Serialized Form (core 1.9.5 API)

Package org.biojava.bibliography
- Class org.biojava.bibliography.BibRefException extends Exception implements Serializable
Package org.biojava.bio
- Class org.biojava.bio.AbstractAnnotation extends AbstractChangeable implements Serializable
- Class org.biojava.bio.AnnotationChanger extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - changer
      
      ChangeTable changer
    - properties
      
      Map properties
    - wrapped
      
      Annotation wrapped
- Class org.biojava.bio.AnnotationRenamer extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - mapper
      
      PropertyChanger mapper
    - properties
      
      Map properties
    - wrapped
      
      Annotation wrapped
- Class org.biojava.bio.BeanAsAnnotation extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - properties
      
      Map properties
- Class org.biojava.bio.BioError extends Error implements Serializable
- Class org.biojava.bio.BioException extends Exception implements Serializable
- Class org.biojava.bio.BioRuntimeException extends RuntimeException implements Serializable
- Class org.biojava.bio.MergeAnnotation extends AbstractChangeable implements Serializable
  - Serialized Fields
    - mergeSet
      
      List mergeSet
- Class org.biojava.bio.OverlayAnnotation extends AbstractChangeable implements Serializable
  - Serialized Fields
    - overlay
      
      Map overlay
    - parent
      
      Annotation parent
- Class org.biojava.bio.SimpleAnnotation extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - properties
      
      Map properties
      
      The properties map. This may be null if no property values have yet been set.
- Class org.biojava.bio.SmallAnnotation extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - properties
      
      Map properties
Package org.biojava.bio.alignment
- Class org.biojava.bio.alignment.SimpleAlignment extends AbstractSymbolList implements Serializable
  
  serialVersionUID:
  
  -1760075176220928440L
  - Serialized Fields
    - alphabet
      
      Alphabet alphabet
    - labels
      
      List<String> labels
    - labelToSymbolList
      
      LinkedHashMap<String,SymbolList> labelToSymbolList
    - length
      
      int length
    - score
      
      int score
Package org.biojava.bio.annodb
- Class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory extends Object implements Serializable
  - Serialized Fields
    - method
      
      Method method
Package org.biojava.bio.dist
- Class org.biojava.bio.dist.AbstractOrderNDistribution extends AbstractDistribution implements Serializable
  
  serialVersionUID:
  
  1406135308618188893L
  - Serialized Fields
    - alphabet
      
      Alphabet alphabet
    - firstA
      
      Alphabet firstA
    - lastA
      
      Alphabet lastA
    - nullModel
      
      Distribution nullModel
- Class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory extends Object implements Serializable
  - Serialization Methods
    - writeReplace
      
      private Object writeReplace() throws ObjectStreamException
      
      Throws:
      
      ObjectStreamException
- Class org.biojava.bio.dist.GapDistribution extends Unchangeable implements Serializable
  
  serialVersionUID:
  
  88622317L
  - Serialized Fields
    - alpha
      
      Alphabet alpha
- Class org.biojava.bio.dist.IndexedCount extends AbstractChangeable implements Serializable
  
  serialVersionUID:
  
  -1764931829553447679L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream stream) throws IOException, ClassNotFoundException
      
      Throws:
      
      IOException
      
      ClassNotFoundException
    - writeObject
      
      private void writeObject(ObjectOutputStream oos) throws IOException
      
      Throws:
      
      IOException
  - Serialized Fields
    - alpha
      
      FiniteAlphabet alpha
- Class org.biojava.bio.dist.PairDistribution extends AbstractChangeable implements Serializable
  - Serialized Fields
    - alphabet
      
      Alphabet alphabet
    - first
      
      Distribution first
    - second
      
      Distribution second
- Class org.biojava.bio.dist.SimpleDistribution extends AbstractDistribution implements Serializable
  
  serialVersionUID:
  
  7252850540926095728L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream stream) throws IOException, ClassNotFoundException
      
      Throws:
      
      IOException
      
      ClassNotFoundException
    - writeObject
      
      private void writeObject(ObjectOutputStream oos) throws IOException
      
      Throws:
      
      IOException
  - Serialized Fields
    - alpha
      
      FiniteAlphabet alpha
    - nullModel
      
      Distribution nullModel
- Class org.biojava.bio.dist.SimpleDistributionTrainer extends Object implements Serializable
  - Serialized Fields
    - c
      
      Map c
      
      Deprecated.
    - dis
      
      Distribution dis
      
      Deprecated.
- Class org.biojava.bio.dist.SimpleDistributionTrainerContext extends Object implements Serializable
  - Serialized Fields
    - distToTrainer
      
      Map distToTrainer
    - nullModelWeight
      
      double nullModelWeight
    - trainers
      
      Set trainers
- Class org.biojava.bio.dist.TranslatedDistribution extends AbstractChangeable implements Serializable
  - Serialized Fields
    - delegate
      
      Distribution delegate
    - other
      
      Distribution other
    - table
      
      ReversibleTranslationTable table
- Class org.biojava.bio.dist.UniformDistribution extends AbstractDistribution implements Serializable
  
  serialVersionUID:
  
  88454038L
  - Serialized Fields
    - alphabet
      
      FiniteAlphabet alphabet
    - nullModel
      
      Distribution nullModel
- Class org.biojava.bio.dist.UntrainableDistribution extends SimpleDistribution implements Serializable
Package org.biojava.bio.dp
- Class org.biojava.bio.dp.BaumWelchSampler extends AbstractTrainer implements Serializable
- Class org.biojava.bio.dp.BaumWelchTrainer extends AbstractTrainer implements Serializable
- Class org.biojava.bio.dp.DP.ReverseIterator extends Object implements Serializable
  - Serialized Fields
    - index
      
      int index
    - sym
      
      SymbolList sym
- Class org.biojava.bio.dp.IllegalTransitionException extends BioException implements Serializable
  - Serialized Fields
    - from
      
      State from
    - to
      
      State to
- Class org.biojava.bio.dp.MagicalState extends SimpleEmissionState implements Serializable
  - Serialization Methods
    - writeReplace
      
      private Object writeReplace() throws ObjectStreamException
      
      Throws:
      
      ObjectStreamException
- Class org.biojava.bio.dp.ProfileHMM extends SimpleMarkovModel implements Serializable
  - Serialized Fields
    - columns
      
      int columns
      
      The number of columns in this model.
    - deleteStates
      
      DotState[] deleteStates
      
      Delete states array.
      From 0 .. columns()-1 corresponding to indexes 1..columns().
    - insertStates
      
      EmissionState[] insertStates
      
      Insert states array.
      From 0 .. columns().
    - matchStates
      
      EmissionState[] matchStates
      
      Match states array.
      matchStates[0] == matchStates[columns+1] == magicalState().
- Class org.biojava.bio.dp.ScoreType.NullModel extends Object implements Serializable
- Class org.biojava.bio.dp.ScoreType.Odds extends Object implements Serializable
- Class org.biojava.bio.dp.ScoreType.Probability extends Object implements Serializable
- Class org.biojava.bio.dp.SimpleDotState extends FundamentalAtomicSymbol implements Serializable
- Class org.biojava.bio.dp.SimpleEmissionState extends AbstractChangeable implements Serializable
  - Serialized Fields
    - advance
      
      int[] advance
    - ann
      
      Annotation ann
    - dis
      
      Distribution dis
    - matches
      
      Alphabet matches
    - name
      
      String name
- Class org.biojava.bio.dp.SimpleMarkovModel extends AbstractChangeable implements Serializable
  
  serialVersionUID:
  
  -3043028839927615753L
  - Serialized Fields
    - emissionAlpha
      
      Alphabet emissionAlpha
    - magicalState
      
      MagicalState magicalState
    - stateAlpha
      
      FiniteAlphabet stateAlpha
    - transFrom
      
      Map transFrom
    - transTo
      
      Map transTo
    - transWeights
      
      Map transWeights
- Class org.biojava.bio.dp.SimpleModelInState extends FundamentalAtomicSymbol implements Serializable
  - Serialized Fields
    - model
      
      MarkovModel model
- Class org.biojava.bio.dp.SimpleModelTrainer extends SimpleDistributionTrainerContext implements Serializable
  - Serialized Fields
    - models
      
      Set models
- Class org.biojava.bio.dp.SimpleStatePath extends Unchangeable implements Serializable
  - Serialized Fields
    - delegate
      
      Alignment delegate
    - score
      
      double score
- Class org.biojava.bio.dp.SimpleWeightMatrix extends Object implements Serializable
  
  serialVersionUID:
  
  73394340224964858L
  - Serialized Fields
    - alpha
      
      Alphabet alpha
    - columns
      
      Distribution[] columns
- Class org.biojava.bio.dp.TrainerTransition extends Object implements Serializable
  - Serialized Fields
    - from
      
      State from
    - to
      
      State to
    - trainer
      
      TransitionTrainer trainer
- Class org.biojava.bio.dp.Transition extends Object implements Serializable
  - Serialized Fields
    - from
      
      State from
    - to
      
      State to
- Class org.biojava.bio.dp.WeightMatrixAnnotator extends Object implements Serializable
  - Serialized Fields
    - matrix
      
      WeightMatrix matrix
    - scoreType
      
      ScoreType scoreType
    - threshold
      
      double threshold
    - wmID
      
      String wmID
- Class org.biojava.bio.dp.WMAsMM extends AbstractChangeable implements Serializable
  - Serialized Fields
    - magicalState
      
      MagicalState magicalState
    - stateAlpha
      
      FiniteAlphabet stateAlpha
    - states
      
      EmissionState[] states
    - transFrom
      
      Map transFrom
    - transTo
      
      Map transTo
    - transWeights
      
      Map transWeights
    - wm
      
      WeightMatrix wm
Package org.biojava.bio.dp.onehead
- Class org.biojava.bio.dp.onehead.SingleDP extends DP implements Serializable
  - Serialized Fields
    - emissionsNull
      
      HashMap emissionsNull
    - emissionsOdds
      
      HashMap emissionsOdds
    - emissionsProb
      
      HashMap emissionsProb
- Class org.biojava.bio.dp.onehead.SingleDPMatrix extends Object implements Serializable
  - Serialized Fields
    - model
      
      MarkovModel model
    - score
      
      double score
    - scores
      
      double[][] scores
    - states
      
      State[] states
    - symList
      
      SymbolList[] symList
Package org.biojava.bio.dp.twohead
- Class org.biojava.bio.dp.twohead.DPInterpreter extends Object implements Serializable
  - Serialized Fields
    - dp
      
      DP dp
- Class org.biojava.bio.dp.twohead.EmissionCache extends Object implements Serializable
  - Serialized Fields
    - alpha
      
      Alphabet alpha
    - dsi
      
      int dsi
    - eMap
      
      Map eMap
    - gap
      
      Symbol[] gap
    - scoreType
      
      ScoreType scoreType
    - states
      
      State[] states
- Class org.biojava.bio.dp.twohead.PairDPMatrix extends Object implements Serializable
  - Serialized Fields
    - finalScore
      
      double finalScore
    - model
      
      MarkovModel model
    - scores
      
      double[][][] scores
    - seqs
      
      SymbolList[] seqs
    - states
      
      State[] states
- Class org.biojava.bio.dp.twohead.PairwiseDP extends DP implements Serializable
  - Serialized Fields
    - ccFactory
      
      CellCalculatorFactory ccFactory
    - emissionCache
      
      HashMap emissionCache
Package org.biojava.bio.molbio
- Class org.biojava.bio.molbio.RestrictionEnzyme extends Object implements Serializable
  - Serialized Fields
    - cutType
      
      int cutType
    - dsCutPositions
      
      int[] dsCutPositions
    - forwardRegex
      
      String forwardRegex
    - name
      
      String name
    - prototype
      
      RestrictionEnzyme prototype
    - reverseRegex
      
      String reverseRegex
    - site
      
      SymbolList site
    - size
      
      double size
    - summary
      
      String summary
    - usCutPositions
      
      int[] usCutPositions
- Class org.biojava.bio.molbio.RestrictionSite.Template extends StrandedFeature.Template implements Serializable
  - Serialized Fields
    - enzyme
      
      RestrictionEnzyme enzyme
      
      enzyme RestrictionEnzyme field.
Package org.biojava.bio.program.gff
- Class org.biojava.bio.program.gff.IgnoreRecordException extends Exception implements Serializable
Package org.biojava.bio.program.hmmer
- Class org.biojava.bio.program.hmmer.FullHmmerProfileHMM extends SimpleMarkovModel implements Serializable
  - Serialized Fields
    - c
      
      EmissionState c
    - hmmState
      
      ModelInState hmmState
    - j
      
      EmissionState j
    - n
      
      EmissionState n
- Class org.biojava.bio.program.hmmer.HmmerProfileHMM extends ProfileHMM implements Serializable
- Class org.biojava.bio.program.hmmer.ProfileEmissionState extends SimpleEmissionState implements Serializable
Package org.biojava.bio.program.homologene
- Class org.biojava.bio.program.homologene.DuplicateTaxonException extends BioException implements Serializable
Package org.biojava.bio.program.phred
- Class org.biojava.bio.program.phred.PhredFormat extends Object implements Serializable
  - Serialized Fields
    - lineWidth
      
      int lineWidth
      
      The line width for output.
    - mListeners
      
      Vector mListeners
- Class org.biojava.bio.program.phred.PhredSequence extends SimpleSequence implements Serializable
Package org.biojava.bio.program.ssaha
- Class org.biojava.bio.program.ssaha.SearchException extends Exception implements Serializable
Package org.biojava.bio.proteomics
- Class org.biojava.bio.proteomics.Protease extends Object implements Serializable
  - Serialization Methods
    - readResolve
      
      protected Object readResolve() throws ObjectStreamException
      
      Prevent duplication of the object during Serialization
      
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - cleavageResidues
      
      SymbolList cleavageResidues
    - endoProtease
      
      boolean endoProtease
    - name
      
      String name
    - notCleaveResidues
      
      SymbolList notCleaveResidues
Package org.biojava.bio.search
- Class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter extends Object implements Serializable
  - Serialized Fields
    - cachedOutcome
      
      TriState cachedOutcome
- Class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable
  - Serialized Fields
    - key
      
      Object key
    - test
      
      FilterTest test
- Class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable
  - Serialized Fields
    - key
      
      Object key
    - test
      
      FilterTest test
- Class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable
  - Serialized Fields
    - key
      
      Object key
    - test
      
      FilterTest test
- Class org.biojava.bio.search.BlastLikeSearchFilter.Not extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable
  - Serialized Fields
    - filter
      
      BlastLikeSearchFilter.AbstractBlastLikeSearchFilter filter
Package org.biojava.bio.seq
- Class org.biojava.bio.seq.CircularView extends ViewSequence implements Serializable
- Class org.biojava.bio.seq.ComponentFeature.Template extends StrandedFeature.Template implements Serializable
  - Serialized Fields
    - componentLocation
      
      Location componentLocation
    - componentSequence
      
      Sequence componentSequence
    - componentSequenceName
      
      String componentSequenceName
- Class org.biojava.bio.seq.Feature.Template extends Object implements Serializable
  - Serialized Fields
    - annotation
      
      Annotation annotation
    - location
      
      Location location
    - source
      
      String source
    - sourceTerm
      
      Term sourceTerm
    - type
      
      String type
    - typeTerm
      
      Term typeTerm
- Class org.biojava.bio.seq.FeatureFilter.And extends Object implements Serializable
  - Serialized Fields
    - c1
      
      FeatureFilter c1
    - c2
      
      FeatureFilter c2
- Class org.biojava.bio.seq.FeatureFilter.AnnotationContains extends FeatureFilter.ByAnnotationType implements Serializable
  - Serialized Fields
    - key
      
      Object key
    - value
      
      Object value
- Class org.biojava.bio.seq.FeatureFilter.ByAncestor extends Object implements Serializable
  - Serialized Fields
    - filter
      
      FeatureFilter filter
- Class org.biojava.bio.seq.FeatureFilter.ByAnnotation extends FeatureFilter.ByAnnotationType implements Serializable
  - Serialized Fields
    - key
      
      Object key
    - value
      
      Object value
- Class org.biojava.bio.seq.FeatureFilter.ByAnnotationType extends Object implements Serializable
  - Serialized Fields
    - type
      
      AnnotationType type
- Class org.biojava.bio.seq.FeatureFilter.ByChild extends Object implements Serializable
  - Serialized Fields
    - filter
      
      FeatureFilter filter
- Class org.biojava.bio.seq.FeatureFilter.ByClass extends Object implements Serializable
  - Serialized Fields
    - clazz
      
      Class clazz
- Class org.biojava.bio.seq.FeatureFilter.ByComponentName extends Object implements Serializable
  - Serialized Fields
    - cname
      
      String cname
- Class org.biojava.bio.seq.FeatureFilter.ByDescendant extends Object implements Serializable
  - Serialized Fields
    - filter
      
      FeatureFilter filter
- Class org.biojava.bio.seq.FeatureFilter.ByFeature extends Object implements Serializable
  - Serialized Fields
    - feature
      
      Feature feature
- Class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore extends Object implements Serializable
  - Serialized Fields
    - hashCode
      
      int hashCode
    - maxScore
      
      double maxScore
    - minScore
      
      double minScore
    - score
      
      double score
- Class org.biojava.bio.seq.FeatureFilter.ByParent extends Object implements Serializable
  - Serialized Fields
    - filter
      
      FeatureFilter filter
- Class org.biojava.bio.seq.FeatureFilter.BySequenceName extends Object implements Serializable
  - Serialized Fields
    - seqName
      
      String seqName
- Class org.biojava.bio.seq.FeatureFilter.BySource extends Object implements Serializable
  - Serialized Fields
    - source
      
      String source
- Class org.biojava.bio.seq.FeatureFilter.ByType extends Object implements Serializable
  - Serialized Fields
    - type
      
      String type
- Class org.biojava.bio.seq.FeatureFilter.ContainedByLocation extends Object implements Serializable
  - Serialized Fields
    - loc
      
      Location loc
- Class org.biojava.bio.seq.FeatureFilter.FrameFilter extends Object implements Serializable
  - Serialized Fields
    - frame
      
      FramedFeature.ReadingFrame frame
- Class org.biojava.bio.seq.FeatureFilter.HasAnnotation extends FeatureFilter.ByAnnotationType implements Serializable
  - Serialized Fields
    - key
      
      Object key
- Class org.biojava.bio.seq.FeatureFilter.Not extends Object implements Serializable
  - Serialized Fields
    - child
      
      FeatureFilter child
- Class org.biojava.bio.seq.FeatureFilter.OnlyChildren extends Object implements Serializable
  - Serialized Fields
    - filter
      
      FeatureFilter filter
- Class org.biojava.bio.seq.FeatureFilter.OnlyDescendants extends Object implements Serializable
  - Serialized Fields
    - filter
      
      FeatureFilter filter
- Class org.biojava.bio.seq.FeatureFilter.Or extends Object implements Serializable
  - Serialized Fields
    - c1
      
      FeatureFilter c1
    - c2
      
      FeatureFilter c2
- Class org.biojava.bio.seq.FeatureFilter.OverlapsLocation extends Object implements Serializable
  - Serialized Fields
    - loc
      
      Location loc
- Class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation extends Object implements Serializable
  - Serialized Fields
    - loc
      
      Location loc
- Class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation extends Object implements Serializable
  - Serialized Fields
    - loc
      
      Location loc
- Class org.biojava.bio.seq.FeatureFilter.StrandFilter extends Object implements Serializable
  - Serialized Fields
    - strand
      
      StrandedFeature.Strand strand
- Class org.biojava.bio.seq.FramedFeature.ReadingFrame extends Object implements Serializable
  - Serialized Fields
    - frame
      
      int frame
    - text
      
      String text
- Class org.biojava.bio.seq.FramedFeature.Template extends StrandedFeature.Template implements Serializable
  - Serialized Fields
    - readingFrame
      
      FramedFeature.ReadingFrame readingFrame
- Class org.biojava.bio.seq.MergeFeatureHolder extends AbstractFeatureHolder implements Serializable
  - Serialized Fields
    - featureHolders
      
      List featureHolders
- Class org.biojava.bio.seq.RemoteFeature.Template extends StrandedFeature.Template implements Serializable
  - Serialized Fields
    - regions
      
      List regions
    - resolver
      
      RemoteFeature.Resolver resolver
- Class org.biojava.bio.seq.SimpleFeatureHolder extends AbstractFeatureHolder implements Serializable
  - Serialized Fields
    - features
      
      List features
      
      The child features.
    - schema
      
      FeatureFilter schema
- Class org.biojava.bio.seq.SimpleFeatureRealizer extends Object implements Serializable
  - Serialized Fields
    - fallBack
      
      FeatureRealizer fallBack
    - templateToImpl
      
      List templateToImpl
- Class org.biojava.bio.seq.StrandedFeature.Strand extends Object implements Serializable
  - Serialization Methods
    - writeReplace
      
      private Object writeReplace() throws ObjectStreamException
      
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - text
      
      String text
    - token
      
      char token
    - value
      
      int value
- Class org.biojava.bio.seq.StrandedFeature.Template extends Feature.Template implements Serializable
  - Serialized Fields
    - strand
      
      StrandedFeature.Strand strand
Package org.biojava.bio.seq.db
- Class org.biojava.bio.seq.db.AnnotatedSequenceDB extends AbstractSequenceDB implements Serializable
  - Serialized Fields
    - annotator
      
      SequenceAnnotator annotator
    - parent
      
      SequenceDB parent
- Class org.biojava.bio.seq.db.CachingSequenceDB extends SequenceDBWrapper implements Serializable
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Throws:
      
      IOException
      
      ClassNotFoundException
- Class org.biojava.bio.seq.db.HashSequenceDB extends AbstractSequenceDB implements Serializable
  - Serialized Fields
    - idMaker
      
      IDMaker idMaker
      
      An object to extract an ID for a sequence.
    - name
      
      String name
      
      The name of this sequence database.
    - sequenceByID
      
      Map sequenceByID
      
      The sequence-by-id map.
- Class org.biojava.bio.seq.db.IDMaker.ByName extends Object implements Serializable
  - Serialization Methods
    - writeReplace
      
      private Object writeReplace() throws IOException
      
      Throws:
      
      IOException
- Class org.biojava.bio.seq.db.IDMaker.ByURN extends Object implements Serializable
  - Serialization Methods
    - writeReplace
      
      private Object writeReplace() throws IOException
      
      Throws:
      
      IOException
- Class org.biojava.bio.seq.db.IllegalIDException extends BioException implements Serializable
- Class org.biojava.bio.seq.db.IndexedSequenceDB extends AbstractSequenceDB implements Serializable
  - Serialized Fields
    - idMaker
      
      IDMaker idMaker
    - indexStore
      
      IndexStore indexStore
- Class org.biojava.bio.seq.db.SequenceDBWrapper extends AbstractSequenceDB implements Serializable
  - Serialized Fields
    - parent
      
      SequenceDB parent
- Class org.biojava.bio.seq.db.SubSequenceDB extends SequenceDBWrapper implements Serializable
  - Serialized Fields
    - ids
      
      Set ids
- Class org.biojava.bio.seq.db.TabIndexStore extends Object implements Serializable
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Throws:
      
      IOException
      
      ClassNotFoundException
  - Serialized Fields
    - files
      
      Set files
    - format
      
      SequenceFormat format
    - indexFile
      
      File indexFile
    - name
      
      String name
    - sbFactory
      
      SequenceBuilderFactory sbFactory
    - seqFileIndex
      
      File[] seqFileIndex
    - storeFile
      
      File storeFile
    - symbolParser
      
      SymbolTokenization symbolParser
- Class org.biojava.bio.seq.db.ViewingSequenceDB extends SequenceDBWrapper implements Serializable
Package org.biojava.bio.seq.homol
- Class org.biojava.bio.seq.homol.HomologyFeature.Template extends StrandedFeature.Template implements Serializable
  - Serialized Fields
    - homology
      
      Homology homology
- Class org.biojava.bio.seq.homol.SimilarityPairFeature.Template extends StrandedFeature.Template implements Serializable
  - Serialized Fields
    - alignment
      
      Alignment alignment
      
      alignment Alignment field.
    - score
      
      double score
      
      score of the search which produced the alignment.
    - sibling
      
      SimilarityPairFeature sibling
      
      sibling SimilarityPairFeature field. May be null if the reciprocal SimilarityPairFeature has not yet been created.
Package org.biojava.bio.seq.impl
- Class org.biojava.bio.seq.impl.RevCompSequence extends SimpleSequence implements Serializable
  - Serialized Fields
    - origSeq
      
      Sequence origSeq
    - pfh
      
      ProjectedFeatureHolder pfh
- Class org.biojava.bio.seq.impl.SimpleFeature extends AbstractChangeable implements Serializable
  - Serialized Fields
    - annotation
      
      Annotation annotation
      
      The annotation object. This is lazily instantiated.
    - featureHolder
      
      SimpleFeatureHolder featureHolder
      
      The FeatureHolder that we will delegate the FeatureHolder interface too. This is lazily instantiated.
    - loc
      
      Location loc
      
      The location of this feature.
    - parent
      
      FeatureHolder parent
      
      Our parent FeatureHolder.
    - source
      
      String source
      
      The source of this feature - the program that generated it. This is included for cheap interoperability with GFF.
    - sourceTerm
      
      Term sourceTerm
    - type
      
      String type
      
      The type of this feature - something like Exon. This is included for cheap interoperability with GFF.
    - typeTerm
      
      Term typeTerm
- Class org.biojava.bio.seq.impl.SimpleFramedFeature extends SimpleStrandedFeature implements Serializable
  - Serialized Fields
    - readingFrame
      
      FramedFeature.ReadingFrame readingFrame
- Class org.biojava.bio.seq.impl.SimpleGappedSequence extends SimpleGappedSymbolList implements Serializable
  
  serialVersionUID:
  
  -791305118810523245L
  - Serialized Fields
    - createOnUnderlying
      
      boolean createOnUnderlying
    - features
      
      MergeFeatureHolder features
    - localFeatures
      
      SimpleFeatureHolder localFeatures
    - projectedFeatures
      
      FeatureHolder projectedFeatures
    - sequence
      
      Sequence sequence
- Class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext extends ReparentContext implements Serializable
  
  serialVersionUID:
  
  8878073952684354286L
- Class org.biojava.bio.seq.impl.SimpleHomologyFeature extends SimpleStrandedFeature implements Serializable
  - Serialized Fields
    - homology
      
      Homology homology
- Class org.biojava.bio.seq.impl.SimpleRemoteFeature extends SimpleStrandedFeature implements Serializable
  - Serialized Fields
    - regions
      
      List regions
    - resolver
      
      RemoteFeature.Resolver resolver
- Class org.biojava.bio.seq.impl.SimpleRestrictionSite extends SimpleStrandedFeature implements Serializable
  - Serialized Fields
    - enzyme
      
      RestrictionEnzyme enzyme
    - position
      
      int position
- Class org.biojava.bio.seq.impl.SimpleSequence extends AbstractChangeable implements Serializable
  
  serialVersionUID:
  
  -8681680737943980721L
  - Serialized Fields
    - annotation
      
      Annotation annotation
    - featureHolder
      
      SimpleFeatureHolder featureHolder
    - name
      
      String name
    - symList
      
      SymbolList symList
      
      Delegate SymbolList.
    - urn
      
      String urn
- Class org.biojava.bio.seq.impl.SimpleSequenceFactory extends Object implements Serializable
  - Serialized Fields
    - realizer
      
      FeatureRealizer realizer
- Class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature extends SimpleStrandedFeature implements Serializable
  - Serialized Fields
    - alignment
      
      Alignment alignment
    - score
      
      double score
    - sibling
      
      SimilarityPairFeature sibling
- Class org.biojava.bio.seq.impl.SimpleStrandedFeature extends SimpleFeature implements Serializable
  - Serialized Fields
    - strand
      
      StrandedFeature.Strand strand
- Class org.biojava.bio.seq.impl.SubSequence extends Object implements Serializable
  - Serialized Fields
    - annotation
      
      Annotation annotation
    - name
      
      String name
    - parent
      
      Sequence parent
    - parentLocation
      
      RangeLocation parentLocation
    - symbols
      
      SymbolList symbols
    - uri
      
      String uri
- Class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext extends ReparentContext implements Serializable
  - Serialized Fields
    - clippingFilter
      
      FeatureFilter clippingFilter
    - parentLocation
      
      RangeLocation parentLocation
    - remoteLocationFilter
      
      FeatureFilter remoteLocationFilter
- Class org.biojava.bio.seq.impl.ViewSequence extends Unchangeable implements Serializable
  
  serialVersionUID:
  
  9866447L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream s) throws IOException, ClassNotFoundException
      
      Throws:
      
      IOException
      
      ClassNotFoundException
  - Serialized Fields
    - addedFeatures
      
      SimpleFeatureHolder addedFeatures
    - anno
      
      Annotation anno
      
      Our annotation.
    - exposedFeatures
      
      MergeFeatureHolder exposedFeatures
      
      FeatureHolder support
    - name
      
      String name
      
      IDs
    - seqDelegate
      
      Sequence seqDelegate
      
      Delegate Sequence.
    - urn
      
      String urn
Package org.biojava.bio.seq.io
- Class org.biojava.bio.seq.io.AlternateTokenization extends Unchangeable implements Serializable
  - Serialized Fields
    - alphabet
      
      Alphabet alphabet
    - caseSensitive
      
      boolean caseSensitive
    - initiated
      
      boolean initiated
    - symbolsToStrings
      
      Map symbolsToStrings
    - width
      
      int width
- Class org.biojava.bio.seq.io.CharacterTokenization extends Unchangeable implements Serializable
  - Serialized Fields
    - alphabet
      
      Alphabet alphabet
    - caseSensitive
      
      boolean caseSensitive
    - charactersToSymbols
      
      Map charactersToSymbols
    - symbolsToCharacters
      
      Map symbolsToCharacters
- Class org.biojava.bio.seq.io.CrossProductTokenization extends WordTokenization implements Serializable
  - Serialized Fields
    - subTokenizations
      
      List subTokenizations
- Class org.biojava.bio.seq.io.DoubleTokenization extends WordTokenization implements Serializable
- Class org.biojava.bio.seq.io.EmblLikeFormat extends Object implements Serializable
  - Serialized Fields
    - elideSymbols
      
      boolean elideSymbols
      
      Deprecated.
    - mListeners
      
      Vector mListeners
      
      Deprecated.
- Class org.biojava.bio.seq.io.EmblProcessor.Factory extends Object implements Serializable
  - Serialized Fields
    - delegateFactory
      
      SequenceBuilderFactory delegateFactory
- Class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory extends Object implements Serializable
  - Serialized Fields
    - delegateFactory
      
      SequenceBuilderFactory delegateFactory
- Class org.biojava.bio.seq.io.FastaFormat extends Object implements Serializable
  - Serialized Fields
    - lineWidth
      
      int lineWidth
      
      Deprecated.
      
      The line width for output.
    - mListeners
      
      Vector mListeners
      
      Deprecated.
- Class org.biojava.bio.seq.io.GenbankFormat extends Object implements Serializable
  - Serialized Fields
    - elideSymbols
      
      boolean elideSymbols
      
      Deprecated.
    - mListeners
      
      Vector mListeners
      
      Deprecated.
- Class org.biojava.bio.seq.io.GenbankProcessor.Factory extends Object implements Serializable
  - Serialized Fields
    - delegateFactory
      
      SequenceBuilderFactory delegateFactory
- Class org.biojava.bio.seq.io.GenbankXmlFormat extends GenbankFormat implements Serializable
  - Serialized Fields
    - m_handler
      
      org.biojava.bio.seq.io.GenbankXmlFormat.GenbankXmlHandler m_handler
      
      Deprecated.
    - m_parsed
      
      boolean m_parsed
      
      Deprecated.
    - m_sequenceIndex
      
      int m_sequenceIndex
      
      Deprecated.
    - m_xmlParser
      
      SAXParser m_xmlParser
      
      Deprecated.
- Class org.biojava.bio.seq.io.GenpeptFormat extends GenbankFormat implements Serializable
- Class org.biojava.bio.seq.io.IntegerTokenization extends WordTokenization implements Serializable
- Class org.biojava.bio.seq.io.NameTokenization extends WordTokenization implements Serializable
  - Serialized Fields
    - caseSensitive
      
      boolean caseSensitive
- Class org.biojava.bio.seq.io.OrganismParser.Factory extends Object implements Serializable
  - Serialized Fields
    - commonNameKey
      
      String commonNameKey
    - delegateFactory
      
      SequenceBuilderFactory delegateFactory
    - ncbiTaxonKey
      
      String ncbiTaxonKey
    - sciNameKey
      
      String sciNameKey
    - taxonFactory
      
      TaxonFactory taxonFactory
    - taxonParser
      
      TaxonParser taxonParser
- Class org.biojava.bio.seq.io.ParseException extends BioException implements Serializable
- Class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory extends Object implements Serializable
  - Serialized Fields
    - delegateFactory
      
      SequenceBuilderFactory delegateFactory
- Class org.biojava.bio.seq.io.ReferenceAnnotation extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - properties
      
      Map properties
      
      Deprecated.
      
      The properties map. This may be null if no property values have yet been set.
- Class org.biojava.bio.seq.io.SubIntegerTokenization extends WordTokenization implements Serializable
- Class org.biojava.bio.seq.io.SwissprotProcessor.Factory extends Object implements Serializable
  - Serialized Fields
    - delegateFactory
      
      SequenceBuilderFactory delegateFactory
- Class org.biojava.bio.seq.io.WordTokenization extends Unchangeable implements Serializable
  - Serialized Fields
    - alphabet
      
      Alphabet alphabet
Package org.biojava.bio.seq.projection
- Class org.biojava.bio.seq.projection.ProjectedFeatureHolder extends AbstractFeatureHolder implements Serializable
  - Serialized Fields
    - context
      
      ProjectionContext context
    - topLevelFeatures
      
      FeatureHolder topLevelFeatures
- Class org.biojava.bio.seq.projection.ReparentContext extends Object implements Serializable
  - Serialized Fields
    - parent
      
      FeatureHolder parent
    - wrapped
      
      FeatureHolder wrapped
- Class org.biojava.bio.seq.projection.TranslateFlipContext extends ReparentContext implements Serializable
  - Serialized Fields
    - oppositeStrand
      
      boolean oppositeStrand
    - translation
      
      int translation
Package org.biojava.bio.symbol
- Class org.biojava.bio.symbol.AbstractAlphabet extends AbstractChangeable implements Serializable
  
  serialVersionUID:
  
  -3043128839927615753L
  - Serialization Methods
    - readResolve
      
      protected Object readResolve() throws ObjectStreamException
      
      To prevent duplication of a what should be a single instance of an existing alphabet. This method was written as protected so that subclasses even from other packages will inherit it. It should only be overridden with care.
      
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - ambCache
      
      Map ambCache
    - registered
      
      boolean registered
    - tokenizationsByName
      
      Map tokenizationsByName
- Class org.biojava.bio.symbol.AbstractLocation extends Object implements Serializable
- Class org.biojava.bio.symbol.AbstractRangeLocation extends AbstractLocation implements Serializable
- Class org.biojava.bio.symbol.ChunkedSymbolList extends AbstractSymbolList implements Serializable
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream stream) throws IOException, ClassNotFoundException
      
      Throws:
      
      IOException
      
      ClassNotFoundException
  - Serialized Fields
    - alpha
      
      Alphabet alpha
    - chunks
      
      SymbolList[] chunks
    - chunkSize
      
      int chunkSize
    - length
      
      int length
- Class org.biojava.bio.symbol.DNAAmbPack extends Object implements Serializable
  - Serialized Fields
    - syms
      
      Symbol[] syms
- Class org.biojava.bio.symbol.DNANoAmbPack extends Object implements Serializable
  - Serialized Fields
    - placeHolder
      
      byte placeHolder
- Class org.biojava.bio.symbol.DoubleAlphabet extends Unchangeable implements Serializable
  - Serialization Methods
    - writeReplace
      
      private Object writeReplace() throws ObjectStreamException
      
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - alphabets
      
      List alphabets
    - doubleToSym
      
      WeakValueHashMap doubleToSym
- Class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange extends Unchangeable implements Serializable
  - Serialized Fields
    - matches
      
      Alphabet matches
    - maxVal
      
      double maxVal
    - minVal
      
      double minVal
- Class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol extends Unchangeable implements Serializable
  - Serialized Fields
    - matches
      
      Alphabet matches
    - val
      
      double val
- Class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet extends Unchangeable implements Serializable
  - Serialization Methods
    - readResolve
      
      protected Object readResolve() throws ObjectStreamException
      
      To prevent duplication of a what should be a single instance of an existing alphabet. This method was written as protected so that subclasses even from other packages will inherit it. It should only be overridden with care.
      
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - max
      
      double max
    - min
      
      double min
    - name
      
      String name
- Class org.biojava.bio.symbol.DummySymbolList extends AbstractSymbolList implements Serializable
  - Serialized Fields
    - alpha
      
      Alphabet alpha
    - length
      
      int length
    - sym
      
      Symbol sym
- Class org.biojava.bio.symbol.Edit extends Object implements Serializable
  - Serialized Fields
    - length
      
      int length
    - pos
      
      int pos
    - props
      
      Map<String,Object> props
    - replacement
      
      SymbolList replacement
- Class org.biojava.bio.symbol.FundamentalAtomicSymbol extends AbstractSymbol implements Serializable
  - Serialized Fields
    - annotation
      
      Annotation annotation
    - name
      
      String name
- Class org.biojava.bio.symbol.FuzzyLocation extends AbstractRangeLocation implements Serializable
  - Serialized Fields
    - innerMax
      
      int innerMax
    - innerMin
      
      int innerMin
    - mIsMaxFuzzy
      
      boolean mIsMaxFuzzy
    - mIsMinFuzzy
      
      boolean mIsMinFuzzy
    - outerMax
      
      int outerMax
    - outerMin
      
      int outerMin
    - resolver
      
      FuzzyLocation.RangeResolver resolver
- Class org.biojava.bio.symbol.FuzzyPointLocation extends AbstractLocation implements Serializable
  - Serialized Fields
    - max
      
      int max
    - min
      
      int min
    - resolver
      
      FuzzyPointLocation.PointResolver resolver
- Class org.biojava.bio.symbol.IllegalAlphabetException extends BioException implements Serializable
- Class org.biojava.bio.symbol.IllegalSymbolException extends BioException implements Serializable
  - Serialized Fields
    - sym
      
      Symbol sym
- Class org.biojava.bio.symbol.IntegerAlphabet extends Unchangeable implements Serializable
  - Serialization Methods
    - writeReplace
      
      private Object writeReplace() throws ObjectStreamException
      
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - intToSym
      
      WeakValueHashMap intToSym
      
      Canonicalization map for ints and references to symbols.
- Class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol extends Unchangeable implements Serializable
  - Serialized Fields
    - matches
      
      Alphabet matches
    - val
      
      int val
- Class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet extends AbstractAlphabet implements Serializable
  - Serialized Fields
    - max
      
      int max
    - min
      
      int min
    - name
      
      String name
- Class org.biojava.bio.symbol.MergeLocation extends RangeLocation implements Serializable
  - Serialized Fields
    - componentLocations
      
      List componentLocations
- Class org.biojava.bio.symbol.PackedSymbolList extends AbstractSymbolList implements Serializable
  - Serialized Fields
    - currentMax
      
      int currentMax
    - currentMin
      
      int currentMin
    - currentWord
      
      long currentWord
    - length
      
      int length
    - mask
      
      byte mask
    - packing
      
      Packing packing
    - syms
      
      long[] syms
    - symsPerElement
      
      byte symsPerElement
    - wordsize
      
      int wordsize
- Class org.biojava.bio.symbol.PointLocation extends AbstractRangeLocation implements Serializable
  - Serialized Fields
    - point
      
      int point
      
      The actual index contained.
- Class org.biojava.bio.symbol.RangeLocation extends AbstractRangeLocation implements Serializable
  - Serialized Fields
    - max
      
      int max
      
      The maximum point contained.
    - min
      
      int min
      
      The minimum point contained.
- Class org.biojava.bio.symbol.SimpleAlphabet extends AbstractAlphabet implements Serializable
  
  serialVersionUID:
  
  216254146L
  - Serialized Fields
    - alphabets
      
      List alphabets
      
      A list of alphabets that make up this one - a singleton list containing this.
    - annotation
      
      Annotation annotation
    - name
      
      String name
    - symbols
      
      Set symbols
- Class org.biojava.bio.symbol.SimpleAtomicSymbol extends org.biojava.bio.symbol.AbstractSimpleBasisSymbol implements Serializable
  - Serialization Methods
    - writeReplace
      
      private Object writeReplace()
- Class org.biojava.bio.symbol.SimpleGappedSymbolList extends AbstractSymbolList implements Serializable
  
  serialVersionUID:
  
  4258621048300499709L
  - Serialized Fields
    - alpha
      
      Alphabet alpha
      
      The Alphabet - the same as source but guaranteed to include the gap character.
    - blocks
      
      List<SimpleGappedSymbolList.Block> blocks
      
      The list of ungapped blocks that align between source and this view.
    - length
      
      int length
      
      The total length of the alignment - necessary to allow leading & trailing gaps.
    - source
      
      SymbolList source
      
      The SymbolList to view.
- Class org.biojava.bio.symbol.SimpleGappedSymbolList.Block extends Object implements Serializable
  
  serialVersionUID:
  
  4090888450309921439L
  - Serialized Fields
    - sourceEnd
      
      int sourceEnd
    - sourceStart
      
      int sourceStart
    - viewEnd
      
      int viewEnd
    - viewStart
      
      int viewStart
- Class org.biojava.bio.symbol.SimpleGeneticCodeTable extends SimpleManyToOneTranslationTable implements Serializable
  - Serialized Fields
    - description
      
      String description
    - table_num
      
      int table_num
- Class org.biojava.bio.symbol.SimpleManyToOneTranslationTable extends AbstractManyToOneTranslationTable implements Serializable
  - Serialized Fields
    - revMap
      
      Map revMap
    - source
      
      FiniteAlphabet source
    - target
      
      Alphabet target
    - transMap
      
      Map transMap
- Class org.biojava.bio.symbol.SimpleReversibleTranslationTable extends AbstractReversibleTranslationTable implements Serializable
  - Serialized Fields
    - revMap
      
      Map revMap
    - source
      
      FiniteAlphabet source
    - target
      
      Alphabet target
    - transMap
      
      Map transMap
- Class org.biojava.bio.symbol.SimpleSymbolList extends AbstractSymbolList implements Serializable
  
  serialVersionUID:
  
  -9015317520644706924L
  - Serialized Fields
    - alphabet
      
      Alphabet alphabet
    - isView
      
      boolean isView
    - length
      
      int length
    - referenceSymbolList
      
      SymbolList referenceSymbolList
    - symbols
      
      Symbol[] symbols
    - viewOffset
      
      int viewOffset
- Class org.biojava.bio.symbol.SimpleTranslationTable extends org.biojava.bio.symbol.AbstractTranslationTable implements Serializable
  - Serialized Fields
    - source
      
      FiniteAlphabet source
    - target
      
      Alphabet target
    - transMap
      
      Map transMap
- Class org.biojava.bio.symbol.SingletonAlphabet extends AbstractAlphabet implements Serializable
  - Serialized Fields
    - alphabets
      
      List alphabets
    - sym
      
      AtomicSymbol sym
- Class org.biojava.bio.symbol.SuffixTree extends Object implements Serializable
  - Serialized Fields
    - alphabet
      
      FiniteAlphabet alphabet
    - counts
      
      List counts
    - indexer
      
      AlphabetIndex indexer
    - root
      
      SuffixTree.SuffixNode root
- Class org.biojava.bio.symbol.SuffixTree.SuffixNode extends Object implements Serializable
Package org.biojava.bio.taxa
- Class org.biojava.bio.taxa.CircularReferenceException extends BioException implements Serializable
Package org.biojava.directory
- Class org.biojava.directory.ProviderNotFoundException extends RegistryException implements Serializable
- Class org.biojava.directory.RegistryException extends Exception implements Serializable
Package org.biojava.ontology
- Class org.biojava.ontology.AlreadyExistsException extends OntologyException implements Serializable
- Class org.biojava.ontology.DefaultOps extends Object implements Serializable
- Class org.biojava.ontology.InvalidTermException extends OntologyException implements Serializable
- Class org.biojava.ontology.Ontology.Impl extends AbstractChangeable implements Serializable
  
  serialVersionUID:
  
  -8064461497813727957L
  - Serialized Fields
    - description
      
      String description
    - localRemoteTerms
      
      Set<Term> localRemoteTerms
    - name
      
      String name
    - objectTriples
      
      Map<Term,Set<Triple>> objectTriples
    - ops
      
      OntologyOps ops
    - relationTriples
      
      Map<Term,Set<Triple>> relationTriples
    - remoteTerms
      
      Map<Term,RemoteTerm> remoteTerms
    - subjectTriples
      
      Map<Term,Set<Triple>> subjectTriples
    - terms
      
      Map<String,Term> terms
    - triples
      
      Set<Triple> triples
- Class org.biojava.ontology.OntologyException extends Exception implements Serializable
- Class org.biojava.ontology.OntologyTerm.Impl extends AbstractChangeable implements Serializable
  - Serialized Fields
    - ontology
      
      Ontology ontology
    - synonyms
      
      Set synonyms
    - target
      
      Ontology target
- Class org.biojava.ontology.RemoteTerm.Impl extends AbstractTerm implements Serializable
  
  serialVersionUID:
  
  922700041939183676L
  - Serialized Fields
    - name
      
      String name
    - ontology
      
      Ontology ontology
    - remoteTerm
      
      Term remoteTerm
    - synonyms
      
      Set synonyms
- Class org.biojava.ontology.Term.Impl extends AbstractTerm implements Serializable
  
  serialVersionUID:
  
  6561668917514377417L
  - Serialized Fields
    - annotation
      
      Annotation annotation
    - name
      
      String name
    - ontology
      
      Ontology ontology
    - synonyms
      
      Set<Object> synonyms
- Class org.biojava.ontology.Triple.Impl extends Unchangeable implements Serializable
  
  serialVersionUID:
  
  3807331980372839221L
  - Serialized Fields
    - description
      
      String description
    - name
      
      String name
    - object
      
      Term object
    - predicate
      
      Term predicate
    - subject
      
      Term subject
    - synonyms
      
      Set<Object> synonyms
- Class org.biojava.ontology.Variable.Impl extends Term.Impl implements Serializable
Package org.biojava.stats.svm
- Class org.biojava.stats.svm.CachingKernel extends NestedKernel implements Serializable
- Class org.biojava.stats.svm.DiagonalAddKernel extends NestedKernel implements Serializable
  - Serialized Fields
    - lambda
      
      double lambda
      
      The scale vactor.
    - negClass
      
      Set negClass
    - posClass
      
      Set posClass
- Class org.biojava.stats.svm.DiagonalCachingKernel extends NestedKernel implements Serializable
- Class org.biojava.stats.svm.LinearKernel extends Object implements Serializable
- Class org.biojava.stats.svm.ListSumKernel extends NestedKernel implements Serializable
- Class org.biojava.stats.svm.NestedKernel extends Object implements Serializable
  - Serialized Fields
    - nested
      
      SVMKernel nested
      
      The SVMKernel being wrapped.
- Class org.biojava.stats.svm.NormalizingKernel extends NestedKernel implements Serializable
- Class org.biojava.stats.svm.PolynomialKernel extends NestedKernel implements Serializable
  - Serialized Fields
    - a
      
      double a
    - c
      
      double c
    - order
      
      double order
- Class org.biojava.stats.svm.RadialBaseKernel extends NestedKernel implements Serializable
  - Serialized Fields
    - width
      
      double width
- Class org.biojava.stats.svm.SparseVector extends Object implements Serializable
  - Serialized Fields
    - keys
      
      int[] keys
    - size
      
      int size
    - values
      
      double[] values
- Class org.biojava.stats.svm.SparseVector.NormalizingKernel extends Object implements Serializable
  - Serialized Fields
    - s
      
      SparseVector s
      
      The sparse vector that performes the normalization.
- Class org.biojava.stats.svm.TrainingEvent extends EventObject implements Serializable
Package org.biojava.stats.svm.tools
- Class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier extends JComponent implements Serializable
  - Serialized Fields
    - addPos
      
      boolean addPos
    - kernel
      
      SVMKernel kernel
    - model
      
      SVMClassifierModel model
    - negPaint
      
      Paint negPaint
    - negShape
      
      Shape negShape
    - plainPaint
      
      Paint plainPaint
    - posPaint
      
      Paint posPaint
    - posShape
      
      Shape posShape
    - svPaint
      
      Paint svPaint
    - target
      
      SVMTarget target
- Class org.biojava.stats.svm.tools.SuffixTreeKernel extends Object implements Serializable
  - Serialized Fields
    - depthScaler
      
      SuffixTreeKernel.DepthScaler depthScaler
      
      The DepthScaler that will scale each sub-space. This defaults to UniformScaler.
- Class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar extends Object implements Serializable
  - Serialized Fields
    - a
      
      SuffixTreeKernel.DepthScaler a
    - b
      
      SuffixTreeKernel.DepthScaler b
- Class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler extends Object implements Serializable
- Class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar extends Object implements Serializable
  - Serialized Fields
    - bSet
      
      BitSet bSet
- Class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler extends Object implements Serializable
Package org.biojava.utils
- Class org.biojava.utils.AssertionFailure extends AssertionError implements Serializable
- Class org.biojava.utils.ChangeEvent extends EventObject implements Serializable
  - Serialized Fields
    - chain
      
      ChangeEvent chain
    - change
      
      Object change
    - previous
      
      Object previous
    - type
      
      ChangeType type
- Class org.biojava.utils.ChangeType extends Object implements Serializable
  - Serialization Methods
    - writeReplace
      
      private Object writeReplace()
      
      Make a placeholder for this object in a serialized stream.
  - Serialized Fields
    - name
      
      String name
    - ourField
      
      Field ourField
    - superType
      
      ChangeType superType
- Class org.biojava.utils.ChangeVetoException extends RuntimeException implements Serializable
  - Serialized Fields
    - change
      
      ChangeEvent change
- Class org.biojava.utils.CommitFailure extends Exception implements Serializable
- Class org.biojava.utils.ListTools extends Object implements Serializable
- Class org.biojava.utils.ListTools.Doublet extends AbstractList implements Serializable
  - Serialized Fields
    - a
      
      Object a
    - b
      
      Object b
- Class org.biojava.utils.ListTools.Triplet extends AbstractList implements Serializable
  - Serialized Fields
    - a
      
      Object a
    - b
      
      Object b
    - c
      
      Object c
- Class org.biojava.utils.ParseErrorEvent extends EventObject implements Serializable
  - Serialized Fields
    - mMessage
      
      String mMessage
- Class org.biojava.utils.ParserException extends Exception implements Serializable
  - Serialized Fields
    - character
      
      int character
    - line
      
      String line
    - lineNumber
      
      int lineNumber
    - locator
      
      String locator
- Class org.biojava.utils.ProcessTimeoutException extends Exception implements Serializable
  - Serialized Fields
    - returnCode
      
      int returnCode
- Class org.biojava.utils.SingletonList extends AbstractList implements Serializable
  - Serialized Fields
    - obj
      
      Object obj
- Class org.biojava.utils.SmallMap extends AbstractMap implements Serializable
  - Serialized Fields
    - mappings
      
      Object[] mappings
    - numMappings
      
      int numMappings
- Class org.biojava.utils.StaticMemberPlaceHolder extends Object implements Serializable
  - Serialization Methods
    - readResolve
      
      public Object readResolve() throws ObjectStreamException
      
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - className
      
      String className
    - fieldName
      
      String fieldName
- Class org.biojava.utils.TypedProperties extends Properties implements Serializable
Package org.biojava.utils.automata
- Class org.biojava.utils.automata.AutomatonException extends BioException implements Serializable
Package org.biojava.utils.candy
- Class org.biojava.utils.candy.CandyException extends Exception implements Serializable
Package org.biojava.utils.lsid
- Class org.biojava.utils.lsid.LifeScienceIdentifier extends Object implements Serializable
  
  serialVersionUID:
  
  8478038493421763123L
  - Serialized Fields
    - authorityId
      
      String authorityId
    - namespaceId
      
      String namespaceId
    - objectId
      
      String objectId
    - revisionId
      
      String revisionId
- Class org.biojava.utils.lsid.LifeScienceIdentifierParseException extends Exception implements Serializable
Package org.biojava.utils.regex
- Class org.biojava.utils.regex.RegexException extends BioException implements Serializable
Package org.biojava.utils.xml
- Class org.biojava.utils.xml.AppException extends Exception implements Serializable
Package org.biojavax
- Class org.biojavax.CrossReferenceResolutionException extends Exception implements Serializable
- Class org.biojavax.EmptyRichAnnotation extends Unchangeable implements Serializable
  - Serialization Methods
    - writeReplace
      
      private Object writeReplace() throws ObjectStreamException
      
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - emptyNotes
      
      Note[] emptyNotes
Package org.biojavax.bio.alignment
Package org.biojavax.bio.alignment.blast
- Class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - param
      
      HashMap<String,String> param
- Class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - alignFormat
      
      String alignFormat
    - alignNumbers
      
      int alignNumbers
    - descNumbers
      
      int descNumbers
    - out
      
      HashMap<String,String> out
    - outFormat
      
      String outFormat
Package org.biojavax.bio.seq
- Class org.biojavax.bio.seq.RichFeature.Template extends Feature.Template implements Serializable
  - Serialized Fields
    - featureRelationshipSet
      
      Set featureRelationshipSet
    - rankedCrossRefs
      
      Set rankedCrossRefs
Package org.biojavax.ga.exception
- Class org.biojavax.ga.exception.IllegalOrganismException extends Exception implements Serializable
Package org.biojavax.ga.util
- Class org.biojavax.ga.util.WeightedSet extends AbstractSet implements Serializable
  - Serialized Fields
    - key2Weight
      
      HashMap key2Weight
    - totalWeight
      
      double totalWeight

Serialized Form

Package org.biojava.bibliography

Class org.biojava.bibliography.BibRefException extends Exception implements Serializable

Package org.biojava.bio

Class org.biojava.bio.AbstractAnnotation extends AbstractChangeable implements Serializable

Class org.biojava.bio.AnnotationChanger extends AbstractAnnotation implements Serializable

Serialized Fields

changer

properties

wrapped

Class org.biojava.bio.AnnotationRenamer extends AbstractAnnotation implements Serializable

Serialized Fields

mapper

properties

wrapped

Class org.biojava.bio.BeanAsAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

properties

Class org.biojava.bio.BioError extends Error implements Serializable

Class org.biojava.bio.BioException extends Exception implements Serializable

Class org.biojava.bio.BioRuntimeException extends RuntimeException implements Serializable

Class org.biojava.bio.MergeAnnotation extends AbstractChangeable implements Serializable

Serialized Fields

mergeSet

Class org.biojava.bio.OverlayAnnotation extends AbstractChangeable implements Serializable

Serialized Fields

overlay

parent

Class org.biojava.bio.SimpleAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

properties

Class org.biojava.bio.SmallAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

properties

Package org.biojava.bio.alignment

Class org.biojava.bio.alignment.SimpleAlignment extends AbstractSymbolList implements Serializable

Serialized Fields

alphabet

labels

labelToSymbolList

length

score

Package org.biojava.bio.annodb

Class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory extends Object implements Serializable

Serialized Fields

method

Package org.biojava.bio.dist

Class org.biojava.bio.dist.AbstractOrderNDistribution extends AbstractDistribution implements Serializable

Serialized Fields

alphabet

firstA

lastA

nullModel

Class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory extends Object implements Serializable

Serialization Methods

writeReplace

Class org.biojava.bio.dist.GapDistribution extends Unchangeable implements Serializable

Serialized Fields

alpha

Class org.biojava.bio.dist.IndexedCount extends AbstractChangeable implements Serializable

Serialization Methods

readObject

writeObject

Serialized Fields

alpha

Class org.biojava.bio.dist.PairDistribution extends AbstractChangeable implements Serializable

Serialized Fields

alphabet

first

second

Class org.biojava.bio.dist.SimpleDistribution extends AbstractDistribution implements Serializable

Serialization Methods

readObject

writeObject

Serialized Fields

alpha

nullModel

Class org.biojava.bio.dist.SimpleDistributionTrainer extends Object implements Serializable

Serialized Fields

c