Index (core 1.9.5 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes All Packages

A

a() - Static method in class org.biojava.bio.seq.DNATools
a() - Static method in class org.biojava.bio.seq.NucleotideTools
a() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Alanine
a() - Static method in class org.biojava.bio.seq.RNATools
A_THALIANA - Static variable in interface org.biojava.bio.program.homologene.Taxon
AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: AA indicates that a sequence contains AA (amino acid) symbols.
AAindex - Class in org.biojava.bio.proteomics.aaindex: Symbol property table based on the Amino Acid Index Database.
AAindex(String) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindex: Initializes the AAindex symbol property table.
AAindexStreamReader - Class in org.biojava.bio.proteomics.aaindex: Iterator over AAindex objects that are stored in a stream in the AAindex1 file format.
AAindexStreamReader(BufferedReader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader: Initializes the iterator.
AAindexStreamReader(Reader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader: Initializes the iterator.
ABBREV_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
abbreviation - Variable in class org.biojava.bibliography.BiblioJournal: An abbreviation of the journal title.
ABORT_PARSING - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
AbortErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
Abstract() - Constructor for class org.biojava.bio.AnnotationType.Abstract
AbstractAlignmentStyler - Class in org.biojava.bio.program.blast2html: Abstract implementation of AlignmentStyler, contains utility methods for generating a set of HTML styles from a list of RGB colours.
AbstractAlignmentStyler() - Constructor for class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
AbstractAlphabet - Class in org.biojava.bio.symbol: An abstract implementation of Alphabet.
AbstractAlphabet() - Constructor for class org.biojava.bio.symbol.AbstractAlphabet
AbstractAnnotation - Class in org.biojava.bio: A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
AbstractAnnotation() - Constructor for class org.biojava.bio.AbstractAnnotation: Protected no-args constructor intended for sub-classes.
AbstractAnnotation(Map) - Constructor for class org.biojava.bio.AbstractAnnotation: Create a new Annotation by copying the key-value pairs from a map.
AbstractAnnotation(Annotation) - Constructor for class org.biojava.bio.AbstractAnnotation: Copy-constructor.
AbstractBioEntryDB - Class in org.biojavax.bio.db: An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.
AbstractBioEntryDB() - Constructor for class org.biojavax.bio.db.AbstractBioEntryDB
AbstractChangeable - Class in org.biojava.utils: Useful base-class for objects implementing Changeable
AbstractChangeable() - Constructor for class org.biojava.utils.AbstractChangeable
AbstractCrossOverFunction - Class in org.biojavax.ga.functions: Abstract implementation of CrossOverFunction.
AbstractCrossOverFunction() - Constructor for class org.biojavax.ga.functions.AbstractCrossOverFunction
AbstractDistribution - Class in org.biojava.bio.dist: An abstract implementation of Distribution.
AbstractDistribution() - Constructor for class org.biojava.bio.dist.AbstractDistribution
AbstractFeatureHolder - Class in org.biojava.bio.seq: An abstract implementation of FeatureHolder.
AbstractFeatureHolder() - Constructor for class org.biojava.bio.seq.AbstractFeatureHolder
AbstractGeneticAlgorithm - Class in org.biojavax.ga.impl: Base class from which most implementations of GeneticAlgorithm will inherit.
AbstractGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.AbstractGeneticAlgorithm
AbstractLocation - Class in org.biojava.bio.symbol: An abstract implementation of Location.
AbstractLocation() - Constructor for class org.biojava.bio.symbol.AbstractLocation
AbstractLocationDecorator - Class in org.biojava.bio.symbol: Abstract Location decorator (wrapper).
AbstractLocationDecorator(Location) - Constructor for class org.biojava.bio.symbol.AbstractLocationDecorator: Construct a new decorator wrapping the specified Location.
AbstractManyToOneTranslationTable - Class in org.biojava.bio.symbol: an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractManyToOneTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
AbstractMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
AbstractMatrixPairDPCursor(SymbolList, SymbolList, int, int, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
AbstractMutationFunction - Class in org.biojavax.ga.functions: Abstract implementation of MutationFunction all custom implementations should inherit from here.
AbstractMutationFunction() - Constructor for class org.biojavax.ga.functions.AbstractMutationFunction
AbstractOrderNDistribution - Class in org.biojava.bio.dist: Simple base class for OrderNDistributions.
AbstractOrderNDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.AbstractOrderNDistribution: Construct a new NthOrderDistribution.
AbstractOrganism - Class in org.biojavax.ga.impl: Abstract implementation of Organism.
AbstractOrganism() - Constructor for class org.biojavax.ga.impl.AbstractOrganism
AbstractOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.AbstractOrganism
AbstractOrthologueSet - Class in org.biojava.bio.program.homologene
AbstractOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthologueSet
AbstractOrthoPairCollection - Class in org.biojava.bio.program.homologene: An abstract implementation of the OrthoPairCollection interface.
AbstractOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
AbstractOrthoPairSet - Class in org.biojava.bio.program.homologene: represents the Homologene Group.
AbstractOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairSet
AbstractPopulation - Class in org.biojavax.ga.impl: Most Population implementations will want to inherit from here.
AbstractPopulation() - Constructor for class org.biojavax.ga.impl.AbstractPopulation
AbstractPopulation(String) - Constructor for class org.biojavax.ga.impl.AbstractPopulation
AbstractRangeLocation - Class in org.biojava.bio.symbol: Base class for simple contiguous Location implementations.
AbstractRangeLocation() - Constructor for class org.biojava.bio.symbol.AbstractRangeLocation
AbstractReversibleTranslationTable - Class in org.biojava.bio.symbol: an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractReversibleTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractReversibleTranslationTable
AbstractRichSequenceDB - Class in org.biojavax.bio.db: An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
AbstractRichSequenceDB() - Constructor for class org.biojavax.bio.db.AbstractRichSequenceDB
AbstractSequenceDB - Class in org.biojava.bio.seq.db: An abstract implementation of SequenceDB that provides the sequenceIterator method.
AbstractSequenceDB() - Constructor for class org.biojava.bio.seq.db.AbstractSequenceDB
AbstractSVMClassifierModel - Class in org.biojava.stats.svm: Abstract implementation of SVMClassifierModel.
AbstractSVMClassifierModel() - Constructor for class org.biojava.stats.svm.AbstractSVMClassifierModel
AbstractSVMTarget - Class in org.biojava.stats.svm: An abstract implementation of an SVMModel.
AbstractSVMTarget() - Constructor for class org.biojava.stats.svm.AbstractSVMTarget
AbstractSymbol - Class in org.biojava.bio.symbol: The base-class for Symbol implementations.
AbstractSymbol() - Constructor for class org.biojava.bio.symbol.AbstractSymbol
AbstractSymbolList - Class in org.biojava.bio.symbol: Abstract helper implementation of the SymbolList core interface.
AbstractSymbolList() - Constructor for class org.biojava.bio.symbol.AbstractSymbolList
AbstractSymbolList.EditScreener - Class in org.biojava.bio.symbol: This adapter screens all edit events to see if they overlap with a window of interest.
AbstractSymbolList.EditTranslater - Class in org.biojava.bio.symbol: This translates edit events that fall within a window into window co-ordinates.
AbstractTaxon - Class in org.biojava.bio.taxa: Deprecated.
replaced by classes in org.biojavax.bio.taxa
AbstractTaxon() - Constructor for class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
AbstractTaxon(String, String) - Constructor for class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
AbstractTerm - Class in org.biojava.ontology: Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
AbstractTerm() - Constructor for class org.biojava.ontology.AbstractTerm
AbstractTrainer - Class in org.biojava.bio.dp: An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.
AbstractTrainer() - Constructor for class org.biojava.bio.dp.AbstractTrainer
AbstractTrainer(DP) - Constructor for class org.biojava.bio.dp.AbstractTrainer
abstractType - Variable in class org.biojava.bibliography.BiblioDescription: It specifies how BiblioDescription.theAbstract is coded.
AbstractWrapper - Class in org.biojava.bio.program.tagvalue: An abstract TagValueWrapper that does nothing!
AbstractWrapper() - Constructor for class org.biojava.bio.program.tagvalue.AbstractWrapper
ACC_VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
accept() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter: returns a TriState indicating the current outcome of evaluating this filter.
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.And
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Or
accept(Object) - Method in interface org.biojava.bio.CollectionConstraint: accept returns true if the value fulfills the constraint.
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.And
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Or
accept(Object) - Method in interface org.biojava.bio.PropertyConstraint: accept returns true if the value fulfills the constraint.
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.And
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByClass
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Or
accept(Object) - Method in interface org.biojava.bio.search.FilterTest
accept(Object) - Method in class org.biojava.bio.search.FilterTest.Equals
accept(Object) - Method in class org.biojava.bio.search.FilterTest.FindRegex
accept(Object) - Method in class org.biojava.bio.search.FilterTest.GreaterThan
accept(Object) - Method in class org.biojava.bio.search.FilterTest.LessThan
accept(Object) - Method in class org.biojava.bio.search.FilterTest.MatchRegex
accept(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFRecordFilter: Return whether or not to accept record.
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
accept(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueFilter
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.And
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Not
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Or
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Xor
accept(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairFilter
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.And
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Not
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Or
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Xor
accept(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairSetFilter
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor
accept(Feature) - Method in interface org.biojava.bio.seq.FeatureFilter: This method determines whether a feature is to be accepted.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.And
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore: Accept a Feature if it is an instance of SimilarityPairFeature and its score is <= filter's minimum score and >= filter's maximum score.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByType: Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation: Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter: Accept the Feature if it is an instance of FramedFeature and matches the value of getFrame().
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Not
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Or
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation: Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation: Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation: Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter: Accept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().
ACCEPT_ALL - Static variable in interface org.biojava.bio.program.gff.GFFRecordFilter: A GFFRecordFilter that accepts everything.
AcceptAll() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
AcceptAll() - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
ACCESSION - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
accessionNumber() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the accession number of the AAindex entry.
AcnumHitReader - Class in org.biojava.bio.seq.db.emblcd: AcnumHitReader reads the "acnum.hit" file of an EMBL CD-ROM format binary index.
AcnumHitReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumHitReader: Creates a new AcnumHitReader.
AcnumTrgReader - Class in org.biojava.bio.seq.db.emblcd: AcnumTrgReader reads the "acnum.trg" file of an EMBL CD-ROM format binary index.
AcnumTrgReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumTrgReader: Creates a new AcnumTrgReader.
ACRONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon: Use this to define acronyms for things.
ACRONYM - Static variable in interface org.biojavax.Namespace
activityFailed(Object, Exception) - Method in interface org.biojava.utils.ActivityListener: Notification of errors behind the scenes.
ActivityListener - Interface in org.biojava.utils: Interface for object which monitor long-running activities.
activityProgress(Object, int, int) - Method in interface org.biojava.utils.ActivityListener: Estimated progress of an activity.
add(Object) - Method in class org.biojava.utils.FileAsList
add(Object) - Method in class org.biojava.utils.MergingSet
add(Object) - Method in class org.biojava.utils.SmallSet
add(Object) - Method in class org.biojavax.ga.util.WeightedSet: Adds a new Object with a weight of zero.
add(String) - Method in class org.biojava.bio.program.gff.GFFEntrySet: Add a comment to the end of this set.
add(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFEntrySet: Add a GFFRecord to the end of this set.
add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
add(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
addAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
addAllFeatures(Sequence, FeatureHolder) - Static method in class org.biojava.bio.seq.SequenceTools: Add features to a sequence that contain the same information as all those in a feature holder.
addAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation: Add a new Annotation to to the end of the list to be merged.
addAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB: Add a DB to be merged in this view.
addBioEntry(String, BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
addBioEntry(BioEntry) - Method in interface org.biojavax.bio.db.BioEntryDBLite: Adds a sequence to the database.
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB: Add a BioEntry, the name of the BioEntry will be used as the ID
addBottomConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite: Add a configuration as the most default place to look.
addChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext: Add a ChangeListener to a projected feature.
addChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
addChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
addChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable: Deprecated.
use addChangeListener(cl, ChangeType.UNKNOWN)
addChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport: Add a listener that will be informed of all changes.
addChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
addChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList: Add a listener that will be informed of all changes.
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
addChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable: Add a listener that will be informed of changes of a given type.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport: Add a listener that will be informed of changes of a given type (and it's subtypes)
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList: Add a listener that will be informed of changes of a given type.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory: Deprecated.
addChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory: Deprecated.

Add a taxon as a child to a parent.
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory: Deprecated.
addCluster(UnigeneCluster) - Method in interface org.biojava.bio.program.unigene.UnigeneDB: Add a cluster to a database.
addComment(Comment) - Method in interface org.biojavax.bio.BioEntry: Adds a comment instance to this bioentry.
addComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry: Adds a comment instance to this bioentry.
addComponentSequence(ComponentFeature.Template) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
addCount(Distribution, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext: Registers that sym was counted in this state.
addCount(Distribution, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainer: Registers that sym was counted in this state.
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer: Deprecated.
addCount(State, State, double) - Method in interface org.biojava.bio.dp.TransitionTrainer: Add 'count' to the transition from->to.
addDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB: Add a distributed data source.
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
addDbId(AGAVEDbId) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs: add @param id
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
addDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple: Adds a descriptor.
addDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple: Adds a descriptor.
addDetailHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler: Extend this FeatureSetHandler to delegate certain detail elements to the specified handler type.
addDigestFeatures() - Method in class org.biojava.bio.proteomics.Digest: Adds peptides as features to the Sequence in this class.
addElementId(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
addEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper: addEnzyme adds an enzyme to be searched for in the Sequence.
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa: Add a silent optimisable transition to instance.
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
addFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder: Add a feature to the featureholder
addFeatureHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler: Extend this FeatureSetHandler to delegate certain feature elements to the specified handler type.
addFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder: Add an extra FeatureHolder to the set of FeatureHolders which are merged.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
addFeatureProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener: Notify the listener of a feature property.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase: Add an annotation-bundle entry to the feature.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Null implementation
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Notify the listener of a feature property.
addFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder: Adds a relationship to this feature holder.
addFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Adds a relationship to this feature holder.
addFeatureToSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
addFile(File) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB: Add sequences from a file to the sequence database.
addFile(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
addForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
addGapInSource(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList: Add a gap at pos within the source coordinates.
addGapInSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addGapInView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList: Add a single gap at pos within the view coordintates.
addGapInView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addGapsInSource(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList: Add length gaps at pos within the source coordinates.
addGapsInSource(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addGapsInView(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList: Add length gaps at pos within the view coordinates.
addGapsInView(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler: Adds a feature to the Handler attribute of the StAXFeatureHandler object
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
addHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler: The addHitProperty method adds a key/value pair containing some property of a particular hit.
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
addIdAlias(AGAVEIdAlias) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
addIdAlias(AGAVEIdAlias) - Method in interface org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf
addImplementation(Class, Class) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer: Install a new mapping from a class of Feature.Template to a class of Feature implementations.
addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
addItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
addItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
addItemAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
addItemTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
addKey(String, int) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory: addKey adds a new identifier namespace.
addKeyPath(String, Object[]) - Method in class org.biojava.bio.program.tagvalue.Index2Model: Add a key and a path to that key in the tag-value hierachy.
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa: Add a silent persistent transition to instance.
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
addListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub: add a ChangeListener associated with given key.
addListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub
addMapPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
addName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon: Adds the name to this taxon in the given name class.
addName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Adds the name to this taxon in the given name class.
addNeg(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
addNode(boolean) - Method in class org.biojava.utils.automata.FiniteAutomaton: Add a node to the FA.
addNode(boolean) - Method in interface org.biojava.utils.automata.NfaBuilder
addNode(boolean) - Method in class org.biojava.utils.automata.NfaSubModel
addNote(Note) - Method in class org.biojavax.EmptyRichAnnotation: Adds a note to this annotation.
addNote(Note) - Method in interface org.biojavax.RichAnnotation: Adds a note to this annotation.
addNote(Note) - Method in class org.biojavax.SimpleRichAnnotation: Adds a note to this annotation.
addOboFileEventListener(OboFileEventListener) - Method in class org.biojava.ontology.obo.OboFileParser
addOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganism(Organism) - Method in interface org.biojavax.ga.Population: Adds an Organism to the Population
addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation
addOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganisms(Set) - Method in interface org.biojavax.ga.Population: Adds several organisms to the population
addOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population: Adds several organisms to the population
addOrganisms(Population) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganisms(Population) - Method in interface org.biojavax.ga.Population: Adds the residents of one population to this one
addOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet: Add an orthologue to the set.
addOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
addOrthologueProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: add a property to the current Orthologue
addOrthologueProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
addOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet: adds a specified OrthoPair relationship to this group.
addOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
addOrthoPairProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: add a property to the current OrthoPair
addOrthoPairProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat: Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor: Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource: Adds a parse error listener to the list of listeners.
addPattern(String) - Method in class org.biojava.utils.automata.PatternBlitz: add the specified regex to the patterns used for searching.
addPattern(String, boolean) - Method in class org.biojava.utils.regex.Search: add a search pattern to the searches to be conducted by this object.
addPattern(String, String, boolean) - Method in class org.biojava.utils.regex.Search: add a search pattern to the searches to be conducted by this object.
addPos(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
addPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
addProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType: Add a value to the specified property slot.
addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
addProperty(AGAVEProperty) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry: Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm: Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable: Adds a ranked cross reference to the existing set.
addRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry: Adds a ranked docref instance to this bioentry.
addRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry: Adds a ranked docref instance to this bioentry.
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
addRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry: Adds a relation instance to this bioentry.
addRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry: Adds a relation instance to this bioentry.
addRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes: Add a repository to FeatureTypes.
addRequest(Runnable) - Method in class org.biojava.utils.SimpleThreadPool
addRequest(Runnable) - Method in interface org.biojava.utils.ThreadPool: addRequest requests that a Runnable be scheduled to be run by one of the threads in the pool.
addRichSequence(String, RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB: Add a sequence.
addRichSequence(RichSequence) - Method in interface org.biojavax.bio.db.RichSequenceDBLite: Adds a sequence to the database.
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
addSearchProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler: The addSearchProperty method adds a key/value pair containing some property of the overall search result.
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
addSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer: Add a secondary key.
addSequence(String, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree: Add a sequence into the tree.
addSequence(String, Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB: Add a sequence under a particular id.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.DummySequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB: addSequence always throws a ChangeVetoException as this implementation is immutable.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
addSequence(Sequence) - Method in interface org.biojava.bio.seq.db.SequenceDBLite: Adds a sequence to the database.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.WebSequenceDB: Not supported, You can't add sequences to a WebDB!
addSequence(Sequence) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
addSequence(Sequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
addSequenceDB(String, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation: This method creates a new (and empty) HashSequenceDB with the given name that will be accessible through this sequence db installation through this name and all given other identifiers.
addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation: As this is a dummy implementation adding a sequenceDB doesn't do anything
addSequenceDB(SequenceDBLite, Set) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation: addSequenceDB adds a new SequenceDB under its own identifier which will additionally be recognised by the set of other identifiers.
addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation: addSequenceDB adds a new SequenceDB which will be accessible via the name returned by its getName() method and via all other given identifiers.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblProcessor: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.OrganismParser: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
addSequenceProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener: Notify the listener of a sequence-wide property.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase: Add an annotation-bundle entry to the sequence.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Notify the listener of a sequence-wide property.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotProcessor: Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Notify the listener of a sequence-wide property.
addSet(Set) - Method in class org.biojava.utils.MergingSet
addState(State) - Method in interface org.biojava.bio.dp.MarkovModel: Adds a state to the model.
addState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
addState(State) - Method in class org.biojava.bio.dp.WMAsMM
addStyle(String, String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler: Add a colour style to this Styler.
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
addSubHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler: The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
addSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet: Adds a symbol to this alphabet.
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolList: Add a new Symbol to the end of this list.
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: SoftMaskedAlphabets cannot add new Symbols.
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
addSymbolList(SymbolList, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory: tool to construct the SymbolList by adding Symbols.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer: Deprecated.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOFilter
addSymbols(Alphabet, Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SeqIOListener: Notify the listener of symbol data.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleSequenceBuilder
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SmartSequenceBuilder
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Prints out the sequences properties in order.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Notify the listener of symbol data.
addSymbols(SymbolList, int) - Method in class org.biojava.bio.symbol.SuffixTree: Add a count for all motifs with length of up to window to this tree.
addSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
addSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl
addSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl
addSynonym(Object) - Method in interface org.biojava.ontology.Term: Add a synonym for this term.
addSynonym(Object) - Method in class org.biojava.ontology.Term.Impl
addSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl
addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm: Add a synonym for this term.
addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple: Add a synonym for this term.
addTable(SymbolPropertyTable) - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB: Adds a symbol property table to the database.
addTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper: Add a tag to retain.
addTitle(int, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: add title information to an Orthologue (this is not in enclosed in the Orthologue element because it comes completely separate in the Homologene data files.
addTitle(int, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
addToCache(String, File) - Static method in class org.biojava.utils.io.FlatFileCache
addToEnvironment(String, Object) - Method in class org.biojava.naming.ObdaContext
addTopConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite: Add a configuration as the most authoritative place to look.
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in interface org.biojava.utils.automata.NfaBuilder
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.NfaSubModel
addTypeWithParent(Class) - Method in class org.biojava.utils.walker.WalkerFactory: Register a type as being a 'container' class.
addVariableModification(char, double[]) - Method in class org.biojava.bio.proteomics.MassCalc: Add Variable modifications.
addVariableModification(Symbol, double[]) - Method in class org.biojava.bio.proteomics.MassCalc: Add Variable modifications.
addVector(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
addVector(Object, double, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
addXMLCollectionConstraintWriter(Class, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter: Register a writer for the specified class of collection constraint
addXMLCollectionConstraintWriter(CollectionConstraint, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter: Register a writer for a singleton property constraint.
addXMLFilterWriter(Class, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter: Add a writer for the specified class of filters
addXMLFilterWriter(FeatureFilter, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter: Add a writer for a singleton filter.
addXMLPropertyConstraintWriter(Class, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter: Register a writer for the specified class of property constraint
addXMLPropertyConstraintWriter(PropertyConstraint, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter: Register a writer for a singleton property constraint.
addXref(AGAVEXref) - Method in interface org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf
addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs: add @param xref
addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
advance() - Method in interface org.biojava.bio.dp.MarkovModel: The maximum advance for this model.
advance() - Method in interface org.biojava.bio.dp.onehead.DPCursor: Advance.
advance() - Method in class org.biojava.bio.dp.onehead.SmallCursor
advance() - Method in class org.biojava.bio.dp.SimpleMarkovModel
advance() - Method in class org.biojava.bio.dp.WMAsMM
ADVANCE - Static variable in interface org.biojava.bio.dp.EmissionState: This signals that the advance array has been altered.
affiliation - Variable in class org.biojava.bibliography.BiblioPerson: Their affiliation.
AGAVE_AGAVE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
AGAVE_ALT_IDS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
AGAVE_ANNOTATIONS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler
AGAVE_ASSEMBLY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler
AGAVE_BIO_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
AGAVE_BIO_SEQUENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
AGAVE_CDS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECdsHandler
AGAVE_CHROMOSOME_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
AGAVE_CLASSIFICATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
AGAVE_COMP_RESULT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
AGAVE_COMPUTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
AGAVE_CONTIG_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
AGAVE_DBID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
AGAVE_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
AGAVE_ELEMENT_ID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
AGAVE_EVIDENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
AGAVE_EXONS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler
AGAVE_FRAGMENT_ORDER_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
AGAVE_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
AGAVE_ID_ALIAS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
AGAVE_KEYWORD_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
AGAVE_MAP_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
AGAVE_MAP_POSITION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
AGAVE_MATCH_ALIGN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
AGAVE_MATCH_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
AGAVE_MATCH_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
AGAVE_MRNA_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
AGAVE_NOTE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
AGAVE_PREDICTED_PROTEIN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
AGAVE_QUALIFIER_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
AGAVE_QUERY_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
AGAVE_RELATED_ANNOT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
AGAVE_RESULT_GROUP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
AGAVE_RESULT_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
AGAVE_SCI_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
AGAVE_SEQ_FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
AGAVE_SEQ_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
AGAVE_SEQ_MAP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
AGAVE_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
AGAVE_TRANSCRIPT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
AGAVE_UNORDERED_FRAGMENTS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler
AGAVE_VIEW_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
AGAVE_XREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
AGAVE_XREF_PROP_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
AGAVE_XREFS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
Agave2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave: Dumping the data from biojava with source of agave into agave format
AGAVEAltIdsPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with alternate sequence IDs
AGAVEAnnotationsHandler - Class in org.biojava.bio.seq.io.agave
AGAVEAnnotFilter - Interface in org.biojava.bio.seq.io.agave: This interface defines mapping from BioJava into AGAVE format.
AGAVEAnnotFilterFactory - Interface in org.biojava.bio.seq.io.agave
AGAVEAssemblyHandler - Class in org.biojava.bio.seq.io.agave
AGAVEBioSeqCallbackItf - Interface in org.biojava.bio.seq.io.agave: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEBioSeqHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <bio_sequence> element
AGAVEBioSequenceHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <bio_sequence> element
AGAVECallbackItf - Interface in org.biojava.bio.seq.io.agave: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVECdsHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <cds> element
AGAVEChromosomeCallbackItf - Interface in org.biojava.bio.seq.io.agave: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEChromosomeHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <chromosome> element
AGAVEClassificationHandler - Class in org.biojava.bio.seq.io.agave
AGAVECompResultHandler - Class in org.biojava.bio.seq.io.agave
AGAVEComputationHandler - Class in org.biojava.bio.seq.io.agave
AGAVEContigCallbackItf - Interface in org.biojava.bio.seq.io.agave: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEContigHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <contig> element
AGAVEDbId - Class in org.biojava.bio.seq.io.agave
AGAVEDbId() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEDbId
AGAVEDbIdCallbackItf - Interface in org.biojava.bio.seq.io.agave: this is the interface implemented by several classes
AGAVEDbIdPropCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEDbIdPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with database crossreferences
AGAVEDescPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with database crossreferences
AGAVEElementIdPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEEvidenceCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEEvidenceHandler - Class in org.biojava.bio.seq.io.agave
AGAVEExonsPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.agave: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEFragmentOrderHandler - Class in org.biojava.bio.seq.io.agave
AGAVEFragmentOrientationHandler - Class in org.biojava.bio.seq.io.agave
AGAVEGeneHandler - Class in org.biojava.bio.seq.io.agave
AGAVEHandler - Class in org.biojava.bio.seq.io.agave: Handles the root AGAVE element modified for agave format
AGAVEHandler() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEHandler
AGAVEIdAlias - Class in org.biojava.bio.seq.io.agave
AGAVEIdAliasCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEIdAliasPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEKeywordPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with AGAVE keywords
AGAVEMapLocation - Class in org.biojava.bio.seq.io.agave
AGAVEMapLocation() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapLocation
AGAVEMapLocationPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEMapPosition - Class in org.biojava.bio.seq.io.agave
AGAVEMapPosition() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapPosition
AGAVEMapPositionPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEMatchAlignPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with match_align
AGAVEMatchDescPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with match_desc
AGAVEMatchRegion - Class in org.biojava.bio.seq.io.agave: match_region
AGAVEMatchRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
AGAVEMatchRegionPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with match_region
AGAVEMrnaHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <mrna> element
AGAVENotePropHandler - Class in org.biojava.bio.seq.io.agave: Deals with note
AGAVEPredictedProteinHandler - Class in org.biojava.bio.seq.io.agave: Handles the AGAVE <predicted_protein> element
AGAVEProperty - Class in org.biojava.bio.seq.io.agave
AGAVEProperty(String, String, String, String) - Constructor for class org.biojava.bio.seq.io.agave.AGAVEProperty
AGAVEQualifierPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEQueryRegion - Class in org.biojava.bio.seq.io.agave
AGAVEQueryRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
AGAVEQueryRegionPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVERelatedAnnot - Class in org.biojava.bio.seq.io.agave
AGAVERelatedAnnot() - Constructor for class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot: construct..
AGAVERelatedAnnotPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEResultGroupHandler - Class in org.biojava.bio.seq.io.agave
AGAVEResultPropertyPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVESciPropertyPropHandler - Class in org.biojava.bio.seq.io.agave: sci_property
AGAVESeqFeatureHandler - Class in org.biojava.bio.seq.io.agave: seq_feature
AGAVESeqLocationPropHandler - Class in org.biojava.bio.seq.io.agave: seq_location
AGAVESeqMapHandler - Class in org.biojava.bio.seq.io.agave: sequence_map
AGAVESeqPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with sequence code
AGAVETranscriptHandler - Class in org.biojava.bio.seq.io.agave: transcript
AGAVEUnorderedFragmentsHandler - Class in org.biojava.bio.seq.io.agave: unordered_fragments
AGAVEViewPropHandler - Class in org.biojava.bio.seq.io.agave: Moves view attributes into annotation properties.
AgaveWriter - Class in org.biojava.bio.seq.io.agave: Writes Sequence into AGAVE XML document.
AgaveWriter() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter: Default constructor uses generic annotation to attribute mapping.
AgaveWriter(AGAVEAnnotFilter) - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter: Construct with data source specific annotation to attribute mapping.
AgaveWriter.Indent - Class in org.biojava.bio.seq.io.agave: Implements indenting for elements.
AGAVEXref - Class in org.biojava.bio.seq.io.agave: xref
AGAVEXref() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXref
AGAVEXrefCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEXrefPropHandler - Class in org.biojava.bio.seq.io.agave: handle AGAVE xref
AGAVEXrefPropPropHandler - Class in org.biojava.bio.seq.io.agave: xref_property
AGAVEXrefs - Class in org.biojava.bio.seq.io.agave: xrefs
AGAVEXrefs() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXrefs
AGAVEXrefsPropHandler - Class in org.biojava.bio.seq.io.agave: Deals with database crossreferences (xrefs)
Aggregator - Class in org.biojava.bio.program.tagvalue: Joins multipel values into single values.
Aggregator(TagValueListener, BoundaryFinder, String) - Constructor for class org.biojava.bio.program.tagvalue.Aggregator
ala() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Alanine (A)
AlignIOConstants - Class in org.biojava.bio.seq.io: AlignIOConstants contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing alignments.
AlignIOConstants() - Constructor for class org.biojava.bio.seq.io.AlignIOConstants
alignment - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template: alignment Alignment field.
alignment(List, SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews: View a SymbolList over a cross-product Alphabet as an Alignment.
alignment(Map) - Static method in class org.biojava.bio.symbol.SymbolListViews: Construct an alignment of the SymbolLists contained in the values collection of labelToSymList.
Alignment - Interface in org.biojava.bio.alignment: An alignment containing multiple SymbolLists.
ALIGNMENT - Static variable in interface org.biojava.bio.seq.homol.Homology: Signals that the alignment describing the homologous sequences has changed.
Alignment.SymbolListIterator - Class in org.biojava.bio.alignment: Iterator implementation looping over symbol lists in an alignment using the labels.
AlignmentFormat - Interface in org.biojava.bio.seq.io
AlignmentMarker - Class in org.biojava.bio.program.blast2html: Class to do simple HTML colouring of sequence alignments.
AlignmentMarker(ColourCommand, AlignmentStyler) - Constructor for class org.biojava.bio.program.blast2html.AlignmentMarker: Creates a new AlignmentMarker instance.
all - Static variable in interface org.biojava.bio.seq.FeatureFilter: All features are selected by this filter.
all() - Static method in class org.biojava.bio.seq.FilterUtils: Return a filter which matches all features.
ALL - Static variable in interface org.biojava.bio.program.xff.ElementRecognizer
ALL - Static variable in interface org.biojava.bio.seq.io.agave.ElementRecognizer
ALL - Static variable in interface org.biojava.bio.seq.io.game.ElementRecognizer
AllElementRecognizer() - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
allIn(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools: Destructive down-cast an annotation to a type.
allOut(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools: allOut returns a new Annotation containing only those values in the Annotation argument which are not of a type specified by the AnnotationType.
AllPairsInCollection(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
AllValuesIn(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.AllValuesIn: Create an AllValuesIn based upon a PropertyConstraint and a cardinality.
alph - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
Alphabet - Interface in org.biojava.bio.symbol: The set of AtomicSymbols which can be concatenated together to make a SymbolList.
alphabetForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager: Retrieve the alphabet for a specific name.
AlphabetIndex - Interface in org.biojava.bio.symbol: Map between Symbols and index numbers.
AlphabetManager - Class in org.biojava.bio.symbol: Utility methods for working with Alphabets.
AlphabetManager() - Constructor for class org.biojava.bio.symbol.AlphabetManager
alphabets() - Static method in class org.biojava.bio.symbol.AlphabetManager: Get an iterator over all alphabets known.
alphaIndex(Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
alphaIndex(Symbol) - Method in class org.biojava.utils.automata.Nfa
AlreadyExistsException - Exception in org.biojava.ontology: Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
AlreadyExistsException() - Constructor for exception org.biojava.ontology.AlreadyExistsException
AlreadyExistsException(String) - Constructor for exception org.biojava.ontology.AlreadyExistsException
ALT_ID - Static variable in class org.biojava.ontology.obo.OboFileHandler
ALT_YEAST_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the alternative yeast nuclear genetic code.
AlternateTokenization - Class in org.biojava.bio.seq.io: Implementation of SymbolTokenization which binds symbols to strings of characters.
AlternateTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.AlternateTokenization
ALTERNATIVE_PRODUCTS - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser: A name for a comment type.
ALWAYS_VETO - Static variable in interface org.biojava.utils.ChangeListener: Convenience implementation which vetoes every change of which it is notified.
AlwaysVetoListener() - Constructor for class org.biojava.utils.ChangeListener.AlwaysVetoListener: Private constructor.
AMBIGUOUS - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: AMBIGUOUS indicates that a sequence contains ambiguity symbols.
aminoAcids - Static variable in class org.biojavax.bio.seq.io.FastaFormat
and(FeatureFilter.And, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
and(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils: Constructs a new filter which matches the intersection of a set of filters.
and(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a new filter which matches the intersection of two other filters.
And(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.And: Create a new And from two child constraints.
And(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.And
And(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.And
And(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
And(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.And: Create a new And from two child constraints.
And(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.And
And(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.And
annot - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
Annotatable - Interface in org.biojava.bio: Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder - Class in org.biojava.bio: Deprecated.
use new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY) instead
annotate(Sequence) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
annotate(Sequence) - Method in class org.biojava.bio.molbio.RestrictionMapper: annotate adds Features which represent restriction sites.
annotate(Sequence) - Method in interface org.biojava.bio.seq.SequenceAnnotator: Return an annotated version of a sequence.
AnnotatedSequenceDB - Class in org.biojava.bio.seq.db: SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
AnnotatedSequenceDB(SequenceDB, SequenceAnnotator) - Constructor for class org.biojava.bio.seq.db.AnnotatedSequenceDB
annotateSequence(Sequence, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools: Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
annotateSequence(Sequence, GFFEntrySet, boolean) - Static method in class org.biojava.bio.program.gff.GFFTools: Annotates a sequence with the features from a GFF entry set.
annotateSequences(SequenceDB, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools: Annotates all sequences in a sequence DB with features from a GFF entry set.
annotateXFF(File, Sequence) - Static method in class org.biojava.bio.program.xff.XFFTools
annotateXFF(File, Sequence, Annotation) - Static method in class org.biojava.bio.program.xff.XFFTools
annotation - Variable in class org.biojava.bio.seq.Feature.Template
annotation - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
Annotation - Interface in org.biojava.bio: Arbitrary annotation associated with one or more objects.
ANNOTATION - Static variable in interface org.biojava.bio.Annotatable: Signals that the associated Annotation has altered in some way.
ANNOTATION_ADD - Static variable in class org.biojava.bio.MergeAnnotation: ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
ANNOTATION_CHANGED - Static variable in class org.biojava.bio.MergeAnnotation: ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
ANNOTATION_REMOVE - Static variable in class org.biojava.bio.MergeAnnotation: ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
AnnotationBuilder - Class in org.biojava.bio.program.tagvalue: Builds an Annotation tree from TagValue events using an AnnotationType to work out which fields are of what type.
AnnotationBuilder(AnnotationType) - Constructor for class org.biojava.bio.program.tagvalue.AnnotationBuilder: Make a new AnnotationBuilder that will build Annotation instances of a given type.
AnnotationChanger - Class in org.biojava.bio: AnnotationChanger remaps the values of an Annotation to new values specified by a ValueChanger.
AnnotationChanger(Annotation, ChangeTable) - Constructor for class org.biojava.bio.AnnotationChanger: Creates a new AnnotationChanger using the specified ValueChanger to remap its values.
AnnotationContains(Object, Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.AnnotationContains: Make a new AnnotationContains that will accept features with an annotation bundle where the value-set assosiated with the property key contains a member equal to value.
AnnotationDB - Interface in org.biojava.bio.annodb: A database of Annotation instances.
AnnotationFactory - Class in org.biojava.bio.program.ssbind: AnnotationFactory is a utility class for making Annotations from Maps.
AnnotationFactory() - Constructor for class org.biojava.bio.program.ssbind.AnnotationFactory
annotationForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
annotationForwarder - Variable in class org.biojava.bio.seq.impl.SubSequence
annotationForwarder - Variable in class org.biojava.bio.seq.NewSimpleAssembly
annotationForwarder - Variable in class org.biojava.bio.seq.SimpleAssembly
annotationForwarder - Variable in class org.biojava.bio.symbol.AbstractSymbol
annotationForwarder - Variable in class org.biojava.bio.symbol.SimpleAlphabet
AnnotationForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.Annotatable.AnnotationForwarder: Deprecated.

Create a new AnnotationForwarder that will forward events for a source using a change support.
AnnotationRenamer - Class in org.biojava.bio: AnnotationRenamer remaps the keys of an Annotation to new keys specified by a TagMapper.
AnnotationRenamer(Annotation, PropertyChanger) - Constructor for class org.biojava.bio.AnnotationRenamer: Creates a new AnnotationRenamer using the specified TagMapper to remap its keys.
AnnotationTools - Class in org.biojava.bio: AnnotationTools is a set of static utility methods for manipulating Annotations and AnnotationTypes.
AnnotationTools() - Constructor for class org.biojava.bio.AnnotationTools
AnnotationType - Interface in org.biojava.bio: A set of constraints on the data contained in an Annotation.
AnnotationType.Abstract - Class in org.biojava.bio: An abstract base class useful for implementing AnnotationType instances.
AnnotationType.Impl - Class in org.biojava.bio: An implementation of AnnotationType.
ANY - Static variable in interface org.biojava.bio.AnnotationType: The type that accepts all annotations and is the supertype of all other annotations.
ANY - Static variable in class org.biojava.bio.CardinalityConstraint: The property can have any number of values, including none.
ANY - Static variable in interface org.biojava.bio.CollectionConstraint: ANY is a constraint which accepts a property for addition under all conditions.
ANY - Static variable in interface org.biojava.bio.PropertyConstraint: ANY is a constraint which accepts a property for addition under all conditions.
ANY - Static variable in class org.biojava.ontology.OntoTools
AppBeanRunner - Class in org.biojava.utils.xml: Create a bean from an XML file, then attempt to enter it.
AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner
append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel
AppEntry - Interface in org.biojava.utils.xml
AppException - Exception in org.biojava.utils.xml
AppException(String) - Constructor for exception org.biojava.utils.xml.AppException
applicants - Variable in class org.biojava.bibliography.BiblioPatent: Array of applicants.
ARCHITECTURE - Static variable in interface org.biojava.bio.dp.MarkovModel: Signals that the architecture of the model is changing.
areDisjoint(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Determines if two queries can be proven to be disjoint.
areEmissionSpectraEqual(Distribution[], Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools: Compares the emission spectra of two distribution arrays.
areEmissionSpectraEqual(Distribution, Distribution) - Static method in class org.biojava.bio.dist.DistributionTools: Compares the emission spectra of two distributions.
areEqual(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Decide if two feature filters accept exactly the same set of features.
areEqual(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools: Return whether two locations are equal.
areProperSubset(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Determines if the set of features matched by sub can be proven to be a proper subset of the features matched by sup.
arg() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Arginine (R)
ARG_C - Static variable in class org.biojava.bio.proteomics.Protease
ARG_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager
ArrayStateMachineToolkit - Class in org.biojava.utils.automata
ASCID_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the ascidian mitochondrial genetic code.
asMap() - Method in class org.biojava.bio.AbstractAnnotation
asMap() - Method in interface org.biojava.bio.Annotation: Return a map that contains the same key/values as this Annotation.
asMap() - Method in class org.biojava.bio.MergeAnnotation
asMap() - Method in class org.biojava.bio.OverlayAnnotation: Return a Map view onto this annotation.
asMap() - Method in class org.biojavax.EmptyRichAnnotation: Return a map that contains the same key/values as this Annotation.
asMap() - Method in class org.biojavax.ga.util.WeightedSet: Converts the Set to a map from key Objects to Double weights.
asMap() - Method in class org.biojavax.SimpleRichAnnotation: Return a map that contains the same key/values as this Annotation.
asn() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Asparagine (N)
asp() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Aspartic Acid (D)
ASP_N - Static variable in class org.biojava.bio.proteomics.Protease
ASP_N - Static variable in class org.biojava.bio.proteomics.ProteaseManager
AssembledSymbolList - Class in org.biojava.bio.seq.impl: Support class for applications which need to patch together sections of sequence into a single SymbolList.
AssembledSymbolList() - Constructor for class org.biojava.bio.seq.impl.AssembledSymbolList
AssertionFailure - Error in org.biojava.utils: An unchecked exception representing an Assertion failure.
AssertionFailure(String) - Constructor for error org.biojava.utils.AssertionFailure
AssertionFailure(String, Throwable) - Constructor for error org.biojava.utils.AssertionFailure
AssertionFailure(Throwable) - Constructor for error org.biojava.utils.AssertionFailure
AtomicSymbol - Interface in org.biojava.bio.symbol: A symbol that is not ambiguous.
ATTR_FORMAT - Static variable in interface org.biojava.bibliography.BibRefSupport: A vocabulary name, or a part of a vocabulary name.
ATTR_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport: A part of a vocabulary name.
ATTR_SCOPE - Static variable in interface org.biojava.bibliography.BibRefSupport: A vocabulary name, or a part of a vocabulary name.
attribute(String, String) - Method in class org.biojava.utils.xml.FastXMLWriter
attribute(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
attribute(String, String) - Method in interface org.biojava.utils.xml.XMLWriter: Add an un-qualified attribute to an element.
attribute(String, String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
attribute(String, String, String) - Method in interface org.biojava.utils.xml.XMLWriter: Add an attribute to an element.
AUTHOR_LIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
AUTHORITY - Static variable in interface org.biojavax.Namespace
authors - Variable in class org.biojava.bibliography.BibRef: The authors and contributors are responsible for creating the contents of the cited resource.
AUTHORS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
AutomatonException - Exception in org.biojava.utils.automata: An exception thrown by classes of this package.
AutomatonException(String) - Constructor for exception org.biojava.utils.automata.AutomatonException
AutomatonException(Throwable) - Constructor for exception org.biojava.utils.automata.AutomatonException
AutomatonException(Throwable, String) - Constructor for exception org.biojava.utils.automata.AutomatonException
available() - Method in class org.biojava.utils.io.UncompressInputStream
average(Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools: Averages two or more distributions.
AverageResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.AverageResolver
AVG_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable

B

b() - Static method in class org.biojava.bio.seq.DNATools
b() - Static method in class org.biojava.bio.seq.NucleotideTools
B_TAURUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
back - Variable in class org.biojava.bio.dp.BackPointer: The previous backpointer (towards origin of DP matrix) in traceback.
BackMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
BackMatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
BackPointer - Class in org.biojava.bio.dp: A backpointer.
BackPointer(State) - Constructor for class org.biojava.bio.dp.BackPointer
BackPointer(State, BackPointer, double) - Constructor for class org.biojava.bio.dp.BackPointer
backPointers - Variable in class org.biojava.bio.dp.twohead.Cell
backward(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backward_initialize(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward_recurse(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward_termination(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backwards(ScoreType) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
backwards(ScoreType) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
backwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
backwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP
BACTERIAL - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the bacterial and plant plastid genetic code.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.program.phred.PhredFormat: This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.

This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat: Deprecated.

This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.

This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.StreamReader: This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in interface org.biojava.utils.ParseErrorListener: Method called when the parser encounters a bad line.
BASE_COUNT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
BASE_COUNT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
BASE_COUNT_TAG_FULL - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
BASEPOSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
BASEPOSITION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
BaseXMLWriter - Class in org.biojava.bio.program.xml: Base XMLWriter class for writing XML representations of Java Value Objects with bespoke architectures.
BaseXMLWriter() - Constructor for class org.biojava.bio.program.xml.BaseXMLWriter
BasicFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
BasicState(String) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState: This is the default constructor
BasicState(String, TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState: when this constructor is used, a fixed listener is used with this state.
BasicXFFHelper - Class in org.biojava.bio.program.xff
BasicXFFHelper() - Constructor for class org.biojava.bio.program.xff.BasicXFFHelper
BasisSymbol - Interface in org.biojava.bio.symbol: A symbol that can be represented as a string of Symbols.
BaumWelchSampler - Class in org.biojava.bio.dp: Train a hidden markov model using a sampling algorithm.
BaumWelchSampler(DP) - Constructor for class org.biojava.bio.dp.BaumWelchSampler
BaumWelchTrainer - Class in org.biojava.bio.dp: Train a hidden markov model using maximum likelihood.
BaumWelchTrainer(DP) - Constructor for class org.biojava.bio.dp.BaumWelchTrainer
BeanAsAnnotation - Class in org.biojava.bio: Create an Annotation with properties matching those of a JavaBean instance.
BeanAsAnnotation(Object) - Constructor for class org.biojava.bio.BeanAsAnnotation: Create a new BeanAsAnnotation for a bean.
BeanAsMap - Class in org.biojava.utils
BeanAsMap(Object) - Constructor for class org.biojava.utils.BeanAsMap
beginWriting() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.INSDseqFormat: Informs the writer that we want to start writing.
beginWriting() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat: Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: Informs the writer that we want to start writing.
BETWEEN_BASES - Static variable in interface org.biojavax.bio.seq.Position: A symbol representing a position that falls in between two bases, eg. 2^3 falls somewhere in the gap between 2 and 3.
BetweenLocation - Class in org.biojava.bio.symbol: Between view onto an underlying Location instance.
BetweenLocation(Location) - Constructor for class org.biojava.bio.symbol.BetweenLocation
BiblioArticle - Class in org.biojava.bibliography: It represents an article.
BiblioArticle() - Constructor for class org.biojava.bibliography.BiblioArticle
BiblioBook - Class in org.biojava.bibliography: It represents a book.
BiblioBook() - Constructor for class org.biojava.bibliography.BiblioBook
BiblioBookArticle - Class in org.biojava.bibliography: It represents a book article.
BiblioBookArticle() - Constructor for class org.biojava.bibliography.BiblioBookArticle
BiblioCriterion - Class in org.biojava.bibliography: The criteria define how the matching or ordering should be done during queries.
BiblioCriterion() - Constructor for class org.biojava.bibliography.BiblioCriterion
BiblioDescription - Class in org.biojava.bibliography: It represents an account of the content of the cited resource.
BiblioDescription() - Constructor for class org.biojava.bibliography.BiblioDescription
BiblioEntryStatus - Class in org.biojava.bibliography: It defines information related to the citation itself rather than to the cited resource.
BiblioEntryStatus() - Constructor for class org.biojava.bibliography.BiblioEntryStatus
BiblioJournal - Class in org.biojava.bibliography: A class describing journals.
BiblioJournal() - Constructor for class org.biojava.bibliography.BiblioJournal
BiblioJournalArticle - Class in org.biojava.bibliography: It represents a journal article.
BiblioJournalArticle() - Constructor for class org.biojava.bibliography.BiblioJournalArticle
BiblioOrganisation - Class in org.biojava.bibliography: It represents an organisation dealing with the bibliographic resources.
BiblioOrganisation() - Constructor for class org.biojava.bibliography.BiblioOrganisation
BiblioPatent - Class in org.biojava.bibliography: It represents a patent.
BiblioPatent() - Constructor for class org.biojava.bibliography.BiblioPatent
BiblioPerson - Class in org.biojava.bibliography: It represents a person dealing with the bibliographic resources.
BiblioPerson() - Constructor for class org.biojava.bibliography.BiblioPerson
BiblioProceeding - Class in org.biojava.bibliography: It represents a conference proceeding.
BiblioProceeding() - Constructor for class org.biojava.bibliography.BiblioProceeding
BiblioProvider - Class in org.biojava.bibliography: This class and its sub-classes define active participants of the process of creation and dissemination of the bibliographic resources.
BiblioProvider() - Constructor for class org.biojava.bibliography.BiblioProvider
BiblioScope - Class in org.biojava.bibliography: It represent an extent or scope of the content of the cited resource.
BiblioScope() - Constructor for class org.biojava.bibliography.BiblioScope
BiblioService - Class in org.biojava.bibliography: It represents a service dealing with the bibliographic resources.
BiblioService() - Constructor for class org.biojava.bibliography.BiblioService
BiblioSubject - Class in org.biojava.bibliography: It represents the topic of the content of the cited resource.
BiblioSubject() - Constructor for class org.biojava.bibliography.BiblioSubject
BiblioTechReport - Class in org.biojava.bibliography: It represents a technical report.
BiblioTechReport() - Constructor for class org.biojava.bibliography.BiblioTechReport
BiblioThesis - Class in org.biojava.bibliography: It represents a thesis.
BiblioThesis() - Constructor for class org.biojava.bibliography.BiblioThesis
BiblioWebResource - Class in org.biojava.bibliography: It represents a WWW resource.
BiblioWebResource() - Constructor for class org.biojava.bibliography.BiblioWebResource
BibRef - Class in org.biojava.bibliography: This class is a core class of the bibliographic data model - it represents a bibliographic reference, a citation.
BibRef() - Constructor for class org.biojava.bibliography.BibRef
BibRefException - Exception in org.biojava.bibliography: An exception raised when communciation with the BibRef APIs fails.
BibRefException(String) - Constructor for exception org.biojava.bibliography.BibRefException: Create a new BibRefException with a message.
BibRefException(String, Throwable) - Constructor for exception org.biojava.bibliography.BibRefException: Create a nw BibRefException with a message and a root cause.
BibRefException(Throwable) - Constructor for exception org.biojava.bibliography.BibRefException: Create a new BibRefException with a root cause.
BibRefQuery - Interface in org.biojava.bibliography: The interface BibRefQuery is a fundamental part of the Bibliographic Query Service.
BibRefSupport - Interface in org.biojava.bibliography: This interface defines supporting utilities for working with bibliographic repositories.
binary(int) - Static method in class org.biojava.bio.symbol.PackingFactory
binary(long) - Static method in class org.biojava.bio.symbol.PackingFactory
BinarySearch - Class in org.biojava.utils.math: solves y = f(x) = 0 by binary search.
BinarySearch() - Constructor for class org.biojava.utils.math.BinarySearch
bind(String, Object) - Method in class org.biojava.naming.ObdaContext
bind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
bind(Name, Object) - Method in class org.biojava.naming.ObdaContext
bind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
bindSymbol(Symbol, char) - Method in class org.biojava.bio.seq.io.CharacterTokenization: Bind a Symbol to a character.
bindSymbol(Symbol, String) - Method in class org.biojava.bio.seq.io.AlternateTokenization: Bind a Symbol to a string.
BioEntry - Interface in org.biojavax.bio: This class relates to the bioentry table in BioSQL.
BioEntryDB - Interface in org.biojavax.bio.db: .
BioEntryDBLite - Interface in org.biojavax.bio.db: A database of BioEntrys.
BioEntryIterator - Interface in org.biojavax.bio: Essentially the same as SequenceIterator.
BioEntryRelationship - Interface in org.biojavax.bio: Represents the relation between two bioentries.
BIOENTRYS - Static variable in interface org.biojavax.bio.db.BioEntryDBLite: Signals that sequences are being added to or remove from the database.
BioError - Error in org.biojava.bio: A nestable biological error.
BioError() - Constructor for error org.biojava.bio.BioError: Create a new BioError.
BioError(String) - Constructor for error org.biojava.bio.BioError: Create a new BioError with a message.
BioError(String, Throwable) - Constructor for error org.biojava.bio.BioError: Create a new BioError with a cause and a message.
BioError(Throwable) - Constructor for error org.biojava.bio.BioError: Create a new BioError with a cause.
BioError(Throwable, String) - Constructor for error org.biojava.bio.BioError: Deprecated.
Use BioError(message, ex) instead.
BioException - Exception in org.biojava.bio: A nestable biological exception.
BioException() - Constructor for exception org.biojava.bio.BioException: Create a new BioException.
BioException(String) - Constructor for exception org.biojava.bio.BioException: Create a new BioException with a message.
BioException(String, Throwable) - Constructor for exception org.biojava.bio.BioException: Create a new BioException with a cause and a message.
BioException(Throwable) - Constructor for exception org.biojava.bio.BioException: Create a new BioException with a cause.
BioException(Throwable, String) - Constructor for exception org.biojava.bio.BioException: Deprecated.
use new BioException(message, ex) instead
BioFetchSequenceDB - Class in org.biojava.bio.seq.db.biofetch: Simple SequenceDB implementation backed by a BioFetch (HTTP) server.
BioFetchSequenceDB(String, String) - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB: Construct a BioFetchSequenceDB which connects to the specified BioFetch server.
BioFetchSequenceDBProvider - Class in org.biojava.bio.seq.db.biofetch: Directory-services plugin for biofetch databases.
BioFetchSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
BioIndex - Class in org.biojava.bio.seq.db: The original object for indexing sequence files.
BioIndex(File) - Constructor for class org.biojava.bio.seq.db.BioIndex: Load an existing index file.
BioIndex(File, String, int) - Constructor for class org.biojava.bio.seq.db.BioIndex
biojavaToFile(int, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Converts a Biojava object to the given filetype.
biojavaToFile(String, String, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Writes a Biojava SequenceIterator, SequenceDB, Sequence or Aligment to an OutputStream
BioMatcher - Interface in org.biojava.bio.search: Interface for things that perform matches.
BioPattern - Interface in org.biojava.bio.search
BIOPHYSICOCHEMICAL_PROPERTIES - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser: A name for a comment type.
BioRuntimeException - Exception in org.biojava.bio: A nestable biological exception.
BioRuntimeException() - Constructor for exception org.biojava.bio.BioRuntimeException: Create a new BioRuntimeException.
BioRuntimeException(String) - Constructor for exception org.biojava.bio.BioRuntimeException: Create a new BioRuntimeException with a message.
BioRuntimeException(String, Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException: Create a new BioRuntimeException with a cause and a message.
BioRuntimeException(Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException: Create a new BioRuntimeException with a cause.
BioRuntimeException(Throwable, String) - Constructor for exception org.biojava.bio.BioRuntimeException: Deprecated.
use new BioRuntimeException(message, ex) instead
BioStore - Class in org.biojava.bio.program.indexdb: BioStores represent directory and file structures which index flat files according to the OBDA specification.
BioStore(File, boolean) - Constructor for class org.biojava.bio.program.indexdb.BioStore: Creates a new BioStore flatfile index at the specified location with the specified caching behaviour.
BioStoreFactory - Class in org.biojava.bio.program.indexdb: BioStoreFactory creates BioStore instances.
BioStoreFactory() - Constructor for class org.biojava.bio.program.indexdb.BioStoreFactory: Creates a new BioStoreFactory.
BIT_PACKED - Static variable in class org.biojava.bio.seq.io.SmartSequenceBuilder
bitsOfInformation(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools: Calculates the total bits of information for a distribution.
Blast2HTMLHandler - Class in org.biojava.bio.program.blast2html: Takes a SAX event stream and a HTMLRenderer to produce a HTML Blast like program report.
Blast2HTMLHandler(HTMLRenderer) - Constructor for class org.biojava.bio.program.blast2html.Blast2HTMLHandler: A content handler for rendering blast like outputs into HTML.
BlastLikeSearchFilter - Interface in org.biojava.bio.search: A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter - Class in org.biojava.bio.search
BlastLikeSearchFilter.And - Class in org.biojava.bio.search
BlastLikeSearchFilter.ByHitProperty - Class in org.biojava.bio.search: Applies test to the value specified by the key in hit properties.
BlastLikeSearchFilter.BySearchProperty - Class in org.biojava.bio.search: Applies test to the value specified by the key in search properties.
BlastLikeSearchFilter.BySubHitProperty - Class in org.biojava.bio.search: Applies test to the value specified by the key in subhit properties.
BlastLikeSearchFilter.Node - Interface in org.biojava.bio.search
BlastLikeSearchFilter.Not - Class in org.biojava.bio.search
BlastLikeSearchFilter.Or - Class in org.biojava.bio.search
BLEPH_MNUC - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the blepharisma macronuclear genetic code.
Block(int, int, int, int) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
Block(SimpleGappedSymbolList.Block) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
blockCount(Location) - Static method in class org.biojava.bio.symbol.LocationTools: Return the number of contiguous blocks in a location.
blockIterator() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
blockIterator() - Method in class org.biojava.bio.symbol.AbstractRangeLocation
blockIterator() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
blockIterator() - Method in interface org.biojava.bio.symbol.Location: Return an Iterator over the set of maximal contiguous sub-locations.
blockIterator() - Method in class org.biojavax.bio.seq.CompoundRichLocation: Return an Iterator over the set of maximal contiguous sub-locations.
blockIterator() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Return an Iterator over the set of maximal contiguous sub-locations.
blockIterator() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Return an Iterator over the set of maximal contiguous sub-locations.
BlockIterator() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Get list of the un-gapped region of the SymbolList.
BLUNT - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme: BLUNT the end type created by enzymes which leave a blunt end.
BooleanElementHandlerBase - Class in org.biojava.utils.stax: StAX handler for any element which just contains a string representation of an boolean.
BooleanElementHandlerBase() - Constructor for class org.biojava.utils.stax.BooleanElementHandlerBase
BOTH_FORWARD_COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
BoundaryFinder - Interface in org.biojava.bio.program.tagvalue
bPointers - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
bPointers - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor: Description of the Field
breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer: Deprecated.

Converts the symbol list passed in into an array of strings.
breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Converts the symbol list passed in into an array of strings.
BROAD_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
BROAD_SYNONYM - Static variable in class org.biojava.ontology.Synonym
buildDataParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools: Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener.
buildDataStore(File, SequenceStreamer, Packing, int, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
buildDataStore(File, SequenceDB, Packing, int, int) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory: Build a new DataStore.
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory
buildLibInfoParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools: Generate a tag-value parser for the library info unigene files.
buildObject(Class, List) - Method in interface org.biojavax.RichObjectBuilder: This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
buildObject(Class, List) - Method in class org.biojavax.SimpleRichObjectBuilder: This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
ByAccession(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
byAncestor(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where at least one of the ancestors matches the specified filter.
byAncestor(FeatureFilter.ByAncestor, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
ByAncestor(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAncestor
byAnnotation(Object, Object) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where the annotation property named key is equal to value.
ByAnnotation(Object, Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotation: Make a new ByAnnotation that will accept features with an annotation bundle containing 'value' associated with 'key'.
byAnnotationType(Object, Class) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where the annotation property named key is an instance of valClass.
byAnnotationType(AnnotationType) - Static method in class org.biojava.bio.seq.FilterUtils: Match features with annotations matching the specified AnnotationType
ByAnnotationType() - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.PropertyConstraint.ByAnnotationType: Create a new constraint by type.
ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
byChild(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where at least one child feature matches the supplied filter.
byChild(FeatureFilter.ByChild, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
ByChild(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByChild
byClass(Class) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches features which are assignable to the specified class or interface.
ByClass(Class) - Constructor for class org.biojava.bio.PropertyConstraint.ByClass: Create a new ByClass instance.
ByClass(Class) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByClass
byComponentName(String) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches all features which implement the ComponentFeature interface and have a componentName property equal to the specified value
ByComponentName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByComponentName
byDescendant(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where at least one decendant feature -- possibly but not necessarily an immediate child -- matches the specified filter.
byDescendant(FeatureFilter.ByDescendant, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
ByDescendant(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByDescendant
ByFeature(Feature) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByFeature
byFrame(FramedFeature.ReadingFrame) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches FramedFeatures with the specified reading frame.
byHitProperty(BlastLikeSearchFilter.ByHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
ByHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
ByHomologeneID(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
ByLocalName(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
ByLocationComparator() - Constructor for class org.biojava.bio.seq.Feature.ByLocationComparator
ByLocationMinMaxComparator - Class in org.biojava.bio.seq: A Comparator similar to Feature.ByLocationComparator except that the min and max positions of the location are both compared
ByLocationMinMaxComparator() - Constructor for class org.biojava.bio.seq.ByLocationMinMaxComparator
ByLocationMinMaxFeatureComparator - Class in org.biojava.bio.seq: Comparator that compares the min and max positions of Features Required by org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer instances.
ByLocationMinMaxFeatureComparator() - Constructor for class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
byLocationOrder - Static variable in interface org.biojava.bio.seq.Feature: byLocationOrder contains a Feature comparator which compares by the minimum base position of their Location.
ByLocusID(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
ByMaxIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
ByMinIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
ByMinIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
byName - Static variable in interface org.biojava.bio.seq.db.IDMaker: A simple implementation of IDMaker that hashes by sequence name.
ByName() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByName
ByName(String) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.ByName
ByNSName(String, String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
byPairwiseScore(double, double) - Static method in class org.biojava.bio.seq.FilterUtils: Match SeqSimilaritiy features with scores in the specified range.
ByPairwiseScore(double, double) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore: Creates a new ByPairwiseScore.
byParent(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Match features where the parent feature matches the specified filter.
byParent(FeatureFilter.ByParent, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
ByParent(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByParent
ByRef(String) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
byScore - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit: byScore contains a SeqSimilaritySearchHit comparator which compares by their score.
byScore - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: byScore contains a SeqSimilaritySearchSubHit comparator which compares by the score of the sub-hit.
ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
bySearchProperty(BlastLikeSearchFilter.BySearchProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
BySearchProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
bySequenceName(String) - Static method in class org.biojava.bio.seq.FilterUtils: Match features attached to sequences with a specified name.
BySequenceName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySequenceName
BySimilarityType(SimilarityType) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
bySource(String) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches features with a specific source value.
BySource(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySource: Create a BySource filter that filters in all features which have sources equal to source.
byStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.FilterUtils: Match StrandedFeatures on the specified strand.
bySubHitCount - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit: bySubHitCount contains a SeqSimilaritySearchHit comparator which compares by their number of sub-hits.
BySubHitCountComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
bySubHitProperty(BlastLikeSearchFilter.BySubHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
BySubHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
bySubjectStart - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: bySubjectStart contains a SeqSimilaritySearchSubHit comparator which compares by the start position of the sub-hit on the subject sequence.
BySubjectStartComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
ByTaxon(Taxon) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
ByTaxon(Taxon) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
ByTaxonID(int) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
ByteElementHandlerBase - Class in org.biojava.utils.stax: StAX handler for any element which just contains a string representation of a byte.
ByteElementHandlerBase() - Constructor for class org.biojava.utils.stax.ByteElementHandlerBase
BYTES_IN_BYTE - Static variable in class org.biojava.utils.Constants
BYTES_IN_CHAR - Static variable in class org.biojava.utils.Constants
BYTES_IN_DOUBLE - Static variable in class org.biojava.utils.Constants
BYTES_IN_FLOAT - Static variable in class org.biojava.utils.Constants
BYTES_IN_INT - Static variable in class org.biojava.utils.Constants
BYTES_IN_LONG - Static variable in class org.biojava.utils.Constants
BYTES_IN_SHORT - Static variable in class org.biojava.utils.Constants
bytesRead - Variable in class org.biojava.ontology.obo.OboFileParser
ByTitle(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
byType(String) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches features with a specific type value.
ByType(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByType: Create a ByType filter that filters in all features with type fields equal to type.
byURN - Static variable in interface org.biojava.bio.seq.db.IDMaker: A simple implementation of IDMaker that hashes by URN.
ByURN() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByURN

C

c() - Static method in class org.biojava.bio.seq.DNATools
c() - Static method in class org.biojava.bio.seq.NucleotideTools
c() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Cysteine
c() - Static method in class org.biojava.bio.seq.RNATools
C_ELEGANS - Static variable in interface org.biojava.bio.program.homologene.Taxon
cache - Variable in class org.biojava.utils.io.CachingInputStream: The byte cache itself.
Cache - Interface in org.biojava.utils.cache: Interface for managing caches of objects.
CACHE_PROPERTY - Static variable in class org.biojava.utils.io.InputStreamProvider
cachedOutcome - Variable in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
CacheMap - Interface in org.biojava.utils.cache: Interface for managing caches of objects fetchable by key.
CacheReference - Interface in org.biojava.utils.cache: Interface for a reference to an object, analogous to java.lang.ref.Referencce, but more flexible.
CachingInputStream - Class in org.biojava.utils.io: A wrapper around InputStream that provides in-memory caching of the input data.
CachingInputStream(InputStream) - Constructor for class org.biojava.utils.io.CachingInputStream
CachingKernel - Class in org.biojava.stats.svm: Caches the results of a nested kernel so that k(a, b) need only be calculated once.
CachingKernel() - Constructor for class org.biojava.stats.svm.CachingKernel
CachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.CachingKernel
CachingSequenceDB - Class in org.biojava.bio.seq.db: SequenceDB implementation that caches the results of another SequenceDB.
CachingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.CachingSequenceDB: Create a new CachingSequenceDB that caches the sequences in parent.
calcCell(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator: Calculate the 'scores' array in the cell at cells[0][0].
calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByName
calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByURN
calcID(Sequence) - Method in interface org.biojava.bio.seq.db.IDMaker: Calculate the id for a sequence.
calcKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
calculatePrimRecLen(int) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory: calculatePrimRecLen calculates the byte length of primary namespace records.
calculateScore(Distribution, Symbol) - Method in interface org.biojava.bio.dp.ScoreType: Calculates the score associated with a distribution and a symbol.
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.NullModel
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Odds
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Probability
calculateSecRecLen(int, String, Map) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory: calculateSecRecLen calculates the byte length of secondary namespace records.
callbackStack - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: this is the stack of handler objects for the current feature.
callbackStack - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler: this is the stack of handler objects for the current feature.
canAccept(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory: Accepts all URLs that are of the file protocol.
canAccept(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory: Accepts all URLs that are of the jdbc protocol.
canAccept(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
canAdvance() - Method in interface org.biojava.bio.dp.onehead.DPCursor: Can we advance?
CANDIES_NOT_SORTED - Static variable in interface org.biojava.utils.candy.CandyVocabulary: A property name.
CandyEntry - Class in org.biojava.utils.candy: This is a basic container for a vocabulary entry.
CandyEntry() - Constructor for class org.biojava.utils.candy.CandyEntry: An empty constructor.
CandyEntry(String) - Constructor for class org.biojava.utils.candy.CandyEntry: It creates an entry instance with given name and empty value.
CandyEntry(String, String) - Constructor for class org.biojava.utils.candy.CandyEntry: It creates an entry instance with given name and value.
CandyEntry(String, String, Hashtable) - Constructor for class org.biojava.utils.candy.CandyEntry: It creates an entry instance with given name, value and additional properties.
CandyException - Exception in org.biojava.utils.candy
CandyException(String) - Constructor for exception org.biojava.utils.candy.CandyException
CandyException(String, Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
CandyException(Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
CandyFinder - Interface in org.biojava.utils.candy: This interface is a main entry point to a set of controlled vocabularies.
CandyVocabulary - Interface in org.biojava.utils.candy: This interface defines functionality of a controlled vocabulary.
canMerge(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools: Determines whether the locations are touching or not (if they could be merged in a single Location.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat: Check to see if a given stream is in our format.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: Check to see if a given stream is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.FastaFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Check to see if a given file is in our format.
canRead(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat: Check to see if a given file is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: Check to see if a given file is in our format.
CardinalityConstraint - Class in org.biojava.bio: A constraint on the number of values a property can have.
Cavg - Static variable in class org.biojava.bio.proteomics.MassCalc: Constant value of Carbon average mass
Cell - Class in org.biojava.bio.dp.twohead: A single cell in the DP matrix.
Cell() - Constructor for class org.biojava.bio.dp.twohead.Cell
CellCalculator - Interface in org.biojava.bio.dp.twohead: The interface for all functions that can calculate the 'scores' array for a given cell.
CellCalculatorFactory - Interface in org.biojava.bio.dp.twohead
CellCalculatorFactoryMaker - Interface in org.biojava.bio.dp.twohead: The interface for all functions that can calculate the 'scores' array for a given cell.
CEREVISIAE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools: Saccharomyces cerevisiae codon preferences
ChainedChanger(ChangeTable.Changer[]) - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
change(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
change(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Changer: Produce a modified value from an old value.
change(Object) - Method in class org.biojava.bio.program.tagvalue.RegexChanger
change(Object, Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
CHANGE_COMMON_NAME - Static variable in interface org.biojava.bio.taxa.Taxon: Deprecated.

Change type to indicate that the common name of this Taxon is changing.
CHANGE_SCIENTIFIC_NAME - Static variable in interface org.biojava.bio.taxa.Taxon: Deprecated.

Change type to indicate that the scientific name of this Taxon is changing.
Changeable - Interface in org.biojava.utils: This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeableCache - Class in org.biojava.utils.cache: A cache that clears values as the keys fire ChangeEvents of a given type.
ChangeableCache(ChangeType) - Constructor for class org.biojava.utils.cache.ChangeableCache
ChangeAdapter - Class in org.biojava.utils: This is a ChangeListener that ignores everything.
ChangeAdapter() - Constructor for class org.biojava.utils.ChangeAdapter
ChangeEvent - Class in org.biojava.utils: Event which encapsulates a change in any mutable BioJava object.
ChangeEvent(Object, ChangeType) - Constructor for class org.biojava.utils.ChangeEvent: Construct a ChangeEvent with no change details.
ChangeEvent(Object, ChangeType, Object) - Constructor for class org.biojava.utils.ChangeEvent: Construct a ChangeEvent specifying a new value for a property, or an object to be added to a collection.
ChangeEvent(Object, ChangeType, Object, Object) - Constructor for class org.biojava.utils.ChangeEvent: Construct a ChangeEvent specifying a new value for a property, and giving the previous value.
ChangeEvent(Object, ChangeType, Object, Object, ChangeEvent) - Constructor for class org.biojava.utils.ChangeEvent: Construct a ChangeEvent to be fired because another ChangeEvent has been received from a property object.
ChangeEventRecorder() - Constructor for class org.biojava.utils.ChangeListener.ChangeEventRecorder
ChangeForwarder - Class in org.biojava.utils: This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeForwarder(Object, ChangeSupport) - Constructor for class org.biojava.utils.ChangeForwarder: Create a new ChangeForwarder for forwarding events.
ChangeForwarder.Retyper - Class in org.biojava.utils: A ChangeForwarder that systematically uses a given type and wraps the old event.
ChangeHub - Interface in org.biojava.utils: Interface implemented by ChangeHubs, i.e.
ChangeListener - Interface in org.biojava.utils: Interface for objects which listen to ChangeEvents.
ChangeListener.AlwaysVetoListener - Class in org.biojava.utils: An implementation that always vetoes everything.
ChangeListener.ChangeEventRecorder - Class in org.biojava.utils: A listener that remembers the ChangeEvent of the last change.
ChangeListener.LoggingListener - Class in org.biojava.utils: A listener that writes information about the event stream to a PrintStream.
changeSupport() - Method in class org.biojava.utils.ChangeForwarder: Return the underlying ChangeSupport instance that can be used to fire ChangeEvents and mannage listeners.
ChangeSupport - Class in org.biojava.utils: A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeSupport() - Constructor for class org.biojava.utils.ChangeSupport: Generate a new ChangeSupport instance.
ChangeSupport(int) - Constructor for class org.biojava.utils.ChangeSupport: Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources.
ChangeSupport(int, int) - Constructor for class org.biojava.utils.ChangeSupport: Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources, and which will grow by delta each time.
ChangeSupport(Set) - Constructor for class org.biojava.utils.ChangeSupport
ChangeSupport(Set, int, int) - Constructor for class org.biojava.utils.ChangeSupport: Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources, and which will grow by delta each time.
ChangeTable - Class in org.biojava.bio.program.tagvalue: A mapping between keys and actions to turn old values into new values.
ChangeTable() - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable
ChangeTable.ChainedChanger - Class in org.biojava.bio.program.tagvalue: An implementation of Changer that applies a list of Changer instances to the value in turn.
ChangeTable.Changer - Interface in org.biojava.bio.program.tagvalue: Callback used to produce a new value from an old one.
ChangeTable.Splitter - Interface in org.biojava.bio.program.tagvalue: Callback used to produce a list of values from a single old one.
ChangeType - Class in org.biojava.utils: Class for all constants which are used to indicate change types.
ChangeType(String, Class, String) - Constructor for class org.biojava.utils.ChangeType: Construct a new ChangeType with supertype UNKNOWN.
ChangeType(String, Class, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType: Construct a new ChangeType.
ChangeType(String, Field) - Constructor for class org.biojava.utils.ChangeType: Construct a new ChangeType with superType UNKNOWN.
ChangeType(String, Field, ChangeType) - Constructor for class org.biojava.utils.ChangeType: Construct a new ChangeType.
ChangeType(String, String, String) - Constructor for class org.biojava.utils.ChangeType
ChangeType(String, String, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
ChangeVetoException - Exception in org.biojava.utils: Exception which is thrown when a ChangeListener does not wish a change to take place.
ChangeVetoException() - Constructor for exception org.biojava.utils.ChangeVetoException
ChangeVetoException(String) - Constructor for exception org.biojava.utils.ChangeVetoException: Create an exception with a detail message
ChangeVetoException(String, Throwable) - Constructor for exception org.biojava.utils.ChangeVetoException
ChangeVetoException(Throwable, String) - Constructor for exception org.biojava.utils.ChangeVetoException: Deprecated.
use new ChangeVetoException(reason, ex);
ChangeVetoException(Throwable, ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException: Propogate an exception without (additional) explanation.
ChangeVetoException(Throwable, ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException: Propogate an exception, giving a detail message
ChangeVetoException(ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException: Construct an exception to veto a change without explanation.
ChangeVetoException(ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException: Construct an exception to veto a change for a specified reason.
CHARACTER - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
characters(char[], int, int) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler: Describe characters method here.
characters(char[], int, int) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase: Signal a span of character data in the XML input.
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.StreamParser
characters(char[], int, int) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.CharElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.IntElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.LongElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
characters(char[], int, int) - Method in interface org.biojava.utils.stax.StAXContentHandler
characters(char[], int, int) - Method in class org.biojava.utils.stax.StAXContentHandlerBase: Signal a span of character data in the XML input.
characters(char[], int, int) - Method in class org.biojava.utils.stax.StringElementHandlerBase
CharacterTokenization - Class in org.biojava.bio.seq.io: Implementation of SymbolTokenization which binds symbols to single unicode characters.
CharacterTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.CharacterTokenization
charAt(int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
charAt(int) - Method in class org.biojava.utils.RepeatedCharSequence
CharElementHandlerBase - Class in org.biojava.utils.stax: StAX handler for any element which just contains a string representation of a char.
CharElementHandlerBase() - Constructor for class org.biojava.utils.stax.CharElementHandlerBase
charValue(Symbol) - Method in class org.biojava.utils.regex.PatternFactory: Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for.
charValue(Symbol) - Method in class org.biojava.utils.regex.Search
checkException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
checkException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
checkIOException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
checkIOException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
checkIOException() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
children - Variable in class org.biojava.bio.taxa.SimpleTaxon: Deprecated.
CHLORO_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the chlorophycean mitochondrial genetic code.
chromosomes - Variable in class org.biojavax.ga.impl.AbstractOrganism
CHROMOSOMES - Static variable in interface org.biojavax.ga.Organism
ChunkedSymbolList - Class in org.biojava.bio.symbol: SymbolList implementation using constant-size chunks.
ChunkedSymbolList(SymbolList[], int, int, Alphabet) - Constructor for class org.biojava.bio.symbol.ChunkedSymbolList
ChunkedSymbolListFactory - Class in org.biojava.bio.seq.io: class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves.
ChunkedSymbolListFactory(SymbolListFactory) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
ChunkedSymbolListFactory(SymbolListFactory, int) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.Protease
CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.ProteaseManager
CILIATE_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the ciliate nuclear genetic code.
CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichLocation
CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichSequence
CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
circularLength - Variable in class org.biojavax.bio.seq.SimpleRichLocation
CircularLocation - Class in org.biojava.bio.symbol: Circular view onto an underlying Location instance.
CircularLocation(Location, int) - Constructor for class org.biojava.bio.symbol.CircularLocation: Constructs a CircularLocation by wrapping another Location It is preferable to use LocationTools to make CircularLocations
CircularLocation(Location, int, int) - Constructor for class org.biojava.bio.symbol.CircularLocation: Makes a CircularLocation where the 5' end of the Location is specified.
CircularReferenceException - Exception in org.biojava.bio.taxa: Deprecated.
replaced by classes in org.biojavax.bio.taxa
CircularReferenceException() - Constructor for exception org.biojava.bio.taxa.CircularReferenceException: Deprecated.
CircularReferenceException(String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException: Deprecated.
CircularReferenceException(Throwable) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException: Deprecated.
CircularReferenceException(Throwable, String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException: Deprecated.
CircularView - Class in org.biojava.bio.seq: A circular view onto another Sequence object.
CircularView(Sequence) - Constructor for class org.biojava.bio.seq.CircularView
CircularView(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.CircularView
CITATION_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_FIRST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_ID_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_INSTITUTE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_ISSUE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_LAST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_PATENT_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_PUB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
CITATION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_VOL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_YEAR_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ClassifierExample - Class in org.biojava.stats.svm.tools: A simple toy example that allows you to put points on a canvas, and find a polynomial hyperplane to seperate them.
ClassifierExample() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample
ClassifierExample.PointClassifier - Class in org.biojava.stats.svm.tools: An extention of JComponent that contains the points & encapsulates the classifier.
classify() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier: Learn a model from the current points.
classify(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
classify(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
classify(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
Classify - Class in org.biojava.stats.svm.tools
Classify() - Constructor for class org.biojava.stats.svm.tools.Classify
ClassTools - Class in org.biojava.utils: Utility methods for manipulating class objects and resources.
clear() - Method in class org.biojava.bio.dp.twohead.EmissionCache
clear() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
clear() - Method in class org.biojava.stats.svm.AbstractSVMTarget
clear() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
clear() - Method in class org.biojava.stats.svm.SimpleSVMTarget
clear() - Method in interface org.biojava.stats.svm.SVMClassifierModel
clear() - Method in interface org.biojava.stats.svm.SVMTarget
clear() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier: Remove all points from the canvas, and discard any model.
clear() - Method in interface org.biojava.utils.cache.CacheReference
clear() - Method in class org.biojava.utils.FileAsList
clear() - Method in class org.biojava.utils.io.FlatFileCache
clear() - Method in class org.biojava.utils.io.SoftHashMap
clear() - Method in class org.biojavax.EmptyRichAnnotation: Removes all notes from this annotation object.
clear() - Method in class org.biojavax.ga.util.WeightedSet
clear() - Method in interface org.biojavax.RichAnnotation: Removes all notes from this annotation object.
clear() - Method in class org.biojavax.SimpleRichAnnotation: Removes all notes from this annotation object.
clearCounts() - Method in interface org.biojava.bio.dist.DistributionTrainerContext: Clears all of the counts to zero.
clearCounts() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
clearCounts() - Method in interface org.biojava.bio.dp.TransitionTrainer: Clears all of the counts to zero.
clearCounts(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.DistributionTrainer: Clears all of the counts to zero.
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer: Deprecated.
clearEnzymes() - Method in class org.biojava.bio.molbio.RestrictionMapper: clearEnzymes removes all enzymes from those to be searched for in the Sequence.
clearLRUCache() - Static method in class org.biojavax.RichObjectFactory: Removes all objects from the LRU cache.
clearLRUCache(Class) - Static method in class org.biojavax.RichObjectFactory: Removes all objects of the specified class from the LRU cache.
clearPatterns() - Method in class org.biojava.utils.regex.Search: remove all patterns from the pattern cache.
clone() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
clone() - Method in class org.biojava.bio.seq.Feature.Template
clone() - Method in class org.biojava.bio.seq.impl.RevCompSequence: clone() should make a complete copy of the Sequence with all features (and children) and return a SimpleSequence that is unconnected from the original sequence.
clone() - Method in class org.biojava.utils.ExecRunner: We override the clone method here to prevent cloning of our class.
clone() - Method in class org.biojava.utils.TypedProperties
close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader: close closes the underlying InputStream.
close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess: close closes the underlying RandomAccessFile.
close() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore: close closes the underlying EntryNamRandomAccess which in turn closes the lower level RandomAccessFile.
close() - Method in interface org.biojava.bio.seq.io.StreamParser
close() - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
close() - Method in class org.biojava.naming.ObdaContext
close() - Method in class org.biojava.utils.io.CountedBufferedReader
close() - Method in class org.biojava.utils.io.RandomAccessReader: close closes the underlying RandomAccessFile.
close() - Method in class org.biojava.utils.xml.PrettyXMLWriter
close() - Method in interface org.biojava.utils.xml.XMLWriter: Close this XMLWriter, and it's underlying stream.
closeTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
closeTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
closeTag(String) - Method in interface org.biojava.utils.xml.XMLWriter: Closes an un-qualified element.
closeTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
closeTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter: Closes an element
CLUSTAL - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: CLUSTAL indicates that the alignment format is Clustal.
CLUSTAL_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: CLUSTAL_AA premade CLUSTAL | AA;
CLUSTAL_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: CLUSTAL_DNA premade CLUSTAL | DNA;
CLUSTAL_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: CLUSTAL_RNA premade CLUSTAL | RNA;
Cmono - Static variable in class org.biojava.bio.proteomics.MassCalc: Constant value of Carbon monoisotopic mass
CNBr - Static variable in class org.biojava.bio.proteomics.Protease
CNBr - Static variable in class org.biojava.bio.proteomics.ProteaseManager
codes - Variable in class org.biojava.bibliography.BiblioSubject: Classification code (call number) is usually either Dewey decimal or Congress classification.
CodonPref - Interface in org.biojava.bio.symbol
CodonPrefFilter - Interface in org.biojava.bio.symbol
CodonPrefFilter.AcceptAll - Class in org.biojava.bio.symbol
CodonPrefFilter.ByName - Class in org.biojava.bio.symbol
CodonPrefFilter.EverythingToXML - Class in org.biojava.bio.symbol
CodonPrefTools - Class in org.biojava.bio.symbol: An utility class for codon preferences
CodonPrefTools() - Constructor for class org.biojava.bio.symbol.CodonPrefTools
CollectionConstraint - Interface in org.biojava.bio: Used by AnnotationType to represent the constraint on the collection of values in a property-slot.
CollectionConstraint.AllValuesIn - Class in org.biojava.bio: CollectionConstraint which validates all members of a Collection.
CollectionConstraint.And - Class in org.biojava.bio: A collection constraint that accpepts collections iff they are accepted by both child constraints.
CollectionConstraint.Contains - Class in org.biojava.bio: CollectionConstraint which validates a portion of a Collection.
CollectionConstraint.Or - Class in org.biojava.bio: A collection constraint that accepts items iff they are accepted by either child constraints.
ColourCommand - Interface in org.biojava.bio.program.blast2html: Interface for specifying whether a particular pair of residues/bases should be coloured.
columns - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
columns() - Method in class org.biojava.bio.dp.ProfileHMM: Retrieve the number of columns in the model.
columns() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
columns() - Method in interface org.biojava.bio.dp.WeightMatrix: The number of columns modeled by the weight matrix.
Comment - Interface in org.biojavax: A simple ranked comment designed to be used for BioEntry comments in BioSQL.
COMMENT - Static variable in class org.biojava.ontology.obo.OboFileHandler
COMMENT - Static variable in interface org.biojavax.bio.BioEntry
COMMENT_ABS_MAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ABSORPTION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ERROR_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_EVENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_EXPERIMENTS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_INTERACT_INTACT_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_INTERACT_LABEL_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_INTERACTANT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ISOFORM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_KIN_KM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_KIN_VMAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_KINETICS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_LINK_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_LINK_URI_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_LOCTYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_METHOD_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ORGANISMS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_PH_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_REDOX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_TEMPERATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
commentLine(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler: A comment line has been encountered.
commentLine(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
commentLine(String) - Method in class org.biojava.bio.program.gff.GFFWriter: Prints the comment directly to the PrintWriter after adding a leading '#'.
commentLine(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler: A comment line has been encountered.
commit() - Method in class org.biojava.bio.program.indexdb.BioStore: commit writes an index to disk.
commit() - Method in class org.biojava.bio.seq.db.BioIndex
commit() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore: commit commits changes.
commit() - Method in interface org.biojava.bio.seq.db.IndexStore: Commit the stored indices to permanent storage.
commit() - Method in class org.biojava.bio.seq.db.TabIndexStore
commit() - Method in interface org.biojava.utils.Commitable: commit commits pending changes.
commit() - Method in class org.biojava.utils.FileAsList
Commitable - Interface in org.biojava.utils: Implementations of Commitable support atomic changes from one known state to another via commit/rollback semantics.
CommitFailure - Exception in org.biojava.utils
CommitFailure(String) - Constructor for exception org.biojava.utils.CommitFailure
CommitFailure(String, Throwable) - Constructor for exception org.biojava.utils.CommitFailure
CommitFailure(Throwable) - Constructor for exception org.biojava.utils.CommitFailure
commitStore() - Method in class org.biojava.bio.seq.db.TabIndexStore
COMMON - Static variable in interface org.biojavax.bio.taxa.NCBITaxon: Use this to define common names for things.
COMMON_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
COMNAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CompactedDataStore - Class in org.biojava.bio.program.ssaha: An implementation of DataStore that will map onto a file using the NIO constructs.
CompactedDataStoreFactory - Class in org.biojava.bio.program.ssaha: Builder for a data store that is backed by a java.nio.MappedByteBuffer.
CompactedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
ComparableOntology - Interface in org.biojavax.ontology: An Ontology that can be compared to another.
ComparableTerm - Interface in org.biojavax.ontology: Makes Term objects comparable properly and adds some extra features to them.
ComparableTriple - Interface in org.biojavax.ontology: Comparable triples, obviously.
comparator() - Static method in class org.biojava.bio.seq.ByLocationMinMaxComparator
COMPARATOR - Static variable in class org.biojava.ontology.Synonym
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.Feature.ByLocationComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.io.EmblReferenceComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblFeatureComparator: Deprecated.
compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblPropertyComparator: Deprecated.
compareTo(Object) - Method in class org.biojavax.bio.seq.CompoundRichLocation: Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
compareTo(Object) - Method in class org.biojavax.bio.seq.EmptyRichLocation: Empty Rich Locations return 0 when compared to other Empty ones, or -1 otherwise.
compareTo(Object) - Method in class org.biojavax.bio.seq.RichLocation.Strand: Strands are compared first by symbol, then by number.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Features are sorted first by rank, then parent, type, and source.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Relations are compared first by rank, then object, subject, then finally term.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichLocation: Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntry: Bioentries are ordered first by namespace, then name, accession, and finally version.
compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntryRelationship: A relationship is compared first by rank, then object, subject, and term.
compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: NCBITaxon objects are compared only by their NCBITaxID fields.
compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName: Taxon names are sorted by class first, then name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableOntology: Ontologies are compared only by name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm: Terms are sorted by ontology first, then name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple: Triples are sorted in order of ontology, subject, object, and finally predicate.
compareTo(Object) - Method in class org.biojavax.SimpleComment: Comments are ordered first by their rank, then by a string comparison of their text values.
compareTo(Object) - Method in class org.biojavax.SimpleCrossRef: Compares cross references first by database name, then by accession, then by version.
compareTo(Object) - Method in class org.biojavax.SimpleDocRef: Document references are compared first by author, then by location, then by title.
compareTo(Object) - Method in class org.biojavax.SimpleDocRefAuthor: Document authors are compared first by name, then consortium status, then editor status.
compareTo(Object) - Method in class org.biojavax.SimpleNamespace: Namespaces are compared only by name.
compareTo(Object) - Method in class org.biojavax.SimpleNote: Notes are compared first by rank, then by the term.
compareTo(Object) - Method in class org.biojavax.SimpleRankedCrossRef: Ranked cross references are sorted first by rank, then by cross reference.
compareTo(Object) - Method in class org.biojavax.SimpleRankedDocRef: Ranked document references are sorted first by rank then location then by actual document reference.
compareTo(Synonym) - Method in class org.biojava.ontology.Synonym
compile(String) - Method in class org.biojava.utils.regex.PatternFactory: Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
compile(String, String) - Method in class org.biojava.utils.regex.PatternFactory: Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
complement(Symbol) - Static method in class org.biojava.bio.seq.DNATools: Complement the symbol.
complement(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools: Complement the symbol.
complement(Symbol) - Static method in class org.biojava.bio.seq.RNATools: Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools: Retrieve a complement view of list.
complement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools: Retrieve a complement view of list.
complement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools: Retrieve a complement view of list.
COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
complementTable() - Static method in class org.biojava.bio.seq.DNATools: Get a translation table for complementing DNA symbols.
complementTable() - Static method in class org.biojava.bio.seq.NucleotideTools: Get a translation table for complementing Nucleotide symbols.
complementTable() - Static method in class org.biojava.bio.seq.RNATools: Get a translation table for complementing DNA symbols.
completeCycle() - Method in interface org.biojava.bio.dp.HMMTrainer: indicate that a cycle of training is completed and the emission/transition matrices should be updated.
completeCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer
completedActivity(Object) - Method in interface org.biojava.utils.ActivityListener: Notification that an activity is complete.
COMPONENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ComponentFeature - Interface in org.biojava.bio.seq: Feature which represents a component in an assembly (contig).
ComponentFeature.Template - Class in org.biojava.bio.seq: Template for constructing a new ComponentFeature.
componentLocation - Variable in class org.biojava.bio.seq.ComponentFeature.Template
componentLocationIterator() - Method in class org.biojava.bio.symbol.MergeLocation
componentSequence - Variable in class org.biojava.bio.seq.ComponentFeature.Template
componentSequenceName - Variable in class org.biojava.bio.seq.ComponentFeature.Template
composeName(String, String) - Method in class org.biojava.naming.ObdaContext
composeName(Name, Name) - Method in class org.biojava.naming.ObdaContext
Composite() - Constructor for class org.biojava.directory.RegistryConfiguration.Composite
Composition - Class in org.biojava.bio.molbio: Computes composition statistics about a SymbolList.
Composition() - Constructor for class org.biojava.bio.molbio.Composition
Compound() - Constructor for class org.biojava.bio.program.formats.Ligand.Compound
CompoundRichLocation - Class in org.biojavax.bio.seq: An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
CompoundRichLocation() - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
CompoundRichLocation(Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation: Constructs a CompoundRichLocation from the given set of members, with the default term of "join".
CompoundRichLocation(ComparableTerm, Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation: Constructs a CompoundRichLocation from the given set of members.
compute(double) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc.ChargeCalculator: computes charge at given pH
compute(double) - Method in interface org.biojava.utils.math.ComputeObject: workhorse method for this class.
ComputeObject - Interface in org.biojava.utils.math: interface for classes that return a single double precision value for a single double precision argument.
conditionedDistributions() - Method in interface org.biojava.bio.dist.OrderNDistribution: Get the conditioned distributions.
CONFIG_FILE - Static variable in class org.biojava.directory.SystemRegistry
CONFIG_LOCATOR - Static variable in class org.biojava.directory.SystemRegistry
connect() - Method in interface org.biojava.bibliography.BibRefQuery: It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication.
connect() - Method in interface org.biojava.bibliography.BibRefSupport: It creates a connection to an object providing the supporting utilities, or/and it makes all necessary initialization steps needed for further communication.
connect() - Method in interface org.biojava.utils.candy.CandyFinder: It creates a connection to an object representing a vocabulary finder, or/and it makes all necessary initialization steps needed for further communication.
connect(byte[]) - Method in interface org.biojava.bibliography.BibRefQuery: It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication, and it makes the collection described by collectionId the current collection.
connectModel() - Method in class org.biojava.bio.dp.ProfileHMM: This is called by constructor in setting up the allowed transitions in the model
connectModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM: This is called by constructor in setting up the allowed transitions in the model
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
Constants - Class in org.biojava.utils: Some usefull constants for working with binary files.
Constants() - Constructor for class org.biojava.utils.Constants
construct(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools: Constructs a RichLocation object based on the given collection of members.
constructSubsets() - Method in class org.biojava.utils.automata.DfaBuilder
containedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils: Construct a filter which matches features with locations wholly contained by the specified Location.
ContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ContainedByLocation: Creates a filter that returns everything contained within loc.
contains(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
contains(int) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
contains(int) - Method in class org.biojava.bio.symbol.CircularLocation
contains(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
contains(int) - Method in interface org.biojava.bio.symbol.Location: Checks if this location contains a point.
contains(int) - Method in class org.biojava.bio.symbol.PointLocation
contains(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation: Checks if this location contains a point.
contains(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation: Checks if this location contains a point.
contains(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation: Checks if this location contains a point.
contains(Object) - Method in class org.biojava.utils.MergingSet
contains(Object) - Method in class org.biojava.utils.SmallSet
contains(Object) - Method in class org.biojavax.ga.util.WeightedSet
contains(String) - Method in interface org.biojava.utils.candy.CandyVocabulary: It checks if a given entry exists in this vocabulary.
contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
contains(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
contains(Location) - Method in class org.biojava.bio.symbol.CircularLocation
contains(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
contains(Location) - Method in interface org.biojava.bio.symbol.Location: Checks if this location contains the other.
contains(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation: Checks if this location contains the other.
contains(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation: Checks if this location contains the other.
contains(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation: Checks if this location contains the other.
contains(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools: Return true iff all indices in locB are also contained by locA.
contains(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
contains(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet: Returns whether or not this Alphabet contains the symbol.
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
contains(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
contains(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
contains(Note) - Method in class org.biojavax.EmptyRichAnnotation: Returns true if the given note exists in this annotation.
contains(Note) - Method in interface org.biojavax.RichAnnotation: Returns true if the given note exists in this annotation.
contains(Note) - Method in class org.biojavax.SimpleRichAnnotation: Returns true if the given note exists in this annotation.
Contains(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.Contains: Create a Contains based upon a PropertyConstraint and a cardinality.
CONTAINS_PREFIX - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
containsAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
containsFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder: Check if the feature is present in this holder.
containsFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence: containsFeature() will return true if this seq contains the feature in question, or if if the original (non reverse complement) sequence contains the feature;
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.MergeFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly
containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly
containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
containsFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Check if the feature is present in this holder.
containsFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence: Check if the feature is present in this holder.
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
containsKey(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
containsKey(Object) - Method in class org.biojava.utils.OverlayMap
containsKey(Object) - Method in class org.biojava.utils.SmallMap
containsName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon: Tests for the presence of a name in a given class.
containsName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Tests for the presence of a name in a given class.
containsNode(FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
containsProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
containsProperty(Object) - Method in interface org.biojava.bio.Annotation: Returns whether there the property is defined.
containsProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
containsProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
containsProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation: Returns whether there the property is defined.
containsProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation: Deprecated.
containsTerm(String) - Method in class org.biojava.ontology.IntegerOntology
containsTerm(String) - Method in interface org.biojava.ontology.Ontology: Determines if this ontology currently contains a term named name
containsTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
containsTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Determines if this ontology currently contains a term named name
containsTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel: Returns wether a transition exists or not.
containsTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
containsTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology
containsTriple(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology: See if a triple exists in this ontology
containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl
containsTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology: See if a triple exists in this ontology
CONTENT - Static variable in interface org.biojava.bio.alignment.Alignment: Signals that SymbolLists will be added to or removed from an alignment.
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
contributors - Variable in class org.biojava.bibliography.BibRef: The authors and contributors are responsible for creating the contents of the cited resource.
COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
COPYRIGHT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
cost - Variable in class org.biojava.bibliography.BiblioWebResource: The cost of accessing the resource.
Count - Interface in org.biojava.bio.dist: An encapsulation of a count over the Symbols within an alphabet.
CountedBufferedReader - Class in org.biojava.utils.io
CountedBufferedReader(Reader) - Constructor for class org.biojava.utils.io.CountedBufferedReader
countFeatures() - Method in interface org.biojava.bio.seq.FeatureHolder: Count how many features are contained.
countFeatures() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.impl.DummySequence
countFeatures() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.impl.RevCompSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleFeature
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
countFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.MergeFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.NewSimpleAssembly
countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.SimpleAssembly
countFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
countFeatures() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Count how many features are contained.
countFeatures() - Method in class org.biojavax.bio.seq.ThinRichSequence: Count how many features are contained.
COUNTS - Static variable in interface org.biojava.bio.dist.Count: Whenever a component count changes the values that would be returned by getCount, they should fire a ChangeEvent with this object as the type.
countToDistribution(Count) - Static method in class org.biojava.bio.dist.DistributionTools: Make a distribution from a count.
coverage - Variable in class org.biojava.bibliography.BibRef: It defines an extent or scope of the content of the cited resource.
coverage(Location) - Static method in class org.biojava.bio.symbol.LocationTools: Return the number of positions which are covered by a Location
CRC64Checksum - Class in org.biojavax.utils: Utility class that calculates a CRC64 checksum on a stream of bytes.
CRC64Checksum() - Constructor for class org.biojavax.utils.CRC64Checksum
CREATE_DATE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
CREATE_REL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
createBinary(String) - Static method in class org.biojavax.ga.util.GATools: Creates a SymbolList in the GABinary Alphabet
createBioStore() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory: createBioStore creates a BioStore reflecting the current state of the factory and returns a reference to it.
createDistribution(Alphabet) - Method in interface org.biojava.bio.dist.DistributionFactory: Generate a new Distribution as requested.
createDistribution(Alphabet) - Method in class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
createDistribution(Alphabet) - Method in class org.biojava.bio.dist.OrderNDistributionFactory: Creates an OrderNDistribution of the appropriate type.
createDNA(String) - Static method in class org.biojava.bio.seq.DNATools: Return a new DNA SymbolList for dna.
createDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools: Return a new DNA Sequence for dna.
createDP(MarkovModel) - Method in interface org.biojava.bio.dp.DPFactory
createDP(MarkovModel) - Method in class org.biojava.bio.dp.DPFactory.DefaultFactory
createDummy(String, String) - Static method in class org.biojava.bio.seq.SequenceTools: Create a new Sequence that has no annotation, no features and a zero-length symbol list.
createDummy(Alphabet, int, Symbol, String, String) - Static method in class org.biojava.bio.seq.SequenceTools: Create a new Sequence that contains a single symbol repeated over and over.
createEmblParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.CircularView: Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.FeatureHolder: Create a new Feature, and add it to this FeatureHolder.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.DummySequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.RevCompSequence: createFeature() will call createFeature() on the underlying Sequence.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SubSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.LazyFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext: Create a projected feature with properties matching the template.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Create a new Feature, and add it to this FeatureHolder.
createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.ThinRichSequence: Create a new Feature, and add it to this FeatureHolder.
createFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence: Deprecated.
Please use new 1-arg createFeature instead.
createFeature(Feature, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext: Create a new projected feature.
createFeature(Feature, Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
createFeatureHolder() - Method in class org.biojava.bio.seq.LazyFeatureHolder
createFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler: Create a new template of the appropriate type.
createFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
createGappedDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools: Get a new dna as a GappedSequence
createGappedProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools: Get a new protein as a GappedSequence
createGFFRecord(Feature, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Internal method to create a GFFRecord from an individual Feature.
createList(Object[]) - Static method in class org.biojava.utils.ListTools
createList(List) - Static method in class org.biojava.utils.ListTools
createMatches() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
createNodeSet() - Method in class org.biojava.utils.automata.FiniteAutomaton
createNodeSet() - Method in interface org.biojava.utils.automata.NfaBuilder
createNodeSet() - Method in class org.biojava.utils.automata.NfaSubModel
createNucleotide(String) - Static method in class org.biojava.bio.seq.NucleotideTools: Return a new Nucleotide SymbolList for nucleotide.
createNucleotideSequence(String, String) - Static method in class org.biojava.bio.seq.NucleotideTools: Return a new Nucleotide Sequence for nucleotide.
createOntology(String, String) - Method in interface org.biojava.ontology.OntologyFactory: Creates a new Ontology
createOntologyTerm(Ontology) - Method in class org.biojava.ontology.Ontology.Impl
createOrthologue(int, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Create an orthologue.
createOrthologue(int, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthologue(Taxon, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Create an orthologue.
createOrthologue(Taxon, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthoPair(Orthologue, Orthologue, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Create a curated orthology entry.
createOrthoPair(Orthologue, Orthologue, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Create a computed orthology entry.
createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthoPairSet() - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Create a Homologene Group.
createOrthoPairSet() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createPhred(SymbolList, SymbolList) - Static method in class org.biojava.bio.program.phred.PhredTools: Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.
createProtease(String, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
createProtease(String, boolean, String, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
createProtease(SymbolList, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
createProtease(SymbolList, boolean, SymbolList, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager: Creates and registers a new Protease.
createProtein(String) - Static method in class org.biojava.bio.seq.ProteinTools: Return a new Protein SymbolList for protein.
createProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools: Return a new PROTEIN Sequence for protein.
createRecord(GFFDocumentHandler, List, String, String) - Method in class org.biojava.bio.program.gff.GFFParser: Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
createRecord(GFF3DocumentHandler, List, String, String, Ontology, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser: Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.
createRegex(SymbolList) - Static method in class org.biojava.bio.symbol.MotifTools: createRegex creates a regular expression which matches the SymbolList.
createRichSequence(String, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Create a new RichSequence in the specified namespace.
createRichSequence(String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Create a new RichSequence in the default namespace.
createRichSequence(String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Create a new RichSequence in the default namespace.
createRichSequence(Namespace, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Create a new RichSequence in the specified namespace.
createRichSequence(Namespace, String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Create a new RichSequence in the specified namespace.
createRNA(String) - Static method in class org.biojava.bio.seq.RNATools: Return a new RNA SymbolList for rna.
createRNASequence(String, String) - Static method in class org.biojava.bio.seq.RNATools: Return a new RNA Sequence for rna.
createSequence(SymbolList, String, String, Annotation) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
createSequence(SymbolList, String, String, Annotation) - Method in interface org.biojava.bio.seq.SequenceFactory: Deprecated.

Creates a sequence using these parameters.
createSequence(SymbolList, String, String, Annotation) - Static method in class org.biojava.bio.seq.SequenceTools
createSeriesList(String, String, int) - Static method in class org.biojava.utils.ListTools: Create a new SeriesList with the given leader, trailer and size.
createState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine
createSubcontext(String) - Method in class org.biojava.naming.ObdaContext
createSubcontext(String, Attributes) - Method in class org.biojava.naming.ObdaContext
createSubcontext(Name) - Method in class org.biojava.naming.ObdaContext
createSubcontext(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
createSwissprotParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
createSymbol(char, String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager: Deprecated.
Use the two-arg version of this method instead.
createSymbol(char, Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Deprecated.
use the new version, without the token argument
createSymbol(char, Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Deprecated.
use the three-arg version of this method instead.
createSymbol(String) - Static method in class org.biojava.bio.symbol.AlphabetManager: Generate a new AtomicSymbol instance with a name and an Empty Annotation.
createSymbol(String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager: Generate a new AtomicSymbol instance with a name and Annotation.
createSymbol(Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Generates a new Symbol instance that represents the tuple of Symbols in symList.
createSymbol(Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Generates a new Symbol instance that represents the tuple of Symbols in symList.
createTaxon(int, String) - Static method in class org.biojava.bio.program.homologene.HomologeneTools: add a Taxon
createTaxon(String, String) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory: Deprecated.
createTaxon(String, String) - Method in interface org.biojava.bio.taxa.TaxonFactory: Deprecated.

Create a new orphan Taxon with a given scientific and common name.
createTaxon(String, String) - Method in class org.biojava.bio.taxa.WeakTaxonFactory: Deprecated.
createTemplate() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: generates a very basic Template for the feature with SmallAnnotation in the annotation field.
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
createTemplate() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: generates a very basic Template for the feature with SmallAnnotation in the annotation field.
createTerm(String) - Method in class org.biojava.ontology.IntegerOntology
createTerm(String) - Method in interface org.biojava.ontology.Ontology: Create a new term in this ontology.
createTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
createTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Create a new term in this ontology.
createTerm(String, String) - Method in class org.biojava.ontology.IntegerOntology
createTerm(String, String) - Method in interface org.biojava.ontology.Ontology: Create a new term in this ontology.
createTerm(String, String) - Method in class org.biojava.ontology.Ontology.Impl
createTerm(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in class org.biojava.ontology.IntegerOntology
createTerm(String, String, Object[]) - Method in interface org.biojava.ontology.Ontology: Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in class org.biojava.ontology.Ontology.Impl
createTerm(String, String, Object[]) - Method in class org.biojavax.ontology.SimpleComparableOntology: Create a new term in this ontology.
createTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel: Makes a transition between two states legal.
createTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
createTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
createTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.IntegerOntology
createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.ontology.Ontology: Creates a new Triple.
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.Ontology.Impl
createTriple(Term, Term, Term, String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Creates a new Triple.
createType(String, FeatureFilter, Set) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl: Create a new type in this repository.
createUnigene(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
createUnigene(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
createUnigene(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
createUnigene(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools: Create a new UnigeneDB instance referred to by a URL.
createURL(Object) - Method in interface org.biojava.utils.net.URLFactory: createURL returns a URL which is relevant to the object in a way specified by the implementation.
createVariable(String, String) - Method in class org.biojava.ontology.IntegerOntology
createVariable(String, String) - Method in interface org.biojava.ontology.Ontology: Create a new term in this ontology that is used as a variable.
createVariable(String, String) - Method in class org.biojava.ontology.Ontology.Impl
createVariable(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Create a new term in this ontology that is used as a variable.
CROSS_OVER_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
CrossOverFunction - Interface in org.biojavax.ga.functions: Crosses two chromosomes.
CrossOverFunction.NoCross - Class in org.biojavax.ga.functions: A place holder CrossOverFunction that doesn't perform cross overs
CrossProductTokenization - Class in org.biojava.bio.seq.io: Tokenization for cross-product alphabets.
CrossProductTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
CrossProductTokenization(Alphabet, List) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
CrossRef - Interface in org.biojavax: Represents a cross reference to another database.
CROSSREF - Static variable in interface org.biojavax.bio.seq.RichFeature
CROSSREF - Static variable in interface org.biojavax.DocRef
CrossReferenceResolutionException - Exception in org.biojavax: An exception that indicates that an attempt to resolve a CrossRef has failed.
CrossReferenceResolutionException() - Constructor for exception org.biojavax.CrossReferenceResolutionException: Creates a new instance of CrossReferenceResolutionException
CrossReferenceResolutionException(String) - Constructor for exception org.biojavax.CrossReferenceResolutionException: Creates a new instance of CrossReferenceResolutionException with a message.
CrossReferenceResolutionException(String, Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException: Creates a new instance of CrossReferenceResolutionException with a message and a cause.
CrossReferenceResolutionException(Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException: Creates a new instance of CrossReferenceResolutionException with a cause.
CrossReferenceResolver - Interface in org.biojavax: This interface returns symbols or sequence for a given cross-reference.
crossReferences - Variable in class org.biojava.bibliography.BibRef: It is an array of identifiers, all of them pointing to the same cited source but usually stored in different bibliographic repositories.
cState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM: Gets the c loop state
CURATED - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
CURATED - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
currentCol() - Method in interface org.biojava.bio.dp.onehead.DPCursor: The current column of the matrix.
currentCol() - Method in class org.biojava.bio.dp.onehead.SmallCursor
currentRes() - Method in interface org.biojava.bio.dp.onehead.DPCursor: The current symbol.
CUT_COMPOUND - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme: CUT_COMPOUND a cut type where the enzyme cuts in two positions relative to the recognition site.
CUT_SIMPLE - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme: CUT_SIMPLE a cut type where the enzyme cuts in one position relative to the recognition site.
cutType - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
cys() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Cysteine (C)

D

d() - Static method in class org.biojava.bio.seq.DNATools
d() - Static method in class org.biojava.bio.seq.NucleotideTools
d() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Aspartic Acid
D_MELANOGASTER - Static variable in interface org.biojava.bio.program.homologene.Taxon
D_RERIO - Static variable in interface org.biojava.bio.program.homologene.Taxon
DATABASE - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser: A name for a comment type.
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
DatabaseURLGenerator - Interface in org.biojava.bio.program.blast2html: Takes a database ID and some configuration properties ( such as base URL ) and returns either a URL or a full anchor tag.
DATASOURCE - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
DATASOURCE_SELECTION - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
DataStore - Interface in org.biojava.bio.program.ssaha: A repository that can be searched with a sequence.
DataStoreFactory - Interface in org.biojava.bio.program.ssaha: Builder for a data store.
date - Variable in class org.biojava.bibliography.BibRef: Defines a date associated with an event in the life cycle of the cited resource when this resource became available.
DATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
DATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
DATE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
DATE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
dateFormat - Variable in class org.biojava.ontology.obo.OboFileParser
DB_NUCLEOTIDE - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
DB_PROTEIN - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
DBREF_DB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBREF_PRIMARY_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBREF_SEC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBREFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBResolver(SequenceDB) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
dbxp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
dbxp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
dbxp - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DBXREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
DEBUG - Static variable in class org.biojava.utils.io.SoftHashMap
DebuggingRichSeqIOListener - Class in org.biojavax.bio.seq.io: This is purely for debugging purposes.
DebuggingRichSeqIOListener(InputStream) - Constructor for class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
declareNamespace(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
declareNamespace(String, String) - Method in interface org.biojava.utils.xml.XMLWriter: Hints that a namespace is going to be used in a sub-tree.
decorate(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
decorate(Location) - Method in class org.biojava.bio.symbol.BetweenLocation
decorate(Location) - Method in class org.biojava.bio.symbol.CircularLocation
DEF - Static variable in class org.biojava.ontology.obo.OboFileHandler
DEFAULT - Static variable in interface org.biojava.bio.dist.DistributionFactory: The default DistributionFactory object.
DEFAULT - Static variable in class org.biojava.bio.dist.OrderNDistributionFactory: Factory which used DistributionFactory.DEFAULT to create conditioned distributions.
DEFAULT - Static variable in interface org.biojava.bio.dp.DPFactory
DEFAULT - Static variable in class org.biojava.bio.program.phred.PhredFormat
DEFAULT - Static variable in class org.biojava.bio.seq.impl.FeatureImpl: Default implementation of FeatureRealizer, which wraps simple implementations of Feature and StrandedFeature.
DEFAULT - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
DEFAULT - Static variable in class org.biojava.bio.seq.io.FastaFormat: Deprecated.
DEFAULT - Static variable in class org.biojava.bio.seq.io.GAMEFormat
DEFAULT - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
DEFAULT - Static variable in class org.biojava.bio.seq.projection.ProjectionEngine: The standard projection engine object.
DEFAULT - Static variable in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
DEFAULT - Static variable in interface org.biojavax.ga.functions.SelectionFunction: Selects all members of a population for replication
DEFAULT_CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
DEFAULT_DELIMITERS - Static variable in class org.biojava.utils.TypedProperties: the default string of delimiter characters used by getAsStringList()
DEFAULT_FINDER_NAME - Static variable in interface org.biojava.utils.candy.CandyFinder: A default name of this (and any) finder.
DEFAULT_LIMIT - Static variable in class org.biojava.utils.io.SoftHashMap
DEFAULT_MAX_CROSS - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
DEFAULT_MUTATION_PROBS - Static variable in interface org.biojavax.ga.functions.MutationFunction
DEFAULT_TERM_CHAR - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree
DefaultDistributionFactory() - Constructor for class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
DefaultFactory(CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.DPFactory.DefaultFactory
DefaultMaskingDetector() - Constructor for class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
DefaultOps - Class in org.biojava.ontology: Default implementation of OntologyOps.
DefaultOps() - Constructor for class org.biojava.ontology.DefaultOps
DefaultURLGeneratorFactory - Class in org.biojava.bio.program.blast2html: A simple default URLGeneratorFactory which returns a single NcbiDatabaseURLGenerator instance.
DefaultURLGeneratorFactory() - Constructor for class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
delegate - Variable in class org.biojava.bio.program.tagvalue.StateMachine
delegate(StAXContentHandler) - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
delegate(StAXContentHandler) - Method in interface org.biojava.utils.stax.DelegationManager
DelegatingTransformer(FilterUtils.FilterTransformer, FilterUtils.FilterTransformer) - Constructor for class org.biojava.bio.seq.FilterUtils.DelegatingTransformer: Create a new DelegatingTransformer that will apply t1 and then t2 if t1 fails.
DelegationManager - Interface in org.biojava.bio.seq.io.agave: Interface which exposes delegation services offered by a StAX event source.
DelegationManager - Interface in org.biojava.utils.stax: Interface which exposes delegation services offered by a StAX event source.
deleteTerm(Term) - Method in class org.biojava.ontology.IntegerOntology
deleteTerm(Term) - Method in interface org.biojava.ontology.Ontology: Remove a term from an ontology, together with all triples which refer to it.
deleteTerm(Term) - Method in class org.biojava.ontology.Ontology.Impl
deleteTerm(Term) - Method in class org.biojavax.ontology.SimpleComparableOntology: Remove a term from an ontology, together with all triples which refer to it.
DELIMITER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
depth - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
depth - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor: Description of the Field
DESC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
describeSequence(Sequence) - Method in class org.biojava.bio.program.phred.PhredFormat: Return a suitable description line for a Sequence.
describeSequence(Sequence) - Method in class org.biojava.bio.seq.io.FastaFormat: Deprecated.

Return a suitable description line for a Sequence.
description - Variable in class org.biojava.bibliography.BibRef: An account of the content of the cited resource.
description - Variable in class org.biojava.ontology.AbstractTerm
description - Variable in class org.biojava.utils.candy.CandyEntry: A value of this entry.
DESCRIPTION - Static variable in interface org.biojavax.bio.BioEntry
DESCRIPTION - Static variable in interface org.biojavax.Namespace
DESCRIPTION - Static variable in interface org.biojavax.ontology.ComparableOntology
DESCRIPTION - Static variable in interface org.biojavax.ontology.ComparableTerm
DESCRIPTOR - Static variable in interface org.biojavax.ontology.ComparableTriple
destination - Variable in class org.biojava.bio.program.tagvalue.StateMachine.Transition: the terminus of this Transition
destroy() - Method in interface org.biojava.bibliography.BibRefQuery: It frees all resources related to this query collection.
destroy() - Method in interface org.biojava.utils.candy.CandyVocabulary: It frees all resources related to this vocabulary.
destroy() - Static method in class org.biojava.utils.io.FlatFileCache
destroySubcontext(String) - Method in class org.biojava.naming.ObdaContext
destroySubcontext(Name) - Method in class org.biojava.naming.ObdaContext
destroyTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel: Breaks a transition between two states legal.
destroyTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
destroyTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
DfaBuilder - Class in org.biojava.utils.automata
DiagonalAddKernel - Class in org.biojava.stats.svm: Adds a class specific constant to k(x, x).
DiagonalAddKernel() - Constructor for class org.biojava.stats.svm.DiagonalAddKernel
DiagonalCachingKernel - Class in org.biojava.stats.svm: Caches the leading diagonal of a kernel matrix.
DiagonalCachingKernel() - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel: Create a new CachingKernel.
DiagonalCachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel: Creates a new DiagonalCachingKernel that nests k.
diddleQueue() - Method in class org.biojava.utils.IndexedChangeHub
Digest - Class in org.biojava.bio.proteomics: This class contains methods for calculating the results of proteolytic digestion of a protein sequence this class is not designed to be thread safe
Digest() - Constructor for class org.biojava.bio.proteomics.Digest: Creates a new Digest Bean
disconnect() - Method in interface org.biojava.bibliography.BibRefQuery: It disconnects from the repository.
disconnect() - Method in interface org.biojava.bibliography.BibRefSupport: It closes connection with a utility object.
disconnect() - Method in interface org.biojava.utils.candy.CandyFinder: It closes connection with the finder object.
DISJOINT_FROM - Static variable in class org.biojava.ontology.obo.OboFileHandler
displayString() - Method in class org.biojava.utils.ChangeSupport
DistDataSource - Interface in org.biojava.bio.seq.distributed: Object which contributes data to a DistributedSequenceDB.
distForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
distOverAlignment(Alignment) - Static method in class org.biojava.bio.dist.DistributionTools: Equivalent to distOverAlignment(a, false, 0.0).
distOverAlignment(Alignment, boolean) - Static method in class org.biojava.bio.dist.DistributionTools: Creates an array of distributions, one for each column of the alignment.
distOverAlignment(Alignment, boolean, double) - Static method in class org.biojava.bio.dist.DistributionTools: Creates an array of distributions, one for each column of the alignment.
DistributedSequenceDB - Class in org.biojava.bio.seq.distributed: Sequence database from the meta-DAS system.
DistributedSequenceDB() - Constructor for class org.biojava.bio.seq.distributed.DistributedSequenceDB
Distribution - Interface in org.biojava.bio.dist: An encapsulation of a probability distribution over the Symbols within an alphabet.
DISTRIBUTION - Static variable in interface org.biojava.bio.dp.EmissionState: This signals that the distribution associate with an EmissionState has been altered.
Distribution.NullModelForwarder - Class in org.biojava.bio.dist: Deprecated.
use new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY) instead
DistributionFactory - Interface in org.biojava.bio.dist: A thing that can make Distributions.
DistributionFactory.DefaultDistributionFactory - Class in org.biojava.bio.dist: The default DistributionFactory implementation.
DistributionTools - Class in org.biojava.bio.dist: A class to hold static methods for calculations and manipulations using Distributions.
DistributionTrainer - Interface in org.biojava.bio.dist: An object that can be used to train a distribution up.
DistributionTrainerContext - Interface in org.biojava.bio.dist: A context within a group of DistributionTrainers can be trained together.
DIVISION - Static variable in interface org.biojavax.bio.BioEntry
DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
DIVISION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DivisionLkpReader - Class in org.biojava.bio.seq.db.emblcd: DivisionLkpReader reads the "division.lkp" file of an EMBL CD-ROM format binary index.
DivisionLkpReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.DivisionLkpReader: Creates a new DivisionLkpReader.
DNA - Static variable in class org.biojava.bio.seq.io.FastaAlignmentFormat
DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: DNA indicates that a sequence contains DNA (deoxyribonucleic acid) symbols.
DNAAmbPack - Class in org.biojava.bio.symbol: Packing utility class for DNA.
DNAAmbPack() - Constructor for class org.biojava.bio.symbol.DNAAmbPack
DNAComposition - Class in org.biojava.bio.molbio: Computes composition statistics about a DNA SymbolList.
DNAComposition() - Constructor for class org.biojava.bio.molbio.DNAComposition
DNANoAmbPack - Class in org.biojava.bio.symbol: A Packing implementation which handles the DNA alphabet, without any support for ambiguity symbols.
DNANoAmbPack(byte) - Constructor for class org.biojava.bio.symbol.DNANoAmbPack: Construct a new packing which returns the specified byte value for unknown Symbols (such as ambiguity symbols).
DNANoAmbPack(Symbol) - Constructor for class org.biojava.bio.symbol.DNANoAmbPack: Construct a new packing which translates unknown symbols into the specified symbol.
dnaSymbolFromPhred(Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools: Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
dnaToken(Symbol) - Static method in class org.biojava.bio.seq.DNATools: Get a single-character token for a DNA symbol
DNATools - Class in org.biojava.bio.seq: Useful functionality for processing DNA sequences.
doAnnotation(Sequence) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB: Apply the annotation to a sequence.
docNumber - Variable in class org.biojava.bibliography.BiblioPatent: The document number.
docOffice - Variable in class org.biojava.bibliography.BiblioPatent: Document office.
DocRef - Interface in org.biojavax: Represents a documentary reference.
DocRefAuthor - Interface in org.biojavax: Represents an author of a documentary reference.
DocRefAuthor.Tools - Class in org.biojavax: Useful tools for working with authors.
docType - Variable in class org.biojava.bibliography.BiblioPatent: Document type.
documentEnd() - Method in interface org.biojava.ontology.obo.OboFileEventListener: end of parsing a new OBO file
documentEnd() - Method in class org.biojava.ontology.obo.OboFileHandler
documentStart() - Method in interface org.biojava.ontology.obo.OboFileEventListener: starting to parse a new OBO file
documentStart() - Method in class org.biojava.ontology.obo.OboFileHandler
DOI_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms: Holds a reference to the key that must be used to store DOI references.
DOMAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
domain1 - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
doPreProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Emit any per-sequence header information.
doProcessFeature(Feature, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Internal method to process an individual Feature.
doProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Internal method to process an individual Sequence.
doRetain() - Method in class org.biojava.bio.program.tagvalue.TagDropper: Find out if known tags are retained or dropped.
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
DotState - Interface in org.biojava.bio.dp: A Dot state.
DoubleAlphabet - Class in org.biojava.bio.symbol: An efficient implementation of an Alphabet over the infinite set of double values.
DoubleAlphabet.DoubleRange - Class in org.biojava.bio.symbol: A range of double values.
DoubleAlphabet.DoubleSymbol - Class in org.biojava.bio.symbol: A single double value.
DoubleAlphabet.SubDoubleAlphabet - Class in org.biojava.bio.symbol: A class to represent a contiguous range of double symbols.
DoubleElementHandlerBase - Class in org.biojava.utils.stax: StAX handler for any element which just contains a string representation of a double.
DoubleElementHandlerBase() - Constructor for class org.biojava.utils.stax.DoubleElementHandlerBase
DoubleRange(double, double) - Constructor for class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
Doublet() - Constructor for class org.biojava.utils.ListTools.Doublet
Doublet(Object, Object) - Constructor for class org.biojava.utils.ListTools.Doublet
DoubleTokenization - Class in org.biojava.bio.seq.io
DoubleTokenization() - Constructor for class org.biojava.bio.seq.io.DoubleTokenization
doubleValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable: this method is expected to reverse-translate any symbol in the source alphabet.
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable: this method is expected to reverse-translate any symbol in the source alphabet.
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
dp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
dp - Static variable in class org.biojavax.bio.seq.io.FastaFormat
DP - Class in org.biojava.bio.dp: Objects that can perform dymamic programming operations upon sequences with HMMs.
DP() - Constructor for class org.biojava.bio.dp.DP: This method will result in a DP with no model.
DP(MarkovModel) - Constructor for class org.biojava.bio.dp.DP
dp_ipi - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
dp_uniprot - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
DP.ReverseIterator - Class in org.biojava.bio.dp
DPCompiler - Class in org.biojava.bio.dp.twohead: This is an implementation of CellCalculatorFactoryMaker that compiles the HMM object down to Java byte-code that is equivalent in behaviour to the interpreter.
DPCompiler(boolean) - Constructor for class org.biojava.bio.dp.twohead.DPCompiler
DPCursor - Interface in org.biojava.bio.dp.onehead: Encapsulates the dynamic programmming matrix, and the context within algorithms work.
DPFactory - Interface in org.biojava.bio.dp: The interface for objects that can generate a DP object for a MarkovModel.
DPFactory.DefaultFactory - Class in org.biojava.bio.dp
DPInterpreter - Class in org.biojava.bio.dp.twohead
DPInterpreter(DP) - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter
DPInterpreter.Maker - Class in org.biojava.bio.dp.twohead
DPMatrix - Interface in org.biojava.bio.dp
DR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
dropBoundaryValues() - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
DROSOPHILA_MELANOGASTER_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools: Drosophila melanogaster codon preferences
dsCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
DummyCrossReferenceResolver - Class in org.biojavax: A simple implementation of CrossReferenceResolver.
DummyCrossReferenceResolver() - Constructor for class org.biojavax.DummyCrossReferenceResolver
DummyRichSequenceHandler - Class in org.biojavax.bio.seq
DummyRichSequenceHandler() - Constructor for class org.biojavax.bio.seq.DummyRichSequenceHandler
DummySequence - Class in org.biojava.bio.seq.impl: A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
DummySequence(String, String) - Constructor for class org.biojava.bio.seq.impl.DummySequence
DummySequenceDB - Class in org.biojava.bio.seq.db: DummySequenceDB is an implementation which contains only a DummySequence.
DummySequenceDB(String) - Constructor for class org.biojava.bio.seq.db.DummySequenceDB
DummySequenceDBInstallation - Class in org.biojava.bio.seq.db: DummySequenceDBInstallation is an implementation which returns the same DummySequenceDB instance regardless of the identifier used to retrieve a database.
DummySequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.DummySequenceDBInstallation
DummySymbolList - Class in org.biojava.bio.symbol: Symbol list which just consists of non-informative symbols.
DummySymbolList(Alphabet, int, Symbol) - Constructor for class org.biojava.bio.symbol.DummySymbolList
DummySymbolList(FiniteAlphabet, int) - Constructor for class org.biojava.bio.symbol.DummySymbolList
dumpBlocks() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Debugging method
duplicate() - Method in class org.biojava.utils.automata.NfaSubModel: Makes a deep clone of this instance.
DuplicateTaxonException - Exception in org.biojava.bio.program.homologene
DuplicateTaxonException() - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
DuplicateTaxonException(String) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
DuplicateTaxonException(Throwable) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
DuplicateTaxonException(Throwable, String) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException

E

e() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Glutamic Acid
EbiDatabaseURLGenerator - Class in org.biojava.bio.program.blast2html: Simple URL generator for EMBL at the EBI.
EbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
EbiFormat - Class in org.biojava.bio.taxa: Deprecated.
replaced by classes in org.biojavax.bio.taxa
EbiFormat() - Constructor for class org.biojava.bio.taxa.EbiFormat: Deprecated.
EC_FROM_STRING - Static variable in class org.biojava.bio.program.formats.FormatTools
EC_PATTERN - Static variable in interface org.biojava.bio.EcNumber: A Pattern that can be used to parse EC strings into the indiidual numbers.
eCache - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
eCache - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor: Description of the Field
ECHIN_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the echinoderm mitochondrial genetic code.
Echo - Class in org.biojava.bio.program.tagvalue: A simple listener that just echoes events back to the console.
Echo() - Constructor for class org.biojava.bio.program.tagvalue.Echo
Echo(PrintStream) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Echo
EcNumber - Interface in org.biojava.bio: An ec (enzyme classification) number.
EcNumber.Impl - Class in org.biojava.bio: A simple implementation of EcNumber.
ECOLI - Static variable in class org.biojava.bio.symbol.CodonPrefTools: Escherichia coli codon preferences
edit(Edit) - Method in class org.biojava.bio.dp.SimpleStatePath
edit(Edit) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
edit(Edit) - Method in class org.biojava.bio.seq.impl.DummySequence
edit(Edit) - Method in class org.biojava.bio.seq.impl.RevCompSequence: edit() will try to edit the underlying Sequence.
edit(Edit) - Method in class org.biojava.bio.seq.impl.SimpleSequence
edit(Edit) - Method in class org.biojava.bio.seq.impl.SubSequence
edit(Edit) - Method in class org.biojava.bio.seq.impl.ViewSequence
edit(Edit) - Method in class org.biojava.bio.seq.NewSimpleAssembly
edit(Edit) - Method in class org.biojava.bio.seq.SimpleAssembly
edit(Edit) - Method in class org.biojava.bio.symbol.AbstractSymbolList
edit(Edit) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
edit(Edit) - Method in class org.biojava.bio.symbol.RelabeledAlignment
edit(Edit) - Method in class org.biojava.bio.symbol.SimpleSymbolList: Apply and edit to the SymbolList as specified by Edit.
edit(Edit) - Method in interface org.biojava.bio.symbol.SymbolList: Apply an edit to the SymbolList as specified by the edit object.
edit(Edit) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList: Apply an edit to the SymbolList as specified by the edit object.
edit(Edit) - Method in class org.biojavax.bio.seq.ThinRichSequence: Apply an edit to the SymbolList as specified by the edit object.
edit(RichSequence, Edit) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler: Apply an edit to the Sequence as specified by the edit object.
edit(RichSequence, Edit) - Method in interface org.biojavax.bio.seq.RichSequenceHandler: Apply an edit to the Sequence as specified by the edit object.
Edit - Class in org.biojava.bio.symbol: Encapsulates an edit operation on a SymbolList.
Edit(int, int, SymbolList) - Constructor for class org.biojava.bio.symbol.Edit: Create a new Edit.
Edit(int, int, SymbolList, Map<String, Object>) - Constructor for class org.biojava.bio.symbol.Edit: Create a new Edit with some properties.
Edit(int, Alphabet, Symbol) - Constructor for class org.biojava.bio.symbol.Edit: Convenience construtor for making single residue changes
EDIT - Static variable in interface org.biojava.bio.symbol.SymbolList: Signals that the SymbolList is being edited.
edition - Variable in class org.biojava.bibliography.BiblioBook: Edition.
editor - Variable in class org.biojava.bibliography.BiblioBook: Editor.
EDITOR_LIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EDITOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
EditScreener(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
EditTranslater(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
ElementRecognizer - Interface in org.biojava.bio.program.xff: Simple interface for filtering SAX/StAX startElement events.
ElementRecognizer - Interface in org.biojava.bio.seq.io.agave: This class is copied to agave package Simple interface for filtering SAX/StAX startElement events
ElementRecognizer - Interface in org.biojava.bio.seq.io.game: Simple interface for filtering SAX/StAX startElement events
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.program.xff
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.seq.io.agave
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.seq.io.game
ElementRecognizer.ByLocalName - Class in org.biojava.bio.program.xff: Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName - Class in org.biojava.bio.seq.io.agave: Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName - Class in org.biojava.bio.seq.io.game: Filter elements by local name (not recommended).
ElementRecognizer.ByNSName - Class in org.biojava.bio.program.xff: Filter elements by name and namespace.
ElementRecognizer.ByNSName - Class in org.biojava.bio.seq.io.agave: Filter elements by name and namespace.
ElementRecognizer.ByNSName - Class in org.biojava.bio.seq.io.game: Filter elements by name and namespace.
ElementRecognizer.HasAttribute - Class in org.biojava.bio.program.xff: Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute - Class in org.biojava.bio.seq.io.agave: Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute - Class in org.biojava.bio.seq.io.game: Filter elements on the existence of a specified attribute.
email - Variable in class org.biojava.bibliography.BiblioPerson: Their e-mail address.
Embl - Class in org.biojava.bio.program.formats
Embl() - Constructor for class org.biojava.bio.program.formats.Embl
EMBL - Static variable in class org.biojava.bio.program.tagvalue.LineSplitParser: A LineSplitParser pre-configured to process EMBL-style flat files.
EMBL - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: EMBL indicates that the sequence format is EMBL.
EMBL_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: EMBL_AA premade EMBL | AA.
EMBL_AGAVE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
EMBL_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: EMBL_DNA premade EMBL | DNA.
EMBL_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLFormat: The name of the current format
EMBL_GENBANK_FEATURE_TABLE_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
EMBL_PRE87_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLFormat: The name of the Pre-87 format
EMBL_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: EMBL_RNA premade EMBL | RNA.
EMBL_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
Embl2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave: Map EMBL data into AGAVE format
EmblCDROMIndexReader - Class in org.biojava.bio.seq.db.emblcd: EmblCDROMIndexReader is an abstract class whose concrete subclasses read EMBL CD-ROM format indices from an underlying InputStream.
EmblCDROMIndexReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader: Creates a new EmblCDROMIndexReader instance.
EmblCDROMIndexStore - Class in org.biojava.bio.seq.db: EmblCDROMIndexStores implement a read-only IndexStore backed by EMBL CD-ROM format binary indices.
EmblCDROMIndexStore(File, File, File, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.EmblCDROMIndexStore: Creates a new EmblCDROMIndexStore backed by a random access binary index.
EmblCDROMIndexStore(File, File, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.EmblCDROMIndexStore: Creates a new EmblCDROMIndexStore backed by a random access binary index.
EmblCDROMRandomAccess - Class in org.biojava.bio.seq.db.emblcd: EmblCDROMRandomAccess is an abstract class whose concrete subclasses can perform fast lookups in EMBL CD-ROM format index files.
EmblCDROMRandomAccess(File, int, int, long) - Constructor for class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess: Creates a new EmblCDROMRandomAccess object.
EmblFileFormer - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
EmblFileFormer() - Constructor for class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.

Creates a new EmblFileFormer using System.out stream.
EmblFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.

Creates a new EmblFileFormer using the specified stream.
EMBLFormat - Class in org.biojavax.bio.seq.io: Format reader for EMBL files.
EMBLFormat() - Constructor for class org.biojavax.bio.seq.io.EMBLFormat
EMBLFormat.Terms - Class in org.biojavax.bio.seq.io: Implements some EMBL-specific terms.
EmblLikeFormat - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io.EMBLFormat instead
EmblLikeFormat() - Constructor for class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
EmblLikeLocationParser - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
EmblProcessor - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
EmblProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.EmblProcessor: Deprecated.
EmblProcessor.Factory - Class in org.biojava.bio.seq.io: Deprecated.

Factory which wraps SequenceBuilders in an EmblProcessor
EmblReferenceComparator - Class in org.biojava.bio.seq.io
EmblReferenceComparator() - Constructor for class org.biojava.bio.seq.io.EmblReferenceComparator
EMBLXML_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat: The name of this format
EMBLxmlFormat - Class in org.biojavax.bio.seq.io: Format reader for EMBLxml files.
EMBLxmlFormat() - Constructor for class org.biojavax.bio.seq.io.EMBLxmlFormat
EMBLxmlFormat.Terms - Class in org.biojavax.bio.seq.io: Implements some EMBLxml-specific terms.
emissionAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel: Alphabet that is emitted by the emission states.
emissionAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel
emissionAlphabet() - Method in class org.biojava.bio.dp.WMAsMM
EmissionCache - Class in org.biojava.bio.dp.twohead: Cache for columns of emission probabilities in pair-wise alignment algorithms.
EmissionCache(Alphabet, State[], int, ScoreType) - Constructor for class org.biojava.bio.dp.twohead.EmissionCache
emissions - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
emissions - Variable in class org.biojava.bio.dp.twohead.Cell
emissionsNull - Variable in class org.biojava.bio.dp.onehead.SingleDP
emissionsOdds - Variable in class org.biojava.bio.dp.onehead.SingleDP
emissionsProb - Variable in class org.biojava.bio.dp.onehead.SingleDP
EmissionState - Interface in org.biojava.bio.dp: A state in a markov process that has an emission spectrum.
empty - Static variable in interface org.biojava.bio.symbol.Location: The Location which contains no points.
EMPTY - Static variable in interface org.biojava.bio.annodb.AnnotationDB: An AnnotationDB that is always empty.
EMPTY - Static variable in interface org.biojava.bio.CollectionConstraint: EMPTY is a constraint which only accepts the empty set.
EMPTY_ALPHABET - Static variable in interface org.biojava.bio.symbol.Alphabet: A really useful static alphabet that is always empty.
EMPTY_ANNOTATION - Static variable in interface org.biojava.bio.Annotation: A really useful empty and immutable annotation object.
EMPTY_ANNOTATION - Static variable in interface org.biojavax.RichAnnotation
EMPTY_FEATURE_HOLDER - Static variable in interface org.biojava.bio.seq.FeatureHolder
EMPTY_LINE_EOR - Static variable in interface org.biojava.bio.program.tagvalue.TagValueParser: EMPTY_LINE_EOR is a special EOR value which allows an empty line to be used as a record separator.
EMPTY_LIST - Static variable in interface org.biojava.bio.symbol.SymbolList: A useful object that represents an empty symbol list, to avoid returning null.
EMPTY_LOCATION - Static variable in interface org.biojavax.bio.seq.RichLocation: The empty location matches nothing.
EMPTY_PAIRWISE - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature: Constant EMPTY_PAIRWISE is an empty alignment for situations where there is no available alignment data or the implementation does not want to create one.
EMPTY_POSITION - Static variable in interface org.biojavax.bio.seq.Position: The empty position lies nowhere.
emptyBP - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
emptyBP - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor: Description of the Field
emptyFeature - Variable in class org.biojavax.bio.seq.io.RichSeqIOAdapter: This is a dummy feature.
EmptyFeatureHolder() - Constructor for class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
emptyList(Alphabet) - Static method in class org.biojava.bio.symbol.SymbolListViews: Get a new immutable, empty symbol list with the given alphabet.
EmptyRichAnnotation - Class in org.biojavax: A place holder for a RichAnnotation that prevents null having to be used
EmptyRichAnnotation() - Constructor for class org.biojavax.EmptyRichAnnotation
EmptyRichLocation - Class in org.biojavax.bio.seq: An Empty implementation of RichLocation.
EmptyRichLocation() - Constructor for class org.biojavax.bio.seq.EmptyRichLocation
end - Variable in class org.biojava.utils.automata.FiniteAutomaton
end() - Method in interface org.biojava.bio.search.BioMatcher: Get the last symbol index that matches the pattern.
end() - Method in class org.biojava.bio.search.MaxMismatchMatcher
end() - Method in class org.biojava.utils.regex.Matcher: Returns the index of the last character matched, plus one.
end(int) - Method in class org.biojava.utils.regex.Matcher: Returns the index of the last Symbol, plus one, of the subsequence captured by the given group during the previous match operation.
END_RECORD_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
END_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
END_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
END_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
endDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: end of data for DB
endDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endDocument() - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler: Indicates that the current GFF document has now ended.
endDocument() - Method in class org.biojava.bio.program.gff.GFFFilterer
endDocument() - Method in class org.biojava.bio.program.gff.GFFWriter: Flushes the PrintWriter to make sure that everything is written.
endDocument() - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler: Indicates that the current GFF document has now ended.
endDocument() - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
endDocument() - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
endElement() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
endElement(String, String, String) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler: Called when the end of an element is reached.
endElement(String, String, String) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
endElement(String, String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
endElement(String, String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
endElement(String, String, String, StAXContentHandler) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.FeatureHandler: StAX callback for element ends.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler: Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.CharElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.IntElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.LongElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in interface org.biojava.utils.stax.StAXContentHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.StringElementHandlerBase
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler: Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler: when exiting, put the DbXrefElement into the annotation bundle
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMESpanPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler: Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEAspectHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler.SeqRelHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEPropertyHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESpanHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler: Element specific exit handler Subclass to do anything useful.
endFeature() - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
endFeature() - Method in class org.biojava.bio.seq.io.FeatureTableParser: Deprecated.
endFeature() - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
endFeature() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
endFeature() - Method in class org.biojava.bio.seq.io.SeqIOFilter
endFeature() - Method in interface org.biojava.bio.seq.io.SeqIOListener: Mark the end of data associated with one specific feature.
endFeature() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
endFeature() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
endFeature() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Null implementation.
endFeature() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
endFeature() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
endFeature() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Mark the end of data associated with one specific feature.
endGroup() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: end of data for group
endGroup() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endHeader() - Method in class org.biojava.bio.search.FilteringContentHandler
endHeader() - Method in class org.biojava.bio.search.SearchContentAdapter
endHeader() - Method in class org.biojava.bio.search.SearchContentFilter
endHeader() - Method in interface org.biojava.bio.search.SearchContentHandler: The endHeader method indicates the end of a formatted header.
endHeader() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endHit() - Method in class org.biojava.bio.search.FilteringContentHandler
endHit() - Method in class org.biojava.bio.search.SearchContentAdapter
endHit() - Method in class org.biojava.bio.search.SearchContentFilter
endHit() - Method in interface org.biojava.bio.search.SearchContentHandler: The endHit method indicates the end of a formatted hit.
endHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endIndex - Variable in class org.biojava.ontology.obo.OboFileParser.SOPair
endLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
endLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
endOrthologue() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: end of data for this Orthologue
endOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endOrthoPair() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: end of data for this OrthoPair
endOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endPrefixMapping(String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
endPrefixMapping(String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
endPrefixMapping(String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
endPrefixMapping(String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
endPrefixMapping(String) - Method in interface org.biojava.utils.stax.StAXContentHandler
endPrefixMapping(String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
endRecord() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
endRecord() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
endRecord() - Method in class org.biojava.bio.program.tagvalue.Echo
endRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer
endRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer2
endRecord() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
endRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine
endRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
endRecord() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener: The current record has ended.
endSearch() - Method in class org.biojava.bio.search.FilteringContentHandler
endSearch() - Method in class org.biojava.bio.search.SearchContentAdapter
endSearch() - Method in class org.biojava.bio.search.SearchContentFilter
endSearch() - Method in interface org.biojava.bio.search.SearchContentHandler: The endSearch method indicates the end of useful search information.
endSearch() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
endSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener: Indicates that a sequence has been searched against a DataStore.
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
endSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.EmblProcessor: Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.OrganismParser: Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
endSequence() - Method in class org.biojava.bio.seq.io.SeqIOFilter
endSequence() - Method in interface org.biojava.bio.seq.io.SeqIOListener: Notify the listener that processing of the sequence is complete.
endSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
endSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
endSequence() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Notify the listener that processing of the sequence is complete.
endSequence() - Method in class org.biojava.bio.seq.io.SwissprotProcessor: Deprecated.
endSequence() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
endSequence() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
endSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Notify the listener that processing of the sequence is complete.
endSubHit() - Method in class org.biojava.bio.search.FilteringContentHandler
endSubHit() - Method in class org.biojava.bio.search.SearchContentAdapter
endSubHit() - Method in class org.biojava.bio.search.SearchContentFilter
endSubHit() - Method in interface org.biojava.bio.search.SearchContentHandler: The endSubHit method indicates the end of a formatted subhit.
endSubHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endTag() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
endTag() - Method in class org.biojava.bio.program.tagvalue.Aggregator
endTag() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
endTag() - Method in class org.biojava.bio.program.tagvalue.Echo
endTag() - Method in class org.biojava.bio.program.tagvalue.Indexer
endTag() - Method in class org.biojava.bio.program.tagvalue.Indexer2
endTag() - Method in class org.biojava.bio.program.tagvalue.MultiTagger
endTag() - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
endTag() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
endTag() - Method in class org.biojava.bio.program.tagvalue.StateMachine
endTag() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
endTag() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
endTag() - Method in class org.biojava.bio.program.tagvalue.TagDropper
endTag() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener: End the current tag.
endTree() - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
endTree() - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
endTree() - Method in interface org.biojava.utils.stax.StAXContentHandler
endTree() - Method in class org.biojava.utils.stax.StAXContentHandlerBase
enrich(Feature) - Static method in class org.biojavax.bio.seq.RichFeature.Tools: Takes a normal Feature and attempts to convert it into a RichFeature.
enrich(Sequence) - Static method in class org.biojavax.bio.seq.RichSequence.Tools: Boldly attempts to convert a Sequence into a RichSequence.
enrich(Location) - Static method in class org.biojavax.bio.seq.RichLocation.Tools: Attempts to convert a plain Location into a RichLocation.
entry - Variable in class org.biojava.utils.candy.CandyEntry: A unique identifier of this entry.
ENTRY_ACCESSION_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_CREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_CREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_DATACLASS_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_NAMESPACE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport: A vocabulary name.
ENTRY_RELCREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_RELUPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_STATUS_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_STATUS_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_SUBACC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_SUBVER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_SUBWGSVER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_TAX_DIVISION_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_UPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_UPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_VERSION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EntryNamIdxReader - Class in org.biojava.bio.seq.db.emblcd: EntryNamIdxReader reads the "entrynam.idx" file of an EMBL CD-ROM format binary index.
EntryNamIdxReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader: Creates a new EntryNamIdxReader.
EntryNamRandomAccess - Class in org.biojava.bio.seq.db.emblcd: EntryNamRandomAccess objects provide random access to records within the "entrynam.idx" file of an EMBL CD-ROM format binary index.
EntryNamRandomAccess(File, int, int, long) - Constructor for class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
entrySet() - Method in class org.biojava.utils.BeanAsMap
entrySet() - Method in class org.biojava.utils.cache.WeakValueHashMap
entrySet() - Method in class org.biojava.utils.io.SoftHashMap
entrySet() - Method in class org.biojava.utils.OverlayMap
entrySet() - Method in class org.biojava.utils.SmallMap
entryStatus - Variable in class org.biojava.bibliography.BibRef: It defines information related to the citation itself rather than to the cited resource.
Enumeration(Object[]) - Constructor for class org.biojava.bio.PropertyConstraint.Enumeration: Creates a new Enumeration using the elements of the specified array as a constraint.
Enumeration(Set) - Constructor for class org.biojava.bio.PropertyConstraint.Enumeration: Creates a new Enumeration using the members of the specified set as a constraint.
enzyme - Variable in class org.biojava.bio.molbio.RestrictionSite.Template: enzyme RestrictionEnzyme field.
Enzyme - Class in org.biojava.bio.program.formats
Enzyme() - Constructor for class org.biojava.bio.program.formats.Enzyme
Enzyme() - Constructor for class org.biojava.bio.program.formats.Ligand.Enzyme
eof() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader: Checks if the end of the file or stream is reached.
equals(boolean[], boolean[]) - Static method in class org.biojava.utils.ObjectUtil
equals(boolean, boolean) - Static method in class org.biojava.utils.ObjectUtil
equals(double[], double[]) - Static method in class org.biojava.utils.ObjectUtil
equals(double, double) - Static method in class org.biojava.utils.ObjectUtil
equals(float[], float[]) - Static method in class org.biojava.utils.ObjectUtil
equals(float, float) - Static method in class org.biojava.utils.ObjectUtil
equals(int[], int[]) - Static method in class org.biojava.utils.ObjectUtil
equals(int, int) - Static method in class org.biojava.utils.ObjectUtil
equals(long[], long[]) - Static method in class org.biojava.utils.ObjectUtil
equals(long, long) - Static method in class org.biojava.utils.ObjectUtil
equals(Object) - Method in class org.biojava.bio.AbstractAnnotation
equals(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
equals(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
equals(Object) - Method in class org.biojava.bio.dist.AbstractDistribution
equals(Object) - Method in class org.biojava.bio.dp.SimpleWeightMatrix
equals(Object) - Method in class org.biojava.bio.dp.TrainerTransition: Two transitions are equal if they have the same trainer, from and to states.
equals(Object) - Method in class org.biojava.bio.dp.Transition: Two transitions are equal if they have the same from and to states.
equals(Object) - Method in class org.biojava.bio.EcNumber.Impl
equals(Object) - Method in class org.biojava.bio.molbio.RestrictionEnzyme
equals(Object) - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
equals(Object) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
equals(Object) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
equals(Object) - Method in class org.biojava.bio.seq.Feature.Template
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.And
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.Not
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.Or
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
equals(Object) - Method in class org.biojava.bio.seq.impl.SimpleFeature
equals(Object) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
equals(Object) - Method in class org.biojava.bio.symbol.AbstractLocation
equals(Object) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
equals(Object) - Method in class org.biojava.bio.symbol.AbstractSymbolList: Provides logical equality for two SymbolLists that share the same list of canonical symbols
equals(Object) - Method in class org.biojava.bio.symbol.CircularLocation
equals(Object) - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
equals(Object) - Method in interface org.biojava.bio.symbol.Location: Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
equals(Object) - Method in interface org.biojava.bio.taxa.Taxon: Deprecated.

Two taxa are equal if they have equivalent children, common and scientific names.
equals(Object) - Method in class org.biojava.ontology.Term.Impl
equals(Object) - Method in interface org.biojava.ontology.Triple: Check to see if an object is an equivalent Triple.
equals(Object) - Method in class org.biojava.ontology.Triple.Impl: Two triples are equal if all their fields are identical.
equals(Object) - Method in class org.biojava.utils.ListTools.Doublet
equals(Object) - Method in class org.biojava.utils.ListTools.Triplet
equals(Object) - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
equals(Object) - Method in class org.biojava.utils.TypedProperties
equals(Object) - Method in class org.biojavax.bio.seq.CompoundRichLocation: Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojavax.bio.seq.EmptyRichLocation: Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojavax.bio.seq.RichLocation.Strand: Strands are equal if their numbers and symbols match.
equals(Object) - Method in class org.biojavax.bio.seq.SimplePosition: Two positions are equal if they share all parameters in common, eg. fuzzy start+end, start, end, type.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Features are equal when they have the same rank, parent, type, and source.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Relations are equal if their objects, subjects and terms are equal.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichLocation: Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojavax.bio.SimpleBioEntry: Two bioentries are equal if they share the same namespace, name, accession and version.
equals(Object) - Method in class org.biojavax.bio.SimpleBioEntryRelationship: Relationships are equal if they share the same rank, object, subject and term.
equals(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: NCBITaxon objects are equal if their NCBITaxID fields match.
equals(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName: Two taxon names are equal if their name and class match.
equals(Object) - Method in class org.biojavax.EmptyRichAnnotation
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableOntology: Ontologies are equal if their names are equal.
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm: Two terms are equal if they are in the same ontology and share the same name.
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple: Check to see if an object is an equivalent Triple.
equals(Object) - Method in class org.biojavax.SimpleComment: Two comments are defined as equal if their text values and rankings are identical.
equals(Object) - Method in class org.biojavax.SimpleCrossRef: Equality is defined as having the same database name, accession and version.
equals(Object) - Method in class org.biojavax.SimpleDocRef: Document references are equal if they have the same author and location and title.
equals(Object) - Method in class org.biojavax.SimpleDocRefAuthor: Document references are equal if they have all fields the same.
equals(Object) - Method in class org.biojavax.SimpleNamespace: Namespaces are equal only by name.
equals(Object) - Method in class org.biojavax.SimpleNote: Notes are equal if they have the same rank and term.
equals(Object) - Method in class org.biojavax.SimpleRankedCrossRef: Ranked cross references are the same if they have the same rank and refer to the same cross reference (cross references are equal).
equals(Object) - Method in class org.biojavax.SimpleRankedDocRef: Two ranked document references are equal if they have the same rank and refer to the same location and same document reference.
equals(Object[], Object[]) - Static method in class org.biojava.utils.ObjectUtil
equals(Object, Object) - Static method in class org.biojava.utils.ObjectUtil
equals(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
Equals(Object) - Constructor for class org.biojava.bio.search.FilterTest.Equals
EQUIVALENCE - Static variable in class org.biojava.ontology.OntoTools
EQUIVALENT - Static variable in interface org.biojavax.bio.taxa.NCBITaxon: Use this to define equivalent names for things.
ERROR_FEATURES_PROPERTY - Static variable in class org.biojava.bio.seq.io.SequenceBuilderBase
escape(String, boolean) - Static method in class org.biojava.ontology.obo.OboFileParser
escapeChars - Static variable in class org.biojava.ontology.obo.OboFileParser
estimatedSize - Variable in class org.biojava.bibliography.BiblioWebResource: An estomated size in kilobytes.
EUPL_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the euplotid nuclear genetic code.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.CachingKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel: Return the dot product of a, b.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.DiagonalCachingKernel: Returns the kernel product of two Objects.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.LinearKernel: Deprecated.

The linear kernel is equal to the dot product of a and b.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.ListSumKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.NormalizingKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.PolynomialKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.RadialBaseKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.SigmoidKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel: Evaluate the kernel function between two SparseVectors.
evaluate(Object, Object) - Method in interface org.biojava.stats.svm.SVMKernel: Return the dot product of two vectors in an arbitrary feature space.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel: Calculate the dot product between the SuffixTrees a and b.
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
evaluate(BlastLikeSearchFilter.Node) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter: computes the outcome of this filter on the specified node and stores it.
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
Event() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Event
EverythingToXML(PrintWriter) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
EVIDENCE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_ATTRIBUTE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_CATEGORY_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EXACT_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
EXACT_SYNONYM - Static variable in class org.biojava.ontology.Synonym
ExactValue(Object) - Constructor for class org.biojava.bio.PropertyConstraint.ExactValue: Get a PropertyConstraint that matches this object and all those that are equal to it (by the Object.equals() method).
ExceptionFound - Variable in class org.biojava.bio.seq.db.GenbankSequenceDB
exec(String) - Method in class org.biojava.utils.ExecRunner: The exec(String) method runs a process inside of a watched thread.
exec(String[], Reader, Writer, Writer) - Static method in class org.biojava.utils.ProcessTools: Deprecated.

Execute the specified command and wait for it to return.
exec(String[], String[], File, Reader, Writer, Writer, long) - Static method in class org.biojava.utils.ProcessTools: Deprecated.

Execute the specified command and wait for it to return, or kill it if the specified timeout expires first.
exec(String, OutputStream, OutputStream) - Method in class org.biojava.utils.ExecRunner: Convenience method for calling exec with OutputStreams.
exec(String, PrintWriter, PrintWriter) - Method in class org.biojava.utils.ExecRunner: The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread.
exec(String, Reader, Writer, Writer) - Static method in class org.biojava.utils.ProcessTools: Deprecated.

Execute the specified command and wait for it to return.
exec(String, String[]) - Method in class org.biojava.utils.ExecRunner: Sometimes special cases may occur that the arguments of an external program are Strings containing white spaces.
exec(String, String[], File, Reader, Writer, Writer, long) - Static method in class org.biojava.utils.ProcessTools: Deprecated.

Execute the specified command and wait for it to return.
exec(String, String[], OutputStream, OutputStream) - Method in class org.biojava.utils.ExecRunner: Convenience method for calling exec with OutputStreams.
exec(String, String[], PrintWriter, PrintWriter) - Method in class org.biojava.utils.ExecRunner: The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread.
ExecRunner - Class in org.biojava.utils: Makes running external executables easier, optionally under a watched thread.
ExecRunner() - Constructor for class org.biojava.utils.ExecRunner: Basic ExecRunner constructor.
ExecRunner(String) - Constructor for class org.biojava.utils.ExecRunner: ExecRunner constructor which also conveniently runs exec(String).
ExecRunner(String, String[]) - Constructor for class org.biojava.utils.ExecRunner: ExecRunner constructor which also conveniently runs exec(String).
execute() - Method in class org.biojava.utils.process.ExternalProcess: Executes the external process and waits for its termination.
execute(String) - Static method in class org.biojava.utils.process.ExternalProcess: Executes an external program.
execute(String, String, StringWriter, StringWriter) - Static method in class org.biojava.utils.process.ExternalProcess: Executes an external program.
execute(Properties) - Method in class org.biojava.utils.process.ExternalProcess: Executes the external process and waits for its termination.
expandCache(int) - Method in class org.biojava.utils.io.CachingInputStream: Expands the cache to hold some number of additionalBytes.
ExternalProcess - Class in org.biojava.utils.process: Utility class to execute an external process and to handle the STDOUT, STDERR and STDIN streams in multiple threads managed by a thread pool.
ExternalProcess() - Constructor for class org.biojava.utils.process.ExternalProcess: Initializes the external process.
ExternalProcess(ThreadPool) - Constructor for class org.biojava.utils.process.ExternalProcess: Initializes the external process.
extractOverlappingLocation(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils: Try to determine the minimal location which all features matching a given filter must overlap.
extras - Variable in class org.biojava.utils.candy.CandyEntry: A container for the additional properties represented by this entry.

F

f() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Phenylalanine
factorize(Alphabet, Set) - Static method in class org.biojava.bio.symbol.AlphabetManager: Return a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.EmblProcessor.Factory: Deprecated.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory: Deprecated.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor.Factory: Deprecated.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory: Deprecated.
Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor.Factory: Deprecated.
Factory(SequenceBuilderFactory, TaxonFactory, TaxonParser, String, String, String) - Constructor for class org.biojava.bio.seq.io.OrganismParser.Factory: Deprecated.
FACTORY - Static variable in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
FACTORY - Static variable in class org.biojava.bio.seq.io.SimpleSequenceBuilder
FACTORY - Static variable in class org.biojava.bio.seq.io.SmartSequenceBuilder
FACTORY - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory: Accessor for the default factory.
FALSE - Static variable in class org.biojava.utils.TriState
FASTA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: FASTA indicates that the alignment format is Fasta.
FASTA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: FASTA indicates that the sequence format is Fasta.
FASTA_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: FASTA_AA premade FASTA | AA;
FASTA_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: FASTA_AA premade FASTA | AA.
FASTA_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: FASTA_DNA premade FASTA | DNA;
FASTA_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: FASTA_DNA premade FASTA | DNA.
FASTA_FORMAT - Static variable in class org.biojavax.bio.seq.io.FastaFormat: The name of this format
FASTA_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants: FASTA_RNA premade FASTA | RNA;
FASTA_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: FASTA_RNA premade FASTA | RNA.
FastaAlignmentFormat - Class in org.biojava.bio.seq.io: This class implements the AlignmentFormat interface to read FASTA alignments.
FastaAlignmentFormat() - Constructor for class org.biojava.bio.seq.io.FastaAlignmentFormat
FastaDescriptionLineParser - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io.FastaFormat
FastaDescriptionLineParser(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.FastaDescriptionLineParser: Deprecated.
FastaDescriptionLineParser.Factory - Class in org.biojava.bio.seq.io: Deprecated.

Factory which wraps SequenceBuilders in a FastaDescriptionLineParser
FastaFormat - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io.FastaFormat
FastaFormat - Class in org.biojavax.bio.seq.io: Format object representing FASTA files.
FastaFormat() - Constructor for class org.biojava.bio.seq.io.FastaFormat: Deprecated.
FastaFormat() - Constructor for class org.biojavax.bio.seq.io.FastaFormat
FastaHeader - Class in org.biojavax.bio.seq.io: This class is used by FastaFormat to determine which fields are in the fasta header.
FastaHeader() - Constructor for class org.biojavax.bio.seq.io.FastaHeader
FastXMLWriter - Class in org.biojava.utils.xml: Simple implementation of XMLWriter, optimized for speed.
FastXMLWriter(PrintWriter) - Constructor for class org.biojava.utils.xml.FastXMLWriter
Feature - Interface in org.biojava.bio.seq: A feature within a sequence, or nested within another feature.
FEATURE - Static variable in interface org.biojavax.bio.seq.RichLocation
FEATURE_ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_DESC_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
FEATURE_FLAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
FEATURE_FROM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.FeatureHandler
FEATURE_HEADER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
FEATURE_INTERBP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_INTERVAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_INTERVALS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_ISCOMP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_KEY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_LINE_PREFIX - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
FEATURE_LOC_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
FEATURE_OPERATOR_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_ORIGINAL_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
FEATURE_PARTIAL3_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_PARTIAL5_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_POINT_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_TABLE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
FEATURE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
FEATURE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
FEATURE_TO_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_VARIATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
Feature.ByLocationComparator - Class in org.biojava.bio.seq: ByLocationComparator compares Features by the minimum base position of their Location.
Feature.Template - Class in org.biojava.bio.seq: Template class for a plain feature.
featureData(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser: Deprecated.
featureFilter(FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
FeatureFilter - Interface in org.biojava.bio.seq: A filter for accepting or rejecting a feature.
FeatureFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
FeatureFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
FeatureFilter.And - Class in org.biojava.bio.seq: A filter that returns all features accepted by both child filter.
FeatureFilter.AnnotationContains - Class in org.biojava.bio.seq: Retrieve features that contain a given annotation, and that the set of values contains the value given.
FeatureFilter.ByAncestor - Class in org.biojava.bio.seq: Filter by applying a nested FeatureFilter to all ancestor features.
FeatureFilter.ByAnnotation - Class in org.biojava.bio.seq: Retrieve features that contain a given annotation with a given value.
FeatureFilter.ByAnnotationType - Class in org.biojava.bio.seq: A filter that returns all features that have an annotation bundle that is of a given annotation type.
FeatureFilter.ByChild - Class in org.biojava.bio.seq: Filter by applying a nested FeatureFilter to the child features.
FeatureFilter.ByClass - Class in org.biojava.bio.seq: Filter which accepts only those filters which are an instance of a specific Java class
FeatureFilter.ByComponentName - Class in org.biojava.bio.seq: Accepts features which are ComponentFeatures and have a componentSequenceName property of the specified value.
FeatureFilter.ByDescendant - Class in org.biojava.bio.seq: Filter by applying a nested FeatureFilter to all descendant features.
FeatureFilter.ByFeature - Class in org.biojava.bio.seq: Accept only features which are equal to the specified feature
FeatureFilter.ByPairwiseScore - Class in org.biojava.bio.seq: ByPairwiseScore is used to filter SimilarityPairFeatures by their score.
FeatureFilter.ByParent - Class in org.biojava.bio.seq: Filter by applying a nested FeatureFilter to the parent feature.
FeatureFilter.BySequenceName - Class in org.biojava.bio.seq: Accept features that reside on a sequence with a particular name.
FeatureFilter.BySource - Class in org.biojava.bio.seq: Construct one of these to filter features by source.
FeatureFilter.ByType - Class in org.biojava.bio.seq: Construct one of these to filter features by type.
FeatureFilter.ContainedByLocation - Class in org.biojava.bio.seq: A filter that returns all features contained within a location.
FeatureFilter.FrameFilter - Class in org.biojava.bio.seq: Accept features with a given reading frame.
FeatureFilter.HasAnnotation - Class in org.biojava.bio.seq: Retrieve features that contain a given annotation with any value.
FeatureFilter.Not - Class in org.biojava.bio.seq: A filter that returns all features not accepted by a child filter.
FeatureFilter.OnlyChildren - Class in org.biojava.bio.seq: Accepts features where all immediate children meet the supplied filter.
FeatureFilter.OnlyDescendants - Class in org.biojava.bio.seq: Accepts features where all descendants meet the supplied filter.
FeatureFilter.Or - Class in org.biojava.bio.seq: A filter that returns all features accepted by at least one child filter.
FeatureFilter.OverlapsLocation - Class in org.biojava.bio.seq: A filter that returns all features overlapping a location.
FeatureFilter.ShadowContainedByLocation - Class in org.biojava.bio.seq: A filter that accepts all features whose shadow is contained by a specified Location.
FeatureFilter.ShadowOverlapsLocation - Class in org.biojava.bio.seq: A filter that accepts all features whose shadow overlaps a specified Location.
FeatureFilter.StrandFilter - Class in org.biojava.bio.seq: Accept features with a given strandedness.
FeatureHandler - Class in org.biojava.bio.program.xff: StAX handler for the basic feature type of XFF.
FeatureHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.FeatureHandler: Construct a new Feature handler, passing in an XFF-parsing environment.
FeatureHolder - Interface in org.biojava.bio.seq: The interface for objects that contain features.
FeatureHolder.EmptyFeatureHolder - Class in org.biojava.bio.seq
featureHolderAllocated() - Method in class org.biojava.bio.seq.impl.SimpleFeature: A utility function to find out if the feature holder delegate has been instantiated yet.
featureHolderAllocated() - Method in class org.biojava.bio.seq.impl.SimpleSequence
featureHolderAsSet(FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils: Returns a FeatureHolder as a Set of Features
FeatureHolderUtils - Class in org.biojava.bio.seq: This class intendes to provide some FeatureHolder utilities.
FeatureHolderUtils() - Constructor for class org.biojava.bio.seq.FeatureHolderUtils
FeatureImpl - Class in org.biojava.bio.seq.impl: Wrap up default sets of Feature implementations.
FeatureImpl() - Constructor for class org.biojava.bio.seq.impl.FeatureImpl
featureListener - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
featureListener - Variable in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
featureListener - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
featureListener - Variable in class org.biojava.bio.seq.io.game.StAXPropertyHandler
FEATUREQUAL_NAME_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATUREQUAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATUREQUAL_VALUE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATUREQUALS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FeatureRealizer - Interface in org.biojava.bio.seq: Interface for translators which map from Feature.Template instances to real Feature objects.
featureRelationshipSet - Variable in class org.biojavax.bio.seq.RichFeature.Template
features - Variable in class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.
features() - Method in interface org.biojava.bio.seq.Feature: Iterate over any child features which are held by this feature.
features() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
features() - Method in interface org.biojava.bio.seq.FeatureHolder: Iterate over the features in no well defined order.
features() - Method in class org.biojava.bio.seq.impl.DummySequence
features() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
features() - Method in class org.biojava.bio.seq.impl.RevCompSequence
features() - Method in class org.biojava.bio.seq.impl.SimpleFeature
features() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
features() - Method in class org.biojava.bio.seq.impl.SimpleSequence
features() - Method in class org.biojava.bio.seq.impl.SubSequence
features() - Method in class org.biojava.bio.seq.impl.ViewSequence
features() - Method in class org.biojava.bio.seq.LazyFeatureHolder
features() - Method in class org.biojava.bio.seq.MergeFeatureHolder: Iterate over all the features in all child FeatureHolders.
features() - Method in class org.biojava.bio.seq.NewSimpleAssembly
features() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
features() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
features() - Method in class org.biojava.bio.seq.SimpleAssembly
features() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
features() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Iterate over any child features which are held by this feature.
features() - Method in class org.biojavax.bio.seq.ThinRichSequence: Iterate over the features in no well defined order.
FEATURES - Static variable in interface org.biojava.bio.seq.FeatureHolder: Signals that features have been added or removed directly within this FeatureHolder.
FEATURES_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FeatureTableParser - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
featureTemplate - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
featureTemplate - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
FeatureTypes - Class in org.biojava.bio.seq: Registry of known types of features.
FeatureTypes() - Constructor for class org.biojava.bio.seq.FeatureTypes
FeatureTypes.Repository - Interface in org.biojava.bio.seq: A named collection of Types.
FeatureTypes.RepositoryImpl - Class in org.biojava.bio.seq: A simple implementation of a Repository.
FeatureTypes.Type - Interface in org.biojava.bio.seq: A type of feature.
fetch(String) - Method in class org.biojava.bio.seq.db.BioIndex
fetch(String) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
fetch(String) - Method in interface org.biojava.bio.seq.db.IndexStore: Fetch an Index based upon an ID.
fetch(String) - Method in class org.biojava.bio.seq.db.TabIndexStore
FetchURL - Class in org.biojava.bio.seq.db
FetchURL(String, String) - Constructor for class org.biojava.bio.seq.db.FetchURL: Constructs a fetchURL object based on the database name and specified return format of sequence.
FileAsList - Class in org.biojava.utils: FileAsList creates a writable List implementation backed by a random access file.
FileAsList(File, boolean) - Constructor for class org.biojava.utils.FileAsList: Creates a new FileAsList instance from an existing backing file.
FileAsList(File, int) - Constructor for class org.biojava.utils.FileAsList: Creates a new FileAsList and corresponding backing file.
FileStreamer(SequenceFormat, SymbolTokenization, File) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
FileStreamer(SequenceFormat, SymbolTokenization, List) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
fileToBiojava(int, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Reads a file and returns the corresponding Biojava object.
fileToBiojava(String, String, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Reads a file with the specified format and alphabet
fillBuffer(StringBuffer, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Simple method that adds spaces onto the buffer passed in.
fillTemplate(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
fillTemplate(FramedFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
fillTemplate(HomologyFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
fillTemplate(SimilarityPairFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
fillTemplate(RemoteFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
fillTemplate(StrandedFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
filter(AnnotationType) - Method in interface org.biojava.bio.annodb.AnnotationDB: Find all Annotation instances in this DB that are of a particular type.
filter(AnnotationType) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
filter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFEntrySet: Filter this entry set into another set.
filter(OrthologueFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthologueSet
filter(OrthologueFilter) - Method in interface org.biojava.bio.program.homologene.OrthologueSet: Filter the contents of a set.
filter(OrthoPairFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairSet
filter(OrthoPairFilter) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet: filter an OrthoPairSet
filter(OrthoPairSetFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
filter(OrthoPairSetFilter) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Filter the database for a specified group.
filter(OrthoPairSetFilter) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
filter(FeatureFilter) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
filter(FeatureFilter) - Method in interface org.biojava.bio.seq.db.SequenceDB: Query features attached to all sequences in this database.
filter(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
filter(FeatureFilter) - Method in interface org.biojava.bio.seq.FeatureHolder: Query this set of features using a supplied FeatureFilter.
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.DummySequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.RevCompSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleFeature
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SubSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.ViewSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.LazyFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.NewSimpleAssembly
filter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
filter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.SimpleAssembly
filter(FeatureFilter) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
filter(FeatureFilter) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Query this set of features using a supplied FeatureFilter.
filter(FeatureFilter) - Method in class org.biojavax.bio.seq.ThinRichSequence: Query this set of features using a supplied FeatureFilter.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
filter(FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.FeatureHolder: Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.DummySequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.RevCompSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleFeature
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SubSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.ViewSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.LazyFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.MergeFeatureHolder: When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.NewSimpleAssembly
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.SimpleAssembly
filter(FeatureFilter, boolean) - Method in class org.biojavax.bio.seq.SimpleRichFeature: Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
filter(FeatureFilter, boolean) - Method in class org.biojavax.bio.seq.ThinRichSequence: Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
FilterByLength(SearchListener, int) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.FilterByLength
FilteringContentHandler - Class in org.biojava.bio.search
FilteringContentHandler(BlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.FilteringContentHandler
FilteringContentHandler(BlastLikeSearchFilter, SearchContentHandler) - Constructor for class org.biojava.bio.search.FilteringContentHandler
FilteringContentHandler.FilterVisitor - Class in org.biojava.bio.search: Visitor class that parses the filter tree
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.program.xff.ElementRecognizer: Recognize an element based upon the start element parameters.
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.seq.io.agave.ElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.seq.io.game.ElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute
FilterTest - Interface in org.biojava.bio.search: Class for implementing tests with BlastLikeSearchFilter objects.
FilterTest.Equals - Class in org.biojava.bio.search: Tests that the value associated with the specified key is equal to the value supplied here by whatever criterion of equality appropriate to those objects.
FilterTest.FindRegex - Class in org.biojava.bio.search: Tests that the value associated with the specified key contains a part matched by the supplied regex.
FilterTest.GreaterThan - Class in org.biojava.bio.search: Tests that the value associated with the specified key is greater than the specified threshold.
FilterTest.LessThan - Class in org.biojava.bio.search: Tests that the value associated with the specified key is less than the specified threshold.
FilterTest.MatchRegex - Class in org.biojava.bio.search: Tests that the value associated with the specified key is matched in its entirety by the supplied regex.
FilterTransformer - Class in org.biojava.bio.seq.filter: Base-class for visitors that re-write a filter tree.
FilterTransformer() - Constructor for class org.biojava.bio.seq.filter.FilterTransformer
FilterUtils - Class in org.biojava.bio.seq: A set of FeatureFilter algebraic operations.
FilterUtils.DelegatingTransformer - Class in org.biojava.bio.seq: An implementation of FilterTransformer that attempts to transform by one transformer, and if that fails, by another.
FilterUtils.FilterTransformer - Interface in org.biojava.bio.seq: An object able to transform some FeatureFilter instances sytematically into others.
FilterVisitor() - Constructor for class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
finalize() - Method in class org.biojava.bio.alignment.SimpleAlignment
finalize() - Method in class org.biojava.bio.seq.io.NameTokenization
finalize() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
finalize() - Method in class org.biojava.bio.symbol.SimpleSymbolList
finalize() - Method in class org.biojava.utils.process.ExternalProcess
find() - Method in interface org.biojava.bio.search.BioMatcher: Attempt to find the next match.
find() - Method in class org.biojava.bio.search.MaxMismatchMatcher
find() - Method in class org.biojava.utils.regex.Matcher: Attempts to find the next subsequence of the input sequence that matches the pattern.
find(int) - Method in class org.biojava.utils.regex.Matcher: Resets this matcher and then attempts to find the next subsequence of the input sequence that matches the pattern, starting at the specified index.
find(String[], String[], Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery: The easiest direct method for querying a repository.
findByAuthor(BiblioProvider, Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery: This is a convenient method for a common query.
findById(String) - Method in interface org.biojava.bibliography.BibRefQuery: This is a convenient method returning just one citation.
findById(String, String[]) - Method in interface org.biojava.bibliography.BibRefQuery: This is a convenient method returning just one citation, perhaps with a limited number of attributes.
findFactory(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools: Find the UnigeneFactory that can accept a URL.
findMatches(SymbolList) - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch: This will return an int[] giving the offsets of the matches in text (ie the location of the first symbol of each match in the text).
findRecord(String) - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess: findRecord performs a binary search within the file for a record specified by an identifier String.
FindRegex(String) - Constructor for class org.biojava.bio.search.FilterTest.FindRegex
findSourceBlock(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Finds the index of the block containing the source coordinate indx.
findSourceGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Finds the index of the Block before the gap at indx within the following gap.
findTaxon(Object[]) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
findUnescaped(String, char) - Static method in class org.biojava.ontology.obo.OboFileParser
findUnescaped(String, char, int, int) - Static method in class org.biojava.ontology.obo.OboFileParser
findUnescaped(String, char, int, int, boolean) - Static method in class org.biojava.ontology.obo.OboFileParser
findViewBlock(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Finds the index of the Block containing indx within the view ranges.
findViewGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Finds the index of the Block before the gap at indx within the view range.
finishWriting() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.INSDseqFormat: Informs the writer that are done writing.
finishWriting() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat: Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: Informs the writer that are done writing.
FiniteAlphabet - Interface in org.biojava.bio.symbol: An alphabet over a finite set of Symbols.
FiniteAutomaton - Class in org.biojava.utils.automata: Class for modelling finite automata.
fireEndFeature() - Method in class org.biojava.bio.program.xff.FeatureHandler: Fire the endFeature event.
fireHits(int, int, SearchListener) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
firePostChange(Object, ChangeEvent) - Method in interface org.biojava.utils.ChangeHub: invoke the firePostChangeEvent on all ChangeListeners associated with a specific key.
firePostChange(Object, ChangeEvent) - Method in class org.biojava.utils.IndexedChangeHub
firePostChangeEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeSupport: Inform the listeners that a change has taken place using their firePostChangeEvent methods.
firePreChange(Object, ChangeEvent) - Method in interface org.biojava.utils.ChangeHub: invoke the firePreChangeEvent on all ChangeListeners associated with a specific key.
firePreChange(Object, ChangeEvent) - Method in class org.biojava.utils.IndexedChangeHub
firePreChangeEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeSupport: Inform the listeners that a change is about to take place using their firePreChangeEvent methods.
fireStartFeature() - Method in class org.biojava.bio.program.xff.FeatureHandler: Fire the startFeature event.
firstName - Variable in class org.biojava.bibliography.BiblioPerson: The person's christian name (first name).
firstNonGap() - Method in interface org.biojava.bio.symbol.GappedSymbolList: Return the index of the first Symbol that is not a Gap character.
firstNonGap() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
firstPage - Variable in class org.biojava.bibliography.BiblioArticle: First page of the article.
firstToken(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
fitness(Organism, Population, GeneticAlgorithm) - Method in interface org.biojavax.ga.functions.FitnessFunction: Calculates the fitness of org.
FITNESS_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
FitnessFunction - Interface in org.biojavax.ga.functions: Calculates the fitness of an Organism in a Population of Organisms
fivePrimeBlockIterator() - Method in class org.biojava.bio.symbol.CircularLocation: Iterates over the location blocks in order starting with the most 5'
FixedSizeCache - Class in org.biojava.utils.cache: Cache which stores up to limit Objects.
FixedSizeCache(int) - Constructor for class org.biojava.utils.cache.FixedSizeCache
FixedSizeMap - Class in org.biojava.utils.cache: A cache that only remembers a given number of keys.
FixedSizeMap(int) - Constructor for class org.biojava.utils.cache.FixedSizeMap
FIXEDWIDTH - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
FLAT_QUERY_ANCHORED - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
FLAT_QUERY_ANCHORED_NO_IDENTITIES - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
FlatFileCache - Class in org.biojava.utils.io: Provides a cache for storing multiple small files in memory.
FlatFileUnigeneFactory - Class in org.biojava.bio.program.unigene: A UnigeneFactory that will use flat-file indexing of the unigene ascii-art files.
FlatFileUnigeneFactory() - Constructor for class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
FlatSequenceDB - Class in org.biojava.bio.seq.db.flat: FlatSequenceDB is an OBDA flatfile sequence databank implementation.
FlatSequenceDB(String, String) - Constructor for class org.biojava.bio.seq.db.flat.FlatSequenceDB
FlatSequenceDBProvider - Class in org.biojava.bio.seq.db.flat: FlatSequenceDBProvider directory-services plugin for flatfile databases.
FlatSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
flatten(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools: Takes a set of locations and returns the set of all members.
flatten(RichLocation) - Static method in class org.biojavax.bio.seq.RichLocation.Tools: Takes a location and returns the set of all members.
flatView(MarkovModel) - Static method in class org.biojava.bio.dp.DP
flip() - Method in class org.biojava.bio.seq.StrandedFeature.Strand: Return a strand that represents flipping this onto the opposite strand.
flip(Location, int) - Static method in class org.biojava.bio.symbol.LocationTools: Flips a location relative to a length.
flip(SymbolList, StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.DNATools: Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
flipLocation(Location, int) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils: Flip a location.
flipStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
FloatElementHandlerBase - Class in org.biojava.utils.stax: StAX handler for any element which just contains a string representation of a float.
FloatElementHandlerBase() - Constructor for class org.biojava.utils.stax.FloatElementHandlerBase
flush() - Method in class org.biojava.utils.RepeatedCharSequence
flushFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
force() - Method in class org.biojava.utils.io.LargeBuffer
forIndex(int) - Static method in class org.biojava.bio.seq.DNATools: Return the symbol for an index - compatible with index.
forIndex(int) - Static method in class org.biojava.bio.seq.NucleotideTools: Return the symbol for an index - compatible with index.
forIndex(int) - Static method in class org.biojava.bio.seq.RNATools: Return the symbol for an index - compatible with index.
format - Variable in class org.biojava.bibliography.BibRef: It describes the physical or digital manifestation of the cited resource.
Format - Interface in org.biojava.bio.program.formats: A file format supported by the tag-value event-based parsing system.
formatLocation(StringBuffer, Location) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

formatLocation creates a String representation of a Location.
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.SeqFileFormer: Deprecated.

formatLocation creates a String representation of a Location.
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

formatLocation creates a String representation of a Location.
formatLocation(Feature) - Method in interface org.biojava.bio.seq.io.SeqFileFormer: Deprecated.

Formats the location of a feature.
formatLocation(Feature) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Creates a string representation of the location of a feature
formatPoint(int, int, boolean) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

Formats the points from fuzzy locations.
Formats - Class in org.biojava.bio.program.tagvalue: This is intended as a repository for tag-value and AnnotationType information about common file formats.
Formats() - Constructor for class org.biojava.bio.program.tagvalue.Formats
formatToFactory(SequenceFormat, Alphabet) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.
as this essentially duplicates the operation available in the method identifyBuilderFactory.
FormatTools - Class in org.biojava.bio.program.formats
forName(String) - Static method in class org.biojavax.bio.seq.RichLocation.Strand: Returns the strand object that matches the symbol given.
forSubset - Variable in class org.biojava.bibliography.BiblioCriterion: A name of a repository subset which this criterion is valid/used for.
forSymbol(char) - Static method in class org.biojava.bio.seq.DNATools: Retrieve the symbol for a symbol.
forSymbol(char) - Static method in class org.biojava.bio.seq.NucleotideTools: Retrieve the symbol for a symbol.
forSymbol(char) - Static method in class org.biojava.bio.seq.RNATools: Retrieve the symbol for a symbol.
forValue(int) - Static method in class org.biojavax.bio.seq.RichLocation.Strand: Returns the strand object that matches the number given.
forward(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
FORWARD - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
forward_initialize(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardChangeEvent(ChangeEvent) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder: Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolder
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
forwardRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
forwards(ScoreType) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
forwards(ScoreType) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
forwardsBackwards(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
forwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP: Returns a matrix for the specified States describing all valid Transitions between those States.
forwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP: Compute the log(score) of all transitions between the specified States.
fp - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
Frame - Interface in org.biojava.bio.seq: Title: Frame.
FRAME_0 - Static variable in interface org.biojava.bio.seq.Frame
FRAME_0 - Static variable in interface org.biojava.bio.seq.FramedFeature
FRAME_1 - Static variable in interface org.biojava.bio.seq.Frame
FRAME_1 - Static variable in interface org.biojava.bio.seq.FramedFeature
FRAME_2 - Static variable in interface org.biojava.bio.seq.Frame
FRAME_2 - Static variable in interface org.biojava.bio.seq.FramedFeature
FramedFeature - Interface in org.biojava.bio.seq: Title: FramedFeature.
FramedFeature.ReadingFrame - Class in org.biojava.bio.seq: A singleton to hold the frame information
FramedFeature.Template - Class in org.biojava.bio.seq
FrameFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
FrameFilter(int) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
FrameFilter(FramedFeature.ReadingFrame) - Constructor for class org.biojava.bio.seq.FeatureFilter.FrameFilter: Build a new filter that matches all features of a reading frame.
frequency(int) - Method in class org.biojava.bio.symbol.SuffixTree: Return the number of motifs of a given length encoded in this SuffixTree.
from - Variable in class org.biojava.bio.dp.TrainerTransition
from - Variable in class org.biojava.bio.dp.Transition
fromArray(double[]) - Static method in class org.biojava.bio.symbol.DoubleAlphabet: Retrieve a SymbolList view of an array of doubles.
fromArray(int[]) - Static method in class org.biojava.bio.symbol.IntegerAlphabet: Retrieve a SymbolList view of an array of integers.
fromBook - Variable in class org.biojava.bibliography.BiblioBookArticle: Book this is from.
fromJournal - Variable in class org.biojava.bibliography.BiblioJournalArticle: The journal that this article is in.
FUGU_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools: Takifugu rubripes codon preferences
full - Static variable in interface org.biojava.bio.symbol.Location: The Location which contains all points.
FULL_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
FullHmmerProfileHMM - Class in org.biojava.bio.program.hmmer: This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
FundamentalAtomicSymbol - Class in org.biojava.bio.symbol: An atomic symbol consisting only of itself.
FundamentalAtomicSymbol(String, Annotation) - Constructor for class org.biojava.bio.symbol.FundamentalAtomicSymbol
FuzzyLocation - Class in org.biojava.bio.symbol: A 'fuzzy' location a-la Embl fuzzy locations.
FuzzyLocation(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver) - Constructor for class org.biojava.bio.symbol.FuzzyLocation: Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).
FuzzyLocation(int, int, int, int, FuzzyLocation.RangeResolver) - Constructor for class org.biojava.bio.symbol.FuzzyLocation: Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).
FuzzyLocation.RangeResolver - Interface in org.biojava.bio.symbol: Determines how a FuzzyLocation should be treated when used as a normal Location.
FuzzyPointLocation - Class in org.biojava.bio.symbol: FuzzyPointLocation represents two types of EMBL-style partially-defined locations.
FuzzyPointLocation(int, int, FuzzyPointLocation.PointResolver) - Constructor for class org.biojava.bio.symbol.FuzzyPointLocation: Creates a new FuzzyPointLocation object.
FuzzyPointLocation.PointResolver - Interface in org.biojava.bio.symbol: Determines how a FuzzyPointLocation should be treated when used as a normal Location.
FWORM_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable: Translation table name for the flatworm mitochondrial genetic code.

G

g() - Static method in class org.biojava.bio.seq.DNATools
g() - Static method in class org.biojava.bio.seq.NucleotideTools
g() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Glycine
g() - Static method in class org.biojava.bio.seq.RNATools
GACross - Interface in org.biojavax.ga.functions: Holds the results of a CrossOver event, objects of this type are made by CrossOverFunctions
GACrossResult - Interface in org.biojavax.ga.functions: Holds the results of a CrossOver event, objects of this type are made by CrossOverFunctions
GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler: Description of the Field
GAME_ASPECT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAspectHandler
GAME_ASPECT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler
GAME_DBXREF_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler: Description of the Field
GAME_DBXREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler
GAME_DESCRIPTION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
GAME_FEATURE_SET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler: Description of the Field
GAME_FEATURE_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler: Description of the Field
GAME_FEATURESET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
GAME_FEATURESET_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler
GAME_FEATURESPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
GAME_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEGeneHandler: Description of the Field
GAME_GENE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
GAME_MAP_POS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
GAME_NAME_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMENamePropHandler
GAME_PROPERTY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEPropertyHandler: Description of the Field
GAME_RESIDUES_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
GAME_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqHandler: Description of the Field
GAME_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
GAME_SEQ_REL_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler: Description of the Field
GAME_SEQREL_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler
GAME_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESpanHandler: Description of the Field
GAME_SPAN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESpanPropHandler
GAME_TYPE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMETypePropHandler
GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <annotation> element
GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <annotation> element
GAMEAspectHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <aspect> element
GAMEAspectPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <aspect> element
GAMEDbxrefHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <dbxref> element
GAMEDbxrefPropHandler - Class in org.biojava.bio.seq.io.game: Deals with database crossreferences
GAMEDbxrefPropHandler.DbXrefElement - Class in org.biojava.bio.seq.io.game
GAMEDescriptionPropHandler - Class in org.biojava.bio.seq.io.game: StAX handler for GAME <description> elements.
GAMEDescriptionPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
GAMEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.game: An interface that can be tested for by nested handlers when trying to do a callback.
GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game: Handles the <feature_set> element
GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <feature_set> element this element is used to represent transcripts.
GAMEFeatureSetPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME element
GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game: Handles the <feature_span> element
GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <feature_span> element
GAMEFeatureSpanHandler.SeqRelHandler - Class in org.biojava.bio.seq.io.game12
GAMEFormat - Class in org.biojava.bio.seq.io: A rudimentary read-only GAME 1.2 Format object.
GAMEFormat() - Constructor for class org.biojava.bio.seq.io.GAMEFormat
GAMEGeneHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <annotation> element
GAMEGenePropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <gene> element
GAMEHandler - Class in org.biojava.bio.seq.io.game: Handles the root GAME element
GAMEHandler - Class in org.biojava.bio.seq.io.game12: Handles the root GAME element
GAMEHandler() - Constructor for class org.biojava.bio.seq.io.game.GAMEHandler
GAMEHandler(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.game12.GAMEHandler: Constructor for the GAMEHandler object
GAMEMapPosPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <map_position> element Currently, it just ignores it!
GAMENameCallbackItf - Interface in org.biojava.bio.seq.io.game: An interface that can be tested for by nested handlers when trying to do a callback.
GAMENamePropHandler - Class in org.biojava.bio.seq.io.game: StAX handler for the GAME <name> element.
GAMENamePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMENamePropHandler
GAMEPropertyHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <dbxref> element
GAMEResiduesPropHandler - Class in org.biojava.bio.seq.io.game: StAX handler for GAME <residues> elements.
GAMEResiduesPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
GAMESeqHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <seq> element
GAMESeqPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <seq> element
GAMESeqRelHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <> element
GAMESeqRelPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <aspect> element
GAMESpanHandler - Class in org.biojava.bio.seq.io.game12: Handles the GAME <> element.
GAMESpanPropHandler - Class in org.biojava.bio.seq.io.game: Handles the GAME <span> element Currently, it just ignores it!
GAMETranscriptCallbackItf - Interface in org.biojava.bio.seq.io.game: An interface that can be tested for by nested handlers when trying to do a callback.
GAMETypePropHandler - Class in org.biojava.bio.seq.io.game: StAX handler for GAME <type> elements.
GAMETypePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMETypePropHandler
GapDistribution - Class in org.biojava.bio.dist: This distribution emits gap symbols.
GapDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.GapDistribution: Get a GapDistribution for an alphabet.
GappedContext() - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
GappedSequence - Interface in org.biojava.bio.seq: Extension of GappedSymbolList which also projects features into the gapped coordinate system.
GappedSymbolList - Interface in org.biojava.bio.symbol: This extends SymbolList with API for manipulating, inserting and deleting gaps.
gappedToLocation(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList: Translates a Location from the gapped view into the underlying sequence.
gappedView(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools: Create a new gapped sequence for a sequence.
GAStoppingCriteria - Interface in org.biojavax.ga: Used by a GeneticAlgorithm.run() method to determine when the algorithm should stop
GAStoppingCriteria.MaximumGeneration - Class in org.biojavax.ga: Simple Implementation of GAStoppingCriteria, signals a GeneticAlgorithm to stop after n generations
GATools - Class in org.biojavax.ga.util: Utility methods for the GA library
GATools() - Constructor for class org.biojavax.ga.util.GATools
GCG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GCG indicates that the sequence format is GCG.
GENBANK - Static variable in class org.biojava.bio.program.tagvalue.LineSplitParser: A LineSplitParser pre-configured to process GENBANK-style flat files.
GENBANK - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GENBANK indicates that the sequence format is GENBANK.
GENBANK_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GENBANK_DNA premade GENBANK | AA.
GENBANK_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GENBANK_DNA premade GENBANK | DNA.
GENBANK_FORMAT - Static variable in class org.biojavax.bio.seq.io.GenbankFormat: The name of this format
GENBANK_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GENBANK_DNA premade GENBANK | RNA.
GenbankFileFormer - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenbankFileFormer() - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.

Creates a new GenbankFileFormer using System.out stream.
GenbankFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.

Creates a new GenbankFileFormer using the specified stream.
GenbankFormat - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io.GenbankFormat
GenbankFormat - Class in org.biojavax.bio.seq.io: Format reader for GenBank files.
GenbankFormat() - Constructor for class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
GenbankFormat() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat
GenbankFormat.Terms - Class in org.biojavax.bio.seq.io: Implements some GenBank-specific terms.
GenbankLocationParser - Class in org.biojavax.bio.seq.io: Parses Genbank location strings into RichLocation objects.
GenbankProcessor - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenbankProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.
GenbankProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor: Deprecated.
GenbankProcessor.Factory - Class in org.biojava.bio.seq.io: Deprecated.

Factory which wraps sequence builders in a GenbankProcessor
GenbankRichSequenceDB - Class in org.biojavax.bio.db.ncbi: This class contains functions accessing DNA sequences in Genbank format.
GenbankRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: The default constructor delegates to the parent class.
GenbankSequenceDB - Class in org.biojava.bio.seq.db: This class contains functions accessing DNA sequences in Genbank format.
GenbankSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenbankSequenceDB
GenbankXmlFormat - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io.INSDseqFormat
GenbankXmlFormat() - Constructor for class org.biojava.bio.seq.io.GenbankXmlFormat: Deprecated.
GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
GENELOCATION_NAME_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
GENELOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
GenEmblFeatureComparator - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenEmblPropertyComparator - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
GENENAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
generate() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Generates a comment string based on the current values of the internal fields.
generate(int) - Method in class org.biojava.bio.dp.DP: Generates an alignment from a model.
generateAuthorString(List<DocRefAuthor>, boolean) - Static method in class org.biojavax.DocRefAuthor.Tools: Takes a set of authors and creates a comma-separated string.
generateBackwardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
generateChangeSupport() - Method in class org.biojava.utils.AbstractChangeable: Called the first time a ChangeSupport object is needed.
generateCrossProductAlphaFromName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager: Generates a new CrossProductAlphabet from the give name.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.Annotatable.AnnotationForwarder: Deprecated.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.dist.Distribution.NullModelForwarder: Deprecated.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.MergeAnnotation.PropertyForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.OverlayAnnotation.PropertyForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder: Return the new event to represent the originating event ce.
generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder.Retyper
generateForardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
generateOrderNSequence(String, OrderNDistribution, int) - Static method in class org.biojava.bio.dist.DistributionTools: Deprecated.
use generateSequence() or generateSymbolList() instead.
generateRecord(byte[], Object) - Method in class org.biojava.utils.FileAsList
generateSequence(String, Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools: Produces a sequence by randomly sampling the Distribution.
generateSymbolList(Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools: Produces a SymbolList by randomly sampling a Distribution.
generateViterbiClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
GENERIC_PROVIDER - Static variable in interface org.biojava.bibliography.BibRefSupport: A name of a provider type.
GENESYNONYM_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
GeneticAlgorithm - Interface in org.biojavax.ga: The class that runs the cycles of reproduction, evolution and selection, potentially on multiple Populations
GENETICCODE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
GeneticCodes - Class in org.biojava.bio.seq: Collects the references to translation methods in one place.
GENPEPT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GENPEPT indicates that the sequence format is GENPEPT.
GenpeptFormat - Class in org.biojava.bio.seq.io: Deprecated.
Use org.biojavax.bio.seq.io framework instead
GenpeptFormat() - Constructor for class org.biojava.bio.seq.io.GenpeptFormat: Deprecated.
GenpeptRichSequenceDB - Class in org.biojavax.bio.db.ncbi: This class contains functions accessing Peptide sequences in Genpept format.
GenpeptRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: The default constructor delegates to the parent class.
GenpeptSequenceDB - Class in org.biojava.bio.seq.db
GenpeptSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenpeptSequenceDB
get() - Method in interface org.biojava.utils.cache.CacheReference
get() - Method in class org.biojava.utils.io.LargeBuffer
get(int) - Method in class org.biojava.stats.svm.SparseVector: Retrieve the value at dimension dim.
get(int) - Method in class org.biojava.utils.FileAsList
get(int) - Method in class org.biojava.utils.ListTools.Doublet
get(int) - Method in class org.biojava.utils.ListTools.SeriesList
get(int) - Method in class org.biojava.utils.ListTools.Triplet
get(int) - Method in class org.biojava.utils.SingletonList
get(long) - Method in class org.biojava.utils.io.LargeBuffer
get(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable: get the Transition associated with the specified tag.
get(Object) - Method in interface org.biojava.utils.cache.CacheMap: Retrieve the Object associated with the key, or null if either no value has been associated or if the key's value has been cleared by the cache.
get(Object) - Method in class org.biojava.utils.cache.ChangeableCache
get(Object) - Method in class org.biojava.utils.cache.FixedSizeMap
get(Object) - Method in class org.biojava.utils.cache.WeakCacheMap
get(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
get(Object) - Method in class org.biojava.utils.io.SoftHashMap
get(Object) - Method in class org.biojava.utils.OverlayMap
get(Object) - Method in class org.biojava.utils.SmallMap
get(String) - Method in class org.biojava.bio.program.indexdb.BioStore
get(String) - Method in interface org.biojava.bio.program.indexdb.IndexStore: get returns a record specified by a primary identifier.
get(String, String) - Method in class org.biojava.bio.program.indexdb.BioStore
get(String, String) - Method in interface org.biojava.bio.program.indexdb.IndexStore: get returns a list of Records by searching against the primary identifiers if the namespace argument is equal to the primary namespace or otherwise by searching the secondary namespaces.
get_() - Method in class org.biojava.bio.proteomics.StructureTools
get3PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation
get5PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation: The point at which indicates the 5' end of the Location.
getA() - Method in class org.biojava.bio.molbio.DNAComposition: Get the relative compositon of 'A'.
getA() - Method in class org.biojava.utils.ListTools.Doublet
getA() - Method in class org.biojava.utils.ListTools.Triplet
getAbsorptionMax() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property absorptionMax.
getAbsorptionNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property absorptionNote.
getAccession() - Method in interface org.biojava.bio.program.homologene.Orthologue: get the Accession ID associated with this orthologue.
getAccession() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getAccession() - Method in interface org.biojavax.bio.BioEntry: Returns the accession of this bioentry.
getAccession() - Method in class org.biojavax.bio.SimpleBioEntry: Returns the accession of this bioentry.
getAccession() - Method in interface org.biojavax.CrossRef: Returns the accession of the object that the crossref refers to.
getAccession() - Method in class org.biojavax.SimpleCrossRef: Returns the accession of the object that the crossref refers to.
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAccession(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAcronym() - Method in interface org.biojavax.Namespace: If the namespace has an acronym, this will return it.
getAcronym() - Method in class org.biojavax.SimpleNamespace: If the namespace has an acronym, this will return it.
getAddedFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
getAddHandler() - Method in class org.biojava.bio.program.gff.GFFEntrySet: Get the GFFDocumentHandler for adding to this set.
getAdditionalAccessionTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the secondary/tertiary/additional accession term
getAddPos() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier: Retrieve the current value of addPos.
getAddress(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB: Get the URL object for locating sequence object using eutils.
getAddress(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getAddress(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getAddress(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getAddress(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Get the URL object for locating sequence object using eutils.
getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: Get the URL object for locating sequence object using eutils.
getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB: Get the URL object for locating sequence object using eutils.
getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getAdvance() - Method in interface org.biojava.bio.dp.EmissionState: Determine the number of symbols this state advances along one or more symbol lists.
getAdvance() - Method in class org.biojava.bio.dp.SimpleEmissionState
getAlignLength(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAlignLength(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAlignment() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.
getAlignment() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getAlignment() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getAlignment() - Method in interface org.biojava.bio.seq.homol.Homology: Retrieve the Alignment that specifies how the homologous regions are aligned.
getAlignment() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature: getAlignment returns the Alignment of two similar features.
getAlignment() - Method in class org.biojava.bio.seq.homol.SimpleHomology: getAlignment returns the alignment, which uses the HomologyFeatures as keys.
getAlignment() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature: getAlignment returns the alignment between the two features.
getAlignmentNumber() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties: A method that simply returns the number of alignments fetched with this RemoteQBlastOutputProperties object.
getAlignmentOption(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
getAlignmentOption(String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties: Method that returns the value associated with the key given in parameter.
getAlignmentOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
getAlignmentOptions() - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties: Method to get all keys to the information stored in this object.
getAlignmentOutputFormat() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties: Method that returns the alignment output format for this actual RemoteQBlastOutputProperties object
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService: This method extracts the actual Blast report for this request ID.
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService: Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.
getAlignmentStyles() - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler: Returns a fragment of HTML that defines the FONT styles to be used in the alignment markup.
getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAlignUnits(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAll() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster: All sequences that map to this cluster.
getAllAmbiguitySymbol(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Return the ambiguity symbol which matches all symbols in a given alphabet.
getAllBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery: It returns all citations from the current collection as a (possibly big) array.
getAllBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery: It returns all citations from the current collection as a (possibly big) array, perhaps with a limited number of attributes.
getAllBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery: It returns all citations from the current collection as an XML stream.
getAllEntries() - Method in interface org.biojava.utils.candy.CandyVocabulary: It returns all available vocabulary entries.
getAllEnzymes() - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getAllEnzymes returns an unmodifable set of all available enzymes.
getAllIDs() - Method in interface org.biojava.bibliography.BibRefQuery: A convenient method returning just identifiers of all current citations.
getAllNames() - Method in interface org.biojava.utils.candy.CandyVocabulary: It return all names (entry identifiers) available in this vocabulary.
getAllNodes(UkkonenSuffixTree.SuffixNode, ArrayList, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getAllProteases() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getAllSymbols(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Return a set containing all possible symbols which can be considered members of a given alphabet, including ambiguous symbols.
getAllVocabularies() - Method in interface org.biojava.utils.candy.CandyFinder: It returns all available vocabularies.
getAllVocabularyNames() - Method in interface org.biojava.utils.candy.CandyFinder: It returns names of all vocabularies known to this vocabulary finder.
getAlpha(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getAlpha(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
getAlpha(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
getAlphabet() - Method in class org.biojava.bio.alignment.SimpleAlignment
getAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
getAlphabet() - Method in interface org.biojava.bio.dist.Count: The alphabet from which this Count is over.
getAlphabet() - Method in interface org.biojava.bio.dist.Distribution: The alphabet from which this spectrum emits symbols.
getAlphabet() - Method in class org.biojava.bio.dist.GapDistribution
getAlphabet() - Method in class org.biojava.bio.dist.IndexedCount
getAlphabet() - Method in class org.biojava.bio.dist.PairDistribution
getAlphabet() - Method in class org.biojava.bio.dist.SimpleDistribution
getAlphabet() - Method in class org.biojava.bio.dist.TranslatedDistribution
getAlphabet() - Method in class org.biojava.bio.dist.UniformDistribution
getAlphabet() - Method in class org.biojava.bio.dp.SimpleStatePath
getAlphabet() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
getAlphabet() - Method in interface org.biojava.bio.dp.WeightMatrix: The alphabet for the sequences that this weight matrix models.
getAlphabet() - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
getAlphabet() - Method in interface org.biojava.bio.program.ssaha.DataStore: The alphabet of symbol lists that can be searched against this DataStore.
getAlphabet() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.WebSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
getAlphabet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
getAlphabet() - Method in class org.biojava.bio.seq.impl.DummySequence
getAlphabet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
getAlphabet() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getAlphabet() - Method in class org.biojava.bio.seq.impl.SubSequence
getAlphabet() - Method in class org.biojava.bio.seq.impl.ViewSequence
getAlphabet() - Method in class org.biojava.bio.seq.io.AlternateTokenization
getAlphabet() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolReader: Find the alphabet of all symbols which may be returned by this SymbolReader.
getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolTokenization: The alphabet to which this tokenization applies.
getAlphabet() - Method in class org.biojava.bio.seq.io.WordTokenization
getAlphabet() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools: Gets the protein alphabet
getAlphabet() - Method in class org.biojava.bio.seq.SimpleAssembly
getAlphabet() - Method in interface org.biojava.bio.symbol.AlphabetIndex: Retrieve the alphabet that this indexes.
getAlphabet() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
getAlphabet() - Method in class org.biojava.bio.symbol.DNAAmbPack
getAlphabet() - Method in class org.biojava.bio.symbol.DNANoAmbPack
getAlphabet() - Method in class org.biojava.bio.symbol.DummySymbolList
getAlphabet() - Method in class org.biojava.bio.symbol.PackedSymbolList
getAlphabet() - Method in interface org.biojava.bio.symbol.Packing: The FiniteAlphabet this packing is for.
getAlphabet() - Method in class org.biojava.bio.symbol.RelabeledAlignment
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolList: Get the alphabet of this SymbolList.
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
getAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
getAlphabet() - Method in class org.biojava.bio.symbol.SuffixTree: Return the Alphabet containing all Symbols which might be found in this SuffixTree.
getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolList: The alphabet that this SymbolList is over.
getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
getAlphabet() - Method in class org.biojava.utils.regex.Pattern
getAlphabet() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList: The alphabet that this SymbolList is over.
getAlphabet() - Method in class org.biojavax.bio.seq.ThinRichSequence: The alphabet that this SymbolList is over.
getAlphabet(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

getAlphabet accepts a value which represents a sequence format and returns the relevant FiniteAlphabet object.
getAlphabetIndex(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Get an indexer for a specified alphabet.
getAlphabetIndex(Symbol[]) - Static method in class org.biojava.bio.symbol.AlphabetManager: Get an indexer for an array of symbols.
getAlphabetName() - Method in class org.biojavax.bio.seq.ThinRichSequence
getAlphabets() - Method in interface org.biojava.bio.symbol.Alphabet: Return an ordered List of the alphabets which make up a compound alphabet.
getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SimpleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SingletonAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Gets the components of the Alphabet.
getAlphaStar(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAltIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: This is not supported.
getAmbiguity(Set<Symbol>) - Method in interface org.biojava.bio.symbol.Alphabet: Get a symbol that represents the set of symbols in syms.
getAmbiguityImpl(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet: Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
getAnnotation() - Method in interface org.biojava.bio.Annotatable: Should return the associated annotation object.
getAnnotation() - Method in class org.biojava.bio.dp.SimpleEmissionState
getAnnotation() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.

getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.

getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit: getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult: getAnnotation returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit: getAnnotation returns the Annotation associated with this sub-hit.
getAnnotation() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getAnnotation() - Method in class org.biojava.bio.seq.impl.DummySequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.SubSequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.ViewSequence
getAnnotation() - Method in class org.biojava.bio.seq.io.AlternateTokenization
getAnnotation() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getAnnotation() - Method in class org.biojava.bio.seq.io.WordTokenization
getAnnotation() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getAnnotation() - Method in class org.biojava.bio.seq.SimpleAssembly
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.SimpleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.SingletonAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: The SoftMaskedAlphabet has no annotation
getAnnotation() - Method in class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
getAnnotation() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getAnnotation() - Method in class org.biojava.ontology.OntologyTerm.Impl
getAnnotation() - Method in class org.biojava.ontology.RemoteTerm.Impl
getAnnotation() - Method in class org.biojava.ontology.Term.Impl
getAnnotation() - Method in class org.biojava.ontology.Triple.Impl
getAnnotation() - Method in class org.biojavax.bio.seq.CompoundRichLocation: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.SimpleBioEntry: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTerm: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTriple: Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.SimpleCrossRef: Should return the associated annotation object.
getAnnotation(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getAnnotation returns an immutable, static annotation describing the enzyme.
getAnnotations() - Method in class org.biojava.bio.MergeAnnotation: Gets an unmodifiable view of the list of Annotations that are part of the MergeAnnotation.
getAnnotationType() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType: Get the AnnotationType used as a constraint.
getAnnotationType() - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler: Return the AnnotationType built by this handler
getAnnotator() - Method in class org.biojava.bio.program.gff.GFFEntrySet: Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.
getAnnotator(boolean) - Method in class org.biojava.bio.program.gff.GFFEntrySet: Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.
getArg_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getArticleAuthors() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the names of the authors which first published an article about the AAindex entry.
getArticleTitle() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the title of the article which describes the AAindex entry.
getAsp_N() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getAttributes(String) - Method in class org.biojava.naming.ObdaContext
getAttributes(String, String[]) - Method in class org.biojava.naming.ObdaContext
getAttributes(Name) - Method in class org.biojava.naming.ObdaContext
getAttributes(Name, String[]) - Method in class org.biojava.naming.ObdaContext
getAuthority() - Method in interface org.biojavax.Namespace: This method will return the authority that governs the namespace.
getAuthority() - Method in class org.biojavax.SimpleNamespace: This method will return the authority that governs the namespace.
getAuthorityId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier: Return the authority id for this identifier.
getAuthorList() - Method in interface org.biojavax.DocRef: Returns the authors of the document reference as a set of DocRefAuthor implementation instances.
getAuthorList() - Method in class org.biojavax.SimpleDocRef: Returns the authors of the document reference as a set of DocRefAuthor implementation instances.
getAuthors() - Method in interface org.biojavax.DocRef: Returns the authors of the document reference.
getAuthors() - Method in class org.biojavax.SimpleDocRef: Returns the authors of the document reference.
getAutomaton() - Method in class org.biojava.utils.automata.FiniteAutomaton
getAutomaton() - Method in interface org.biojava.utils.automata.NfaBuilder
getAutomaton() - Method in class org.biojava.utils.automata.NfaSubModel
getB() - Method in class org.biojava.bio.proteomics.StructureTools
getB() - Method in class org.biojava.utils.ListTools.Doublet
getB() - Method in class org.biojava.utils.ListTools.Triplet
getBackwardTransitions() - Method in class org.biojava.bio.dp.DP
getBackwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
getBases() - Method in class org.biojava.bio.dp.SimpleEmissionState
getBases() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getBases() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getbaseURL() - Method in class org.biojava.bio.seq.db.FetchURL
getBibRefAsXML(BibRef) - Method in interface org.biojava.bibliography.BibRefQuery: A convenient utility method converting a given citation to its XML representation.
getBibRefCount() - Method in interface org.biojava.bibliography.BibRefQuery: It returns the number of citations in the current collection.
getBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery: It returns an enumeration of all citations from the current collection.
getBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery: It returns an enumeration of all citations from the current collection, perhaps with a limited number of attributes.
getBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery: It returns an enumeration of all citations from the current collection.
getBinaryAlphabet() - Static method in class org.biojavax.ga.util.GATools: Gets a Reference to the FlyWeight GA_Binary Alphabet.
getBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite: Retrieve a single BioEntry by its id.
getBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB
getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractBioEntryDB
getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntryIterator() - Method in interface org.biojavax.bio.db.BioEntryDB: Returns a BioEntryIterator over all BioEntrys in the database.
getBioEntrys(Set) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntrys(Set) - Method in interface org.biojavax.bio.db.BioEntryDBLite: Retrieve multiple BioEntry by their ids.
getBioEntrys(Set) - Method in class org.biojavax.bio.db.HashBioEntryDB
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntrys(Set, BioEntryDB) - Method in interface org.biojavax.bio.db.BioEntryDBLite: Retrieve multiple BioEntry into a specific sequence database.
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.HashBioEntryDB
getBlastAdvancedOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties: Simply return the string given as argument via setBlastAdvancedOptions
getBlastDatabase() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties: This method returns the value of the database used for this particular blast run.
getBlastProgram() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties: This method returns the value of the program used for this particular blast run.
getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.Aggregator
getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.MultiTagger
getBuilderFactory(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

getBuilderFactory accepts a value which represents a sequence format and returns the relevant SequenceBuilderFactory object.
getC() - Method in class org.biojava.bio.molbio.DNAComposition: Get the relative compositon of 'C'.
getC() - Method in class org.biojava.bio.proteomics.StructureTools
getC() - Method in class org.biojava.stats.svm.SMOTrainer
getC() - Method in class org.biojava.utils.ListTools.Triplet
getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn: Get the cardinality constraint used to validate the number of property values.
getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains: Get the cardinality constraint used to validate the number of property values.
getCategory() - Method in class org.biojava.ontology.Synonym
getCell(int[]) - Method in interface org.biojava.bio.dp.DPMatrix
getCell(int[]) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
getCell(int[]) - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
getChainedEvent() - Method in class org.biojava.utils.ChangeEvent: Return the event which caused this to be fired, or null if this change was not caused by another event.
getChange() - Method in class org.biojava.utils.ChangeEvent: Return an object which is to be the new value of some property, or is to be added to a collection.
getChangeEvent() - Method in exception org.biojava.utils.ChangeVetoException: Return the ChangeEvent which is being vetoed.
getChanger() - Method in class org.biojava.bio.AnnotationChanger: getMapper returns the ValueChanger being used to remap the Annotation.
getChanger(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable: Get the Changer currently registered to handle a tag.
getChangeSupport() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
getChangeSupport() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractDistribution
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.TranslatedDistribution
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleEmissionState
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleMarkovModel
getChangeSupport(ChangeType) - Method in class org.biojava.bio.MergeAnnotation
getChangeSupport(ChangeType) - Method in class org.biojava.bio.OverlayAnnotation
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleFeature
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleSequence
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.LazyFeatureHolder
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.NewSimpleAssembly
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.SimpleAssembly
getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.AbstractSymbol
getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.SimpleAlphabet
getChangeSupport(ChangeType) - Method in class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.ontology.AbstractTerm
getChangeSupport(ChangeType) - Method in class org.biojava.ontology.OntologyTerm.Impl
getChangeSupport(ChangeType) - Method in class org.biojava.utils.AbstractChangeable: Called to retrieve the ChangeSupport for this object.
getChangeTable() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
getChangeTypes(Class) - Static method in class org.biojava.utils.ChangeType: Get all ChangeType objects defined within a class.
getChar() - Method in class org.biojava.utils.io.LargeBuffer
getChar(long) - Method in class org.biojava.utils.io.LargeBuffer
getCharacter() - Method in class org.biojava.utils.RepeatedCharSequence
getCharacterOffset() - Method in exception org.biojava.utils.ParserException: Get the character offset in the line where an error was detected.
getChild() - Method in class org.biojava.bio.seq.FeatureFilter.Not
getChild(SuffixTree.SuffixNode, int) - Method in class org.biojava.bio.symbol.SuffixTree: Get the n'th child of a node.
getChild(SuffixTree.SuffixNode, Symbol) - Method in class org.biojava.bio.symbol.SuffixTree: Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
getChild1() - Method in class org.biojava.bio.CollectionConstraint.And: Get the first child CollectionConstraint.
getChild1() - Method in class org.biojava.bio.CollectionConstraint.Or: Get the first child CollectionConstraint.
getChild1() - Method in class org.biojava.bio.PropertyConstraint.And: Get the first child PropertyConstraint.
getChild1() - Method in class org.biojava.bio.PropertyConstraint.Or: Get the first child PropertyConstraint.
getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.And
getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.Or
getChild2() - Method in class org.biojava.bio.CollectionConstraint.And: Get the seccond child CollectionConstraint.
getChild2() - Method in class org.biojava.bio.CollectionConstraint.Or: Get the seccond child CollectionConstraint.
getChild2() - Method in class org.biojava.bio.PropertyConstraint.And: Get the seccond child PropertyConstraint.
getChild2() - Method in class org.biojava.bio.PropertyConstraint.Or: Get the seccond child PropertyConstraint.
getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.And
getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.Or
getChildren() - Method in class org.biojava.bio.taxa.SimpleTaxon: Deprecated.
getChildren() - Method in interface org.biojava.bio.taxa.Taxon: Deprecated.

The children of this Taxon.
getChildren() - Method in class org.biojava.bio.taxa.WeakTaxon: Deprecated.
getChildrenRaw() - Method in class org.biojava.bio.taxa.WeakTaxon: Deprecated.
getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getChromNum(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getChromosome() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getChromosome(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getChromosomes() - Method in interface org.biojavax.ga.functions.GACross: Gets the chromosomes after the cross
getChromosomes() - Method in interface org.biojavax.ga.functions.GACrossResult: Gets the chromosomes after the cross
getChromosomes() - Method in class org.biojavax.ga.functions.SimpleGACrossResult
getChromosomes() - Method in class org.biojavax.ga.impl.AbstractOrganism
getChromosomes() - Method in interface org.biojavax.ga.Organism: Gets the organisms 'chromosome' sequences
getChymotrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getCircular() - Method in interface org.biojavax.bio.seq.RichSequence: Is the sequence circular?
getCircular() - Method in class org.biojavax.bio.seq.ThinRichSequence: Is the sequence circular?
getCircularLength() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the circular length of this location.
getCircularLength() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: Retrieves the circular length of this location.
getCircularLength() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the circular length of this location.
getCircularLength() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the circular length of this location.
getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifyId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifySystem(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifyType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassLoader(Class) - Static method in class org.biojava.utils.ClassTools: Get the classloader which loaded clazz.
getClassLoader(Object) - Static method in class org.biojava.utils.ClassTools: Get the classloader which loaded the class of obj.
getClassNumber(int) - Method in interface org.biojava.bio.EcNumber: Get the class number associated with the particular level of the ec number.
getClassNumber(int) - Method in class org.biojava.bio.EcNumber.Impl
getCleaveageResidues() - Method in class org.biojava.bio.proteomics.Protease: The list of residues that the protease will cleave at.
getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCloneId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCloneLibrary(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCluster(String) - Method in interface org.biojava.bio.program.unigene.UnigeneDB: Fetch a cluster by its cluster id.
getCNBr() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getCodonAlphabet() - Static method in class org.biojava.bio.seq.DNATools: Gets the (DNA x DNA x DNA) Alphabet
getCodonAlphabet() - Static method in class org.biojava.bio.seq.RNATools: Gets the (RNA x RNA x RNA) Alphabet
getCodonPref() - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
getCodonPreference(String) - Static method in class org.biojava.bio.symbol.CodonPrefTools: get the specified codon preference.
getCodonPrefs() - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
getCollectionConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandler
getCollectionId() - Method in interface org.biojava.bibliography.BibRefQuery: It returns an identification of the current query collection.
getColourClass(String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler: Returns the colour class for the specified colour (in hex).
getColumn(int) - Method in class org.biojava.bio.dp.SimpleWeightMatrix
getColumn(int) - Method in interface org.biojava.bio.dp.WeightMatrix: Retrieve a column as an EmissionState.
getCommands() - Method in class org.biojava.utils.process.ExternalProcess: Gets the command line including the path or name of the external program and its command line arguments.
getComment() - Method in interface org.biojava.bio.AnnotationType: Get the comment for the whole AnnotationType.
getComment() - Method in class org.biojava.bio.AnnotationType.Impl
getComment() - Method in interface org.biojava.bio.program.gff.GFFRecord: The feature comment.
getComment() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getComment() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the user comment for the AAindex entry.
getComment() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
getComment() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event: Getter for property comment.
getComment() - Method in interface org.biojavax.Comment: Returns the comment part of this comment.
getComment() - Method in class org.biojavax.SimpleComment: Returns the comment part of this comment.
getComment(Object) - Method in interface org.biojava.bio.AnnotationType: Get the comment for a particular property.
getComment(Object) - Method in class org.biojava.bio.AnnotationType.Impl
getComments() - Method in interface org.biojavax.bio.BioEntry: Returns a set of all comments associated with this bioentry.
getComments() - Method in class org.biojavax.bio.SimpleBioEntry: Returns a set of all comments associated with this bioentry.
getCommentType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property commentType.
getCommonName() - Method in class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
getCommonName() - Method in interface org.biojava.bio.taxa.Taxon: Deprecated.

The common name of the Taxon.
getComparator() - Method in class org.biojava.utils.FileAsList
getComponentList(boolean) - Method in class org.biojava.bio.symbol.MergeLocation: Gets the component locations that make up this one
getComponentLocation() - Method in interface org.biojava.bio.seq.ComponentFeature: Return a location which identifies a portion of the component sequence which is to be included in the assembly.
getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
getComponentName() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
getComponentSequence() - Method in interface org.biojava.bio.seq.ComponentFeature: Get the sequence object which provides a component of this feature's parent sequence.
getComponentSequenceName() - Method in interface org.biojava.bio.seq.ComponentFeature: Get the name of the component sequence.
getConditionedAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution: Get the conditioned alphabet.
getConditionedAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution: Get the conditioned alphabet.
getConditioningAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution: Get the conditioning alphabet of this distribution.
getConditioningAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution: Get the conditioning alphabet of this distribution.
getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getConfidence(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Composite
getConfigLocator() - Method in interface org.biojava.directory.RegistryConfiguration: getConfigLocator returns a locator for the configuration.
getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Impl
getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Composite
getConfiguration() - Method in interface org.biojava.directory.RegistryConfiguration: getConfiguration returns a mapping of registry database names to collections of tag-value pairs.
getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Impl
getConstant() - Method in class org.biojava.stats.svm.PolynomialKernel
getConstant() - Method in class org.biojava.stats.svm.SigmoidKernel
getConstraint(Object) - Method in interface org.biojava.bio.AnnotationType: Retrieve the constraint that will be applied to all properties with a given key.
getConstraint(Object) - Method in class org.biojava.bio.AnnotationType.Impl
getContainsTerm() - Static method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Gets the default CONTAINS term used for defining the relationship between features.
getContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
getContext() - Method in class org.biojava.stats.svm.TrainingEvent
getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser: See if empty tags are treated as a continuation of previous tags or as a new tag with the value of the empty string.
getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser: Report whether empty tags will be treated as continuations of the last non -empty tag.
getCopyrightTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the copyright term
getCoreOntology() - Static method in class org.biojava.ontology.OntoTools: Get the Ontology that defines our core "central dogma".
getCount() - Method in interface org.biojava.utils.candy.CandyVocabulary: It returns a number of entries contained in this vocabulary.
getCount(Distribution, Symbol) - Method in interface org.biojava.bio.dist.DistributionTrainerContext: Return the number of counts of a particular symbol which will be used to train the specified distribution.
getCount(Distribution, Symbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
getCount(DistributionTrainerContext, AtomicSymbol) - Method in interface org.biojava.bio.dist.DistributionTrainer: Get the current count for this state.
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer: Deprecated.
getCount(AtomicSymbol) - Method in interface org.biojava.bio.dist.Count: Return the counts for a given Symbol.
getCount(AtomicSymbol) - Method in class org.biojava.bio.dist.IndexedCount
getCRC() - Method in interface org.biojavax.DocRef: Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references.
getCRC() - Method in class org.biojavax.SimpleDocRef: Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references.
getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCreateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCreateOnUnderlyingSequence() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getCrossOverFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
getCrossOverFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACross: Returns the collection of cross over locations from the last cross
getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACrossResult: Returns the collection of cross over locations from the last cross
getCrossOverPositions() - Method in class org.biojavax.ga.functions.SimpleGACrossResult
getCrossOverProbs() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
getCrossOverProbs() - Method in interface org.biojavax.ga.functions.CrossOverFunction
getCrossOverProbs() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
getCrossProductAlphabet(List) - Static method in class org.biojava.bio.symbol.AlphabetManager: Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCrossProductAlphabet(List, String) - Static method in class org.biojava.bio.symbol.AlphabetManager: Attempts to create a cross product alphabet and register it under a name.
getCrossProductAlphabet(List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager: Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCrossref() - Method in interface org.biojavax.DocRef: The document reference may refer to an object in another database.
getCrossref() - Method in class org.biojavax.SimpleDocRef: The document reference may refer to an object in another database.
getCrossRef() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the crossref associated with this location.
getCrossRef() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: Retrieves the crossref associated with this location.
getCrossRef() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the crossref associated with this location.
getCrossRef() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the crossref associated with this location.
getCrossRef() - Method in interface org.biojavax.RankedCrossRef: Return the cross reference associated with this object.
getCrossRef() - Method in class org.biojavax.SimpleRankedCrossRef: Return the cross reference associated with this object.
getCrossResults() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm: Get a List containing details of all the cross over events during the run.
getCurrentCycle() - Method in interface org.biojava.stats.svm.TrainingContext
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
getCurrentFeature() - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener: Gets the feature currently being created.
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder: Gets the feature currently being created.
getCurrentScore() - Method in class org.biojava.bio.dp.AbstractTrainer
getCurrentScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getCutoff() - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold
getCuttingSize() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: The cutting size of a restriction enzyme is defined has the number of nucleotides that are directly involved in the recognition sequence.
getCutType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getCutType returns the type of cut produced by the enzyme.
getCycle() - Method in class org.biojava.bio.dp.AbstractTrainer
getCycle() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getDatabase(String) - Method in class org.biojava.directory.Registry: getDatabase retrieves a database instance known by a name String.
getDataBase() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getDatabaseName() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property databaseName.
getDatabaseURLGenerators() - Method in class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
getDatabaseURLGenerators() - Method in interface org.biojava.bio.program.blast2html.URLGeneratorFactory: Returns a list of 0, 1 or more DatabaseURLGenerator The first is used to link from the id in the summary table, all are used as a list of links in the detail section.
getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms: Getter for the Ensembl-specific 'dataClass' term
getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms: Getter for the Ensembl-specific 'dataClass' term
getDataClassTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the DataClass term
getDataSource(String, String, String, String) - Static method in class org.biojava.utils.JDBCPooledDataSource
getDataSources() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB: Get the current set of all currently registered data sources.
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
getDataStore(File) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory: Get a pre-built data store associated with a file.
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory
getDataType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
getDateAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the date annotated term
getDateCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the date created term
getDateUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the date updated term
getDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder: retrieve the DB that has just been built
getDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
getDB() - Method in class org.biojava.bio.seq.db.FetchURL
getDbCode() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getDbId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs: return a set of DbId
getDbname() - Method in interface org.biojavax.CrossRef: Returns the name of the database the cross reference refers to.
getDbname() - Method in class org.biojavax.SimpleCrossRef: Returns the name of the database the cross reference refers to.
getDbXrefId() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
getDbxrefList(String, int, int) - Method in class org.biojava.ontology.obo.OboFileParser
getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocation
getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getDecorator(Class) - Method in interface org.biojava.bio.symbol.Location: Checks the decorator chain for an instance of decoratorClass and return it if found.
getDecorator(Class) - Method in class org.biojavax.bio.seq.CompoundRichLocation: Checks the decorator chain for an instance of decoratorClass and return it if found.
getDecorator(Class) - Method in class org.biojavax.bio.seq.EmptyRichLocation: Checks the decorator chain for an instance of decoratorClass and return it if found.
getDecorator(Class) - Method in class org.biojavax.bio.seq.SimpleRichLocation: Checks the decorator chain for an instance of decoratorClass and return it if found.
getDefaultChanger() - Method in class org.biojava.bio.program.tagvalue.ValueChanger: Get the changer that will be applied to values of tags with no specific handler registered.
getDefaultConstraint() - Method in interface org.biojava.bio.AnnotationType: Get the CollectionConstraint that will be applied to all properties without an explicit binding.
getDefaultConstraint() - Method in class org.biojava.bio.AnnotationType.Impl
getDefaultCrossReferenceResolver() - Static method in class org.biojavax.RichObjectFactory: Returns the default cross ref resolver object.
getDefaultFactory() - Static method in class org.biojava.ontology.OntoTools
getDefaultFormat() - Method in class org.biojava.bio.program.phred.PhredFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.FastaFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GAMEFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankXmlFormat: Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenpeptFormat: Deprecated.
getDefaultFormat() - Method in interface org.biojava.bio.seq.io.SequenceFormat: Deprecated.
new implementations should only write a single format.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.FastaFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.GenbankFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.INSDseqFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
getDefaultNamespace() - Static method in class org.biojavax.RichObjectFactory: Returns the default namespace object.
getDefaultOntology() - Static method in class org.biojavax.RichObjectFactory: Returns the default ontology object.
getDefaultPositionResolver() - Static method in class org.biojavax.RichObjectFactory: Returns the default position resolver object.
getDefaultRichSequenceHandler() - Static method in class org.biojavax.RichObjectFactory: Returns the default sequence resolver object.
getDefaultSplitter() - Method in class org.biojava.bio.program.tagvalue.ValueChanger: Get the splitter that will be applied to values of tags with no specific handler registered.
getDelegate() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
getDelegate() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
getDelegate() - Method in class org.biojava.bio.program.tagvalue.StateMachine
getDelegate() - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper: get listener to which all calls will be delegated
getDelegate() - Method in class org.biojava.bio.seq.io.SeqIOFilter: Retrieve the delegate that is wrapped.
getDelegate() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter: Retrieve the delegate that is wrapped.
getDelegate() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: The compound alpha that holds the symbols used by this wrapper
getDelegateParser() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getDelete(int) - Method in class org.biojava.bio.dp.ProfileHMM: Retrieves the delete state for column indx.
getDepth() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
getDepth() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor: Gets the Depth attribute of the LightPairDPCursor object
getDepth() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor: retrieve the depth of this cursor
getDepthScaler() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel: Retrieve the current DepthScaler.
getDescription() - Method in class org.biojava.bio.program.homologene.SimilarityType.PlaceHolder
getDescription() - Method in interface org.biojava.bio.program.homologene.Taxon: returns the name of the Taxon
getDescription() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
getDescription() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the description for the AAindex entry.
getDescription() - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
getDescription() - Method in class org.biojava.ontology.IntegerOntology
getDescription() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getDescription() - Method in interface org.biojava.ontology.Ontology: Return a human-readable description of this ontology, or the empty string if none is available
getDescription() - Method in class org.biojava.ontology.Ontology.Impl
getDescription() - Method in class org.biojava.ontology.OntologyTerm.Impl
getDescription() - Method in class org.biojava.ontology.RemoteTerm.Impl
getDescription() - Method in interface org.biojava.ontology.Term: Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojava.ontology.Term.Impl
getDescription() - Method in class org.biojava.ontology.Triple.Impl
getDescription() - Method in interface org.biojava.utils.candy.CandyVocabulary: It returns a description of this vocabulary.
getDescription() - Method in interface org.biojavax.bio.BioEntry: Returns a description of this sequence.
getDescription() - Method in class org.biojavax.bio.SimpleBioEntry: Returns a description of this sequence.
getDescription() - Method in interface org.biojavax.Namespace: Returns a description of this namespace.
getDescription() - Method in interface org.biojavax.ontology.ComparableOntology: Return a human-readable description of this ontology.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableOntology: Return a human-readable description of this ontology.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableTerm: Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableTriple: Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojavax.SimpleNamespace: Returns a description of this namespace.
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getDescription(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getDescriptionNumber() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties: A method that simply returns the number of descriptions fetched with this RemoteQBlastOutputProperties object.
getDescriptors() - Method in interface org.biojavax.ontology.ComparableTriple: Returns all descriptors.
getDescriptors() - Method in class org.biojavax.ontology.SimpleComparableTriple: Returns all descriptors.
getDetailsHandler() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler: Return a handler for the XFF details element.
getDFA() - Method in class org.biojava.utils.automata.DfaBuilder
getDimAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector: Retrieve the dimension at a specific index.
getDinucleotideAlphabet() - Static method in class org.biojava.bio.symbol.CodonPrefTools: returns an RNA dinucleotide alphabet.
getDisplayName() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific
getDisplayName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific or if there are no scientific names at all, the empty string.
getDistribution() - Method in interface org.biojava.bio.dp.EmissionState: Get the Distribution associated with this state.
getDistribution() - Method in class org.biojava.bio.dp.SimpleEmissionState
getDistribution() - Method in class org.biojava.bio.molbio.Composition: Returns the distribution backing this class.
getDistribution(Symbol) - Method in interface org.biojava.bio.dist.OrderNDistribution
getDivision() - Method in interface org.biojavax.bio.BioEntry: Returns the division of this bioentry.
getDivision() - Method in class org.biojavax.bio.SimpleBioEntry: Returns the division of this bioentry.
getDNA() - Method in class org.biojava.bio.program.phred.PhredSequence: Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
getDNA() - Static method in class org.biojava.bio.seq.DNATools: Return the DNA alphabet.
getDNAAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence
getDNADistribution(double) - Static method in class org.biojava.bio.seq.DNATools: return a SimpleDistribution of specified GC content.
getDNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools: Creates a DNA symbol tokenizer.
getDNAxDNA() - Static method in class org.biojava.bio.seq.DNATools: Gets the (DNA x DNA) Alphabet
getDNAxDNADistribution(double, double) - Static method in class org.biojava.bio.seq.DNATools: return a (DNA x DNA) cross-product Distribution with specified DNA contents in each component Alphabet.
getDocumentReference() - Method in interface org.biojavax.RankedDocRef: Represents a reference to a document.
getDocumentReference() - Method in class org.biojavax.SimpleRankedDocRef: Represents a reference to a document.
getDotStatesIndex() - Method in class org.biojava.bio.dp.DP
getDouble() - Method in class org.biojava.utils.io.LargeBuffer
getDouble(long) - Method in class org.biojava.utils.io.LargeBuffer
getDoubleValue(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
getDoubleValue(Symbol) - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
getDownstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getDownstreamCut returns the cut site within or downstream of the recognition site.
getDownstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getDownstreamEndType returns the double-stranded end type produced by the primary (intra-site or downstream) cut.
getDP() - Method in class org.biojava.bio.dp.AbstractTrainer
getDP() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getE() - Method in class org.biojava.bio.proteomics.StructureTools
getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getEcNumber(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getEdgeLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getEdgeLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree: Tree navigation methods
getElementId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getElementId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getElementIds() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getElementIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getElideComments() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Is the format going to emit events when comments data or remarks from bibliographic references are read?
getElideComments() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Is the format going to emit events when comments data or remarks from bibliographic references are read?
getElideFeatures() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Is the format going to emit events when feature data is read?
getElideFeatures() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Is the format going to emit events when feature data is read?
getElideReferences() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Is the format going to emit events when bibliographic reference data is read?
getElideReferences() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Is the format going to emit events when bibliographic reference data is read?
getElideSymbols() - Method in class org.biojava.bio.seq.io.EmblLikeFormat: Deprecated.

Return a flag indicating if symbol data will be skipped when parsing streams.
getElideSymbols() - Method in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
getElideSymbols() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Is the format going to emit events when sequence data is read?
getElideSymbols() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Is the format going to emit events when sequence data is read?
getEmail() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService: Get the email for QBlast.
getEmail() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Get the email for Entrez.
getEmblBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Get a default SequenceBuilderFactory for handling EMBL files.
getEMBLTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms: Getter for the EMBL term
getEMBLxmlTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms: Getter for the EMBLxml term
getEmission(Symbol, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP: This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache.
getEmissions(List) - Method in class org.biojava.bio.dp.twohead.EmissionCache
getEmissions(List, boolean) - Method in class org.biojava.bio.dp.twohead.EmissionCache: Retrieve the emission scores from the cache for every EmissionState for the specified symbols.
getEnd() - Method in interface org.biojava.bio.program.gff.GFFRecord: The end of this feature within the source sequence.
getEnd() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getEnd() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getEnd() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getEnd() - Method in class org.biojava.bio.seq.impl.SubSequence
getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
getEnd() - Method in class org.biojava.utils.automata.FiniteAutomaton
getEnd() - Method in interface org.biojava.utils.automata.NfaBuilder
getEnd() - Method in class org.biojava.utils.automata.NfaSubModel
getEnd() - Method in interface org.biojavax.bio.seq.Position: Returns the end of the range of bases this base could lie in.
getEnd() - Method in class org.biojavax.bio.seq.SimplePosition: Returns the end of the range of bases this base could lie in.
getEnd() - Method in interface org.biojavax.RankedDocRef: The end position in the sequence that this reference is referred to from.
getEnd() - Method in class org.biojavax.SimpleRankedDocRef: The end position in the sequence that this reference is referred to from.
getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser: Get the current string indicating that a record has ended.
getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.RegexParser: Get the explicit end-of-record string.
getEntryByName(String) - Method in interface org.biojava.utils.candy.CandyVocabulary: It returns a selected vocabulary entry.
getEnvironment() - Method in class org.biojava.naming.ObdaContext
getEnvironmentProperties() - Method in class org.biojava.utils.process.ExternalProcess: Gets environment variables for the external process.
getEnzyme() - Method in interface org.biojava.bio.molbio.RestrictionSite: getEnzyme returns the enzyme which cuts at this site.
getEnzyme() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
getEnzyme(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getEnzyme returns an enzyme by name.
getEpsilon() - Method in class org.biojava.stats.svm.SMOTrainer
getErrorHandler() - Method in class org.biojava.bio.program.gff.GFFParser: Find the error handler used by this parser.
getErrorHandler() - Method in class org.biojava.bio.program.gff3.GFF3Parser: Find the error handler used by this parser.
getErrorHandler() - Method in class org.biojava.utils.process.ExternalProcess: Gets the output error handler which is responsible for the standard error output of the external process.
getErrString() - Method in class org.biojava.utils.ExecRunner: Returns the error string if exec(String) was invoked.
getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return the overall E-value of this hit.
getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return the E-value of this sub-hit.
getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getEvent() - Method in class org.biojava.utils.ChangeListener.ChangeEventRecorder
getEvents() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property events.
getEvidenceAttrTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the evidence attr term
getEvidenceCategoryTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the evidence category term
getEvidenceDateTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the evidence date term
getEvidenceTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the evidence type term
getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getExonIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getExtendedName() - Method in interface org.biojavax.DocRefAuthor: Returns the extended version of the authors name.
getExtendedName() - Method in class org.biojavax.SimpleDocRefAuthor: Returns the extended version of the authors name.
getFactory() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Getter for property factory.
getFactory() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: Getter for property factory.
getFactory(String, FiniteAutomaton) - Method in class org.biojava.utils.automata.ArrayStateMachineToolkit
getFastaBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Get a default SequenceBuilderFactory for handling FASTA files.
getFeature() - Method in interface org.biojava.bio.program.gff.GFFRecord: The feature type filed.
getFeature() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter: Retrieve the current feature.
getFeature() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getFeature() - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
getFeature() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the feature this location is associated with.
getFeature() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the feature this location is associated with.
getFeature() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the feature this location is associated with.
getFeatureDescTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the FeatureDesc term
getFeatureFilter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Return the current FeatureFilter.
getFeatureFilter() - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandler
getFeatureFromOriginal(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence: getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am including this method so that you can get the corresponding feature from the original sequence.
getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleFeature: A utility function to retrieve the feature holder delegate, creating it if necessary.
getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getFeatureID(Feature) - Method in class org.biojava.bio.program.xff.BasicXFFHelper
getFeatureID(Feature) - Method in interface org.biojava.bio.program.xff.XFFHelper
getFeatureListener() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler: Return the object which receives startFeature/endFeature notifications.
getFeatureListener() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: Return current feature listener
getFeatureListener() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: Return current feature listener
getFeatureOriginalTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the feature original term
getFeatureRealizer() - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory: Returns the FeatureRealizer set by "setFeatureRealizer".
getFeatureRefTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the feature ref term
getFeatureRelationshipSet() - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder: Returns the set of relationships held in this feature holder.
getFeatureRelationshipSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Returns the set of relationships held in this feature holder.
getFeatures() - Method in interface org.biojava.bio.seq.homol.Homology: Retrieve the set of features that mark homologous regions.
getFeatures() - Method in class org.biojava.bio.seq.homol.SimpleHomology: getFeatures returns the constituent HomologyFeatures which are also used as the keys in the alignment.
getFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
getFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder: Returns the list of features in this featureholder.
getFeatures(String, FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource: Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
getFeatures(FeatureFilter) - Method in interface org.biojava.bio.seq.distributed.DistDataSource: Get all features matching a FeatureFilter provided by this DistDataSource.
getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
getFeatureSet() - Method in interface org.biojavax.bio.seq.RichSequence: The features for this sequence.
getFeatureSet() - Method in class org.biojavax.bio.seq.ThinRichSequence: The features for this sequence.
getFeatureStatusTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the feature status term
getFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler: Get the template for the feature being constructed.
getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getFeatureType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getFeatureVariationTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the feature variation term
getField() - Method in class org.biojava.utils.ChangeType: Return a Field object where this change type is declared.
getFile() - Method in interface org.biojava.bio.program.indexdb.Record: getFile returns the random access file in which the record belongs.
getFile() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getFile() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess: getFile returns the File wrapped.
getFile() - Method in interface org.biojava.bio.seq.db.Index: The file to retrieve from.
getFile() - Method in class org.biojava.bio.seq.db.SimpleIndex
getFile() - Method in class org.biojava.utils.io.RAF
getFileIndex(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
getFilePointer() - Method in class org.biojava.utils.io.CountedBufferedReader
getFilePointer() - Method in class org.biojava.utils.io.RandomAccessReader: getFilePointer returns the effective position of the pointer in the underlying RandomAccessFile.
getFiles() - Method in class org.biojava.bio.seq.db.BioIndex
getFiles() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getFiles() - Method in interface org.biojava.bio.seq.db.IndexStore: Retrieve the Set of files that are currently indexed.
getFiles() - Method in class org.biojava.bio.seq.db.TabIndexStore
getFilter() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
getFinderName() - Method in interface org.biojava.utils.candy.CandyFinder: It returns a name of this vocabulary finder.
getFirstIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction: Getter for property firstIntActID.
getFirstOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair: gets the first orthologue in the orthology relationship.
getFirstOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getFitness() - Method in class org.biojavax.ga.impl.AbstractOrganism
getFitness() - Method in interface org.biojavax.ga.Organism: Returns the current fitness of this organism.
getFitnessFunction() - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
getFitnessFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm: Returns the fitness function, i.e. the class that computes the fitness of each organism in a population.
getFitnessFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getFloat() - Method in class org.biojava.utils.io.LargeBuffer
getFloat(long) - Method in class org.biojava.utils.io.LargeBuffer
getFormat() - Method in class org.biojava.bio.seq.db.BioIndex
getFormat() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getFormat() - Method in interface org.biojava.bio.seq.db.IndexStore: Retrieve the format of the index file.
getFormat() - Method in class org.biojava.bio.seq.db.TabIndexStore
getFormat(String) - Static method in class org.biojava.bio.program.formats.FormatTools: Attempt to find aformat for a format identifer string.
getForwarders(ChangeType) - Method in class org.biojava.utils.Unchangeable
getForwardRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getForwardRegex returns a regular expression which matches the forward strand of the recognition site.
getForwardTransitions() - Method in class org.biojava.bio.dp.DP
getForwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
getFrame() - Method in interface org.biojava.bio.program.gff.GFFRecord: The frame of the feature.
getFrame() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
getFrame() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getFrame() - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter: Retrieve the reading frame this filter matches.
getFrame() - Method in interface org.biojava.bio.seq.Frame: A method to get the frame information of the implementing object
getFrame() - Method in class org.biojava.bio.seq.FramedFeature.ReadingFrame
getFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
getFrequency() - Method in interface org.biojava.bio.symbol.CodonPref: returns a Distribution giving the frequency of codons (sums to one over the totality of codons).
getFrequency() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getFrequencyForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref: returns a Distribution giving the frequency of synonymous codons.
getFrequencyForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref
getFrequencyOfNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution: returns the frequency with which synonymous codons start with a specified pair of bases.
getFrom() - Method in exception org.biojava.bio.dp.IllegalTransitionException
getFTIdTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the FTId term
getFuzzyEnd() - Method in interface org.biojavax.bio.seq.Position: Returns true if the position has a fuzzy end.
getFuzzyEnd() - Method in class org.biojavax.bio.seq.SimplePosition: Returns true if the position has a fuzzy end.
getFuzzyStart() - Method in interface org.biojavax.bio.seq.Position: Returns true if the position has a fuzzy start.
getFuzzyStart() - Method in class org.biojavax.bio.seq.SimplePosition: Returns true if the position has a fuzzy start.
getG() - Method in class org.biojava.bio.molbio.DNAComposition: Get the relative compositon of 'G'.
getG() - Method in class org.biojava.bio.proteomics.StructureTools
getGapSymbol() - Method in class org.biojava.bio.symbol.AbstractAlphabet
getGapSymbol() - Method in interface org.biojava.bio.symbol.Alphabet: Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
getGapSymbol() - Static method in class org.biojava.bio.symbol.AlphabetManager: Get the special `gap' Symbol.
getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
getGapSymbol(List) - Static method in class org.biojava.bio.symbol.AlphabetManager: Get the gap symbol appropriate to this list of alphabets.
getGenbankBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Get a default SequenceBuilderFactory for handling GenBank files.
getGenBankTerm() - Static method in class org.biojavax.bio.seq.io.GenbankFormat.Terms: Getter for the Genbank term
getGeneNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the GeneName term
getGenerateSequenceHeader() - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Discover if per-sequence header lines will be generated.
getGeneration() - Method in interface org.biojavax.ga.GeneticAlgorithm
getGeneration() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm: The current generation
getGeneSynonymTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the GeneSynonym term
getGeneticCode() - Method in interface org.biojava.bio.symbol.CodonPref: the genetic code that this codon preference is based on.
getGeneticCode() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Returns the genetic code of this taxon, which may be null if not known.
getGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Returns the genetic code of this taxon, which may be null if not known.
getGeneticCode(int) - Static method in class org.biojava.bio.seq.RNATools: Retrieve a TranslationTable by number.
getGeneticCode(String) - Static method in class org.biojava.bio.seq.RNATools: Retrieve a TranslationTable by name.
getGeneticCodeName() - Method in interface org.biojava.bio.symbol.CodonPref: get the name of the genetic code
getGeneticCodeName() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getGeneticCodeNames() - Static method in class org.biojava.bio.seq.RNATools: Retrieve a Set containing the name of each genetic code.
getGenomicTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms: Getter for the Ensembl-specific 'genomic' term
getGenpeptBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Get a default SequenceBuilderFactory for handling Genpept files.
getGlu_C_bicarbonate() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getGlu_C_phosphate() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getGroupAttributes() - Method in interface org.biojava.bio.program.gff.GFFRecord: A Map containing the group / attribute information.
getGroupAttributes() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getGroupOrder(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getH() - Method in class org.biojava.bio.proteomics.StructureTools
getHandler(String, String) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler: Retrieve a FilterHandler for the specified tag name.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.agave.StAXHandlerFactory: Return a suitable StAX content handler.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game.StAXHandlerFactory: Return a suitable StAX content handler.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game12.StAXHandlerFactory: Return a suitable StAX content handler.
getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler: get iterator for current stack starting at the position below mine.
getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler: get iterator for current stack starting at the position below mine.
getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: return iterator to callbackStack
getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: return iterator to callbackStack
getHeader() - Method in class org.biojavax.bio.seq.io.FastaFormat
getHeaderDefinitions() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer: Returns the appropriate style and javascript definitions for this renderer.
getHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
getHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
getHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult: Return all hits in this sequence similarity search result.
getHits() - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
getHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getHomologeneID() - Method in interface org.biojava.bio.program.homologene.Orthologue: get the Homologene ID.
getHomologeneID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getHomology() - Method in interface org.biojava.bio.seq.homol.HomologyFeature
getHomology() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
getI() - Method in class org.biojava.bio.proteomics.StructureTools
getId() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getId() - Method in class org.biojavax.bio.seq.SimplePosition: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.SimpleBioEntry: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.SimpleBioEntryRelationship: Gets the Hibernate ID.
getId() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Gets the Hibernate ID.
getId() - Method in class org.biojavax.ontology.SimpleComparableOntology: Gets the Hibernate ID.
getId() - Method in class org.biojavax.ontology.SimpleComparableTerm: Gets the Hibernate ID.
getId() - Method in class org.biojavax.ontology.SimpleComparableTriple: Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleComment: Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleCrossRef: Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleDocRef: Gets the Hibernate ID.
getId() - Method in class org.biojavax.SimpleNamespace: Gets the Hibernate ID.
getID() - Method in interface org.biojava.bio.program.indexdb.Record: getID returns the primary identifier of the record.
getID() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getID() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster: The public unigene ID.
getID() - Method in interface org.biojava.bio.seq.db.Index: The ID of the sequence at this position in this file.
getID() - Method in class org.biojava.bio.seq.db.SimpleIndex
getID() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
getID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction: Getter for property ID.
getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getIdAlias(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getIdentifier() - Method in interface org.biojava.utils.lsid.Identifiable: Return the identifier of this object.
getIdentifier() - Method in interface org.biojavax.bio.BioEntry: Returns the identifier of this bioentry.
getIdentifier() - Method in class org.biojavax.bio.SimpleBioEntry: Returns the identifier of this bioentry.
getIdentifier() - Method in interface org.biojavax.ontology.ComparableTerm: Returns the (optional) identifier associated with this term.
getIdentifier() - Method in class org.biojavax.ontology.SimpleComparableTerm: Returns the (optional) identifier associated with this term.
getIDMaker() - Method in class org.biojava.bio.seq.db.HashSequenceDB: Retrieve the IDMaker associated with this database.
getIDMaker() - Method in class org.biojavax.bio.db.HashRichSequenceDB: Retrieve the IDMaker associated with this database.
getIDs() - Method in class org.biojava.bio.seq.db.BioIndex
getIDs() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getIDs() - Method in interface org.biojava.bio.seq.db.IndexStore: Retrieve the set of all current IDs.
getIDs() - Method in class org.biojava.bio.seq.db.TabIndexStore
getImplementationNames(Class) - Static method in class org.biojava.utils.Services: Return a Set of names of implementations of the given service interface in the classloader from which BioJava was loaded.
getImplementationNames(Class, ClassLoader) - Static method in class org.biojava.utils.Services: Return a List of names of implementations of the given service interface available in a given classloader.
getIndexStore() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB: Retrieve the IndexStore.
getInitialContext(Hashtable) - Method in class org.biojava.naming.ObdaInitialContextFactory
getInnerMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
getInnerMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
getInput() - Method in interface org.biojava.utils.process.OutputHandler: Gets the input stream.
getInput() - Method in class org.biojava.utils.process.StreamPipe: Gets the input stream
getInput() - Method in class org.biojava.utils.process.WriterOutputHandler: Gets the input stream.
getInputHandler() - Method in class org.biojava.utils.process.ExternalProcess: Gets the input handler which is responsible for the standard input of the external process.
getInputStream(File) - Method in class org.biojava.utils.io.InputStreamProvider: get an InputStream for the file
getInputStream(String) - Static method in class org.biojava.utils.io.FlatFileCache
getInputStream(String) - Method in class org.biojava.utils.io.InputStreamProvider: get an InputStream for this file
getInputStream(URL) - Method in class org.biojava.utils.io.InputStreamProvider
getINSDseqTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms: Getter for the INSDseq term
getInsert(int) - Method in class org.biojava.bio.dp.ProfileHMM: Retrieves the insert state at column indx.
getInstance() - Static method in class org.biojava.bio.dist.IgnoreCountsTrainer: Returns the global singleton instance of the IgnoreCountsTrainer.
getInstance() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getInstance() - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory
getInstance() - Static method in class org.biojava.bio.symbol.DoubleAlphabet: Retrieve the single DoubleAlphabet instance.
getInstance() - Static method in class org.biojava.bio.symbol.IntegerAlphabet: Retrieve the single IntegerAlphabet instance.
getInstance() - Static method in class org.biojava.bio.taxa.EbiFormat: Deprecated.
getInstance() - Static method in class org.biojava.naming.ObdaUriParser
getInstance() - Static method in class org.biojava.utils.io.FlatFileCache
getInstance() - Static method in class org.biojava.utils.walker.WalkerFactory
getInstance(Class) - Static method in class org.biojava.utils.walker.WalkerFactory: Make a WalkerFactory that handles a Visitor for a class of type typeClazz.
getInstance(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.
getInstance(FiniteAlphabet, SoftMaskedAlphabet.MaskingDetector) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any Symbol is soft masked or not.
getInt() - Method in class org.biojava.utils.io.LargeBuffer
getInt(long) - Method in class org.biojava.utils.io.LargeBuffer
getIntegerOntology() - Static method in class org.biojava.ontology.OntoTools: Get the Ontology that defines integers.
getInteractions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property interactions.
getInternalSymbolList() - Method in interface org.biojavax.bio.seq.RichSequence: A special function that returns the SymbolList that this RichSequence is based around.
getInternalSymbolList() - Method in class org.biojavax.bio.seq.SimpleRichSequence: A special function that returns the SymbolList that this RichSequence is based around.
getInternalSymbolList() - Method in class org.biojavax.bio.seq.ThinRichSequence: A special function that returns the SymbolList that this RichSequence is based around.
getIsoelectricPoint(SymbolList) - Static method in class org.biojava.bio.proteomics.IsoelectricPointCalc: Static public method to compute the pI for a polypeptide in denaturating and reduced conditions with both free ends.
getIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property isoforms.
getIsoIDs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform: Getter for property isoIDs.
getIsoschizomers(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getIsoschizomers returns an unmodifable set of the isoschizomers of this enzyme.
getItem() - Method in interface org.biojava.stats.svm.ItemValue
getItem() - Method in class org.biojava.stats.svm.SimpleItemValue
getIterator() - Method in class org.biojava.utils.ListTools.Doublet
getIterator() - Method in class org.biojava.utils.ListTools.Triplet
getJoiner() - Method in class org.biojava.bio.program.tagvalue.Aggregator
getJoinTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation: Getter for the "join" term
getJournalReference() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets a reference to the journal which published the article about the AAindex entry.
getKernel() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
getKernel() - Method in interface org.biojava.stats.svm.SVMClassifierModel
getKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
getKernel() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier: Retrieve the currently used kernel
getKernelValue(int, int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.HasAnnotation
getKey() - Method in class org.biojava.utils.cache.KeyedWeakReference
getKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
getKeys() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getKeys() - Method in class org.biojava.bio.program.tagvalue.Index2Model
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getKeyword(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getKeywordTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the keyword term
getKineticsNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property kineticsNote.
getKmpNextTable() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch: Returns the table of border lengths
getKMs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property KMs.
getLabel() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState: return the label of this class.
getLabel() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
getLabel() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
getLabel() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction: Getter for property label.
getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getLabel(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getLabels() - Method in interface org.biojava.bio.alignment.Alignment: The list of SymbolLists in the alignment.
getLabels() - Method in class org.biojava.bio.alignment.SimpleAlignment
getLabels() - Method in class org.biojava.bio.dp.SimpleStatePath
getLabels() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
getLabels() - Method in class org.biojava.bio.symbol.RelabeledAlignment
getLambda() - Method in class org.biojava.stats.svm.DiagonalAddKernel: Retrieve the scale factor.
getLast() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder: Get the last complete annotation built.
getLastScore() - Method in class org.biojava.bio.dp.AbstractTrainer
getLastScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getLeader() - Method in class org.biojava.utils.ListTools.SeriesList
getLeftValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Gets the left value.
getLeftValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Gets the left value.
getLength() - Method in interface org.biojava.bio.program.indexdb.Record: getLength returns the length of the record in bytes.
getLength() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getLength() - Method in class org.biojava.bio.search.SeqContentPattern: Get the current length.
getLength() - Method in interface org.biojava.bio.seq.db.Index: The entry can be slurped out of the file by grabbing length bytes from start.
getLength() - Method in class org.biojava.bio.seq.db.SimpleIndex
getLength() - Method in class org.biojava.bio.symbol.CircularLocation
getLength() - Method in class org.biojava.utils.RepeatedCharSequence
getLevel() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler: return current stack level.
getLevel() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler: return current stack level.
getLimit() - Method in class org.biojava.utils.cache.FixedSizeCache
getLine() - Method in exception org.biojava.utils.ParserException: Get the text of the line where the exception occured.
getLineNumber() - Method in exception org.biojava.utils.ParserException: Get the line number in the stream where this exception occured.
getLineWidth() - Method in class org.biojava.bio.program.phred.PhredFormat: Retrive the current line width.
getLineWidth() - Method in class org.biojava.bio.seq.io.FastaFormat: Deprecated.

Retrive the current line width.
getLineWidth() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Retrive the current line width.
getLineWidth() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Retrive the current line width.
getListener() - Method in class org.biojava.bio.program.tagvalue.ParserListener: getListener returns the listener of the pair.
getListener() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState: return the TagValueListener assigned to this State.
getListener() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
getListener(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getListeners(ChangeType) - Method in class org.biojava.utils.Unchangeable
getLITDBEntryNumbers() - Method in class org.biojava.bio.proteomics.aaindex.AAindex: Gets the list of literature database identifiers for the AAindex entry.
getLocation() - Method in class org.biojava.bio.program.indexdb.BioStore: getLocation returns the directory where the index is located.
getLocation() - Method in interface org.biojava.bio.seq.Feature: The location of this feature.
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
getLocation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getLocation() - Method in class org.biojava.bio.seq.RemoteFeature.Region: Retrieve the Location of the Region.
getLocation() - Method in class org.biojavax.bio.seq.SimpleRichFeature: The location of this feature.
getLocation() - Method in interface org.biojavax.DocRef: Returns a textual description of the document reference.
getLocation() - Method in interface org.biojavax.RankedDocRef: If this object was constructed using a location instead of two integers, then this method will return that location.
getLocation() - Method in class org.biojavax.SimpleDocRef: Returns a textual description of the document reference.
getLocation() - Method in class org.biojavax.SimpleRankedDocRef
getLocationHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getLocationSequenceTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the location seq term
getLocator() - Method in exception org.biojava.utils.ParserException: Get a locator for the stream which caused this exception.
getLocusID() - Method in interface org.biojava.bio.program.homologene.Orthologue: get the locus ID associated with this orthologue.
getLocusID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getLong() - Method in class org.biojava.utils.io.LargeBuffer
getLong(long) - Method in class org.biojava.utils.io.LargeBuffer
getLSID() - Method in class org.biojava.bio.program.formats.Embl
getLSID() - Method in class org.biojava.bio.program.formats.Enzyme
getLSID() - Method in interface org.biojava.bio.program.formats.Format: Retrieve the LSID associated with this format.
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Compound
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Reaction
getLSID() - Method in class org.biojava.bio.program.formats.Swissprot
getLys_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getMagicalState() - Method in class org.biojava.bio.program.tagvalue.StateMachine
getMagicalState(Alphabet, int) - Static method in class org.biojava.bio.dp.MagicalState
getMapAll() - Method in class org.biojava.bio.molbio.RestrictionMapper: getMapAll returns whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it.
getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMapLocation(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMapper() - Method in class org.biojava.bio.AnnotationRenamer: getMapper returns the TagMapper being used to remap the Annotation.
getMapper() - Method in class org.biojava.bio.program.tagvalue.TagRenamer: Retrieve the mapper used to rename tags
getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMapPosition(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMapType() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getMaskedAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Gets the Alphabet upon which masking is being applied
getMaskingDetector() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Getter for the MaskingDetector
getMass(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc: Get the Mass of this peptide.
getMass(SymbolList, String, boolean) - Static method in class org.biojava.bio.proteomics.MassCalc: getMass calculates the mass of this peptide.
getMatch(int) - Method in class org.biojava.bio.dp.ProfileHMM: Retrieve the match state at column indx.
getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchAlign(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchDesc(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMatches() - Method in class org.biojava.bio.dp.SimpleEmissionState
getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getMatches() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
getMatches() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getMatches() - Method in interface org.biojava.bio.symbol.Symbol: The alphabet containing the symbols matched by this ambiguity symbol.
getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMax() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getMax() - Method in class org.biojava.bio.symbol.CircularLocation: This will give you the coordinate of the maximum point contained by this Location.
getMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
getMax() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
getMax() - Method in interface org.biojava.bio.symbol.Location: The maximum position contained.
getMax() - Method in class org.biojava.bio.symbol.PointLocation
getMax() - Method in class org.biojava.bio.symbol.RangeLocation
getMax() - Method in class org.biojavax.bio.seq.EmptyRichLocation: The maximum position contained.
getMax() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: The maximum position contained.
getMax() - Method in class org.biojavax.bio.seq.SimpleRichLocation: The maximum position contained.
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver: Resolves the maximum possible base for this position.
getMax(Position) - Method in interface org.biojavax.bio.seq.PositionResolver: Resolves the maximum possible base for this position.
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver: Resolves the maximum possible base for this position.
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver: Resolves the maximum possible base for this position.
getMaxCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern: Get the maximum counts required for a symbol.
getMaxCrossOvers() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
getMaxCrossOvers() - Method in interface org.biojavax.ga.functions.CrossOverFunction
getMaxCrossOvers() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
getMaxGenerations() - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
getMaxPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the end position of this location.
getMaxPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: Retrieves the end position of this location.
getMaxPosition() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the end position of this location.
getMaxPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the end position of this location.
getMaxRunTimeExceeded() - Method in class org.biojava.utils.ExecRunner: Returns whether the maximum runtime was exceeded or not.
getMaxRunTimeSecs() - Method in class org.biojava.utils.ExecRunner: Returns the maximum run time in seconds for this object.
getMaxScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore: getMaxScore returns the maximum score accepted.
getMaxSize() - Method in class org.biojava.utils.cache.FixedSizeMap
getMaxValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getMergeAnnotation() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
getMerged() - Method in class org.biojava.bio.annodb.MergingAnnotationDB: Return a list of merged DBs.
getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser: See if tags are being merged.
getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser: Report whether empty tags will be treated as continuations of the last non -empty tag.
getMessage() - Method in class org.biojava.utils.ParseErrorEvent: Find the message about this event
getMetaData() - Method in class org.biojava.bio.program.indexdb.BioStore
getMetaData() - Method in interface org.biojava.bio.program.indexdb.IndexStore: getMetaData returns a data structure which represents an OBDA "config.dat" flatfile indexing configuration file.
getMethod() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory: Get the Method used.
getMin() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getMin() - Method in class org.biojava.bio.symbol.CircularLocation: This will give you the coordinate of the minimum point contained by this Location.
getMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
getMin() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
getMin() - Method in interface org.biojava.bio.symbol.Location: The minimum position contained.
getMin() - Method in class org.biojava.bio.symbol.PointLocation
getMin() - Method in class org.biojava.bio.symbol.RangeLocation
getMin() - Method in class org.biojavax.bio.seq.EmptyRichLocation: The minimum position contained.
getMin() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: The minimum position contained.
getMin() - Method in class org.biojavax.bio.seq.SimpleRichLocation: The minimum position contained.
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver: Resolves the minimum possible base for this position.
getMin(Position) - Method in interface org.biojavax.bio.seq.PositionResolver: Resolves the minimum possible base for this position.
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver: Resolves the minimum possible base for this position.
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver: Resolves the minimum possible base for this position.
getMinCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern: Get the minimum counts required for a symbol.
getMinIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet: get the lowest level of identity observed in this Group
getMinIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
getMinPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the start position of this location.
getMinPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: Retrieves the start position of this location.
getMinPosition() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the start position of this location.
getMinPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the start position of this location.
getMinScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore: getMinScore returns the minimum score accepted.
getMinValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getMismatches() - Method in class org.biojava.bio.search.MaxMismatchPattern
getMitoGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Returns the mitochondrial genetic code of this taxon, which may be null if not known.
getMitoGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Getter for property mitoGeneticCode.
getModel() - Method in class org.biojava.bio.dp.DP
getModel() - Method in interface org.biojava.bio.dp.ModelInState: The model that is inside this state.
getModel() - Method in class org.biojava.bio.dp.SimpleModelInState
getModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
getModifiable() - Method in class org.biojava.utils.MergingSet
getMolecularWeight() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property molecularWeight.
getMolecularWeight(SymbolList) - Static method in class org.biojava.bio.proteomics.MassCalc: Calculate the molecular weight of a protein, making estimates whenever it is possible like averaging mass values for ambiguity symbols or counting zero when gaps are encountered.
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMolType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMolTypeTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: getter for the MolType term
getMolWeightError() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property molWeightError.
getMolWeightMethod() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property molWeightMethod.
getMolWeightRangeEnd() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property molWeightRangeEnd.
getMolWeightRangeStart() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property molWeightRangeStart.
getMoreSearches() - Method in class org.biojava.bio.search.SearchContentAdapter
getMoreSearches() - Method in class org.biojava.bio.search.SearchContentFilter
getMoreSearches() - Method in interface org.biojava.bio.search.SearchContentHandler: getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source.
getMoreSearches() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
getMotifs() - Method in class org.biojava.bio.program.Meme
getMultiplier() - Method in class org.biojava.stats.svm.PolynomialKernel
getMultiplier() - Method in class org.biojava.stats.svm.SigmoidKernel
getMutationFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
getMutationFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getMutationProbs() - Method in class org.biojavax.ga.functions.AbstractMutationFunction
getMutationProbs() - Method in interface org.biojavax.ga.functions.MutationFunction
getMutationProbs() - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
getMutationSpectrum() - Method in class org.biojavax.ga.functions.AbstractMutationFunction
getMutationSpectrum() - Method in interface org.biojavax.ga.functions.MutationFunction
getMutationSpectrum() - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
getMyComponents(Name) - Method in class org.biojava.naming.ObdaContext
getName() - Method in interface org.biojava.bio.annodb.AnnotationDB: The name of this AnnotationDB.
getName() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
getName() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
getName() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
getName() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
getName() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
getName() - Method in class org.biojava.bio.dp.SimpleEmissionState
getName() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getName returns the enzyme name.
getName() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet: retrieves name of this group.
getName() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
getName() - Method in class org.biojava.bio.program.indexdb.BioStore: The name of this store or null if the name has not been set.
getName() - Method in class org.biojava.bio.proteomics.Protease: Gets the name of this Protease
getName() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
getName() - Method in class org.biojava.bio.seq.db.BioIndex
getName() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
getName() - Method in class org.biojava.bio.seq.db.DummySequenceDB
getName() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore: getName returns the database name as defined within the EMBL CD-ROM index.
getName() - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
getName() - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
getName() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
getName() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getName() - Method in class org.biojava.bio.seq.db.HashSequenceDB
getName() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB: Get the name of this sequence database.
getName() - Method in interface org.biojava.bio.seq.db.IndexStore: Retrieve the name of this store.
getName() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getName() - Method in interface org.biojava.bio.seq.db.SequenceDBLite: Get the name of this sequence database.
getName() - Method in class org.biojava.bio.seq.db.SubSequenceDB
getName() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getName() - Method in class org.biojava.bio.seq.db.TabIndexStore
getName() - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
getName() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
getName() - Method in interface org.biojava.bio.seq.FeatureTypes.Repository: The name of this repository.
getName() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getName() - Method in interface org.biojava.bio.seq.FeatureTypes.Type: Get the name of this type.
getName() - Method in class org.biojava.bio.seq.impl.DummySequence
getName() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getName() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getName() - Method in class org.biojava.bio.seq.impl.SubSequence
getName() - Method in class org.biojava.bio.seq.impl.ViewSequence
getName() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getName() - Method in interface org.biojava.bio.seq.Sequence: The name of this sequence.
getName() - Method in class org.biojava.bio.seq.SimpleAssembly
getName() - Method in interface org.biojava.bio.symbol.Alphabet: Get the name of the alphabet.
getName() - Method in interface org.biojava.bio.symbol.CodonPref: get name of object
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getName() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getName() - Method in class org.biojava.bio.symbol.SimpleAlphabet
getName() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getName() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
getName() - Method in class org.biojava.bio.symbol.SingletonAlphabet
getName() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: The name of the Alphabet
getName() - Method in interface org.biojava.bio.symbol.Symbol: The long name for the symbol.
getName() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
getName() - Method in class org.biojava.bio.taxa.SimpleTaxonFactory: Deprecated.
getName() - Method in interface org.biojava.bio.taxa.TaxonFactory: Deprecated.

Name for this TaxonFactory.
getName() - Method in class org.biojava.bio.taxa.WeakTaxonFactory: Deprecated.
getName() - Method in interface org.biojava.directory.SequenceDBProvider: The name of this provider.
getName() - Method in class org.biojava.ontology.IntegerOntology
getName() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getName() - Method in interface org.biojava.ontology.Ontology: Return the name of this ontology
getName() - Method in class org.biojava.ontology.Ontology.Impl
getName() - Method in class org.biojava.ontology.OntologyTerm.Impl
getName() - Method in class org.biojava.ontology.RemoteTerm.Impl
getName() - Method in class org.biojava.ontology.Synonym
getName() - Method in interface org.biojava.ontology.Term: Return the name of this term.
getName() - Method in class org.biojava.ontology.Term.Impl
getName() - Method in class org.biojava.ontology.Triple.Impl
getName() - Method in interface org.biojava.utils.candy.CandyVocabulary: It returns a name of this vocabulary.
getName() - Method in class org.biojava.utils.ChangeType: Return the name of this change.
getName() - Method in class org.biojava.utils.regex.Pattern: return the String label associated with this pattern.
getName() - Method in interface org.biojavax.bio.BioEntry: Returns the name of this bioentry.
getName() - Method in interface org.biojavax.bio.db.BioEntryDBLite: Get the name of this sequence database.
getName() - Method in class org.biojavax.bio.db.HashBioEntryDB
getName() - Method in class org.biojavax.bio.db.HashRichSequenceDB
getName() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
getName() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
getName() - Method in interface org.biojavax.bio.seq.RichFeature: Returns the name of this feature.
getName() - Method in class org.biojavax.bio.seq.RichLocation.Strand: Returns the string symbol of this strand.
getName() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Returns the name of this feature.
getName() - Method in class org.biojavax.bio.SimpleBioEntry: Returns the name of this bioentry.
getName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName: Returns this name.
getName() - Method in interface org.biojavax.DocRefAuthor: Returns a textual description of the authors name.
getName() - Method in class org.biojavax.ga.impl.AbstractOrganism
getName() - Method in class org.biojavax.ga.impl.AbstractPopulation
getName() - Method in interface org.biojavax.ga.Organism: Gets the organisms name
getName() - Method in interface org.biojavax.ga.Population
getName() - Method in interface org.biojavax.Namespace: The name of the namespace is immutable and must be set by the constructor of the instantiating class.
getName() - Method in class org.biojavax.ontology.SimpleComparableOntology: Return the name of this ontology
getName() - Method in class org.biojavax.ontology.SimpleComparableTerm: Return the name of this term.
getName() - Method in class org.biojavax.ontology.SimpleComparableTriple: Return the name of this term.
getName() - Method in class org.biojavax.SimpleDocRefAuthor: Returns a textual description of the authors name.
getName() - Method in class org.biojavax.SimpleNamespace: The name of the namespace is immutable and must be set by the constructor of the instantiating class.
getNameClass() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName: Returns the class of this name.
getNameClasses() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Returns all the name classes available for a taxon.
getNameClasses() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Returns all the name classes available for a taxon.
getNamedIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event: Getter for property namedIsoforms.
getNameHierarchy() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Returns the taxonomy hierarchy of this taxon entry in the form: least specific; more specific; ...; most specific.
getNameHierarchy() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific.
getNameInNamespace() - Method in class org.biojava.naming.ObdaContext
getNameParser(String) - Method in class org.biojava.naming.ObdaContext
getNameParser(Name) - Method in class org.biojava.naming.ObdaContext
getNames() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getNames() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform: Getter for property names.
getNames(String) - Method in interface org.biojavax.bio.taxa.NCBITaxon: Returns all the names available for a taxon in a given class.
getNames(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Returns all the names available for a taxon in a given class.
getNameSet() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
getNamesMap() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
getNamespace() - Method in interface org.biojavax.bio.BioEntry: Returns the namespace of this bioentry.
getNamespace() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Getter for property namespace.
getNamespace() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: Getter for property namespace.
getNamespace() - Method in class org.biojavax.bio.SimpleBioEntry: Returns the namespace of this bioentry.
getNamespaceId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier: Return the namespace id for this identifier within the authority.
getNameToSymbol() - Method in class org.biojava.bio.seq.io.NameTokenization
getNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Gets the NCBI taxon ID.
getNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Gets the NCBI taxon ID.
getNCutters(int) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getNCutters returns an unmodifable set of all enzymes with a cut site of size n.
getNegShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier: Retrieve the shape used to represent negative points.
getNestedKernel() - Method in class org.biojava.stats.svm.NestedKernel: Retrieve the currently nested SVMKernel.
getNestedValue(NestedValue, String, int) - Method in class org.biojava.ontology.obo.OboFileParser
getNewTag(Object) - Method in interface org.biojava.bio.program.tagvalue.PropertyChanger: getNewTag returns the tag which substitutes the specified value.
getNewTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper
getNodeRank() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Gets the node rank of this taxon.
getNodeRank() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Gets the node rank of this taxon.
getNodes() - Method in class org.biojava.utils.automata.FiniteAutomaton: get all Nodes within this instance.
getNodes() - Method in interface org.biojava.utils.automata.NfaBuilder
getNodes() - Method in class org.biojava.utils.automata.NfaSubModel
getNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution: returns Set containing the nonWobbleBases that occur in codons that encode this residue
getNormalizingVector() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel: Retrive the current normalizing vector.
getNotCleaveResidues() - Method in class org.biojava.bio.proteomics.Protease: The list of residues that will prevent cleavage if they follow the cleavage residue.
getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property note.
getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform: Getter for property note.
getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getNote(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getNote(Note) - Method in class org.biojavax.EmptyRichAnnotation: Uses the term and rank to lookup a note in this annotation.
getNote(Note) - Method in interface org.biojavax.RichAnnotation: Uses the term and rank to lookup a note in this annotation.
getNote(Note) - Method in class org.biojavax.SimpleRichAnnotation: Uses the term and rank to lookup a note in this annotation.
getNoteSet() - Method in class org.biojavax.bio.seq.CompoundRichLocation: Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.bio.SimpleBioEntry: Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.EmptyRichAnnotation: Returns an immutable set of all notes in this annotation.
getNoteSet() - Method in interface org.biojavax.RichAnnotatable: Returns the set of notes associated with this object.
getNoteSet() - Method in interface org.biojavax.RichAnnotation: Returns an immutable set of all notes in this annotation.
getNoteSet() - Method in class org.biojavax.SimpleCrossRef: Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.SimpleRichAnnotation: Returns an immutable set of all notes in this annotation.
getNucleotide() - Static method in class org.biojava.bio.seq.NucleotideTools: Return the Nucleotide alphabet.
getNucleotideParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools: Creates a nucleotide symbol tokenizer.
getNullModel() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
getNullModel() - Method in interface org.biojava.bio.dist.Distribution: Retrieve the null model Distribution that this Distribution recognizes.
getNullModel() - Method in class org.biojava.bio.dist.GapDistribution
getNullModel() - Method in class org.biojava.bio.dist.PairDistribution
getNullModel() - Method in class org.biojava.bio.dist.SimpleDistribution
getNullModel() - Method in class org.biojava.bio.dist.TranslatedDistribution
getNullModel() - Method in class org.biojava.bio.dist.UniformDistribution
getNullModel(Distribution, Distribution) - Static method in class org.biojava.bio.dist.PairDistribution: Get a uniform null model over a PairDistribution over [first,second].
getNullModelWeight() - Method in interface org.biojava.bio.dist.DistributionTrainerContext: Return the number of pseudocounts added to the distribution when training.
getNullModelWeight() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
getNumber() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode: Return a number (usually, but not always, a motif count) associated with this node of the tree.
getNumberExperiments() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction: Getter for property numberExperiments.
getNumCount() - Method in interface org.biojava.utils.candy.CandyFinder: It returns the number of available vocabularies.
getObject() - Method in interface org.biojava.ontology.Triple: Return the object term of this triple.
getObject() - Method in class org.biojava.ontology.Triple.Impl
getObject() - Method in interface org.biojavax.bio.BioEntryRelationship: Returns the object of this relationship (ie. the BioEntry which this relationship starts from).
getObject() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship: Returns the object of this relationship (ie. the feature which this relationship starts from).
getObject() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Returns the object of this relationship (ie. the feature which this relationship starts from).
getObject() - Method in class org.biojavax.bio.SimpleBioEntryRelationship: Returns the object of this relationship (ie. the BioEntry which this relationship starts from).
getObject() - Method in class org.biojavax.ontology.SimpleComparableTriple: Return the object term of this triple.
getObject(Class, Object[]) - Static method in class org.biojavax.RichObjectFactory: Delegates to a RichObjectBuilder to construct/retrieve the object, and returns it.
getObjectId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier: Return the object id of this identifier.
getOboFileEventListener() - Method in class org.biojava.ontology.obo.OboFileParser
getObsolete() - Method in interface org.biojavax.ontology.ComparableTerm: Checks to see if this term is obsolete.
getObsolete() - Method in class org.biojavax.ontology.SimpleComparableTerm: Checks to see if this term is obsolete.
getOffset() - Method in interface org.biojava.bio.program.indexdb.Record: getOffset returns the byte offset in the file at which the record begins.
getOffset() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getOldIDHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getOntology() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getOntology() - Method in interface org.biojava.ontology.OntologyTerm: Get the remote ontology referenced by this term
getOntology() - Method in class org.biojava.ontology.OntologyTerm.Impl
getOntology() - Method in class org.biojava.ontology.RemoteTerm.Impl
getOntology() - Method in interface org.biojava.ontology.Term: Return the ontology in which this term exists.
getOntology() - Method in class org.biojava.ontology.Term.Impl
getOntology() - Method in class org.biojava.ontology.Triple.Impl
getOntology() - Method in class org.biojavax.ontology.SimpleComparableTerm: Return the ontology in which this term exists.
getOntology() - Method in class org.biojavax.ontology.SimpleComparableTriple: Return the ontology in which this term exists.
getOps() - Method in class org.biojava.ontology.IntegerOntology
getOps() - Method in interface org.biojava.ontology.Ontology: Return the associated OntologyOps.
getOps() - Method in class org.biojava.ontology.Ontology.Impl
getOps() - Method in class org.biojavax.ontology.SimpleComparableOntology: Return the associated OntologyOps.
getOrCreateTerm(String) - Method in interface org.biojavax.ontology.ComparableOntology: Looks for a term with the given name and returns it.
getOrCreateTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Looks for a term with the given name and returns it.
getOrCreateTriple(Term, Term, Term) - Method in interface org.biojavax.ontology.ComparableOntology: Looks for a triple with the given subject object and predicate and returns it.
getOrCreateTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology: Looks for a triple with the given subject object and predicate and returns it.
getOrder() - Method in class org.biojava.stats.svm.PolynomialKernel
getOrderedLocusNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the OrderedLocusName term
getOrderTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation: Getter for the "order" term
getORFNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the ORFName term
getOrganelleTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the Organelle term
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getOrganism(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getOrganismByName(String) - Method in class org.biojavax.ga.impl.SimplePopulation
getOrganismByName(String) - Method in interface org.biojavax.ga.Population: Gets the specified organism
getOrganisms() - Method in class org.biojavax.ga.impl.SimplePopulation
getOrganisms() - Method in interface org.biojavax.ga.Population: Gets the Set of Organisms
getOrientation() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getOrImportTerm(Term) - Method in interface org.biojavax.ontology.ComparableOntology: Looks for a term with the same name as the given term and returns it.
getOrImportTerm(Term) - Method in class org.biojavax.ontology.SimpleComparableOntology: Looks for a term with the same name as the given term and returns it.
getOrthologue(String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Returns an orthologue of specified ID.
getOrthologue(String) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
getOrthologue(String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
getOrthologue(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
getOrthoPairSets() - Method in interface org.biojava.bio.program.homologene.HomologeneDB: Get the HomologeneGroups in this database.
getOrthoPairSets() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getOS(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getOtherSeqIdTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms: Getter for the INSDseq term
getOuterMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
getOuterMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
getOutput() - Method in interface org.biojava.utils.process.InputHandler: Gets the output stream.
getOutput() - Method in class org.biojava.utils.process.ReaderInputHandler: Gets the output stream.
getOutput() - Method in class org.biojava.utils.process.StreamPipe: Gets the output stream.
getOutputFormat() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties: Simply returns stream output format for the actual RemoteQBlastOutputProperties object
getOutputHandler() - Method in class org.biojava.utils.process.ExternalProcess: Gets the output handler which is responsible for the standard output of the external process.
getOutputOption(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties: Method that returns any value associated to any key for this RemoteQBlastOutputProperties object.
getOutputOption(String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties: Method that returns the value associated with the key given in parameter.
getOutputOptions() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
getOutputOptions() - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties: Method to get all keys to the information stored in this object.
getOutString() - Method in class org.biojava.utils.ExecRunner: Returns the output string if exec(String) was invoked.
getOverlay() - Method in class org.biojava.bio.OverlayAnnotation: Get the map used for the overlay.
getOverlayMap() - Method in class org.biojava.utils.OverlayMap: Return the object containing the overlay mappings.
getPacking(FiniteAlphabet, boolean) - Static method in class org.biojava.bio.symbol.PackingFactory: Get the default packing for an alphabet.
getParent() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB: Get the original sequenceDB from this annotated sequenceDB.
getParent() - Method in class org.biojava.bio.seq.db.SequenceDBWrapper: Return the parent SequenceDB.
getParent() - Method in interface org.biojava.bio.seq.Feature: Return the FeatureHolder to which this feature has been attached.
getParent() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getParent() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getParent() - Method in class org.biojava.bio.seq.projection.ReparentContext
getParent() - Method in class org.biojava.bio.taxa.SimpleTaxon: Deprecated.
getParent() - Method in interface org.biojava.bio.taxa.Taxon: Deprecated.

The parent of this Taxon.
getParent() - Method in class org.biojava.bio.taxa.WeakTaxon: Deprecated.
getParent() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Return the FeatureHolder to which this feature has been attached.
getParent(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
getParent(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
getParentMap() - Method in class org.biojava.utils.OverlayMap: Return the object containing the fallback mappings.
getParentNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Returns the parent NCBI taxon ID, if known.
getParentNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Returns the parent NCBI taxon ID, if known.
getParents() - Method in interface org.biojava.bio.seq.FeatureTypes.Type: Get a set of URIs for parent types.
getParser() - Method in class org.biojava.bio.program.tagvalue.ParserListener: getParser returns the parser of the pair.
getParser(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getParserListener(TagValueListener) - Method in interface org.biojava.bio.annodb.IndexedAnnotationDB.ParserListenerFactory: Get the ParserListener for a TagValueListener.
getParserListener(TagValueListener) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Embl
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Enzyme
getParserListener(TagValueListener) - Method in interface org.biojava.bio.program.formats.Format: Retrieve a ParserListener pair for the format that will pass all events on to a listener.
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Compound
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Reaction
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Swissprot
getParserListenerFactory() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB: Get the ParserListenerFactory used by this IndexedAnnotationDB.
getPartHandler(XFFFeatureSetHandler) - Method in interface org.biojava.bio.program.xff.XFFPartHandlerFactory: Return a suitable StAX content handler.
getPathEnd(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getPathLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getPathPrefix() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore: getPathPrefix returns the abstract path currently being appended to the raw sequence database filenames extracted from the binary index.
getPattern() - Method in class org.biojava.bio.program.tagvalue.RegexParser: Get the Pattern currently used to split lines.
getPattern() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
getPattern() - Method in class org.biojava.bio.search.MaxMismatchPattern
getPatterns(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getPatterns returns two Pattern objects for an enzyme, one matches the forward strand and one the reverse.
getPercentIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPair: get percentage identity.
getPercentIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getPhase() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getPhase() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getPHDependence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property PHDependence.
getPhredAlphabet() - Static method in class org.biojava.bio.program.phred.PhredTools: Retrieves the PHRED alphabet from the AlphabetManager.
getPhredSymbol(Symbol, Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools: Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
getPI(SymbolList, boolean, boolean) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc: Computes isoelectric point of specified peptide.
getPlasmidTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the Plasmid term
getPopulation() - Method in interface org.biojavax.ga.GeneticAlgorithm: The registered Population
getPopulation() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getPos() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
getPosition() - Method in interface org.biojava.bio.molbio.RestrictionSite: getPosition returns the common, forward strand cut site.
getPosition() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
getPosition1() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getPosition2() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getPositions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
getPosShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier: Retrieve the shape used to represent positive points.
getPredicate() - Method in interface org.biojava.ontology.Triple: Return a Term which defines the type of relationship between the subject and object terms.
getPredicate() - Method in class org.biojava.ontology.Triple.Impl
getPredicate() - Method in class org.biojavax.ontology.SimpleComparableTriple: Return a Term which defines the type of relationship between the subject and object terms.
getPrevious() - Method in class org.biojava.utils.ChangeEvent: Return the old value of a property being changed.
getPrimaryKey() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory: getPrimaryKey returns the primary identifier namespace.
getPrimaryKeyName() - Method in class org.biojava.bio.program.tagvalue.Index2Model: Retrieve the tag currently used as primary key.
getPrimaryKeyName() - Method in class org.biojava.bio.program.tagvalue.Indexer: Retrieve the tag currently used as primary key.
getPrintStream() - Method in class org.biojava.bio.seq.io.EmblFileFormer: Deprecated.
getPrintStream() - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.
getPrintStream() - Method in interface org.biojava.bio.seq.io.SeqFileFormer: Deprecated.

getPrintStream returns the PrintStream to which an instance will write the formatted data.
getPrintStream() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer: Deprecated.

getPrintStream returns the PrintStream to which an instance of SwissprotFileFormer will write the formatted data.
getPrintStream() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: Gets the print stream currently being written to.
getPrintStream() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: Gets the print stream currently being written to.
getProjectAccessionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms: Getter for the ProjectAccession term
getProjectedFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getProjectionContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getProjectionContext() - Method in interface org.biojava.bio.seq.projection.Projection
getPropClass() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
getProperties() - Method in class org.biojava.bio.AbstractAnnotation: Implement this to return the Map delegate.
getProperties() - Method in class org.biojava.bio.AnnotationChanger: getProperties returns the mapped contents of the underlying Annotation as a Map.
getProperties() - Method in class org.biojava.bio.AnnotationRenamer: getProperties returns the mapped contents of the underlying Annotation as a Map.
getProperties() - Method in interface org.biojava.bio.AnnotationType: Retrieve the set of properties for which constraints have been explicity specified.
getProperties() - Method in class org.biojava.bio.AnnotationType.Impl
getProperties() - Method in class org.biojava.bio.BeanAsAnnotation
getProperties() - Method in class org.biojava.bio.seq.io.ReferenceAnnotation: Deprecated.
getProperties() - Method in class org.biojava.bio.SimpleAnnotation: Get the property value pairs in this annotation
getProperties() - Method in class org.biojava.bio.SmallAnnotation
getProperties(Object) - Method in class org.biojavax.EmptyRichAnnotation: Find all the Notes with any rank that match the key.
getProperties(Object) - Method in interface org.biojavax.RichAnnotation: Find all the Notes with any rank that match the key.
getProperties(Object) - Method in class org.biojavax.SimpleRichAnnotation: Deprecated.
getProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
getProperty(Object) - Method in interface org.biojava.bio.Annotation: Retrieve the value of a property by key.
getProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
getProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
getProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation: Retrieve the value of a property by key.
getProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation: Deprecated.
getProperty(Annotation, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
getProperty(Annotation, Object) - Method in interface org.biojava.bio.AnnotationType: Get the Collection of values associated with an Annotation bundle according to the type we believe it to be.
getProperty(Annotation, String) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getProperty(Annotation, String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getProperty(Annotation, String) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter: ThomasD made this a bit safer...
getProperty(Annotation, String) - Static method in class org.biojava.bio.seq.io.agave.UtilHelper: inhibit the getProperty(key) of Annotation from throw exception when key does not exist.
getPropertyAsBoolean(String) - Method in class org.biojava.utils.TypedProperties: Searches for the property with the specified key in this property list.
getPropertyAsDouble(String) - Method in class org.biojava.utils.TypedProperties: Searches for the property with the specified key in this property list.
getPropertyAsInteger(String) - Method in class org.biojava.utils.TypedProperties: Searches for the property with the specified key in this property list.
getPropertyAsLong(String) - Method in class org.biojava.utils.TypedProperties: Searches for the property with the specified key in this property list.
getPropertyAsStringList(String) - Method in class org.biojava.utils.TypedProperties: just like getPropertyAsStringList(String key, String delims) but uses ',' (comma), ';' (semicolon) and '\t' (tab) as the possible delimiters.
getPropertyAsStringList(String, String) - Method in class org.biojava.utils.TypedProperties: Searches for the property with the specified key in this property list.
getPropertyClass() - Method in class org.biojava.bio.PropertyConstraint.ByClass: Get the Class used as the constraint.
getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn: Get the PropertyConstraint used to validate each property value.
getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains: Get the PropertyConstraint used to validate each property value.
getPropertyConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandler
getProps() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
getPropType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
getProteaseByName(String) - Static method in class org.biojava.bio.proteomics.Protease: Retrieves a reference to the named Protease.
getProteaseByName(String) - Static method in class org.biojava.bio.proteomics.ProteaseManager: Gets a Protease instance by name.
getProteaseList() - Static method in class org.biojava.bio.proteomics.Protease: Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager.
getProteinExistsTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms: Getter for the protein exists term
getProteinExistsTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the protein exists term
getProteinParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools: Creates a protein symbol tokenizer.
getProteinTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the protein type term
getPrototype() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: The prototype is a RestrictionEnzyme that represents a set of isoshizomers.
getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return the overall P-value of this hit.
getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return the P-value of this sub-hit.
getPValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getPValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getQuality() - Method in class org.biojava.bio.program.phred.PhredSequence: Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.
getQuality() - Method in interface org.biojava.bio.program.phred.Qualitative: Retreives the list of quality symbols from the underlying object.
getQualityAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence
getQualityAt(int) - Method in interface org.biojava.bio.program.phred.Qualitative: Retreives the quality symbol for the specified index.
getQueryEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return the end position of the last sub-hit in the query sequence.
getQueryEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return the end position of the sub-hit in the query sequence.
getQueryEnd() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getQueryEnd() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getQueryEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getQueryEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getQueryRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getQuerySequence() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult: Returns the query sequence which was used to perform the search.
getQuerySequence() - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
getQuerySequence() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getQueryStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return the start position of the first sub-hit in the query sequence.
getQueryStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return the start position of the sub-hit in the query sequence.
getQueryStart() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getQueryStart() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getQueryStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getQueryStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getQueryStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return the strand of the hit with respect to the query sequence.
getQueryStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return the strand of the sub-hit with respect to the query sequence.
getQueryStrand() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getQueryStrand() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getQueryStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getQueryStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getRank() - Method in interface org.biojavax.bio.BioEntryRelationship: Returns the rank of this relationship.
getRank() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the rank associated with this location.
getRank() - Method in interface org.biojavax.bio.seq.RichFeature: Returns the rank of this feature.
getRank() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship: Gets the rank of this relationship.
getRank() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the rank associated with this location.
getRank() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Returns the rank of this feature.
getRank() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Gets the rank of this relationship.
getRank() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the rank associated with this location.
getRank() - Method in class org.biojavax.bio.SimpleBioEntryRelationship: Returns the rank of this relationship.
getRank() - Method in interface org.biojavax.Comment: Returns the rank of this comment.
getRank() - Method in interface org.biojavax.Note: Gets the rank that defines this note.
getRank() - Method in interface org.biojavax.RankedCrossRef: Return the rank associated with the cross reference.
getRank() - Method in interface org.biojavax.RankedDocRef: The rank of this reference.
getRank() - Method in class org.biojavax.SimpleComment: Returns the rank of this comment.
getRank() - Method in class org.biojavax.SimpleNote: Gets the rank that defines this note.
getRank() - Method in class org.biojavax.SimpleRankedCrossRef: Return the rank associated with the cross reference.
getRank() - Method in class org.biojavax.SimpleRankedDocRef: The rank of this reference.
getRankedCrossRefs() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Returns the set of all ranked cross references associated with an object.
getRankedCrossRefs() - Method in class org.biojavax.bio.SimpleBioEntry: Returns the set of all ranked cross references associated with an object.
getRankedCrossRefs() - Method in class org.biojavax.ontology.SimpleComparableTerm: Returns the set of all ranked cross references associated with an object.
getRankedCrossRefs() - Method in interface org.biojavax.RankedCrossRefable: Returns the set of all ranked cross references associated with an object.
getRankedDocRefs() - Method in interface org.biojavax.bio.BioEntry: Returns a set of all bioentrydocrefs associated with this bioentry.
getRankedDocRefs() - Method in class org.biojavax.bio.SimpleBioEntry: Returns a set of all bioentrydocrefs associated with this bioentry.
getReader() - Method in class org.biojava.bio.program.tagvalue.Indexer: Retrieve the reader that can be safely used to index this file.
getReader() - Method in class org.biojava.bio.program.tagvalue.Indexer2: Retrieve the reader that can be safely used to index this file.
getReader() - Method in class org.biojava.utils.process.ReaderWriterPipe: Gets the reader.
getReadingFrame() - Method in interface org.biojava.bio.seq.FramedFeature: return the reading frame of the feature.
getReadingFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
getRecognitionSequence(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getRecognitionSequence returns a string that describes the recognition site of this enzyme.
getRecognitionSite() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getRecognitionSite returns the forward strand of the recognition site.
getRecordKey(Object[]) - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess: getRecordKey returns the field from the record on which the records were sorted in the index.
getRecordKey(Object[]) - Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess: getRecordKey returns the field from the record on which the records were sorted in the index.
getRecordList() - Method in class org.biojava.bio.program.indexdb.BioStore: getRecordList returns all the Records in the index.
getRecurse() - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Return whether features will be filtered recursively or not.
getRecursive() - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
getRedoxPotential() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property redoxPotential.
getRef() - Method in interface org.biojava.bio.program.homologene.OrthoPair: get reference to evidence for orthology.
getRef() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getRegions() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
getRegions() - Method in interface org.biojava.bio.seq.RemoteFeature: Retrieve the list of Regions that locate this feature both localy and remotely.
getRegistryConfiguration() - Method in class org.biojava.directory.Registry: getRegistryConfiguration returns the configuration of the registry.
getRegistryPath() - Static method in class org.biojava.directory.SystemRegistry: Get the list of places that will be searched for registry files.
getRel() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
getRel() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
getRelAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the release annotated term
getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getRelatedAnnot(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getRelationships() - Method in interface org.biojavax.bio.BioEntry: Returns a set of all relationships associated with this bioentry.
getRelationships() - Method in class org.biojavax.bio.SimpleBioEntry: Returns a set of all relationships associated with this bioentry.
getRelCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the release created term
getRelUpdatedRecordVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms: Getter for the RelUpdatedRecordVersion term
getRelUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the release updated term
getRemark() - Method in interface org.biojavax.DocRef: If remarks have been made about this document reference, this method will return them.
getRemark() - Method in class org.biojavax.SimpleDocRef: If remarks have been made about this document reference, this method will return them.
getRemoteBioEntry(CrossRef) - Method in interface org.biojavax.CrossReferenceResolver: Given the CrossRef return the corresponding BioEntry
getRemoteBioEntry(CrossRef) - Method in class org.biojavax.DummyCrossReferenceResolver: Given the CrossRef return the corresponding BioEntry
getRemoteFeature() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
getRemoteFeature() - Method in interface org.biojava.bio.seq.RemoteFeature: Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.
getRemoteSymbolList(CrossRef, Alphabet) - Method in interface org.biojavax.CrossReferenceResolver: Given a cross reference, return the corresponding symbol list.
getRemoteSymbolList(CrossRef, Alphabet) - Method in class org.biojavax.DummyCrossReferenceResolver: Given a cross reference, return the corresponding symbol list.
getRemoteTerm() - Method in interface org.biojava.ontology.RemoteTerm: Return the imported term
getRemoteTerm() - Method in class org.biojava.ontology.RemoteTerm.Impl
getRemoteTerms() - Method in interface org.biojava.ontology.OntologyOps: Get the set of all remote terms.
getRepository(String) - Static method in class org.biojava.bio.seq.FeatureTypes: Fetch a repository by name.
getRepositoryNames() - Static method in class org.biojava.bio.seq.FeatureTypes: Find the names of all known repositories.
getResidue() - Method in interface org.biojava.bio.symbol.WobbleDistribution: returns the residue encoded by this WobbleDistribution
getResolver() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
getResolver() - Method in interface org.biojava.bio.seq.RemoteFeature
getResolver() - Method in class org.biojava.bio.symbol.FuzzyLocation: Retrieve the Location that this decorates.
getResolver() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getResultType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getRetrievalMode() - Method in class org.biojava.bio.seq.db.FetchURL: Get the retrieval mode
getRetrievalType() - Method in class org.biojava.bio.seq.db.FetchURL: Get the retrieval type
getReturnCode() - Method in exception org.biojava.utils.ProcessTimeoutException: Get the return code from the dying child process.
getReturnFormat() - Method in class org.biojava.bio.seq.db.FetchURL
getReverseRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getReverseRegex returns a regular expression which matches the reverse strand of the recognition site.
getReverter() - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
getReverter() - Method in class org.biojava.bio.seq.projection.ReparentContext
getReverter() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
getRevisionId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier: Return the revision id of this identifier.
getRichAnnotation() - Method in class org.biojavax.bio.seq.CompoundRichLocation: Return the associated annotation object.
getRichAnnotation() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Return the associated annotation object.
getRichAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Return the associated annotation object.
getRichAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Return the associated annotation object.
getRichAnnotation() - Method in class org.biojavax.bio.SimpleBioEntry: Return the associated annotation object.
getRichAnnotation() - Method in interface org.biojavax.RichAnnotatable: Return the associated annotation object.
getRichAnnotation() - Method in class org.biojavax.SimpleCrossRef: Return the associated annotation object.
getRichSequence(String) - Method in class org.biojavax.bio.db.HashRichSequenceDB
getRichSequence(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Given the appropriate Genbank ID, return the matching RichSequence object.
getRichSequence(String) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: Given the appropriate Genbank ID, return the matching RichSequence object.
getRichSequence(String) - Method in interface org.biojavax.bio.db.RichSequenceDBLite: Retrieve a single RichSequence by its id.
getRichSequence(String, Namespace) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Given the appropriate Genbank ID, return the matching RichSequence object.
getRichSequence(String, Namespace) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: Given the appropriate Genbank ID, return the matching RichSequence object.
getRichSequenceIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getRichSequenceIterator() - Method in interface org.biojavax.bio.db.RichSequenceDB: Returns a RichSequenceIterator over all sequences in the database.
getRichSequences(Set) - Method in class org.biojavax.bio.db.HashRichSequenceDB
getRichSequences(Set) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Retrieve rich sequences from a Genbank
getRichSequences(Set) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: Retrieve rich sequences from a Genbank
getRichSequences(Set) - Method in interface org.biojavax.bio.db.RichSequenceDBLite: Retrieve multiple RichSequence by its id.
getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.HashRichSequenceDB
getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Retrieve rich sequences from a Genbank
getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB: Retrieve rich sequences from a Genbank
getRichSequences(Set, RichSequenceDB) - Method in interface org.biojavax.bio.db.RichSequenceDBLite: Retrieve multiple RichSequence into a specific sequence database.
getRightValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon: Gets the right value.
getRightValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon: Gets the right value.
getRNA() - Static method in class org.biojava.bio.seq.RNATools: Return the RNA alphabet.
getRNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools: Creates a RNA symbol tokenizer.
getRoot() - Method in class org.biojava.bio.symbol.SuffixTree: Return the node object which is the root of this suffix tree.
getRoot() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getRoot() - Method in class org.biojava.bio.taxa.SimpleTaxonFactory: Deprecated.
getRoot() - Method in interface org.biojava.bio.taxa.TaxonFactory: Deprecated.

Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.
getRoot() - Method in class org.biojava.bio.taxa.WeakTaxonFactory: Deprecated.
getS() - Method in class org.biojava.bio.proteomics.StructureTools
getSBFactory() - Method in class org.biojava.bio.seq.db.BioIndex
getSBFactory() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getSBFactory() - Method in interface org.biojava.bio.seq.db.IndexStore: Retrieve the SequenceBuilderFactory used to build Sequence instances.
getSBFactory() - Method in class org.biojava.bio.seq.db.TabIndexStore
getScale(int) - Method in interface org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler: Retrieve the scaling factor at a given depth
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
getSchema() - Method in interface org.biojava.bio.annodb.AnnotationDB: Get an AnnotationType that accepts all Annotation instances in this DB.
getSchema() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
getSchema() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
getSchema() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
getSchema() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
getSchema() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
getSchema() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
getSchema() - Method in interface org.biojava.bio.seq.FeatureHolder: Return a schema-filter for this FeatureHolder.
getSchema() - Method in interface org.biojava.bio.seq.FeatureTypes.Type: Get the schema for this type.
getSchema() - Method in class org.biojava.bio.seq.impl.DummySequence
getSchema() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSchema() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getSchema() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getSchema() - Method in class org.biojava.bio.seq.impl.SubSequence
getSchema() - Method in class org.biojava.bio.seq.impl.ViewSequence
getSchema() - Method in class org.biojava.bio.seq.LazyFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.MergeFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getSchema() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.SimpleAssembly
getSchema() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
getSchema() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Return a schema-filter for this FeatureHolder.
getSchema() - Method in class org.biojavax.bio.seq.ThinRichSequence: Return a schema-filter for this FeatureHolder.
getSchema(String) - Method in class org.biojava.naming.ObdaContext
getSchema(Name) - Method in class org.biojava.naming.ObdaContext
getSchema(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
getSchemaClassDefinition(String) - Method in class org.biojava.naming.ObdaContext
getSchemaClassDefinition(Name) - Method in class org.biojava.naming.ObdaContext
getScientificName() - Method in class org.biojava.bio.taxa.AbstractTaxon: Deprecated.
getScientificName() - Method in interface org.biojava.bio.taxa.Taxon: Deprecated.

The scientific name of this taxon.
getScope() - Method in class org.biojava.ontology.Synonym
getScore() - Method in class org.biojava.bio.alignment.SimpleAlignment
getScore() - Method in interface org.biojava.bio.dp.DPMatrix
getScore() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
getScore() - Method in class org.biojava.bio.dp.SimpleStatePath
getScore() - Method in interface org.biojava.bio.dp.StatePath: Return the overall score for this state-path and it's emissions.
getScore() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
getScore() - Method in interface org.biojava.bio.program.gff.GFFRecord: The score of the feature.
getScore() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getScore() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getScore() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return the overall score of this hit in the units defined by the search algorithm.
getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return the score of this sub-hit in the units defined by the search algorithm.
getScore() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getScore() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getScore() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature: getScore returns the alignment score.
getScore() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature: getScore returns the alignment score.
getScore() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
getSearchableDBs() - Method in interface org.biojava.bio.search.SeqSimilaritySearcher: Return a set of all databases that can be searched with this sequence similarity searcher.
getSearchParameters() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult: Returns the search parameters used in the search that produced this search result.
getSearchParameters() - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
getSearchParameters() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getSearchProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
getSearchProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
getSecondIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction: Getter for property secondIntActID.
getSecondOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair: gets the first orthologue in the orthology relationship.
getSecondOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getSelectionFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
getSelectionFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getSeqCautions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property seqCautions.
getSeqDB() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
getSeqDBs() - Method in interface org.biojava.bio.seq.homol.HomologyDB: Retrieve the SeqDBs that have been searched against each other.
getSeqID() - Method in class org.biojava.bio.seq.RemoteFeature.Region: Return the remote Sequence ID if this Region is on another Sequence (isRemote will return true), null otherwise.
getSeqIDs() - Method in class org.biojava.bio.program.Meme
getSeqIOEvents(Sequence, SeqIOListener) - Method in class org.biojava.bio.seq.io.SeqIOEventEmitter: Deprecated.

getSeqIOEvents scans a Sequence object and sends events describing its data to the SeqIOListener.
getSeqName() - Method in interface org.biojava.bio.program.gff.GFFRecord: The sequence name field.
getSeqName() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter: Retrieve the current sequence name.
getSeqName() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getSequence() - Method in class org.biojava.bio.proteomics.Digest
getSequence() - Method in interface org.biojava.bio.seq.Feature: Return the Sequence object to which this feature is (ultimately) attached.
getSequence() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSequence() - Method in class org.biojava.bio.seq.impl.SubSequence: Return the parent sequence of which this is a partial view
getSequence() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getSequence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
getSequence() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Return the Sequence object to which this feature is (ultimately) attached.
getSequence(String) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.CachingSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
getSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDBLite: Retrieve a single sequence by its id.
getSequence(String) - Method in class org.biojava.bio.seq.db.SubSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB: Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
getSequence(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource: Get a Sequence object for an ID.
getSequence(String) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
getSequence(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
getSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getSequence(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext: Get the sequence for a feature.
getSequence(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
getSequenceDB() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult: Returns the sequence database against which the search was performed.
getSequenceDB() - Method in class org.biojava.bio.search.SequenceDBSearchResult: Deprecated.
getSequenceDB() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getSequenceDB(String) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
getSequenceDB(String) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation: Return the SequenceDB for the given identifier.
getSequenceDB(String) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation: If the given identifier is known to this sequence db installation because it has been used in a call to addSequenceDB(), then this method returns the SequenceDB associated with this identifier.
getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
getSequenceDB(Map) - Method in interface org.biojava.directory.SequenceDBProvider: Get a sequence database.
getSequenceDBs() - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
getSequenceDBs() - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation: Return all sequence dbs available in this sequence db installation.
getSequenceDBs() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation: Return a newly created set of the SequenceDB objects that were already created through method addSequenceDB().
getSequenceFormat() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory: getSequenceFormat returns the current sequence format name.
getSequenceFormat() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
getSequenceFormat() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getSequenceFormat() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getSequenceFormat() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getSequenceFormat() - Method in class org.biojava.bio.seq.db.WebSequenceDB
getSequenceFormat(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

getSequenceFormat accepts a value which represents a sequence format and returns the relevant SequenceFormat object.
getSequenceId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getSequenceId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getSequenceID() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getSequenceID() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getSequenceLength() - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler: Gets the sequenceLength attribute of the GAMESeqHandler object
getSequenceLength() - Method in class org.biojavax.bio.seq.SimpleRichSequence
getSequenceLength() - Method in class org.biojavax.bio.seq.ThinRichSequence
getSequenceName() - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
getSequenceRef() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform: Getter for property sequenceRef.
getSequences() - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
getSequences() - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler: get all the top level sequences bio_sequence --> SimpleSequence contig --> SimpleAssembly --> SimpleSequence( if only one sequence ) chromosome -> SimpleAssembly -> SimpleSequence( if only one sequence)
getSequences(Set) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB: Retrieve sequences from a Genbank
getSequences(Set, SequenceDB) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB: Retrieve sequences from a Genbank
getSequenceType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform: Getter for property sequenceType.
getSeqVersion() - Method in interface org.biojavax.bio.seq.RichSequence: The version of the associated symbol list.
getSeqVersion() - Method in class org.biojavax.bio.seq.ThinRichSequence: The version of the associated symbol list.
getShatter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF: Determine if features with non-contiguous locations will be broken into multiple GFF records.
getShort() - Method in class org.biojava.utils.io.LargeBuffer
getShort(long) - Method in class org.biojava.utils.io.LargeBuffer
getSibling() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature: getSibling returns the sibling Feature, query for subject and vice versa.
getSibling() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature: getSibling returns the sibling feature of the pair.
getSimilarity() - Method in interface org.biojava.bio.program.homologene.OrthoPair: gets the second orthologue in the orthology relationship.
getSimilarity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getSleepTime() - Method in class org.biojava.utils.process.ExternalProcess: Gets the number of milliseconds the ExternalProcess.execute(Properties) method should pauses after the external process is terminated.
getSource() - Method in interface org.biojava.bio.program.gff.GFFRecord: The source, or creator of this feature.
getSource() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter: Retrieve the current source.
getSource() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getSource() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getSource() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getSource() - Method in interface org.biojava.bio.seq.Feature: The source of the feature.
getSource() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
getSource() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSource() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getSource() - Method in class org.biojava.utils.ChangeForwarder: Retrieve the 'source' object for ChangeEvents fired by this forwarder.
getSource() - Method in class org.biojavax.bio.seq.SimpleRichFeature: The source of the feature.
getSourceAlphabet() - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
getSourceAlphabet() - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable
getSourceAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable: The alphabet of Symbols that can be translated.
getSourceHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getSourceSymbolList() - Method in interface org.biojava.bio.symbol.GappedSymbolList: Return the underlying (ungapped) SymbolList.
getSourceSymbolList() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
getSourceTerm() - Method in interface org.biojava.bio.seq.Feature: An ontology term defining the source of this feature.
getSourceTerm() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSourceTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeature: An ontology term defining the source of this feature.
getSpeciesForShortName(String) - Static method in class org.biojava.bio.program.unigene.UnigeneTools: Converts short species names (like Hs) to long species names (like Homo Sapiens).
getSpeciesTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the Species term
getSplitOffset() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser: Get the current offset at which lines are split.
getSplitter(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable: Get the Splitter currently registered to handle a tag.
getStart() - Method in interface org.biojava.bio.program.gff.GFFRecord: The start of this feature within the source sequence.
getStart() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getStart() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getStart() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getStart() - Method in interface org.biojava.bio.seq.db.Index: Skipping this number of bytes through the file should put the file pointer to the first byte of the sequence.
getStart() - Method in class org.biojava.bio.seq.db.SimpleIndex
getStart() - Method in class org.biojava.bio.seq.impl.SubSequence
getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
getStart() - Method in class org.biojava.utils.automata.FiniteAutomaton
getStart() - Method in interface org.biojava.utils.automata.NfaBuilder
getStart() - Method in class org.biojava.utils.automata.NfaSubModel
getStart() - Method in interface org.biojava.utils.automata.StateMachineInstance
getStart() - Method in interface org.biojavax.bio.seq.Position: Returns the beginning of the range of bases this base could lie in.
getStart() - Method in class org.biojavax.bio.seq.SimplePosition: Returns the beginning of the range of bases this base could lie in.
getStart() - Method in interface org.biojavax.RankedDocRef: The start position in the sequence that this reference is referred to from.
getStart() - Method in class org.biojavax.SimpleRankedDocRef: The start position in the sequence that this reference is referred to from.
getState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine
getStates() - Method in class org.biojava.bio.dp.DP
getStatusDateTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms: Getter for the StatusDate term
getStatusTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms: Getter for the Status term
getStAXContentHandler() - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler: Return a StAXContentHandler which can deal with any FilterXML construct known to this class.
getStoreLocation() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory: getStoreLocation returns the directory of the bew index.
getStoreName() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory: getStoreName returns the name to be given to the new index.
getStrainTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the Strain term
getStrand() - Method in interface org.biojava.bio.program.gff.GFFRecord: The strand of the feature.
getStrand() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
getStrand() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getStrand() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getStrand() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getStrand() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter: Retrieve the strand this matches.
getStrand() - Method in interface org.biojava.bio.seq.FramedFeature
getStrand() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
getStrand() - Method in interface org.biojava.bio.seq.StrandedFeature: Retrieve the strand that this feature lies upon.
getStrand() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the strand associated with this location.
getStrand() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation: Retrieves the strand associated with this location.
getStrand() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the strand associated with this location.
getStrand() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Retrieve the strand that this feature lies upon.
getStrand() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the strand associated with this location.
getStrandedFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
getStrandedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the Strand term; legal values are "single", "double", and "mixed".
getStringSequence() - Method in class org.biojavax.bio.seq.SimpleRichSequence
getStructure() - Method in class org.biojava.bio.proteomics.StructureTools
getStyle(String, String, String[]) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler: Return the styles for the two aligned characters.
getStyle(String, String, String[]) - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler: Returns the styles for the two aligned characters in the form of predefined font classes.
getSubAlphabet(double, double) - Static method in class org.biojava.bio.symbol.DoubleAlphabet
getSubAlphabet(int, int) - Static method in class org.biojava.bio.symbol.IntegerAlphabet: Construct a finite contiguous subset of the IntegerAlphabet.
getSubHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
getSubHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
getSubHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return all sub-hits for this sequence similarity search hit.
getSubHits() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getSubHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getSubject() - Method in interface org.biojava.ontology.Triple: Return the subject term of this triple
getSubject() - Method in class org.biojava.ontology.Triple.Impl
getSubject() - Method in interface org.biojavax.bio.BioEntryRelationship: Returns the subject of this relationship (ie. the BioEntry which this relationship targets).
getSubject() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship: Gets the feature that this relationship refers to.
getSubject() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Gets the feature that this relationship refers to.
getSubject() - Method in class org.biojavax.bio.SimpleBioEntryRelationship: Returns the subject of this relationship (ie. the BioEntry which this relationship targets).
getSubject() - Method in class org.biojavax.ontology.SimpleComparableTriple: Return the subject term of this triple
getSubjectEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return the end position of the last sub-hit in the subject sequence.
getSubjectEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return the start position of the sub-hit in the subject sequence.
getSubjectEnd() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getSubjectEnd() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getSubjectEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getSubjectEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getSubjectID() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: The sequence identifier of this hit within the sequence database against which the search was performed.
getSubjectID() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getSubjectID() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getSubjectStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return the start position of the first sub-hit in the subject sequence.
getSubjectStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return the start position of the sub-hit in the subject sequence.
getSubjectStart() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getSubjectStart() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getSubjectStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getSubjectStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getSubjectStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit: Return the strand of the sub-hit with respect to the subject sequence.
getSubjectStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit: Return the strand of the sub-hit with respect to the subject sequence.
getSubjectStrand() - Method in class org.biojava.bio.search.SequenceDBSearchHit: Deprecated.
getSubjectStrand() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit: Deprecated.
getSubjectStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getSubjectStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getSubmitterAccessionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms: Getter for the SubmitterAccession term
getSubmitterVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms: Getter for the SubmitterVersion term
getSubmitterWgsVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms: Getter for the SubmitterWgsVersion term
getSubSeqStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getSuppliers(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager: getSuppliers returns a string describing the suppliers of this enzyme according to REBASE encoding for commercial sources or an empty String if the enzyme is not commecially available.
getSupportedCriteria() - Method in interface org.biojava.bibliography.BibRefSupport: It returns all supported searching and sorting criteria for the whole bibliographic repository.
getSupportedCriteria(String) - Method in interface org.biojava.bibliography.BibRefSupport: It returns all supported searching and sorting criteria in the given repository subset.
getSupportedValues(String, String) - Method in interface org.biojava.bibliography.BibRefSupport: It returns a controlled vocabulary containing all possible values of the attribute given in attrName in the context given in resourceType.
getSwissprotBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.

Get a default SequenceBuilderFactory for handling Swissprot files.
getSymbol() - Method in exception org.biojava.bio.symbol.IllegalSymbolException: Retrieve the symbol that caused this exception, or null.
getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet: Retrieve the Symbol for a double.
getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getSymbol(double, double) - Method in class org.biojava.bio.symbol.DoubleAlphabet: Retrieve the symbol for a range of doubles.
getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet: Retrieve the Symbol for an int.
getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getSymbol(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet
getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet
getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getSymbol(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet
getSymbol(List) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet: Gets the compound symbol composed of the Symbols in the List.
getSymbol(List<Symbol>) - Method in interface org.biojava.bio.symbol.Alphabet: Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
getSymbolArray() - Method in class org.biojava.bio.symbol.SimpleSymbolList: Return the Java Symbol[] array that backs this object.
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.SimpleAlphabet
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.SingletonAlphabet
getSymbolParser() - Method in class org.biojava.bio.seq.db.BioIndex
getSymbolParser() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getSymbolParser() - Method in interface org.biojava.bio.seq.db.IndexStore: Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
getSymbolParser() - Method in class org.biojava.bio.seq.db.TabIndexStore
getSymbolPropertyTable(String) - Static method in class org.biojava.bio.seq.ProteinTools
getSymbols() - Method in class org.biojava.bio.dp.SimpleEmissionState
getSymbols() - Method in interface org.biojava.bio.seq.Feature: Return a list of symbols that are contained in this feature.
getSymbols() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSymbols() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
getSymbols() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getSymbols() - Method in interface org.biojava.bio.seq.StrandedFeature: Return a list of symbols that are contained in this feature.
getSymbols() - Method in interface org.biojava.bio.symbol.BasisSymbol: The list of symbols that this symbol is composed from.
getSymbols() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getSymbols() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getSymbols() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
getSymbols() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getSymbols() - Method in class org.biojavax.bio.seq.SimpleRichFeature: Return a list of symbols that are contained in this feature.
getSyms() - Method in class org.biojava.bio.symbol.PackedSymbolList: Return the long array within which the symbols are bit-packed.
getSynonyms() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getSynonyms() - Method in class org.biojava.ontology.OntologyTerm.Impl
getSynonyms() - Method in class org.biojava.ontology.RemoteTerm.Impl
getSynonyms() - Method in interface org.biojava.ontology.Term: Return the synonyms for this term.
getSynonyms() - Method in class org.biojava.ontology.Term.Impl
getSynonyms() - Method in class org.biojava.ontology.Triple.Impl
getSynonyms() - Method in class org.biojavax.ontology.SimpleComparableTerm: Return the synonyms for this term.
getSynonyms() - Method in class org.biojavax.ontology.SimpleComparableTriple: Return the synonyms for this term.
getT() - Method in class org.biojava.bio.molbio.DNAComposition: Get the relative compositon of 'T'.
getT() - Method in class org.biojava.bio.proteomics.StructureTools
getTable() - Method in class org.biojava.bio.dist.TranslatedDistribution: Retrieve the translation table encapsulating the map from this emission spectrum to the underlying one.
getTableNumber() - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
getTag() - Method in class org.biojava.bio.program.tagvalue.TagValue
getTagGroup() - Method in class org.biojava.bio.program.tagvalue.RegexParser: Get the group number that matches the tag.
getTags() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getTags() - Method in class org.biojava.bio.program.tagvalue.TagDropper: Get the complete set of tags that are currently recognized.
getTAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools: Gets the protein alphabet including the translation termination symbols
getTarget(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
getTarget(Object) - Method in interface org.biojava.stats.svm.SVMTarget
getTargetAlphabet() - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
getTargetAlphabet() - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable
getTargetAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable: The alphabet of Symbols that will be produced.
getTargetOntology() - Method in class org.biojava.ontology.OntologyTerm.Impl
getTaxa() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet: get the taxa represented in this group
getTaxa() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
getTaxon() - Method in interface org.biojava.bio.program.homologene.Orthologue: return the Taxon associated with this orthologue
getTaxon() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getTaxon() - Method in interface org.biojavax.bio.BioEntry: Gets the taxon associated with this bioentry.
getTaxon() - Method in class org.biojavax.bio.SimpleBioEntry: Gets the taxon associated with this bioentry.
getTaxon(int) - Static method in class org.biojava.bio.program.homologene.HomologeneTools: get the Taxon corresponding to this Taxon ID
getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getTaxonId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getTaxonID() - Method in interface org.biojava.bio.program.homologene.Orthologue: a convenience method to return the TaxonID for thsi orhtologue.
getTaxonID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getTaxonID() - Method in interface org.biojava.bio.program.homologene.Taxon: returns the taxon ID
getTaxonID() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
getTempBuffer() - Method in class org.biojava.ontology.obo.OboFileParser
getTemperatureDependence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property temperatureDependence.
getTerm() - Method in interface org.biojavax.bio.BioEntryRelationship: Returns the term describing the relationship.
getTerm() - Method in class org.biojavax.bio.seq.EmptyRichLocation: Retrieves the term associated with this location.
getTerm() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship: Gets the term that describes this relationship.
getTerm() - Method in interface org.biojavax.bio.seq.RichLocation: Retrieves the term associated with this location.
getTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship: Gets the term that describes this relationship.
getTerm() - Method in class org.biojavax.bio.seq.SimpleRichLocation: Retrieves the term associated with this location.
getTerm() - Method in class org.biojavax.bio.SimpleBioEntryRelationship: Returns the term describing the relationship.
getTerm() - Method in interface org.biojavax.Note: Gets the term that defines this note.
getTerm() - Method in class org.biojavax.SimpleNote: Gets the term that defines this note.
getTerm(String) - Method in class org.biojava.ontology.IntegerOntology
getTerm(String) - Method in interface org.biojava.ontology.Ontology: Fetch the term with the specified name.
getTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
getTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology: Fetch the term with the specified name.
getTermMass() - Method in class org.biojava.bio.proteomics.MassCalc: getTermMass returns the terminal mass being used by the instance methods.
getTerms() - Method in class org.biojava.ontology.IntegerOntology
getTerms() - Method in interface org.biojava.ontology.Ontology: Return all the terms in this ontology
getTerms() - Method in class org.biojava.ontology.Ontology.Impl
getTerms() - Method in class org.biojavax.ontology.SimpleComparableOntology: Return all the terms in this ontology
getTermSet() - Method in interface org.biojavax.ontology.ComparableOntology: Returns the set of terms in this ontology.
getTermSet() - Method in class org.biojavax.ontology.SimpleComparableOntology: Returns the set of terms in this ontology.
getTestClass() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
getText() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property text.
getThreshold() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
getThreshold() - Method in interface org.biojava.stats.svm.SVMClassifierModel
getThreshold() - Method in class org.biojava.stats.svm.SVMRegressionModel
getTissueTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the Tissue term
getTitle() - Method in interface org.biojava.bio.program.homologene.Orthologue: return the title used by Genbank for this protein
getTitle() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getTitle() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster: The cluster title.
getTitle() - Method in interface org.biojavax.DocRef: Returns the title of the document reference.
getTitle() - Method in class org.biojavax.SimpleDocRef: Returns the title of the document reference.
getTo() - Method in exception org.biojava.bio.dp.IllegalTransitionException
getToken() - Method in class org.biojava.bio.dp.SimpleEmissionState
getToken() - Method in class org.biojava.bio.seq.StrandedFeature.Strand: Returns the token for strandedness.
getTokenization(String) - Method in class org.biojava.bio.symbol.AbstractAlphabet
getTokenization(String) - Method in interface org.biojava.bio.symbol.Alphabet: Get a SymbolTokenization by name.
getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet
getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet: Creates a new parser (Mark Schreiber 3 May 2001).
getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getTokenization(String) - Method in class org.biojava.bio.symbol.SingletonAlphabet
getTokenization(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
getTokenTable() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getTokenType() - Method in class org.biojava.bio.seq.io.AlternateTokenization: Tokens have fixed size.
getTokenType() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getTokenType() - Method in interface org.biojava.bio.seq.io.SymbolTokenization: Determine the style of tokenization represented by this object.
getTokenType() - Method in class org.biojava.bio.seq.io.WordTokenization
getTokenType() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
getTool() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService: Get the tool identifier for QBlast.
getTool() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB: Get the tool identifier for Entrez.
getTotalWeight() - Method in class org.biojavax.ga.util.WeightedSet: The total weight that has been added to this Set.
getTrailer() - Method in class org.biojava.utils.ListTools.SeriesList
getTrainer(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext: Return the Distribution trainer object from the current context.
getTrainer(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
getTransformer() - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
getTransformer() - Method in class org.biojava.bio.seq.projection.ReparentContext
getTransformer() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
getTransitions() - Method in class org.biojava.utils.automata.FiniteAutomaton: retrieve Set of all transitions in instance.
getTransitions() - Method in interface org.biojava.utils.automata.NfaBuilder
getTransitions() - Method in class org.biojava.utils.automata.NfaSubModel
getTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState: retrieve the TransitionTable for this State.
getTranslation() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
getTransposonTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms: Getter for the Transposon term
getTrimTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser: See if tag trimming is enabled.
getTrimTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser: See if trimming of tags is enabled.
getTrimValue() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser: See if value trimming is enabled.
getTrimValue() - Method in class org.biojava.bio.program.tagvalue.RegexParser: See if trimming of values is enabled.
getTriples(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology
getTriples(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology: Return all triples from this ontology which match the supplied pattern.
getTriples(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl
getTriples(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology: Return all triples from this ontology which match the supplied pattern.
getTripleSet() - Method in interface org.biojavax.ontology.ComparableOntology: Returns the set of triples in this ontology.
getTripleSet() - Method in class org.biojavax.ontology.SimpleComparableOntology: Returns the set of triples in this ontology.
getTrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getType() - Method in class org.biojava.bio.program.formats.Embl
getType() - Method in class org.biojava.bio.program.formats.Enzyme
getType() - Method in interface org.biojava.bio.program.formats.Format: Get the AnnotationType that constrains the events that will be fired.
getType() - Method in class org.biojava.bio.program.formats.Ligand.Compound
getType() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
getType() - Method in class org.biojava.bio.program.formats.Ligand.Reaction
getType() - Method in class org.biojava.bio.program.formats.Swissprot
getType() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getType() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getType() - Method in interface org.biojava.bio.seq.Feature: The type of the feature.
getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
getType() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getType() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
getType() - Method in class org.biojava.utils.ChangeEvent: Find the type of this event.
getType() - Method in class org.biojava.utils.ChangeForwarder.Retyper
getType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event: Getter for property type.
getType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
getType() - Method in interface org.biojavax.bio.seq.Position: Returns the type of this position if it is not a point/single position.
getType() - Method in class org.biojavax.bio.seq.SimplePosition: Returns the type of this position if it is not a point/single position.
getType() - Method in class org.biojavax.bio.seq.SimpleRichFeature: The type of the feature.
getType(String) - Static method in class org.biojava.bio.seq.FeatureTypes: Get a Type by URI.
getType(String) - Method in interface org.biojava.bio.seq.FeatureTypes.Repository: Find the type for a name.
getType(String) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getTypeClass() - Method in class org.biojava.utils.walker.WalkerFactory
getTypeHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getTypes() - Method in interface org.biojava.bio.seq.FeatureTypes.Repository: Get a set of all type names defined in this repository.
getTypes() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getTypeTerm() - Method in interface org.biojava.bio.seq.Feature: An ontology term defining the type of feature.
getTypeTerm() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getTypeTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeature: An ontology term defining the type of feature.
getUngappedLocation() - Method in interface org.biojava.bio.symbol.GappedSymbolList: Get a Location that contains exactly those positions that are not gaps.
getUngappedLocation() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
getUniProtDBNameTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms: Getter for the UniProt combined database term
getUniprotKWOnto() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the private uniprot ontology.
getUniProtTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms: Getter for the UniProt term
getUniProtXMLTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms: Getter for the UniProtXML term
getUnique() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster: The unique sequence that is used as a representative for this cluster.
getUnits() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getUnprojectedFeatures() - Method in interface org.biojava.bio.seq.projection.ProjectionContext: Get the features before projection.
getUnprojectedFeatures() - Method in class org.biojava.bio.seq.projection.ReparentContext
getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getUpdateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getUpstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getUpstreamCut returns the cut site upstream of the recognition site.
getUpstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme: getUpstreamEndType returns the double-stranded end type produced by the secondary (upstream) cut.
getUri() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property uri.
getURI() - Method in interface org.biojava.bio.seq.FeatureTypes.Type: Get the URI for this type.
getURI() - Method in interface org.biojavax.Namespace: If the namespace has a URI, this will return it.
getURI() - Method in class org.biojavax.SimpleNamespace: If the namespace has a URI, this will return it.
getURN() - Method in class org.biojava.bio.seq.impl.DummySequence
getURN() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getURN() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getURN() - Method in class org.biojava.bio.seq.impl.SubSequence
getURN() - Method in class org.biojava.bio.seq.impl.ViewSequence
getURN() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getURN() - Method in interface org.biojava.bio.seq.Sequence: A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.
getURN() - Method in class org.biojava.bio.seq.SimpleAssembly
getURN() - Method in class org.biojavax.bio.seq.ThinRichSequence: A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.
getValue() - Method in class org.biojava.bio.program.tagvalue.TagValue
getValue() - Method in class org.biojava.bio.PropertyConstraint.ExactValue: Get the value that all properties must match.
getValue() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains
getValue() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation
getValue() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
getValue() - Method in class org.biojava.bio.seq.StrandedFeature.Strand: Returns the integer label for strandedness.
getValue() - Method in interface org.biojava.stats.svm.ItemValue
getValue() - Method in class org.biojava.stats.svm.SimpleItemValue
getValue() - Method in interface org.biojava.utils.walker.Walker: If the visitor has a return value, then the result of applying the visitor to the tree can be obtained using this method, otherwise the result will be null.
getValue() - Method in interface org.biojavax.Note: Gets the value that defines this note.
getValue() - Method in class org.biojavax.SimpleNote: Gets the value that defines this note.
getValue() - Method in class org.biojavax.utils.CRC64Checksum
getValueAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector: Retrieve the value at a specific index.
getValueGroup() - Method in class org.biojava.bio.program.tagvalue.RegexParser: Get the group number that matches the value.
getValues() - Method in class org.biojava.bio.PropertyConstraint.Enumeration: getValues returns the set of values which constrain the property.
getVariableMasses(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc: Get all masses including the variable mass.
getVector() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
getVector(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getVectorNTISupport() - Method in class org.biojava.bio.seq.io.GenbankFileFormer: Deprecated.

Is VectorNTI compatable output being produced?
getVersion() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getVersion() - Method in interface org.biojava.utils.candy.CandyVocabulary: It returns a vesrion of this vocabulary.
getVersion() - Method in interface org.biojavax.bio.BioEntry: Gets the version of this bioentry.
getVersion() - Method in class org.biojavax.bio.SimpleBioEntry: Gets the version of this bioentry.
getVersion() - Method in interface org.biojavax.CrossRef: Returns the version of the object that the crossref refers to.
getVersion() - Method in class org.biojavax.SimpleCrossRef: Returns the version of the object that the crossref refers to.
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getVersion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getVersionLineTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms: Getter for the Ensembl-specific 'versionLine' term
getViewedFeature() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getViewedFeature() - Method in interface org.biojava.bio.seq.projection.Projection
getVMaxes() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser: Getter for property VMaxes.
getVocabularyByName(String) - Method in interface org.biojava.utils.candy.CandyFinder: It returns a selected vocabulary.
getVocabularyFinder() - Method in interface org.biojava.bibliography.BibRefSupport: It returns an object representing a central place where all controlled vocabularies can be received from and shared by all users.
getWalker(Visitor) - Method in class org.biojava.utils.walker.WalkerFactory: Get a Walker that is customosed to a particular visitor.
getWeight(Object) - Method in class org.biojavax.ga.util.WeightedSet: Determines the normalized weight for o
getWeight(Symbol) - Method in class org.biojava.bio.dist.AbstractDistribution: Retrieve the weight for this distribution.
getWeight(Symbol) - Method in interface org.biojava.bio.dist.Distribution: Return the probability that Symbol s is emitted by this spectrum.
getWeight(Symbol) - Method in class org.biojava.bio.dist.GapDistribution
getWeight(Symbol) - Method in class org.biojava.bio.dist.PairDistribution
getWeight(Symbol) - Method in class org.biojava.bio.dist.TranslatedDistribution
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.AbstractDistribution: Override this method to implement getting the weight for an atomic symbol.
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution: Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.UniformDistribution
getWeightMatrixID() - Method in class org.biojava.bio.dp.WeightMatrixAnnotator: Get the value of the weight matrix id.
getWeights() - Method in class org.biojava.bio.dist.SimpleDistribution: Get the underlying array that stores the weights.
getWeights(State) - Method in interface org.biojava.bio.dp.MarkovModel: Get a probability Distribution over the transition from 'source'.
getWeights(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
getWeights(State) - Method in class org.biojava.bio.dp.WMAsMM
getWidth() - Method in class org.biojava.bio.seq.io.AlternateTokenization: Get the width of the tokens.
getWidth() - Method in class org.biojava.stats.svm.RadialBaseKernel
getWobbleDistributionForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref: returns a WobbleDistribution for a specified residue.
getWobbleDistributionForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref
getWobbleFrequency(Symbol) - Method in interface org.biojava.bio.symbol.WobbleDistribution: returns the frequency of a specific wobble base in a set of synonymous codons that start with the same two bases.
getWorkingDirectory() - Method in class org.biojava.utils.process.ExternalProcess: Gets the working directory for the external process.
getWrapped() - Method in class org.biojava.bio.AnnotationChanger: getWrapped returns the Annotation being remapped.
getWrapped() - Method in class org.biojava.bio.AnnotationRenamer: getWrapped returns the Annotation being remapped.
getWrapped() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getWrappedKernel() - Method in class org.biojava.stats.svm.SigmoidKernel
getWriter() - Method in class org.biojava.utils.process.ReaderWriterPipe: Gets the writer.
getXFFEnvironment() - Method in class org.biojava.bio.program.xff.FeatureHandler: Return the XFF processing environment passed in when this handler was created.
getXrefDb() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
getXrefProps() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
getXrefs() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs: return a set of AGAVEXref
getXrefs(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getXrefs(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getXrefs(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
GFF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants: GFF indicates that the sequence format is GFF.
GFF3DocumentHandler - Interface in org.biojava.bio.program.gff3: The interface for things that listen to GFF event streams.
GFF3Parser - Class in org.biojava.bio.program.gff3: Parse a stream of GFF text into a stream of records and comments.
GFF3Parser() - Constructor for class org.biojava.bio.program.gff3.GFF3Parser
GFF3Record - Interface in org.biojava.bio.program.gff3: A record in a GFF3 formatted file.
GFF3Record.Impl - Class in org.biojava.bio.program.gff3
GFFDataSource - Class in org.biojava.bio.seq.distributed: Use a GFFEntrySet as a DataSource for adding annotation to sequences.
GFFDataSource(GFFEntrySet) - Constructor for class org.biojava.bio.seq.distributed.GFFDataSource
GFFDocumentHandler - Interface in org.biojava.bio.program.gff: The interface for things that listen to GFF event streams.
GFFEntrySet - Class in org.biojava.bio.program.gff: A set of entries and comments as a representation of a GFF file.
GFFEntrySet() - Constructor for class org.biojava.bio.program.gff.GFFEntrySet: Make an empty GFFEntrySet.
GFFErrorHandler - Interface in org.biojava.bio.program.gff: Interface which captures any errors which occur when parsing a GFF stream.
GFFErrorHandler.AbortErrorHandler - Class in org.biojava.bio.program.gff
GFFErrorHandler.SkipRecordErrorHandler - Class in org.biojava.bio.program.gff
GFFFilterer - Class in org.biojava.bio.program.gff: An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others.
GFFFilterer(GFFDocumentHandler, GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFFilterer: Create a new GFFFilterer that will forward to handler everything that filter accepts.
gffFromSeqDB(SequenceDB) - Static method in class org.biojava.bio.program.gff.GFFTools: Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.
gffFromSequence(Sequence) - Static method in class org.biojava.bio.program.gff.GFFTools: Creates a GFFEntrySet containing one entry for each feature on a sequence.
GFFParser - Class in org.biojava.bio.program.gff: Parse a stream of GFF text into a stream of records and comments.
GFFParser() - Constructor for class org.biojava.bio.program.gff.GFFParser
GFFRecord - Interface in org.biojava.bio.program.gff: A single GFF record.
GFFRecordFilter - Interface in org.biojava.bio.program.gff: A filter that will accept or reject a GFFEntry.
GFFRecordFilter.AcceptAll - Class in org.biojava.bio.program.gff: Implementation of GFFRecordFilter that accepts everything.
GFFRecordFilter.FeatureFilter - Class in org.biojava.bio.program.gff: Implementation of GFFRecordFilter that accepts records based upon the feature field.
GFFRecordFilter.FrameFilter - Class in org.biojava.bio.program.gff
GFFRecordFilter.NotFilter - Class in org.biojava.bio.program.gff
GFFRecordFilter.SequenceFilter - Class in org.biojava.bio.program.gff: Implementation of GFFRecordFilter that accepts records based upon the sequence name.
GFFRecordFilter.SourceFilter - Class in org.biojava.bio.program.gff: Implementation of GFFRecordFilter that accepts records based upon the source field.
GFFRecordFilter.StrandFilter - Class in org.biojava.bio.program.gff
GFFTools - Class in org.biojava.bio.program.gff
GFFTools() - Constructor for class org.biojava.bio.program.gff.GFFTools
GFFWriter - Class in org.biojava.bio.program.gff: Listens to a stream of GFF events and writes the lines to a PrintWriter.
GFFWriter(PrintWriter) - Constructor for class org.biojava.bio.program.gff.GFFWriter: Create a new GFFWriter that will write to out.
GI_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat: Deprecated.
gln() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Glutamine (Q)
GLOBAL - Static variable in class org.biojava.bio.taxa.SimpleTaxonFactory: Deprecated.

The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.
GLOBAL - Static variable in class org.biojava.bio.taxa.WeakTaxonFactory: Deprecated.

The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.
glu() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Glutamic Acid (E)
GLU_C_BICARB - Static variable in class org.biojava.bio.proteomics.Protease
GLU_C_BICARB - Static variable in class org.biojava.bio.proteomics.ProteaseManager
GLU_C_PHOS - Static variable in class org.biojava.bio.proteomics.Protease
GLU_C_PHOS - Static variable in class org.biojava.bio.proteomics.ProteaseManager
gly() - Static method in class org.biojava.bio.seq.ProteinTools: Returns the AtomicSymbol for the amino acid Glycine (G)
GOParser - Class in org.biojava.ontology.io: Simple parser for the Gene Ontology (GO) flatfile format.
GOParser() - Constructor for class org.biojava.ontology.io.GOParser
GreaterThan(double) - Constructor for class org.biojava.bio.search.FilterTest.GreaterThan
group() - Method in interface org.biojava.bio.search.BioMatcher: Get the matching region as a SymbolList.
group() - Method in class org.biojava.bio.search.MaxMismatchMatcher
group() - Method in class org.biojava.utils.regex.Matcher: Returns the input subsequence matched by the previous match.
group(int) - Method in class org.biojava.utils.regex.Matcher: Returns the input subsequence captured by the given group during the previous match operation.
groupCount() - Method in class org.biojava.utils.regex.Matcher: Returns the number of capturing groups in this matcher's pattern.
groups - Variable in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
growIfNecessary() - Method in class org.biojava.utils.ChangeSupport: Grows the internal resources if by adding one more listener they would be full.
guessFileType(File) - Static method in class org.biojava.bio.seq.io.SeqIOTools: Deprecated.
because there is no standard file naming convention and guessing by file name is inherantly error prone and bad.
guessRecLen(RandomAccessFile) - Method in class org.biojava.bio.seq.db.BioIndex
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat: On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat: On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat: On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat: On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat: On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat: On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat: On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.FastaFormat: On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat: On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat: On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat: On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat: On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat: On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat: On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
GZIP_MAGIC - Static variable in class org.biojava.utils.io.InputStreamProvider: The magic number found at the start of a GZIP stream.





H

h() - Static method in class org.biojava.bio.seq.DNATools
 
h() - Static method in class org.biojava.bio.seq.NucleotideTools
 
h() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Histidine

H_SAPIENS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
H_VULGARE - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
handlesAmbiguity() - Method in class org.biojava.bio.symbol.DNAAmbPack
 
handlesAmbiguity() - Method in class org.biojava.bio.symbol.DNANoAmbPack
 
handlesAmbiguity() - Method in interface org.biojava.bio.symbol.Packing


 Flag to state if ambiguities are stored.

hasAnnotation(Object) - Static method in class org.biojava.bio.seq.FilterUtils

Match features where the property key has been defined as having
 some value, regardless of the exact value.

HasAnnotation(Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.HasAnnotation

Make a new ByAnnotation that will accept features with an annotation
 bundle containing any value associated with 'key'.

HasAttribute(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
 
HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute
 
HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute
 
hasBoundedMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
hasBoundedMax() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
hasBoundedMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
hasBoundedMin() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
hasChangeSupport() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
hasChild(int) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode

Determine if this node has a child corresponding to a given
 index number.

hasChild(Character) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode

Determine if this node has a child corresponding to a given character

hasFeatures(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource

Find out if this DistDataSource can provide features on a sequence with a particular ID.

hasFeatures(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
 
hasFeatures(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
HashBioEntryDB - Class in org.biojavax.bio.db

An implementation of RichSequenceDB that uses an underlying HashMap to store the
 RichSequence objects.

HashBioEntryDB() - Constructor for class org.biojavax.bio.db.HashBioEntryDB

Generate a HashRichSequenceDB object that will use byName to generate ids for
 sequences and have a null name.

HashBioEntryDB(String) - Constructor for class org.biojavax.bio.db.HashBioEntryDB

Generate a HashRichSequenceDB object that will use byName to generate ids and
 will have the requested name.

hashCode() - Method in class org.biojava.bio.AbstractAnnotation
 
hashCode() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
hashCode() - Method in class org.biojava.bio.CollectionConstraint.Contains
 
hashCode() - Method in class org.biojava.bio.dist.AbstractDistribution
 
hashCode() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
 
hashCode() - Method in class org.biojava.bio.dp.TrainerTransition

The hash code is model.hashCode() ^ from.hashCode() ^ to.hashCode()

hashCode() - Method in class org.biojava.bio.dp.Transition

The hash code is from.hashCode() ^ to.hashCode()

hashCode() - Method in class org.biojava.bio.EcNumber.Impl
 
hashCode() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
 
hashCode() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
 
hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchHit

Deprecated.
 
hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchResult

Deprecated.
 
hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit

Deprecated.
 
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
hashCode() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
 
hashCode() - Method in class org.biojava.bio.seq.Feature.Template
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.And
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.Not
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
 
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
 
hashCode() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
hashCode() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
hashCode() - Method in class org.biojava.bio.symbol.AbstractLocation
 
hashCode() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
hashCode() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
hashCode() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
hashCode() - Method in class org.biojava.bio.taxa.AbstractTaxon

Deprecated.
 
hashCode() - Method in interface org.biojava.bio.taxa.Taxon

Deprecated.
The hash-code of a Taxon is equal to the hash-code of it's
 scientific name.

hashCode() - Method in class org.biojava.ontology.Term.Impl
 
hashCode() - Method in interface org.biojava.ontology.Triple

The hashcode for a Triple.

hashCode() - Method in class org.biojava.ontology.Triple.Impl
 
hashCode() - Method in class org.biojava.utils.ListTools.Doublet
 
hashCode() - Method in class org.biojava.utils.ListTools.Triplet
 
hashCode() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
 
hashCode() - Method in class org.biojava.utils.TypedProperties
 
hashCode() - Method in class org.biojavax.bio.seq.CompoundRichLocation
hashCode() - Method in class org.biojavax.bio.seq.EmptyRichLocation


 ALWAYS RETURNS 17

hashCode() - Method in class org.biojavax.bio.seq.RichLocation.Strand
hashCode() - Method in class org.biojavax.bio.seq.SimpleRichFeature
hashCode() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
hashCode() - Method in class org.biojavax.bio.seq.SimpleRichLocation
hashCode() - Method in class org.biojavax.bio.SimpleBioEntry
hashCode() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
hashCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
hashCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
hashCode() - Method in class org.biojavax.EmptyRichAnnotation
hashCode() - Method in class org.biojavax.ontology.SimpleComparableOntology
hashCode() - Method in class org.biojavax.ontology.SimpleComparableTerm
hashCode() - Method in class org.biojavax.ontology.SimpleComparableTriple

The hashcode for a Triple.

hashCode() - Method in class org.biojavax.SimpleComment
hashCode() - Method in class org.biojavax.SimpleCrossRef
hashCode() - Method in class org.biojavax.SimpleDocRef
hashCode() - Method in class org.biojavax.SimpleDocRefAuthor
hashCode() - Method in class org.biojavax.SimpleNamespace
hashCode() - Method in class org.biojavax.SimpleNote
hashCode() - Method in class org.biojavax.SimpleRankedCrossRef
hashCode() - Method in class org.biojavax.SimpleRankedDocRef
hashCode(int, boolean) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, boolean[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, double) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, double[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, float) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, float[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, int) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, int[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, long) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, long[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, Object) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, Object[]) - Static method in class org.biojava.utils.ObjectUtil
 
HashedFastaIterator - Class in org.biojavax.bio.seq.io

Iterates over a Fasta file that is kept in memory for optimized access.

HashedFastaIterator(BufferedInputStream, Alphabet, Namespace) - Constructor for class org.biojavax.bio.seq.io.HashedFastaIterator
 
HashRichSequenceDB - Class in org.biojavax.bio.db

An implementation of RichSequenceDB that uses an underlying HashMap to store the
 RichSequence objects.

HashRichSequenceDB() - Constructor for class org.biojavax.bio.db.HashRichSequenceDB

Generate a HashRichSequenceDB object that will use byName to generate ids for
 sequences and have a null name.

HashRichSequenceDB(String) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB

Generate a HashRichSequenceDB object that will use byName to generate ids and
 will have the requested name.

HashRichSequenceDB(IDMaker) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB

Generate a HashRichSequenceDB object that will use idMaker to generate ids for
 sequences and have a null name.

HashRichSequenceDB(IDMaker, String) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB

Generate a HashRichSequenceDB object that will use idMaker to generate ids for
 sequences and have the requested name.

HashSequenceDB - Class in org.biojava.bio.seq.db

An implementation of SequenceDB that uses an underlying HashMap to store the
 sequence objects.

HashSequenceDB() - Constructor for class org.biojava.bio.seq.db.HashSequenceDB

Generate a HashSequenceDB object that will use byName to generate ids for
 sequences and have a null name.

HashSequenceDB(String) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB

Generate a HashSequenceDB object that will use byName to generate ids and
 will have the requested name.

HashSequenceDB(IDMaker) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB

Generate a HashSequenceDB object that will use idMaker to generate ids for
 sequences and have a null name.

HashSequenceDB(IDMaker, String) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB

Generate a HashSequenceDB object that will use idMaker to generate ids for
 sequences and have the requested name.

hasListeners() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
hasListeners() - Method in class org.biojava.utils.AbstractChangeable

Discover if we have any listeners registered.

hasListeners() - Method in class org.biojava.utils.ChangeSupport

Return true if we have any listeners registered at all.

hasListeners(ChangeType) - Method in class org.biojava.utils.AbstractChangeable

Discover if we have listeners registered for a particular change type.

hasListeners(ChangeType) - Method in class org.biojava.utils.ChangeSupport

Return true if we have listeners registered for a particular change type.

hasMoreSymbols() - Method in interface org.biojava.bio.seq.io.SymbolReader

Determine if there are more symbols left to read in this stream.

hasNext() - Method in class org.biojava.bio.alignment.Alignment.SymbolListIterator
 
hasNext() - Method in class org.biojava.bio.dp.DP.ReverseIterator
 
hasNext() - Method in class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
 
hasNext() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor

Are there further Cells to be computed?

hasNext() - Method in class org.biojava.bio.dp.twohead.MatrixPairDPCursor
 
hasNext() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor

test wether the cursor can be advanced further

hasNext() - Method in interface org.biojava.bio.program.homologene.OrthologueSet.Iterator
 
hasNext() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection.Iterator

are more OrthoPairSets available?

hasNext() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet.Iterator
 
hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet.Iterator
 
hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection.Iterator
 
hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet.Iterator
 
hasNext() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
 
hasNext() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
 
hasNext() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
 
hasNext() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader

Checks if there is a further 
 SymbolPropertyTable object.

hasNext() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator

Checks if there is a further 
 SymbolPropertyTable object.

hasNext() - Method in class org.biojava.bio.seq.io.StreamReader
 
hasNext() - Method in interface org.biojava.bio.seq.SequenceIterator

Returns whether there are more sequences to iterate over.

hasNext() - Method in class org.biojava.utils.MergingIterator
 
hasNext() - Method in interface org.biojavax.bio.BioEntryIterator

Returns whether there are more sequences to iterate over.

hasNext() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator
 
hasNext() - Method in class org.biojavax.bio.seq.io.RichStreamReader

Returns whether there are more sequences to iterate over.

hasNext() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator

Returns whether there are more sequences to iterate over.

hasSequence(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource

Find out if this DistDataSource provides the sequence information for a sequence ID.

hasSequence(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
 
hasSequence(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
hasWeights() - Method in class org.biojava.bio.dist.SimpleDistribution

Indicate whether the weights array has been allocated yet.

Havg - Static variable in class org.biojava.bio.proteomics.MassCalc

Constant value of Hydrogen average mass

HeaderlessFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
 
headerLine - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
headerLine - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
headerLine - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
heads() - Method in interface org.biojava.bio.dp.MarkovModel

Deprecated.
use advance().length


heads() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
heads() - Method in class org.biojava.bio.dp.WMAsMM
 
HIDDEN - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
his() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Histidine (H)

hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.HitMerger
 
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
 
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.FilterByLength
 
hit(int, int, int, int) - Method in interface org.biojava.bio.program.ssaha.SearchListener

There has been a hit between the query sequence and a database
 sequence.

hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
 
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
 
HitMerger - Class in org.biojava.bio.program.ssaha

A listener that merges overlapping hits and culls all hits under a given
 length.

HitMerger(SearchListener, int) - Constructor for class org.biojava.bio.program.ssaha.HitMerger

Build a new HitMerger that will pass events on to a delegate.

hmm - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
hmm() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM

Gets the inner HmmerProfileHMM state

HmmerProfileHMM - Class in org.biojava.bio.program.hmmer

This is a class for representing HMMER generated Profile HMM.

HmmerProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory, String) - Constructor for class org.biojava.bio.program.hmmer.HmmerProfileHMM
 
HmmerProfileParser - Class in org.biojava.bio.program.hmmer

A class for parsing in Hmmer markov models from HMM_ls files generated by HMMER training
 note that this class is still currently experimental.

HmmerProfileParser(String) - Constructor for class org.biojava.bio.program.hmmer.HmmerProfileParser
 
HMMTrainer - Interface in org.biojava.bio.dp

interface implemented by objects that train HMMs.

Hmono - Static variable in class org.biojava.bio.proteomics.MassCalc

Constant value of  Hydrogen monoisotopic mass

HOMOID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
HomologeneBuilder - Interface in org.biojava.bio.program.homologene

an interface for Homologene dataset Builders

HomologeneDB - Interface in org.biojava.bio.program.homologene

Homologene is a NCBI dataset that curates sets
 of orthologues from the reference model organisms.

HomologeneTools - Class in org.biojava.bio.program.homologene

Homologene is a NCBI dataset that curates sets
 of orthologues from the reference model ogranisms.

HomologeneTools() - Constructor for class org.biojava.bio.program.homologene.HomologeneTools
 
homology - Variable in class org.biojava.bio.seq.homol.HomologyFeature.Template
 
Homology - Interface in org.biojava.bio.seq.homol


 Signifies that two or more features are homologous.

HomologyDB - Interface in org.biojava.bio.seq.homol
 
HomologyFeature - Interface in org.biojava.bio.seq.homol
 
HomologyFeature.Template - Class in org.biojava.bio.seq.homol
 
hp - Static variable in class org.biojavax.bio.seq.io.FastaFormat
 
HTML - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
HTMLRenderer - Class in org.biojava.bio.program.blast2html

Renders HTML version of blast-like output.

HTMLRenderer(PrintWriter, String, int, URLGeneratorFactory, AlignmentMarker, Properties) - Constructor for class org.biojava.bio.program.blast2html.HTMLRenderer

Creates an HTMLRenderer, that outputs the HTML to the specified
 PrintWriter.

HYDROPATHICITY - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 




I

i() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Isoleucine

ID_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ID_KEY - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
ID_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
ID_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
Identifiable - Interface in org.biojava.utils.lsid

Marks an implementor as having a LifeScienceIdentifier.

identifier - Variable in class org.biojava.bibliography.BibRef

It is an unambiguous reference to this citation "within the world".

IDENTIFIER - Static variable in interface org.biojavax.bio.BioEntry
 
IDENTIFIER - Static variable in interface org.biojavax.ontology.ComparableTerm
 
identifyFormat(String, String) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
identifyFormat performs a case-insensitive mapping
 of a pair of common sequence format name (such as 'embl',
 'genbank' or 'fasta') and alphabet name (such as 'dna', 'rna',
 'protein', 'aa') to an integer.

IDMaker - Interface in org.biojava.bio.seq.db

Interface for objects that define how to make an ID for a sequence.

IDMaker.ByName - Class in org.biojava.bio.seq.db
 
IDMaker.ByURN - Class in org.biojava.bio.seq.db
 
ids() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.DummySequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
 
ids() - Method in interface org.biojava.bio.seq.db.SequenceDB

Get an immutable set of all of the IDs in the database.

ids() - Method in class org.biojava.bio.seq.db.SubSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
 
ids() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
ids() - Method in interface org.biojavax.bio.db.BioEntryDB

Get an immutable set of all of the IDs in the database.

ids() - Method in class org.biojavax.bio.db.HashBioEntryDB
 
ids() - Method in class org.biojavax.bio.db.HashRichSequenceDB
 
ids() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
 
ids() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
 
ids(boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource

Get the complete set of sequence IDs provided by this DistDataSource.

ids(boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
 
ids(boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
IG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

IG indicates that the sequence format is IG.

ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
ignorableWhitespace(char[], int, int) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
ignorableWhitespace(char[], int, int) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
ignorableWhitespace(char[], int, int) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
ignorableWhitespace(char[], int, int) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
IgnoreCountsTrainer - Class in org.biojava.bio.dist

A distribution trainer that just ignores all counts.

IgnoreCountsTrainer() - Constructor for class org.biojava.bio.dist.IgnoreCountsTrainer

Constructor intended for sub-classes.

IgnoreRecordException - Exception in org.biojava.bio.program.gff

Ignore this record in the stream.

IgnoreRecordException() - Constructor for exception org.biojava.bio.program.gff.IgnoreRecordException
 
ile() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Isoleucine (I)

IllegalAlphabetException - Exception in org.biojava.bio.symbol


 The exception to indicate that an invalid alphabet has been used.

IllegalAlphabetException() - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException

Just make the exception.

IllegalAlphabetException(String) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException

Make the exception with a message.

IllegalAlphabetException(Throwable) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException
 
IllegalAlphabetException(Throwable, String) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException
 
IllegalIDException - Exception in org.biojava.bio.seq.db
 
IllegalIDException() - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
 
IllegalIDException(String) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
 
IllegalIDException(Throwable) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
 
IllegalIDException(Throwable, String) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
 
IllegalOrganismException - Exception in org.biojavax.ga.exception

Indicates an invalid organism

IllegalOrganismException() - Constructor for exception org.biojavax.ga.exception.IllegalOrganismException
 
IllegalOrganismException(String) - Constructor for exception org.biojavax.ga.exception.IllegalOrganismException
 
IllegalSymbolException - Exception in org.biojava.bio.symbol

The exception to indicate that a symbol is not valid within a context.

IllegalSymbolException(String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException

Make the exception with a message.

IllegalSymbolException(Throwable, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException
 
IllegalSymbolException(Throwable, Symbol, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException
 
IllegalSymbolException(Symbol, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException

Make the exception with a message and a symbol.

IllegalTransitionException - Exception in org.biojava.bio.dp

This exception indicates that there is no transition between two states.

IllegalTransitionException() - Constructor for exception org.biojava.bio.dp.IllegalTransitionException
 
IllegalTransitionException(State, State) - Constructor for exception org.biojava.bio.dp.IllegalTransitionException
 
IllegalTransitionException(State, State, String) - Constructor for exception org.biojava.bio.dp.IllegalTransitionException
 
Impl() - Constructor for class org.biojava.bio.AnnotationType.Impl

Create a new Impl with no constraints.

Impl() - Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl
 
Impl(int, int, int, int) - Constructor for class org.biojava.bio.EcNumber.Impl

Make a new EcNumber.Impl with the data provided.

Impl(String, String) - Constructor for class org.biojava.ontology.Ontology.Impl
 
Impl(String, Map) - Constructor for class org.biojava.directory.RegistryConfiguration.Impl
 
Impl(String, RAF, long, int) - Constructor for class org.biojava.bio.program.indexdb.Record.Impl

Creates a new Impl record.

Impl(CollectionConstraint) - Constructor for class org.biojava.bio.AnnotationType.Impl

Create a new Impl with a default collection constraint.

Impl(GFF3Record) - Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl
 
Impl(PropertyConstraint, Location) - Constructor for class org.biojava.bio.AnnotationType.Impl

Create a new Impl with a default property and cardinality constraint.

Impl(Ontology, String) - Constructor for class org.biojava.ontology.Term.Impl
 
Impl(Ontology, String, String) - Constructor for class org.biojava.ontology.Term.Impl
 
Impl(Ontology, String, String) - Constructor for class org.biojava.ontology.Variable.Impl
 
Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.ontology.Term.Impl
 
Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.ontology.Variable.Impl
 
Impl(Ontology, Ontology) - Constructor for class org.biojava.ontology.OntologyTerm.Impl
 
Impl(Ontology, Ontology, Object[]) - Constructor for class org.biojava.ontology.OntologyTerm.Impl
 
Impl(Ontology, Term, String) - Constructor for class org.biojava.ontology.RemoteTerm.Impl
 
Impl(Ontology, Term, String, Object[]) - Constructor for class org.biojava.ontology.RemoteTerm.Impl
 
Impl(Term, Term, Term) - Constructor for class org.biojava.ontology.Triple.Impl
 
Impl(Term, Term, Term, Object[]) - Constructor for class org.biojava.ontology.Triple.Impl
 
Impl(Term, Term, Term, String, String) - Constructor for class org.biojava.ontology.Triple.Impl
 
Impl(Term, Term, Term, String, String, Object[]) - Constructor for class org.biojava.ontology.Triple.Impl
 
importTaxon(Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory

Deprecated.
 
importTaxon(Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory

Deprecated.
Import a Taxon and all its children into the implementation
 provided by this factory.

importTaxon(Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory

Deprecated.
 
importTerm(Term, String) - Method in class org.biojava.ontology.IntegerOntology
 
importTerm(Term, String) - Method in class org.biojava.ontology.Ontology.Impl
 
importTerm(Term, String) - Method in interface org.biojava.ontology.Ontology

Create a view of a term from another ontology.

importTerm(Term, String) - Method in class org.biojavax.ontology.SimpleComparableOntology

Create a view of a term from another ontology.

in - Variable in class org.biojava.utils.io.CachingInputStream

The underlying input stream whose data we're caching

IN_RANGE - Static variable in interface org.biojavax.bio.seq.Position

A symbol representing a position that occupies a single base somewhere
 in a range, eg. 5.10 falls on some base between 5 and 10.

incCounts(int, int) - Method in class org.biojava.bio.symbol.SuffixTree
 
INCLUDES_PREFIX - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
increaseCount(AtomicSymbol, double) - Method in interface org.biojava.bio.dist.Count

Set the probability or odds that Symbol s is emitted by this state.

increaseCount(AtomicSymbol, double) - Method in class org.biojava.bio.dist.IndexedCount
 
indent() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
indent() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent

Add a level of indentation

Indent() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
 
INDENT - Static variable in class org.biojava.bio.seq.io.agave.AgaveWriter

use a two space indent

INDETERMINATE - Static variable in class org.biojava.utils.TriState
 
index - Variable in class org.biojava.ontology.obo.OboFileParser.SOPair
 
index(State) - Method in class org.biojava.bio.dp.WMAsMM
 
index(Symbol) - Static method in class org.biojava.bio.seq.DNATools

Return an integer index for a symbol - compatible with
 forIndex.

index(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools

Return an integer index for a symbol - compatible with

 forIndex.

index(Symbol) - Static method in class org.biojava.bio.seq.RNATools

Return an integer index for a symbol - compatible with forIndex.

Index - Interface in org.biojava.bio.seq.db

This defines an index entry for an individual sequence within a set of
 indexed files.

INDEX - Static variable in interface org.biojava.bio.symbol.AlphabetIndex


 Indicates that the index is changing, probably due to the underlying
 alphabet changing.

Index2Model - Class in org.biojava.bio.program.tagvalue
 
Index2Model() - Constructor for class org.biojava.bio.program.tagvalue.Index2Model
 
IndexedAnnotationDB - Class in org.biojava.bio.annodb

A database of Annotation instances backed by an indexed file set.

IndexedAnnotationDB(String, File, Index2Model, List, int, AnnotationType, IndexedAnnotationDB.ParserListenerFactory) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB

Create a new IndexedAnnotationDB.

IndexedAnnotationDB(BioStore) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB

Initialise the db from a store.

IndexedAnnotationDB.ParserListenerFactory - Interface in org.biojava.bio.annodb

A factory for retrieving parsers and listeners.

IndexedAnnotationDB.StaticMethodRPFactory - Class in org.biojava.bio.annodb

An implementation of ParserListenerFactory that uses a static method.

IndexedChangeHub - Class in org.biojava.utils

implements Changeable support with a ChangeHub that
 stores ChangeListener by key.

IndexedChangeHub() - Constructor for class org.biojava.utils.IndexedChangeHub
 
IndexedChangeHub.ListenerMemento - Class in org.biojava.utils
 
IndexedCount - Class in org.biojava.bio.dist

An encapsulation of a count over the Symbols within a FiniteAlphabet using
 an AlphabetIndex object.

IndexedCount(AlphabetIndex) - Constructor for class org.biojava.bio.dist.IndexedCount

Get a new InexedCount for an alphabet indexer.

IndexedCount(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.IndexedCount

Get a new IdexedCount for an alphabet using the default indexer.

IndexedSequenceDB - Class in org.biojava.bio.seq.db


 This class implements SequenceDB on top of a set of sequence files
 and sequence offsets within these files.

IndexedSequenceDB(IDMaker, IndexStore) - Constructor for class org.biojava.bio.seq.db.IndexedSequenceDB

Create an IndexedSequenceDB by specifying both the IDMaker and
 IndexStore used.

IndexedSequenceDB(IndexStore) - Constructor for class org.biojava.bio.seq.db.IndexedSequenceDB

Create an IndexedSequenceDB by specifying IndexStore used.

indexEmbl(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools

indexEmbl indexes DNA, RNA or protein EMBL format
 sequence files on ID as primary identifier and AC as secondary.

Indexer - Class in org.biojava.bio.program.tagvalue


 Listens to tag-value events and passes on indexing events to an IndexStore.

Indexer(File, IndexStore) - Constructor for class org.biojava.bio.program.tagvalue.Indexer

Build a new Indexer.

Indexer2 - Class in org.biojava.bio.program.tagvalue


 Listens to tag-value events and passes on indexing events to an IndexStore.

Indexer2(File, IndexStore, Index2Model) - Constructor for class org.biojava.bio.program.tagvalue.Indexer2

Build a new Indexer.

indexFasta(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools

indexFasta indexes DNA, RNA or protein Fasta
 format sequence files on primary identifier.

indexForSymbol(Symbol) - Method in interface org.biojava.bio.symbol.AlphabetIndex

Return the unique index for a symbol.

indexGenbank(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools

indexGenbank indexes DNA, RNA or protein Genbank
 format sequence files on LOCUS as primary identifier and
 ACCESSION as secondary.

IndexStore - Interface in org.biojava.bio.program.indexdb

IndexStore is an interface for indexing flatfiles
 according to the OBDA specification.

IndexStore - Interface in org.biojava.bio.seq.db

This defines the objects that IndexedSequenceDB uses to store all of the
 database state, such as name, format, sequence builder and the actual file
 offsets.

indexSwissprot(String, File, File[]) - Static method in class org.biojava.bio.program.indexdb.IndexTools

indexSwissprot indexes Swissprot format protein
 sequence files on ID as primary identifier.

IndexTools - Class in org.biojava.bio.program.indexdb

IndexTools contains static utility methods for
 creating flatfile indices according to the OBDA standard.

inFeature() - Method in class org.biojava.bio.seq.io.FeatureTableParser

Deprecated.
 
InfinitelyAmbiguousSymbolList - Class in org.biojavax.bio.seq

A symbol list that is Integer.MAX_VALUElong, never gives index out of
 bounds and always returns ambiguity symbols for everything.

InfinitelyAmbiguousSymbolList(FiniteAlphabet) - Constructor for class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

Creates a new instance of InfinitelyAmbiguousSymbolList

init() - Method in interface org.biojava.utils.xml.Initializable
 
INIT_PROP_LOG - Static variable in interface org.biojava.bibliography.BibRefSupport


 A property name ("log").

INIT_PROP_SUPPORT - Static variable in interface org.biojava.bibliography.BibRefSupport


 A property name ("bibrefsupport").

initialiseProfileHMM(int) - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
Initializable - Interface in org.biojava.utils.xml
 
initialize() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
initialize(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator

Initialize the cell at [0][0] to the recursion initial parameters.

initializeVariables(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver) - Method in class org.biojava.bio.symbol.FuzzyLocation

Refactored initialization code from the constructors.

initPopulation() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm

Assigns a fitness value to each organism within the population according to
 the currently set fitness function.

input - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
 
InputHandler - Interface in org.biojava.utils.process

Interface to a threadable input handler for
 an external process.

InputStreamProvider - Class in org.biojava.utils.io

A class that provides an InputStream from a File.

InputStreamProvider() - Constructor for class org.biojava.utils.io.InputStreamProvider
 
INSDSEQ_FORMAT - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat

The name of this format

INSDSEQ_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
INSDseqFormat - Class in org.biojavax.bio.seq.io

Format reader for INSDseq files.

INSDseqFormat() - Constructor for class org.biojavax.bio.seq.io.INSDseqFormat
 
INSDseqFormat.Terms - Class in org.biojavax.bio.seq.io

Implements some INSDseq-specific terms.

INSDSEQS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
instance() - Static method in class org.biojava.bio.symbol.AlphabetManager

Deprecated.
all AlphabetManager methods have become static


instance() - Static method in class org.biojava.directory.SystemRegistry

Get the singleton Registry instance representing the system-wide
 default registry.

INSTANCE - Static variable in class org.biojava.bio.seq.io.GenEmblFeatureComparator

Deprecated.
 
INSTANCE - Static variable in class org.biojava.bio.seq.io.GenEmblPropertyComparator

Deprecated.
 
INSTANCE - Static variable in class org.biojava.bio.symbol.DoubleAlphabet
 
INSTANCE - Static variable in class org.biojava.bio.symbol.IntegerAlphabet

The singleton instance of the IntegerAlphabet class.

INSTANCE - Static variable in class org.biojava.utils.xml.XMLBeans
 
instanceOf(Annotation) - Method in class org.biojava.bio.AnnotationType.Abstract
 
instanceOf(Annotation) - Method in interface org.biojava.bio.AnnotationType

Validate an Annotation against this AnnotationType.

instantiateBean(Element) - Method in class org.biojava.utils.xml.XMLBeans
 
instantiateBean(Element, ClassLoader, Map) - Method in class org.biojava.utils.xml.XMLBeans
 
instantiateDB(URL, HomologeneBuilder) - Static method in class org.biojava.bio.program.homologene.HomologeneTools

instantiate a HomologeneDB.

instantiateTemplate(Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils

This attempts to divine the 'best' template class for a feature and return
 a new instance readly for pupulating.

INTEGER - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

INTEGER indicates that a sequence contains integer
 alphabet symbols, such as used to describe sequence quality
 data.

IntegerAlphabet - Class in org.biojava.bio.symbol


 An efficient implementation of an Alphabet over the infinite set of integer
 values.

IntegerAlphabet.IntegerSymbol - Class in org.biojava.bio.symbol

A single int value.

IntegerAlphabet.SubIntegerAlphabet - Class in org.biojava.bio.symbol

A class to represent a finite contiguous subset of the infinite IntegerAlphabet

IntegerOntology - Class in org.biojava.ontology
 
IntegerOntology.IntTerm - Class in org.biojava.ontology
 
IntegerSymbol(int) - Constructor for class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
integerSymbolFromPhred(Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools

Retrives the IntegerSymbol component of the Phred BasisSymbol from the
 PHRED alphabet.

IntegerTokenization - Class in org.biojava.bio.seq.io
 
IntegerTokenization() - Constructor for class org.biojava.bio.seq.io.IntegerTokenization
 
IntElementHandlerBase - Class in org.biojava.utils.stax

StAX handler for any element which just contains a string representation of
 an integer.

IntElementHandlerBase() - Constructor for class org.biojava.utils.stax.IntElementHandlerBase
 
Interaction() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
 
INTERACTION - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser

A name for a comment type.

internalClassify(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
intersect(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils

Operator: Intersect FeatureHolder1 with FeatureHolder2

intersection(AnnotationType, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools

Calculate an AnnotationType that matches all Annotation instances matched
 by both types.

intersection(CollectionConstraint, CollectionConstraint) - Static method in class org.biojava.bio.AnnotationTools

Return the CollectionConstraint which accept only collections accepted by
 both of those specified.

intersection(PropertyConstraint, PropertyConstraint) - Static method in class org.biojava.bio.AnnotationTools

Calculate the intersection of two PropertyConstraint instances.

intersection(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
 
intersection(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
intersection(Location) - Method in class org.biojava.bio.symbol.CircularLocation
 
intersection(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
intersection(Location) - Method in interface org.biojava.bio.symbol.Location

Returns a Location that contains all points common to both ranges.

intersection(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Returns a Location that contains all points common to both ranges.

intersection(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Returns a Location that contains all points common to both ranges.

intersection(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Returns a Location that contains all points common to both ranges.

intersection(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools

Return the intersection of two locations.

INTERSECTION_OF - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
IntTerm(int) - Constructor for class org.biojava.ontology.IntegerOntology.IntTerm
 
IntTerm(int, Object[]) - Constructor for class org.biojava.ontology.IntegerOntology.IntTerm
 
intValue() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
intValue() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
intValue() - Method in class org.biojavax.bio.seq.RichLocation.Strand

Returns the numeric value of this strand.

iNumberOfColours - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler

The number of unique colours.

invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidEnd(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler

The `end' field of the GFF entry was not a valid value.

invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidEnd(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidFrame(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidFrame(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler

The `frame' field of the GFF entry was not a valid value.

invalidFrame(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidFrame(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidScore(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidScore(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler

The `score' field of the GFF entry was not a valid value.

invalidScore(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidScore(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidStart(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidStart(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler

The `start' field of the GFF entry was not a valid value.

invalidStart(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidStart(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidStrand(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler

The `strand' field of the GFF entry was not a valid value.

invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFWriter
 
InvalidTermException - Exception in org.biojava.ontology

Thrown to indicate that an ontology term is not acceptable or
 appropriate in a given context

InvalidTermException() - Constructor for exception org.biojava.ontology.InvalidTermException
 
InvalidTermException(String) - Constructor for exception org.biojava.ontology.InvalidTermException
 
InvalidTermException(String, Throwable) - Constructor for exception org.biojava.ontology.InvalidTermException
 
InvalidTermException(Throwable) - Constructor for exception org.biojava.ontology.InvalidTermException
 
INVERT_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable

Translation table name for the invertebrate mitochondrial
 genetic code.

IOExceptionFound - Variable in class org.biojava.bio.seq.db.GenbankSequenceDB
 
IS_A - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
IS_A - Static variable in class org.biojava.ontology.OntoTools
 
IS_OBSOLETE - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
isbn - Variable in class org.biojava.bibliography.BiblioBook

ISBN number.

isBoundaryEnd(Object) - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
 
isBoundaryStart(Object) - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
 
isCaseSensitive() - Method in interface org.biojava.utils.candy.CandyVocabulary

It returns true if the vocabulary entries should
  be considered as case-sensitive.

isColoured(String, String) - Method in interface org.biojava.bio.program.blast2html.ColourCommand

Returns true if the alignment pair should be coloured
 else false.

isComponentResolvable() - Method in interface org.biojava.bio.seq.ComponentFeature

Determine if the sequence references by this ComponentFeature
 is available in this context.

isConsortium() - Method in interface org.biojavax.DocRefAuthor

Is this author actually a consortium?

isConsortium() - Method in class org.biojavax.SimpleDocRefAuthor

Is this author actually a consortium?

isContiguous() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
isContiguous() - Method in class org.biojava.bio.symbol.AbstractRangeLocation
 
isContiguous() - Method in class org.biojava.bio.symbol.CircularLocation

Delegates to the wrapped location.

isContiguous() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
isContiguous() - Method in interface org.biojava.bio.symbol.Location

Determine if a Location is contiguous.

isContiguous() - Method in class org.biojavax.bio.seq.CompoundRichLocation

Determine if a Location is contiguous.

isContiguous() - Method in class org.biojavax.bio.seq.EmptyRichLocation

Determine if a Location is contiguous.

isContiguous() - Method in class org.biojavax.bio.seq.SimpleRichLocation

Determine if a Location is contiguous.

isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
 
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
 
isDisjoint(FeatureFilter) - Method in interface org.biojava.bio.seq.OptimizableFilter

Returns true if this filter is disjoint from filt - that is, there is no
 Feature that is accepted by both filters.

isEditor() - Method in interface org.biojavax.DocRefAuthor

Is this author actually an editor?

isEditor() - Method in class org.biojavax.SimpleDocRefAuthor

Is this author actually an editor?

isEmpty() - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
 
isEmpty() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
 
isEmpty() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
 
isEmpty() - Method in class org.biojavax.ga.util.WeightedSet
 
isEndoProtease() - Method in class org.biojava.bio.proteomics.Protease
 
isEscapeStarter(char) - Static method in class org.biojava.ontology.obo.OboFileParser
 
isHaploid() - Method in class org.biojavax.ga.impl.AbstractOrganism
 
isHaploid() - Method in class org.biojavax.ga.impl.SimpleOrganism

Simple Organisms are Halpoid

isHaploid() - Method in interface org.biojavax.ga.Organism

Is the organism Haploid?

isMasked(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector

Default Behaivour is that if the whole token is lower case it is
 masked.

isMasked(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
 
isMasked(BasisSymbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet

Determines if a Symbol is masked.

isMatchingType(ChangeType) - Method in class org.biojava.utils.ChangeType

Return true iff ct is equal to this type
 or any of it's supertypes (including ChangeType.UNKNOWN).

isMaxFuzzy() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
isMinFuzzy() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
isMultiSource(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools

Returns false if all the locations in the set are from the same
 strand of the same sequence.

isMyChangeEvent(ChangeEvent, IndexedChangeHub.ListenerMemento) - Method in class org.biojava.utils.IndexedChangeHub
 
isNewTag() - Method in class org.biojava.bio.program.tagvalue.TagValue
 
IsoelectricPointCalc - Class in org.biojava.bio.proteomics

Class that computes isoelectric point for denaturated proteins.

IsoelectricPointCalc() - Constructor for class org.biojava.bio.proteomics.IsoelectricPointCalc
 
IsoelectricPointCalc.ChargeCalculator - Class in org.biojava.bio.proteomics
 
Isoform() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform

Creates a new instance.

isOppositeStrand() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
isOrganismsDiffer() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction

Getter for property organismsDiffer.

isPalindromic() - Method in class org.biojava.bio.molbio.RestrictionEnzyme

isPalindromic returns true if the recognition site
 is palindromic.

isParseable(String) - Static method in class org.biojavax.bio.seq.io.UniProtCommentParser

Returns true if the comment may be parseable (starts with -!

isParseable(Comment) - Static method in class org.biojavax.bio.seq.io.UniProtCommentParser

Returns true if the comment may be parseable (starts with -!

isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
 
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
 
isProperSubset(FeatureFilter) - Method in interface org.biojava.bio.seq.OptimizableFilter

Returns true if this filter is a proper subset of sup - that is, for every
 feature that matches this, it also matches sup.

isPrototype() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
 
isQuote(char) - Static method in class org.biojava.ontology.obo.OboFileParser
 
isReady() - Method in interface org.biojava.bibliography.BibRefQuery

It checks if the repository is available.

isReady() - Method in interface org.biojava.bibliography.BibRefSupport

It checks if a utility object is available.

isReady() - Method in interface org.biojava.utils.candy.CandyFinder

It checks if a vocabulary finder object is available.

isReady(String, long) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService


 This method is used only for the executeBlastSearch method to check for
 completion of request using the NCBI specified RTOE variable

isReady(String, long) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService

Simple method to check if the specified request has been completed by the service used.

isRemote() - Method in class org.biojava.bio.seq.RemoteFeature.Region

Return whether this Region is remote or local.

isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
 
isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
 
isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
 
isRequired(String) - Method in interface org.biojava.bio.symbol.CodonPrefFilter

indicates if the current CodonPref is to be accepted

isSane() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
isSane() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
isShowAccession() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
isShowDescription() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
isShowIdentifier() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
isShowName() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
isShowNamespace() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
isShowVersion() - Method in class org.biojavax.bio.seq.io.FastaHeader
 
issn - Variable in class org.biojava.bibliography.BiblioJournal


 A standard number for journals.

isStrict() - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter

Determine if this writer is in strict mode.

isStrict() - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter

Determine if this writer is in strict mode.

isSubTypeOf(FeatureTypes.Type, FeatureTypes.Type) - Static method in class org.biojava.bio.seq.FeatureTypes

Work out if one type is a sub-type of another.

issue - Variable in class org.biojava.bibliography.BiblioJournalArticle

The issue of the journal.

issueSupplement - Variable in class org.biojava.bibliography.BiblioJournalArticle

Suplement.

isTaxonHidden() - Method in interface org.biojavax.bio.taxa.NCBITaxon

used in getNameHierarchy() to determine whether this taxonomy level is displayed

isTaxonHidden() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Returns the taxonomy hierarchy of this taxon entry in the form:
   most specific; less specific; ...; least specific.

isTerminal() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode

Determine is this node is terminal (has no children).

isTerminal() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode

Determine is this node is terminal (has no children).

isTrainingComplete(TrainingAlgorithm) - Method in interface org.biojava.bio.dp.StoppingCriteria

Decide if the training has completed.

isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
 
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
isUnchanging(ChangeType) - Method in class org.biojava.utils.AbstractChangeable
 
isUnchanging(ChangeType) - Method in interface org.biojava.utils.Changeable


 A particular ChangeType can never be raised by this Changeable.

isUnchanging(ChangeType) - Method in class org.biojava.utils.ChangeSupport
 
isUnchanging(ChangeType) - Method in class org.biojava.utils.Unchangeable
 
isUnchanging(ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList


 A particular ChangeType can never be raised by this Changeable.

isUnchanging(ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
isUnchanging(ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
itemAlphas() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
itemAlphas() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
items() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
items() - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
items() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
items() - Method in interface org.biojava.stats.svm.SVMTarget
 
itemTargets() - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
itemTargets() - Method in interface org.biojava.stats.svm.SVMTarget
 
ItemValue - Interface in org.biojava.stats.svm

A simple Object-double tuple.

iterator() - Method in interface org.biojava.bio.annodb.AnnotationDB

Loop over each Annotation in this db.

iterator() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
 
iterator() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
 
iterator() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
 
iterator() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
 
iterator() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
 
iterator() - Method in class org.biojava.bio.dp.SimpleStatePath
 
iterator() - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
 
iterator() - Method in interface org.biojava.bio.program.homologene.OrthologueSet

Return an iterator to the contents of the set.

iterator() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
 
iterator() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet

returns an iterator to the members of this set

iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
 
iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
 
iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
iterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
iterator() - Method in class org.biojava.bio.seq.impl.DummySequence
 
iterator() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
iterator() - Method in class org.biojava.bio.seq.impl.SubSequence
 
iterator() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
iterator() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
iterator() - Method in class org.biojava.bio.seq.SimpleAssembly
 
iterator() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
iterator() - Method in interface org.biojava.bio.symbol.FiniteAlphabet

Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.

iterator() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
iterator() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
iterator() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
iterator() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
iterator() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
 
iterator() - Method in interface org.biojava.bio.symbol.SymbolList

An Iterator over all Symbols in this SymbolList.

iterator() - Method in class org.biojava.utils.FileAsList
 
iterator() - Method in class org.biojava.utils.MergingSet
 
iterator() - Method in class org.biojava.utils.SmallSet
 
iterator() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

An Iterator over all Symbols in this SymbolList.

iterator() - Method in class org.biojavax.bio.seq.ThinRichSequence

An Iterator over all Symbols in this SymbolList.

iterator() - Method in class org.biojavax.ga.util.WeightedSet

Returns an unmodifiable iterator over the keys of the set.

iterator(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler

An Iterator over all Symbols in this SymbolList.

iterator(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler

An Iterator over all Symbols in this SymbolList.





J

JDBCConnectionPool - Class in org.biojava.utils

Really simple connection pool for JDBC databases.

JDBCConnectionPool(String) - Constructor for class org.biojava.utils.JDBCConnectionPool
 
JDBCConnectionPool(String, String, String) - Constructor for class org.biojava.utils.JDBCConnectionPool
 
JDBCPooledDataSource - Class in org.biojava.utils

Returns a DataSource that implements connection pooling

 Uses Jakarta Commons DBCP and Pool packages.

JDBCPooledDataSource() - Constructor for class org.biojava.utils.JDBCPooledDataSource
 
joinCommands(Object[]) - Static method in class org.biojava.utils.process.ExternalProcess

Joins a command list to a single command string.

jointDistOverAlignment(Alignment, boolean, double, int[]) - Static method in class org.biojava.bio.dist.DistributionTools

Creates a joint distribution.

JOURNAL_ABBREV - Static variable in interface org.biojava.bibliography.BibRefSupport

A vocabulary name.

JOURNAL_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
JOURNAL_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
JOURNAL_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
JOURNAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
JOURNAL_TITLES - Static variable in interface org.biojava.bibliography.BibRefSupport

A vocabulary name.

jState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM

Gets the J loop state

jumpTo(UkkonenSuffixTree.SuffixNode, CharSequence, int, int) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree

Just like walkTo, but faster when used during tree construction, as it
 assumes that a mismatch can only occurs with the last character of the
 target string.





K

k() - Static method in class org.biojava.bio.seq.DNATools
 
k() - Static method in class org.biojava.bio.seq.NucleotideTools
 
k() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Lysine

kernel - Static variable in class org.biojava.stats.svm.SparseVector
 
KEY_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
KEY_QUERY_ID - Static variable in interface org.biojava.bio.search.BlastLikeSearchFilter
 
KeyedWeakReference - Class in org.biojava.utils.cache

Subclass of WeakReference which includes and extra field (the key)
 which can be used to help cleanup once this reference has been
 enqueued.

KeyedWeakReference(Object, Object) - Constructor for class org.biojava.utils.cache.KeyedWeakReference
 
KeyedWeakReference(Object, Object, ReferenceQueue) - Constructor for class org.biojava.utils.cache.KeyedWeakReference
 
keys() - Method in class org.biojava.bio.AbstractAnnotation
 
keys() - Method in interface org.biojava.bio.Annotation

Get a set of key objects.

keys() - Method in class org.biojava.bio.MergeAnnotation
 
keys() - Method in class org.biojava.bio.OverlayAnnotation

Return a Set containing all key objects
 visible in this annotation.

keys() - Method in class org.biojavax.EmptyRichAnnotation

Get a set of key objects.

keys() - Method in class org.biojavax.SimpleRichAnnotation

Get a set of key objects.

KEYS - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory

KEYS is the key used to identify the secondary
 namespaces in the OBDA config.dat files.

keySet() - Method in class org.biojava.utils.OverlayMap
 
keySet() - Method in class org.biojava.utils.SmallMap
 
KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
keywords - Variable in class org.biojava.bibliography.BiblioSubject

The keywords are usually (but not limited to) one word long.

KEYWORDS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
KEYWORDS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
KEYWORDS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
KLDistance(Distribution, Distribution, double) - Static method in class org.biojava.bio.dist.DistributionTools

A method to calculate the Kullback-Liebler Distance (relative entropy).

KnuthMorrisPrattSearch - Class in org.biojava.bio.search

An object to find exact subsequences within a sequence.

KnuthMorrisPrattSearch(SymbolList) - Constructor for class org.biojava.bio.search.KnuthMorrisPrattSearch

Constructs a KMP matcher to find exact occurances of
 pattern in text using the
 Knuth-Morris-Pratt algorithm.





L

l() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Leucine

L_ESCULENTUM - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
LabelledVector(SparseVector, double) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
LabelledVector(SparseVector, double, String) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
language - Variable in class org.biojava.bibliography.BiblioDescription


 It defines a language used for BiblioDescription.theAbstract and BiblioDescription.tableOfContents.

language - Variable in class org.biojava.bibliography.BibRef


 It defines a language of the intellectual contents of the cited resource.

LANGUAGES - Static variable in interface org.biojava.bibliography.BibRefSupport

A vocabulary name.

LargeBuffer - Class in org.biojava.utils.io

Wrapper arround MappedByteBuffers to allow long-indexed access to files
 larger than 2 gigs.

LargeBuffer(FileChannel, FileChannel.MapMode, long, long) - Constructor for class org.biojava.utils.io.LargeBuffer
 
lastCol() - Method in interface org.biojava.bio.dp.onehead.DPCursor

The previous column.

lastCol() - Method in class org.biojava.bio.dp.onehead.SmallCursor
 
lastModifiedDate - Variable in class org.biojava.bibliography.BiblioEntryStatus


 It defines when the citation record was added or last modified.

lastNonGap() - Method in interface org.biojava.bio.symbol.GappedSymbolList

Return the index of the last Symbol that is not a Gap character.

lastNonGap() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
lastPage - Variable in class org.biojava.bibliography.BiblioArticle

Last page of the article.

lastRes() - Method in interface org.biojava.bio.dp.onehead.DPCursor

The previous symbol.

LazyFeatureHolder - Class in org.biojava.bio.seq

Wrapper implementation of FeatureHolder which calls a method
 to create a contained FeatureHolder on demand.

LazyFeatureHolder() - Constructor for class org.biojava.bio.seq.LazyFeatureHolder

Construct a LazyFeatureHolder with the schema of its contained featureholder

LazyFeatureHolder(FeatureFilter) - Constructor for class org.biojava.bio.seq.LazyFeatureHolder

Construct a LazyFeatureHolder with the specified schema

LazyFilteredAnnotationDB - Class in org.biojava.bio.annodb

An implementation of AnnotationDB that lazily applies a filter.

LazyFilteredAnnotationDB(String, AnnotationDB, AnnotationType) - Constructor for class org.biojava.bio.annodb.LazyFilteredAnnotationDB

Create a new DB by wrapping another with a schema.

LazyFilterFeatureHolder - Class in org.biojava.bio.seq.impl

FeatureHolder which lazily applies a specified filter to another FeatureHolder.

LazyFilterFeatureHolder(FeatureHolder, FeatureFilter) - Constructor for class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
LazySearchedAnnotationDB - Class in org.biojava.bio.annodb

An implementation of AnnotationDB that does a JIT search on another set.

LazySearchedAnnotationDB(String, AnnotationDB, AnnotationType) - Constructor for class org.biojava.bio.annodb.LazySearchedAnnotationDB

Create a new DB from an old one by applying a schema.

leaf - Static variable in interface org.biojava.bio.seq.FeatureFilter

A filter which accepts features with no children

leaf() - Static method in class org.biojava.bio.seq.FilterUtils

Return a filter which matches features with zero children.

leftIndent(String, int) - Static method in class org.biojavax.utils.StringTools

Takes an input string and appends spaces to the left.

leftPad(String, char, int) - Static method in class org.biojavax.utils.StringTools

Pads a string to be a certain width by prepending given symbols.

leftPad(String, int) - Static method in class org.biojavax.utils.StringTools

Pads a string to be a certain width by prepending spaces.

LEFTVALUE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
length - Variable in class org.biojava.bio.symbol.Edit
 
length() - Method in class org.biojava.bio.alignment.SimpleAlignment
 
length() - Method in interface org.biojava.bio.dp.onehead.DPCursor


 The length of the sequence.

length() - Method in class org.biojava.bio.dp.onehead.SmallCursor
 
length() - Method in class org.biojava.bio.dp.SimpleStatePath
 
length() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
length() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
length() - Method in class org.biojava.bio.seq.impl.DummySequence
 
length() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
length() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
length() - Method in class org.biojava.bio.seq.impl.SubSequence
 
length() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
length() - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
 
length() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
length() - Method in class org.biojava.bio.seq.SimpleAssembly
 
length() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
 
length() - Method in class org.biojava.bio.symbol.DummySymbolList
 
length() - Method in class org.biojava.bio.symbol.PackedSymbolList
 
length() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
length() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
length() - Method in class org.biojava.bio.symbol.SimpleSymbolList

Get the length of this SymbolList.

length() - Method in interface org.biojava.bio.symbol.SymbolList

The number of symbols in this SymbolList.

length() - Method in class org.biojava.utils.io.RandomAccessReader

length returns the length of the underlying
 RandomAccessFile.

length() - Method in class org.biojava.utils.RepeatedCharSequence
 
length() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

The number of symbols in this SymbolList.

length() - Method in class org.biojavax.bio.seq.SimpleRichSequence

The number of symbols in this SymbolList.

length() - Method in class org.biojavax.bio.seq.ThinRichSequence

The number of symbols in this SymbolList.

LENGTH_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
LessThan(double) - Constructor for class org.biojava.bio.search.FilterTest.LessThan
 
leu() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Leucine (L)

LIBRARY_ANNOTATION - Static variable in class org.biojava.bio.program.unigene.UnigeneTools


 Annotation schema for all Unigene libraries.

LifeScienceIdentifier - Class in org.biojava.utils.lsid

Life Science Identifier (LSID).

LifeScienceIdentifierParseException - Exception in org.biojava.utils.lsid

Exception thrown in the event of an error in
 parsing a LSID-formatted string.

LifeScienceIdentifierParseException() - Constructor for exception org.biojava.utils.lsid.LifeScienceIdentifierParseException

Construct a new parse exception with no message.

LifeScienceIdentifierParseException(String) - Constructor for exception org.biojava.utils.lsid.LifeScienceIdentifierParseException

Construct a new parse exception with the
 specified error message.

Ligand - Class in org.biojava.bio.program.formats
 
Ligand.Compound - Class in org.biojava.bio.program.formats
 
Ligand.Enzyme - Class in org.biojava.bio.program.formats
 
Ligand.Reaction - Class in org.biojava.bio.program.formats
 
LightPairDPCursor - Class in org.biojava.bio.dp.twohead

A LIGHT implementation of PairDPCursor.

LightPairDPCursor(SymbolList, SymbolList, int, int, int, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.LightPairDPCursor

Constructor for the LightPairDPCursor object

line - Variable in class org.biojava.ontology.obo.OboFileParser
 
LINEAGE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LINEAGE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LinearKernel - Class in org.biojava.stats.svm

Deprecated.
Just use SparseVector.kernel instead...


LinearKernel() - Constructor for class org.biojava.stats.svm.LinearKernel

Deprecated.
 
lineIterator() - Method in class org.biojava.bio.program.gff.GFFEntrySet

Loop over all lines in the set.

linenum - Variable in class org.biojava.ontology.obo.OboFileParser
 
LineSplitParser - Class in org.biojava.bio.program.tagvalue


 A parser that splits a line into tag/value at a given column number.

LineSplitParser() - Constructor for class org.biojava.bio.program.tagvalue.LineSplitParser
 
LineSplitParser(LineSplitParser) - Constructor for class org.biojava.bio.program.tagvalue.LineSplitParser
 
lineWidth - Variable in class org.biojava.bio.seq.io.FastaFormat

Deprecated.
The line width for output.

list(String) - Method in class org.biojava.naming.ObdaContext
 
list(Name) - Method in class org.biojava.naming.ObdaContext
 
listBindings(String) - Method in class org.biojava.naming.ObdaContext
 
listBindings(Name) - Method in class org.biojava.naming.ObdaContext
 
listener - Variable in class org.biojava.utils.IndexedChangeHub.ListenerMemento
 
ListenerMemento(ChangeType, Reference) - Constructor for class org.biojava.utils.IndexedChangeHub.ListenerMemento
 
ListSumKernel - Class in org.biojava.stats.svm

This kernel computes the sum of the dot products between items of two lists
 at corresponding indexes.

ListSumKernel() - Constructor for class org.biojava.stats.svm.ListSumKernel
 
ListTools - Class in org.biojava.utils
 
ListTools() - Constructor for class org.biojava.utils.ListTools
 
ListTools.Doublet - Class in org.biojava.utils
 
ListTools.Mapper - Interface in org.biojava.utils

Maps one object to another.

ListTools.SeriesList - Class in org.biojava.utils

A list that represents a series of values.

ListTools.Triplet - Class in org.biojava.utils
 
load(Class, String) - Method in class org.biojava.utils.TypedProperties

Reads a property list (key and element pairs) from the given
 file which is interpreted as a resource of the given class.

load(String) - Method in class org.biojava.utils.TypedProperties

Reads a property list (key and element pairs) from the file with the given file name.

loadAlphabets(InputSource) - Static method in class org.biojava.bio.symbol.AlphabetManager

Load additional Alphabets, defined in XML format, into the AlphabetManager's registry.

loadEnzymeFile(InputStream, boolean) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager

loadEnzymeFile loads a new REBASE file (or any file using
 REBASE format #31).

loadUnigene(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
 
loadUnigene(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
 
loadUnigene(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
 
loadUnigene(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools

Load a UnigeneDB instance referred to by a URL.

LOC_ELEMENT_ACC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOC_ELEMENT_COMPL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOC_ELEMENT_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOC_ELEMENT_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOC_FUZZY_END_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
LOC_FUZZY_START_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
location - Variable in class org.biojava.bio.seq.Feature.Template
 
Location - Interface in org.biojava.bio.symbol

A set of integers, often used to represent positions on biological sequences.

LOCATION - Static variable in interface org.biojava.bio.seq.Feature

The location of this feature is being altered.

LOCATION - Static variable in interface org.biojavax.bio.seq.RichFeature
 
LOCATION - Static variable in interface org.biojavax.RankedDocRef
 
LOCATION_BEGIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_COMPL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOCATION_ELEMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOCATION_END_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_POSITION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_SEQ_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
LOCATION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LocationHandlerBase - Class in org.biojava.bio.program.xff

Handler to the XFF location type.

LocationHandlerBase() - Constructor for class org.biojava.bio.program.xff.LocationHandlerBase
 
locationToGapped(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList

Translate a Location onto the gapped view, splitting blocks if necessary

LocationTools - Class in org.biojava.bio.symbol

Tools class containing a number of operators for working with Location objects.

LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
lock() - Method in class org.biojava.utils.automata.PatternBlitz
 
lockModel() - Method in class org.biojava.bio.dp.DP
 
LOCUS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
LOCUSID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
LOG_TO_OUT - Static variable in interface org.biojava.utils.ChangeListener

Convenience implementation that echoes all events to out.

log2(double) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
 
log2(double) - Static method in class org.biojava.bio.program.hmmer.ProfileEmissionState
 
LoggingListener(PrintStream) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener

Create a LoggingListener that will log all events to 'out'.

LoggingListener(PrintStream, String) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener

Create a LoggingListener that will log all events to 'out' with a prefix.

logProb(Symbol) - Method in class org.biojava.bio.program.hmmer.ProfileEmissionState
 
LongElementHandlerBase - Class in org.biojava.utils.stax

StAX handler for any element which just contains a string representation of
 a long.

LongElementHandlerBase() - Constructor for class org.biojava.utils.stax.LongElementHandlerBase
 
lookingAt() - Method in class org.biojava.utils.regex.Matcher

Attempts to match the input SymbolList, starting at the beginning, against the pattern.

lookup(String) - Method in class org.biojava.naming.ObdaContext
 
lookup(Name) - Method in class org.biojava.naming.ObdaContext
 
lookupLink(String) - Method in class org.biojava.naming.ObdaContext
 
lookupLink(Name) - Method in class org.biojava.naming.ObdaContext
 
lp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
lp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
lp_ipi - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
lp_uniprot - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
lpPre87 - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
LSID_EMBL_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

LSID_EMBL_AA sequence format LSID for EMBL AA.

LSID_EMBL_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

LSID_EMBL_DNA sequence format LSID for EMBL DNA.

LSID_EMBL_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

LSID_EMBL_RNA sequence format LSID for EMBL RNA.

LSID_FASTA_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

LSID_FASTA_AA sequence format LSID for Fasta AA.

LSID_FASTA_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

LSID_FASTA_DNA sequence format LSID for Fasta DNA.

LSID_FASTA_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

LSID_FASTA_RNA sequence format LSID for Fasta RNA.

LSID_GENBANK_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

LSID_GENBANK_AA sequence format LSID for Genbank
 AA.

LSID_GENBANK_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

LSID_GENBANK_DNA sequence format LSID for Genbank
 DNA.

LSID_GENBANK_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

LSID_GENBANK_RNA sequence format LSID for Genbank
 RNA.

LSID_SWISSPROT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

LSID_SWISSPROT sequence format LSID for Swissprot.

lys() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Lysine (K)

LYS_C - Static variable in class org.biojava.bio.proteomics.Protease
 
LYS_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager
 




M

m() - Static method in class org.biojava.bio.seq.DNATools
 
m() - Static method in class org.biojava.bio.seq.NucleotideTools
 
m() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Methionine

M_MUSCULUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
M_TRUNCULATA - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
MAGICAL_STATE - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
 
magicalState() - Method in interface org.biojava.bio.dp.MarkovModel

The MagicalState for this model.

magicalState() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
magicalState() - Method in class org.biojava.bio.dp.WMAsMM
 
MagicalState - Class in org.biojava.bio.dp

Start/end state for HMMs.

main(String[]) - Static method in class org.biojava.bio.search.KnuthMorrisPrattSearch

Demo and Test method

main(String[]) - Static method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation

Test this class

main(String[]) - Static method in class org.biojava.bio.seq.io.MSFAlignmentFormat

used to quick test the code

main(String[]) - Static method in class org.biojava.stats.svm.tools.ClassifierExample

Entry point for the application.

main(String[]) - Static method in class org.biojava.stats.svm.tools.Classify
 
main(String[]) - Static method in class org.biojava.stats.svm.tools.Train
 
main(String[]) - Static method in class org.biojava.stats.svm.tools.TrainRegression
 
main(String[]) - Static method in class org.biojava.utils.ExecRunner

This is for unit testing of the class.

main(String[]) - Static method in class org.biojava.utils.io.UncompressInputStream
 
main(String[]) - Static method in class org.biojava.utils.JDBCPooledDataSource
 
main(String[]) - Static method in class org.biojava.utils.process.ExternalProcess

Runs an external program from the command line.

main(String[]) - Static method in class org.biojava.utils.xml.AppBeanRunner
 
make(DP) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker
 
make(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
 
make(DP) - Method in class org.biojava.bio.dp.twohead.DPInterpreter.Maker
 
make(SymbolReader) - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory

Method to create a Sequence with a SymbolReader.

makeAnnotation(Map) - Static method in class org.biojava.bio.program.ssbind.AnnotationFactory

makeAnnotation creates the annotation.

makeBatchRequest(URL, Set) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB

Create the Http Post Request to fetch (in batch mode) a list of sequence
 with Genbank.

makeBatchRequest(URL, Set) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

Create the Http Post Request to fetch (in batch mode) a list of sequence
 with Genbank.

makeBatchRequest(URL, Set) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB

Create the Http Post Request to fetch (in batch mode) a list of sequence
 with Genbank.

makeCircularLocation(int, int, int) - Static method in class org.biojava.bio.symbol.LocationTools

A simple method to generate a RangeLocation wrapped
 in a CircularLocation.

makeConfigFile(File) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory

makeConfigFile returns a file which represents an
 OBDA "config.dat" in the specified index directory.

makeEmptyFeature() - Static method in class org.biojavax.bio.seq.RichFeature.Tools

A way to make a dummy feature

makeFactory(FiniteAlphabet) - Static method in class org.biojava.utils.regex.PatternFactory

Returns a factory for Patterns in the specified Alphabet.

makeHandler(String, String) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory
 
makeHandler(String, String) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory
 
makeHandler(String, String, XMLFilterHandler) - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandlerFactory
 
makeLocation(int, int) - Static method in class org.biojava.bio.symbol.LocationTools

Return a contiguous Location from min to max.

makeName(String, MarkovModel) - Static method in class org.biojava.bio.dp.twohead.DPCompiler
 
makeNewInsertState(String, Annotation, int[], Distribution) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
 
makeNewMatchState(String, Annotation, int[], Distribution) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
 
makePrimaryKeyFile(File, String) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory

makePrimaryKeyFile returns a file which represents
 an OBDA "key_<primary namespace>.key" primary key file on the
 specified index directory.

makeProjectionSet(FeatureHolder) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder

Called internally to construct a lightweight projected view of a set of
 features

Maker() - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter.Maker
 
makeReference(Object) - Method in interface org.biojava.utils.cache.Cache

Construct a temporary reference to an object.

makeReference(Object) - Method in class org.biojava.utils.cache.FixedSizeCache
 
makeReference(Object) - Method in class org.biojava.utils.cache.SoftReferenceCache
 
makeRichSequence() - Method in interface org.biojavax.bio.seq.io.RichSequenceBuilder

Build a RichSequence.

makeRichSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Build a RichSequence.

makeSearchResult() - Method in interface org.biojava.bio.search.SearchBuilder

The makeSearchResult method returns a
 SeqSimilaritySearchResult instance created from
 accumulated data.

makeSecondaryFile(File, String) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory

makeSecondaryFile returns a file which represents
 an OBDA "id_<secondary namespace>.index" secondary key file on
 the specified.

makeSequence() - Method in interface org.biojava.bio.seq.io.SequenceBuilder

Return the Sequence object which has been constructed
 by this builder.

makeSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
makeSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
makeSequence() - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
 
makeSequence() - Method in class org.biojava.bio.seq.io.SimpleSequenceBuilder
 
makeSequence() - Method in class org.biojava.bio.seq.io.SmartSequenceBuilder
 
makeSequence() - Method in interface org.biojavax.bio.seq.io.RichSequenceBuilder

Return the Sequence object which has been constructed
 by this builder.

makeSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Return the Sequence object which has been constructed
 by this builder.

makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.EmblProcessor.Factory

Deprecated.
 
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory

Deprecated.
 
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.GenbankProcessor.Factory

Deprecated.
 
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.OrganismParser.Factory

Deprecated.
 
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory

Deprecated.
 
makeSequenceBuilder() - Method in interface org.biojava.bio.seq.io.SequenceBuilderFactory
 
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.SwissprotProcessor.Factory

Deprecated.
 
makeSequenceBuilder() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
makeSequenceBuilder(String) - Method in class org.biojava.bio.seq.io.GenbankProcessor.Factory

Deprecated.
 
makeSequenceBuilder(String) - Method in class org.biojava.bio.seq.io.SwissprotProcessor.Factory

Deprecated.
 
makeSymbolList() - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory

Converts accumulated Symbols to a SymbolList

makeSymbolList(Symbol[], int, Alphabet) - Method in class org.biojava.bio.symbol.PackedSymbolListFactory

Makes a packed SymbolList out of a list of Symbols.

makeSymbolList(Symbol[], int, Alphabet) - Method in class org.biojava.bio.symbol.SimpleSymbolListFactory

Create a factory for SimpleSymbolLists.

makeSymbolList(Symbol[], int, Alphabet) - Method in interface org.biojava.bio.symbol.SymbolListFactory

makes a SymbolList containing size Symbols from a Symbol array.

makeTemplate() - Method in interface org.biojava.bio.seq.Feature

Create a new Template that could be used to generate a feature identical
 to this one.

makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
makeTemplate() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
makeTemplate() - Method in class org.biojavax.bio.seq.SimpleRichFeature

Create a new Template that could be used to generate a feature identical
 to this one.

makeTemplate(Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils
 
MAN_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools

Homo sapiens codon preferences

mAnnotFilter - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter

The AnnotationMap to use for getting
 AGAVE XML attributes from a Sequence Annotation.

ManyToOneTranslationTable - Interface in org.biojava.bio.symbol

A translation table that will handle the many-to-one mappings
 that you see, for example, with genetic codes.

map(Object) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
map(Object) - Method in interface org.biojava.utils.ListTools.Mapper

Map the object.

map(Set<String>) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
mapList(List, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools
 
mapLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
 
mapMap(Map, ListTools.Mapper, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools
 
MappedDataStoreFactory - Class in org.biojava.bio.program.ssaha


 Builder for a data store that is backed by a java.nio.MappedByteBuffer.

MappedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.MappedDataStoreFactory
 
mapSet(Set, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools
 
mark(int) - Method in class org.biojava.utils.io.CountedBufferedReader
 
MarkovModel - Interface in org.biojava.bio.dp

A markov model.

markSupported() - Method in class org.biojava.utils.io.CountedBufferedReader
 
markSupported() - Method in class org.biojava.utils.io.UncompressInputStream

This stream does not support mark/reset on the stream.

mask(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector

Masks a token by making it lowercase

mask(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector

Present the token for a Symbol as it would appear if masked

maskSequence(Sequence, RangeLocation) - Static method in class org.biojava.bio.seq.SequenceTools

Mask of a sequence.

MASS_SPECTROMETRY - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser

A name for a comment type.

MassCalc - Class in org.biojava.bio.proteomics

MassCalc calculates the mass of peptides which for our
 purposes are SymbolLists which contain
 Symbolsfrom the protein Alphabet.

MassCalc(String, boolean) - Constructor for class org.biojava.bio.proteomics.MassCalc

Creates a new MassCalc.

matcher(SymbolList) - Method in interface org.biojava.bio.search.BioPattern

Get a matcher that will use these parameters to search a SymbolList.

matcher(SymbolList) - Method in class org.biojava.bio.search.MaxMismatchPattern
 
matcher(SymbolList) - Method in class org.biojava.bio.search.SeqContentPattern
 
matcher(SymbolList) - Method in class org.biojava.utils.regex.Pattern

Creates a matcher that will match the given input against this pattern.

Matcher - Class in org.biojava.utils.regex

This class is analogous to java.util.Matcher except that it works
 on SymbolLists instead of Strings.

matches() - Method in class org.biojava.utils.regex.Matcher

Attempts to match the entire input sequence against the pattern.

matchingTypes() - Method in class org.biojava.utils.ChangeType

Return an iterator which contains this type, and all supertypes.

MatchRegex(String) - Constructor for class org.biojava.bio.search.FilterTest.MatchRegex
 
mathExp(double) - Method in class org.biojava.bio.dp.BaumWelchTrainer
 
MatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
 
MatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.MatrixPairDPCursor
 
max - Variable in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
 
MAX_CROSSES - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
 
MaximalResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.MaximalResolver
 
MaximumGeneration(int) - Constructor for class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration

Public Constructer

maxIndex() - Method in class org.biojava.stats.svm.SparseVector
 
maxLength() - Method in class org.biojava.bio.symbol.SuffixTree

Return the length of the longest motif represented in this
 SuffixTree

MaxMismatchMatcher - Class in org.biojava.bio.search

A BioMatcher class returned by MaxMismatchPattern.matcher() that implements
 searching of a SymbolList.

MaxMismatchPattern - Class in org.biojava.bio.search

This class permits searching a SymbolList with another SymbolList while
 permitting a specified number of mismatches.

MaxMismatchPattern() - Constructor for class org.biojava.bio.search.MaxMismatchPattern
 
MaxMismatchPattern(SymbolList, int) - Constructor for class org.biojava.bio.search.MaxMismatchPattern
 
MEDLINE_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms

Holds a reference to the key that must be used to store Medline
 references.

MEDLINE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
MEDLINE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
members - Variable in class org.biojavax.bio.seq.CompoundRichLocation
 
Meme - Class in org.biojava.bio.program

The results of a meme run.

Meme(InputStream, SymbolTokenization) - Constructor for class org.biojava.bio.program.Meme
 
merge(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools

Takes a set of locations and tries to merge all pairs where the union
 operation results in a simple rich location, not a compound one.

merge(Set, Set) - Static method in class org.biojava.utils.MergingSet
 
MergeAnnotation - Class in org.biojava.bio

Merged view onto a list of underlying Annotation objects.

MergeAnnotation() - Constructor for class org.biojava.bio.MergeAnnotation
 
MergeAnnotation.PropertyForwarder - Class in org.biojava.bio

Listener used to forward changes for any of the underlying annotations to
 listeners on this annotation.

MergeFeatureHolder - Class in org.biojava.bio.seq

FeatureHolder which exposes all the features in a set
 of sub-FeatureHolders.

MergeFeatureHolder() - Constructor for class org.biojava.bio.seq.MergeFeatureHolder

Create a new, empty, MergeFeatureHolder.

MergeLocation - Class in org.biojava.bio.symbol

Produced by LocationTools as a result of union operations.

mergeLocations(List) - Static method in class org.biojava.bio.symbol.MergeLocation

Static Factory method for getting an instance of a MergeLocation

mergeLocations(Location, Location) - Static method in class org.biojava.bio.symbol.MergeLocation
 
MergingAnnotationDB - Class in org.biojava.bio.annodb

An AnnotationDB that provides a merged view of a list of underlying DBs.

MergingAnnotationDB(String) - Constructor for class org.biojava.bio.annodb.MergingAnnotationDB

Create a new MergingAnnotationDB with a name and no DBs to merge.

MergingAnnotationDB(String, List) - Constructor for class org.biojava.bio.annodb.MergingAnnotationDB

Create a new MergingAnnotationDB with a name and a list of DBs to merge.

MergingIterator - Class in org.biojava.utils
 
MergingIterator(Iterator) - Constructor for class org.biojava.utils.MergingIterator
 
MergingSet - Class in org.biojava.utils
 
MergingSet() - Constructor for class org.biojava.utils.MergingSet
 
MergingSet(Set) - Constructor for class org.biojava.utils.MergingSet
 
met() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Methionine (M)

META_DATA_TYPE - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory

AnnotationType that all meta-data files should fit.

mFilter - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter

writes PCDATA replacing XML characters with escape entities

midInitials - Variable in class org.biojava.bibliography.BiblioPerson

Any middle innitials.

min - Variable in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
 
mIndent - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent

Base indent

mIndent - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter

indent

MinimalResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.MinimalResolver
 
mismatchCount() - Method in class org.biojava.bio.search.MaxMismatchMatcher

Returns number of mismatches

MITOGENETICCODE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
mListeners - Variable in class org.biojava.bio.seq.io.FastaFormat

Deprecated.
 
model - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
model() - Method in interface org.biojava.bio.dp.DPMatrix
 
model() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
model() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
 
ModelInState - Interface in org.biojava.bio.dp

A state that contains an entire sub-model.

ModelTrainer - Interface in org.biojava.bio.dp

Encapsulates the training of an entire model.

modifiableMerge() - Static method in class org.biojava.utils.MergingSet
 
modifiableMerge(Set) - Static method in class org.biojava.utils.MergingSet
 
MODIFY - Static variable in interface org.biojava.bio.program.homologene.OrthologueSet
 
MODIFY - Static variable in interface org.biojava.bio.program.homologene.OrthoPairSet
 
modifyAttributes(String, int, Attributes) - Method in class org.biojava.naming.ObdaContext
 
modifyAttributes(String, ModificationItem[]) - Method in class org.biojava.naming.ObdaContext
 
modifyAttributes(Name, int, Attributes) - Method in class org.biojava.naming.ObdaContext
 
modifyAttributes(Name, ModificationItem[]) - Method in class org.biojava.naming.ObdaContext
 
modulateCircularIndex(int, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools

Takes a point on a circular location and moves it left until it falls
 at the earliest possible point that represents the same base.

modulateCircularLocation(int, int, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools

Takes a start and end position on a circular location of given
 length, and shifts them left along the sequence until they sit at the
 earliest possible point where they still would represent the same
 sequence.

modulateCircularLocationPair(Location, Location, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools

Takes two circular locations of given length, and shifts them left
 along the sequence until they sit at the earliest possible point
 where they still would represent the same sequence.

MOLD_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable

Translation table name for the mold mitochondrial genetic code.

MOLTYPE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
MONO_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 
MotifTools - Class in org.biojava.bio.symbol

MotifTools contains utility methods for sequence
 motifs.

MotifTools() - Constructor for class org.biojava.bio.symbol.MotifTools
 
MOUSE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools

Mus musculus codon preferences

mOut - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter

Write to XML document

MSF - Static variable in class org.biojava.bio.seq.io.AlignIOConstants

MSF indicates that the alignment format is MSF.

MSF_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants

MSF_AA premade MSF | AA;

MSF_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants

MSF_DNA premade MSF | DNA;

MSF_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants

MSF_DNA premade MSF | RNA;

MSFAlignmentFormat - Class in org.biojava.bio.seq.io
 
MSFAlignmentFormat() - Constructor for class org.biojava.bio.seq.io.MSFAlignmentFormat
 
MULTIPLE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
MULTIPLE - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
 
MultipleScalar(SuffixTreeKernel.DepthScaler, SuffixTreeKernel.DepthScaler) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
 
MultiSourceCompoundRichLocation - Class in org.biojavax.bio.seq

An implementation of RichLocation which possibly covers multiple locations, 
 on different strands, different circular lengths, or different sequences.

MultiSourceCompoundRichLocation(Collection) - Constructor for class org.biojavax.bio.seq.MultiSourceCompoundRichLocation

Constructs a MultiSourceCompoundRichLocation from the given set of members, with
 the default term of "join".

MultiSourceCompoundRichLocation(ComparableTerm, Collection) - Constructor for class org.biojavax.bio.seq.MultiSourceCompoundRichLocation

Constructs a MultiSourceCompoundRichLocation from the given set of members.

MultiTagger - Class in org.biojava.bio.program.tagvalue

Partician multiple values for a tag into their own tag groups.

MultiTagger(TagValueListener, BoundaryFinder) - Constructor for class org.biojava.bio.program.tagvalue.MultiTagger
 
mutate(SymbolList) - Method in interface org.biojavax.ga.functions.MutationFunction

Produces a new SymbolList by mutation.

mutate(SymbolList) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
mutate(SymbolList) - Method in class org.biojavax.ga.functions.SimpleMutationFunction
 
mutate(SymbolList) - Method in class org.biojavax.ga.functions.SwapMutationFunction
 
MUTATION_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
 
MUTATION_PROBS - Static variable in interface org.biojavax.ga.functions.MutationFunction
 
MUTATION_SPECTRUM - Static variable in interface org.biojavax.ga.functions.MutationFunction
 
MutationFunction - Interface in org.biojavax.ga.functions

A class that mutates a SymbolList

MutationFunction.NoMutation - Class in org.biojavax.ga.functions

 Place Holder class that doesn't mutate its SymbolLists

mutuallyExclusiveWith - Variable in class org.biojava.bibliography.BiblioCriterion


 A list of other criteria names that this criterion is mutually exclusive with.

mWriteDocType - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter

write DOCTYPE if true

myLocalName - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 




N

n() - Static method in class org.biojava.bio.seq.DNATools
 
n() - Static method in class org.biojava.bio.seq.NucleotideTools
 
n() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Asparagine

n() - Static method in class org.biojava.bio.seq.RNATools
 
name - Variable in class org.biojava.bibliography.BiblioCriterion


 Each Criterion is identified by its name.

name - Variable in class org.biojava.bibliography.BiblioJournal

A journal title.

name - Variable in class org.biojava.bibliography.BiblioOrganisation

The name of the organisation.

name - Variable in class org.biojava.bibliography.BiblioService

The name of a bibliographic service.

name - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
name - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
 
NAME - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
NAME - Static variable in interface org.biojavax.bio.seq.RichFeature
 
NAME - Static variable in interface org.biojavax.ga.Organism
 
NAME - Static variable in interface org.biojavax.ga.Population
 
NAME - Static variable in interface org.biojavax.Namespace
 
NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
NAME_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
names - Variable in class org.biojavax.bio.taxa.SimpleNCBITaxon
 
names() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB

Returns the set of unique table names.

names() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB

Returns the set of unique table names.

NAMES - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
 
NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
 
NameSetStringValue(String) - Method in interface org.biojava.bio.seq.io.game.GAMENameCallbackItf

Callback implemented by nesting class to allow
 nested class to pass string to nesting class for
 handling.

NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
 
Namespace - Interface in org.biojavax

The namespace of an entry in a database schema.

NameTokenization - Class in org.biojava.bio.seq.io

Simple implementation of SymbolTokenization which uses the `name'
 field of the symbols.

NameTokenization(FiniteAlphabet) - Constructor for class org.biojava.bio.seq.io.NameTokenization

Construct a new NameTokenization, defaulting to case-insensitive.

NameTokenization(FiniteAlphabet, boolean) - Constructor for class org.biojava.bio.seq.io.NameTokenization
 
NARROW_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
NARROW_SYNONYM - Static variable in class org.biojava.ontology.Synonym
 
NATURAL_ORDER - Static variable in interface org.biojava.bio.program.gff.GFFRecord

Comparator which defines a useful sort order for GFF records.

naturalOrder - Static variable in interface org.biojava.bio.symbol.Location

Comparator which orders Locations naturally.

Navg - Static variable in class org.biojava.bio.proteomics.MassCalc

Constant value of Nitrogen average mass

NBRF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

NBRF indicates that the sequence format is NBRF.

NCBI_TAXON_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
NcbiDatabaseURLGenerator - Class in org.biojava.bio.program.blast2html

Simple URL generator for Entrez at the NCBI.

NcbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator
 
NCBISequenceDB - Class in org.biojava.bio.seq.db
 
NCBISequenceDB() - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB

Default constructor, querys the Genbank nucleotide database on "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
 and retrieves sequences in FastaFormat.

NCBISequenceDB(String, String, String, SequenceFormat) - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB

Parameterized constructor

NCBISequenceDB(String, SequenceFormat) - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB

Parameterized constructor

NCBITaxon - Interface in org.biojavax.bio.taxa

Represents an NCBI Taxon entry, a combination of the taxon and taxon_name
 tables in BioSQL.

NCBITaxonomyLoader - Interface in org.biojavax.bio.taxa.io

Implementors are able to load taxonomy files and generate sets of NCBITaxon objects
 that represent them.

NEGATIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature

Flag to indicate that a feature is on the negative strand.

NEGATIVE_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand

The negative strand is represented by the symbol '-' and has the
 number -1.

NestedKernel - Class in org.biojava.stats.svm

Encapsulates a kernel that wraps another kernel up.

NestedKernel() - Constructor for class org.biojava.stats.svm.NestedKernel

Create a new NestedKernel.

NestedKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NestedKernel

Create a new NestedKernel that wraps
 k.

NewAssembledSymbolList - Class in org.biojava.bio.seq.impl

Support class for applications which need to patch together sections
 of sequence into a single SymbolList.

NewAssembledSymbolList() - Constructor for class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
newInstance(Constructor, Object[]) - Method in interface org.biojava.bio.seq.projection.ProjectionEngine.Instantiator
 
newInstance(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
 
newInstance(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
newInstance(Location) - Method in interface org.biojava.bio.symbol.Location

Create a new instance of Location with all of the same decorators as this
 instance but with the data stored in loc.

newInstance(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Create a new instance of Location with all of the same decorators as this
 instance but with the data stored in loc.

newInstance(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Create a new instance of Location with all of the same decorators as this
 instance but with the data stored in loc.

newInstance(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Create a new instance of Location with all of the same decorators as this
 instance but with the data stored in loc.

newKey(String, String) - Method in interface org.biojava.ontology.obo.OboFileEventListener

found a new key in the file

newKey(String, String) - Method in class org.biojava.ontology.obo.OboFileHandler
 
newMessage(Class, String, String, String, String) - Static method in exception org.biojava.bio.seq.io.ParseException

Make a new error message.

newOboFileHeader() - Method in interface org.biojava.ontology.obo.OboFileEventListener

parsed a new OBO file header

newOboFileHeader() - Method in class org.biojava.ontology.obo.OboFileHandler
 
NewSimpleAssembly - Class in org.biojava.bio.seq

A Sequence which is assembled from other sequences contained
 in a set of ComponentFeature objects.

NewSimpleAssembly(int, String, String) - Constructor for class org.biojava.bio.seq.NewSimpleAssembly

Construct a new SimpleAssembly using the DNA alphabet.

NewSimpleAssembly(String, String) - Constructor for class org.biojava.bio.seq.NewSimpleAssembly

Construct a new NewSimpleAssembly using the DNA alphabet.

newStanza(String) - Method in interface org.biojava.ontology.obo.OboFileEventListener

parsed a new stanza in the file

newStanza(String) - Method in class org.biojava.ontology.obo.OboFileHandler
 
newSynonym(Synonym) - Method in interface org.biojava.ontology.obo.OboFileEventListener

a new synonym has been found

newSynonym(Synonym) - Method in class org.biojava.ontology.obo.OboFileHandler
 
next() - Method in class org.biojava.bio.alignment.Alignment.SymbolListIterator
 
next() - Method in class org.biojava.bio.dp.DP.ReverseIterator
 
next() - Method in class org.biojava.utils.MergingIterator
 
next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
 
next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor

Description of the Method

next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.MatrixPairDPCursor
 
next(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.PairDPCursor

retrieve the next block of cells

nextBioEntry() - Method in interface org.biojavax.bio.BioEntryIterator
 
nextBioEntry() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator
 
nextBioEntry() - Method in class org.biojavax.bio.seq.io.RichStreamReader
nextBioEntry() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
nextOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthologueSet.Iterator
 
nextOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet.Iterator
 
nextOrthoPair() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet.Iterator
 
nextOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet.Iterator
 
nextRequest() - Method in class org.biojava.utils.SimpleThreadPool

nextRequest gets the next Runnable
 from the queue.

nextRichSequence() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator
 
nextRichSequence() - Method in class org.biojavax.bio.seq.io.RichStreamReader
nextRichSequence() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
nextRichSequence() - Method in interface org.biojavax.bio.seq.RichSequenceIterator
 
nextSequence() - Method in class org.biojava.bio.seq.io.StreamReader

Pull the next sequence out of the stream.

nextSequence() - Method in interface org.biojava.bio.seq.SequenceIterator

Returns the next sequence in the iterator.

nextSequence() - Method in class org.biojavax.bio.seq.io.HashedFastaIterator
 
nextSequence() - Method in class org.biojavax.bio.seq.io.RichStreamReader

Returns the next sequence in the iterator.

nextSequence() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator

Returns the next sequence in the iterator.

nextSet() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection.Iterator

returns the next OrthoPairSet

nextSet() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection.Iterator
 
nextTable() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader

Returns the next SymbolPropertyTable 
 object.

nextTable() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator

Returns the next SymbolPropertyTable 
 object.

nextWord(SymbolList, int, int, int, Packing) - Static method in class org.biojava.bio.symbol.PackingFactory
 
Nfa - Class in org.biojava.utils.automata

Class for modelling non-deterministic finite automata.

Nfa(String, FiniteAlphabet) - Constructor for class org.biojava.utils.automata.Nfa
 
NfaBuilder - Interface in org.biojava.utils.automata
 
NfaSubModel - Class in org.biojava.utils.automata

This class caches a reference to all objects that
 it directs its delegate to make.

NIODataStoreFactory - Class in org.biojava.bio.program.ssaha


 Builder for a datastore that has no practical file size limit.

NIODataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.NIODataStoreFactory
 
nl() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
Nmono - Static variable in class org.biojava.bio.proteomics.MassCalc

Constant value of Nitrogen monoisotopic mass

NO_CROSS - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
 
NO_FRAME - Static variable in interface org.biojava.bio.program.gff.GFFRecord

Deprecated.
Use GFFTools.NO_FRAME instead


NO_FRAME - Static variable in class org.biojava.bio.program.gff.GFFTools

Flag to indicate that there is no frame info.

NO_MUTATION - Static variable in interface org.biojavax.ga.functions.MutationFunction
 
NO_SCORE - Static variable in interface org.biojava.bio.program.gff.GFFRecord

Deprecated.
Use GFFTools.NO_SCORE instead


NO_SCORE - Static variable in class org.biojava.bio.program.gff.GFFTools

Flag to indicate that there is no score info.

NoCross() - Constructor for class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
NODERANK - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
nodes - Variable in class org.biojava.utils.automata.FiniteAutomaton
 
NoMutation() - Constructor for class org.biojavax.ga.functions.MutationFunction.NoMutation
 
none - Static variable in interface org.biojava.bio.seq.FeatureFilter

No features are selected by this filter.

none() - Static method in class org.biojava.bio.seq.FilterUtils

Return a filter which matches no features.

NONE - Static variable in interface org.biojava.bio.AnnotationType

The type that accepts no annotations at all and is the subtype of all
 other annotations.

NONE - Static variable in class org.biojava.bio.CardinalityConstraint

This cardinality contains no intengers, not even zero.

NONE - Static variable in interface org.biojava.bio.CollectionConstraint

NONE is a constraint which accepts no value for a property
 under any condition.

NONE - Static variable in interface org.biojava.bio.PropertyConstraint

NONE is a constraint which accepts no value for a property
 under any condition.

NONE - Static variable in class org.biojava.ontology.OntoTools
 
nonRemoveIterator(Iterator) - Static method in class org.biojava.utils.ListTools
 
NormalizingKernel - Class in org.biojava.stats.svm

Performs a normalization on the results of a nested kernel.

NormalizingKernel() - Constructor for class org.biojava.stats.svm.NormalizingKernel
 
NormalizingKernel(List) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel

Generate a normalizing kernel defined by the SparseVectors in vectors.

NormalizingKernel(SparseVector) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel

Generate a normalizing kernel with the normalizing vector s.

NormalizingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NormalizingKernel
 
normalLengthVector(SparseVector, double) - Static method in class org.biojava.stats.svm.SparseVector
 
not(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils

Construct a new filter which is the negation of filter.

not(FeatureFilter.Not, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
not(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils

Operator: FeatureHolder 1 NOT FeatureHolder2

Not(OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Not
 
Not(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Not
 
Not(OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not
 
Not(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.Not
 
Not(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Not
 
Note - Interface in org.biojavax

Note is a generic class intended to hold a term describing the note, 
 a value to associate with that term, and a rank.

NOTE - Static variable in interface org.biojavax.bio.seq.RichLocation
 
NOTE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
NotFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
 
NotFilter(GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
 
notifyExit() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.ExitNotification
 
notifyHit(String, int, int, boolean) - Method in interface org.biojava.utils.automata.PatternListener
 
notifyOnExit - Variable in class org.biojava.bio.program.tagvalue.StateMachine.Transition

should the State listener be notified
 that this transition is leaving the state.

notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.program.phred.PhredFormat

Passes the event on to all the listeners registered for ParseErrorEvents.

notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.

notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblProcessor

Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.

notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat

Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.

notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.

notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankProcessor

Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.

notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.SwissprotProcessor

Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.

nState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM

Gets the n loop state

nucleotideToken(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools

Get a single-character token for a Nucleotide symbol

NucleotideTools - Class in org.biojava.bio.seq

Useful functionality for processing nucleotide sequences.

NULL_MAPPER - Static variable in class org.biojava.utils.ListTools
 
NULL_MODEL - Static variable in interface org.biojava.bio.dist.Distribution


 Whenever the null model distribution changes the values that would be
 returned by getWeight, either by being edited or by being replaced, a
 ChangeEvent with this object as the type should be thrown.

NULL_MODEL - Static variable in interface org.biojava.bio.dp.ScoreType
 
NullModel() - Constructor for class org.biojava.bio.dp.ScoreType.NullModel
 
nullModelForwarder - Variable in class org.biojava.bio.dist.AbstractDistribution

Forwarder for modifications to the null model.

NullModelForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.dist.Distribution.NullModelForwarder

Deprecated.
Create a new forwarder.

NullModelScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
 
numericalEntity(char) - Method in class org.biojava.utils.xml.FastXMLWriter
 
numericalEntity(char) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
numStates - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
numStates - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor

Description of the Field

numTables() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB

Returns the number of symbol property tables in the database.

numTables() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB

Returns the number of symbol property tables in the database.





O

o() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Pyrrolysine

O_SATIVA - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
Oavg - Static variable in class org.biojava.bio.proteomics.MassCalc

Constant value of Oxygen average mass

OBDA_SEARCH_ENV - Static variable in class org.biojava.directory.SystemRegistry
 
ObdaContext - Class in org.biojava.naming
 
ObdaInitialContextFactory - Class in org.biojava.naming
 
ObdaInitialContextFactory() - Constructor for class org.biojava.naming.ObdaInitialContextFactory
 
OBDARegistryParser - Class in org.biojava.directory

This class encapsulates all the parsing of the OBDA registry
 configuration file.

OBDARegistryParser() - Constructor for class org.biojava.directory.OBDARegistryParser
 
ObdaUriParser - Class in org.biojava.naming

Singleton class for parsers that understand OBDA URIs.

ObjectUtil - Class in org.biojava.utils

utility methods for implementing the equals() and hashCode() methods of Objects.

ObjectUtil() - Constructor for class org.biojava.utils.ObjectUtil
 
OboFileEventListener - Interface in org.biojava.ontology.obo

an interface for events that occur during parsing of .obo files

OboFileHandler - Class in org.biojava.ontology.obo

A  file handler for .obo files

OboFileHandler(Ontology) - Constructor for class org.biojava.ontology.obo.OboFileHandler
 
OboFileParser - Class in org.biojava.ontology.obo

A class to parse the content of an OBO file.

OboFileParser() - Constructor for class org.biojava.ontology.obo.OboFileParser
 
OboFileParser.SOPair - Class in org.biojava.ontology.obo
 
OboParser - Class in org.biojava.ontology.io

Parses an OBO file.

OboParser() - Constructor for class org.biojava.ontology.io.OboParser
 
OBSOLETE - Static variable in interface org.biojavax.ontology.ComparableTerm
 
oColourClassMap - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler


 Stores mapping from a Colour to a FONT Class.

oColourMap - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler


 Map between Char and the Colour class.

oColourSet - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler

Store the unique colours for markup.

Odds() - Constructor for class org.biojava.bio.dp.ScoreType.Odds
 
ODDS - Static variable in interface org.biojava.bio.dp.ScoreType
 
Omono - Static variable in class org.biojava.bio.proteomics.MassCalc

Constant value of Oxygen monoisotopic mass

one() - Static method in class org.biojavax.ga.util.GATools
 
ONE - Static variable in class org.biojava.bio.CardinalityConstraint

The property should have exactly one value.

ONE_OR_MORE - Static variable in class org.biojava.bio.CardinalityConstraint

The property should have one or more values.

onlyChildren(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils

Construct a filter which matches features whose children all match the
 specified filter.

onlyChildren(FeatureFilter.OnlyChildren, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
OnlyChildren(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
onlyDescendants(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils

Construct a filter which matches features whose decendants all match the
 specified filter.

onlyDescendants(FeatureFilter.OnlyDescendants, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
OnlyDescendants(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
 
Ontology - Interface in org.biojava.ontology

An ontology.

ONTOLOGY - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
ONTOLOGY - Static variable in interface org.biojava.ontology.Term

ChangeType which indicates that this term's ontology has been
 altered

Ontology.Impl - Class in org.biojava.ontology

A basic in-memory implementation of an ontology

OntologyException - Exception in org.biojava.ontology

Thrown to indicate an error in an Ontology object

OntologyException() - Constructor for exception org.biojava.ontology.OntologyException
 
OntologyException(String) - Constructor for exception org.biojava.ontology.OntologyException
 
OntologyException(String, Throwable) - Constructor for exception org.biojava.ontology.OntologyException
 
OntologyException(Throwable) - Constructor for exception org.biojava.ontology.OntologyException
 
OntologyFactory - Interface in org.biojava.ontology

A factory for Ontology instances.

OntologyOps - Interface in org.biojava.ontology

This is an interface for optimizing ontology operators.

OntologyTerm - Interface in org.biojava.ontology

A term in an ontology which identifies another ontology.

OntologyTerm.Impl - Class in org.biojava.ontology

Simple in-memory implementation of a remote ontology term.

OntoTools - Class in org.biojava.ontology

Tools for manipulating ontologies.

open(File) - Static method in class org.biojava.bio.seq.db.TabIndexStore

Open an existing index store.

openTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
openTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
openTag(String) - Method in interface org.biojava.utils.xml.XMLWriter

Open a new unqualified XML tag.

openTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
openTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter

Open a new namespace-qualified XML tag.

OptimizableFilter - Interface in org.biojava.bio.seq

The interface for filters that can potentialy optimize themselves, and
 compare themselves with other filters.

optimize(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils

Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with
 fewer terms.

or(FeatureFilter.Or, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
 
or(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils

Construct a new filter which matches the intersection of two filters.

or(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils

Construct a new filter which matches the union of two filters.

Or(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.Or

Create a new Or from two child constraints.

Or(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Or
 
Or(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Or
 
Or(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or
 
Or(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.Or

Create a new Or from two child constraints.

Or(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.Or
 
Or(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Or
 
OrderCrossover - Class in org.biojavax.ga.functions

This does a 2-point-crossover on two chromosomes keeping the Symbols in each
 chromosome constant.

OrderCrossover() - Constructor for class org.biojavax.ga.functions.OrderCrossover

Sets the maximal number of crossover points to two and the crossover
 probability to 0.5 and initializes this object.

OrderNDistribution - Interface in org.biojava.bio.dist

Provides an N'th order distribution.

OrderNDistributionFactory - Class in org.biojava.bio.dist

Default factory for Order-N distributions.

OrderNDistributionFactory(DistributionFactory) - Constructor for class org.biojava.bio.dist.OrderNDistributionFactory

Construct a new OrderNDistributionFactory with a specified factory
 for conditioned distributions.

orderNSymbolList(SymbolList, int) - Static method in class org.biojava.bio.symbol.SymbolListViews

An n-th order view of another SymbolList.

ORDLOCNAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
ORFNAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
org.biojava.bibliography - package org.biojava.bibliography

The data structures and interfaces included in this package define an
interoperable framework for bibliographic searches.

org.biojava.bio - package org.biojava.bio

The core classes that will be used throughout the bio packages.

org.biojava.bio.alignment - package org.biojava.bio.alignment
 
org.biojava.bio.annodb - package org.biojava.bio.annodb


Databases of generic structured data (annotation) objects.

org.biojava.bio.dist - package org.biojava.bio.dist


Probability distributions over Alphabets.

org.biojava.bio.dp - package org.biojava.bio.dp

HMM and Dynamic Programming Algorithms.

org.biojava.bio.dp.onehead - package org.biojava.bio.dp.onehead
 
org.biojava.bio.dp.twohead - package org.biojava.bio.dp.twohead
 
org.biojava.bio.molbio - package org.biojava.bio.molbio

The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.

org.biojava.bio.program - package org.biojava.bio.program


Java wrappers for interacting with external bioinformatics tools.

org.biojava.bio.program.blast2html - package org.biojava.bio.program.blast2html

Code for generating HTML reports from blast output

org.biojava.bio.program.formats - package org.biojava.bio.program.formats


Experimental parsers using the tagvalue framework.

org.biojava.bio.program.gff - package org.biojava.bio.program.gff

GFF manipulation.

org.biojava.bio.program.gff3 - package org.biojava.bio.program.gff3


Support for reading and writing GFF3.

org.biojava.bio.program.hmmer - package org.biojava.bio.program.hmmer


Tools for working with profile Hidden Markov Models from the HMMer package.

org.biojava.bio.program.homologene - package org.biojava.bio.program.homologene


Support classes for Homologene data.

org.biojava.bio.program.indexdb - package org.biojava.bio.program.indexdb

A flat-file ascii index of ascii flat files as per the OBDA specification.

org.biojava.bio.program.phred - package org.biojava.bio.program.phred

Parser for Phred output

org.biojava.bio.program.ssaha - package org.biojava.bio.program.ssaha

SSAHA sequence searching API.

org.biojava.bio.program.ssbind - package org.biojava.bio.program.ssbind
 
org.biojava.bio.program.tagvalue - package org.biojava.bio.program.tagvalue

 Process files as streams of records, each with tags with values.

org.biojava.bio.program.unigene - package org.biojava.bio.program.unigene

Objects for representing Unigene clusters.

org.biojava.bio.program.xff - package org.biojava.bio.program.xff

Event-driven parsing system for the Extensible Feature Format (XFF).

org.biojava.bio.program.xml - package org.biojava.bio.program.xml

Utility classes for the org.biojava.bio.program.sax
package.

org.biojava.bio.proteomics - package org.biojava.bio.proteomics

Utilities to aid in performing various physical analysis of proteins.

org.biojava.bio.proteomics.aaindex - package org.biojava.bio.proteomics.aaindex

Classes and interfaces to load Amino Acid Index database files.

org.biojava.bio.search - package org.biojava.bio.search


Interfaces and classes for representing sequence similarity search results.

org.biojava.bio.seq - package org.biojava.bio.seq

Classes and interfaces for defining biological sequences and informatics
objects.

org.biojava.bio.seq.db - package org.biojava.bio.seq.db


Collections of biological sequence data.

org.biojava.bio.seq.db.biofetch - package org.biojava.bio.seq.db.biofetch

Client for the OBDA BioFetch protocol.

org.biojava.bio.seq.db.emblcd - package org.biojava.bio.seq.db.emblcd


Readers for the EMBL CD-ROM format binary index files used by EMBOSS and Staden packages.

org.biojava.bio.seq.db.flat - package org.biojava.bio.seq.db.flat


Support for OBDA flatfile databases.

org.biojava.bio.seq.distributed - package org.biojava.bio.seq.distributed

Sequences and SequenceDBs which are composed from data taken
from a number of data sources.

org.biojava.bio.seq.filter - package org.biojava.bio.seq.filter
 
org.biojava.bio.seq.homol - package org.biojava.bio.seq.homol

The classes and interfaces for defining sequence similarity and
honology.

org.biojava.bio.seq.impl - package org.biojava.bio.seq.impl

Standard in-memory implementations of Sequence and
Feature.

org.biojava.bio.seq.io - package org.biojava.bio.seq.io

Classes and interfaces for processing and producing flat-file representations
of sequences.

org.biojava.bio.seq.io.agave - package org.biojava.bio.seq.io.agave

Classes for converting between AGAVE XML and BioJava objects.

org.biojava.bio.seq.io.filterxml - package org.biojava.bio.seq.io.filterxml

Tools for reading and writing an XML representation of BioJava's FeatureFilter language.

org.biojava.bio.seq.io.game - package org.biojava.bio.seq.io.game

Event-driven parsing system for the Gene Annotation Markup Elements (GAME).

org.biojava.bio.seq.io.game12 - package org.biojava.bio.seq.io.game12


Event-driven parsing system for the Gene Annotation Markup Elements (GAME).

org.biojava.bio.seq.projection - package org.biojava.bio.seq.projection

Code for projecting Feature objects and systematically altering their
properties.

org.biojava.bio.symbol - package org.biojava.bio.symbol

Representation of the Symbols that make up a sequence, and locations within
them.

org.biojava.bio.taxa - package org.biojava.bio.taxa

Taxonomy object for representing species information.

org.biojava.directory - package org.biojava.directory

Open Bio Sequence Database Access (OBDA) registry support.

org.biojava.naming - package org.biojava.naming
 
org.biojava.ontology - package org.biojava.ontology


A general-purpose API for ontologies.

org.biojava.ontology.io - package org.biojava.ontology.io


Tools for loading and saving ontologies.

org.biojava.ontology.obo - package org.biojava.ontology.obo
 
org.biojava.stats.svm - package org.biojava.stats.svm


Support Vector Machine classification and regression.

org.biojava.stats.svm.tools - package org.biojava.stats.svm.tools

Tools for use of the SVM package.

org.biojava.utils - package org.biojava.utils


Miscellaneous utility classes used by other BioJava components.

org.biojava.utils.automata - package org.biojava.utils.automata
 
org.biojava.utils.cache - package org.biojava.utils.cache

A simple cache system with pluggable caching behaviours.

org.biojava.utils.candy - package org.biojava.utils.candy

The data structures and interfaces included in this package define an
interoperable framework for simple controlled vocabularies.

org.biojava.utils.io - package org.biojava.utils.io

I/O utility classes.

org.biojava.utils.lsid - package org.biojava.utils.lsid

Life Science Identifier (LSID) package.

org.biojava.utils.math - package org.biojava.utils.math


Mathematical utility classes.

org.biojava.utils.net - package org.biojava.utils.net


Network programming utility classes.

org.biojava.utils.process - package org.biojava.utils.process

Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.

org.biojava.utils.regex - package org.biojava.utils.regex

This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.

org.biojava.utils.stax - package org.biojava.utils.stax

The Stack API for XML (StAX).

org.biojava.utils.walker - package org.biojava.utils.walker
 
org.biojava.utils.xml - package org.biojava.utils.xml


Utility classes for handling and generating XML documents.

org.biojavax - package org.biojavax

The Biojava extensions packages, classes that extend the core biojava 
     functionality

org.biojavax.bio - package org.biojavax.bio

Classes to represent biological entities and their relationships.

org.biojavax.bio.alignment - package org.biojavax.bio.alignment

This package contains the interfaces that need to be implemented by discrete alignment services.

org.biojavax.bio.alignment.blast - package org.biojavax.bio.alignment.blast

This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services
  through the WWW.

org.biojavax.bio.db - package org.biojavax.bio.db

Interactions between biojavax objects and a DB.

org.biojavax.bio.db.ncbi - package org.biojavax.bio.db.ncbi

Interfaces to NCBI data.

org.biojavax.bio.seq - package org.biojavax.bio.seq

Rich implementations of Sequences, Locations and Features.

org.biojavax.bio.seq.io - package org.biojavax.bio.seq.io

Classes to support the I/O of RichSequence and 
     Bioentry objects.

org.biojavax.bio.taxa - package org.biojavax.bio.taxa

Objects that model the NCBI taxonomy schema as described in the BioSQL
  schema.

org.biojavax.bio.taxa.io - package org.biojavax.bio.taxa.io
 
org.biojavax.ga - package org.biojavax.ga

Classes to provide a genetic algorithm framework

org.biojavax.ga.exception - package org.biojavax.ga.exception

Exceptions related to the GA framework

org.biojavax.ga.functions - package org.biojavax.ga.functions

GA functions

org.biojavax.ga.impl - package org.biojavax.ga.impl

Default implementations and abstract classes.

org.biojavax.ga.util - package org.biojavax.ga.util

Utility functions and helper classes

org.biojavax.ontology - package org.biojavax.ontology

Extensions to the biojava ontology model that represent BioSQL ontology.

org.biojavax.utils - package org.biojavax.utils

Utility classes that are used by biojavax objects but could have wider utility
  to other applications.

ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
Organism - Interface in org.biojavax.ga

A GA 'organism' contains one or more Chromosomes

ORGANISM_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
ORGANISM_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ORGANISM_XREF_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
OrganismParser - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.taxa framework instead


OrganismParser(SequenceBuilder, TaxonFactory, TaxonParser, String, String, String) - Constructor for class org.biojava.bio.seq.io.OrganismParser

Deprecated.
 
OrganismParser.Factory - Class in org.biojava.bio.seq.io

Deprecated.
Factory which wraps SequenceBuilders in an OrganismParser.

organisms() - Method in class org.biojavax.ga.impl.SimplePopulation
 
organisms() - Method in interface org.biojavax.ga.Population
 
ORGANISMS - Static variable in interface org.biojavax.ga.Population
 
origSeq - Variable in class org.biojava.bio.seq.impl.RevCompSequence
 
Orthologue - Interface in org.biojava.bio.program.homologene

this entry contains data about the orthologue.

OrthologueFilter - Interface in org.biojava.bio.program.homologene
 
OrthologueFilter.AcceptAll - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.And - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByAccession - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByHomologeneID - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByLocusID - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByTaxon - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByTaxonID - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.ByTitle - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.Not - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.Or - Class in org.biojava.bio.program.homologene
 
OrthologueFilter.Xor - Class in org.biojava.bio.program.homologene
 
OrthologueSet - Interface in org.biojava.bio.program.homologene

Interface for classes that store and manipulate
 orthologues.

OrthologueSet.Iterator - Interface in org.biojava.bio.program.homologene

An iterator for the contents of
 an OrthologueSet.

OrthoPair - Interface in org.biojava.bio.program.homologene

Each HomologeneEntry represents a single
 Homologene record that relates two
 presumptive orthologues.

OrthoPairCollection - Interface in org.biojava.bio.program.homologene

Interface for a Set of OrthoPairSets

OrthoPairCollection.Iterator - Interface in org.biojava.bio.program.homologene

Iterator for a OrthoPairCollection

OrthoPairFilter - Interface in org.biojava.bio.program.homologene
 
OrthoPairFilter.AcceptAll - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.And - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.ByMaxIdentity - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.ByMinIdentity - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.ByRef - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.BySimilarityType - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.Not - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.Or - Class in org.biojava.bio.program.homologene
 
OrthoPairFilter.Xor - Class in org.biojava.bio.program.homologene
 
OrthoPairSet - Interface in org.biojava.bio.program.homologene

represents the Homologene Group.

OrthoPairSet.Iterator - Interface in org.biojava.bio.program.homologene
 
OrthoPairSetFilter - Interface in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.AcceptAll - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.AllPairsInCollection - Class in org.biojava.bio.program.homologene

all OrthoPairs must meet the requirement
 defined by filter.

OrthoPairSetFilter.And - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.ByMinIdentity - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.ByTaxon - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.Not - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.Or - Class in org.biojava.bio.program.homologene
 
OrthoPairSetFilter.SomePairsInCollection - Class in org.biojava.bio.program.homologene

at least one OrthoPair must meet the requirement
 defined by filter.

OrthoPairSetFilter.Xor - Class in org.biojava.bio.program.homologene
 
OTHER_SEQID_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
OTHER_SEQIDS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
OutputHandler - Interface in org.biojava.utils.process

Interface to a threadable output handler for
 an external process.

OVERHANG_3PRIME - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme

OVERHANG_3PRIME the sticky end type created by
 enzymes which leave a 3' overhang (e.g. a stretch of single-stranded
 DNA with a free 3' end).

OVERHANG_5PRIME - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme

OVERHANG_5PRIME the sticky end type created by
 enzymes which leave a 5' overhang (e.g. a stretch of single-stranded
 DNA with a free 5' end).

overlaps(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
 
overlaps(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
overlaps(Location) - Method in class org.biojava.bio.symbol.CircularLocation
 
overlaps(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
overlaps(Location) - Method in interface org.biojava.bio.symbol.Location

Checks if these two locations overlap, using this location's
 concept of overlapping.

overlaps(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Checks if these two locations overlap, using this location's
 concept of overlapping.

overlaps(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Checks if these two locations overlap, using this location's
 concept of overlapping.

overlaps(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Checks if these two locations overlap, using this location's
 concept of overlapping.

overlaps(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools

Determines whether the locations overlap or not.

overlapsLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils

Construct a filter which matches features with locations contained by or
 overlapping the specified Location.

OverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.OverlapsLocation

Creates a filter that returns everything overlapping loc.

overlapsOrigin() - Method in class org.biojava.bio.symbol.CircularLocation

Does the Location overlap the origin (position 1) of the sequence?

OverlayAnnotation - Class in org.biojava.bio

Annotation implementation which allows new key-value
 pairs to be layered on top of an underlying Annotation.

OverlayAnnotation(Annotation) - Constructor for class org.biojava.bio.OverlayAnnotation

Construct an annotation which can overlay new key-value
 pairs onto an underlying annotation.

OverlayAnnotation.PropertyForwarder - Class in org.biojava.bio

Forwards change events from the underlying Annotation to this one.

OverlayMap - Class in org.biojava.utils


 Overlap one map onto another.

OverlayMap(Map) - Constructor for class org.biojava.utils.OverlayMap

Build a new map with default key-value pairs.

OverlayMap(Map, Map) - Constructor for class org.biojava.utils.OverlayMap

Build a new map with default key-value pairs.





P

p() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Proline

pack(Symbol) - Method in class org.biojava.bio.symbol.DNAAmbPack
 
pack(Symbol) - Method in class org.biojava.bio.symbol.DNANoAmbPack
 
pack(Symbol) - Method in interface org.biojava.bio.symbol.Packing


 Return a byte representing the packing of a symbol.

PACKED - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory

Accessor for a factory that produces builders that compress the
 SymbolList of a RichSequence.

PackedSymbolList - Class in org.biojava.bio.symbol


 A SymbolList that stores symbols as bit-patterns in an array of longs.

PackedSymbolList(Packing, long[], int) - Constructor for class org.biojava.bio.symbol.PackedSymbolList


 Create a new PackedSymbolList directly from a bit pattern.

PackedSymbolList(Packing, Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.PackedSymbolList


 Create a new PackedSymbolList from an array of Symbols.

PackedSymbolList(Packing, SymbolList) - Constructor for class org.biojava.bio.symbol.PackedSymbolList


 Create a new PackedSymbolList as a packed copy of another symbol list.

PackedSymbolListFactory - Class in org.biojava.bio.symbol

This class makes PackedSymbolLists.

PackedSymbolListFactory() - Constructor for class org.biojava.bio.symbol.PackedSymbolListFactory

Create a factory for PackedSymbolLists.

PackedSymbolListFactory(boolean) - Constructor for class org.biojava.bio.symbol.PackedSymbolListFactory

Deprecated.
the argumentless constructor creates a SymbolListFactory
   that will autoselect the packing appropriately.


Packing - Interface in org.biojava.bio.symbol


 An encapsulation of the way symbols map to bit-patterns.

PackingFactory - Class in org.biojava.bio.symbol


 A factory that is used to maintain associations between alphabets and
 preferred bit-packings for them.

PackingFactory() - Constructor for class org.biojava.bio.symbol.PackingFactory
 
paintComponent(Graphics) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier

Renders this component to display the points, and if present, the
 support vector machine.

PairDistribution - Class in org.biojava.bio.dist

Class for pairing up two independant distributions.

PairDistribution(Distribution, Distribution) - Constructor for class org.biojava.bio.dist.PairDistribution

Create a new PairDistribution that represents the product of two other
 distributions.

PairDPCursor - Interface in org.biojava.bio.dp.twohead

A cursor over a DP matrix.

PairDPMatrix - Class in org.biojava.bio.dp.twohead

Storage structure for intermediate values from a pairwise
 dynamic programming run.

PairDPMatrix(DP, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.twohead.PairDPMatrix
 
PAIRWISE - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
PairwiseDP - Class in org.biojava.bio.dp.twohead

Algorithms for dynamic programming (alignments) between pairs
 of SymbolLists.

PairwiseDP(MarkovModel, CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.twohead.PairwiseDP
 
PARAMETER - Static variable in interface org.biojava.bio.dp.MarkovModel

Signals that one or more parameters have altered.

parent - Variable in class org.biojava.bio.taxa.SimpleTaxon

Deprecated.
 
parent - Variable in class org.biojava.bio.taxa.WeakTaxon

Deprecated.
 
parent() - Method in interface org.biojava.utils.automata.StateMachineInstance
 
PARENT - Static variable in interface org.biojavax.bio.seq.RichFeature
 
PARENT - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
parse(BufferedReader, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFParser

Informs handler of each line of
 gff read from bReader.

parse(BufferedReader, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.GFFParser

Informs handler of each line of
 GFF read from bReader

parse(BufferedReader, GFF3DocumentHandler, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser

Informs handler of each line of
 gff read from bReader.

parse(BufferedReader, GFF3DocumentHandler, Ontology, String) - Method in class org.biojava.bio.program.gff3.GFF3Parser

Informs handler of each line of
 GFF read from bReader

parse(BufferedReader, OntologyFactory) - Method in class org.biojava.ontology.io.TabDelimParser

Parse an ontology from a reader.

parse(File) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileParser

Returns a profile HMM representing the core HMMER hmm

parse(Object) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
 
parse(Object) - Method in class org.biojava.bio.program.tagvalue.RegexParser
 
parse(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueParser
 
parse(String) - Method in class org.biojava.naming.ObdaUriParser
 
parse(TaxonFactory, String) - Method in class org.biojava.bio.taxa.EbiFormat

Deprecated.
 
parse(TaxonFactory, String) - Method in interface org.biojava.bio.taxa.TaxonParser

Deprecated.
Convert a stringified Taxon into a Taxon instance.

parseAttribute(String) - Method in class org.biojava.bio.program.gff.GFFParser

Parse attValList into a
 Map of attributes and value lists.

parseAttribute(String, Annotation, Ontology, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser

Parse attValList into a
 Map of attributes and value lists.

parseAuthorString(String) - Static method in class org.biojavax.DocRefAuthor.Tools

Takes a list of authors and returns a set of DocRefAuthor objects.

parseComment(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Parses the comment string from the given comment and populates
 the internal fields appropriately.

parseComment(Comment) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Parses the comment string from the given comment and populates
 the internal fields appropriately.

ParseErrorEvent - Class in org.biojava.utils

Event which signals a bad line when parsing a record.

ParseErrorEvent(Object) - Constructor for class org.biojava.utils.ParseErrorEvent

Construct a ParseErrorEvent with no other information.

ParseErrorEvent(Object, String) - Constructor for class org.biojava.utils.ParseErrorEvent

Construct a ParseErrorEvent with a message.

ParseErrorListener - Interface in org.biojava.utils

Listener for a ParseErrorEvent.

ParseErrorSource - Interface in org.biojava.utils

Source for a ParseErrorEvent.

parseExample(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
ParseException - Exception in org.biojava.bio.seq.io

ParseException should be thrown to indicate that there was a problem with
 parsing sequence information.

ParseException() - Constructor for exception org.biojava.bio.seq.io.ParseException
 
ParseException(String) - Constructor for exception org.biojava.bio.seq.io.ParseException
 
ParseException(Throwable) - Constructor for exception org.biojava.bio.seq.io.ParseException
 
ParseException(Throwable, String) - Constructor for exception org.biojava.bio.seq.io.ParseException
 
parseFull(File) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileParser

Returns the full markov model - including the core model + J,C,N loop states.

parseGO(BufferedReader, String, String, OntologyFactory) - Method in class org.biojava.ontology.io.GOParser
 
parseLocation(String) - Static method in class org.biojavax.bio.seq.io.UniProtLocationParser

Parses a location.

parseLocation(String, Feature.Template) - Method in class org.biojava.bio.seq.io.EmblLikeLocationParser

Deprecated.
parseLocation creates a Location from
 the String and returns a stranded location.

parseLocation(Namespace, String, String) - Static method in class org.biojavax.bio.seq.io.GenbankLocationParser

Parses a location.

parseModel(File) - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
parseOBO(BufferedReader) - Method in class org.biojava.ontology.obo.OboFileParser

parse an ontology file

parseOBO(BufferedReader, String, String) - Method in class org.biojava.ontology.io.OboParser

Parse a OBO file and return its content as a BioJava Ontology object

Parser - Class in org.biojava.bio.program.tagvalue


 Encapsulate the parsing of lines from a buffered reader into tag-value
 events.

Parser() - Constructor for class org.biojava.bio.program.tagvalue.Parser
 
parseRecord(byte[]) - Method in class org.biojava.utils.FileAsList
 
parseRegistry(BufferedReader, String) - Static method in class org.biojava.directory.OBDARegistryParser

parseRegistry parses an Open Bioinformatics Database
 Access (OBDA) configuration file.

ParserException - Exception in org.biojava.utils

Exception thrown when an error occurs in document parsing.

ParserException(String) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(String, String) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(String, String, int) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(String, String, int, String) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(String, String, int, String, int) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(String, Throwable) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(Throwable) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(Throwable, String) - Constructor for exception org.biojava.utils.ParserException

Deprecated.
use new ParserException(detail, t)


ParserException(Throwable, String, String) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(Throwable, String, String, int) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(Throwable, String, String, int, String) - Constructor for exception org.biojava.utils.ParserException
 
ParserException(Throwable, String, String, int, String, int) - Constructor for exception org.biojava.utils.ParserException
 
ParserListener - Class in org.biojava.bio.program.tagvalue

ParserListener is an immutable pairing of a parser and
 listener.

ParserListener(TagValueParser, TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.ParserListener

Creates a new ParserListener instance.

PARSERS - Static variable in interface org.biojava.bio.symbol.Alphabet

This signals that the available parsers have changed.

parseStrand(String) - Static method in class org.biojava.bio.seq.StrandParser
 
parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.AlternateTokenization

Will throw an exception.

parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
parseStream(SeqIOListener) - Method in interface org.biojava.bio.seq.io.SymbolTokenization

Return an object which can parse an arbitrary character stream into
 symbols.

parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.WordTokenization
 
parseStream(SeqIOListener) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization

The current implementation only supports character parsing.

parseString(String) - Method in class org.biojava.bio.seq.io.WordTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.AlternateTokenization

Will throw an exception.

parseToken(String) - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.CrossProductTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.DoubleTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.IntegerTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.NameTokenization
 
parseToken(String) - Method in class org.biojava.bio.seq.io.SubIntegerTokenization
 
parseToken(String) - Method in interface org.biojava.bio.seq.io.SymbolTokenization

Returns the symbol for a single token.

parseToken(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
 
parseTokenChar(char) - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
parseXML(InputStream) - Method in class org.biojava.bio.dist.XMLDistributionReader

Reads an XML representation of a Distribution from a file.

parseXref(String, int, int) - Method in class org.biojava.ontology.obo.OboFileParser
 
PART_OF - Static variable in class org.biojava.ontology.OntoTools
 
PARTIAL_ORDER - Static variable in class org.biojava.ontology.OntoTools
 
PATENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
pattern() - Method in class org.biojava.utils.regex.Matcher

Returns the Pattern object that compiled this Matcher.

Pattern - Class in org.biojava.utils.regex

A class analogous to java.util.regex.Pattern but for SymbolLists.

patternAsString() - Method in class org.biojava.utils.regex.Pattern

returns the Pattern to be matched as a String.

PatternBlitz - Class in org.biojava.utils.automata
 
PatternBlitz(FiniteAlphabet, StateMachineToolkit) - Constructor for class org.biojava.utils.automata.PatternBlitz
 
patternExpanded() - Method in class org.biojava.utils.regex.Pattern

returns the actual String used to construct the regex with all
 ambiguities expanded.

PatternFactory - Class in org.biojava.utils.regex

A class that creates Patterns for regex matching on 
 SymbolLists of a specific Alphabet.

PatternListener - Interface in org.biojava.utils.automata
 
PatternMaker - Class in org.biojava.utils.automata
 
PDB - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

PDB indicates that the sequence format is
 PDB.

PEPTIDE_FEATURE_TYPE - Static variable in class org.biojava.bio.proteomics.Digest
 
PERCENTIDENTITY - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
performCrossOver(SymbolList, SymbolList) - Method in interface org.biojavax.ga.functions.CrossOverFunction

Performs a cross between the pair of chromosomes

performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.OrderCrossover
 
performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.SimpleCrossOverFunction
 
PERSON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
pFromQuality(double) - Static method in class org.biojava.bio.program.phred.PhredTools

Calculates the probability of an error from the quality score via the formula
  P_e = 10**(QV/-10)

pFromQuality(int) - Static method in class org.biojava.bio.program.phred.PhredTools

Calculates the probability of an error from the quality score via the formula
  P_e = 10**(QV/-10)

pFromQuality(IntegerAlphabet.IntegerSymbol) - Static method in class org.biojava.bio.program.phred.PhredTools

Calculates the probability of an error from the quality score via the formula
  P_e = 10**(QV/-10)

phe() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Phenylalanine (F)

PHRED - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

PHRED indicates that the sequence format is
 PHRED.

phredAlignmentToDistArray(Alignment) - Static method in class org.biojava.bio.program.phred.PhredTools

converts an Alignment of PhredSequences to a Distribution[] where each position is the average
 distribution of the underlying column of the alignment.

PhredFormat - Class in org.biojava.bio.program.phred

Format object representing Phred Quality files.

PhredFormat() - Constructor for class org.biojava.bio.program.phred.PhredFormat
 
PhredSequence - Class in org.biojava.bio.program.phred

PhredSequence is an extension of SimpleSequence that implements
 Qualitative to hold Phred quality scores.

PhredSequence(SymbolList, String, String, Annotation) - Constructor for class org.biojava.bio.program.phred.PhredSequence

Constructs a new PhredSequence.

phredToDistArray(PhredSequence) - Static method in class org.biojava.bio.program.phred.PhredTools

Converts a Phred sequence to an array of distributions.

PhredTools - Class in org.biojava.bio.program.phred

PhredTools contains static methods for working with phred
 quality data.

PhredTools() - Constructor for class org.biojava.bio.program.phred.PhredTools
 
PK - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 
PK_Cterm - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 
PK_Nterm - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
 
PLASMID_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
 
PointClassifier() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier

Make a new PointClassifier.

PointLocation - Class in org.biojava.bio.symbol

A location representing a single point.

PointLocation(int) - Constructor for class org.biojava.bio.symbol.PointLocation
 
polyKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
 
PolynomialKernel - Class in org.biojava.stats.svm

This kernel computes all possible products of order features in feature
 space.

PolynomialKernel() - Constructor for class org.biojava.stats.svm.PolynomialKernel
 
PolynomialKernel(SVMKernel, double, double, double) - Constructor for class org.biojava.stats.svm.PolynomialKernel
 
POMBE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools

Schizosaccharomyces pombe codon preferences

pop() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler

pop a StAXContentHandler off the stack.

pop() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler

pop a StAXContentHandler off the stack.

populate(Feature.Template, Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils

This attempts to populate the fields of a template using
 the publically accessible information in a feature.

population - Variable in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
Population - Interface in org.biojavax.ga

A collection of GA organisms

POPULATION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
 
pos - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
pos - Variable in class org.biojava.bio.symbol.Edit
 
position() - Method in class org.biojava.utils.io.LargeBuffer
 
position(long) - Method in class org.biojava.utils.io.LargeBuffer
 
Position - Interface in org.biojavax.bio.seq

Holds info about base positions.

PositionResolver - Interface in org.biojavax.bio.seq

Resolves a position that is fuzzy or covers a range of bases by
 converting it to a single base.

PositionResolver.AverageResolver - Class in org.biojavax.bio.seq

The minimal resolver returns the base which provides the
 average range, halfway between maximal and minimal.

PositionResolver.MaximalResolver - Class in org.biojavax.bio.seq

The maximal resolver returns the base which provides the
 largest possible range.

PositionResolver.MinimalResolver - Class in org.biojavax.bio.seq

The minimal resolver returns the base which provides the
 smallest possible range.

POSITIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature

Flag to indicate that a feature is on the positive strand.

POSITIVE_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand

The positive strand is represented by the symbol '+' and has the
 number 1.

posmax(Position, Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
posmin(Position, Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
postalAddress - Variable in class org.biojava.bibliography.BiblioPerson

Their postal address.

postChange(ChangeEvent) - Method in class org.biojava.bio.symbol.SimpleSymbolList
 
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeAdapter
 
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder
 
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.AlwaysVetoListener
 
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.LoggingListener
 
postChange(ChangeEvent) - Method in interface org.biojava.utils.ChangeListener


 Called when a change has just taken place.

preChange(ChangeEvent) - Method in class org.biojava.bio.symbol.SimpleSymbolList

On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols

preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeAdapter
 
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder
 
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.AlwaysVetoListener
 
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.ChangeEventRecorder
 
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.LoggingListener
 
preChange(ChangeEvent) - Method in interface org.biojava.utils.ChangeListener


 Called before a change takes place.

press() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
press() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor

Returns the minimal context of the DP matrix
 necessary to compute the value of a single point
 in that matrix.

press() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor

press out a new correctly sized cell array

PrettyXMLWriter - Class in org.biojava.utils.xml

Implementation of XMLWriter which emits nicely formatted documents
 to a PrintWriter.

PrettyXMLWriter(PrintWriter) - Constructor for class org.biojava.utils.xml.PrettyXMLWriter
 
PRIMARY_KEY_NAME - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory

PRIMARY_KEY_NAME is the key used to identify the
 primary namespace in the OBDA config.dat files.

PRIME - Static variable in class org.biojava.utils.ObjectUtil

the current hashCode is always first multiplied with this prime before the hashCode value for a particular field is
 added.

primeWord(SymbolList, int, Packing) - Static method in class org.biojava.bio.symbol.PackingFactory
 
print(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
print(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
print(String) - Method in interface org.biojava.utils.xml.XMLWriter

Prints some textual content in an element.

printAttributeValue(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
printAttributeValue(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
printChars(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
printChars(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
println(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
println(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
println(String) - Method in interface org.biojava.utils.xml.XMLWriter

Prints some textual content, terminated with a newline character.

printOutSequenceHeaderLine(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer

Deprecated.
Prints out sequence header with only length data.

printRaw(String) - Method in class org.biojava.utils.xml.FastXMLWriter
 
printRaw(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
printRaw(String) - Method in interface org.biojava.utils.xml.XMLWriter

Send raw data to the stream.

printRemoteBlastInfo() - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService

A simple method to check the availability of the QBlast service

printTree() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
priority - Variable in class org.biojava.utils.SimpleThreadPool
 
pro() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Proline (P)

Probability() - Constructor for class org.biojava.bio.dp.ScoreType.Probability
 
PROBABILITY - Static variable in interface org.biojava.bio.dp.ScoreType
 
processDB(SequenceDB, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF

Process all Sequences within a
 SequenceDB, informing
 handler of any suitable features.

processHeader(String, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat

Parse the Header information from the Fasta Description line

processingInstruction(String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
processingInstruction(String, String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
processingInstruction(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
processingInstruction(String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
processingInstruction(String, String) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
processingInstruction(String, String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
processSequence(Sequence, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF

Process an individual Sequence, informing
 handler of any suitable features.

processSequenceLine(String, StreamParser) - Method in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
Dispatch symbol data from SQ-block line of an EMBL-like file.

ProcessTimeoutException - Exception in org.biojava.utils

Exception which is thrown if a child process managed by ProcessTools
 exceeds a specified time limit.

ProcessTimeoutException(int) - Constructor for exception org.biojava.utils.ProcessTimeoutException
 
ProcessTimeoutException(int, String) - Constructor for exception org.biojava.utils.ProcessTimeoutException
 
ProcessTools - Class in org.biojava.utils

Deprecated.
preferable to use org.biojava.utils.ExecRunner 
 or the org.biojava.utils.process package.


ProfileEmissionState - Class in org.biojava.bio.program.hmmer

A state in a HMMer model.

ProfileEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.program.hmmer.ProfileEmissionState
 
ProfileHMM - Class in org.biojava.bio.dp
 
ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory) - Constructor for class org.biojava.bio.dp.ProfileHMM

Deprecated. 

ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory, String) - Constructor for class org.biojava.bio.dp.ProfileHMM

Create a new ProfileHMM.

PROJ_ACC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
projectChildFeatures(Feature, FeatureHolder) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
 
projectChildFeatures(Feature, FeatureHolder) - Method in interface org.biojava.bio.seq.projection.ProjectionContext

Project all features that are children of feature so that they become
 children of parent.

projectChildFeatures(Feature, FeatureHolder) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
ProjectedFeature - Class in org.biojava.bio.seq.projection

Internal class used by ProjectionEngine to wrap Feature objects.

ProjectedFeature(Feature, ProjectionContext) - Constructor for class org.biojava.bio.seq.projection.ProjectedFeature
 
ProjectedFeatureHolder - Class in org.biojava.bio.seq.projection

Helper class for projecting Feature objects into an alternative
 coordinate system.

ProjectedFeatureHolder(ProjectionContext) - Constructor for class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
projectFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
 
projectFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext

Project a single feature.

projectFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext

Create a single projected feature using the rules of this ProjectedFeatureHolder.

projectFeature(Feature, ProjectionContext) - Method in class org.biojava.bio.seq.projection.ProjectionEngine

Return a projection of Feature f into the system
 defined by a given ProjectionContext.

projectFeatures(FeatureHolder) - Method in interface org.biojava.bio.seq.projection.ProjectionContext

Project all of the features in a FeatureHolder.

projectFeatures(FeatureHolder) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
projectFilter(FeatureFilter) - Method in interface org.biojava.bio.seq.projection.ProjectionContext

Transform a filter on unprojected features so that it applies to projected
 features.

projectFilter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
Projection - Interface in org.biojava.bio.seq.projection

Interface implemented by all projected feature objects.

ProjectionContext - Interface in org.biojava.bio.seq.projection

Interface that defines the projection between original features and
 projected features.

ProjectionEngine - Class in org.biojava.bio.seq.projection

Factory for proxy objects which project BioJava features
 into alternate coordinate systems.

ProjectionEngine.Instantiator - Interface in org.biojava.bio.seq.projection

Internal helper class.

ProjectionEngine.TemplateProjector - Interface in org.biojava.bio.seq.projection

This is an interface for things that project feature templates.

ProjectionUtils - Class in org.biojava.bio.seq.projection

Some common things you want to do while projecting features.

ProjectionUtils() - Constructor for class org.biojava.bio.seq.projection.ProjectionUtils
 
projectLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
 
projectLocation(Location) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
 
projectLocation(Location) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
projectStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
PROP_CASE_SENSITIVE - Static variable in interface org.biojava.utils.candy.CandyVocabulary

A property name.

PROP_CRITERIONS - Static variable in interface org.biojava.bibliography.BibRefQuery

A property name specifying a list of searching and ordering criteria
 names (type of the property value should be String[]).

PROP_ENTRY_COUNT - Static variable in interface org.biojava.utils.candy.CandyVocabulary

A property name.

PROP_EXCLUDED_ATTRS - Static variable in interface org.biojava.bibliography.BibRefQuery


 A property name specifying a list of excluded attribute names
 (the type of the property value should be String[]).

PROP_VOCAB_DESC - Static variable in interface org.biojava.utils.candy.CandyVocabulary

A property name.

PROP_VOCAB_NAME - Static variable in interface org.biojava.utils.candy.CandyVocabulary

A property name.

PROP_VOCAB_VERSION - Static variable in interface org.biojava.utils.candy.CandyVocabulary

A property name.

PROP_VOCABULARY - Static variable in interface org.biojava.utils.candy.CandyFinder


 A property name.

PROP_VOCABULARY - Static variable in interface org.biojava.utils.candy.CandyVocabulary

A property name.

PROPDETAIL_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.PropDetailHandler
 
PropDetailHandler - Class in org.biojava.bio.program.xff

StAX handler for xff:prop detail elements.

PropDetailHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.PropDetailHandler
 
properties - Variable in class org.biojava.bibliography.BiblioEntryStatus


 The dynamic properties may be used to add features related to
 the citation itself.

properties - Variable in class org.biojava.bibliography.BiblioJournal

Additional properties used when the explicit attributes
 are not sufficient.

properties - Variable in class org.biojava.bibliography.BiblioProvider

Additional properties used when the explicit attributes of the
 sub-classes are not sufficient.

properties - Variable in class org.biojava.bibliography.BiblioScope

It may contain additional properties related to the extend or
 scope of the cited resource.

properties - Variable in class org.biojava.bibliography.BibRef

Additional attributes of this citation.

propertiesAllocated() - Method in class org.biojava.bio.AbstractAnnotation

A convenience method to see if we have allocated the properties
 Map.

propertiesAllocated() - Method in class org.biojava.bio.AnnotationChanger

propertiesAllocated is a convenience method to see
 if we have allocated the properties Map.

propertiesAllocated() - Method in class org.biojava.bio.AnnotationRenamer

propertiesAllocated Javadoc FIXME - this overrides
 a protected method and I'm not sure why (KJ).

propertiesAllocated() - Method in class org.biojava.bio.BeanAsAnnotation
 
propertiesAllocated() - Method in class org.biojava.bio.seq.io.ReferenceAnnotation

Deprecated.
 
propertiesAllocated() - Method in class org.biojava.bio.SimpleAnnotation

Test to see if any properties have been allocated

propertiesAllocated() - Method in class org.biojava.bio.SmallAnnotation
 
PROPERTY - Static variable in interface org.biojava.bio.Annotation

This type symbolizes that one or more properties have changed.

PROPERTY_DATA_KEY - Static variable in interface org.biojava.bio.seq.Feature

This is used as a key in the Annotation where it
 identifies internal data.

PROPERTY_DESCRIPTIONLINE - Static variable in class org.biojava.bio.program.phred.PhredFormat

Constant string which is the property key used to notify
 listeners of the description lines of Phred sequences.

PROPERTY_DESCRIPTIONLINE - Static variable in class org.biojava.bio.seq.io.FastaFormat

Deprecated.
Constant string which is the property key used to notify
 listeners of the description lines of FASTA sequences.

PROPERTY_EMBL_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.EmblProcessor

Deprecated.
 
PROPERTY_GENBANK_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.GenbankProcessor

Deprecated.
 
PROPERTY_GFF_SCORE - Static variable in class org.biojava.bio.program.gff.GFFEntrySet
 
PROPERTY_NCBI_TAXON - Static variable in class org.biojava.bio.taxa.EbiFormat

Deprecated.
 
PROPERTY_ORGANISM - Static variable in class org.biojava.bio.seq.io.OrganismParser

Deprecated.
 
PROPERTY_SWISSPROT_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor

Deprecated.
 
PROPERTY_SWISSPROT_COMMENT - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor

Deprecated.
 
PROPERTY_SWISSPROT_FEATUREATTRIBUTE - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor

Deprecated.
 
PROPERTY_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
PROPERTY_TAXON_NAMES - Static variable in class org.biojava.bio.taxa.EbiFormat

Deprecated.
 
PROPERTY_XFF_ID - Static variable in class org.biojava.bio.program.xff.XFFFeatureSetHandler
 
PropertyChanger - Interface in org.biojava.bio.program.tagvalue

Interface for objects that change tag names or properties systematically.

PropertyConstraint - Interface in org.biojava.bio

PropertyConstraints describes a constraint applied
 to the members of an annotation bundle.

PropertyConstraint.And - Class in org.biojava.bio

A property constraint that accpepts items iff they are accepted by both
 child constraints.

PropertyConstraint.ByAnnotationType - Class in org.biojava.bio

ByAnnotationType accepts a property value if it
 belongs to type defined by AnnotationType.

PropertyConstraint.ByClass - Class in org.biojava.bio

ByClass accepts a property value if it is an
 instance of a specific Java class.

PropertyConstraint.Enumeration - Class in org.biojava.bio

Enumeration accepts a property if it is present
 in the specified set of values.

PropertyConstraint.ExactValue - Class in org.biojava.bio

Matches properties if they have exactly this one value.

PropertyConstraint.Or - Class in org.biojava.bio

A property constraint that accepts items iff they are accepted by either
 child constraints.

PropertyForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.MergeAnnotation.PropertyForwarder

Create a new forwarder on behalf of a source using the change support.

PropertyForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.OverlayAnnotation.PropertyForwarder

Forward on behalf of source using the change support provided.

PropertyWriter - Class in org.biojava.bio.program.xff
 
PropertyWriter() - Constructor for class org.biojava.bio.program.xff.PropertyWriter
 
ProportionalSelection - Class in org.biojavax.ga.functions


 A Selection function that determines the proportion of individuals in a new
 population proportionally to their fitness.

ProportionalSelection() - Constructor for class org.biojavax.ga.functions.ProportionalSelection
 
props - Variable in class org.biojava.bio.symbol.Edit
 
Protease - Class in org.biojava.bio.proteomics

The protease class stores parameters needed by Digest to digest a protein sequence.

Protease(String, boolean) - Constructor for class org.biojava.bio.proteomics.Protease

Deprecated.
Creating a Protease with this constructor will not register it
 with the ProteaseManager (use ProteaseManager.createProtease())


Protease(String, boolean, String) - Constructor for class org.biojava.bio.proteomics.Protease

Deprecated.
Creating a Protease with this constructor will not register it
 with the ProteaseManager (use ProteaseManager.createProtease())


Protease(SymbolList, boolean, SymbolList) - Constructor for class org.biojava.bio.proteomics.Protease

Deprecated.
Creating a Protease with this constructor will not register it
 with the ProteaseManager (use ProteaseManager.createProtease())


Protease(SymbolList, boolean, SymbolList, String) - Constructor for class org.biojava.bio.proteomics.Protease
 
ProteaseManager - Class in org.biojava.bio.proteomics

Registry and utility methods for Proteases.

ProteaseManager() - Constructor for class org.biojava.bio.proteomics.ProteaseManager
 
PROTEIN - Static variable in class org.biojava.bio.seq.io.FastaAlignmentFormat
 
PROTEIN_ALPHABET - Static variable in class org.biojava.bio.proteomics.aaindex.AAindex

The alphabet of the symbol property table, that is 
 protein.

PROTEIN_EXIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
PROTEIN_EXISTS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
PROTEIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
PROTEIN_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ProteinRefSeqFileFormer - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead


ProteinRefSeqFileFormer() - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqFileFormer

Deprecated.
 
ProteinRefSeqFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqFileFormer

Deprecated.
 
ProteinRefSeqProcessor - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead


ProteinRefSeqProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqProcessor

Deprecated.
 
ProteinRefSeqProcessor.Factory - Class in org.biojava.bio.seq.io

Deprecated.
Factory which wraps sequence builders in a ProteinRefSeqProcessor

ProteinTools - Class in org.biojava.bio.seq

The central port-of-call for all information and functionality specific to
 SymbolLists over the protein alphabet.

PROVIDER_ORGANISATION - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a provider type.

PROVIDER_PERSON - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a provider type.

PROVIDER_SERVICE - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a provider type.

ProviderNotFoundException - Exception in org.biojava.directory

ProviderNotFoundException is thrown when a sequence
 database provider can not be located.

ProviderNotFoundException() - Constructor for exception org.biojava.directory.ProviderNotFoundException

Creates a ProviderNotFoundException with no detail
 message.

ProviderNotFoundException(String) - Constructor for exception org.biojava.directory.ProviderNotFoundException

Creates a ProviderNotFoundException with the
 specified detail message.

PTM - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser

A name for a comment type.

ptr - Variable in class org.biojava.utils.io.CachingInputStream

The 0-based index into cache of the _next_ byte to return.

publisher - Variable in class org.biojava.bibliography.BibRef

A publisher is responsible for making the resource available.

PUBMED_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms

Holds a reference to the key that must be used to store PubMed
 references.

PUBMED_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
PUBMED_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
PUBMED_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
push(StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler

Push StAXContentHandler object onto stack

push(StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler

Push StAXContentHandler object onto stack

pushParser(TagValueParser, TagValueListener) - Method in interface org.biojava.bio.program.tagvalue.TagValueContext


 Push a parser and listener pair onto the parser stack.

put(byte) - Method in class org.biojava.utils.io.LargeBuffer
 
put(int, double) - Method in class org.biojava.stats.svm.SparseVector

Set the value at a particular dimension.

put(long, byte) - Method in class org.biojava.utils.io.LargeBuffer
 
put(Object, Object) - Method in class org.biojava.utils.BeanAsMap
 
put(Object, Object) - Method in interface org.biojava.utils.cache.CacheMap

Associate a value with a key.

put(Object, Object) - Method in class org.biojava.utils.cache.ChangeableCache
 
put(Object, Object) - Method in class org.biojava.utils.cache.FixedSizeMap
 
put(Object, Object) - Method in class org.biojava.utils.cache.WeakCacheMap
 
put(Object, Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
 
put(Object, Object) - Method in class org.biojava.utils.io.SoftHashMap

Here we put the key, value pair into the HashMap using a SoftValue

 object.

put(Object, Object) - Method in class org.biojava.utils.OverlayMap
 
put(Object, Object) - Method in class org.biojava.utils.SmallMap
 
put(Object, StateMachine.Transition) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable

set a Transition within this TransitionTable (2-argument form)

put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
 
put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
 
put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
 
put(CodonPref) - Method in interface org.biojava.bio.symbol.CodonPrefFilter

handles storage of a CodonPref object

putChar(char) - Method in class org.biojava.utils.io.LargeBuffer
 
putChar(long, char) - Method in class org.biojava.utils.io.LargeBuffer
 
putComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
putComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
putComponent(Location, SymbolList) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
putConnection(Connection) - Method in class org.biojava.utils.JDBCConnectionPool
 
putDouble(double) - Method in class org.biojava.utils.io.LargeBuffer
 
putDouble(long, double) - Method in class org.biojava.utils.io.LargeBuffer
 
putFloat(float) - Method in class org.biojava.utils.io.LargeBuffer
 
putFloat(long, float) - Method in class org.biojava.utils.io.LargeBuffer
 
putInt(int) - Method in class org.biojava.utils.io.LargeBuffer
 
putInt(long, int) - Method in class org.biojava.utils.io.LargeBuffer
 
putLong(long) - Method in class org.biojava.utils.io.LargeBuffer
 
putLong(long, long) - Method in class org.biojava.utils.io.LargeBuffer
 
putShort(long, short) - Method in class org.biojava.utils.io.LargeBuffer
 
putShort(short) - Method in class org.biojava.utils.io.LargeBuffer
 
putStatement(Statement) - Method in class org.biojava.utils.JDBCConnectionPool
 
putTokenization(String, SymbolTokenization) - Method in class org.biojava.bio.symbol.AbstractAlphabet


 Assigns a symbol parser to a String object.

pyl() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Pyrrolysine (O)





Q

q() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Glutamine

QUALIFIER - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
QUALIFIER_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
QUALIFIER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
Qualitative - Interface in org.biojava.bio.program.phred

Qualitative is an interface for classes wanting to hold quality
 data in symbolic form such as Phred scores.

qualityFromP(double) - Static method in class org.biojava.bio.program.phred.PhredTools

The quality value is related to the base call error probability
 by the formula  QV = - 10 * log_10( P_e )
 where P_e is the probability that the base call is an error.

query(String, Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery


 It queries the current collection using a query language.

QUERY_ANCHORED - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
QUERY_ANCHORED_NO_IDENTITIES - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
QUERY_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion

A query criterion.

QUERY_LABEL - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit

This object is used as the label for the query sequence in the
 alignment of the query sequence with this sub-hit sequence.

QUERY_LABEL - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature

Constant QUERY_LABEL is the alignment label used
 for all query sequences.





R

r() - Static method in class org.biojava.bio.seq.DNATools
 
r() - Static method in class org.biojava.bio.seq.NucleotideTools
 
r() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Arginine

R_NORVEGICUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
RadialBaseKernel - Class in org.biojava.stats.svm

This kernel computes the radial base kernel that corresponds to a gausian
 distribution.

RadialBaseKernel() - Constructor for class org.biojava.stats.svm.RadialBaseKernel
 
RadialBaseKernel(SVMKernel, double) - Constructor for class org.biojava.stats.svm.RadialBaseKernel
 
RAF - Class in org.biojava.utils.io
 
RAF(File, String) - Constructor for class org.biojava.utils.io.RAF
 
RAF(String, String) - Constructor for class org.biojava.utils.io.RAF
 
raIndexFile - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
 
RandomAccessReader - Class in org.biojava.utils.io

RandomAccessReader extends Reader to
 provide a means to create buffered Readers from
 RandomAccessFiles.

RandomAccessReader(RandomAccessFile) - Constructor for class org.biojava.utils.io.RandomAccessReader

Creates a new RandomAccessReader wrapping the
 RandomAccessFile and using a default-sized buffer
 (8192 bytes).

RandomAccessReader(RandomAccessFile, int) - Constructor for class org.biojava.utils.io.RandomAccessReader

Creates a new RandomAccessReader wrapping the
 RandomAccessFile and using a buffer of the
 specified size.

randomizeDistribution(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools

Randomizes the weights of a Distribution.

RangeLocation - Class in org.biojava.bio.symbol

A simple implementation of Location that contains all points between
 getMin and getMax inclusive.

RangeLocation(int, int) - Constructor for class org.biojava.bio.symbol.RangeLocation

Construct a new RangeLocation from min to max.

RANK - Static variable in interface org.biojavax.bio.BioEntryRelationship
 
RANK - Static variable in interface org.biojavax.bio.seq.RichFeature
 
RANK - Static variable in interface org.biojavax.bio.seq.RichFeatureRelationship
 
RANK - Static variable in interface org.biojavax.bio.seq.RichLocation
 
RANK - Static variable in interface org.biojavax.Comment
 
RANK - Static variable in interface org.biojavax.Note
 
RANK - Static variable in interface org.biojavax.RankedCrossRef
 
RANK - Static variable in interface org.biojavax.RankedDocRef
 
RankedCrossRef - Interface in org.biojavax

Allows cross-references to other databases to be ranked.

RANKEDCROSSREF - Static variable in interface org.biojavax.bio.BioEntry
 
RANKEDCROSSREF - Static variable in interface org.biojavax.ontology.ComparableTerm
 
RankedCrossRefable - Interface in org.biojavax

Defines an object as being able to have ranked cross references associated
 with it.

rankedCrossRefs - Variable in class org.biojavax.bio.seq.RichFeature.Template
 
RankedDocRef - Interface in org.biojavax

Represents a documentary reference.

RANKEDDOCREF - Static variable in interface org.biojavax.bio.BioEntry
 
RAT_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools

Rattus norvegicus codon preferences

RAW - Static variable in class org.biojava.bio.seq.io.AlignIOConstants

RAW indicates that the alignment format is raw
 (symbols only).

RAW - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

RAW indicates that the sequence format is raw
 (symbols only).

RAW_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants

RAW_AA premade RAW | AA.

RAW_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants

RAW_DNA premade RAW | DNA.

RAW_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants

RAW_RNA premade RAW | RNA.

rawGet(int) - Method in class org.biojava.utils.FileAsList

rawGet reads the record at the specified index as
 a raw byte array.

rbfKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
 
RC_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
RC_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RC_PLASMID_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RC_SPECIES_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RC_STRAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RC_TISSUE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
RC_TRANSP_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
Reaction() - Constructor for class org.biojava.bio.program.formats.Ligand.Reaction
 
read() - Method in class org.biojava.utils.io.CachingInputStream
 
read() - Method in class org.biojava.utils.io.CountedBufferedReader
 
read() - Method in class org.biojava.utils.io.RandomAccessReader

read reads one byte from the underlying
 RandomAccessFile.

read() - Method in class org.biojava.utils.io.UncompressInputStream
 
read() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
read(byte[], int, int) - Method in class org.biojava.utils.io.CachingInputStream
 
read(byte[], int, int) - Method in class org.biojava.utils.io.UncompressInputStream
 
read(char[]) - Method in class org.biojava.utils.io.CountedBufferedReader
 
read(char[], int, int) - Method in class org.biojava.utils.io.CountedBufferedReader
 
read(char[], int, int) - Method in class org.biojava.utils.io.RandomAccessReader

read reads from the underlying
 RandomAccessFile into an array.

read(BufferedReader) - Method in interface org.biojava.bio.seq.io.AlignmentFormat

Read in an alignment from a buffered reader object

read(BufferedReader) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat

Reads an alignment in FASTA format.

read(BufferedReader) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat

Reads an MSF Alignment File

read(BufferedReader, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.Parser
 
readableFileNames - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
readableFiles - Static variable in class org.biojavax.bio.seq.io.FastaFormat
 
readableFiles - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
readColourMap() - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler

Read the the properties file that specifies the character/colour mapping.

readColourMapFromProperties(String) - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler

Setup styles from java property file.

readDBDate() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader

readDBDate reads the date from the index
 header.

readDBName() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader

readDBName returns the database name from the
 index header.

readDBRelease() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader

readDBRelease returns the database release from
 the index header.

readEmbl(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Iterate over the sequences in an EMBL-format stream.

readEMBL(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Read a EMBL file using a custom type of SymbolList.

readEMBLDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an EMBL-format stream of DNA sequences.

readEmblNucleotide(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Iterate over the sequences in an EMBL-format stream.

readEMBLProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an EMBL-format stream of Protein
 sequences.

readEmblRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Iterate over the sequences in an EMBL-format stream, but for RNA.

readEMBLRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an EMBL-format stream of RNA sequences.

readEMBLxml(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Read a EMBLxml file using a custom type of SymbolList.

readEMBLxmlDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an EMBLxml-format stream of DNA
 sequences.

readEMBLxmlProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an EMBLxml-format stream of Protein
 sequences.

readEMBLxmlRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an EMBLxml-format stream of RNA
 sequences.

ReaderInputHandler - Class in org.biojava.utils.process

Reader input handler 
 that reads the input for an external process from a 
 reader.

ReaderInputHandler(Reader, String) - Constructor for class org.biojava.utils.process.ReaderInputHandler

Initializes the reader input handler.

ReaderWriterPipe - Class in org.biojava.utils.process

A multi threaded class
 which pipes the contents of an input reader to an output 
 writer.

ReaderWriterPipe(Reader, Writer, String) - Constructor for class org.biojava.utils.process.ReaderWriterPipe

Initializes the reader writer pipe.

readFasta(BufferedReader, SymbolTokenization) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Read a fasta file.

readFasta(BufferedReader, SymbolTokenization, SequenceBuilderFactory) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Read a fasta file using a custom type of SymbolList.

readFasta(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Read a fasta file building a custom type of RichSequence
 .

readFasta(BufferedReader, SymbolTokenization, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Read a fasta file.

readFasta(InputStream, Alphabet) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Create a sequence database from a fasta file provided as an
 input stream.

readFastaDNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Iterate over the sequences in an FASTA-format stream of DNA sequences.

readFastaDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an FASTA-format stream of DNA
 sequences.

readFastaProtein(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Iterate over the sequences in an FASTA-format stream of Protein sequences.

readFastaProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an FASTA-format stream of Protein
 sequences.

readFastaRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Iterate over the sequences in an FASTA-format stream of RNA sequences.

readFastaRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an FASTA-format stream of RNA
 sequences.

readFile(File, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Guess which format a file is then attempt to read it.

readFile(File, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Guess which format a file is then attempt to read it.

readFileLength() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader

readFileLength returns the file length in bytes
 (stored within the file's header by the indexing program).

readFromXML(InputStream) - Static method in class org.biojava.bio.dist.DistributionTools

Read a distribution from XML.

readFromXML(InputStream) - Static method in class org.biojava.bio.symbol.CodonPrefTools
 
readFromXML(InputStream, String) - Static method in class org.biojava.bio.symbol.CodonPrefTools

reads a specified CodonPref from an file.

readFromXML(InputStream, CodonPrefFilter) - Static method in class org.biojava.bio.symbol.CodonPrefTools

read an CodonPref XML stream and handle it with a CodonPrefFilter object.

readGenbank(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Iterate over the sequences in an Genbank-format stream.

readGenbank(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Read a GenBank file using a custom type of SymbolList.

readGenbankDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an GenBank-format stream of DNA
 sequences.

readGenbankProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an GenBank-format stream of Protein
 sequences.

readGenbankRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an GenBank-format stream of RNA
 sequences.

readGenbankXml(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Iterate over the sequences in an GenbankXML-format stream.

readGenpept(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Iterate over the sequences in an Genpept-format stream.

readGFF(BufferedReader) - Static method in class org.biojava.bio.program.gff.GFFTools

Read all GFF entries from a buffered reader.

readGFF(BufferedReader, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools

Read all GFF entries matching a filter from a buffered reader.

readGFF(File) - Static method in class org.biojava.bio.program.gff.GFFTools

Reads a GFFEntrySet from a file with no filtering.

readGFF(File, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools

Reads a GFFEntrySet from a file with the specified filter.

readGFF(String) - Static method in class org.biojava.bio.program.gff.GFFTools

Deprecated.
use: readGff(File)


readGFF(String, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools

Deprecated.
use: readGff(File,GFFRecordFilter)


readHashedFastaDNA(BufferedInputStream, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an FASTA-format stream of DNA
 sequences.

readingFrame - Variable in class org.biojava.bio.seq.FramedFeature.Template
 
readINSDseq(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Read a INSDseq file using a custom type of SymbolList.

readINSDseqDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an INSDseq-format stream of DNA
 sequences.

readINSDseqProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an INSDseq-format stream of Protein
 sequences.

readINSDseqRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an INSDseq-format stream of RNA
 sequences.

readLine() - Method in class org.biojava.utils.io.CountedBufferedReader
 
readMatrix(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
readModel(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
readModelFile(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
readName(BufferedReader) - Method in interface org.biojavax.bio.taxa.io.NCBITaxonomyLoader

Reads the next entry from the names.dmp file and returns the corresponding 
 NCBITaxon object with the name added in already.

readName(BufferedReader) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader

Reads the next entry from the names.dmp file and returns the corresponding 
 NCBITaxon object with the name added in already.

readNode(BufferedReader) - Method in interface org.biojavax.bio.taxa.io.NCBITaxonomyLoader

Reads the next entry from the nodes.dmp file and returns the corresponding 
 NCBITaxon object.

readNode(BufferedReader) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader

Reads the next entry from the nodes.dmp file and returns the corresponding 
 NCBITaxon object.

readPhredQuality(BufferedReader) - Static method in class org.biojava.bio.program.phred.PhredTools

Constructs a StreamReader to read in Phred quality data in FASTA format.

readPhredSequence(BufferedReader) - Static method in class org.biojava.bio.program.phred.PhredTools

Calls SeqIOTools.readFastaDNA(br), added here for convinience.

readQuotedString(String, int, int, char, boolean, boolean) - Method in class org.biojava.ontology.obo.OboFileParser
 
readRawRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader

readRawRecord returns the raw bytes of a single
 record from the index.

readRecord() - Method in class org.biojava.bio.seq.db.emblcd.AcnumHitReader

readRecord creates an array of Objects from the
 raw byte array of a single record.

readRecord() - Method in class org.biojava.bio.seq.db.emblcd.AcnumTrgReader

readRecord creates an array of Objects from the
 raw byte array of a single record.

readRecord() - Method in class org.biojava.bio.seq.db.emblcd.DivisionLkpReader

readRecord creates an array of Objects from the
 raw byte array of a single record.

readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader

readRecord returns an array of objects parsed from
 a single record.

readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess

readRecord returns an array of objects parsed from
 a single record.

readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader

readRecord creates an array of Objects from the
 raw byte array of a single record.

readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess

readRecord creates an array of Objects from the
 raw byte array of a single record.

readRecordCount() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader

readRecordCount returns the number of records in
 the file.

readRecordLength() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader

readRecordLength returns the record length
 (bytes).

readResolve() - Method in class org.biojava.bio.proteomics.Protease

Prevent duplication of the object during Serialization

readResolve() - Method in class org.biojava.bio.symbol.AbstractAlphabet

To prevent duplication of a what should be a
 single instance of an existing alphabet.

readResolve() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet

To prevent duplication of a what should be a
 single instance of an existing alphabet.

readResolve() - Method in class org.biojava.utils.StaticMemberPlaceHolder
 
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat

Reads a sequence from the given buffered reader using the given tokenizer to parse
 sequence symbols.

readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat

Reads a sequence from the given buffered reader using the given tokenizer to parse
 sequence symbols.

readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat

Reads a sequence from the given buffered reader using the given tokenizer to parse
 sequence symbols.

readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.GenbankFormat

Reads a sequence from the given buffered reader using the given tokenizer to parse
 sequence symbols.

readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.INSDseqFormat

Reads a sequence from the given buffered reader using the given tokenizer to parse
 sequence symbols.

readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Reads a sequence from the given buffered reader using the given tokenizer to parse
 sequence symbols.

readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtFormat

Reads a sequence from the given buffered reader using the given tokenizer to parse
 sequence symbols.

readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat

Reads a sequence from the given buffered reader using the given tokenizer to parse
 sequence symbols.

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.program.phred.PhredFormat
 
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.FastaFormat

Deprecated.
Reads information from a flatfile to a SeqIOListener
 using a SymbolTokenizer to convert sequence strings
 to Symbol objects.

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GAMEFormat

this version only reads annotations (no symbols)

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
Reads a sequence from the specified reader using the Symbol
 parser and Sequence Factory provided.

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GenbankXmlFormat

Deprecated.
 
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in interface org.biojava.bio.seq.io.SequenceFormat

Read a sequence and pass data on to a SeqIOListener.

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.EMBLFormat

Read a sequence and pass data on to a SeqIOListener.

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat

Read a sequence and pass data on to a SeqIOListener.

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.FastaFormat

Read a sequence and pass data on to a SeqIOListener.

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.GenbankFormat

Read a sequence and pass data on to a SeqIOListener.

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.INSDseqFormat

Read a sequence and pass data on to a SeqIOListener.

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.UniProtFormat

Read a sequence and pass data on to a SeqIOListener.

readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat

Read a sequence and pass data on to a SeqIOListener.

readStream(BufferedInputStream, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Guess which format a stream is then attempt to read it.

readStream(BufferedInputStream, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Guess which format a stream is then attempt to read it.

readSwissprot(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Iterate over the sequences in an Swissprot-format stream.

readSymbol() - Method in interface org.biojava.bio.seq.io.SymbolReader

Return a single symbol from the stream.

readSymbols(Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SymbolReader

Read one or more symbols from the stream.

readUniProt(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Read a UniProt file using a custom type of SymbolList.

readUniProt(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an UniProt-format stream of RNA
 sequences.

readUniProtXML(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Read a UniProt XML file using a custom type of SymbolList.

readUniProtXML(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Iterate over the sequences in an UniProt XML-format stream of RNA
 sequences.

readXFF(File, String) - Static method in class org.biojava.bio.program.xff.XFFTools
 
readXFF(File, String, FiniteAlphabet) - Static method in class org.biojava.bio.program.xff.XFFTools
 
readXMLChunk(BufferedReader, DefaultHandler, String) - Static method in class org.biojavax.utils.XMLTools

Attempts to read XML file in chunks, passing each chunk to a SAX parser.

ready() - Method in class org.biojava.utils.io.CountedBufferedReader
 
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
realizeFeature(FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.RealizingFeatureHolder

Realize a feature template.

realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
 
realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.FeatureRealizer

Install a feature on the specified sequence.

realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer
 
realizeSubFeatures(Feature) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler

recursively attach children features to parent

RealizingFeatureHolder - Interface in org.biojava.bio.seq

Interface for FeatureHolder objects which know how to
 instantiate new child Features.

reapGarbageListeners() - Method in class org.biojava.utils.ChangeSupport

Remove all references to listeners which have been cleared by the
 garbage collector.

REBASE_DATA_KEY - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager

REBASE_DATA_KEY the ResourceBundle key which
 specifies the location of the REBASE flat file.

REBASE_TAG_COMM - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager

REBASE_TAG_COMM the REBASE tag containing the
 commercial suppliers.

REBASE_TAG_ISZR - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager

REBASE_TAG_ISZR the REBASE tag containing the
 enzyme isoschizomers.

REBASE_TAG_METH - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager

REBASE_TAG_METH the REBASE tag containing the
 methylation site.

REBASE_TAG_NAME - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager

REBASE_TAG_NAME the REBASE tag containing the
 enzyme name.

REBASE_TAG_ORGN - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager

REBASE_TAG_ORGN the REBASE tag containing the
 organism.

REBASE_TAG_REFS - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager

REBASE_TAG_REFS the REBASE tag containing the
 references.

REBASE_TAG_SITE - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager

REBASE_TAG_SITE the REBASE tag containing the
 enzyme site.

REBASE_TAG_SRCE - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager

REBASE_TAG_SRCE the REBASE tag containing the
 source.

rebind(String, Object) - Method in class org.biojava.naming.ObdaContext
 
rebind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
 
rebind(Name, Object) - Method in class org.biojava.naming.ObdaContext
 
rebind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
 
recBytes - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
 
Record - Interface in org.biojava.bio.program.indexdb

Record represents a record within an indexed flat file
 databank as defined by the OBDA standard.

Record.Impl - Class in org.biojava.bio.program.indexdb

Impl is the default implementation of Record.

recordEmittedSymbol(State, Symbol, double) - Method in interface org.biojava.bio.dp.HMMTrainer

record that the specified symbol was emitted from the specified state.

recordEmittedSymbol(State, Symbol, double) - Method in class org.biojava.bio.dp.SimpleHMMTrainer
 
recordLine(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler

A record line has been encountered.

recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFFilterer

Only forward the GFFRecords that match a filter.

recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFWriter

Prints record to the PrintWriter.

recordLine(GFF3Record) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler

A record line has been encountered.

recordTransition(State, State, double) - Method in interface org.biojava.bio.dp.HMMTrainer

record that a transition was observed between the specified states.

recordTransition(State, State, double) - Method in class org.biojava.bio.dp.SimpleHMMTrainer
 
recParser - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
 
recParser - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess

A recParser for implementing
 readRecord() specific to each concrete subclass.

REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
REF_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
REF_POS_BEGIN_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
REF_POS_END_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
REF_XREF_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
REFERENCE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
REFERENCE_LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
REFERENCE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
REFERENCE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
ReferenceAnnotation - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead


ReferenceAnnotation() - Constructor for class org.biojava.bio.seq.io.ReferenceAnnotation

Deprecated.
 
REFERENCES_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
REFLEXIVE - Static variable in class org.biojava.ontology.OntoTools
 
refp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
refRange - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
REFSEQ - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

REFSEQ indicates that the sequence format is
 REFSEQ.

REFSEQ_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

REFSEQ_AA premade REFSEQ | AA.

REFSEQ_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

REFSEQ_DNA premade REFSEQ | DNA.

REFSEQ_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

REFSEQ_RNA premade REFSEQ | RNA.

RegexChanger - Class in org.biojava.bio.program.tagvalue


 A ValueChanger.Changer that returns a specific match value using a regex
 Pattern.

RegexChanger(Pattern, int) - Constructor for class org.biojava.bio.program.tagvalue.RegexChanger

Create a new RegexChanger with a pattern.

RegexException - Exception in org.biojava.utils.regex

An exception thrown by classes of this package.

RegexException(String) - Constructor for exception org.biojava.utils.regex.RegexException
 
RegexException(Throwable) - Constructor for exception org.biojava.utils.regex.RegexException
 
RegexException(Throwable, String) - Constructor for exception org.biojava.utils.regex.RegexException
 
RegexFieldFinder - Class in org.biojava.bio.program.tagvalue
 
RegexFieldFinder(TagValueListener, Pattern, String[], boolean) - Constructor for class org.biojava.bio.program.tagvalue.RegexFieldFinder

Creates a new RegexFiledFinder.

RegexParser - Class in org.biojava.bio.program.tagvalue


 A TagValueParser that splits a line based upon a regular expression.

RegexParser() - Constructor for class org.biojava.bio.program.tagvalue.RegexParser

Create a new RegexParser with all boolean values set to false.

RegexSplitter - Class in org.biojava.bio.program.tagvalue


 A ValueChanger.Splitter that splits a line of text using a regular
 expression, returning one value per match.

RegexSplitter(Pattern, int) - Constructor for class org.biojava.bio.program.tagvalue.RegexSplitter

Create a new RegexSplitter with a pattern.

Region(Location, String, boolean) - Constructor for class org.biojava.bio.seq.RemoteFeature.Region

Create a new Region.

regions - Variable in class org.biojava.bio.seq.RemoteFeature.Template
 
register(RestrictionEnzyme, Set) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager

register regisiters a new
 RestrictionEnzyme with the manager.

registerAlphabet(String[], Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager

Register and Alphabet by more than one name.

registerAlphabet(String, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager

Register an alphabet by name.

registerCollectionHandlerFactory(String, String, XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler

Register a factory used to create handlers for the specified tag in an
 XML AnnotationType

registerDistribution(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext


 Register a distribution object with this context.

registerDistribution(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
registered(String) - Static method in class org.biojava.bio.proteomics.ProteaseManager

Has a Protease been registered with that name?

registered(String) - Static method in class org.biojava.bio.symbol.AlphabetManager

Has an Alphabet been registered by that name

registerFactory(UnigeneFactory) - Static method in class org.biojava.bio.program.unigene.UnigeneTools

Register a UnigeneFactory.

registerFormat(Class) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Register a new format with IOTools for auto-guessing.

registerHandlerFactory(String, String, XMLFilterHandler.FilterHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler

Register a factory used to create handlers for the specified tag name

registerModel(MarkovModel) - Method in interface org.biojava.bio.dp.ModelTrainer

Registers an HMM with this trainer.

registerModel(MarkovModel) - Method in class org.biojava.bio.dp.SimpleModelTrainer
 
registerPropertyHandlerFactory(String, String, XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler

Register a factory used to create handlers for the specified tag in an
 XML AnnotationType

registerProtease(Protease) - Static method in class org.biojava.bio.proteomics.ProteaseManager

Registers a protease and ensures its flyweight status

registerTrainer(Distribution, DistributionTrainer) - Method in interface org.biojava.bio.dist.DistributionTrainerContext


 Register a Distribution and an associated DistributionTrainer object.

registerTrainer(Distribution, DistributionTrainer) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractDistribution

Register an IgnoreCountsTrainer instance as the trainer for this
 distribution.

registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.Distribution


 Register this distribution with a training context.

registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.GapDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.PairDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution

Register an SimpleDistribution.Trainer instance as the trainer for this distribution.

registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.TranslatedDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UniformDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UntrainableDistribution
 
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dist.PairDistribution

Register this paired distribution with a model trainer.

registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
registerWithTrainer(ModelTrainer) - Method in interface org.biojava.bio.dp.Trainable

Perform any registration that is necessary with mt.

registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.WMAsMM
 
registrations() - Static method in class org.biojava.bio.symbol.AlphabetManager

A set of names under which Alphabets have been registered.

Registry - Class in org.biojava.directory

Registry is a factory which gets implementations of
 the BioJava SequenceDBLite interface.

Registry(RegistryConfiguration) - Constructor for class org.biojava.directory.Registry

Creates a new OBDA Registry with the specified
 configuration.

RegistryConfiguration - Interface in org.biojava.directory

The BioDirectory Registry is a simple system for specifying
 where to find services which provide sequence databases.

RegistryConfiguration.Composite - Class in org.biojava.directory

A RegistryConfiguration that allows you to treat other
 configurations as providing important or default configuration
 information.

RegistryConfiguration.Impl - Class in org.biojava.directory

A simple implementation of RegistryConfiguration backed by a Map.

RegistryException - Exception in org.biojava.directory

A RegistryException thrown when the registry cannot
 find an implementation of a requested SequenceDB.

RegistryException() - Constructor for exception org.biojava.directory.RegistryException

Creates a new RegistryException with no detail
 message.

RegistryException(String) - Constructor for exception org.biojava.directory.RegistryException

Creates a new RegistryException with the specified
 detail message.

RegistryException(String, Throwable) - Constructor for exception org.biojava.directory.RegistryException
 
RegistryException(Throwable) - Constructor for exception org.biojava.directory.RegistryException

Creates a new RegistryException with no detail
 message, wrapping another Throwable.

RegistryException(Throwable, String) - Constructor for exception org.biojava.directory.RegistryException

Deprecated.
use new RegistryException(message, cause)


REL_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
RelabeledAlignment - Class in org.biojava.bio.symbol

An alignment that relabels another alignment.

RelabeledAlignment(Alignment) - Constructor for class org.biojava.bio.symbol.RelabeledAlignment
 
RELATED_SYNONYM - Static variable in class org.biojava.ontology.Synonym
 
RELATION - Static variable in class org.biojava.ontology.OntoTools
 
RELATION - Static variable in interface org.biojavax.bio.seq.RichFeature
 
RELATIONS - Static variable in interface org.biojavax.bio.BioEntry
 
RELATIONSHIP - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
REMARK - Static variable in interface org.biojavax.DocRef
 
REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
RemoteFeature - Interface in org.biojava.bio.seq

A feature that indicates that there is some remote feature that can't be
 represented entirely on a single Sequence.

RemoteFeature.Region - Class in org.biojava.bio.seq

A tuple of Location and sequence ID.

RemoteFeature.Resolver - Interface in org.biojava.bio.seq

The interface for objects that actually can take a RemoteFeature and
 return a Sequence object with the feature resolved into a real feature.

RemoteFeature.Template - Class in org.biojava.bio.seq
 
RemotePairwiseAlignmentOutputProperties - Interface in org.biojavax.bio.alignment

RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding 
 output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object.

RemotePairwiseAlignmentProperties - Interface in org.biojavax.bio.alignment

RemotePairwiseAlignmentProperties is a interface that contains the barest of 
 methods for setting and getting Alignment properties.

RemotePairwiseAlignmentService - Interface in org.biojavax.bio.alignment

This interface specifies minimal information needed to execute a pairwise alignment on a remote service.

RemoteQBlastAlignmentProperties - Class in org.biojavax.bio.alignment.blast

This class implements RemotePairwiseAlignmentProperties by specifying several
 convenient methods used to wrap the addition of Blast alignment parameters.

RemoteQBlastAlignmentProperties() - Constructor for class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
 
RemoteQBlastOutputFormat - Enum in org.biojavax.bio.alignment.blast

The RemoteQBlastOutputFormat enum acts like static fields for specifiying various
 values for certain output options.

RemoteQBlastOutputProperties - Class in org.biojavax.bio.alignment.blast

The actual implementation of the RemotePairwiseAlignmentOutputProperties 
 interface for the QBlast service.

RemoteQBlastOutputProperties() - Constructor for class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties

This constructor build the parameters for the default output of the GET command sent to the QBlast service.

RemoteQBlastService - Class in org.biojavax.bio.alignment.blast

RemoteQBlastService - A simple way of submitting BLAST request to the QBlast
 service at NCBI.

RemoteQBlastService() - Constructor for class org.biojavax.bio.alignment.blast.RemoteQBlastService

The constructor for a QBlast service request.

RemoteTerm - Interface in org.biojava.ontology

A term in another ontology.

RemoteTerm.Impl - Class in org.biojava.ontology

Simple in-memory implementation of a remote ontology term.

remove() - Method in class org.biojava.bio.alignment.Alignment.SymbolListIterator
 
remove() - Method in class org.biojava.bio.dp.DP.ReverseIterator
 
remove() - Method in class org.biojava.utils.MergingIterator
 
remove(Object) - Method in interface org.biojava.utils.cache.CacheMap

Explicitly remove an object.

remove(Object) - Method in class org.biojava.utils.cache.FixedSizeMap
 
remove(Object) - Method in class org.biojava.utils.cache.WeakCacheMap
 
remove(Object) - Method in class org.biojava.utils.io.SoftHashMap
 
remove(Object) - Method in class org.biojava.utils.MergingSet
 
remove(Object) - Method in class org.biojavax.ga.util.WeightedSet
 
removeAllOrganisms() - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeAllOrganisms() - Method in interface org.biojavax.ga.Population

Removes all the Organisms in this Population

removeAllOrganismsImpl() - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeAllOrganismsImpl() - Method in class org.biojavax.ga.impl.SimplePopulation
 
removeAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation

Remove an Annotation from the list.

removeAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB

Remove a DB from this view.

removeBioEntry(String) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
 
removeBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
removeBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite

Remove the BioEntry associated with an ID from the database.

removeBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB
 
removeChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext

Remove a ChangeListener from a projected feature.

removeChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
 
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
removeChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
 
removeChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable

Deprecated.
use removeChangeListener(cl, ChangeType.UNKNOWN)


removeChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport

Remove a listener that was interested in all types of changes.

removeChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
 
removeChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

Remove a listener that was interested in all types of changes.

removeChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
removeChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
 
removeChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable

Remove a listener that was interested in a specific types of changes.

removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport

Remove a listener that was interested in a specific types of changes.

removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

Remove a listener that was interested in a specific types of changes.

removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory

Deprecated.
 
removeChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory

Deprecated.
Remove a Taxon as a child to this one.

removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory

Deprecated.
 
removeComment(Comment) - Method in interface org.biojavax.bio.BioEntry

Removes a comment instance from this bioentry.

removeComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry

Removes a comment instance from this bioentry.

removeComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
removeComponent(Location) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
removeDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB

Remove a distributed data source.

removeDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple

Removes a descriptor.

removeDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple

Removes a descriptor.

removeEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper

removeEnzyme removes an enzyme from those to be
 searched for in the Sequence.

removeFeature(Feature) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
removeFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder

Remove a feature from this FeatureHolder.

removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence

Remove a feature attached to this sequence.

removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence

Remove a feature from this sequence.

removeFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
 
removeFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext

Remove the dying child.

removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
 
removeFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Remove a feature from this FeatureHolder.

removeFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence

Remove a feature from this FeatureHolder.

removeFeature(Feature, Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext

Remove the dying child.

removeFeature(Feature, Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
removeFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder

Remove a FeatureHolder from the set of FeatureHolders which
 are merged.

removeFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder

Removes a relationship from this feature holder.

removeFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Removes a relationship from this feature holder.

removeForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
 
removeFromEnvironment(String) - Method in class org.biojava.naming.ObdaContext
 
removeGap(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList

Remove a single gap at position pos in this GappedSymbolList.

removeGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
removeGaps(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList

Remove some gaps at position pos in this GappedSymbolList.

removeGaps(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
removeItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
removeItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
 
removeKey(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory

removeKey removes the specified
 key.

removeKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model

Remove a key.

removeListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub

remove a ChangeListener associated with given key.

removeListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub
 
removeName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon

Removes the name from the given name class.

removeName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Removes the name from the given name class.

removeNote(Note) - Method in class org.biojavax.EmptyRichAnnotation

Removes a note from this annotation.

removeNote(Note) - Method in interface org.biojavax.RichAnnotation

Removes a note from this annotation.

removeNote(Note) - Method in class org.biojavax.SimpleRichAnnotation

Removes a note from this annotation.

removeOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeOrganism(Organism) - Method in interface org.biojavax.ga.Population

Kills off the organism

removeOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation
 
removeOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeOrganisms(Set) - Method in interface org.biojavax.ga.Population

Removes all the Organisms in orgs

removeOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
removeOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population

Removes all the Organisms in orgs

removeOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet

Remove an orthologue from the set.

removeOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
 
removeOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet

removes a specified OrthoPair relationship
 from this group.

removeOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat

Removes a parse error listener from the list of listeners if it is
 included.

removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
Removes a parse error listener from the list of listeners if it is
 included.

removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor

Deprecated.
Removes a parse error listener from the list of listeners if it is
 included.

removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat

Deprecated.
Removes a parse error listener from the list of listeners if it is
 included.

removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
Removes a parse error listener from the list of listeners if it is
 included.

removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor

Deprecated.
Removes a parse error listener from the list of listeners if it is
 included.

removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor

Deprecated.
Removes a parse error listener from the list of listeners if it is
 included.

removeParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource

Removes a parse error listener from the list of listeners.

removeProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
 
removeProperty(Object) - Method in interface org.biojava.bio.Annotation

Delete a property.

removeProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
 
removeProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
 
removeProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation

Delete a property.

removeProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation

Deprecated. 

removeProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
 
removeProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType

Remove a value from the specified property slot.

removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Removes a ranked cross reference from the existing set.

removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry

Removes a ranked cross reference from the existing set.

removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm

Removes a ranked cross reference from the existing set.

removeRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable

Removes a ranked cross reference from the existing set.

removeRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry

Removes a ranked docref instance from this bioentry.

removeRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry

Removes a ranked docref instance from this bioentry.

removeRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry

Removes a relation instance from this bioentry.

removeRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry

Removes a relation instance from this bioentry.

removeRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes

Remove a repository from FeaturTypes.

removeRichSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
removeRichSequence(String) - Method in interface org.biojavax.bio.db.RichSequenceDBLite

Remove the RichSequence associated with an ID from the database.

removeSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer

Remove a secondary key.

removeSequence(String) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
 
removeSequence(String) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
 
removeSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB
 
removeSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB

removeSequence always throws a
 ChangeVetoException as this implementation is
 immutable.

removeSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
removeSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDBLite

Remove the sequence associated with an ID from the database.

removeSequence(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB

Not supported, you can't remove a sequence from a WebDB!

removeSequence(String) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
 
removeSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
removeSequence(String) - Method in class org.biojavax.bio.db.HashRichSequenceDB
 
removeSet(Set) - Method in class org.biojava.utils.MergingSet
 
removeState(State) - Method in interface org.biojava.bio.dp.MarkovModel

Remove a state from the model.

removeState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
removeState(State) - Method in class org.biojava.bio.dp.WMAsMM
 
removeSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet

Remove a symbol from this alphabet.

removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet

SoftMaskedAlphabets cannot remove Symbols.

removeSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
removeSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl
 
removeSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl
 
removeSynonym(Object) - Method in class org.biojava.ontology.Term.Impl
 
removeSynonym(Object) - Method in interface org.biojava.ontology.Term

Remove a synonym for this term.

removeSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl
 
removeSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm

Remove a synonym for this term.

removeSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple

Remove a synonym for this term.

removeTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper

Remove a tag so that it will not be retained.

removeVariableModifications(char) - Method in class org.biojava.bio.proteomics.MassCalc

Remove all variable modifications assocaited with this residue.

removeVariableModifications(Symbol) - Method in class org.biojava.bio.proteomics.MassCalc

Remove all variable modifications assocaited with this residue.

rename(String, String) - Method in class org.biojava.naming.ObdaContext
 
rename(Name, Name) - Method in class org.biojava.naming.ObdaContext
 
renumber(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList

Renumber the view indexes from block, adding delta to each offset.

ReparentContext - Class in org.biojava.bio.seq.projection

A good base class to implement ProjectionContext from.

ReparentContext(FeatureHolder, FeatureHolder) - Constructor for class org.biojava.bio.seq.projection.ReparentContext
 
RepeatedCharSequence - Class in org.biojava.utils
 
RepeatedCharSequence() - Constructor for class org.biojava.utils.RepeatedCharSequence
 
RepeatedCharSequence(int, char) - Constructor for class org.biojava.utils.RepeatedCharSequence
 
replacement - Variable in class org.biojava.bio.symbol.Edit
 
replicate(String) - Method in class org.biojavax.ga.impl.SimpleOrganism
 
replicate(String) - Method in interface org.biojavax.ga.Organism

Creates a replica of this Organism with a new name.

reportDna(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
 
reportDna(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
reportDna(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
 
reportDna(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
 
reportExon(RangeLocation, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
 
reportExon(RangeLocation, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf

Allows nesting class that manages a transcript template
 to gain information about its extent from nested
 elements that represent exons.

reportFeature(Location) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf

Allows nesting class that manages a gene template
 to gain information about its extent from nested
 elements.

reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
 
reportFeature(Location) - Method in interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
 
reportFeature(Location) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
 
reportFeature(Location) - Method in interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf

Allows nesting class that manages a gene template
 to gain information about its extent from nested
 elements.

reportMatch(SymbolList, Pattern, int, int) - Method in interface org.biojava.utils.regex.Search.Listener
 
reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVECallbackItf
 
reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf
 
reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
 
reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
 
reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
 
reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
 
reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
 
reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
 
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
 
reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf
 
REPOSITORY_SUBSETS - Static variable in interface org.biojava.bibliography.BibRefSupport

A vocabulary name.

RepositoryImpl(String) - Constructor for class org.biojava.bio.seq.FeatureTypes.RepositoryImpl

Create a named repository.

repositorySubset - Variable in class org.biojava.bibliography.BiblioEntryStatus


 Some bibliographic repositories consist of several, or even
 many, databases.

requestsQueued() - Method in class org.biojava.utils.SimpleThreadPool

requestsQueued returns the number of
 Runnables currently queued.

reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
 
reset() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
 
reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
 
reset() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
 
reset() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter

resets the internal state of this filter including
 any cached evaluations.

reset() - Method in class org.biojava.utils.io.CountedBufferedReader
 
reset() - Method in class org.biojava.utils.regex.Matcher

Resets this matcher.

reset() - Method in class org.biojavax.utils.CRC64Checksum
 
reset(SymbolList) - Method in class org.biojava.utils.regex.Matcher

Resets this matcher with a new input SymbolList.

resolve(RemoteFeature) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
 
resolve(RemoteFeature) - Method in interface org.biojava.bio.seq.RemoteFeature.Resolver

Resolve rFeat.

resolve(FuzzyPointLocation) - Method in interface org.biojava.bio.symbol.FuzzyPointLocation.PointResolver

Return the actual point that the specified location should claim to
 occupy.

RESOLVE_AVERAGE - Static variable in class org.biojava.bio.symbol.FuzzyLocation

Use the arithmetic mean of the `inner' and `outer' values, unless the
 outer value is unbounded.

RESOLVE_AVERAGE - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
 
RESOLVE_INNER - Static variable in class org.biojava.bio.symbol.FuzzyLocation

Always use the `inner' values.

RESOLVE_MAX - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
 
RESOLVE_MIN - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
 
RESOLVE_OUTER - Static variable in class org.biojava.bio.symbol.FuzzyLocation

Use the `outer' values, unless they are unbounded in which case the
 `inner' values are used.

resolveCommands(String, Properties) - Static method in class org.biojava.utils.process.ExternalProcess

Resolves the given command line by replacing all placeholder of the 
 format %NAME% with the values from the given properties
 for the corresponding keys of the format NAME.

resolveEntity(String, String) - Method in class org.biojava.utils.xml.ResourceEntityResolver
 
resolveInt(int) - Method in class org.biojava.ontology.IntegerOntology
 
resolveMax(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver

Delegate for the getMax() method.

resolveMin(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver

Delegate for the getMin() method.

resolver - Variable in class org.biojava.bio.seq.RemoteFeature.Template
 
RESOURCE_TYPES - Static variable in interface org.biojava.bibliography.BibRefSupport

A vocabulary name.

ResourceEntityResolver - Class in org.biojava.utils.xml

SAX EntityResolve which looks up system IDs as resources
 from a Java ClassLoader.

ResourceEntityResolver(String) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver

Construct a resolver which searches for resources in the specified
 path relative to the current classloader.

ResourceEntityResolver(String[]) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver

Construct a resolver which searches for resources in the specified
 list of directories relative to the current classloader.

ResourceEntityResolver(String[], ClassLoader) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver

Construct a resolver which searches for resources in the specified
 list of directories relative to the supplied classloader.

ResourceEntityResolver(String, ClassLoader) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver

Construct a resolver which searches for resources in the specified
 path relative to the supplied classloader.

RestrictionEnzyme - Class in org.biojava.bio.molbio

RestrictionEnzyme represents a restriction enzyme
 according to the REBASE standard.

RestrictionEnzyme(String, SymbolList, int, int) - Constructor for class org.biojava.bio.molbio.RestrictionEnzyme

Creates a new RestrictionEnzyme which cuts within
 or downstream of the recognition site.

RestrictionEnzyme(String, SymbolList, int, int, int, int) - Constructor for class org.biojava.bio.molbio.RestrictionEnzyme

Creates a new RestrictionEnzyme of the unusual
 type which cuts both upstream and downstream of its recognition
 site.

RestrictionEnzymeManager - Class in org.biojava.bio.molbio

RestrictionEnzymeManager manages collections of
 static RestrictionEnzyme instances.

RestrictionMapper - Class in org.biojava.bio.molbio

RestrictionMapper is a class for annotating
 Sequences with Features which represent
 restriction sites.

RestrictionMapper(ExecutorService) - Constructor for class org.biojava.bio.molbio.RestrictionMapper

Creates a new RestrictionMapper which will use
 the specified ExecutorService.

RestrictionMapper(ThreadPool) - Constructor for class org.biojava.bio.molbio.RestrictionMapper

Creates a new RestrictionMapper which will use
 the specified ThreadPool.

RestrictionSite - Interface in org.biojava.bio.molbio

RestrictionSite represents the recognition site of a
 restriction enzyme.

RestrictionSite.Template - Class in org.biojava.bio.molbio

Template for construction of
 RestrictionSites.

RESULT_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
retainAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
 
returnData(Object) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler

provides a standardised way of returning an
  object that represents the result of parsing the
  child element

Retyper(Object, ChangeSupport, ChangeType) - Constructor for class org.biojava.utils.ChangeForwarder.Retyper

Create a new Retyper for forwarding events.

RevCompSequence - Class in org.biojava.bio.seq.impl

A reverse complement view onto Sequence interface.

RevCompSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.RevCompSequence

URN, Name and Annotation are copied as is from the original Sequence, unless you use the
  the other contructor that sets these.

RevCompSequence(Sequence, String, String, Annotation) - Constructor for class org.biojava.bio.seq.impl.RevCompSequence
 
reverse(SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews

A reversed view onto a SymbolList.

reverseComplement(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools

Reverse-complement a sequence, and flip all of its features.

reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools

Retrieve a reverse-complement view of list.

reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools

Retrieve a reverse-complement view of list.

reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools

Retrieve a reverse-complement view of list.

ReverseIterator(SymbolList) - Constructor for class org.biojava.bio.dp.DP.ReverseIterator
 
reverseRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
ReversibleTranslationTable - Interface in org.biojava.bio.symbol

A translation table that can also translate from the target to source
 alphabet.

revertFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
 
revertFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext

Unproject a feature.

revertFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
revertFilter(FeatureFilter) - Method in interface org.biojava.bio.seq.projection.ProjectionContext

Transform a filter on projected features so that it applies to unprojected
 features.

revertFilter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ReparentContext
 
revertLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
 
revertLocation(Location) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
revertLocation(Location, int, boolean) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils

Revert a location, translating and flipping as required.

revertStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
 
revertTemplate(Feature.Template, ProjectionContext) - Method in class org.biojava.bio.seq.projection.ProjectionEngine

Revert a template so that it can be used on the original feature-space.

revertTemplate(ProjectionContext, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionEngine.TemplateProjector
 
RichAnnotatable - Interface in org.biojavax

Annotatable objects that can have rich annotations.

RichAnnotation - Interface in org.biojavax

An annotation collection which stores annotations as Note objects.

RichFeature - Interface in org.biojavax.bio.seq

Represents a feature that can be given name and rank and be
 moved from one sequence to another.

RichFeature.Template - Class in org.biojavax.bio.seq

Added-value extension of Feature.Template including bits we're 
 interested in, eg. featureRelationshipSet for relationships with
 other features, and rankedCrossRefs for lookups into other databases.

RichFeature.Tools - Class in org.biojavax.bio.seq

Some useful tools for working with features.

RichFeatureRelationship - Interface in org.biojavax.bio.seq

Represents the relation between two features.

RichFeatureRelationshipHolder - Interface in org.biojavax.bio.seq

Holds feature relationships.

RichLocation - Interface in org.biojavax.bio.seq

Describes locations, and adds the concepts of circularity, fuzziness,
 annotations, and cross-references to other databases.

RichLocation.Strand - Class in org.biojavax.bio.seq

This class represents a strand on which a location may lie.

RichLocation.Tools - Class in org.biojavax.bio.seq

Some useful tools for working with Locations.

RichObjectBuilder - Interface in org.biojavax

This interface allows a class to generate Rich objects based on a class
 name and some parameters.

RichObjectFactory - Class in org.biojavax

Runs a service that builds rich objects, and provides some default values
 for things like default ontology, default namespace, etc.

RichSeqIOAdapter - Class in org.biojavax.bio.seq.io

This class implements all methods of RichSeqIOListener and takes no action.

RichSeqIOAdapter() - Constructor for class org.biojavax.bio.seq.io.RichSeqIOAdapter

Creates a new instance of RichSeqIOAdapter

RichSeqIOListener - Interface in org.biojavax.bio.seq.io

An interface for classes that listen to BioEntry or 
 RichSequence I/O streams.

RichSequence - Interface in org.biojavax.bio.seq

A rich sequence is a combination of a org.biojavax.bio.Bioentry and a
 Sequence.

RichSequence.IOTools - Class in org.biojavax.bio.seq

A set of convenience methods for handling common file formats.

RichSequence.IOTools.SingleRichSeqIterator - Class in org.biojavax.bio.seq

Used to iterate over a single rich sequence

RichSequence.Terms - Class in org.biojavax.bio.seq

Stores a number of useful terms used across many sequence formats for
 consistency's sake.

RichSequence.Tools - Class in org.biojavax.bio.seq

Some useful tools for working with RichSequence objects.

RichSequenceBuilder - Interface in org.biojavax.bio.seq.io

An interface for objects that can build RichSequences.

RichSequenceBuilderFactory - Interface in org.biojavax.bio.seq.io

Simple factory for constructing new RichSequenceBuilder objects.

RichSequenceDB - Interface in org.biojavax.bio.db

A database of RichSequences with accessible keys and iterators over all
 sequences.

RichSequenceDBLite - Interface in org.biojavax.bio.db

A database of RichSequences.

RichSequenceFormat - Interface in org.biojavax.bio.seq.io

Allows a file format to be read/written as RichSequences.

RichSequenceFormat.BasicFormat - Class in org.biojavax.bio.seq.io

Provides a basic format with simple things like line-widths precoded.

RichSequenceFormat.HeaderlessFormat - Class in org.biojavax.bio.seq.io

Provides the basic implementation required for simple header/footer-less files such as Genbank.

RichSequenceHandler - Interface in org.biojavax.bio.seq

An interface for classes that know how to handle subsequence operations.

RichSequenceIterator - Interface in org.biojavax.bio.seq

Essentially the same as SequenceIterator.

RichStreamReader - Class in org.biojavax.bio.seq.io

Parses a stream into sequences.

RichStreamReader(BufferedReader, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Constructor for class org.biojavax.bio.seq.io.RichStreamReader

Creates a new stream reader on the given reader, which will attempt to read
 sequences in the given format, having symbols from the given tokenization, and
 pass them to the given factory to be transformed into RichSequence objects in
 the given namespace.

RichStreamReader(InputStream, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Constructor for class org.biojavax.bio.seq.io.RichStreamReader

Creates a new stream reader on the given input stream, which will attempt to read
 sequences in the given format, having symbols from the given tokenization, and
 pass them to the given factory to be transformed into RichSequence objects in
 the given namespace.

RichStreamWriter - Class in org.biojavax.bio.seq.io

Writes all of the sequences from a SequenceIterator to a stream with a
 particular format.

RichStreamWriter(OutputStream, RichSequenceFormat) - Constructor for class org.biojavax.bio.seq.io.RichStreamWriter

Generate a new RichStreamWriter to the stream os and using format.

rightPad(String, char, int) - Static method in class org.biojavax.utils.StringTools

Pads a string to be a certain width by appending given symbols.

rightPad(String, int) - Static method in class org.biojavax.utils.StringTools

Pads a string to be a certain width by appending spaces.

rights - Variable in class org.biojava.bibliography.BibRef


 It specifies information about rights over the cited resource.

RIGHTVALUE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
 
RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

RNA indicates that a sequence contains RNA
 (ribonucleic acid) symbols.

RNATools - Class in org.biojava.bio.seq

Useful functionality for processing DNA and RNA sequences.

ROLE_ATTR_QUERYABLE - Static variable in interface org.biojava.bibliography.BibRefSupport


 A role of an attribute.

ROLE_ATTR_RETRIEVABLE - Static variable in interface org.biojava.bibliography.BibRefSupport


 A role of an attribute.

rollback() - Method in class org.biojava.bio.seq.db.BioIndex
 
rollback() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore

rollback rolls back changes made since the last
 commit.

rollback() - Method in interface org.biojava.bio.seq.db.IndexStore

Discard all uncommited changes.

rollback() - Method in class org.biojava.bio.seq.db.TabIndexStore
 
rollback() - Method in interface org.biojava.utils.Commitable

rollback reverses pending changes to restore
 initial (or prior commit) state.

rollback() - Method in class org.biojava.utils.FileAsList
 
RP_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
RP_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
rpp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
rppat - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
rppat - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
run() - Method in class org.biojava.utils.process.ReaderInputHandler
run() - Method in class org.biojava.utils.process.ReaderWriterPipe
run() - Method in class org.biojava.utils.process.SimpleInputHandler
run() - Method in class org.biojava.utils.process.StreamPipe
run(GAStoppingCriteria) - Method in interface org.biojavax.ga.GeneticAlgorithm

Iterates the Algorithm until the stopping criteria are met.

run(GAStoppingCriteria) - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm
 




S

s() - Static method in class org.biojava.bio.seq.DNATools
 
s() - Static method in class org.biojava.bio.seq.NucleotideTools
 
s() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Serine

S_SCROFA - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
sample() - Method in class org.biojavax.ga.util.WeightedSet

Randomly samples an Object from the Set according
 to its weight.

sampleSymbol() - Method in class org.biojava.bio.dist.AbstractDistribution
 
sampleSymbol() - Method in interface org.biojava.bio.dist.Distribution

Sample a symbol from this state's probability distribution.

sampleSymbol() - Method in class org.biojava.bio.dist.GapDistribution
 
sampleSymbol() - Method in class org.biojava.bio.dist.PairDistribution
 
sampleSymbol() - Method in class org.biojava.bio.dist.TranslatedDistribution
 
SAX2StAXAdaptor - Class in org.biojava.bio.seq.io.agave

Lightweight adaptor which translates SAX content events into
 StAX form, and provides delegation services.

SAX2StAXAdaptor - Class in org.biojava.utils.stax

Lightweight adaptor which translates SAX content events into
 StAX form, and provides delegation services.

SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor

Construct a new SAX Content handler which wraps a StAX
 handler.

SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.utils.stax.SAX2StAXAdaptor

Construct a new SAX Content handler which wraps a StAX
 handler.

sb - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
 
SCENE_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable

Translation table name for the scenedesmus obliquus mitochondrial genetic
 code.

SCHEMA - Static variable in interface org.biojava.bio.seq.FeatureHolder

Signals that the schema of this FeatureHolder has changed.

SCI_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
SCIENTIFIC - Static variable in interface org.biojavax.bio.taxa.NCBITaxon

Use this to define scientific names for things.

SCIENTIFIC_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
SCINAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
score - Variable in class org.biojava.bio.dp.BackPointer

The score of this element of the DP matrix.

score - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
score - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template

score of the search which produced the
 alignment.

scores - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
scores - Variable in class org.biojava.bio.dp.twohead.Cell
 
SCORES - Static variable in interface org.biojava.bio.dp.StatePath

Alignment label for the likelyhood at each step.

ScoreType - Interface in org.biojava.bio.dp

This class computes the score that is used to be used
 in a DP optimisation.

ScoreType.NullModel - Class in org.biojava.bio.dp

In this class, calculateScore returns the probability of
 a Symbol being emitted by the null model.

ScoreType.Odds - Class in org.biojava.bio.dp

In this class, calculateScore returns the odds ratio
 of a symbol being emitted.

ScoreType.Probability - Class in org.biojava.bio.dp

In this class, calculateScore returns the probability
 of a Symbol being emitted.

scoreWeightMatrix(WeightMatrix, SymbolList, int) - Static method in class org.biojava.bio.dp.DP

Scores the SymbolList from symbol start to symbol (start+columns) with a
 weight matrix.

scoreWeightMatrix(WeightMatrix, SymbolList, ScoreType, int) - Static method in class org.biojava.bio.dp.DP

Scores the SymbolList from symbol start to symbol (start+columns) with a
 weight matrix using a particular ScoreType.

search(Object) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory

Deprecated.
 
search(Object) - Method in interface org.biojava.bio.taxa.TaxonFactory

Deprecated.
Retrieve a Taxon that matches some ID.

search(Object) - Method in class org.biojava.bio.taxa.WeakTaxonFactory

Deprecated.
 
search(String, String, Object[], SearchControls) - Method in class org.biojava.naming.ObdaContext
 
search(String, String, SearchControls) - Method in class org.biojava.naming.ObdaContext
 
search(String, Attributes) - Method in class org.biojava.naming.ObdaContext
 
search(String, Attributes, String[]) - Method in class org.biojava.naming.ObdaContext
 
search(String, SymbolList, SearchListener) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
 
search(String, SymbolList, SearchListener) - Method in interface org.biojava.bio.program.ssaha.DataStore

Search the DataStore with a symbol list.

search(Name, String, Object[], SearchControls) - Method in class org.biojava.naming.ObdaContext
 
search(Name, String, SearchControls) - Method in class org.biojava.naming.ObdaContext
 
search(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
 
search(Name, Attributes, String[]) - Method in class org.biojava.naming.ObdaContext
 
search(AnnotationType) - Method in interface org.biojava.bio.annodb.AnnotationDB

Find all Annotation instances in this DB and any Annotations that are child
 properties of these that match an AnnotationType.

search(AnnotationType) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
 
search(AnnotationType) - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
 
search(AnnotationType) - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
 
search(AnnotationType) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
 
search(AnnotationType) - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
 
search(SymbolList) - Method in class org.biojava.utils.automata.PatternBlitz
 
search(SymbolList) - Method in class org.biojava.utils.regex.Search

search the Sequence with the patterns already registered with this object.

search(SymbolList, int, int) - Method in class org.biojava.utils.regex.Search

search part of the SymbolList with the patterns already registered with this object.

search(SymbolList, SequenceDB, Map) - Method in interface org.biojava.bio.search.SeqSimilaritySearcher

Using this sequence similarity searcher, search with the given
 sequence against the given sequence database.

Search - Class in org.biojava.utils.regex

A utility class to make searching a Sequence with many regex patterns
 easier.

Search(FiniteAlphabet) - Constructor for class org.biojava.utils.regex.Search
 
Search.Listener - Interface in org.biojava.utils.regex

Interface for a class that will recieve match information
 from this class.

searchAnnotation(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools


 Scans an Annotation with an AnnotationType and returns all Annotation
 instances matching a Type.

SearchBuilder - Interface in org.biojava.bio.search

The SearchBuilder interface is to be used by objects
 which accumulate state via a SearchContentHandler and
 then construct a SeqSimilaritySearchResult object.

SearchContentAdapter - Class in org.biojava.bio.search


 An adapter for SearchContentHandler.

SearchContentAdapter() - Constructor for class org.biojava.bio.search.SearchContentAdapter
 
SearchContentFilter - Class in org.biojava.bio.search


 Filtering implementation of SearchContentHandler that by default passes
 all messages on to the next delegate in the chain.

SearchContentFilter(SearchContentHandler) - Constructor for class org.biojava.bio.search.SearchContentFilter
 
SearchContentHandler - Interface in org.biojava.bio.search

SearchContentHandler is a notification interface for
 objects which listen to search stream parsers.

SearchContentHandlerDebugger - Class in org.biojava.bio.search

This class prints to a PrintStream
 calls to the SearchContentHandler interface
 in human readable form.

SearchContentHandlerDebugger() - Constructor for class org.biojava.bio.search.SearchContentHandlerDebugger

Create an instance that dumps to System.out.

SearchContentHandlerDebugger(PrintStream) - Constructor for class org.biojava.bio.search.SearchContentHandlerDebugger
 
SearchException - Exception in org.biojava.bio.program.ssaha

There has been some failure that prevents a search from completing.

SearchException(String) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
 
SearchException(String, Throwable) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
 
SearchException(Throwable) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
 
SearchListener - Interface in org.biojava.bio.program.ssaha

The interface used to inform interested parties that some sequence has
 been searched and something found.

SearchListener.Echo - Class in org.biojava.bio.program.ssaha

A SearchListener that prints events out to a PrintStream.

SearchListener.FilterByLength - Class in org.biojava.bio.program.ssaha

A simple listener that filters out all hits that are too short.

SearchListener.Tee - Class in org.biojava.bio.program.ssaha

A SearchListener that passes events on to two delegate listeners.

SearchListener.Wrapper - Class in org.biojava.bio.program.ssaha

A simple wrapper implementation.

sec() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Selenocysteine (U)

SEC_ACC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SECONDARY_ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
SECONDARY_ACCESSIONS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
sectp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
seek(long) - Method in class org.biojava.utils.io.CachingInputStream
 
seek(long) - Method in class org.biojava.utils.io.RandomAccessReader

seek moves the pointer to the specified position.

seek(long) - Method in interface org.biojava.utils.io.Seekable

Moves the pointer in the inputstream such that the byte starting  at 
 pos are returned by the next read.

Seekable - Interface in org.biojava.utils.io

This interface provides a collective name for IO classes that implement a
 seek function (e.g., RandomAccessFile).

select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.ProportionalSelection
 
select(Population, GeneticAlgorithm) - Method in interface org.biojavax.ga.functions.SelectionFunction

Selects a Population of Organisms for
 replication based on their fitness.

select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
 
select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold

Selects individuals whose fitness (as determined by the
 FitnessFunction) is more than the cutoff.

select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.TournamentSelection

Standard call to select organisms, will select a number of Organisms
 corresponding to 75 % of the population.

SelectAll() - Constructor for class org.biojavax.ga.functions.SelectionFunction.SelectAll
 
SELECTION_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
 
SelectionFunction - Interface in org.biojavax.ga.functions

Selects Organisms for Replication and returns the offspring.

SelectionFunction.SelectAll - Class in org.biojavax.ga.functions
 
SelectionFunction.Threshold - Class in org.biojavax.ga.functions


 Selects individuals who's fitness exceeds a threshold value.

SelectionScalar(BitSet) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar

Make a new SelectionScalar that masks in different
 depths.

selectNIndividuals(Population, GeneticAlgorithm, int) - Method in class org.biojavax.ga.functions.TournamentSelection

This method selects n Organism from the population it is given, using the
 tournament selection method

sendAlignmentRequest(int, RemotePairwiseAlignmentProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService

This method is a wrapper that executes the Blast request via the Put
 command of the CGI-BIN interface with the specified parameters and a
 GenBank GID.

sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService

This method is a wrapper that executes the Blast request via the Put
 command of the CGI-BIN interface with the specified parameters and a
 string representing the sequence.

sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService

Doing the actual analysis on the instantiated service using specified parameters on the string representation
 of the Sequence object

sendAlignmentRequest(RichSequence, RemotePairwiseAlignmentProperties) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService

This method is a wrapper that executes the Blast request via the Put
 command of the CGI-BIN interface with the specified parameters and a
 RichSequence.

sendAlignmentRequest(RichSequence, RemotePairwiseAlignmentProperties) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentService

Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object

SEPARATED - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
 
SEPARATOR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
seq - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
 
SeqCaution() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution

Creates a new instance.

SeqContentPattern - Class in org.biojava.bio.search

A pattern that can be used to find regions with given sequence content.

SeqContentPattern(FiniteAlphabet) - Constructor for class org.biojava.bio.search.SeqContentPattern

Create a new SeqContentPattern over an alphabet.

SeqFileFormer - Interface in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead


SeqIOAdapter - Class in org.biojava.bio.seq.io

Adapter class for SeqIOListener that has empty methods.

SeqIOAdapter() - Constructor for class org.biojava.bio.seq.io.SeqIOAdapter
 
SeqIOConstants - Class in org.biojava.bio.seq.io

SeqIOConstants contains constants used to identify
 sequence formats, alphabets etc, in the context of reading and
 writing sequences.

SeqIOConstants() - Constructor for class org.biojava.bio.seq.io.SeqIOConstants
 
SeqIOEventEmitter - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead


SeqIOEventEmitter(Comparator, Comparator) - Constructor for class org.biojava.bio.seq.io.SeqIOEventEmitter

Deprecated.
 
SeqIOFilter - Class in org.biojava.bio.seq.io

Base-class for listeners that pass filtered events onto another listener.

SeqIOFilter(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.SeqIOFilter

Create a new SeqIOFilter that will forward events on to another listener.

SeqIOListener - Interface in org.biojava.bio.seq.io

Notification interface for objects which listen to a sequence stream
 parser.

SeqIOTools - Class in org.biojava.bio.seq.io

Deprecated.
use org.biojavax.bio.seq.RichSequence.IOTools


seqNameForID(int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
 
seqNameForID(int) - Method in interface org.biojava.bio.program.ssaha.DataStore

Resolve an ID to a sequence name.

seqs - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
SeqSimilaritySearcher - Interface in org.biojava.bio.search

Objects of this type represent one particular installation (not
 just implementation) of a sequence similarity searcher such as
 BLASTP.

SeqSimilaritySearchHit - Interface in org.biojava.bio.search

Objects of this type represent one particular hit (sequence and
 associated information) from a sequence similarity search.

SeqSimilaritySearchHit.ByScoreComparator - Class in org.biojava.bio.search

ByScoreComparator compares
 SeqSimilaritySearchHits by their score.

SeqSimilaritySearchHit.BySubHitCountComparator - Class in org.biojava.bio.search

BySubHitCountComparator compares
 SeqSimilaritySearchHits by their number of
 sub-hits.

SeqSimilaritySearchResult - Interface in org.biojava.bio.search

Objects of this type represent one particular result of a sequence
 similarity search.

SeqSimilaritySearchSubHit - Interface in org.biojava.bio.search

Objects of this type represent one particular sub-hit (one concrete
 sequence stretch within a sequence and associated information) from
 a sequence similarity search hit.

SeqSimilaritySearchSubHit.ByScoreComparator - Class in org.biojava.bio.search

ByScoreComparator compares
 SeqSimilaritySearchSubHits by their score.

SeqSimilaritySearchSubHit.BySubjectStartComparator - Class in org.biojava.bio.search

BySubjectStartComparator compares
 SeqSimilaritySearchSubHits by their start position
 on the subject sequence.

seqString() - Method in class org.biojava.bio.dp.SimpleStatePath
 
seqString() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
seqString() - Method in class org.biojava.bio.seq.impl.DummySequence
 
seqString() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
seqString() - Method in class org.biojava.bio.seq.impl.SubSequence
 
seqString() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
seqString() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
seqString() - Method in class org.biojava.bio.seq.SimpleAssembly
 
seqString() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
seqString() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
seqString() - Method in interface org.biojava.bio.symbol.SymbolList

Stringify this symbol list.

seqString() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

Stringify this symbol list.

seqString() - Method in class org.biojavax.bio.seq.ThinRichSequence

Stringify this symbol list.

seqString(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler

Stringify this Sequences.

seqString(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler

Stringify this Sequences.

sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
 
Sequence - Interface in org.biojava.bio.seq


 A biological sequence.

SEQUENCE - Static variable in interface org.biojava.bio.dp.StatePath

Alignment label for the emitted sequence.

SEQUENCE_CAUTION - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser

A name for a comment type.

SEQUENCE_CHECKSUM_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SEQUENCE_FORMAT - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory

SEQUENCE_FORMAT is the key used to identify the
 format of the indexed sequence files represented by the store
 in the OBDA config.dat files.

SEQUENCE_LENGTH_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SEQUENCE_LENGTH_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SEQUENCE_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SEQUENCE_MODIFIED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SEQUENCE_TOPOLOGY_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SEQUENCE_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SEQUENCE_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
SEQUENCE_VERSION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
SequenceAnnotator - Interface in org.biojava.bio.seq

An object which adds some additional information to a Sequence.

SequenceBuilder - Interface in org.biojava.bio.seq.io

Interface for objects which accumulate state via SeqIOListener,
 then construct a Sequence object.

SequenceBuilderBase - Class in org.biojava.bio.seq.io

Basic SequenceBuilder implementation which accumulates all
 notified information.

SequenceBuilderBase() - Constructor for class org.biojava.bio.seq.io.SequenceBuilderBase
 
SequenceBuilderFactory - Interface in org.biojava.bio.seq.io

Simple factory for constructing new SequenceBuilder objects.

SequenceBuilderFilter - Class in org.biojava.bio.seq.io

Base-class for builders that pass filtered events onto another builder.

SequenceBuilderFilter(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SequenceBuilderFilter

Create a new SeqIOFilter that will forward events on to another listener.

SequenceContentHandlerBase - Class in org.biojava.bio.seq.io.game

StAX handler for elements containing sequence

SequenceContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
 
SequenceDB - Interface in org.biojava.bio.seq.db

A database of sequences with accessible keys and iterators over all
 sequences.

SequenceDBDataSource - Class in org.biojava.bio.seq.distributed

Turn an entire SequenceDB instance into a DistDataSource.

SequenceDBDataSource(SequenceDB) - Constructor for class org.biojava.bio.seq.distributed.SequenceDBDataSource
 
SequenceDBInstallation - Interface in org.biojava.bio.seq.db


 A SequenceDBInstallation has the functionality of a factory for
 SequenceDB objects and additionally manages the SequenceDB objects
 created by itself such that the minimum number of SequenceDB
 objects is created by a particular SequenceDBInstallation
 object.

SequenceDBLite - Interface in org.biojava.bio.seq.db

A database of sequences.

SequenceDBProvider - Interface in org.biojava.directory

Interfaces for named resources that can provide sequences via a
 database given some configuration information as defined by the
 OBDA standard.

SequenceDBSearchHit - Class in org.biojava.bio.search

Deprecated.
SimpleSeqSimilaritySearchHit has been made Annotatable
 and is now functionally identical.


SequenceDBSearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List) - Constructor for class org.biojava.bio.search.SequenceDBSearchHit

Deprecated.
Creates a new SequenceDBSearchHit object.

SequenceDBSearchResult - Class in org.biojava.bio.search

Deprecated.
SimpleSeqSimilaritySearchResult has been made
 Annotatable and is now functionally identical.


SequenceDBSearchResult(Sequence, SequenceDB, Map, List, Annotation) - Constructor for class org.biojava.bio.search.SequenceDBSearchResult

Deprecated.
Creates a new SequenceDBSearchResult.

SequenceDBSearchSubHit - Class in org.biojava.bio.search

Deprecated.
SimpleSeqSimilaritySearchSubHit has been made
 Annotatable and is now functionally identical.


SequenceDBSearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation) - Constructor for class org.biojava.bio.search.SequenceDBSearchSubHit

Deprecated.
Creates a new SequenceDBSearchSubHit object.

SequenceDBStreamer(SequenceDB) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
 
SequenceDBWrapper - Class in org.biojava.bio.seq.db

An abstract implementation of SequenceDB that wraps up another database.

SequenceDBWrapper(SequenceDB) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper
 
SequenceDBWrapper.SequencesForwarder - Class in org.biojava.bio.seq.db
 
SequenceFactory - Interface in org.biojava.bio.seq

Deprecated.
use org.biojavax.bio.seq.io.RichSequenceBuilder or 
 use org.biojavax.bio.seq.io.SequenceBuilder


SequenceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
 
SequenceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
 
SequenceFormat - Interface in org.biojava.bio.seq.io

Defines what a sequence format does.

SequenceHandler - Interface in org.biojava.bio.seq.io.agave

mark interface

sequenceIterator() - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.DummySequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
 
sequenceIterator() - Method in interface org.biojava.bio.seq.db.SequenceDB

Returns a SequenceIterator over all sequences in the database.

sequenceIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
 
sequenceIterator() - Method in interface org.biojavax.bio.db.RichSequenceDB

Returns a SequenceIterator over all sequences in the database.

SequenceIterator - Interface in org.biojava.bio.seq

An iterator over a bag of sequences.

SEQUENCES - Static variable in interface org.biojava.bio.seq.db.SequenceDBLite

Signals that sequences are being added to or remove from the database.

SequencesAsGFF - Class in org.biojava.bio.program.gff

Turns a sequence database into a GFF event stream.

SequencesAsGFF() - Constructor for class org.biojava.bio.program.gff.SequencesAsGFF
 
SequencesForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
 
SequenceStreamer - Interface in org.biojava.bio.program.ssaha
 
SequenceStreamer.FileStreamer - Class in org.biojava.bio.program.ssaha
 
SequenceStreamer.SequenceDBStreamer - Class in org.biojava.bio.program.ssaha
 
SequenceTools - Class in org.biojava.bio.seq

Methods for manipulating sequences.

SEQVERSION - Static variable in interface org.biojavax.bio.BioEntry
 
ser() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Serine (S)

serialize(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat

Deprecated.
 
serialize(Taxon) - Method in interface org.biojava.bio.taxa.TaxonParser

Deprecated.
Convert a Taxon into a stringified representation.

serializeSource(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat

Deprecated.
 
serializeXRef(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat

Deprecated.
 
serialVersionUID - Static variable in class org.biojava.bio.dp.SimpleMarkovModel
 
serialVersionUID - Static variable in class org.biojava.bio.symbol.AbstractAlphabet
 
serialVersionUID - Static variable in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties
 
serialVersionUID - Static variable in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties
 
series - Variable in class org.biojava.bibliography.BiblioBook

Book series.

Services - Class in org.biojava.utils

Utility methods for handling META-INF/services files

Services() - Constructor for class org.biojava.utils.Services
 
set(int, Object) - Method in class org.biojava.utils.FileAsList

This always returns null, not the previous object.

set(Object, Object) - Method in class org.biojava.utils.ListTools.Doublet
 
set(Object, Object, Object) - Method in class org.biojava.utils.ListTools.Triplet
 
setA(Object) - Method in class org.biojava.utils.ListTools.Doublet
 
setA(Object) - Method in class org.biojava.utils.ListTools.Triplet
 
setAbsorptionMax(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property absorptionMax.

setAbsorptionNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property absorptionNote.

setAccession(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setAccession(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setAccession(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 the accession of the record being read.

setAccession(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 the accession of the record being read.

setAcronym(String) - Method in interface org.biojavax.Namespace

Sets an optional acronym for the namespace.

setAcronym(String) - Method in class org.biojavax.SimpleNamespace

Sets an optional acronym for the namespace.

setAddPos(boolean) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier

Set a flag so that newly added points will be in the positive class or
 negative class, depending on wether addPos is true or false respectively.

setAdvance(int[]) - Method in interface org.biojava.bio.dp.EmissionState

Set the advance array.

setAdvance(int[]) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setAdvancedOptions(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties


 This method is to be used if a request is to use non-default values at
 submission.

setAlignementOption(String, String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
 
setAlignementOption(String, String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties

Method to set the value for a specific alignment parameter using a key to store in a map.

setAlignment(Alignment) - Method in class org.biojava.bio.seq.homol.SimpleHomology

setAlignment sets the alignment which describes
 the homology.

setAlignmentNumber(int) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties

A method to set the number of alignments to fetch to the GET command.

setAlignmentOutputFormat(RemoteQBlastOutputFormat) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties

This method is use to set the alignment output format to get from the QBlast service

setAlpha(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
setAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
setAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
setAlphabetName(String) - Method in class org.biojavax.bio.seq.SimpleRichSequence
 
setAlphabetName(String) - Method in class org.biojavax.bio.seq.ThinRichSequence
 
setAlphaStar(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setAnnotation(Annotation) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setAnnotation(Annotation) - Method in class org.biojava.ontology.Term.Impl
 
setApplicationClass(Class, Class) - Static method in class org.biojavax.RichObjectFactory

Allow application to override the default biojava class created in getObject - subclass restriction is checked in the builder.

setArticleAuthors(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Sets the names of the authors which first published an article about the
 AAindex entry.

setArticleTitle(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Sets the title of the article which describes the AAindex entry.

setAuthority(String) - Method in interface org.biojavax.Namespace

This method sets the authority that governs the namespace.

setAuthority(String) - Method in class org.biojavax.SimpleNamespace

This method sets the authority that governs the namespace.

setB(Object) - Method in class org.biojava.utils.ListTools.Doublet
 
setB(Object) - Method in class org.biojava.utils.ListTools.Triplet
 
setBlastDatabase(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties

This method set the database to be use with blastall

setBlastProgram(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties

This method set the program to be use with blastall.

setBooleanValue(boolean) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase


 Override this method to do something useful with the
 boolean we collect.

setBoundaryFinder(BoundaryFinder) - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
setByteValue(byte) - Method in class org.biojava.utils.stax.ByteElementHandlerBase


 Override this method to do something useful with the
 byte we collect.

setC(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer
 
setC(double) - Method in class org.biojava.stats.svm.SMOTrainer
 
setC(Object) - Method in class org.biojava.utils.ListTools.Triplet
 
setCategory(String) - Method in class org.biojava.ontology.Synonym
 
setChanger(Object, ChangeTable.Changer) - Method in class org.biojava.bio.program.tagvalue.ChangeTable

Set the Changer to be used for all values of a particular tag.

setChangeTable(ChangeTable) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
 
setCharacter(char) - Method in class org.biojava.utils.RepeatedCharSequence
 
setCharValue(char) - Method in class org.biojava.utils.stax.CharElementHandlerBase


 Override this method to do something useful with the
 char we collect.

setChildrenRaw(Set) - Method in class org.biojava.bio.taxa.WeakTaxon

Deprecated.
 
setChromImpl(SymbolList[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
 
setChromImpl(SymbolList[]) - Method in class org.biojavax.ga.impl.SimpleOrganism
 
setChromosome(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setChromosomes(SymbolList[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
 
setChromosomes(SymbolList[]) - Method in interface org.biojavax.ga.Organism

Sets the organisms 'chromosome' sequences.

setCircular(boolean) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setCircular(boolean) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setCircular(boolean) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Defined this sequence being parser as circular.

setCircular(boolean) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Defined this sequence being parser as circular.

setCircular(boolean) - Method in interface org.biojavax.bio.seq.RichSequence

Circularises the Sequence.

setCircular(boolean) - Method in class org.biojavax.bio.seq.ThinRichSequence

Circularises the Sequence.

setCircularLength(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Sets the circular length of this location.

setCircularLength(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Sets the circular length of this location.

setCircularLength(int) - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation

Sets the circular length of this location.

setCircularLength(int) - Method in interface org.biojavax.bio.seq.RichLocation

Sets the circular length of this location.

setCircularLength(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Sets the circular length of this location.

setCommands(String) - Method in class org.biojava.utils.process.ExternalProcess

Sets the command line including the path or name of the external program
 and its command line arguments.

setComment(Object, String) - Method in class org.biojava.bio.AnnotationType.Impl
 
setComment(Object, String) - Method in interface org.biojava.bio.AnnotationType

Set the comment for a particular property.

setComment(String) - Method in class org.biojava.bio.AnnotationType.Impl
 
setComment(String) - Method in interface org.biojava.bio.AnnotationType

Set the comment for the whole AnnotationType.

setComment(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

Set the comment to comment.

setComment(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Sets the user comment for the AAindex entry.

setComment(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setComment(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setComment(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 about a comment in the record being read.

setComment(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 about a comment in the record being read.

setComment(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event

Setter for property comment.

setComment(String) - Method in class org.biojavax.SimpleComment
 
setCommentType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property commentType.

setCommonName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon

Deprecated.
 
setCommonName(String) - Method in interface org.biojava.bio.taxa.Taxon

Deprecated.
Set the new common name of this Taxon.

setConstant(double) - Method in class org.biojava.stats.svm.PolynomialKernel
 
setConstant(double) - Method in class org.biojava.stats.svm.SigmoidKernel
 
setConstraint(Object, CollectionConstraint) - Method in class org.biojava.bio.AnnotationType.Impl
 
setConstraint(Object, CollectionConstraint) - Method in interface org.biojava.bio.AnnotationType

Specifies the constraint to apply to the specified property.

setConstraints(Object, PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract
 
setConstraints(Object, PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType

Set the constraints associated with a property.

setContinueOnEmptyTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser

Choose whether to treat empty tags as a continuation of previous tags or as a
 new tag with the value of the empty string.

setContinueOnEmptyTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser

Decide whether to treat empty tags as continuations of the previous non
 -empty tag.

setCount(AtomicSymbol, double) - Method in interface org.biojava.bio.dist.Count

Set the count for the Symbol s.

setCount(AtomicSymbol, double) - Method in class org.biojava.bio.dist.IndexedCount
 
setCounts(Count) - Method in interface org.biojava.bio.dist.Count

Set the counts in this Counts to be equal to the counts in c.

setCounts(Count) - Method in class org.biojava.bio.dist.IndexedCount
 
setCreateOnUnderlyingSequence(boolean) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
 
setCrossOverFunction(CrossOverFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm

Changes the CrossOverFunction used to CrossOver Chromosomes

setCrossOverFunction(CrossOverFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
setCrossOverProbs(double[]) - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
 
setCrossOverProbs(double[]) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
setCrossOverProbs(double[]) - Method in interface org.biojavax.ga.functions.CrossOverFunction

Sets the probability of crossing at each base.

setCrossref(CrossRef) - Method in interface org.biojavax.DocRef

The document reference may refer to an object in another database.

setCrossref(CrossRef) - Method in class org.biojavax.SimpleDocRef

The document reference may refer to an object in another database.

setCrossRef(CrossRef) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Sets the cross ref resolver to use when retrieving remote symbols.

setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Sets the cross ref resolver to use when retrieving remote symbols.

setCrossRefResolver(CrossReferenceResolver) - Method in interface org.biojavax.bio.seq.RichLocation

Sets the cross ref resolver to use when retrieving remote symbols.

setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Sets the cross ref resolver to use when retrieving remote symbols.

setDatabase(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
 
setDatabaseID(String) - Method in class org.biojava.bio.search.FilteringContentHandler
 
setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentAdapter
 
setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentFilter
 
setDatabaseID(String) - Method in interface org.biojava.bio.search.SearchContentHandler

setDatabaseID identifies the database searched by
 a name, ID or URN.

setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
setDatabaseName(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property databaseName.

setDbCode(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
 
setDefaultChanger(ChangeTable.Changer) - Method in class org.biojava.bio.program.tagvalue.ValueChanger

The changer that will be applied to the values of tags not registered
 explicitly to any changer or splitter instance.

setDefaultConstraint(CollectionConstraint) - Method in class org.biojava.bio.AnnotationType.Impl
 
setDefaultConstraint(CollectionConstraint) - Method in interface org.biojava.bio.AnnotationType

Specifies the default constraint to apply to properties where no
 other constraint is specified.

setDefaultConstraints(PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract
 
setDefaultConstraints(PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType

Set the constraints that will apply to all properties without an
 explicitly defined set of constraints.

setDefaultCrossReferenceResolver(CrossReferenceResolver) - Static method in class org.biojavax.RichObjectFactory

Sets the default crossref resolver to use when resolving remote entries.

setDefaultNamespaceName(String) - Static method in class org.biojavax.RichObjectFactory

Sets the default namespace name to use when loading sequences.

setDefaultOntologyName(String) - Static method in class org.biojavax.RichObjectFactory

Sets the default ontology name to use when loading sequences.

setDefaultPositionResolver(PositionResolver) - Static method in class org.biojavax.RichObjectFactory

Sets the default position resolver to use when creating new rich feature locations.

setDefaultRichSequenceHandler(RichSequenceHandler) - Static method in class org.biojavax.RichObjectFactory

Sets the default sequence handler to use when performing sequence manipulation.

setDefaultSplitter(ChangeTable.Splitter) - Method in class org.biojava.bio.program.tagvalue.ValueChanger

The splitter that will be applied to the values of tags not registered
 explicitly to any changer or splitter instance.

setDefaultTransitions(StateMachine.TransitionTable) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState

specify fallback TransitionTable for this State

setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.StateMachine

TagValueWrapper interface

setDelegate(TagValueListener) - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper

set listener to which all calls will be delegated

setDelegateParser(TagValueParser) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
setDepthScaler(SuffixTreeKernel.DepthScaler) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel

Change the current DepthScaler to
 depthScaler.

setDescription(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Sets the description for the AAindex entry.

setDescription(String) - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
 
setDescription(String) - Method in class org.biojava.ontology.AbstractTerm
 
setDescription(String) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
 
setDescription(String) - Method in class org.biojava.ontology.IntegerOntology
 
setDescription(String) - Method in class org.biojava.ontology.Ontology.Impl
 
setDescription(String) - Method in interface org.biojava.ontology.Ontology

set the description of this ontology

setDescription(String) - Method in class org.biojava.ontology.OntologyTerm.Impl
 
setDescription(String) - Method in interface org.biojava.ontology.Term

set the description of the term;

setDescription(String) - Method in class org.biojava.ontology.Triple.Impl
 
setDescription(String) - Method in interface org.biojavax.bio.BioEntry

Sets the description for this bioentry.

setDescription(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setDescription(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setDescription(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 the description of the record being read.

setDescription(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 the description of the record being read.

setDescription(String) - Method in class org.biojavax.bio.SimpleBioEntry

Sets the description for this bioentry.

setDescription(String) - Method in interface org.biojavax.Namespace

This method sets a description for the namespace.

setDescription(String) - Method in interface org.biojavax.ontology.ComparableOntology

Sets a human-readable description of this ontology.

setDescription(String) - Method in interface org.biojavax.ontology.ComparableTerm

Sets the description associated with this term.

setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableOntology

Sets a human-readable description of this ontology.

setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableTerm

Sets the description associated with this term.

setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableTriple

set the description of the term;

setDescription(String) - Method in class org.biojavax.SimpleNamespace

This method sets a description for the namespace.

setDescriptionNumber(int) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties

A method to set the number of descriptions to fetch to the GET command.

setDescriptors(Set) - Method in interface org.biojavax.ontology.ComparableTriple

Clears the current set of descriptors and replaces it with the content of 
 the set passed.

setDescriptors(Set) - Method in class org.biojavax.ontology.SimpleComparableTriple

Clears the current set of descriptors and replaces it with the content of 
 the set passed.

setDistribution(Distribution) - Method in interface org.biojava.bio.dp.EmissionState

Set the Distribution associated with this state.

setDistribution(Distribution) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setDistribution(Symbol, Distribution) - Method in interface org.biojava.bio.dist.OrderNDistribution

Set the distribution assocated with a symbol.

setDivision(String) - Method in interface org.biojavax.bio.BioEntry

Sets the division of this bioentry.

setDivision(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setDivision(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setDivision(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 the division of the record being read.

setDivision(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 the division of the record being read.

setDivision(String) - Method in class org.biojavax.bio.SimpleBioEntry

Sets the division of this bioentry.

setDocumentLocator(Locator) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
setDocumentLocator(Locator) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
setDocumentLocator(Locator) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
setDocumentLocator(Locator) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
setDocumentLocator(Locator) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
setDocumentLocator(Locator) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
setDoubleProperty(Symbol, String) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
 
setDoubleValue(double) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase


 Override this method to do something useful with the
 double we collect.

setElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
setElideComments(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Use this method to toggle reading of comments data.

setElideComments(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Use this method to toggle reading of comments data.

setElideFeatures(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Use this method to toggle reading of feature data.

setElideFeatures(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Use this method to toggle reading of feature data.

setElideReferences(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Use this method to toggle reading of bibliographic reference data.

setElideReferences(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Use this method to toggle reading of bibliographic reference data.

setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
Specifies whether the symbols (SQ) part of the entry should
 be ignored.

setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
Use this method to toggle reading of sequence data.

setElideSymbols(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Use this method to toggle reading of sequence data.

setElideSymbols(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Use this method to toggle reading of sequence data.

setEmail(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService

Set the email for QBlast.

setEmail(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

Set the email for Entrez.

setEnd(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

Set the end coordinate to end.

setEnd(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setEnd(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
setEnd(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser

Set the string indicating that a record has ended.

setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.RegexParser

Set the explicit end-of-record string.

setEnvironmentProperties(String[]) - Method in class org.biojava.utils.process.ExternalProcess

Sets environment variables for the external process.

setEpsilon(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer
 
setEpsilon(double) - Method in class org.biojava.stats.svm.SMOTrainer
 
setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff.GFFParser

Set the error handler used by this parser.

setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff3.GFF3Parser

Set the error handler used by this parser.

setErrorHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess

Sets the output error handler which is responsible for the standard error
 output of the external process.

setEvents(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property events.

setExceptionOnNullDelegate(boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener

determines if an exception is thrown when an event
 arrives without the delegate being set.

setFactory(RichSequenceBuilderFactory) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

Setter for property factory.

setFactory(RichSequenceBuilderFactory) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB

Setter for property factory.

setFallback(StateMachine.TransitionTable) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable

set the specified TransitionTable to be looked
 looked up if the Transition cannot be found in
 this one.

setFeature(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter

Set the feature to feature.

setFeature(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

Set the feature type to type.

setFeature(RichFeature) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Sets the feature this location is associated with.

setFeature(RichFeature) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Sets the feature this location is associated with.

setFeature(RichFeature) - Method in interface org.biojavax.bio.seq.RichLocation

Sets the feature this location is associated with.

setFeature(RichFeature) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Sets the feature this location is associated with.

setFeatureFilter(FeatureFilter) - Method in class org.biojava.bio.program.gff.SequencesAsGFF

Replace the current FeatureFilter with
 filter.

setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler

Set the object which receives startFeature/endFeature notifications.

setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
setFeatureProperty(Object, Object) - Method in class org.biojava.bio.program.xff.FeatureHandler

Set a property.

setFeatureRealizer(FeatureRealizer) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory

Set the FeatureRealizer used by new sequences created by this
 factory.

setFeatureRelationshipSet(Set<RichFeatureRelationship>) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder

Clears the relations from this feature holder and replaces them with a new set.

setFeatureRelationshipSet(Set<RichFeatureRelationship>) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Clears the relations from this feature holder and replaces them with a new set.

setFeatureSet(Set<Feature>) - Method in interface org.biojavax.bio.seq.RichSequence

Sets the features of this sequence.

setFeatureSet(Set<Feature>) - Method in class org.biojavax.bio.seq.ThinRichSequence

Sets the features of this sequence.

setFilter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
 
setFirstIntActID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction

Setter for property firstIntActID.

setFitness(double[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
 
setFitness(double[]) - Method in interface org.biojavax.ga.Organism

This method allows to set the fitness of this organism to the specified
 value.

setFitnessFunction(FitnessFunction) - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
 
setFitnessFunction(FitnessFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm

The fitness function that will be used to compute the fitness of each
 organism.

setFitnessFunction(FitnessFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
setFloatValue(float) - Method in class org.biojava.utils.stax.FloatElementHandlerBase

Override this method to do something useful with the
 float we collect.

setFrame(int) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
 
setFrame(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

Set the frame to frame.

setGenerateSequenceHeader(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF

Specify whether a per-sequence header line, giving the length of the
 sequence, should be generated.

setGeneticCode(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon

Sets the genetic code of this taxon, which may be null, which will unset it.

setGeneticCode(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Sets the genetic code of this taxon, which may be null, which will unset it.

setGroupAttributes(Map) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

Replace the group-attribute Map with
 ga.

setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler

Sets the element name that the class responds to.

setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler

Sets the element name that the class responds to.

setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler

Sets the element name that the class responds to.

setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler

Sets the element name that the class responds to.

setHeader(FastaHeader) - Method in class org.biojavax.bio.seq.io.FastaFormat
 
setId(Integer) - Method in class org.biojavax.bio.seq.SimplePosition

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.bio.SimpleBioEntry

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.bio.SimpleBioEntryRelationship

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableOntology

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableTerm

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableTriple

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.SimpleComment

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.SimpleCrossRef

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.SimpleDocRef

Sets the Hibernate ID.

setId(Integer) - Method in class org.biojavax.SimpleNamespace

Sets the Hibernate ID.

setId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
setID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction

Setter for property ID.

setIdentifier(String) - Method in interface org.biojavax.bio.BioEntry

Sets the identifier of this bioentry.

setIdentifier(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setIdentifier(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setIdentifier(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 the identifier of the record being read.

setIdentifier(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 the identifier of the record being read.

setIdentifier(String) - Method in class org.biojavax.bio.SimpleBioEntry

Sets the identifier of this bioentry.

setIdentifier(String) - Method in interface org.biojavax.ontology.ComparableTerm

Sets the (optional) identifier associated with this term.

setIdentifier(String) - Method in class org.biojavax.ontology.SimpleComparableTerm

Sets the (optional) identifier associated with this term.

setInput(InputStream) - Method in interface org.biojava.utils.process.OutputHandler

Sets the input stream.

setInput(InputStream) - Method in class org.biojava.utils.process.StreamPipe

Sets the input stream

setInput(InputStream) - Method in class org.biojava.utils.process.WriterOutputHandler

Sets the input stream.

setInputHandler(InputHandler) - Method in class org.biojava.utils.process.ExternalProcess

Sets the input handler which is responsible for the standard input
 of the external process.

setInteractions(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property interactions.

setIntValue(int) - Method in class org.biojava.utils.stax.IntElementHandlerBase

Override this method to do something useful with the
 int we collect.

setIsoforms(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property isoforms.

setIsoIDs(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform

Setter for property isoIDs.

setIsStrict(boolean) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter

Selects strict mode.

setIsStrict(boolean) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter

Selects strict mode.

setJoiner(String) - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
setJournalReference(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Sets a reference to the journal which published the article about the
 AAindex entry.

setKernel(SVMKernel) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setKernel(SVMKernel) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier

Set the kernel used for classification.

setKineticsNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property kineticsNote.

setKMs(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property KMs.

setLabel(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction

Setter for property label.

setLambda(double) - Method in class org.biojava.stats.svm.DiagonalAddKernel

Set the scale factor.

setLeftValue(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon

Sets the left value.

setLeftValue(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Sets the left value.

setLength(int) - Method in class org.biojava.bio.search.SeqContentPattern

Set the pattern length.

setLength(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
setLength(int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
setLength(int) - Method in class org.biojava.utils.RepeatedCharSequence
 
setLimit(int) - Method in class org.biojava.utils.cache.FixedSizeCache
 
setLineWidth(int) - Method in class org.biojava.bio.program.phred.PhredFormat

Set the line width.

setLineWidth(int) - Method in class org.biojava.bio.seq.io.FastaFormat

Deprecated.
Set the line width.

setLineWidth(int) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Set the line width.

setLineWidth(int) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Set the line width.

setListener(Object, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
setListener(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState

set a TagValueListener for this State.

setListener(PatternListener) - Method in class org.biojava.utils.automata.PatternBlitz
 
setListener(PatternListener) - Method in interface org.biojava.utils.automata.StateMachineFactory
 
setListener(Search.Listener) - Method in class org.biojava.utils.regex.Search
 
setLITDBEntryNumbers(String[]) - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Sets the list of literature database identifiers for the AAindex entry.

setLocation(Location) - Method in interface org.biojava.bio.seq.Feature

The new location for this feature.

setLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
setLocation(Location) - Method in class org.biojavax.bio.seq.SimpleRichFeature

The new location for this feature.

setLocation(RichLocation) - Method in interface org.biojavax.RankedDocRef

Set the location of this reference.

setLocation(RichLocation) - Method in class org.biojavax.SimpleRankedDocRef

Set the location of this reference.

setLocationValue(Location) - Method in class org.biojava.bio.program.xff.LocationHandlerBase

Override this method to do something useful with the
 location we collect.

setLongValue(long) - Method in class org.biojava.utils.stax.LongElementHandlerBase

Override this method to do something useful with the
 long we collect.

setLRUCacheSize(int) - Static method in class org.biojavax.RichObjectFactory

Sets the size of the LRU cache.

setLRUCacheSize(Class, int) - Static method in class org.biojavax.RichObjectFactory

Sets the size of the LRU cache.

setMapAll(boolean) - Method in class org.biojava.bio.molbio.RestrictionMapper

setMapAll sets whether all sites should be marked,
 including those which have recognition sites within the
 sequence, but cut outside it.

setMapType(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setMaxCounts(AtomicSymbol, int) - Method in class org.biojava.bio.search.SeqContentPattern

Set the maximum counts required for a symbol.

setMaxCrossOvers(int) - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
 
setMaxCrossOvers(int) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
 
setMaxCrossOvers(int) - Method in interface org.biojavax.ga.functions.CrossOverFunction

Sets an upper limit on the number of crosses.

setMaxMissedCleavages(int) - Method in class org.biojava.bio.proteomics.Digest

Sets the maximum number of partial digest products to be annotated.

setMaxPosition(Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
setMaxRunTimeSecs(int) - Method in class org.biojava.utils.ExecRunner

Sets the maximum run time in seconds.

setMergeAnnotation(Annotation) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
 
setMergeSameTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser

Enable or disable treating runs of identical tags as a single tag start
 event with multiple values or each as a separate tag start, value, and tag
 end.

setMergeSameTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser

Decide if multiple examples of a single tag should be merged into a single
 start/endTag pair with multiple values, or multiple start/endTag pairs each
 with a single value.

setMinCounts(AtomicSymbol, int) - Method in class org.biojava.bio.search.SeqContentPattern

Set the minimum counts required for a symbol.

setMinPosition(Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
setMismatches(int) - Method in class org.biojava.bio.search.MaxMismatchPattern
 
setMitoGeneticCode(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon

Sets the mitochondrial genetic code of this taxon, which may be null, 
 which will unset it.

setMitoGeneticCode(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Sets the mitochondrial genetic code of this taxon, which may be null, 
 which will unset it.

setModel(MarkovModel) - Method in class org.biojava.bio.dp.DP
 
setMolecularWeight(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property molecularWeight.

setMolWeightError(Integer) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property molWeightError.

setMolWeightMethod(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property molWeightMethod.

setMolWeightRangeEnd(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property molWeightRangeEnd.

setMolWeightRangeStart(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property molWeightRangeStart.

setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentAdapter
 
setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentFilter
 
setMoreSearches(boolean) - Method in interface org.biojava.bio.search.SearchContentHandler

setMoreSearches sets the state of the
 SearchContentHandler's expectation of receiving
 more results.

setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
setMultiplier(double) - Method in class org.biojava.stats.svm.PolynomialKernel
 
setMultiplier(double) - Method in class org.biojava.stats.svm.SigmoidKernel
 
setMutationFunction(MutationFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm

Sets the current MutationFunction

setMutationFunction(MutationFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
setMutationProbs(double[]) - Method in class org.biojavax.ga.functions.AbstractMutationFunction
 
setMutationProbs(double[]) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
setMutationProbs(double[]) - Method in interface org.biojavax.ga.functions.MutationFunction

Set the probability of a mutation occuring at a certain position
 Position 0 in the array corresponds to the
 probability of the first residue of seq mutating.

setMutationSpectrum(OrderNDistribution) - Method in class org.biojavax.ga.functions.AbstractMutationFunction
 
setMutationSpectrum(OrderNDistribution) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
 
setMutationSpectrum(OrderNDistribution) - Method in interface org.biojavax.ga.functions.MutationFunction

Sets the Distribution of Symbols that will be selected
 from when a mutation occurs.

setName(String) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setName(String) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet

set the name of this group.

setName(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
setName(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence

Assign a name to this sequence

setName(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer

Deprecated.
 
setName(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer

Deprecated.
 
setName(String) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
setName(String) - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
setName(String) - Method in interface org.biojava.bio.seq.io.SeqIOListener

Notify the listener that the current sequence is generally known
 by a particular name.

setName(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
setName(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
setName(String) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer

Deprecated.
The name is printed out as part of the identifier line.

setName(String) - Method in class org.biojava.bio.symbol.SimpleAlphabet

Assign a name to the alphabet

setName(String) - Method in class org.biojava.ontology.IntegerOntology
 
setName(String) - Method in class org.biojava.ontology.Ontology.Impl
 
setName(String) - Method in interface org.biojava.ontology.Ontology

Set the name for this ontology

setName(String) - Method in class org.biojava.ontology.Synonym
 
setName(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setName(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setName(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Notify the listener that the current sequence is generally known
 by a particular name.

setName(String) - Method in interface org.biojavax.bio.seq.RichFeature

Sets the name of this feature.

setName(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Sets the name of this feature.

setName(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName

Changes the name.

setName(String) - Method in class org.biojavax.ga.impl.AbstractOrganism
 
setName(String) - Method in class org.biojavax.ga.impl.AbstractPopulation
 
setName(String) - Method in interface org.biojavax.ga.Organism

Sets the organisms name

setName(String) - Method in interface org.biojavax.ga.Population

Sets the name of the population

setName(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
 
setNameClass(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName

Changes the class of this name.

setNamedIsoforms(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event

Setter for property namedIsoforms.

setNames(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform

Setter for property names.

setNamespace(Namespace) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

Setter for property namespace.

setNamespace(Namespace) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB

Setter for property namespace.

setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setNamespace(Namespace) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 the namespace of the record being read.

setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 the namespace of the record being read.

setNegShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier

Set the Shape to represent the negative points.

setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.CachingKernel
 
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.DiagonalCachingKernel


 Set the kernel to nest.

setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.NestedKernel

Set the SVMKernel to nest to
 k.

setNewTag(Object, Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper

setNewTag.

setNodeRank(String) - Method in interface org.biojavax.bio.taxa.NCBITaxon

Sets the node rank of this taxon.

setNodeRank(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Setter for property nodeRank.

setNormalizingVector(SparseVector) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel

Set the normalizing vector.

setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform

Setter for property note.

setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property note.

setNoteSet(Set) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Clears the notes associated with this object and replaces them with
 the contents of this set.

setNoteSet(Set) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Clears the notes associated with this object and replaces them with
 the contents of this set.

setNoteSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Clears the notes associated with this object and replaces them with
 the contents of this set.

setNoteSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Clears the notes associated with this object and replaces them with
 the contents of this set.

setNoteSet(Set) - Method in class org.biojavax.EmptyRichAnnotation

Clears the notes from this annotation and replaces them with
 those from the given set.

setNoteSet(Set) - Method in class org.biojavax.SimpleCrossRef

Clears the notes associated with this object and replaces them with
 the contents of this set.

setNoteSet(Set<Note>) - Method in class org.biojavax.bio.SimpleBioEntry

Clears the notes associated with this object and replaces them with
 the contents of this set.

setNoteSet(Set<Note>) - Method in interface org.biojavax.RichAnnotatable

Clears the notes associated with this object and replaces them with
 the contents of this set.

setNoteSet(Set<Note>) - Method in interface org.biojavax.RichAnnotation

Clears the notes from this annotation and replaces them with
 those from the given set.

setNoteSet(Set<Note>) - Method in class org.biojavax.SimpleRichAnnotation

Clears the notes from this annotation and replaces them with
 those from the given set.

setNullModel(Distribution) - Method in class org.biojava.bio.dist.AbstractDistribution
 
setNullModel(Distribution) - Method in interface org.biojava.bio.dist.Distribution

Set the null model Distribution that this Distribution recognizes.

setNullModel(Distribution) - Method in class org.biojava.bio.dist.GapDistribution
 
setNullModel(Distribution) - Method in class org.biojava.bio.dist.PairDistribution
 
setNullModel(Distribution) - Method in class org.biojava.bio.dist.TranslatedDistribution
 
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.AbstractDistribution

Implement this to set the null model.

setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
 
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.SimpleDistribution
 
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.UniformDistribution

Assign a background distribution.

setNullModelWeight(double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext

Set the number of pseudocounts to add when training the distribution.

setNullModelWeight(double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
setNumber(float) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode

Set the number associated with this node.

setNumberExperiments(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction

Setter for property numberExperiments.

setObsolete(Boolean) - Method in interface org.biojavax.ontology.ComparableTerm

Sets the obsolescence flag associated with this term.

setObsolete(Boolean) - Method in class org.biojavax.ontology.SimpleComparableTerm

Sets the obsolescence flag associated with this term.

setOrder(double) - Method in class org.biojava.stats.svm.PolynomialKernel
 
setOrganismsDiffer(boolean) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction

Setter for property organismsDiffer.

setOrientation(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setOutput(OutputStream) - Method in interface org.biojava.utils.process.InputHandler

Sets the output stream.

setOutput(OutputStream) - Method in class org.biojava.utils.process.ReaderInputHandler

Sets the output stream.

setOutput(OutputStream) - Method in class org.biojava.utils.process.StreamPipe

Sets the output stream

setOutputFormat(RemoteQBlastOutputFormat) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties

This method is use to set the stream output format to get from the QBlast service

setOutputHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess

Sets the output handler which is responsible for the standard output
 of the external process.

setOutputOption(String, String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
 
setOutputOption(String, String) - Method in interface org.biojavax.bio.alignment.RemotePairwiseAlignmentOutputProperties

Method to set the value for a specific output parameter using a key to store in a map.

setParent(FeatureHolder) - Method in interface org.biojavax.bio.seq.RichFeature

Sets the parent of this feature.

setParent(FeatureHolder) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Sets the parent of this feature.

setParentNCBITaxID(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon

Sets the parent NCBI taxon ID.

setParentNCBITaxID(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Sets the parent NCBI taxon ID.

setParserListener(Object, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
setPathPrefix(File) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore

setPathPrefix sets the abstract path to be
 appended to sequence database filenames retrieved from the
 binary index.

setPattern(Pattern) - Method in class org.biojava.bio.program.tagvalue.RegexParser

Set the Pattern used to split lines.

setPattern(SymbolList) - Method in class org.biojava.bio.search.MaxMismatchPattern
 
setPhase(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setPHDependence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property PHDependence.

setPopulation(Population) - Method in interface org.biojavax.ga.GeneticAlgorithm

Sets the Population of Organisms to the
 Algorithm.

setPopulation(Population) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
setPos(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
 
setPositionResolver(PositionResolver) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Sets the resolver to use when working out actual base coordinates from
 fuzzy positions.

setPositionResolver(PositionResolver) - Method in interface org.biojavax.bio.seq.RichLocation

Sets the resolver to use when working out actual base coordinates from
 fuzzy positions.

setPositionResolver(PositionResolver) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Sets the resolver to use when working out actual base coordinates from
 fuzzy positions.

setPositions(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
setPosShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier

Set the Shape to represent the positive points.

setPrimaryKey(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory

setPrimaryKey sets the primary identifier
 namespace.

setPrimaryKeyName(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model


 Set the tag to use as a primary key in the index.

setPrimaryKeyName(String) - Method in class org.biojava.bio.program.tagvalue.Indexer


 Set the tag to use as a primary key in the index.

setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.EmblFileFormer

Deprecated.
 
setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFileFormer

Deprecated.
 
setPrintStream(PrintStream) - Method in interface org.biojava.bio.seq.io.SeqFileFormer

Deprecated.
setPrintStream informs an instance which
 PrintStream to use.

setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer

Deprecated.
setPrintStream informs an instance which
 PrintStream to use.

setPrintStream(PrintStream) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Sets the stream to write to.

setPrintStream(PrintStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Sets the stream to write to.

setPrintWriter(PrintWriter) - Method in class org.biojava.bio.program.blast2html.HTMLRenderer

Set the PrintWriter to output the HTML
 to.

setProfileHMM() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
 
setProperty(Object, Object) - Method in class org.biojava.bio.AbstractAnnotation
 
setProperty(Object, Object) - Method in interface org.biojava.bio.Annotation


 Set the value of a property.

setProperty(Object, Object) - Method in class org.biojava.bio.MergeAnnotation
 
setProperty(Object, Object) - Method in class org.biojava.bio.OverlayAnnotation
 
setProperty(Object, Object) - Method in class org.biojavax.EmptyRichAnnotation


 Set the value of a property.

setProperty(Object, Object) - Method in class org.biojavax.SimpleRichAnnotation

Deprecated. 

setProperty(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
 
setProperty(String, String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
setProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
 
setProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType

Set the property in an annotation bundle according to the type we believe
 it should be.

setProtease(Protease) - Method in class org.biojava.bio.proteomics.Digest
 
setProtype(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionEnzyme

Set the prototype of this RestrictionEnzyme.

setQueryID(String) - Method in class org.biojava.bio.search.FilteringContentHandler
 
setQueryID(String) - Method in class org.biojava.bio.search.SearchContentAdapter
 
setQueryID(String) - Method in class org.biojava.bio.search.SearchContentFilter
 
setQueryID(String) - Method in interface org.biojava.bio.search.SearchContentHandler

setQueryID identifies the query sequence by a
 name, ID or URN.

setQueryID(String) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
setRank(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Sets the rank for this location.

setRank(int) - Method in interface org.biojavax.bio.seq.RichFeature

Sets the rank of this feature.

setRank(int) - Method in interface org.biojavax.bio.seq.RichFeatureRelationship

Sets the rank of this relationship.

setRank(int) - Method in interface org.biojavax.bio.seq.RichLocation

Sets the rank for this location.

setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Sets the rank of this feature.

setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship

Sets the rank of this relationship.

setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Sets the rank for this location.

setRank(int) - Method in interface org.biojavax.Comment

Sets the rank of this comment.

setRank(int) - Method in interface org.biojavax.Note

Sets the rank for this note.

setRank(int) - Method in interface org.biojavax.RankedCrossRef

Set the rank associated with the cross reference.

setRank(int) - Method in interface org.biojavax.RankedDocRef

Set the rank of this reference.

setRank(int) - Method in class org.biojavax.SimpleComment

Sets the rank of this comment.

setRank(int) - Method in class org.biojavax.SimpleNote

Sets the rank for this note.

setRank(int) - Method in class org.biojavax.SimpleRankedCrossRef

Set the rank associated with the cross reference.

setRank(int) - Method in class org.biojavax.SimpleRankedDocRef

Set the rank of this reference.

setRank(Integer) - Method in interface org.biojavax.bio.BioEntryRelationship

Sets the rank of this relationship.

setRank(Integer) - Method in class org.biojavax.bio.SimpleBioEntryRelationship

Sets the rank of this relationship.

setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener about a cross reference.

setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener about a cross reference.

setRankedCrossRefs(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Sets the ranked cross references associated with an object.

setRankedCrossRefs(Set) - Method in class org.biojavax.ontology.SimpleComparableTerm

Sets the ranked cross references associated with an object.

setRankedCrossRefs(Set<RankedCrossRef>) - Method in class org.biojavax.bio.SimpleBioEntry
 
setRankedCrossRefs(Set<RankedCrossRef>) - Method in interface org.biojavax.RankedCrossRefable

Sets the ranked cross references associated with an object.

setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 about a literature reference in the record being read.

setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 about a literature reference in the record being read.

setReader(Reader) - Method in class org.biojava.utils.process.ReaderWriterPipe

Sets the reader.

setRecurse(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF

Set whether features will be filtered recursively to
 recurse.

setRecursive(boolean) - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
 
setRedoxPotential(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property redoxPotential.

setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
 
setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 about a relationship between the bioentry or sequence in the
 record being read and another bioentry.

setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 about a relationship between the bioentry or sequence in the
 record being read and another bioentry.

setRemark(String) - Method in interface org.biojavax.DocRef

Set the remarks for this document reference using this method.

setRemark(String) - Method in class org.biojavax.SimpleDocRef

Set the remarks for this document reference using this method.

setRetain(boolean) - Method in class org.biojava.bio.program.tagvalue.TagDropper

Set wether known tags are to be retained or dropped.

setRichObjectBuilder(RichObjectBuilder) - Static method in class org.biojavax.RichObjectFactory

Sets the builder to use when instantiating new Rich objects.

setRightValue(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon

Sets the right value.

setRightValue(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon

Sets the right value.

setScientificName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon

Deprecated.
 
setScientificName(String) - Method in interface org.biojava.bio.taxa.Taxon

Deprecated.
Change the scientific name of this species.

setScope(int) - Method in class org.biojava.ontology.Synonym
 
setScore(double) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
setScore(double) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

Set the score to score.

setScore(double) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setScore(int) - Method in class org.biojava.bio.alignment.SimpleAlignment
 
setScore(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.search.FilteringContentHandler
 
setSecondIntActID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction

Setter for property secondIntActID.

setSelectionFunction(SelectionFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm

Changes the SelectionFunction used to select candidates for
 the next generation

setSelectionFunction(SelectionFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
 
setSelectionPressure(int) - Method in class org.biojavax.ga.functions.TournamentSelection

sets the parameter controlling selection pressure

setSeqCautions(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property seqCautions.

setSeqID(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser

Deprecated.
 
setSeqName(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter

Set the sequence name to seqName.

setSeqName(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

Set the sequence name to seqName.

setSequence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
setSequence(Sequence) - Method in class org.biojava.bio.proteomics.Digest
 
setSequenceFormat(SequenceFormat) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
 
setSequenceFormat(LifeScienceIdentifier) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory

setSequenceFormat sets the sequence format name
 which will be indicated in the index.

setSequenceID(String) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setSequenceLength(int) - Method in class org.biojavax.bio.seq.SimpleRichSequence
 
setSequenceLength(int) - Method in class org.biojavax.bio.seq.ThinRichSequence
 
setSequenceRef(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform

Setter for property sequenceRef.

setSequenceType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform

Setter for property sequenceType.

setSeqVersion(Double) - Method in interface org.biojavax.bio.seq.RichSequence

Sets the version of the associated symbol list.

setSeqVersion(Double) - Method in class org.biojavax.bio.seq.ThinRichSequence

Sets the version of the associated symbol list.

setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setSeqVersion(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 the version of the sequence of the record being read.

setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 the version of the sequence of the record being read.

setShatter(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF

Specify whether features with non-contiguous locations should be broken
 up such that a GFF feature line is emitted for each contiguous block.

setShowAccession(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
 
setShowDescription(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
 
setShowIdentifier(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
 
setShowName(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
 
setShowNamespace(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
 
setShowVersion(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader

Determines if the version number of a sequence should be displayed.

setSibling(SimilarityPairFeature) - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature

setSibling sets the sibling feature of the
 pair.

setSibling(SimilarityPairFeature) - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
 
setSleepTime(int) - Method in class org.biojava.utils.process.ExternalProcess

Sets the number of milliseconds the ExternalProcess.execute(Properties)
 method should pauses after the external process is terminated.

setSource(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter

Set the source to source.

setSource(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

Set the feature source to source.

setSource(String) - Method in interface org.biojava.bio.seq.Feature

Change the source of the Feature.

setSource(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
setSource(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setSource(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Change the source of the Feature.

setSource(Term) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setSourceTerm(Term) - Method in interface org.biojava.bio.seq.Feature

Set the source ontology-term for this feature.

setSourceTerm(Term) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
setSourceTerm(Term) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Set the source ontology-term for this feature.

setSplitOffset(int) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser

Set the offset to split lines at.

setSplitter(Object, ChangeTable.Splitter) - Method in class org.biojava.bio.program.tagvalue.ChangeTable

Set the Splitter to be used for all values of a particular tag.

setStart(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

Set the start coordinate to start.

setStart(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
setStoreLocation(File) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory

setStoreLocation sets the directory of the new
 index.

setStoreName(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory

setStoreName sets the name to be given to the new
 index.

setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
 
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord

Set the strand to strand.

setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
setStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.StrandedFeature

Set the strand that this feature lies upon.

setStrand(StrandedFeature.Strand) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Set the strand that this feature lies upon.

setStrand(RichLocation.Strand) - Method in class org.biojavax.bio.seq.SimpleRichLocation
 
setStreamParser(StreamParser) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase

assign a StreamParser object to instance.

setStringSequence(String) - Method in class org.biojavax.bio.seq.SimpleRichSequence
 
setStringValue(String) - Method in class org.biojava.bio.program.xff.PropDetailHandler
 
setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
 
setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMENamePropHandler
 
setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMETypePropHandler
 
setStringValue(String) - Method in class org.biojava.utils.stax.StringElementHandlerBase

Override this method to do something useful with the
 string we collect.

setSubSeqStart(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setSymbolList(SymbolList) - Method in class org.biojava.bio.molbio.Composition

Set the SymbolList to calculation the composition of.

setSymbolModification(char, double) - Method in class org.biojava.bio.proteomics.MassCalc

Use this to set a post translational modification for the
 Symbol represented by this character.

setSynonyms(Set<Object>) - Method in class org.biojava.ontology.Term.Impl
 
setTableNumber(int) - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
 
setTagGroup(int) - Method in class org.biojava.bio.program.tagvalue.RegexParser

Set the group number that will match the tag.

setTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
setTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
setTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
 
setTaxon(NCBITaxon) - Method in interface org.biojavax.bio.BioEntry

Sets the taxon for this bioentry.

setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setTaxon(NCBITaxon) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 the Taxon of the record being read.

setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 the Taxon of the record being read.

setTaxon(NCBITaxon) - Method in class org.biojavax.bio.SimpleBioEntry

Sets the taxon for this bioentry.

setTaxonHidden(boolean) - Method in interface org.biojavax.bio.taxa.NCBITaxon

determines whether this taxonomy level is displayed in etNameHierarchy()

setTaxonHidden(boolean) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
 
setTemperatureDependence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property temperatureDependence.

setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Sets the term for this location.

setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Sets the term for this location.

setTerm(ComparableTerm) - Method in interface org.biojavax.bio.seq.RichLocation

Sets the term for this location.

setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Sets the term for this location.

setTerm(ComparableTerm) - Method in interface org.biojavax.Note

Sets the term for this note.

setTerm(ComparableTerm) - Method in class org.biojavax.SimpleNote

Sets the term for this note.

setTermSet(Set) - Method in interface org.biojavax.ontology.ComparableOntology

Clears out all the terms and populates the ontology with the contents
 of the set passed.

setTermSet(Set) - Method in class org.biojavax.ontology.SimpleComparableOntology

Clears out all the terms and populates the ontology with the contents
 of the set passed.

setText(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property text.

setThreshold() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
setThreshold(double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
setThreshold(double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
setThreshold(double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setTitle(String) - Method in interface org.biojava.bio.program.homologene.Orthologue
 
setTitle(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
 
setTool(String) - Method in class org.biojavax.bio.alignment.blast.RemoteQBlastService

Set the tool identifier for QBlast.

setTool(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

Set the tool identifier for Entrez.

setTransition(Object, StateMachine.State) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState

set a Transition for this State setting notifyOnExit to false.

setTransition(Object, StateMachine.State, boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState

set a Transition for this State

setTransition(Object, StateMachine.State, boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable

set a Transition within this TransitionTable (3-argument form)

setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable

Alter the translation mapping.

setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable

Alter the translation mapping.

setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable

Alter the translation mapping.

setTrimTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser

Enable or disable trimming of tags.

setTrimTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser

Enable trimming of the tag using String.trim().

setTrimValue(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser

Enable or disable trimming of values.

setTrimValue(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser

Enable trimming of the value using String.trim().

setTripleSet(Set) - Method in interface org.biojavax.ontology.ComparableOntology

Clears out all the triples and populates the ontology with the contents
 of the set passed.

setTripleSet(Set) - Method in class org.biojavax.ontology.SimpleComparableOntology

Clears out all the triples and populates the ontology with the contents
 of the set passed.

setType(String) - Method in interface org.biojava.bio.seq.Feature

Change the type of this feature.

setType(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
setType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event

Setter for property type.

setType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
 
setType(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Change the type of this feature.

setType(AnnotationType) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
setType(Term) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
 
setTypeTerm(Term) - Method in interface org.biojava.bio.seq.Feature

Set the type ontology-term for this feature.

setTypeTerm(Term) - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
setTypeTerm(Term) - Method in class org.biojavax.bio.seq.SimpleRichFeature

Set the type ontology-term for this feature.

setUnits(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
setUri(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property uri.

setURI(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer

Deprecated.
 
setURI(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer

Deprecated.
 
setURI(String) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
setURI(String) - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
setURI(String) - Method in interface org.biojava.bio.seq.io.SeqIOListener

Notify the listener of a URI identifying the current sequence.

setURI(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
setURI(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
setURI(String) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer

Deprecated.
Null implementation.

setURI(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setURI(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setURI(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Deprecated.
There is no clear mapping between URI and BioSQL. This
  method is no longer used or supported in biojavax. Don't use it. Calling
  it may result in exceptions. Use instead setName(String name),
  setAccession(String accession), setVersion(int version) etc as
  appropriate.


setURI(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Notify the listener of a URI identifying the current sequence.

setURI(URI) - Method in interface org.biojavax.Namespace

Sets an optional URI for the namespace.

setURI(URI) - Method in class org.biojavax.SimpleNamespace

Sets an optional URI for the namespace.

setURN(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence

Provide the URN for this sequence

setValue(double) - Method in interface org.biojava.stats.svm.ItemValue
 
setValue(double) - Method in class org.biojava.stats.svm.SimpleItemValue
 
setValue(String) - Method in interface org.biojavax.Note

Sets the value for this note, or null for no value.

setValue(String) - Method in class org.biojavax.SimpleNote

Sets the value for this note, or null for no value.

setValueGroup(int) - Method in class org.biojava.bio.program.tagvalue.RegexParser

Set the group number that will match the value.

setVectorNTISupport(boolean) - Method in class org.biojava.bio.seq.io.GenbankFileFormer

Deprecated.
VectorNTI requires GenBank format to be a little more specific than
 required by the GenBank definition.

setVersion(int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
setVersion(int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
setVersion(int) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener

Call back method so the event emitter can tell the listener
 the version of the record being read.

setVersion(int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Call back method so the event emitter can tell the listener
 the version of the record being read.

setVersion(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
setVMaxes(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser

Setter for property VMaxes.

setWeight(Object, double) - Method in class org.biojavax.ga.util.WeightedSet

Sets the weight of an Object.

setWeight(Symbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution

Set the weight of a given symbol in this distribution.

setWeight(Symbol, double) - Method in interface org.biojava.bio.dist.Distribution

Set the probability or odds that Symbol s is emitted by this state.

setWeight(Symbol, double) - Method in class org.biojava.bio.dist.GapDistribution
 
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.PairDistribution
 
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.TranslatedDistribution
 
setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution

Implement this to actually set the weight.

setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution

Set a weight in one of the conditioned distributions.

setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution
 
setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.UniformDistribution
 
setWeightMatrixID(String) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator

Set the weight matrix id.

setWeights(State, Distribution) - Method in interface org.biojava.bio.dp.MarkovModel

Set the probability distribution over the transitions from 'source'.

setWeights(State, Distribution) - Method in class org.biojava.bio.dp.SimpleMarkovModel

Use this methods to customize the transition probabilities.

setWeights(State, Distribution) - Method in class org.biojava.bio.dp.WMAsMM
 
setWidth(double) - Method in class org.biojava.stats.svm.RadialBaseKernel
 
setWorkingDirectory(File) - Method in class org.biojava.utils.process.ExternalProcess

Sets the working directory for the external process.

setWrappedKernel(SVMKernel) - Method in class org.biojava.stats.svm.SigmoidKernel
 
setWriteDocType(boolean) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter

Set flag that determines if XML DOCTYPE is written
 or not.

setWriter(Writer) - Method in class org.biojava.utils.process.ReaderWriterPipe

Sets the writer.

shadow(Location) - Static method in class org.biojava.bio.symbol.LocationTools

Return a contiguous location running from the minimum to the maximum points of
 the specified location.

shadowContainedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils

Construct a filter which matches features with locations where the interval
 between the min and max positions are contained by 
 the specified Location.

ShadowContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation

Creates a filter that returns everything contained within loc.

shadowOverlapsLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils

Construct a filter which matches features with locations where the interval
 between the min and max positions are contained by or
 overlap the specified Location.

ShadowOverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation

Creates a filter that returns everything overlapping loc.

shannonEntropy(Distribution, double) - Static method in class org.biojava.bio.dist.DistributionTools

A method to calculate the Shannon Entropy for a Distribution.

SHOW_ALL - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler

Return default styles

SHOW_DIFF - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler

As NORMAL except only return if the two colour classes for
 query and subject are the different

SHOW_SAME - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler

Only return if the two colour classes for
 query and subject are the same

sibling - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template

sibling SimilarityPairFeature
 field.

SIBLING - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature

The sibling of this feature has altered.

SigmoidKernel - Class in org.biojava.stats.svm

This kernel implements a three layer neural net.

SigmoidKernel() - Constructor for class org.biojava.stats.svm.SigmoidKernel
 
sign(double) - Static method in class org.biojava.stats.svm.tools.Classify
 
similarEntries() - Method in class org.biojava.bio.proteomics.aaindex.AAindex

Returns a map with the names of similar AAindex entries and its 
 correlation coefficients.

SimilarityPairFeature - Interface in org.biojava.bio.seq.homol

SimilarityPairFeature describes a pairwise
 similarity between two nucleotide sequences (as it extends
 StrandedFeature).

SimilarityPairFeature.EmptyPairwiseAlignment - Class in org.biojava.bio.seq.homol

EmptyPairwiseAlignment empty pairwise alignment
 which has labels to empty symbol lists.

SimilarityPairFeature.Template - Class in org.biojava.bio.seq.homol

Template for construction of
 SimilarityPairFeatures.

SimilarityType - Interface in org.biojava.bio.program.homologene

Each HomologeneEntry represents a single
 Homologene record that relates two
 presumptive orthologues.

SIMILARITYTYPE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
SimilarityType.PlaceHolder - Class in org.biojava.bio.program.homologene
 
SIMPLE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
 
SimpleAlignment - Class in org.biojava.bio.alignment

A simple implementation of an Alignment.

SimpleAlignment(Map<String, SymbolList>) - Constructor for class org.biojava.bio.alignment.SimpleAlignment

Generate an alignment from a list of SymbolLists.

SimpleAlignmentStyler - Class in org.biojava.bio.program.blast2html

Simple implementation for specifying markup styles.

SimpleAlignmentStyler(int) - Constructor for class org.biojava.bio.program.blast2html.SimpleAlignmentStyler

Creates a new SimpleAlignmentStyler instance.

SimpleAlphabet - Class in org.biojava.bio.symbol

A simple no-frills implementation of the FiniteAlphabet interface.

SimpleAlphabet() - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
 
SimpleAlphabet(String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
 
SimpleAlphabet(Set) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
 
SimpleAlphabet(Set, String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
 
SimpleAnnotation - Class in org.biojava.bio

A no-frills implementation of Annotation that is just a wrapper
 around a LinkedHashMap.

SimpleAnnotation() - Constructor for class org.biojava.bio.SimpleAnnotation

Create a new, empty SimpleAnnotation instance.

SimpleAnnotation(Map) - Constructor for class org.biojava.bio.SimpleAnnotation

Create a new SimpleAnnotation using the values in a Map.

SimpleAnnotation(Annotation) - Constructor for class org.biojava.bio.SimpleAnnotation

Create a new SimpleAnnotation by copying the properties from another
 one.

SimpleAnnotationDB - Class in org.biojava.bio.annodb

A no-frills implementation of AnnotationDB.

SimpleAnnotationDB(String, Set, AnnotationType) - Constructor for class org.biojava.bio.annodb.SimpleAnnotationDB

Create a no-frills AnnotationDB instancec.

SimpleAnnotFilter - Class in org.biojava.bio.seq.io.agave

Basic implementation of AGAVEAnnotFilter

SimpleAssembly - Class in org.biojava.bio.seq

A Sequence which is assembled from other sequences contained
 in a set of ComponentFeature objects.

SimpleAssembly(int, String, String) - Constructor for class org.biojava.bio.seq.SimpleAssembly

Construct a new SimpleAssembly using the DNA alphabet.

SimpleAssembly(String, String) - Constructor for class org.biojava.bio.seq.SimpleAssembly

Construct a new SimpleAssembly using the DNA alphabet.

SimpleAssemblyBuilder - Class in org.biojava.bio.seq.io

Basic SequenceBuilder implementation which accumulates all
 notified information and creates a SimpleAssembly.

SimpleAssemblyBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleAssemblyBuilder
 
SimpleAtomicSymbol - Class in org.biojava.bio.symbol

A basic implementation of AtomicSymbol.

SimpleAtomicSymbol(Annotation, List) - Constructor for class org.biojava.bio.symbol.SimpleAtomicSymbol
 
SimpleBioEntry - Class in org.biojavax.bio

Reference implementation of a BioEntry object which has no features or sequence.

SimpleBioEntry() - Constructor for class org.biojavax.bio.SimpleBioEntry
 
SimpleBioEntry(Namespace, String, String, int) - Constructor for class org.biojavax.bio.SimpleBioEntry

Creates a new bioentry representing the sequence in the given namespace
 with the given name, accession and version.

SimpleBioEntryRelationship - Class in org.biojavax.bio

Represents a relationship between two bioentries that is described by a term 
 and given a rank.

SimpleBioEntryRelationship() - Constructor for class org.biojavax.bio.SimpleBioEntryRelationship
 
SimpleBioEntryRelationship(BioEntry, BioEntry, ComparableTerm, Integer) - Constructor for class org.biojavax.bio.SimpleBioEntryRelationship

Creates a new instance of SimpleBioEntryRelationship.

SimpleCodonPref - Class in org.biojava.bio.symbol

a simple no-frills implementation of the
 CodonPref object that encapsulates
 codon preference data.

SimpleCodonPref(String, Distribution, String) - Constructor for class org.biojava.bio.symbol.SimpleCodonPref
 
SimpleComment - Class in org.biojavax

An implementaion of Comment.

SimpleComment() - Constructor for class org.biojavax.SimpleComment
 
SimpleComment(String, int) - Constructor for class org.biojavax.SimpleComment

Constructs a new, immutable comment, given some text and a rank.

SimpleComparableOntology - Class in org.biojavax.ontology

Represents an ontology that can be compared to other ontologies.

SimpleComparableOntology() - Constructor for class org.biojavax.ontology.SimpleComparableOntology
 
SimpleComparableOntology(String) - Constructor for class org.biojavax.ontology.SimpleComparableOntology

Creates a new instance of SimpleComparableOntology with the given,
 immutable, non-nullable name.

SimpleComparableTerm - Class in org.biojavax.ontology

A Term object that can be compared and thus sorted.

SimpleComparableTerm() - Constructor for class org.biojavax.ontology.SimpleComparableTerm
 
SimpleComparableTriple - Class in org.biojavax.ontology

Basic comparable triple, BioSQL style.

SimpleComparableTriple() - Constructor for class org.biojavax.ontology.SimpleComparableTriple
 
SimpleCrossOverFunction - Class in org.biojavax.ga.functions

Simple Implementation of the CrossOverFunction interface

SimpleCrossOverFunction() - Constructor for class org.biojavax.ga.functions.SimpleCrossOverFunction
 
SimpleCrossRef - Class in org.biojavax

A basic CrossRef implementation.

SimpleCrossRef() - Constructor for class org.biojavax.SimpleCrossRef
 
SimpleCrossRef(String, String, int) - Constructor for class org.biojavax.SimpleCrossRef

Creates a new instance of SimpleCrossRef with the values to use for
 the immutable database name, accession and version.

SimpleCrossRef(String, String, Integer) - Constructor for class org.biojavax.SimpleCrossRef

Creates a new instance of SimpleCrossRef with the values to use for
 the immutable database name, accession and version.

SimpleDistribution - Class in org.biojava.bio.dist

A simple implementation of a distribution, which works with any finite alphabet.

SimpleDistribution(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistribution

make an instance of SimpleDistribution with weights identical
 to the specified Distribution.

SimpleDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.SimpleDistribution

make an instance of SimpleDistribution for the specified Alphabet.

SimpleDistribution.Trainer - Class in org.biojava.bio.dist

A simple implementation of a trainer for this class.

SimpleDistributionTrainer - Class in org.biojava.bio.dist

Deprecated.
Distribution impls should be providing custom trainers.


SimpleDistributionTrainer(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainer

Deprecated.
 
SimpleDistributionTrainerContext - Class in org.biojava.bio.dist

A no-frills implementation of DistributionTrainerContext.

SimpleDistributionTrainerContext() - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainerContext

Create a new context with no initial distributions or trainers.

SimpleDocRef - Class in org.biojavax

A basic DocRef implementation.

SimpleDocRef() - Constructor for class org.biojavax.SimpleDocRef
 
SimpleDocRef(String, String) - Constructor for class org.biojavax.SimpleDocRef

Creates a new document reference from the given immutable authors and
 location and title.

SimpleDocRef(String, String, String) - Constructor for class org.biojavax.SimpleDocRef

Creates a new document reference from the given immutable authors and
 location and title.

SimpleDocRef(String, String, String, String, String, Integer) - Constructor for class org.biojavax.SimpleDocRef

Construct a doc ref with populated cross ref.

SimpleDocRef(List<DocRefAuthor>, String) - Constructor for class org.biojavax.SimpleDocRef

Creates a new document reference from the given immutable authors and
 location and title.

SimpleDocRef(List<DocRefAuthor>, String, String) - Constructor for class org.biojavax.SimpleDocRef

Creates a new document reference from the given immutable authors and
 location and title.

SimpleDocRef(List, String, String, String, String, Integer) - Constructor for class org.biojavax.SimpleDocRef

Construct a doc ref with populated cross ref.

SimpleDocRefAuthor - Class in org.biojavax

Represents an author of a documentary reference.

SimpleDocRefAuthor(String) - Constructor for class org.biojavax.SimpleDocRefAuthor

Constructs a new author instance from a string.

SimpleDocRefAuthor(String, boolean, boolean) - Constructor for class org.biojavax.SimpleDocRefAuthor

Constructs a new author instance.

SimpleDotState - Class in org.biojava.bio.dp

A Dot state that you can make and use.

SimpleDotState(char, String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState

Deprecated.
token is ignored since 1.2.  Use the 2-arg constructor instead.


SimpleDotState(String) - Constructor for class org.biojava.bio.dp.SimpleDotState
 
SimpleDotState(String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState

Construct a new state with the specified name and annotation

SimpleEmissionState - Class in org.biojava.bio.dp
 
SimpleEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.dp.SimpleEmissionState
 
SimpleFeature - Class in org.biojava.bio.seq.impl

A no-frills implementation of a feature.

SimpleFeature(Sequence, FeatureHolder, Feature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFeature

Create a SimpleFeature on the given sequence.

SimpleFeatureHolder - Class in org.biojava.bio.seq

A no-frills implementation of FeatureHolder.

SimpleFeatureHolder() - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder

Construct a new SimpleFeatureHolder with a non-informative schema.

SimpleFeatureHolder(FeatureFilter) - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder

Construct a new SimpleFeatureHolder with the specified schema.

SimpleFeatureRealizer - Class in org.biojava.bio.seq

FeatureRealizer which uses a lookup table to map template classes
 to implementations.

SimpleFeatureRealizer() - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer
 
SimpleFeatureRealizer(FeatureRealizer) - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer
 
SimpleFramedFeature - Class in org.biojava.bio.seq.impl

Title:        SimpleFramedFeature.

SimpleFramedFeature(Sequence, FeatureHolder, FramedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFramedFeature
 
SimpleGACrossResult - Class in org.biojavax.ga.functions

Simple implementation of the GACross interface.

SimpleGACrossResult(PointLocation[], SymbolList[]) - Constructor for class org.biojavax.ga.functions.SimpleGACrossResult
 
SimpleGappedSequence - Class in org.biojava.bio.seq.impl

Simple implementation of GappedSequence.

SimpleGappedSequence(GappedSequence) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence
 
SimpleGappedSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence
 
SimpleGappedSequence(Alphabet) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence
 
SimpleGappedSequence.GappedContext - Class in org.biojava.bio.seq.impl
 
SimpleGappedSymbolList - Class in org.biojava.bio.symbol

This implementation of GappedSymbolList wraps a SymbolList, allowing you to
 insert gaps.

SimpleGappedSymbolList(Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList
 
SimpleGappedSymbolList(GappedSymbolList) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList

Create a new SimpleGappedSymbolList that will view source, inheriting all
 existing gaps.

SimpleGappedSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList

Create a new SimpleGappedSymbolList that will view source.

SimpleGappedSymbolList.Block - Class in org.biojava.bio.symbol

An aligned block.

SimpleGeneticAlgorithm - Class in org.biojavax.ga.impl

A simple implementation of the GeneticAlgorithm interface it
 is not intended that this class be overidden, hence it is final.

SimpleGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.SimpleGeneticAlgorithm
 
SimpleGeneticAlgorithm(Population, MutationFunction, CrossOverFunction, SelectionFunction) - Constructor for class org.biojavax.ga.impl.SimpleGeneticAlgorithm
 
SimpleGeneticCodeTable - Class in org.biojava.bio.symbol

A genetic code translation table representing a translation table in the 
 DDBJ/EMBL/GenBank Feature Table (appendix V).

SimpleGeneticCodeTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleGeneticCodeTable

Creates a new instance of SimpleGeneticCodeTable

SimpleGFFRecord - Class in org.biojava.bio.program.gff

A no-frills implementation of a GFFRecord.

SimpleGFFRecord() - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord

Create a new SimpleGFFRecord with values set to null or zero

SimpleGFFRecord(String, String, String, int, int, double, StrandedFeature.Strand, int, String, Map) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
 
SimpleGFFRecord(GFFRecord) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord

Create a new SimpleGFFRecord from GFFRecord object

SimpleHMMTrainer - Class in org.biojava.bio.dp
 
SimpleHMMTrainer(MarkovModel) - Constructor for class org.biojava.bio.dp.SimpleHMMTrainer
 
SimpleHomologeneBuilder - Class in org.biojava.bio.program.homologene

A simple no-frills implementation of the HomologeneBuilder interface.

SimpleHomologeneBuilder() - Constructor for class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
SimpleHomologeneDB - Class in org.biojava.bio.program.homologene
 
SimpleHomologeneDB() - Constructor for class org.biojava.bio.program.homologene.SimpleHomologeneDB
 
SimpleHomology - Class in org.biojava.bio.seq.homol

A no-frills implementation of Homology.

SimpleHomology() - Constructor for class org.biojava.bio.seq.homol.SimpleHomology

Creates a new empty SimpleHomology containing no
 Alignment and no FeatureHolder.

SimpleHomologyFeature - Class in org.biojava.bio.seq.impl
 
SimpleHomologyFeature(Sequence, FeatureHolder, HomologyFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleHomologyFeature
 
SimpleIndex - Class in org.biojava.bio.seq.db

This is a no-frills implementation of the Index interface.

SimpleIndex(File, long, int, String) - Constructor for class org.biojava.bio.seq.db.SimpleIndex

Build the index using the given file, start and id

SimpleInputHandler - Class in org.biojava.utils.process

Simple input handler 
 that reads the input for an external process from an 
 input stream.

SimpleInputHandler(InputStream, String) - Constructor for class org.biojava.utils.process.SimpleInputHandler

Initializes the simple input handler.

SimpleItemValue - Class in org.biojava.stats.svm

A no-frills implementation of ItemValue.

SimpleItemValue(Object, double) - Constructor for class org.biojava.stats.svm.SimpleItemValue
 
SimpleManyToOneTranslationTable - Class in org.biojava.bio.symbol

A no-frills implementation of a translation table that
 maps between two alphabets.

SimpleManyToOneTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleManyToOneTranslationTable

Construct a new translation table.

SimpleMarkovModel - Class in org.biojava.bio.dp
 
SimpleMarkovModel(int, Alphabet) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel

Deprecated. 

SimpleMarkovModel(int, Alphabet, String) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
 
SimpleModelInState - Class in org.biojava.bio.dp
 
SimpleModelInState(MarkovModel, String) - Constructor for class org.biojava.bio.dp.SimpleModelInState
 
SimpleModelTrainer - Class in org.biojava.bio.dp
 
SimpleModelTrainer() - Constructor for class org.biojava.bio.dp.SimpleModelTrainer
 
SimpleMutationFunction - Class in org.biojavax.ga.functions

 Simple no frills Implementation of the MutationFunction interface

SimpleMutationFunction() - Constructor for class org.biojavax.ga.functions.SimpleMutationFunction
 
SimpleNamespace - Class in org.biojavax

A basic Namespace implemenation.

SimpleNamespace() - Constructor for class org.biojavax.SimpleNamespace
 
SimpleNamespace(String) - Constructor for class org.biojavax.SimpleNamespace

Creates a new instance of SimpleNamespace with the given name,
 which cannot be null.

SimpleNCBITaxon - Class in org.biojavax.bio.taxa

Reference implementation of NCBITaxon.

SimpleNCBITaxon() - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon
 
SimpleNCBITaxon(int) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon

Creates a new instance of SimpleNCBITaxon based on the given taxon ID.

SimpleNCBITaxon(Integer) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon

Creates a new instance of SimpleNCBITaxon based on the given taxon ID.

SimpleNCBITaxonName - Class in org.biojavax.bio.taxa

Represents a name class plus name combination for an NCBITaxon object.

SimpleNCBITaxonName() - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxonName
 
SimpleNCBITaxonName(String, String) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxonName

Creates a new taxon name based on the given class and name, both of
 which cannot be null.

SimpleNCBITaxonomyLoader - Class in org.biojavax.bio.taxa.io

Loads NCBI taxon information from names.dmp and nodes.dmp, which are
 two of the files in the archive downloadable at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ .

SimpleNCBITaxonomyLoader() - Constructor for class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
 
SimpleNote - Class in org.biojavax

Simple implementation of Note.

SimpleNote() - Constructor for class org.biojavax.SimpleNote
 
SimpleNote(ComparableTerm, String, int) - Constructor for class org.biojavax.SimpleNote

Creates a new instance of SimpleNote with a given term, value and rank.

SimpleOrganism - Class in org.biojavax.ga.impl

A Simple Haploid Organism implementation

SimpleOrganism() - Constructor for class org.biojavax.ga.impl.SimpleOrganism
 
SimpleOrganism(String) - Constructor for class org.biojavax.ga.impl.SimpleOrganism
 
SimpleOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.SimpleOrganism
 
SimpleOrthologue - Class in org.biojava.bio.program.homologene

this entry contains data about the orthologue.

SimpleOrthologue(int, String, String, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologue

this constructor does the Taxon lookup for you too

SimpleOrthologue(Taxon, String, String, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologue
 
SimpleOrthologueSet - Class in org.biojava.bio.program.homologene
 
SimpleOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologueSet
 
SimpleOrthologueSet.Iterator - Class in org.biojava.bio.program.homologene
 
SimpleOrthoPair - Class in org.biojava.bio.program.homologene

A no-frills implementation of the OrthoPair interface

SimpleOrthoPair(Orthologue, Orthologue, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPair

constructor for the curated form
 of an orthology relationship

SimpleOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPair

constructor for the computed form
 of an orthology relationship.

SimpleOrthoPairCollection - Class in org.biojava.bio.program.homologene
 
SimpleOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
 
SimpleOrthoPairCollection.Iterator - Class in org.biojava.bio.program.homologene
 
SimpleOrthoPairSet - Class in org.biojava.bio.program.homologene

a no-frills implementation of a Homologene Group

SimpleOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
SimpleOrthoPairSet.Iterator - Class in org.biojava.bio.program.homologene
 
SimpleOutputHandler - Class in org.biojava.utils.process

Simple output handler 
 that pipes the output of an external process to an 
 output stream.

SimpleOutputHandler(OutputStream, String) - Constructor for class org.biojava.utils.process.SimpleOutputHandler

Initializes the simple output handler.

SimplePopulation - Class in org.biojavax.ga.impl

Simple concrete implementation of the Population interface

SimplePopulation() - Constructor for class org.biojavax.ga.impl.SimplePopulation
 
SimplePopulation(String) - Constructor for class org.biojavax.ga.impl.SimplePopulation
 
SimplePosition - Class in org.biojavax.bio.seq

A simple implementation of the Position interface.

SimplePosition() - Constructor for class org.biojavax.bio.seq.SimplePosition
 
SimplePosition(boolean, boolean, int) - Constructor for class org.biojavax.bio.seq.SimplePosition

Constructs a point position, with optionally fuzzy start and
 end.

SimplePosition(boolean, boolean, int, int, String) - Constructor for class org.biojavax.bio.seq.SimplePosition

Constructs a range position, with optionally fuzzy start and
 end.

SimplePosition(int) - Constructor for class org.biojavax.bio.seq.SimplePosition

Constructs a point position, with no fuzzy start or
 end.

SimplePosition(int, int) - Constructor for class org.biojavax.bio.seq.SimplePosition

Constructs a range position, with no fuzzy start or
 end.

SimpleRankedCrossRef - Class in org.biojavax

Simple implementation of RankedCrossRef.

SimpleRankedCrossRef() - Constructor for class org.biojavax.SimpleRankedCrossRef
 
SimpleRankedCrossRef(CrossRef, int) - Constructor for class org.biojavax.SimpleRankedCrossRef

Constructs a new crossref with a rank.

SimpleRankedDocRef - Class in org.biojavax

Represents a documentary reference.

SimpleRankedDocRef() - Constructor for class org.biojavax.SimpleRankedDocRef
 
SimpleRankedDocRef(DocRef, Integer, Integer, int) - Constructor for class org.biojavax.SimpleRankedDocRef

Constructs a new docref for a given location.

SimpleRankedDocRef(DocRef, RichLocation, int) - Constructor for class org.biojavax.SimpleRankedDocRef

Constructs a new docref for a given location.

SimpleRemoteFeature - Class in org.biojava.bio.seq.impl

A no-frills implementation of a remote feature.

SimpleRemoteFeature(Sequence, FeatureHolder, RemoteFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature
 
SimpleRemoteFeature.DBResolver - Class in org.biojava.bio.seq.impl
 
SimpleRestrictionSite - Class in org.biojava.bio.seq.impl

SimpleRestrictionSite represents the recognition site
 of a restriction enzyme.

SimpleRestrictionSite(Sequence, FeatureHolder, RestrictionSite.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleRestrictionSite

Creates a new SimpleRestrictionSite.

SimpleReversibleTranslationTable - Class in org.biojava.bio.symbol

A no-frills implementation of TranslationTable that uses a Map to map from
 symbols in a finite source alphabet into a target alphabet.

SimpleReversibleTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleReversibleTranslationTable

Construct a new translation table.

SimpleRichAnnotation - Class in org.biojavax

Simple annotation wrapper.

SimpleRichAnnotation() - Constructor for class org.biojavax.SimpleRichAnnotation

Creates a new, empty instance of SimpleRichAnnotation

SimpleRichFeature - Class in org.biojavax.bio.seq

A simple implementation of RichFeature.

SimpleRichFeature() - Constructor for class org.biojavax.bio.seq.SimpleRichFeature
 
SimpleRichFeature(FeatureHolder, Feature.Template) - Constructor for class org.biojavax.bio.seq.SimpleRichFeature

Creates a new instance of SimpleRichFeature based on a template.

SimpleRichFeatureRelationship - Class in org.biojavax.bio.seq

Represents a relationship between two features that is described by a term.

SimpleRichFeatureRelationship() - Constructor for class org.biojavax.bio.seq.SimpleRichFeatureRelationship
 
SimpleRichFeatureRelationship(RichFeature, RichFeature, ComparableTerm, int) - Constructor for class org.biojavax.bio.seq.SimpleRichFeatureRelationship

Creates a new instance of SimpleRichFeatureRelationship.

SimpleRichLocation - Class in org.biojavax.bio.seq

A simple implementation of RichLocation.

SimpleRichLocation() - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
 
SimpleRichLocation(Position, int) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation

Creates a new instance of SimpleRichSequenceLocation that points to a
 single position on the positive strand.

SimpleRichLocation(Position, int, RichLocation.Strand) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation

Creates a new instance of SimpleRichSequenceLocation that points to a
 single position.

SimpleRichLocation(Position, int, RichLocation.Strand, CrossRef) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation

Creates a new instance of SimpleRichSequenceLocation that points to a
 single position on another sequence.

SimpleRichLocation(Position, Position, int) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation

Creates a new instance of SimpleRichSequenceLocation that points to a
 range position on the positive strand.

SimpleRichLocation(Position, Position, int, RichLocation.Strand) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation

Creates a new instance of SimpleRichSequenceLocation that points to a
 range position.

SimpleRichLocation(Position, Position, int, RichLocation.Strand, CrossRef) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation

Creates a new instance of SimpleRichSequenceLocation that points to a
 range position on another sequence.

SimpleRichObjectBuilder - Class in org.biojavax

Creates objects and returns them, and stores them in an internal
 map of singletons for reference.

SimpleRichObjectBuilder() - Constructor for class org.biojavax.SimpleRichObjectBuilder
 
SimpleRichSequence - Class in org.biojavax.bio.seq

A simple implementation of RichSequence.

SimpleRichSequence() - Constructor for class org.biojavax.bio.seq.SimpleRichSequence
 
SimpleRichSequence(Namespace, String, String, int, SymbolList, Double) - Constructor for class org.biojavax.bio.seq.SimpleRichSequence

Creates a new instance of SimpleRichSequence.

SimpleRichSequenceBuilder - Class in org.biojavax.bio.seq.io

Constructs BioEntry objects by listening to events.

SimpleRichSequenceBuilder() - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Creates a new instance of SimpleRichSequenceBuilder using a SimpleSymbolListFactory
 with a threshold of zero.

SimpleRichSequenceBuilder(SymbolListFactory) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Creates a new instance of SimpleRichSequenceBuilder with the
 desired symbollistfactory and threshold of zero.

SimpleRichSequenceBuilder(SymbolListFactory, int) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Creates a new instance of SimpleRichSequenceBuilder with the
 desired symbollistfactory and threshold.

SimpleRichSequenceBuilderFactory - Class in org.biojavax.bio.seq.io

Generates RichSequenceBuilder objects.

SimpleRichSequenceBuilderFactory() - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory

Creates a new instance of SimpleRichSequenceBuilderFactory

SimpleRichSequenceBuilderFactory(SymbolListFactory) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory

Creates a new instance of SimpleRichSequenceBuilderFactory

SimpleRichSequenceBuilderFactory(SymbolListFactory, int) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory

Creates a new instance of SimpleRichSequenceBuilderFactory that uses
 a specified factory for SymbolLists longer than a specified
 length.

SimpleSeqSimilaritySearchHit - Class in org.biojava.bio.search

SimpleSeqSimilaritySearchHit objects represent a
 similarity search hit of a query sequence to a sequence referenced
 in a SequenceDB object.

SimpleSeqSimilaritySearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchHit

Creates a new SimpleSeqSimilaritySearchHit object.

SimpleSeqSimilaritySearchResult - Class in org.biojava.bio.search

SimpleSeqSimilaritySearchResult objects represent a
 result of a search of a SymbolList against the
 sequences within a SequenceDB object.

SimpleSeqSimilaritySearchResult(Sequence, SequenceDB, Map, List, Annotation) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchResult

Creates a new SimpleSeqSimilaritySearchResult.

SimpleSeqSimilaritySearchSubHit - Class in org.biojava.bio.search

SimpleSeqSimilaritySearchSubHit objects represent
 sub-hits which make up a hit.

SimpleSeqSimilaritySearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit

Creates a new SimpleSeqSimilaritySearchSubHit
 object.

SimpleSequence - Class in org.biojava.bio.seq.impl

A basic implementation of the Sequence interface.

SimpleSequence(SymbolList, String, String, Annotation) - Constructor for class org.biojava.bio.seq.impl.SimpleSequence

Create a SimpleSequence with the symbols and alphabet of sym, and the
 sequence properties listed.

SimpleSequence(SymbolList, String, String, Annotation, FeatureRealizer) - Constructor for class org.biojava.bio.seq.impl.SimpleSequence

Create a SimpleSequence using a specified FeatureRealizer.

SimpleSequenceBuilder - Class in org.biojava.bio.seq.io

Basic SequenceBuilder implementation which accumulates all
 notified information and creates a SimpleSequence.

SimpleSequenceBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleSequenceBuilder
 
SimpleSequenceDBInstallation - Class in org.biojava.bio.seq.db

This class is an implementation of interface SequenceDBInstallation
 that manages a set of SequenceDB objects.

SimpleSequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.SimpleSequenceDBInstallation

create an initially empty SimpleSequenceDBInstallation

SimpleSequenceFactory - Class in org.biojava.bio.seq.impl

A no-frills implementation of SequenceFactory that produces SimpleSequence
 objects.

SimpleSequenceFactory() - Constructor for class org.biojava.bio.seq.impl.SimpleSequenceFactory
 
SimpleSimilarityPairFeature - Class in org.biojava.bio.seq.impl

SimpleSimilarityPairFeature represents a similarity
 between a query sequence and a subject sequence as produced by a
 search program.

SimpleSimilarityPairFeature(Sequence, FeatureHolder, SimilarityPairFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature

Creates a new SimpleSimilarityPairFeature.

SimpleStateListener() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
 
SimpleStatePath - Class in org.biojava.bio.dp

A no-frills implementation of StatePath.

SimpleStatePath(double, SymbolList, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.SimpleStatePath
 
SimpleStrandedFeature - Class in org.biojava.bio.seq.impl

A no-frills implementation of StrandedFeature.

SimpleStrandedFeature(Sequence, FeatureHolder, StrandedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
SimpleSVMClassifierModel - Class in org.biojava.stats.svm

A no-frills implementation of an SVM classifier model.

SimpleSVMClassifierModel(SVMKernel) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
 
SimpleSVMClassifierModel(SVMKernel, Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
 
SimpleSVMClassifierModel(SVMKernel, SVMTarget) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
 
SimpleSVMTarget - Class in org.biojava.stats.svm

No-frills implementation of SVMTarget.

SimpleSVMTarget() - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
 
SimpleSVMTarget(Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
 
SimpleSymbolList - Class in org.biojava.bio.symbol

Basic implementation of SymbolList.

SimpleSymbolList(SymbolTokenization, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList

Construct a SymbolList from a string.

SimpleSymbolList(Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList

Construct an empty SimpleSymbolList.

SimpleSymbolList(Alphabet, List) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList

Construct a SymbolList containing the symbols in the specified list.

SimpleSymbolList(Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList

Construct a SimpleSymbolList given the Symbol array that backs it.

SimpleSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList

Construct a copy of an existing SymbolList.

SimpleSymbolListFactory - Class in org.biojava.bio.symbol

This class makes SimpleSymbolLists.

SimpleSymbolListFactory() - Constructor for class org.biojava.bio.symbol.SimpleSymbolListFactory
 
SimpleSymbolPropertyTable - Class in org.biojava.bio.symbol

Class that implements the SymbolPropertyTable interface

SimpleSymbolPropertyTable(Alphabet, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolPropertyTable
 
SimpleSymbolPropertyTableDB - Class in org.biojava.bio.proteomics.aaindex

A simple implementation of a symbol property table database.

SimpleSymbolPropertyTableDB() - Constructor for class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB

Initializes the database.

SimpleSymbolPropertyTableDB(SymbolPropertyTableIterator) - Constructor for class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB

Initializes the database by copying all symbol property tables from 
 a given iterator into the database.

SimpleTagValueWrapper - Class in org.biojava.bio.program.tagvalue


 Helper class to wrap one TagValueListener inside another one.

SimpleTagValueWrapper() - Constructor for class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
SimpleTagValueWrapper(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper

Build a SimpleTagValueWrapper that will forward everything to a delegate.

SimpleTaxon - Class in org.biojava.bio.taxa

Deprecated.
replaced by classes in org.biojavax.bio.taxa


SimpleTaxon() - Constructor for class org.biojava.bio.taxa.SimpleTaxon

Deprecated.
 
SimpleTaxon(String, String) - Constructor for class org.biojava.bio.taxa.SimpleTaxon

Deprecated.
Create a new instance with no parent, no children and given
 scientific and common names.

SimpleTaxonFactory - Class in org.biojava.bio.taxa

Deprecated.
replaced by classes in org.biojavax.bio.taxa


SimpleTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.SimpleTaxonFactory

Deprecated.
 
SimpleThreadPool - Class in org.biojava.utils

SimpleThreadPool is a basic implementation of
 ThreadPool for use where we don't wish to introduce a
 dependency on a 3rd-party pool.

SimpleThreadPool() - Constructor for class org.biojava.utils.SimpleThreadPool

Creates a new SimpleThreadPool containing 4
 non-daemon threads and starts them.

SimpleThreadPool(int, boolean) - Constructor for class org.biojava.utils.SimpleThreadPool

Creates a new SimpleThreadPool containing the
 specified number of threads and starts them.

SimpleThreadPool(int, boolean, int) - Constructor for class org.biojava.utils.SimpleThreadPool

Creates a new SimpleThreadPool containing the
 specified number of threads and starts them.

SimpleTranslationTable - Class in org.biojava.bio.symbol

A no-frills implementation of TranslationTable that uses a Map to map from
 symbols in a finite source alphabet into a target alphabet.

SimpleTranslationTable(FiniteAlphabet, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable

Create a new translation table that will translate symbols from source to
 target.

SimpleTranslationTable(FiniteAlphabet, Alphabet, Map) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable

Create a new translation table that will translate symbols from source to
 target.

SimpleWeightMatrix - Class in org.biojava.bio.dp
 
SimpleWeightMatrix(Distribution[]) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
 
SimpleWeightMatrix(Alphabet, int, DistributionFactory) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
 
SimpleXMLEmitter - Class in org.biojava.bio.program.xml

A simple XML DocumentHandler that processes SAX2 events
 to create a sensibly formatted XML as it parsed
 without populating objects with data.

SimpleXMLEmitter() - Constructor for class org.biojava.bio.program.xml.SimpleXMLEmitter
 
SimpleXMLEmitter(boolean) - Constructor for class org.biojava.bio.program.xml.SimpleXMLEmitter
 
SingleDP - Class in org.biojava.bio.dp.onehead

An implementation of DP that aligns a single sequence against a single model.

SingleDP(MarkovModel) - Constructor for class org.biojava.bio.dp.onehead.SingleDP
 
SingleDPMatrix - Class in org.biojava.bio.dp.onehead

The dynamic programming matrix for a single sequence.

SingleDPMatrix(DP, SymbolList) - Constructor for class org.biojava.bio.dp.onehead.SingleDPMatrix
 
SingleRichSeqIterator(Sequence) - Constructor for class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator

Creates an iterator over a single sequence.

singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.AbstractTrainer
 
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchSampler
 
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchTrainer
 
singleSequenceIteration(ModelTrainer, SymbolList, ScoreType) - Method in class org.biojava.bio.dp.BaumWelchSampler
 
SingletonAlphabet - Class in org.biojava.bio.symbol

An alphabet that contains a single atomic symbol.

SingletonAlphabet(AtomicSymbol) - Constructor for class org.biojava.bio.symbol.SingletonAlphabet
 
SingletonList - Class in org.biojava.utils
 
SingletonList(Object) - Constructor for class org.biojava.utils.SingletonList
 
site - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
SITE_FEATURE_SOURCE - Static variable in class org.biojava.bio.molbio.RestrictionMapper

SITE_FEATURE_SOURCE the source String
 used by RestrictionMapper when creating
 restriction site Features.

SITE_FEATURE_TYPE - Static variable in class org.biojava.bio.molbio.RestrictionMapper

SITE_FEATURE_TYPE the type String
 used by RestrictionMapper when creating
 restriction site Features.

size - Variable in class org.biojavax.bio.seq.CompoundRichLocation
 
size() - Method in interface org.biojava.bio.annodb.AnnotationDB

The number of Annotation instances in the DB.

size() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
 
size() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
 
size() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
 
size() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
 
size() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
 
size() - Method in class org.biojava.bio.program.gff.GFFEntrySet

Return how many lines are in this set.

size() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet

returns an iterator to the contents of the set.
    /**
 no. of entries in this Homologene group

size() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
 
size() - Method in interface org.biojava.bio.symbol.FiniteAlphabet

The number of symbols in the alphabet.

size() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
 
size() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
size() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
size() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
 
size() - Method in class org.biojava.stats.svm.SparseVector

The number of used dimensions.

size() - Method in class org.biojava.stats.svm.SVMRegressionModel
 
size() - Method in class org.biojava.utils.BeanAsMap
 
size() - Method in class org.biojava.utils.FileAsList
 
size() - Method in class org.biojava.utils.io.FlatFileCache
 
size() - Method in class org.biojava.utils.io.SoftHashMap
 
size() - Method in class org.biojava.utils.ListTools.Doublet
 
size() - Method in class org.biojava.utils.ListTools.SeriesList
 
size() - Method in class org.biojava.utils.ListTools.Triplet
 
size() - Method in class org.biojava.utils.MergingSet
 
size() - Method in class org.biojava.utils.SingletonList
 
size() - Method in class org.biojava.utils.SmallMap
 
size() - Method in class org.biojava.utils.SmallSet
 
size() - Method in class org.biojavax.ga.impl.SimplePopulation
 
size() - Method in interface org.biojavax.ga.Population

Gets the Size of the population

size() - Method in class org.biojavax.ga.util.WeightedSet
 
SIZE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
SIZE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
skip(long) - Method in class org.biojava.utils.io.CachingInputStream
 
skip(long) - Method in class org.biojava.utils.io.CountedBufferedReader
 
skip(long) - Method in class org.biojava.utils.io.UncompressInputStream
 
SKIP_RECORD - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
 
skippedEntity(String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
skippedEntity(String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
skippedEntity(String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
skippedEntity(String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
skippedEntity(String) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
skippedEntity(String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
SkipRecordErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
SLEEP_TIME - Static variable in class org.biojava.utils.process.ExternalProcess

Number of milliseconds the execute method should pauses after the 
 external process has finished the execution.

SmallAnnotation - Class in org.biojava.bio

Annotation that is optimized for memory usage.

SmallAnnotation() - Constructor for class org.biojava.bio.SmallAnnotation

Return a new SmallAnnotation optimised for small sets of properties.

SmallAnnotation(Map) - Constructor for class org.biojava.bio.SmallAnnotation

Return a new SmallAnnotation that copies all values from a Map.

SmallAnnotation(Annotation) - Constructor for class org.biojava.bio.SmallAnnotation

Return a new SmallAnnotation that copies all values from another annoation.

SmallCursor - Class in org.biojava.bio.dp.onehead

Constant-memory implementation of single-head DP cursor.

SmallCursor(State[], SymbolList, Iterator) - Constructor for class org.biojava.bio.dp.onehead.SmallCursor
 
SmallMap - Class in org.biojava.utils

Lightweight implementation of Map which uses little memory to store a
 small number of mappings, at the expense of scalability.

SmallMap() - Constructor for class org.biojava.utils.SmallMap
 
SmallMap(int) - Constructor for class org.biojava.utils.SmallMap
 
SmallMap(Map) - Constructor for class org.biojava.utils.SmallMap
 
SmallSet - Class in org.biojava.utils

Lightweight implementation of Set which uses little memory to store a small
 number of items, at the expense of scalability.

SmallSet() - Constructor for class org.biojava.utils.SmallSet
 
SmallSet(int) - Constructor for class org.biojava.utils.SmallSet
 
SmallSet(Collection) - Constructor for class org.biojava.utils.SmallSet
 
SmartSequenceBuilder - Class in org.biojava.bio.seq.io

Basic SequenceBuilder implementation which accumulates all
 notified information and chooses a sequence implementation
 suited to the size of the sequence.

sMatrix - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
SMORegressionTrainer - Class in org.biojava.stats.svm

Train a regression support vector machine using the Sequential Minimal
 Optimization algorithm.

SMORegressionTrainer() - Constructor for class org.biojava.stats.svm.SMORegressionTrainer
 
SMOTrainer - Class in org.biojava.stats.svm

Train a support vector machine using the Sequential Minimal
 Optimization algorithm.

SMOTrainer() - Constructor for class org.biojava.stats.svm.SMOTrainer
 
SoftHashMap - Class in org.biojava.utils.io

A in memory cache using soft references.

SoftHashMap() - Constructor for class org.biojava.utils.io.SoftHashMap
 
SoftHashMap(int) - Constructor for class org.biojava.utils.io.SoftHashMap
 
SoftMaskedAlphabet - Class in org.biojava.bio.symbol

Soft masking is usually displayed by making the masked regions somehow
 different from the non masked regions.

SoftMaskedAlphabet.CaseSensitiveTokenization - Class in org.biojava.bio.symbol

This SymbolTokenizer works with a delegate to softmask
 symbol tokenization as appropriate.

SoftMaskedAlphabet.MaskingDetector - Interface in org.biojava.bio.symbol

Implementations will define how soft masking looks.

SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector - Class in org.biojava.bio.symbol
 
SoftReferenceCache - Class in org.biojava.utils.cache

Cache which is cleared according to memory pressure.

SoftReferenceCache() - Constructor for class org.biojava.utils.cache.SoftReferenceCache
 
solve(double, double, double, ComputeObject) - Static method in class org.biojava.utils.math.BinarySearch

method that will attempt solving the equation.

SomePairsInCollection(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection
 
SOPair(String, int) - Constructor for class org.biojava.ontology.obo.OboFileParser.SOPair
 
SOPair(String, int, int) - Constructor for class org.biojava.ontology.obo.OboFileParser.SOPair
 
sort() - Method in class org.biojavax.bio.seq.CompoundRichLocation

Sorts the member locations of a compound location.

sort() - Method in class org.biojavax.bio.seq.EmptyRichLocation

Sorts the member locations of a compound location.

sort() - Method in interface org.biojavax.bio.seq.RichLocation

Sorts the member locations of a compound location.

sort() - Method in class org.biojavax.bio.seq.SimpleRichLocation

Sorts the member locations of a compound location.

sort(String[], Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery


 It sorts the current collection and returns another collection which is
 a sorted copy of the current collection.

SORT_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion

A sort criterion.

source - Variable in class org.biojava.bio.seq.Feature.Template
 
SOURCE - Static variable in interface org.biojava.bio.seq.Feature

The source of this feature has altered

SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
sourceEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
SourceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
 
SourceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
 
sourceStart - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
sourceTerm - Variable in class org.biojava.bio.seq.Feature.Template
 
SOURCETERM - Static variable in interface org.biojava.bio.seq.Feature

The ontological source of this feature has altered

SOURCETERM - Static variable in interface org.biojavax.bio.seq.RichFeature
 
sourceToView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList

Coordinate conversion from source to view.

sourceToView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
sourceToView(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList

Coordinate conversion from source to view.

SparseVector - Class in org.biojava.stats.svm

An implementation of a sparse vector.

SparseVector() - Constructor for class org.biojava.stats.svm.SparseVector
 
SparseVector(int) - Constructor for class org.biojava.stats.svm.SparseVector
 
SparseVector.NormalizingKernel - Class in org.biojava.stats.svm

A version of the standard dot-product kernel that scales each column
 independently.

spatialLocation - Variable in class org.biojava.bibliography.BiblioScope


 It defines a spatial location of the cited resource.

SPECIES_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
 
split(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Splitter


 Produce a list of values from an old value.

split(Object) - Method in class org.biojava.bio.program.tagvalue.RegexSplitter
 
splitString(String) - Method in class org.biojava.bio.seq.io.WordTokenization
 
SQLUnigeneFactory - Class in org.biojava.bio.program.unigene

An implementatoin of UnigeneFactory that manages it's data in an SQL
 database.

SQLUnigeneFactory() - Constructor for class org.biojava.bio.program.unigene.SQLUnigeneFactory
 
stackLevel - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
stackLevel - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
standardMutationDistribution(FiniteAlphabet) - Static method in class org.biojavax.ga.util.GATools

Makes a mutation Distribution where the probability
 of a Symbol being mutated to itself is zero and the
 probability of it being changed to any other Symbol in
 the Alphabet a is 1.0 / (a.size() - 1.0)

start - Variable in class org.biojava.utils.automata.FiniteAutomaton
 
start() - Method in interface org.biojava.bio.search.BioMatcher

Get the first symbol index that matches the pattern.

start() - Method in class org.biojava.bio.search.MaxMismatchMatcher
 
start() - Method in class org.biojava.utils.regex.Matcher

Returns the start index of the previous match.

start(int) - Method in class org.biojava.utils.regex.Matcher

Returns the start index of the subsequence captured by the given group during the previous match operation.

start(String[]) - Method in interface org.biojava.utils.xml.AppEntry
 
START_RECORD_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
 
START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
startCycle() - Method in interface org.biojava.bio.dp.HMMTrainer

called to put the trainer into an initial state for a new
 round of training.

startCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer
 
startDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder

indicates start of data for a HomologeneDB

startDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
startDocument() - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
startDocument() - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
startDocument(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler

Indicates that a new GFF document has been started.

startDocument(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
 
startDocument(String) - Method in class org.biojava.bio.program.gff.GFFWriter
 
startDocument(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler

Indicates that a new GFF document has been started.

startedActivity(Object) - Method in interface org.biojava.utils.ActivityListener

Notification that an activity has started.

startElement(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.dist.XMLDistributionReader

Required by SAXParser to be public.

startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler

This is called when an element is entered.

startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
 
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
startElement(String, String, String, Attributes) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
startElement(String, String, String, Attributes, DelegationManager) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler

Handles basic entry processing for all feature handlers.

startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler

Override this to do any processing required but call this
 prior to returning.

startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.FeatureHandler

StAX callback for element starts.

startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.PropDetailHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMENamePropHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMETypePropHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler

Handles basic entry processing for all feature handlers.

startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler

Override this to do any processing required but call this
 prior to returning.

startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler

Handles basic entry processing for all feature handlers.

startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.CharElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.IntElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.LongElementHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StringElementHandlerBase
 
startElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVECdsHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler

currently we do not handler >computation< as subtag of sciobj yet

startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler

Element-specific handler.

startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler

Element-specific handler.

startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler

Element-specific handler.

startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler

Element-specific handler.

startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEHandler

Description of the Method

startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
 
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler

Element-specific handler.

startElementHandler(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
 
startElementHandler(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEHandler
 
startFeature(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser

Deprecated.
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.EmblFileFormer

Deprecated.
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.GenbankFileFormer

Deprecated.
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer

Deprecated.
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
startFeature(Feature.Template) - Method in interface org.biojava.bio.seq.io.SeqIOListener

Notify the listener that a new feature object is starting.

startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer

Deprecated.
Null implementation.

startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Notify the listener that a new feature object is starting.

startGroup() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder

indicates start of data for a OrthoPairSet

startGroup() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
startHeader() - Method in class org.biojava.bio.search.FilteringContentHandler
 
startHeader() - Method in class org.biojava.bio.search.SearchContentAdapter
 
startHeader() - Method in class org.biojava.bio.search.SearchContentFilter
 
startHeader() - Method in interface org.biojava.bio.search.SearchContentHandler

The startHeader method indicates the start of a
 formatted header.

startHeader() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
startHit() - Method in class org.biojava.bio.search.FilteringContentHandler
 
startHit() - Method in class org.biojava.bio.search.SearchContentAdapter
 
startHit() - Method in class org.biojava.bio.search.SearchContentFilter
 
startHit() - Method in interface org.biojava.bio.search.SearchContentHandler

The startHit method indicates the start of a
 formatted hit.

startHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
startInstance(int, int) - Method in interface org.biojava.utils.automata.StateMachineFactory

Return a StateMachineInstance if the Symbol represented
 by the symbol index is valid as the initial symbol of
 the pattern.

startLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
startLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
startOrthologue() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder

indicates start of data for an orthologue

startOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
startOrthoPair() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder

indicates start of data for an OrthoPair

startOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
 
startPrefixMapping(String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
 
startPrefixMapping(String, String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
startPrefixMapping(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
startPrefixMapping(String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
 
startPrefixMapping(String, String) - Method in interface org.biojava.utils.stax.StAXContentHandler
 
startPrefixMapping(String, String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.Echo
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer2
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
 
startRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
startRecord() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener

A new record is about to start.

startSearch() - Method in class org.biojava.bio.search.FilteringContentHandler
 
startSearch() - Method in class org.biojava.bio.search.SearchContentAdapter
 
startSearch() - Method in class org.biojava.bio.search.SearchContentFilter
 
startSearch() - Method in interface org.biojava.bio.search.SearchContentHandler

The startSearch method indicates the start of
 useful search information.

startSearch() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
startSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger
 
startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
 
startSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener

Indicates that a sequence is about to be searched against a DataStore.

startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
 
startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
 
startSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer

Deprecated.
 
startSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer

Deprecated.
 
startSequence() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
 
startSequence() - Method in class org.biojava.bio.seq.io.SeqIOFilter
 
startSequence() - Method in interface org.biojava.bio.seq.io.SeqIOListener

Start the processing of a sequence.

startSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
 
startSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
 
startSequence() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer

Deprecated.
Start the processing of a sequence.

startSequence() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
 
startSequence() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
 
startSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder

Start the processing of a sequence.

startSubHit() - Method in class org.biojava.bio.search.FilteringContentHandler
 
startSubHit() - Method in class org.biojava.bio.search.SearchContentAdapter
 
startSubHit() - Method in class org.biojava.bio.search.SearchContentFilter
 
startSubHit() - Method in interface org.biojava.bio.search.SearchContentHandler

The startSubHit method indicates the start of a
 formatted subhit.

startSubHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Echo
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Indexer
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Indexer2
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.MultiTagger
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine

TagValueListener interface

startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
 
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagRenamer
 
startTag(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueListener

Start a new tag.

startTag(Object) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
 
startThreads() - Method in class org.biojava.utils.SimpleThreadPool
 
startThreads() - Method in interface org.biojava.utils.ThreadPool

startThreads starts all the threads running and
 opens the pool to requests.

startTree() - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
 
startTree() - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
startTree() - Method in interface org.biojava.utils.stax.StAXContentHandler
 
startTree() - Method in class org.biojava.utils.stax.StAXContentHandlerBase
 
state - Variable in class org.biojava.bio.dp.BackPointer

The state with which this backpointer is associated.

State - Interface in org.biojava.bio.dp

A state in a markov process.

stateAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel

FiniteAlphabet of the states.

stateAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
stateAlphabet() - Method in class org.biojava.bio.dp.WMAsMM
 
stateList(MarkovModel) - Method in class org.biojava.bio.dp.DP
 
StateMachine - Class in org.biojava.bio.program.tagvalue

This class implements a state machine for parsing events from
 the Parser class.

StateMachine() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine
 
StateMachine.BasicState - Class in org.biojava.bio.program.tagvalue

Implementation of a State in a state machine

StateMachine.ExitNotification - Interface in org.biojava.bio.program.tagvalue

Interface implemented by State listeners that
 want notification when a transition leaves the State.

StateMachine.SimpleStateListener - Class in org.biojava.bio.program.tagvalue

a basic listener for a State.

StateMachine.State - Interface in org.biojava.bio.program.tagvalue

Interface for a State within this StateMachine

StateMachine.Transition - Class in org.biojava.bio.program.tagvalue

class to represent a State Transition

StateMachine.TransitionTable - Class in org.biojava.bio.program.tagvalue

Table of Transition destination States
 and their corresponding Tags.

StateMachineFactory - Interface in org.biojava.utils.automata

Class that produces StateMachineInstance objects.

StateMachineInstance - Interface in org.biojava.utils.automata
 
StatePath - Interface in org.biojava.bio.dp

Extends the Alignment interface so that it is explicitly used to represent
 a state path through an HMM, and the associated emitted sequence and
 likelihoods.

states - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
states() - Method in interface org.biojava.bio.dp.DPMatrix
 
states() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
states() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
 
STATES - Static variable in interface org.biojava.bio.dp.StatePath

Alignment label for the state path.

StaticMemberPlaceHolder - Class in org.biojava.utils
 
StaticMemberPlaceHolder() - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
 
StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
 
StaticMethodRPFactory(Method) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory

Create a new StaticMethodRPFactory for a method.

STATUS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
StAXContentHandler - Interface in org.biojava.bio.seq.io.agave

Interface for StAX content handlers.

StAXContentHandler - Interface in org.biojava.utils.stax

Interface for StAX content handlers.

StAXContentHandlerBase - Class in org.biojava.bio.seq.io.agave

Simple implementation of the StAXContentHandler
 interface, with empty implementations for all the methods.

StAXContentHandlerBase - Class in org.biojava.utils.stax

Simple implementation of the StAXContentHandler
 interface, with empty implementations for all the methods.

StAXContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
 
StAXContentHandlerBase() - Constructor for class org.biojava.utils.stax.StAXContentHandlerBase
 
staxenv - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
staxenv - Variable in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
 
staxenv - Variable in class org.biojava.bio.seq.io.game.StAXPropertyHandler
 
staxenv - Variable in class org.biojava.bio.seq.io.game12.StAXFeatureHandler

Nesting class that provides callback interfaces to nested class

StAXFeatureHandler - Class in org.biojava.bio.seq.io.agave

StAX handler shamelessly ripped off from Thomas Down's

 XFFFeatureSetHandler.

StAXFeatureHandler - Class in org.biojava.bio.seq.io.game

StAX handler shamelessly ripped off from Thomas Down's
 XFFFeatureSetHandler.

StAXFeatureHandler - Class in org.biojava.bio.seq.io.game12

StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.

StAXFeatureHandler() - Constructor for class org.biojava.bio.seq.io.game.StAXFeatureHandler
 
StAXHandlerFactory - Interface in org.biojava.bio.seq.io.agave

Factory for StAX content handlers.

StAXHandlerFactory - Interface in org.biojava.bio.seq.io.game

Factory for StAX content handlers.

StAXHandlerFactory - Interface in org.biojava.bio.seq.io.game12

Factory for StAX content handlers.

StAXPropertyHandler - Class in org.biojava.bio.seq.io.agave

StAX handler shamelessly ripped off from Thomas Down's
 XFFFeatureSetHandler.

StAXPropertyHandler - Class in org.biojava.bio.seq.io.game

StAX handler shamelessly ripped off from Thomas Down's
 XFFFeatureSetHandler.

stop(GeneticAlgorithm) - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration

Stops the Algorithm if the iterations are >= maxGenerations

stop(GeneticAlgorithm) - Method in interface org.biojavax.ga.GAStoppingCriteria

Determines if an Algorithm should stop spawning new generations

StoppingCriteria - Interface in org.biojava.bio.dp

A callback that is invoked during the training of an HMM.

stopThreads() - Method in class org.biojava.utils.SimpleThreadPool

Waits for all working threads to return and then stops them.

stopThreads() - Method in interface org.biojava.utils.ThreadPool

stopThreads causes all running threads to stop
 when their current task is complete.

store(Index) - Method in class org.biojava.bio.seq.db.BioIndex
 
store(Index) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore

store adds an Index to the store.

store(Index) - Method in interface org.biojava.bio.seq.db.IndexStore

Add the Index to the store.

store(Index) - Method in class org.biojava.bio.seq.db.TabIndexStore
 
STORE_NAME - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory

STORE_NAME is the key used to identify the
 arbitrary name of the store in the OBDA config.dat files.

str - Variable in class org.biojava.ontology.obo.OboFileParser.SOPair
 
STRAIN_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
 
strand - Variable in class org.biojava.bio.seq.StrandedFeature.Template
 
STRAND - Static variable in interface org.biojava.bio.seq.StrandedFeature

The strand of this feature is being altered.

STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
STRANDED_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
StrandedFeature - Interface in org.biojava.bio.seq

Adds the concept of 'strand' to features.

STRANDEDFEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.StrandedFeatureHandler
 
StrandedFeature.Strand - Class in org.biojava.bio.seq

Class to represent the 'strandedness' of a feature.

StrandedFeature.Template - Class in org.biojava.bio.seq

Template class for parameterizing the creation of a new
 StrandedFeature.

StrandedFeatureHandler - Class in org.biojava.bio.program.xff

StAX handler for XFF strandedFeature type.

StrandedFeatureHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.StrandedFeatureHandler
 
StrandFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
 
StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
 
StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.seq.FeatureFilter.StrandFilter

Build a new filter that matches all features of a given strand.

StrandParser - Class in org.biojava.bio.seq

Process strings and return strand objects.

StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser
 
streamNext(SeqIOListener) - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
 
streamNext(SeqIOListener) - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
 
streamNext(SeqIOListener) - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
 
StreamParser - Interface in org.biojava.bio.seq.io

Parse a stream of characters into BioJava symbols.

StreamPipe - Class in org.biojava.utils.process

A multi threaded class 
 which pipes the contents of an input stream to an output stream.

StreamPipe(InputStream, OutputStream, String) - Constructor for class org.biojava.utils.process.StreamPipe

Initializes the stream pipe.

StreamReader - Class in org.biojava.bio.seq.io

Parses a stream into sequences.

StreamReader(BufferedReader, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
 
StreamReader(InputStream, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
 
streamRecords(GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFEntrySet

Write all records in this set out to a handler.

StreamWriter - Class in org.biojava.bio.seq.io

Writes all of the sequences from a SequenceIterator to a stream with a
 particular format.

StreamWriter(OutputStream, SequenceFormat) - Constructor for class org.biojava.bio.seq.io.StreamWriter

Generate a new StreamWriter to the stream os and using format.

STRING_TO_INT - Static variable in class org.biojava.bio.program.tagvalue.ChangeTable
 
StringElementHandlerBase - Class in org.biojava.utils.stax

StAX handler for any element which just contains a string.

StringElementHandlerBase() - Constructor for class org.biojava.utils.stax.StringElementHandlerBase
 
stringifyAttributes(Map) - Static method in class org.biojava.bio.program.gff.SimpleGFFRecord

Create a String representation of
 attMap.

StringTools - Class in org.biojavax.utils

Utility class for formatting strings into regular-sized blocks.

StructureTools - Class in org.biojava.bio.proteomics

Simple access to protein seccondary structure assignments.

StructureTools() - Constructor for class org.biojava.bio.proteomics.StructureTools
 
subAlignment(Set<String>, Location) - Method in interface org.biojava.bio.alignment.Alignment


 Make a view onto this alignment.

subAlignment(Set<String>, Location) - Method in class org.biojava.bio.alignment.SimpleAlignment
 
subAlignment(Set<String>, Location) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
subAlignment(Set<String>, Location) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
subAlignment(Set, Location) - Method in class org.biojava.bio.dp.SimpleStatePath
 
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.And
 
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.Contains
 
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.Or
 
subConstraintOf(CollectionConstraint) - Method in interface org.biojava.bio.CollectionConstraint

subConstraintOf returns true if the constraint
 is a sub-constraint.

subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.And
 
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
 
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ByClass
 
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
 
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
 
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.Or
 
subConstraintOf(PropertyConstraint) - Method in interface org.biojava.bio.PropertyConstraint

subConstraintOf returns true if the constraint
 is a sub-constraint.

subFeatures - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
 
SubIntegerTokenization - Class in org.biojava.bio.seq.io
 
SubIntegerTokenization(IntegerAlphabet.SubIntegerAlphabet) - Constructor for class org.biojava.bio.seq.io.SubIntegerTokenization
 
subject - Variable in class org.biojava.bibliography.BibRef

It defines the topic of the content of the cited resource.

SUBJECT_HEADINGS - Static variable in interface org.biojava.bibliography.BibRefSupport

A vocabulary name.

SUBJECT_LABEL - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature

Constant SUBJECT_LABEL is the alignment label used
 for all subject sequences.

subjectHeadings - Variable in class org.biojava.bibliography.BiblioSubject

The subject headings usually come from standard lists
 such as Sears List of Subject Headings,
 or Library of Congress Subject Headings (LCSH).

subjectHeadingsSource - Variable in class org.biojava.bibliography.BiblioSubject

The source of subject headings.

subList(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
subList(int, int) - Method in class org.biojava.bio.seq.CircularView


 Over rides ViewSequence.

subList(int, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.DummySequence
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.SubSequence
 
subList(int, int) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
subList(int, int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
subList(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly
 
subList(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
subList(int, int) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
 
subList(int, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
subList(int, int) - Method in class org.biojava.bio.symbol.SimpleSymbolList

create a subList of the original, this will be a view until
 either the original symbolList or the sublist is edited

subList(int, int) - Method in interface org.biojava.bio.symbol.SymbolList

Return a new SymbolList for the symbols start to end inclusive.

subList(int, int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

Return a new SymbolList for the symbols start to end inclusive.

subList(int, int) - Method in class org.biojavax.bio.seq.ThinRichSequence

Return a new SymbolList for the symbols start to end inclusive.

subList(SymbolList, int, int) - Static method in class org.biojava.bio.symbol.SymbolListViews

View a portion of a SymbolList.

subList(RichSequence, int, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler

Return a new SymbolList for the symbols start to end inclusive.

subList(RichSequence, int, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler

Return a new SymbolList for the symbols start to end inclusive.

subSequence(int, int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
 
subSequence(int, int) - Method in class org.biojava.utils.RepeatedCharSequence
 
subSequence(Sequence, int, int) - Static method in class org.biojava.bio.seq.SequenceTools

Extract a sub-sequence from a sequence.

subSequence(Sequence, int, int, String) - Static method in class org.biojava.bio.seq.SequenceTools

Extract a sub-sequence from a sequence.

subSequence(Sequence, int, int, String, StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.SequenceTools

Extract a sub-sequence from a sequence.

subSequence(RichSequence, int, int, Namespace, String, String, String, int, Double) - Static method in class org.biojavax.bio.seq.RichSequence.Tools


 Creates a new sequence from a subregion of another sequence.

SubSequence - Class in org.biojava.bio.seq.impl

View a sub-section of a given sequence object, including all the
 features intersecting that region.

SubSequence(Sequence, int, int) - Constructor for class org.biojava.bio.seq.impl.SubSequence

Construct a new SubSequence of the specified sequence.

SubSequence(Sequence, int, int, String) - Constructor for class org.biojava.bio.seq.impl.SubSequence

Construct a new SubSequence of the specified sequence.

SubSequence.SubProjectedFeatureContext - Class in org.biojava.bio.seq.impl

TargetContext that implements the mapping between the parent sequence and this
 sub-sequence.

SubSequenceDB - Class in org.biojava.bio.seq.db
 
SubSequenceDB(SequenceDB, Set) - Constructor for class org.biojava.bio.seq.db.SubSequenceDB
 
SUBSET - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
subStr(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
subStr(int, int) - Method in class org.biojava.bio.seq.CircularView


 Over rides ViewSequence.

subStr(int, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
subStr(int, int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
subStr(int, int) - Method in class org.biojava.bio.seq.impl.DummySequence
 
subStr(int, int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
subStr(int, int) - Method in class org.biojava.bio.seq.impl.SubSequence
 
subStr(int, int) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
subStr(int, int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
subStr(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly
 
subStr(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
subStr(int, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
subStr(int, int) - Method in interface org.biojava.bio.symbol.SymbolList

Return a region of this symbol list as a String.

subStr(int, int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

Return a region of this symbol list as a String.

subStr(int, int) - Method in class org.biojavax.bio.seq.ThinRichSequence

Return a region of this symbol list as a String.

subStr(RichSequence, int, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler

Return a region of this sequence as a String.

subStr(RichSequence, int, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler

Return a region of this sequence as a String.

subStringExists(String) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
 
subtract(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools

Subtract one location from another.

subTypeOf(AnnotationType) - Method in class org.biojava.bio.AnnotationType.Abstract
 
subTypeOf(AnnotationType) - Method in interface org.biojava.bio.AnnotationType

See if an AnnotationType is a specialisation of this type.

SuffixNode() - Constructor for class org.biojava.bio.symbol.SuffixTree.SuffixNode
 
SuffixNode() - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode
 
SuffixTree - Class in org.biojava.bio.symbol

Suffix tree implementation.

SuffixTree(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SuffixTree

Construct a new SuffixTree to contain motifs over the
 specified alphabet.

SuffixTree.SuffixNode - Class in org.biojava.bio.symbol

A node in the suffix tree.

SuffixTreeKernel - Class in org.biojava.stats.svm.tools

Computes the dot-product of two suffix-trees as the sum of the products
 of the counts of all nodes they have in common.

SuffixTreeKernel() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel
 
SuffixTreeKernel.DepthScaler - Interface in org.biojava.stats.svm.tools

Encapsulates the scale factor to apply at a given depth.

SuffixTreeKernel.MultipleScalar - Class in org.biojava.stats.svm.tools

Scale using a multiple of two DepthScalers.

SuffixTreeKernel.NullModelScaler - Class in org.biojava.stats.svm.tools

Scales by 4^depth - equivalent to dividing by a probablistic flatt prior
 null model

SuffixTreeKernel.SelectionScalar - Class in org.biojava.stats.svm.tools

Scale using a BitSet to allow/disallow depths.

SuffixTreeKernel.UniformScaler - Class in org.biojava.stats.svm.tools

Scale all depths by 1.0

surname - Variable in class org.biojava.bibliography.BiblioPerson

The person's sirname (family name).

SVM_Light - Class in org.biojava.stats.svm.tools
 
SVM_Light() - Constructor for class org.biojava.stats.svm.tools.SVM_Light
 
SVM_Light.LabelledVector - Class in org.biojava.stats.svm.tools
 
SVMClassifierModel - Interface in org.biojava.stats.svm

An SVM classifier model.

SVMKernel - Interface in org.biojava.stats.svm

Kernel for support vector machines and related methods.

SVMRegressionModel - Class in org.biojava.stats.svm
 
SVMRegressionModel() - Constructor for class org.biojava.stats.svm.SVMRegressionModel
 
SVMRegressionModel(int) - Constructor for class org.biojava.stats.svm.SVMRegressionModel
 
SVMTarget - Interface in org.biojava.stats.svm

An SVM classifier model.

SwapMutationFunction - Class in org.biojavax.ga.functions

This class does a sort of mutation by exchanging two positions on the
 chromosome.

SwapMutationFunction(double[]) - Constructor for class org.biojavax.ga.functions.SwapMutationFunction

Sets the mutation probabilities to the designated values.

Swissprot - Class in org.biojava.bio.program.formats
 
Swissprot() - Constructor for class org.biojava.bio.program.formats.Swissprot
 
SWISSPROT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

SWISSPROT indicates that the sequence format is
 SWISSPROT.

SWISSPROT_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
 
SwissprotFileFormer - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead


SwissprotFileFormer() - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer

Deprecated.
Creates a new SwissprotFileFormer using
 System.out stream.

SwissprotFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer

Deprecated.
Creates a new SwissprotFileFormer using the
 specified stream.

SwissprotProcessor - Class in org.biojava.bio.seq.io

Deprecated.
Use org.biojavax.bio.seq.io framework instead


SwissprotProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor

Deprecated.
 
SwissprotProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor

Deprecated.
Constructor that sets the source of the feature to theSource.

SwissprotProcessor.Factory - Class in org.biojava.bio.seq.io

Deprecated.
Factory which wraps SequenceBuilders in a SwissprotProcessor

SwissprotSequenceDB - Class in org.biojava.bio.seq.db

This class contains functions accessing sequences in swiss-prot.

SwissprotSequenceDB() - Constructor for class org.biojava.bio.seq.db.SwissprotSequenceDB
 
Symbol - Interface in org.biojava.bio.symbol

A single symbol.

symbolAt(int) - Method in class org.biojava.bio.alignment.SimpleAlignment
 
symbolAt(int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolAt(int) - Method in class org.biojava.bio.seq.CircularView


 Over rides ViewSequence.

symbolAt(int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.DummySequence
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.SubSequence
 
symbolAt(int) - Method in class org.biojava.bio.seq.impl.ViewSequence
 
symbolAt(int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
symbolAt(int) - Method in class org.biojava.bio.seq.SimpleAssembly
 
symbolAt(int) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.DummySymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.PackedSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleSymbolList

Find a symbol at a specified offset in the SymbolList.

symbolAt(int) - Method in interface org.biojava.bio.symbol.SymbolList

Return the symbol at index, counting from 1.

symbolAt(int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

Return the symbol at index, counting from 1.

symbolAt(int) - Method in class org.biojavax.bio.seq.ThinRichSequence

Return the symbol at index, counting from 1.

symbolAt(String, int) - Method in interface org.biojava.bio.alignment.Alignment

Retrieve a symbol by label and column.

symbolAt(String, int) - Method in class org.biojava.bio.alignment.SimpleAlignment
 
symbolAt(String, int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolAt(String, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
symbolAt(String, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
symbolAt(RichSequence, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler

Return the symbol at index, counting from 1.

symbolAt(RichSequence, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler

Return the symbol at index, counting from 1.

symbolForIndex(int) - Method in interface org.biojava.bio.symbol.AlphabetIndex

Retrieve the symbol for an index.

symbolForLifeScienceID(LifeScienceIdentifier) - Static method in class org.biojava.bio.symbol.AlphabetManager

Retreives the Symbol for the LSID

symbolForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager

Deprecated.
use symbolForLifeScienceID() instead


SymbolList - Interface in org.biojava.bio.symbol

A sequence of symbols that belong to an alphabet.

SymbolListCharSequence - Class in org.biojava.bio.seq.io

SymbolListCharSequence is a CharSequence
 implementation which wraps a SymbolList.

SymbolListCharSequence(SymbolList) - Constructor for class org.biojava.bio.seq.io.SymbolListCharSequence

Creates a new SymbolListCharSequence wrapping a
 SymbolList.

SymbolListFactory - Interface in org.biojava.bio.symbol

This interface exists to hide implementational details
 of SymbolLists when making chunked symbol lists.

symbolListForLabel(String) - Method in interface org.biojava.bio.alignment.Alignment

Retrieve a single row of the alignment by label.

symbolListForLabel(String) - Method in class org.biojava.bio.alignment.SimpleAlignment
 
symbolListForLabel(String) - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolListForLabel(String) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
symbolListForLabel(String) - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
symbolListIterator() - Method in interface org.biojava.bio.alignment.Alignment

Creates an Iterator over the SymbolLists in the alignment.

symbolListIterator() - Method in class org.biojava.bio.alignment.SimpleAlignment
 
symbolListIterator() - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolListIterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
symbolListIterator() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
SymbolListIterator(Alignment) - Constructor for class org.biojava.bio.alignment.Alignment.SymbolListIterator

Creates a SymbolListIterator for a given alignment object.

SymbolListViews - Class in org.biojava.bio.symbol

Tools class for constructing views of SymbolList objects.

SymbolPropertyTable - Interface in org.biojava.bio.symbol

class for maintaining properties associated with a symbol

SymbolPropertyTableDB - Interface in org.biojava.bio.proteomics.aaindex

Database of SymbolPropertyTable objects.

SymbolPropertyTableIterator - Interface in org.biojava.bio.proteomics.aaindex

Iterator over SymbolPropertyTable objects.

SymbolReader - Interface in org.biojava.bio.seq.io

Encapsulate a stream of Symbols being parsed from some input
 stream.

symbols(SymbolList) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
symbols(SymbolList) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
 
symbols(SymbolList) - Method in class org.biojava.bio.symbol.CircularLocation
 
symbols(SymbolList) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
symbols(SymbolList) - Method in interface org.biojava.bio.symbol.Location

Return the symbols in a sequence that fall within this range.

symbols(SymbolList) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Return the symbols in a sequence that fall within this range.

symbols(SymbolList) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Return the symbols in a sequence that fall within this range.

symbols(SymbolList) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Return the symbols in a sequence that fall within this range.

SYMBOLS - Static variable in interface org.biojava.bio.symbol.Alphabet


 This ChangeType indicates that some symbols have been added or removed from
 the alphabet.

SymbolTokenization - Interface in org.biojava.bio.seq.io

Encapsulate a mapping between BioJava Symbol objects and
 some string representation.

SymbolTokenization.TokenType - Class in org.biojava.bio.seq.io
 
symList - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
symList() - Method in interface org.biojava.bio.dp.DPMatrix
 
symList() - Method in interface org.biojava.bio.dp.onehead.DPCursor

The symbol list being looped over.

symList() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
 
symList() - Method in class org.biojava.bio.dp.onehead.SmallCursor
 
symList() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
 
SYMLISTVERSION - Static variable in interface org.biojavax.bio.seq.RichSequence
 
SYMMETRIC - Static variable in class org.biojava.ontology.OntoTools
 
Synonym - Class in org.biojava.ontology
 
Synonym() - Constructor for class org.biojava.ontology.Synonym
 
SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
SYNONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon

Use this to define common names for things.

SYNONYM_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
SystemRegistry - Class in org.biojava.directory

A registry that loads up the standard biodirectory files.

SystemRegistry() - Constructor for class org.biojava.directory.SystemRegistry
 




T

t() - Static method in class org.biojava.bio.seq.DNATools
 
t() - Static method in class org.biojava.bio.seq.NucleotideTools
 
t() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Threonine

T_AESTIVUM - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
TabDelimParser - Class in org.biojava.ontology.io

Parse tab-delimited ontology files into Ontology objects.

TabDelimParser() - Constructor for class org.biojava.ontology.io.TabDelimParser
 
TabIndexStore - Class in org.biojava.bio.seq.db


 Implements IndexStore as a serialized file for the java data and a
 tab-delimited file of offsets.

TabIndexStore(File, File, String, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.TabIndexStore

Create a new TabIndexStore.

table(String) - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB

Returns the table with the specified name.

table(String) - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB

Returns the table with the specified name.

tableIterator() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB

Returns an iterator over 
 SymbolPropertyTable objects.

tableIterator() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB

Returns an iterator over 
 SymbolPropertyTable objects.

tableOfContents - Variable in class org.biojava.bibliography.BiblioDescription


 It is a table of contents of the cited resource.

tableOfContentsType - Variable in class org.biojava.bibliography.BiblioDescription


 It specifies how BiblioDescription.tableOfContents is coded.

TABULAR - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
TagDelegator - Class in org.biojava.bio.program.tagvalue


 Pushes a new parser and listener, or delegate to a listener depending on the
 tag.

TagDelegator() - Constructor for class org.biojava.bio.program.tagvalue.TagDelegator
 
TagDelegator(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.TagDelegator
 
TagDropper - Class in org.biojava.bio.program.tagvalue

Silently drop all tags except those specified, and pass the rest onto a
 delegate.

TagDropper() - Constructor for class org.biojava.bio.program.tagvalue.TagDropper
 
TagDropper(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.TagDropper

Create a new TagDropper that will pass on all retained tags and values to
 tvl.

TagMapper - Class in org.biojava.bio.program.tagvalue


 TagMapper maps arbitrary object keys to new keys.

TagMapper() - Constructor for class org.biojava.bio.program.tagvalue.TagMapper

Creates a new, empty TagMapper.

TagRenamer - Class in org.biojava.bio.program.tagvalue


 Rename tags using a TagMapper.

TagRenamer(TagValueListener, PropertyChanger) - Constructor for class org.biojava.bio.program.tagvalue.TagRenamer

Build a new TagRenamer with a delegate and mapper.

TagValue - Class in org.biojava.bio.program.tagvalue


 Utility class for representing tag-value pairs for TagValueParser
 implementors.

TagValue(Object, Object, boolean) - Constructor for class org.biojava.bio.program.tagvalue.TagValue

Build a new TagValue with a tag, a value and a flag indicating if this is a
 new example of this tag or a continuation of an old example.

TagValueContext - Interface in org.biojava.bio.program.tagvalue

Communication interface between Parser and a TagValueListener that allows
 listeners to request that a parser/listener pair be pushed onto the stack to
 handle the current tag.

TagValueListener - Interface in org.biojava.bio.program.tagvalue


 An object that wishes to be informed of events during the parsing of a file.

TagValueParser - Interface in org.biojava.bio.program.tagvalue


 Tokenize single records (lines of text, objects) into a tag and a value.

TagValueWrapper - Interface in org.biojava.bio.program.tagvalue


 Interface for TagValueListeners that wrap other TagValueListeners

takeConnection() - Method in class org.biojava.utils.JDBCConnectionPool
 
takeStatement() - Method in class org.biojava.utils.JDBCConnectionPool
 
tanh(double) - Method in class org.biojava.stats.svm.SigmoidKernel
 
taxa - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
TAXID_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
Taxon - Interface in org.biojava.bio.program.homologene
 
Taxon - Interface in org.biojava.bio.taxa

Deprecated.
replaced by classes in org.biojavax.bio.taxa


TAXON - Static variable in interface org.biojavax.bio.BioEntry
 
TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
Taxon.TaxonStub - Class in org.biojava.bio.program.homologene
 
TaxonFactory - Interface in org.biojava.bio.taxa

Deprecated.
replaced by classes in org.biojavax.bio.taxa


TAXONID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
TAXONOMY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
TaxonParser - Interface in org.biojava.bio.taxa

Deprecated.
replaced by classes in org.biojavax.bio.taxa


Tee(SearchListener, SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Tee
 
tempBuffer - Variable in class org.biojava.ontology.obo.OboFileParser
 
Template() - Constructor for class org.biojava.bio.molbio.RestrictionSite.Template
 
Template() - Constructor for class org.biojava.bio.seq.ComponentFeature.Template
 
Template() - Constructor for class org.biojava.bio.seq.Feature.Template
 
Template() - Constructor for class org.biojava.bio.seq.FramedFeature.Template
 
Template() - Constructor for class org.biojava.bio.seq.homol.HomologyFeature.Template
 
Template() - Constructor for class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
 
Template() - Constructor for class org.biojava.bio.seq.RemoteFeature.Template
 
Template() - Constructor for class org.biojava.bio.seq.StrandedFeature.Template
 
Template() - Constructor for class org.biojavax.bio.seq.RichFeature.Template
 
Template(Feature.Template) - Constructor for class org.biojava.bio.seq.RemoteFeature.Template

Creates a RemoteFeature.Template that has the same values as the
 template passed in.

TemplateUtils - Class in org.biojava.bio.seq.impl

Common things you may want to do with feature templates.

temporalPeriod - Variable in class org.biojava.bibliography.BiblioScope

It defines temporal period of the cited resource.

ter() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the termination (*)
 placeholder

term - Variable in class org.biojavax.bio.seq.SimpleRichLocation
 
Term - Interface in org.biojava.ontology

A term in an ontology.

TERM - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
TERM - Static variable in interface org.biojava.ontology.Ontology
 
TERM - Static variable in interface org.biojavax.bio.seq.RichLocation
 
TERM - Static variable in interface org.biojavax.Note
 
TERM - Static variable in interface org.biojavax.ontology.ComparableOntology
 
Term.Impl - Class in org.biojava.ontology

Simple in-memory implementation of an ontology term.

Terms() - Constructor for class org.biojavax.bio.seq.io.EMBLFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.io.INSDseqFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.io.UniProtFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
 
Terms() - Constructor for class org.biojavax.bio.seq.RichSequence.Terms
 
TEXT - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
TEXT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
theAbstract - Variable in class org.biojava.bibliography.BiblioDescription


 It is an abstract of the cited resource.

ThinRichSequence - Class in org.biojavax.bio.seq

A simple implementation of RichSequence.

ThinRichSequence() - Constructor for class org.biojavax.bio.seq.ThinRichSequence
 
ThinRichSequence(Namespace, String, String, int, Alphabet, Double) - Constructor for class org.biojavax.bio.seq.ThinRichSequence

Creates a new instance of ThinRichSequence.

thr() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Threonine (T)

THREAD_POOL_SIZE - Static variable in class org.biojava.utils.process.ExternalProcess

Size of the thread pool for the static execute methods.

threadPool() - Method in class org.biojava.utils.process.ExternalProcess

Gets the thread pool which is used for the input and output handlers.

ThreadPool - Interface in org.biojava.utils

ThreadPool specifies basic thread-pooling
 operations such that third-party implementations may be used
 without requiring changes to BioJava.

threads - Variable in class org.biojava.utils.SimpleThreadPool
 
threadsAlive() - Method in class org.biojava.utils.SimpleThreadPool

threadsAlive returns the number of threads
 currently alive.

threadsIdle() - Method in class org.biojava.utils.SimpleThreadPool

threadsIdle returns the number of threads
 currently waiting for work.

threadsWorking() - Method in class org.biojava.utils.SimpleThreadPool

threadsWorking returns the number of threads
 currently performing work.

Threshold(double) - Constructor for class org.biojavax.ga.functions.SelectionFunction.Threshold
 
THRESHOLD - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory

Accessor for a factory that produces builders that compress the
 SymbolList of a RichSequence when the length of the
 SymbolList exceeds THRESHOLD.

THRESHOLD_VALUE - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory

The value that will be used as a threshold for the THRESHOLD
 builder.

TISSUE_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
 
title - Variable in class org.biojava.bibliography.BibRef

A title given to the cited resource (a name by which the resource is formally known).

TITLE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
TITLE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
 
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
to - Variable in class org.biojava.bio.dp.TrainerTransition
 
to - Variable in class org.biojava.bio.dp.Transition
 
TO_A_LEAF - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree
 
toArray() - Method in class org.biojavax.ga.util.WeightedSet
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.AlternateTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.CrossProductTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.DoubleTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.IntegerTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.NameTokenization
 
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.SubIntegerTokenization
 
tokenizeSymbol(Symbol) - Method in interface org.biojava.bio.seq.io.SymbolTokenization

Return a token representing a single symbol.

tokenizeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
 
tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.AlternateTokenization
 
tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.CharacterTokenization
 
tokenizeSymbolList(SymbolList) - Method in interface org.biojava.bio.seq.io.SymbolTokenization

Return a string representation of a list of symbols.

tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.WordTokenization
 
tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
 
toLink(String, Properties) - Method in interface org.biojava.bio.program.blast2html.DatabaseURLGenerator

Returns a full retrieve item anchor
 for the given database id.

toLink(String, Properties) - Method in class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
 
toLink(String, Properties) - Method in class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator
 
toList() - Method in class org.biojava.bio.dp.SimpleStatePath
 
toList() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
 
toList() - Method in class org.biojava.bio.seq.impl.DummySequence
 
toList() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
toList() - Method in class org.biojava.bio.seq.impl.SubSequence
 
toList() - Method in class org.biojava.bio.seq.impl.ViewSequence
 
toList() - Method in class org.biojava.bio.seq.NewSimpleAssembly
 
toList() - Method in class org.biojava.bio.seq.SimpleAssembly
 
toList() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
toList() - Method in class org.biojava.bio.symbol.RelabeledAlignment
 
toList() - Method in interface org.biojava.bio.symbol.SymbolList

Returns a List of symbols.

toList() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

Returns a List of symbols.

toList() - Method in class org.biojavax.bio.seq.ThinRichSequence

Returns a List of symbols.

toList(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler

Returns a List of symbols.

toList(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler

Returns a List of symbols.

top_level - Static variable in interface org.biojava.bio.seq.FeatureFilter

A filter which accepts only top-level Features.

topLevel() - Static method in class org.biojava.bio.seq.FilterUtils

Return a filter which matches all top-level features.

TOPOLOGY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
toProtein(SymbolList) - Static method in class org.biojava.bio.seq.DNATools

Convenience method that directly converts a DNA sequence to RNA then to
 protein.

toProtein(SymbolList, int, int) - Static method in class org.biojava.bio.seq.DNATools

Convenience method to translate a region of a DNA sequence directly into
 protein.

toRNA(SymbolList) - Static method in class org.biojava.bio.seq.DNATools

Converts a SymbolList from the DNA Alphabet to the
 RNA Alphabet.

toString() - Method in class org.biojava.bio.AbstractAnnotation
 
toString() - Method in class org.biojava.bio.AnnotationType.Abstract
 
toString() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
toString() - Method in class org.biojava.bio.CollectionConstraint.And
 
toString() - Method in class org.biojava.bio.CollectionConstraint.Contains
 
toString() - Method in class org.biojava.bio.CollectionConstraint.Or
 
toString() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
toString() - Method in class org.biojava.bio.EcNumber.Impl
 
toString() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
 
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
 
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
 
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
 
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
 
toString() - Method in class org.biojava.bio.PropertyConstraint.And
 
toString() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
 
toString() - Method in class org.biojava.bio.PropertyConstraint.ByClass
 
toString() - Method in class org.biojava.bio.PropertyConstraint.Enumeration
 
toString() - Method in class org.biojava.bio.PropertyConstraint.ExactValue
 
toString() - Method in class org.biojava.bio.PropertyConstraint.Or
 
toString() - Method in class org.biojava.bio.search.SequenceDBSearchHit

Deprecated.
 
toString() - Method in class org.biojava.bio.search.SequenceDBSearchResult

Deprecated.
 
toString() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit

Deprecated.
 
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
toString() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
 
toString() - Method in class org.biojava.bio.seq.Feature.Template
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.And
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.Not
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
 
toString() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
 
toString() - Method in class org.biojava.bio.seq.FramedFeature.ReadingFrame
 
toString() - Method in class org.biojava.bio.seq.homol.SimpleHomology
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleFeature
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleSequence
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
 
toString() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
toString() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent

Return the current indent

toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref

return the agave xml representation of this instance

toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs

the agave xml representation of xrefs

toString() - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
 
toString() - Method in class org.biojava.bio.seq.io.SymbolTokenization.TokenType
 
toString() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
 
toString() - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
toString() - Method in class org.biojava.bio.symbol.AbstractSymbol
 
toString() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
toString() - Method in class org.biojava.bio.symbol.CircularLocation
 
toString() - Method in class org.biojava.bio.symbol.FuzzyLocation
 
toString() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
toString() - Method in class org.biojava.bio.symbol.PointLocation
 
toString() - Method in class org.biojava.bio.symbol.RangeLocation
 
toString() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
toString() - Method in class org.biojava.bio.taxa.AbstractTaxon

Deprecated.
 
toString() - Method in class org.biojava.ontology.Ontology.Impl
 
toString() - Method in class org.biojava.ontology.OntologyTerm.Impl
 
toString() - Method in class org.biojava.ontology.RemoteTerm.Impl
 
toString() - Method in class org.biojava.ontology.Synonym
 
toString() - Method in class org.biojava.ontology.Term.Impl
 
toString() - Method in class org.biojava.ontology.Triple.Impl
 
toString() - Method in class org.biojava.stats.svm.CachingKernel
 
toString() - Method in class org.biojava.stats.svm.DiagonalAddKernel
 
toString() - Method in class org.biojava.stats.svm.DiagonalCachingKernel
 
toString() - Method in class org.biojava.stats.svm.ListSumKernel
 
toString() - Method in class org.biojava.stats.svm.NormalizingKernel
 
toString() - Method in class org.biojava.stats.svm.PolynomialKernel
 
toString() - Method in class org.biojava.stats.svm.RadialBaseKernel
 
toString() - Method in class org.biojava.stats.svm.SigmoidKernel
 
toString() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
 
toString() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
 
toString() - Method in class org.biojava.utils.automata.FiniteAutomaton

dumps internal data of Nodes and Transitions that describe
 this FiniteAutomaton.

toString() - Method in interface org.biojava.utils.automata.NfaBuilder
 
toString() - Method in class org.biojava.utils.automata.NfaSubModel
 
toString() - Method in class org.biojava.utils.candy.CandyEntry

It prints the entry contents.

toString() - Method in class org.biojava.utils.ChangeEvent
 
toString() - Method in class org.biojava.utils.ChangeType

Return a string representation of this change.

toString() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
 
toString() - Method in class org.biojava.utils.ParseErrorEvent
 
toString() - Method in exception org.biojava.utils.ParserException

Represent this exception as a string.

toString() - Method in class org.biojava.utils.RepeatedCharSequence
 
toString() - Method in class org.biojava.utils.TypedProperties
 
toString() - Method in class org.biojavax.bio.seq.CompoundRichLocation


 Form: "start..end" or just "point" for point locations

toString() - Method in class org.biojavax.bio.seq.EmptyRichLocation


 ALWAYS RETURNS "empty"

toString() - Method in class org.biojavax.bio.seq.RichLocation.Strand

 Form: "symbol" (eg. +,-,?)

toString() - Method in class org.biojavax.bio.seq.SimplePosition
toString() - Method in class org.biojavax.bio.seq.SimpleRichFeature


 Form: "(#rank) parent:type,source(location)"

toString() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship


 Form: "(#rank) term(object,subject)"

toString() - Method in class org.biojavax.bio.seq.SimpleRichLocation


 Form: "start..end" or just "point" for point locations

toString() - Method in class org.biojavax.bio.SimpleBioEntry

 
 Form: namespace:name/accession.version

toString() - Method in class org.biojavax.bio.SimpleBioEntryRelationship


 Form is "(#rank) term(object,subject)"

toString() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon


 Form: "taxid:[name,name...]"

toString() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName


 Form: "class:name"

toString() - Method in class org.biojavax.ontology.SimpleComparableOntology


 Form: "name"

toString() - Method in class org.biojavax.ontology.SimpleComparableTerm


 Form: "ontology:name [obsolete]" where [obsolete] is optional

toString() - Method in class org.biojavax.ontology.SimpleComparableTriple


 Form: "ontology:predicate(subject,object)"

toString() - Method in class org.biojavax.SimpleComment


 Form: "(#rank) comment"

toString() - Method in class org.biojavax.SimpleCrossRef


 Form: "dbname:accession.version"

toString() - Method in class org.biojavax.SimpleDocRef


 Form: "authors; location"

toString() - Method in class org.biojavax.SimpleDocRefAuthor


 Form: "name (consortium) (ed.)" where sections in brackets are optional.

toString() - Method in class org.biojavax.SimpleNamespace


 Form: "name"

toString() - Method in class org.biojavax.SimpleNote


 Form: "(#rank) term: value"

toString() - Method in class org.biojavax.SimpleRankedCrossRef


 Form: "(#rank) crossref"

toString() - Method in class org.biojavax.SimpleRankedDocRef


 Form: "(#rank) docref"

toString() - Method in class org.biojavax.SimpleRichAnnotation


 Form: list of "[note]" values separated by commas

toString() - Method in class org.biojavax.utils.CRC64Checksum

Returns a zero-padded 16 character wide string containing the current
 value of this checksum in uppercase hexadecimal format.

toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
 
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref

return the agave xml representation of this instance

toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
 
totalEntropy(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools

Calculates the total Entropy for a Distribution.

totalSize - Variable in class org.biojava.ontology.obo.OboFileParser
 
toURL(String, Properties) - Method in interface org.biojava.bio.program.blast2html.DatabaseURLGenerator

Returns a string representation of a URL to the 
 specified ID.

toURL(String, Properties) - Method in class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
 
toURL(String, Properties) - Method in class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator
 
TournamentSelection - Class in org.biojavax.ga.functions

Tournament Selection chooses the best organisms from n random subsets of a
 given population.

TournamentSelection() - Constructor for class org.biojavax.ga.functions.TournamentSelection

Default constructor: sets the selection pressure to the value of 10.

TPA_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
train() - Method in interface org.biojava.bio.dist.DistributionTrainerContext


 Trains the Distribution, given a null model.

train() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
train(double, double) - Method in interface org.biojava.bio.dp.TransitionTrainer

Trains the transition, given an expected probability, and a weight for
 that probability.

train(DistributionTrainerContext, double) - Method in interface org.biojava.bio.dist.DistributionTrainer


 Trains the Distribution, given a null model.

train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
 
train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
 
train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer

Deprecated.
 
train(SequenceDB, double, StoppingCriteria) - Method in class org.biojava.bio.dp.AbstractTrainer

Trains the sequences in db until stopper says to finnish.

train(SequenceDB, double, StoppingCriteria) - Method in interface org.biojava.bio.dp.TrainingAlgorithm

Trains the sequences in db untill stopper says to finnish.

Train - Class in org.biojava.stats.svm.tools
 
Train() - Constructor for class org.biojava.stats.svm.tools.Train
 
Trainable - Interface in org.biojava.bio.dp

Flags an object as being able to register itself with a model trainer.

trainer - Variable in class org.biojava.bio.dp.TrainerTransition
 
trainer - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
 
Trainer() - Constructor for class org.biojava.bio.dist.SimpleDistribution.Trainer

Create a new trainer.

TrainerTransition - Class in org.biojava.bio.dp

This is a small and ugly class for storing a trainer and a transition.

TrainerTransition(TransitionTrainer, State, State) - Constructor for class org.biojava.bio.dp.TrainerTransition
 
trainImpl(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
 
TrainingAlgorithm - Interface in org.biojava.bio.dp
 
trainingComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener
 
TrainingContext - Interface in org.biojava.stats.svm
 
trainingCycleComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener
 
TrainingEvent - Class in org.biojava.stats.svm
 
TrainingEvent(TrainingContext) - Constructor for class org.biojava.stats.svm.TrainingEvent
 
TrainingListener - Interface in org.biojava.stats.svm
 
trainModel(SVMRegressionModel, double[]) - Method in class org.biojava.stats.svm.SMORegressionTrainer
 
trainModel(SVMTarget, SVMKernel, TrainingListener) - Method in class org.biojava.stats.svm.SMOTrainer
 
TrainRegression - Class in org.biojava.stats.svm.tools
 
TrainRegression() - Constructor for class org.biojava.stats.svm.tools.TrainRegression
 
transcribe(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes

Transcribe DNA into RNA.

transcribe(SymbolList) - Static method in class org.biojava.bio.seq.RNATools

Deprecated.
The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or
 DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.


transcribeToRNA(SymbolList) - Static method in class org.biojava.bio.seq.DNATools

Transcribes DNA to RNA.

transcriptionTable() - Static method in class org.biojava.bio.seq.RNATools

Get a translation table for converting DNA to RNA.

transform(FeatureFilter) - Method in class org.biojava.bio.seq.FilterUtils.DelegatingTransformer
 
transform(FeatureFilter) - Method in interface org.biojava.bio.seq.FilterUtils.FilterTransformer

Transform a filter, or return null if it can not be transformed.

transformFilter(FeatureFilter, FilterUtils.FilterTransformer) - Static method in class org.biojava.bio.seq.FilterUtils

This is a general framework method for transforming one filter into another.

transformLocation(Location, int, boolean) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils

Transform a location, translating and flipping as required.

transit(int) - Method in interface org.biojava.utils.automata.StateMachineInstance

invoke transition from current state indicated by Symbol represented by symbol index.

transit(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState

Find the destination State when the specified tag
 is encountered.

transit(Object) - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
 
Transition - Class in org.biojava.bio.dp

This is a small and ugly class for storing a transition.

Transition(State, State) - Constructor for class org.biojava.bio.dp.Transition
 
transitions - Variable in class org.biojava.utils.automata.FiniteAutomaton
 
transitionsFrom(State) - Method in interface org.biojava.bio.dp.MarkovModel

Returns the FiniteAlphabet of all states that have a transition from 'source'.

transitionsFrom(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
transitionsFrom(State) - Method in class org.biojava.bio.dp.WMAsMM
 
transitionsTo(State) - Method in interface org.biojava.bio.dp.MarkovModel

Returns the FiniteAlphabet of all states that have a transition to 'dest'.

transitionsTo(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
transitionsTo(State) - Method in class org.biojava.bio.dp.WMAsMM
 
TransitionTable() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
 
TransitionTrainer - Interface in org.biojava.bio.dp

An object that can be used to train the transitions within a MarkovModel.

TRANSITIVE - Static variable in class org.biojava.ontology.OntoTools
 
translate(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
translate(int) - Method in class org.biojava.bio.symbol.FuzzyLocation
 
translate(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
 
translate(int) - Method in interface org.biojava.bio.symbol.Location

Create a location that is a translation of this location.

translate(int) - Method in class org.biojava.bio.symbol.PointLocation
 
translate(int) - Method in class org.biojava.bio.symbol.RangeLocation
 
translate(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Create a location that is a translation of this location.

translate(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Create a location that is a translation of this location.

translate(int) - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation

Create a location that is a translation of this location.

translate(int) - Method in interface org.biojavax.bio.seq.Position

Takes this position and returns a copy translated by 'distance' bases.

translate(int) - Method in class org.biojavax.bio.seq.SimplePosition

Takes this position and returns a copy translated by 'distance' bases.

translate(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Create a location that is a translation of this location.

translate(Symbol) - Method in interface org.biojava.bio.symbol.TranslationTable

Translate a single symbol from source alphabet to the target alphabet.

translate(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes

Translate RNA into protein (with termination symbols).

translate(SymbolList) - Static method in class org.biojava.bio.seq.RNATools

Translate RNA into protein (with termination symbols).

translate(SymbolList, TranslationTable) - Static method in class org.biojava.bio.symbol.SymbolListViews

Provides a 'translated' view of an underlying SymbolList.

translateCUD(InputStream, OutputStream) - Static method in class org.biojava.bio.symbol.CodonPrefTools

reads in a file in Codon Usage Database format and
 translate it into our XML format
 These can be obtained from the
 Codon Usage Database.

TranslatedDistribution - Class in org.biojava.bio.dist

A translated view of some underlying distribution.

TranslatedDistribution(ReversibleTranslationTable, Distribution, DistributionFactory) - Constructor for class org.biojava.bio.dist.TranslatedDistribution

Create a new TranslatedDistribution.

TranslateFlipContext - Class in org.biojava.bio.seq.projection

A ProjectionContext that translates and optionaly flips features.

TranslateFlipContext(FeatureHolder, FeatureHolder, int) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext

Create a new TranslateFlipContext with translation only.

TranslateFlipContext(FeatureHolder, FeatureHolder, int, boolean) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext

Create a new TranslateFlipContext with explicit translation and flip.

TranslateFlipContext(FeatureHolder, FeatureHolder, int, int) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext

Create a new TranslateFlipContext that flips all featurs arround min and
 max.

TranslationTable - Interface in org.biojava.bio.symbol

Encapsulates the mapping from a source to a destination
 alphabet.

TRANSPOSON_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
 
transScore(State, State, Symbol, Symbol) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
 
TREMA_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable

Translation table name for the trematode mitochondrial genetic
 code.

Triple - Interface in org.biojava.ontology

A triple in an ontology.

TRIPLE - Static variable in interface org.biojava.ontology.Ontology
 
TRIPLE - Static variable in interface org.biojavax.ontology.ComparableOntology
 
Triple.Impl - Class in org.biojava.ontology

Basic in-memory implementation of a Triple in an ontology

 This can be used to implement Ontology.createTriple

Triplet() - Constructor for class org.biojava.utils.ListTools.Triplet
 
Triplet(Object, Object, Object) - Constructor for class org.biojava.utils.ListTools.Triplet
 
TriState - Class in org.biojava.utils

Class that represents the tristate values possible in
 a logical operation: true, false and indeterminate.

trp() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Tryptophan (W)

TRUE - Static variable in class org.biojava.utils.TriState
 
TRYPSIN - Static variable in class org.biojava.bio.proteomics.Protease
 
TRYPSIN - Static variable in class org.biojava.bio.proteomics.ProteaseManager
 
TWIN - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
 
TWIN - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
 
type - Variable in class org.biojava.bibliography.BiblioCriterion

The criteria can be used for defining rules for matching
 (type BiblioCriterion.QUERY_CRITERION), or for ordering (type BiblioCriterion.SORT_CRITERION).

type - Variable in class org.biojava.bibliography.BibRef


 It defines the nature or genre of the cited resource.

type - Variable in class org.biojava.bio.seq.Feature.Template
 
type - Variable in class org.biojava.utils.IndexedChangeHub.ListenerMemento
 
TYPE - Static variable in interface org.biojava.bio.seq.Feature

The type of this feature has altered.

TYPE_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a bibliographic resource type.

TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
TYPE_BOOK - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a bibliographic resource type.

TYPE_BOOK_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a bibliographic resource type.

TYPE_JOURNAL_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a bibliographic resource type.

TYPE_PATENT - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a bibliographic resource type.

TYPE_PROCEEDING - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a bibliographic resource type.

TYPE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
TYPE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
TYPE_TECH_REPORT - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a bibliographic resource type.

TYPE_THESIS - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a bibliographic resource type.

TYPE_WEB_RESOURCE - Static variable in interface org.biojava.bibliography.BibRefSupport

A name of a bibliographic resource type.

TYPEDEF - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
TypedProperties - Class in org.biojava.utils

a sub-class of java.util.Properties that provides the same constructors, adds two convenient load methods to load
 the properties from files and, most importantly, adds getPropertyAsXXX() methods to get a property as an object of
 type XXX.

TypedProperties() - Constructor for class org.biojava.utils.TypedProperties

Creates an empty property list with no default values.

TypedProperties(Properties) - Constructor for class org.biojava.utils.TypedProperties

Creates an empty property list with the specified defaults.

typeTerm - Variable in class org.biojava.bio.seq.Feature.Template
 
TYPETERM - Static variable in interface org.biojava.bio.seq.Feature

The ontological type of this feature has altered.

TYPETERM - Static variable in interface org.biojavax.bio.seq.RichFeature
 
tyr() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Tyrosine (Y)





U

u() - Static method in class org.biojava.bio.seq.NucleotideTools
 
u() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Selenocysteine

u() - Static method in class org.biojava.bio.seq.RNATools
 
UkkonenSuffixTree - Class in org.biojava.bio.symbol


 A suffix tree is an efficient method for encoding the frequencies
 of motifs in a sequence.

UkkonenSuffixTree() - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree

Initializes a new UkkonenSuffixTree instance.

UkkonenSuffixTree(String) - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree
 
UkkonenSuffixTree(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree
 
UkkonenSuffixTree.SuffixNode - Class in org.biojava.bio.symbol

end Tree modification methods

unbind(String) - Method in class org.biojava.naming.ObdaContext
 
unbind(Name) - Method in class org.biojava.naming.ObdaContext
 
Unchangeable - Class in org.biojava.utils

This is a utility implementation of Changeable that doesn't fire any events
 or keep references to any listeners.

Unchangeable() - Constructor for class org.biojava.utils.Unchangeable
 
UNCLASSIFIED - Static variable in interface org.biojava.bio.EcNumber

Constant that represents EC number components that are as yet unclassified.

uncompress(String, FileOutputStream) - Static method in class org.biojava.utils.io.UncompressInputStream
 
UncompressInputStream - Class in org.biojava.utils.io

This class decompresses an input stream containing data compressed with
 the unix "compress" utility (LZC, a LZW variant).

UncompressInputStream(InputStream) - Constructor for class org.biojava.utils.io.UncompressInputStream
 
UNDEFINED - Static variable in interface org.biojava.bio.EcNumber

Constant that represents EC number components that are not defined.

unescape(String) - Method in class org.biojava.ontology.obo.OboFileParser
 
unescape(String, char, int, boolean) - Method in class org.biojava.ontology.obo.OboFileParser
 
unescape(String, char, int, int, boolean) - Method in class org.biojava.ontology.obo.OboFileParser
 
unescapeChars - Static variable in class org.biojava.ontology.obo.OboFileParser
 
UniformDistribution - Class in org.biojava.bio.dist

An implementation of an uniform distribution

UniformDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.UniformDistribution

Create a new UniformDistribution.

uniformMutationDistribution(FiniteAlphabet) - Static method in class org.biojavax.ga.util.GATools

Makes a 1st order distribution which is infact uniform (equivalent to a
 uniform zero order distribution).

UniformScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
 
UNIGENE_ANNOTATION - Static variable in class org.biojava.bio.program.unigene.UnigeneTools


 Annotation schema for all UnigeneCluster instances.

UnigeneCluster - Interface in org.biojava.bio.program.unigene


 A single unigene cluster.

UnigeneDB - Interface in org.biojava.bio.program.unigene

A database of Unigene clusters.

UnigeneFactory - Interface in org.biojava.bio.program.unigene

Objects that can be used to produce a UnigeneDB instance
 given a URL.

UnigeneTools - Class in org.biojava.bio.program.unigene

Usefull tools for working with Unigene.

UnigeneTools() - Constructor for class org.biojava.bio.program.unigene.UnigeneTools
 
unIndent() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent

Remove a level of indentation

union(Collection) - Static method in class org.biojava.bio.symbol.LocationTools

The n-way union of a Collection of locations.

union(BibRefQuery[], Hashtable) - Method in interface org.biojava.bibliography.BibRefSupport


 It merges all given collections together.

union(AnnotationType, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools

Create an AnnotationType that matches all Anntotations that are accepted
 by two others.

union(CollectionConstraint, CollectionConstraint) - Static method in class org.biojava.bio.AnnotationTools

Calculate a CollectionConstaint that will accept all items accepted by
 either constraint.

union(PropertyConstraint, PropertyConstraint) - Static method in class org.biojava.bio.AnnotationTools

Create a PropertyConstraint that matches all Objects that are accepted
 by two others.

union(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils

Operator: Union of FeatureHolder1 and FeatureHolder2

union(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
 
union(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
 
union(Location) - Method in class org.biojava.bio.symbol.CircularLocation
 
union(Location) - Method in interface org.biojava.bio.symbol.Location

Return a Location containing all points in either ranges.

union(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation

Return a Location containing all points in either ranges.

union(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation

Return a Location containing all points in either ranges.

union(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation

Return a Location containing all points in either ranges.

union(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools

Return the union of two locations.

UNIPROT_FORMAT - Static variable in class org.biojavax.bio.seq.io.UniProtFormat

The name of this format

UniProtCommentParser - Class in org.biojavax.bio.seq.io
 
UniProtCommentParser() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser

Creates a new instance of UniProtCommentParser.

UniProtCommentParser.Event - Class in org.biojavax.bio.seq.io

A class to describe events for alternative product comments.

UniProtCommentParser.Interaction - Class in org.biojavax.bio.seq.io

A class to describe protein-protein interactions.

UniProtCommentParser.Isoform - Class in org.biojavax.bio.seq.io

A class to describe isoforms for alternative product comments.

UniProtCommentParser.SeqCaution - Class in org.biojavax.bio.seq.io

A class to describe seq caution entries.

UniProtFormat - Class in org.biojavax.bio.seq.io

Format reader for UniProt files.

UniProtFormat() - Constructor for class org.biojavax.bio.seq.io.UniProtFormat
 
UniProtFormat.Terms - Class in org.biojavax.bio.seq.io

Implements some UniProt-specific terms.

UniProtLocationParser - Class in org.biojavax.bio.seq.io

Parses UniProt location strings into RichLocation objects.

UNIPROTXML_FORMAT - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat

The name of this format

UniProtXMLFormat - Class in org.biojavax.bio.seq.io

Format reader for UniProtXML files.

UniProtXMLFormat() - Constructor for class org.biojavax.bio.seq.io.UniProtXMLFormat
 
UniProtXMLFormat.Terms - Class in org.biojavax.bio.seq.io

Implements some UniProtXML-specific terms.

UNIVERSAL - Static variable in interface org.biojava.bio.symbol.TranslationTable

Translation table name for the universal genetic code.

UNKNOWN - Static variable in class org.biojava.bio.seq.io.AlignIOConstants

UNKNOWN indicates that the alignment format is
 unknown.

UNKNOWN - Static variable in class org.biojava.bio.seq.io.SeqIOConstants

UNKNOWN indicates that the sequence format is
 unknown.

UNKNOWN - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
 
UNKNOWN - Static variable in interface org.biojava.bio.seq.StrandedFeature

Flag to indicate that a feature has an unknown strand.

UNKNOWN - Static variable in class org.biojava.utils.ChangeType

Constant ChangeType field which indicates that a change has
 occured which can't otherwise be represented.

UNKNOWN_SCOPE - Static variable in class org.biojava.ontology.Synonym
 
UNKNOWN_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand

The unknown strand is represented by the symbol '?'

unlockModel() - Method in class org.biojava.bio.dp.DP
 
unmask(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector

Un-masks the token by making it upper case.

unmask(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector

Present the token for a Symbol as it would appear if
 it wasn't softmasked

unpack(byte) - Method in class org.biojava.bio.symbol.DNAAmbPack
 
unpack(byte) - Method in class org.biojava.bio.symbol.DNANoAmbPack
 
unpack(byte) - Method in interface org.biojava.bio.symbol.Packing


 Return the symbol for a packing.

unregisterFactory(UnigeneFactory) - Static method in class org.biojava.bio.program.unigene.UnigeneTools

Register a UnigeneFactory.

UntrainableDistribution - Class in org.biojava.bio.dist

A distribution which does not interact with the training framework.

UntrainableDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.UntrainableDistribution

Construct a new untrainable distribution over the specified alphabet.

untranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable

returns a Set of Atomic Symbols that are the reverse translation
 of the specified Symbol in the target alphabet.

untranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
 
untranslate(Symbol) - Method in interface org.biojava.bio.symbol.ManyToOneTranslationTable

Translate a single symbol from target alphabet to the source alphabet.

untranslate(Symbol) - Method in interface org.biojava.bio.symbol.ReversibleTranslationTable

Translate a single symbol from target alphabet to the source alphabet.

update() - Method in class org.biojava.bio.dp.DP
 
update() - Method in class org.biojava.bio.dp.onehead.SingleDP
 
update() - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
update(byte[], int, int) - Method in class org.biojavax.utils.CRC64Checksum
 
update(int) - Method in class org.biojavax.utils.CRC64Checksum
 
update(String) - Method in class org.biojavax.utils.CRC64Checksum
 
UPDATE_DATE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
UPDATE_REL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
uri - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
 
URI - Static variable in interface org.biojavax.Namespace
 
URI_PREFIX - Static variable in class org.biojava.bio.seq.FeatureTypes

The standard prefix for all type URIs

url - Variable in class org.biojava.bibliography.BiblioWebResource

The URL of the resource.

urlBatchSequences - Static variable in class org.biojava.bio.seq.db.GenbankSequenceDB
 
urlBatchSequences - Static variable in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
 
urlBatchSequences - Static variable in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
 
URLFactory - Interface in org.biojava.utils.net

URLFactory defines a means of obtaining a URL
 associated with an object.

URLGeneratorFactory - Interface in org.biojava.bio.program.blast2html

Interface for a factory method to return a list of
 0, 1 or more DatabaseURLGenerator instances.

usCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
 
useSuppliedSymListFactory() - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory

Call this to convert from default SymbolList implementation
 to user-supplied implementation.

UtilHelper - Class in org.biojava.bio.seq.io.agave

Just make the property follow the common case

UtilHelper() - Constructor for class org.biojava.bio.seq.io.agave.UtilHelper
 




V

v() - Static method in class org.biojava.bio.seq.DNATools
 
v() - Static method in class org.biojava.bio.seq.NucleotideTools
 
v() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Valine

val() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid Valine (V)

validate(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
validate(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet


 Throws a precanned IllegalSymbolException if the symbol is not contained
 within this Alphabet.

validate(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
 
validate(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
validate(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
validate(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
 
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.And
 
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
 
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Or
 
validateAddValue(Collection, Object) - Method in interface org.biojava.bio.CollectionConstraint

Return true iff the Collection formed by adding
 newValue to current would be accepted
 by this constraint.

validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
 
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.And
 
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
 
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Or
 
validateRemoveValue(Collection, Object) - Method in interface org.biojava.bio.CollectionConstraint

Return true iff the Collection formed by removing
 newValue from current would be accepted
 by this constraint.

validLen - Variable in class org.biojava.utils.io.CachingInputStream

A count of the number of bytes in CachingInputStream.cache that contain
  data read from the stream.

value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Aggregator
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Echo
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Indexer
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Indexer2
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.MultiTagger
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
 
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
 
value(TagValueContext, Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueListener

A value has been seen.

value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
 
VALUE - Static variable in interface org.biojavax.Note
 
VALUE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
ValueChanger - Class in org.biojava.bio.program.tagvalue


 Intercept the values associated with some tags and change them
 systematically.

ValueChanger(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.ValueChanger
 
ValueChanger(TagValueListener, ChangeTable) - Constructor for class org.biojava.bio.program.tagvalue.ValueChanger

Create a new changer that will pass the modified event stream to a
 delegate.

valueOf(String) - Static method in class org.biojava.bio.EcNumber.Impl

Process a string into an EcNumber.

valueOf(String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier

Create a new LifeScienceIdentifier parsed
 from the properly formatted string lsid.

valueOf(String) - Static method in enum org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat

Returns the enum constant of this type with the specified name.

valueOf(String, String, String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier

Create a new LifeScienceIdentifier from the
 specified parameters.

valueOf(String, String, String, String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier

Create a new LifeScienceIdentifier from the
 specified parameters.

values() - Static method in enum org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat

Returns an array containing the constants of this enum type, in
the order they are declared.

Variable - Interface in org.biojava.ontology
 
Variable.Impl - Class in org.biojava.ontology
 
vectorToString(SparseVector) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
VERSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
VERSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 
VERT_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable

Translation table name for the vertebrate mitochondrial genetic
 code.

view(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools

Create a new sequence that has all of the data in the original, but allows
 new features and top-level annotations to be added independantly.

view(Sequence, String) - Static method in class org.biojava.bio.seq.SequenceTools

Create a new sequence that has all of the data in the original, but allows
 new features and top-level annotations to be added independantly.

view(Sequence, FeatureRealizer) - Static method in class org.biojava.bio.seq.SequenceTools

Creates a new Sequence with the data of the old but with a different
 FeatureRealizer that will be applied to new Features.

viewEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
ViewingSequenceDB - Class in org.biojava.bio.seq.db

SequenceDB implementation that returns new SequenceView instances
 wrapping the sequences in an underlying database.

ViewingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.ViewingSequenceDB

Create a new ViewingSequenceDB that views the sequences in parent.

ViewSequence - Class in org.biojava.bio.seq.impl

A view onto another Sequence object.

ViewSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.ViewSequence

Construct a view onto an existing sequence which takes on that
 sequence's name.

ViewSequence(Sequence, String) - Constructor for class org.biojava.bio.seq.impl.ViewSequence

Construct a view onto an existing sequence and give it a new
 name.

ViewSequence(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.impl.ViewSequence

Construct a view onto a sequence, using a specific FeatureRealizer.

viewStart - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
 
viewToSource(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList

Coordinate conversion from view to source.

viewToSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
 
viewToSource(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList

Coordinate conversion from view to source.

visitFilter(FeatureFilter, Visitor) - Static method in class org.biojava.bio.seq.FilterUtils

Applies a visitor to a filter, and returns the visitor's result or null.

Visitor - Interface in org.biojava.utils.walker

Things that will be shown filters.

viterbi(ScoreType, BackPointer) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
 
viterbi(ScoreType, BackPointer) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
 
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
 
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
 
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
 
volume - Variable in class org.biojava.bibliography.BiblioBook

Book volume.

volume - Variable in class org.biojava.bibliography.BiblioJournalArticle

The journal volume.

vp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
 
vp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
 




W

w() - Static method in class org.biojava.bio.seq.DNATools
 
w() - Static method in class org.biojava.bio.seq.NucleotideTools
 
w() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Tryptophan

waitForThreads() - Method in class org.biojava.utils.SimpleThreadPool
 
waitForThreads() - Method in interface org.biojava.utils.ThreadPool

waitForThreads temporarily closes the pool to new
 requests until such time as the current request queue has been
 emptied and all running tasks completed.

walk(Object, Visitor) - Method in interface org.biojava.utils.walker.Walker

This walks the feature tree, showing the visitor each filter in
 the expression.

Walker - Interface in org.biojava.utils.walker

Objects that can walk over a filter expression, showing each element to a
 visitor.

WalkerFactory - Class in org.biojava.utils.walker
 
walkTo(UkkonenSuffixTree.SuffixNode, String, int, int) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree

This method is used to walk down the tree, from a given node.

wasEmpty() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer

Returns true if  no HitSummary and no Hit elements were
 encountered

WeakCacheMap - Class in org.biojava.utils.cache

A cache which retains weak references to objects

WeakCacheMap() - Constructor for class org.biojava.utils.cache.WeakCacheMap
 
WeakTaxon - Class in org.biojava.bio.taxa

Deprecated.
replaced by classes in org.biojavax.bio.taxa


WeakTaxon() - Constructor for class org.biojava.bio.taxa.WeakTaxon

Deprecated.
 
WeakTaxon(String, String) - Constructor for class org.biojava.bio.taxa.WeakTaxon

Deprecated.
 
WeakTaxonFactory - Class in org.biojava.bio.taxa

Deprecated.
replaced by classes in org.biojavax.bio.taxa


WeakTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.WeakTaxonFactory

Deprecated.
 
WeakValueHashMap - Class in org.biojava.utils.cache

Map implementation which keeps weak references to values.

WeakValueHashMap() - Constructor for class org.biojava.utils.cache.WeakValueHashMap
 
WebSequenceDB - Class in org.biojava.bio.seq.db

Functions for access to a web based database that returns sequences
 in a variety of formats.

WebSequenceDB() - Constructor for class org.biojava.bio.seq.db.WebSequenceDB
 
WeightedSet - Class in org.biojavax.ga.util

Inspred by the BioJava Distribution objects the WeightedSet is a map from
 a Key to a Weight.

WeightedSet() - Constructor for class org.biojavax.ga.util.WeightedSet
 
weightForwarder - Variable in class org.biojava.bio.dist.AbstractOrderNDistribution

The listener that will forward events from the underlying distributions to
 listeners for this distribution.

WeightMatrix - Interface in org.biojava.bio.dp

A log odds weight matrix.

WeightMatrixAnnotator - Class in org.biojava.bio.dp

Annotates a sequence with hits to a weight-matrix.

WeightMatrixAnnotator(WeightMatrix, double) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator

Create a new annotator that uses PROBABILITY score type.

WeightMatrixAnnotator(WeightMatrix, ScoreType, double) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator

Create a new annotator that uses a specific score type.

WeightMatrixAnnotator(WeightMatrix, ScoreType, double, String) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator

Create a new annotator that uses the PROBABILITY score type and an ID
   for the weight matrix.

WEIGHTS - Static variable in interface org.biojava.bio.dist.Distribution


 Whenever a distribution changes the values that would be returned by
 getWeight, they should fire a ChangeEvent with this object as the type.

windowedSymbolList(SymbolList, int) - Static method in class org.biojava.bio.symbol.SymbolListViews

A view of windows onto another SymbolList.

WMAsMM - Class in org.biojava.bio.dp

Wraps a weight matrix up so that it appears to be a very simple HMM.

WMAsMM(WeightMatrix) - Constructor for class org.biojava.bio.dp.WMAsMM
 
WobbleDistribution - Interface in org.biojava.bio.symbol

an object to return statistics about
 the frequency of the wobble base
 in a set of synonymous codons.

wordSize() - Method in class org.biojava.bio.symbol.DNAAmbPack
 
wordSize() - Method in class org.biojava.bio.symbol.DNANoAmbPack
 
wordSize() - Method in interface org.biojava.bio.symbol.Packing


 The number of bits required to pack a symbol.

WordTokenization - Class in org.biojava.bio.seq.io

Base class for tokenizations which accept whitespace-separated
 `words'.

WordTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.WordTokenization
 
wordWrap(String, String, int) - Static method in class org.biojavax.utils.StringTools

Word-wraps a string into an array of lines of no more than the given width.

WORM_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools

Caenorhabditis elegans codon preferences

Wrapper(SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Wrapper
 
write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat

Writes out the alignment to an FASTA file.

write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
 
write(Sequence) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter

Writing Sequence.

writeAnnotations(FeatureHolder) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeAnnotationType(AnnotationType, XMLWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter

Write an AnnotationType to the specified XMLWriter.

writeAssembly(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeBioSequence(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeClassification(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeCollectionConstraint(CollectionConstraint, XMLWriter, XMLAnnotationTypeWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLCollectionConstraintWriter
 
writeCompResult(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeContig(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeDetails(XMLWriter, Feature) - Method in class org.biojava.bio.program.xff.BasicXFFHelper
 
writeDetails(XMLWriter, Feature) - Method in class org.biojava.bio.program.xff.PropertyWriter
 
writeDetails(XMLWriter, Feature) - Method in interface org.biojava.bio.program.xff.XFFHelper
 
writeDistribution(Distribution, OutputStream) - Method in class org.biojava.bio.dist.XMLDistributionWriter

Writes an OrderNDistribution or simple Distribution to an XML file.

writeDna(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
 
writeDna(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
 
writeEmbl(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Writes a single Sequence to an OutputStream in EMBL format.

writeEmbl(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Writes a stream of Sequences to an OutputStream in EMBL format.

writeEMBL(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes sequences from a SequenceIterator to an
 OutputStream in EMBL Format.

writeEMBL(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes a single Sequence to an OutputStream
 in EMBL format.

writeEMBLxml(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes sequences from a SequenceIterator to an
 OutputStream in EMBLxml Format.

writeEMBLxml(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes a single Sequence to an OutputStream
 in EMBLxml format.

writeEmptyElement(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
writeEmptyElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
writeFasta(OutputStream, SequenceDB) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Write a sequenceDB to an output stream in fasta format.

writeFasta(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Writes a single Sequence to an OutputStream in Fasta format.

writeFasta(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Writes sequences from a SequenceIterator to an OutputStream in
 Fasta Format.

writeFasta(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes Sequences from a SequenceIterator to
 an OutputStream in Fasta Format.

writeFasta(OutputStream, SequenceIterator, Namespace, FastaHeader) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes Sequences from a SequenceIterator to
 an OutputStream in Fasta Format.

writeFasta(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes a single Sequence to an OutputStream
 in Fasta format.

writeFasta(OutputStream, Sequence, Namespace, FastaHeader) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes a single Sequence to an OutputStream
 in Fasta format.

writeFeatureSet(FeatureHolder, XMLWriter) - Method in class org.biojava.bio.program.xff.XFFWriter
 
writeFilter(FeatureFilter, XMLWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter

Write a FeatureFilter to the supplied XMLWriter

writeFilter(FeatureFilter, XMLWriter, XMLFilterWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterWriter.FilterWriter
 
writeFooter() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter

Write </sciobj>

writeGenbank(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Writes a single Sequence to an OutputStream in Genbank format.

writeGenbank(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Writes a stream of Sequences to an OutputStream in Genbank
 format.

writeGenbank(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes sequences from a SequenceIterator to an
 OutputStream in GenBank Format.

writeGenbank(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes a single Sequence to an OutputStream
 in GenBank format.

writeGene(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeGenpept(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Writes a single Sequence to an OutputStream in Genpept format.

writeGenpept(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Writes a stream of Sequences to an OutputStream in Genpept
 format.

writeGFF(File, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools

Writes a GFFEntrySet to a file.

writeGFF(PrintWriter, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools

Writes a GFFEntrySet to a PrintWriter.

writeGFF(String, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools

Writes a GFFEntrySet to a file.

writeHeader() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
writeHeader() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter

Write <sciobj>

writeIndent() - Method in class org.biojava.utils.xml.PrettyXMLWriter
 
writeINSDseq(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes sequences from a SequenceIterator to an
 OutputStream in INSDseq Format.

writeINSDseq(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes a single Sequence to an OutputStream
 in INSDseq format.

writeKeyValueLine(String, String, int, int, PrintStream) - Static method in class org.biojavax.utils.StringTools

Writes some text to the output stream in the following format:
    key         text
                continuation of text
 where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth,
 and the text is split over multiple lines at the nearest occurrence of whitespace.

writeKeyValueLine(String, String, int, int, String, PrintStream) - Static method in class org.biojavax.utils.StringTools

Writes some text to the output stream in the following format:
    key         text
                continuation of text
 where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth,
 and the text is split over multiple lines at the nearest occurrence of separator sep.

writeKeyValueLine(String, String, int, int, String, String, PrintStream) - Static method in class org.biojavax.utils.StringTools

Writes some text to the output stream in the following format:
    key         text
    wrappedKey  continuation of text
 where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth,
 and the text is split over multiple lines at the nearest occurrence of separator sep.

writeLocation(RichLocation) - Static method in class org.biojavax.bio.seq.io.GenbankLocationParser

Writes a location in Genbank format.

writeLocation(RichLocation) - Static method in class org.biojavax.bio.seq.io.UniProtLocationParser

Writes a location in UniProt format.

writeMatrix(WeightMatrix, PrintStream) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
writeModel(MarkovModel, PrintStream) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
writeModelFile(SVMClassifierModel, String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
writePCData(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
 
writePhredQuality(OutputStream, OutputStream, SequenceDB) - Static method in class org.biojava.bio.program.phred.PhredTools

Writes Phred quality data in a Fasta type format.

writePropertyConstraint(PropertyConstraint, XMLWriter, XMLAnnotationTypeWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLPropertyConstraintWriter
 
writeProtein(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
 
writeProtein(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
 
writeRecord(RAF, long, int, String, Map) - Method in class org.biojava.bio.program.indexdb.BioStore
 
writeRecord(RAF, long, int, String, Map) - Method in interface org.biojava.bio.program.indexdb.IndexStore

writeRecord creates and writes a new
 Record

WriterOutputHandler - Class in org.biojava.utils.process

Simple output handler 
 that writes the output of an external process to an 
 writer.

WriterOutputHandler(Writer, String) - Constructor for class org.biojava.utils.process.WriterOutputHandler

Initializes the writer output handler.

writeSeqFeature(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter

Write SeqFeature XML

writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.program.phred.PhredFormat

This method will print symbols to the line width followed by a
 new line etc.

writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter

Write sequence into AGAVE XML format.

writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
 
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat

Deprecated.
Writes a Sequence or RichSequence to a 
 PrintStream in FASTA format.

writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GAMEFormat
 
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
 
writeSequence(Sequence, PrintStream) - Method in interface org.biojava.bio.seq.io.SequenceFormat

writeSequence writes a sequence to the specified
 PrintStream, using the default format.

writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat

writeSequence writes a sequence to the specified
 PrintStream, using the default format.

writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat

writeSequence writes a sequence to the specified
 PrintStream, using the default format.

writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.FastaFormat

writeSequence writes a sequence to the specified
 PrintStream, using the default format.

writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat

writeSequence writes a sequence to the specified
 PrintStream, using the default format.

writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat

writeSequence writes a sequence to the specified
 PrintStream, using the default format.

writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat

writeSequence writes a sequence to the specified
 PrintStream, using the default format.

writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat

writeSequence writes a sequence to the specified
 PrintStream, using the default format.

writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.program.phred.PhredFormat

Deprecated.
use writeSequence(Sequence seq, PrintStream os)


writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.EmblLikeFormat

Deprecated.
use writeSequence(Sequence seq, PrintStream os)


writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat

Deprecated.
use writeSequence(Sequence seq, PrintStream os)


writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.GAMEFormat
 
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat

Deprecated.
use writeSequence(Sequence seq, PrintStream os)


writeSequence(Sequence, String, PrintStream) - Method in interface org.biojava.bio.seq.io.SequenceFormat

Deprecated.
use writeSequence(Sequence seq, PrintStream os)


writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat

writeSequence writes a sequence to the specified
 PrintStream, using the specified format.

writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat

writeSequence writes a sequence to the specified
 PrintStream, using the specified format.

writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.FastaFormat

writeSequence writes a sequence to the specified
 PrintStream, using the specified format.

writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat

writeSequence writes a sequence to the specified
 PrintStream, using the specified format.

writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat

writeSequence writes a sequence to the specified
 PrintStream, using the specified format.

writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat

writeSequence writes a sequence to the specified
 PrintStream, using the specified format.

writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat

writeSequence writes a sequence to the specified
 PrintStream, using the specified format.

writeSequence(Sequence, String, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat

As per EMBLFormat.writeSequence(Sequence, Namespace), except
 that it also takes a format parameter.

writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat

Writes a sequence out to the outputstream given by beginWriting() using the default format of the
 implementing class.

writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat

Writes a sequence out to the outputstream given by beginWriting() using the default format of the
 implementing class.

writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat

Writes a sequence out to the outputstream given by beginWriting() using the default format of the
 implementing class.

writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.GenbankFormat

Writes a sequence out to the outputstream given by beginWriting() using the default format of the
 implementing class.

writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.INSDseqFormat

Writes a sequence out to the outputstream given by beginWriting() using the default format of the
 implementing class.

writeSequence(Sequence, Namespace) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat

Writes a sequence out to the outputstream given by beginWriting() using the default format of the
 implementing class.

writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtFormat

Writes a sequence out to the outputstream given by beginWriting() using the default format of the
 implementing class.

writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat

Writes a sequence out to the outputstream given by beginWriting() using the default format of the
 implementing class.

writeSequenceMap(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter

group sequence_map by getSource()

writeSequenceMap2(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter

Write SequenceMap XML

writeStream(SequenceIterator) - Method in class org.biojava.bio.seq.io.StreamWriter

Write each of the sequences in ss to the stream in the given format.

writeStream(SequenceIterator, Namespace) - Method in class org.biojavax.bio.seq.io.RichStreamWriter

Write each of the sequences in ss to the stream in the given format.

writeSwissprot(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Writes a single Sequence to an OutputStream in SwissProt format.

writeSwissprot(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools

Deprecated.
Writes a stream of Sequences to an OutputStream in SwissProt
 format.

writeToXML(Distribution, OutputStream) - Static method in class org.biojava.bio.dist.DistributionTools

Writes a Distribution to XML that can be read with the readFromXML method.

writeToXML(CodonPref, PrintWriter) - Static method in class org.biojava.bio.symbol.CodonPrefTools

write out a specified CodonPref object in XML format.

writeTranscript(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
 
writeUniProt(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes sequences from a SequenceIterator to an
 OutputStream in UniProt Format.

writeUniProt(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes a single Sequence to an OutputStream
 in UniProt format.

writeUniProtXML(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes sequences from a SequenceIterator to an
 OutputStream in UniProt XML Format.

writeUniProtXML(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools

Writes a single Sequence to an OutputStream
 in UniProt XML format.

writeXFF(File, FeatureHolder) - Static method in class org.biojava.bio.program.xff.XFFTools
 
writeXFF(PrintWriter, FeatureHolder) - Static method in class org.biojava.bio.program.xff.XFFTools
 
writeXML(XMLWriter) - Method in interface org.biojava.utils.xml.XMLWritable
 




X

X_LAEVIS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
XFF_BIOJAVA_NS - Static variable in class org.biojava.bio.program.xff.XFFTools
 
XFF_NS - Static variable in class org.biojava.bio.program.xff.XFFTools
 
XFFFeatureSetHandler - Class in org.biojava.bio.program.xff

StAX handler which converts and stream of parse events for an XFF
 featureSet element into BioJava SeqIO events.

XFFFeatureSetHandler() - Constructor for class org.biojava.bio.program.xff.XFFFeatureSetHandler

Construct a new XFFFeatureSetHandler with the default set of handlers.

XFFHelper - Interface in org.biojava.bio.program.xff
 
XFFPartHandlerFactory - Interface in org.biojava.bio.program.xff

Factory for StAX content handlers.

XFFTools - Class in org.biojava.bio.program.xff

Common functionality for manipulating XFF.

XFFTools() - Constructor for class org.biojava.bio.program.xff.XFFTools
 
XFFWriter - Class in org.biojava.bio.program.xff

Simple XFF writing code, ripped off from Dazzle 0.08.

XFFWriter() - Constructor for class org.biojava.bio.program.xff.XFFWriter
 
XFFWriter(XFFHelper) - Constructor for class org.biojava.bio.program.xff.XFFWriter
 
XML - org.biojavax.bio.alignment.blast.RemoteQBlastOutputFormat
 
XML_ANNOTATIONTYPE_NS - Static variable in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter

XML namespace string used to the AnnotationType representation

XML_FILTER_NS - Static variable in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
 
XMLAnnotationTypeHandler - Class in org.biojava.bio.seq.io.filterxml

StAX handler for parsing AnnotationTypes in FilterXML documents.

XMLAnnotationTypeHandler() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler

Construct a new XMLAnnotationTypeHandler which can parse the builtin PropertyConstraints.

XMLAnnotationTypeHandler.CollectionConstraintHandler - Interface in org.biojava.bio.seq.io.filterxml

Handler for an individual CollectionConstraint in an AnnotationType.

XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml

Handler Factory for a CollectionConstraint in an AnnotationType.

XMLAnnotationTypeHandler.PropertyConstraintHandler - Interface in org.biojava.bio.seq.io.filterxml

Handler for an individual PropertyConstraint in an AnnotationType.

XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml

Handler Factory for a PropertyConstraint in an AnnotationType.

XMLAnnotationTypeWriter - Class in org.biojava.bio.seq.io.filterxml

Main class for writing AnnotationTypes as XML.

XMLAnnotationTypeWriter() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter

Construct a new AnnotationTypeWriter which knows about the builtin types of PropertyConstraint

XMLAnnotationTypeWriter.XMLCollectionConstraintWriter - Interface in org.biojava.bio.seq.io.filterxml

Writer for types of CollectionConstraint.

XMLAnnotationTypeWriter.XMLPropertyConstraintWriter - Interface in org.biojava.bio.seq.io.filterxml

Writer for types of PropertyConstraint.

XMLBeans - Class in org.biojava.utils.xml

Construct java beans from XML elements

XMLBeans() - Constructor for class org.biojava.utils.xml.XMLBeans
 
XMLDistributionReader - Class in org.biojava.bio.dist

A SAX parser that reads an XML representation of a
 Distribution from a file and recreates it as a Distribution Object.

XMLDistributionReader() - Constructor for class org.biojava.bio.dist.XMLDistributionReader
 
XMLDistributionWriter - Class in org.biojava.bio.dist

Writes an OrderNDistribution or simple Distribution to an XML file.

XMLDistributionWriter() - Constructor for class org.biojava.bio.dist.XMLDistributionWriter
 
XMLFilterHandler - Class in org.biojava.bio.seq.io.filterxml

Factory producing content handlers for parsing FilterXML elements.

XMLFilterHandler() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLFilterHandler

Construct a new XMLFilterHandler which can parse the builtin types of FeatureFilter.

XMLFilterHandler.FilterHandler - Interface in org.biojava.bio.seq.io.filterxml

StAXContentHandler for a particular type of FeatureFilter.

XMLFilterHandler.FilterHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml

Factory of StAXContentHandlers for a particular type of FeatureFilter.

XMLFilterWriter - Class in org.biojava.bio.seq.io.filterxml

Write FeatureFilters in XML format.

XMLFilterWriter() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLFilterWriter

Construct a new XMLFilterWriter which can serialize the buildin types of
 FeatureFilter.

XMLFilterWriter.FilterWriter - Interface in org.biojava.bio.seq.io.filterxml

Interface for an object which can write a FeatureFilter as XML.

XmlMarkovModel - Class in org.biojava.bio.dp
 
XmlMarkovModel() - Constructor for class org.biojava.bio.dp.XmlMarkovModel
 
xmlSchema - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
 
xmlSchema - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
xmlSchema - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
 
XMLTools - Class in org.biojavax.utils

Utility class for reading chunks of XML files and feeding them to SAX.

XMLWritable - Interface in org.biojava.utils.xml

Object which knows how to represent itself as an XML element.

XMLWriter - Interface in org.biojava.utils.xml

Simple interface for building XML documents.

Xor(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Xor
 
Xor(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Xor
 
Xor(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor
 
XREF_ANALOG - Static variable in class org.biojava.ontology.obo.OboFileHandler
 
XREF_DBNAME_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
XREF_ID_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 
XREF_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
 
XREF_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
 




Y

y() - Static method in class org.biojava.bio.seq.DNATools
 
y() - Static method in class org.biojava.bio.seq.NucleotideTools
 
y() - Static method in class org.biojava.bio.seq.ProteinTools

Returns the AtomicSymbol for the amino acid
 Tyrosine

YEAST_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable

Translation table name for the yeast mitochondrial genetic
 code.





Z

Z_MAYS - Static variable in interface org.biojava.bio.program.homologene.Taxon
 
zero() - Static method in class org.biojavax.ga.util.GATools
 
ZERO - Static variable in class org.biojava.bio.CardinalityConstraint

The property should have zero values.

ZERO_OR_ONE - Static variable in class org.biojava.bio.CardinalityConstraint

The property should have zero or one values.

zeroCol - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
 
zeroCol - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor

Description of the Field

zeroCounts() - Method in interface org.biojava.bio.dist.Count

Reset all the counts to zero.

zeroCounts() - Method in class org.biojava.bio.dist.IndexedCount
 

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