Uses of Interface
org.biojava.bio.symbol.SymbolList

Packages that use SymbolList

Package	Description
org.biojava.bio.alignment
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead
org.biojava.bio.dp.twohead
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.phred	Parser for Phred output
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
org.biojava.bio.proteomics	Utilities to aid in performing various physical analysis of proteins.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.projection	Code for projecting Feature objects and systematically altering their properties.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.utils.automata
org.biojava.utils.regex	This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.ga	Classes to provide a genetic algorithm framework
org.biojavax.ga.functions	GA functions
org.biojavax.ga.impl	Default implementations and abstract classes.
org.biojavax.ga.util	Utility functions and helper classes

Uses of SymbolList in org.biojava.bio.alignment

Subinterfaces of SymbolList in org.biojava.bio.alignment

Modifier and Type	Interface	Description
interface	Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment that implement SymbolList

Modifier and Type	Class	Description
class	SimpleAlignment	A simple implementation of an Alignment.

Methods in org.biojava.bio.alignment that return SymbolList

Modifier and Type	Method	Description
SymbolList	Alignment.SymbolListIterator.next()
SymbolList	Alignment.symbolListForLabel(String label)	Retrieve a single row of the alignment by label.
SymbolList	SimpleAlignment.symbolListForLabel(String label)

Methods in org.biojava.bio.alignment that return types with arguments of type SymbolList

Modifier and Type	Method	Description
Iterator<SymbolList>	Alignment.symbolListIterator()	Creates an Iterator over the SymbolLists in the alignment.
Iterator<SymbolList>	SimpleAlignment.symbolListIterator()

Constructor parameters in org.biojava.bio.alignment with type arguments of type SymbolList

Constructor	Description
SimpleAlignment(Map<String,SymbolList> labelToResList)	Generate an alignment from a list of SymbolLists.

Uses of SymbolList in org.biojava.bio.dist

Methods in org.biojava.bio.dist that return SymbolList

Modifier and Type	Method	Description
static SymbolList	DistributionTools.generateSymbolList(Distribution d, int length)	Produces a SymbolList by randomly sampling a Distribution.

Uses of SymbolList in org.biojava.bio.dp

Subinterfaces of SymbolList in org.biojava.bio.dp

Modifier and Type	Interface	Description
interface	StatePath	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.

Classes in org.biojava.bio.dp that implement SymbolList

Modifier and Type	Class	Description
class	SimpleStatePath	A no-frills implementation of StatePath.

Methods in org.biojava.bio.dp that return SymbolList

Modifier and Type	Method	Description
SymbolList	SimpleStatePath.subList(int start, int end)
SymbolList	SimpleStatePath.symbolListForLabel(String label)
SymbolList[]	DPMatrix.symList()

Methods in org.biojava.bio.dp that return types with arguments of type SymbolList

Modifier and Type	Method	Description
Iterator<SymbolList>	SimpleStatePath.symbolListIterator()

Methods in org.biojava.bio.dp with parameters of type SymbolList

Modifier and Type	Method	Description
abstract double	DP.backward(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.backwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)
abstract DPMatrix	DP.backwardMatrix(SymbolList[] symList, ScoreType scoreType)
abstract double	DP.forward(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.forwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)
abstract DPMatrix	DP.forwardMatrix(SymbolList[] symList, ScoreType scoreType)
DPMatrix	DP.forwardsBackwards(SymbolList[] symList, ScoreType scoreType)
static double	DP.scoreWeightMatrix(WeightMatrix matrix, SymbolList symList, int start)	Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.
static double	DP.scoreWeightMatrix(WeightMatrix matrix, SymbolList symList, ScoreType scoreType, int start)	Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType.
protected abstract double	AbstractTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected double	BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected double	BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType)
protected double	BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
abstract StatePath	DP.viterbi(SymbolList[] symList, ScoreType scoreType)

Constructors in org.biojava.bio.dp with parameters of type SymbolList

Constructor	Description
ReverseIterator(SymbolList sym)
SimpleStatePath(double score, SymbolList sequence, SymbolList states, SymbolList scores)

Uses of SymbolList in org.biojava.bio.dp.onehead

Fields in org.biojava.bio.dp.onehead declared as SymbolList

Modifier and Type	Field	Description
protected SymbolList[]	SingleDPMatrix.symList

Methods in org.biojava.bio.dp.onehead that return SymbolList

Modifier and Type	Method	Description
SymbolList	DPCursor.symList()	The symbol list being looped over.
SymbolList[]	SingleDPMatrix.symList()
SymbolList	SmallCursor.symList()

Methods in org.biojava.bio.dp.onehead with parameters of type SymbolList

Modifier and Type	Method	Description
double	SingleDP.backward(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)
double	SingleDP.forward(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, ScoreType scoreType)
StatePath	SingleDP.viterbi(SymbolList[] symList, ScoreType scoreType)

Constructors in org.biojava.bio.dp.onehead with parameters of type SymbolList

Constructor	Description
SingleDPMatrix(DP dp, SymbolList symList)
SmallCursor(State[] states, SymbolList symList, Iterator symIterator)

Uses of SymbolList in org.biojava.bio.dp.twohead

Fields in org.biojava.bio.dp.twohead declared as SymbolList

Modifier and Type	Field	Description
protected SymbolList[]	AbstractMatrixPairDPCursor.seqs

Methods in org.biojava.bio.dp.twohead that return SymbolList

Modifier and Type	Method	Description
SymbolList[]	PairDPMatrix.symList()

Methods in org.biojava.bio.dp.twohead with parameters of type SymbolList

Modifier and Type	Method	Description
double	PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
double	PairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType)
StatePath	PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)

Constructors in org.biojava.bio.dp.twohead with parameters of type SymbolList

Constructor	Description
AbstractMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int start1, int start2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)
BackMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)
LightPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, int numStates, EmissionCache eCache)	Constructor for the LightPairDPCursor object
MatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)
PairDPMatrix(DP dp, SymbolList seq0, SymbolList seq1)

Uses of SymbolList in org.biojava.bio.molbio

Fields in org.biojava.bio.molbio declared as SymbolList

Modifier and Type	Field	Description
protected SymbolList	RestrictionEnzyme.site

Methods in org.biojava.bio.molbio that return SymbolList

Modifier and Type	Method	Description
SymbolList	RestrictionEnzyme.getRecognitionSite()	getRecognitionSite returns the forward strand of the recognition site.

Methods in org.biojava.bio.molbio with parameters of type SymbolList

Modifier and Type	Method	Description
void	Composition.setSymbolList(SymbolList symbolList)	Set the SymbolList to calculation the composition of.

Constructors in org.biojava.bio.molbio with parameters of type SymbolList

Constructor	Description
RestrictionEnzyme(String name, SymbolList site, int dsForward, int dsReverse)	Creates a new RestrictionEnzyme which cuts within or downstream of the recognition site.
RestrictionEnzyme(String name, SymbolList site, int usForward, int usReverse, int dsForward, int dsReverse)	Creates a new RestrictionEnzyme of the unusual type which cuts both upstream and downstream of its recognition site.

Uses of SymbolList in org.biojava.bio.program.phred

Classes in org.biojava.bio.program.phred that implement SymbolList

Modifier and Type	Class	Description
class	PhredSequence	PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.

Methods in org.biojava.bio.program.phred that return SymbolList

Modifier and Type	Method	Description
static SymbolList	PhredTools.createPhred(SymbolList dna, SymbolList quality)	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.
SymbolList	PhredSequence.getDNA()	Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
SymbolList	PhredSequence.getQuality()	Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.
SymbolList	Qualitative.getQuality()	Retreives the list of quality symbols from the underlying object.

Methods in org.biojava.bio.program.phred with parameters of type SymbolList

Modifier and Type	Method	Description
static SymbolList	PhredTools.createPhred(SymbolList dna, SymbolList quality)	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.

Constructors in org.biojava.bio.program.phred with parameters of type SymbolList

Constructor	Description
PhredSequence(SymbolList phredSequence, String name, String urn, Annotation anno)	Constructs a new PhredSequence.

Uses of SymbolList in org.biojava.bio.program.ssaha

Methods in org.biojava.bio.program.ssaha with parameters of type SymbolList

Modifier and Type	Method	Description
void	CompactedDataStore.search(String seqID, SymbolList symList, SearchListener listener)
void	DataStore.search(String id, SymbolList symList, SearchListener listener)	Search the DataStore with a symbol list.

Uses of SymbolList in org.biojava.bio.proteomics

Methods in org.biojava.bio.proteomics that return SymbolList

Modifier and Type	Method	Description
SymbolList	Protease.getCleaveageResidues()	The list of residues that the protease will cleave at.
SymbolList	Protease.getNotCleaveResidues()	The list of residues that will prevent cleavage if they follow the cleavage residue.

Methods in org.biojava.bio.proteomics with parameters of type SymbolList

Modifier and Type	Method	Description
static Protease	ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, String name)
static Protease	ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name)	Creates and registers a new Protease.
static double	IsoelectricPointCalc.getIsoelectricPoint(SymbolList peptide)	Static public method to compute the pI for a polypeptide in denaturating and reduced conditions with both free ends.
double	MassCalc.getMass(SymbolList proteinSeq)	Get the Mass of this peptide.
static double	MassCalc.getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS)	getMass calculates the mass of this peptide.
static double	MassCalc.getMolecularWeight(SymbolList proteinSeq)	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.
double	IsoelectricPointCalc.getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm)	Computes isoelectric point of specified peptide.
double[]	MassCalc.getVariableMasses(SymbolList peptide)	Get all masses including the variable mass.

Constructors in org.biojava.bio.proteomics with parameters of type SymbolList

Constructor	Description
Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes)	Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name)

Uses of SymbolList in org.biojava.bio.search

Methods in org.biojava.bio.search that return SymbolList

Modifier and Type	Method	Description
SymbolList	KnuthMorrisPrattSearch.getPattern()
SymbolList	MaxMismatchPattern.getPattern()
SymbolList	BioMatcher.group()	Get the matching region as a SymbolList.
SymbolList	MaxMismatchMatcher.group()

Methods in org.biojava.bio.search with parameters of type SymbolList

Modifier and Type	Method	Description
int[]	KnuthMorrisPrattSearch.findMatches(SymbolList text)	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).
BioMatcher	BioPattern.matcher(SymbolList symList)	Get a matcher that will use these parameters to search a SymbolList.
BioMatcher	MaxMismatchPattern.matcher(SymbolList symList)
BioMatcher	SeqContentPattern.matcher(SymbolList symList)
SeqSimilaritySearchResult	SeqSimilaritySearcher.search(SymbolList querySeq, SequenceDB db, Map searchParameters)	Using this sequence similarity searcher, search with the given sequence against the given sequence database.
void	MaxMismatchPattern.setPattern(SymbolList pattern)

Constructors in org.biojava.bio.search with parameters of type SymbolList

Constructor	Description
KnuthMorrisPrattSearch(SymbolList pattern)	Constructs a KMP matcher to find exact occurances of pattern in text using the Knuth-Morris-Pratt algorithm.
MaxMismatchPattern(SymbolList pattern, int mismatches)

Uses of SymbolList in org.biojava.bio.seq

Subinterfaces of SymbolList in org.biojava.bio.seq

Modifier and Type	Interface	Description
interface	GappedSequence	Extension of GappedSymbolList which also projects features into the gapped coordinate system.
interface	Sequence	A biological sequence.

Classes in org.biojava.bio.seq that implement SymbolList

Modifier and Type	Class	Description
class	CircularView	A circular view onto another Sequence object.
class	NewSimpleAssembly	A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
class	SimpleAssembly	A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.

Methods in org.biojava.bio.seq that return SymbolList

Modifier and Type	Method	Description
static SymbolList	DNATools.complement(SymbolList list)	Retrieve a complement view of list.
static SymbolList	NucleotideTools.complement(SymbolList list)	Retrieve a complement view of list.
static SymbolList	RNATools.complement(SymbolList list)	Retrieve a complement view of list.
static SymbolList	DNATools.createDNA(String dna)	Return a new DNA SymbolList for dna.
static SymbolList	NucleotideTools.createNucleotide(String nucleotide)	Return a new Nucleotide SymbolList for nucleotide.
static SymbolList	ProteinTools.createProtein(String theProtein)	Return a new Protein SymbolList for protein.
static SymbolList	RNATools.createRNA(String rna)	Return a new RNA SymbolList for rna.
static SymbolList	DNATools.flip(SymbolList list, StrandedFeature.Strand strand)	Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
SymbolList	Feature.getSymbols()	Return a list of symbols that are contained in this feature.
SymbolList	StrandedFeature.getSymbols()	Return a list of symbols that are contained in this feature.
static SymbolList	DNATools.reverseComplement(SymbolList list)	Retrieve a reverse-complement view of list.
static SymbolList	NucleotideTools.reverseComplement(SymbolList list)	Retrieve a reverse-complement view of list.
static SymbolList	RNATools.reverseComplement(SymbolList list)	Retrieve a reverse-complement view of list.
SymbolList	CircularView.subList(int start, int end)	Over rides ViewSequence.
SymbolList	NewSimpleAssembly.subList(int start, int end)
SymbolList	SimpleAssembly.subList(int start, int end)
static SymbolList	DNATools.toProtein(SymbolList syms)	Convenience method that directly converts a DNA sequence to RNA then to protein.
static SymbolList	DNATools.toProtein(SymbolList syms, int start, int end)	Convenience method to translate a region of a DNA sequence directly into protein.
static SymbolList	DNATools.toRNA(SymbolList syms)	Converts a SymbolList from the DNA Alphabet to the RNA Alphabet.
static SymbolList	GeneticCodes.transcribe(SymbolList theList)	Transcribe DNA into RNA.
static SymbolList	RNATools.transcribe(SymbolList list)	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.
static SymbolList	DNATools.transcribeToRNA(SymbolList syms)	Transcribes DNA to RNA.
static SymbolList	GeneticCodes.translate(SymbolList theList)	Translate RNA into protein (with termination symbols).
static SymbolList	RNATools.translate(SymbolList syms)	Translate RNA into protein (with termination symbols).

Methods in org.biojava.bio.seq with parameters of type SymbolList

Modifier and Type	Method	Description
static SymbolList	DNATools.complement(SymbolList list)	Retrieve a complement view of list.
static SymbolList	NucleotideTools.complement(SymbolList list)	Retrieve a complement view of list.
static SymbolList	RNATools.complement(SymbolList list)	Retrieve a complement view of list.
Sequence	SequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation)	Deprecated. Creates a sequence using these parameters.
static Sequence	SequenceTools.createSequence(SymbolList syms, String uri, String name, Annotation ann)
static SymbolList	DNATools.flip(SymbolList list, StrandedFeature.Strand strand)	Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
static SymbolList	DNATools.reverseComplement(SymbolList list)	Retrieve a reverse-complement view of list.
static SymbolList	NucleotideTools.reverseComplement(SymbolList list)	Retrieve a reverse-complement view of list.
static SymbolList	RNATools.reverseComplement(SymbolList list)	Retrieve a reverse-complement view of list.
static SymbolList	DNATools.toProtein(SymbolList syms)	Convenience method that directly converts a DNA sequence to RNA then to protein.
static SymbolList	DNATools.toProtein(SymbolList syms, int start, int end)	Convenience method to translate a region of a DNA sequence directly into protein.
static SymbolList	DNATools.toRNA(SymbolList syms)	Converts a SymbolList from the DNA Alphabet to the RNA Alphabet.
static SymbolList	GeneticCodes.transcribe(SymbolList theList)	Transcribe DNA into RNA.
static SymbolList	RNATools.transcribe(SymbolList list)	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.
static SymbolList	DNATools.transcribeToRNA(SymbolList syms)	Transcribes DNA to RNA.
static SymbolList	GeneticCodes.translate(SymbolList theList)	Translate RNA into protein (with termination symbols).
static SymbolList	RNATools.translate(SymbolList syms)	Translate RNA into protein (with termination symbols).

Uses of SymbolList in org.biojava.bio.seq.homol

Classes in org.biojava.bio.seq.homol that implement SymbolList

Modifier and Type	Class	Description
static class	SimilarityPairFeature.EmptyPairwiseAlignment	EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists.

Methods in org.biojava.bio.seq.homol that return SymbolList

Modifier and Type	Method	Description
SymbolList	SimilarityPairFeature.EmptyPairwiseAlignment.subList(int index1, int index2)
SymbolList	SimilarityPairFeature.EmptyPairwiseAlignment.symbolListForLabel(String label)

Methods in org.biojava.bio.seq.homol that return types with arguments of type SymbolList

Modifier and Type	Method	Description
Iterator<SymbolList>	SimilarityPairFeature.EmptyPairwiseAlignment.symbolListIterator()

Uses of SymbolList in org.biojava.bio.seq.impl

Classes in org.biojava.bio.seq.impl that implement SymbolList

Modifier and Type	Class	Description
class	AssembledSymbolList	Support class for applications which need to patch together sections of sequence into a single SymbolList.
class	DummySequence	A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
class	NewAssembledSymbolList	Support class for applications which need to patch together sections of sequence into a single SymbolList.
class	RevCompSequence	A reverse complement view onto Sequence interface.
class	SimpleGappedSequence	Simple implementation of GappedSequence.
class	SimpleSequence	A basic implementation of the Sequence interface.
class	SubSequence	View a sub-section of a given sequence object, including all the features intersecting that region.
class	ViewSequence	A view onto another Sequence object.

Methods in org.biojava.bio.seq.impl that return SymbolList

Modifier and Type	Method	Description
SymbolList	SimpleFeature.getSymbols()
SymbolList	SimpleStrandedFeature.getSymbols()
SymbolList	AssembledSymbolList.subList(int start, int end)
SymbolList	DummySequence.subList(int start, int end)
SymbolList	NewAssembledSymbolList.subList(int start, int end)
SymbolList	SimpleSequence.subList(int start, int end)
SymbolList	SubSequence.subList(int start, int end)
SymbolList	ViewSequence.subList(int start, int end)

Methods in org.biojava.bio.seq.impl with parameters of type SymbolList

Modifier and Type	Method	Description
Sequence	SimpleSequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation)
void	AssembledSymbolList.putComponent(Location l, SymbolList sl)

Constructors in org.biojava.bio.seq.impl with parameters of type SymbolList

Constructor	Description
SimpleSequence(SymbolList sym, String urn, String name, Annotation annotation)	Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed.
SimpleSequence(SymbolList sym, String urn, String name, Annotation annotation, FeatureRealizer realizer)	Create a SimpleSequence using a specified FeatureRealizer.

Uses of SymbolList in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io that return SymbolList

Modifier and Type	Method	Description
SymbolList	ChunkedSymbolListFactory.make(SymbolReader sr)	Method to create a Sequence with a SymbolReader.
SymbolList	ChunkedSymbolListFactory.makeSymbolList()	Converts accumulated Symbols to a SymbolList

Methods in org.biojava.bio.seq.io with parameters of type SymbolList

Modifier and Type	Method	Description
String	AlternateTokenization.tokenizeSymbolList(SymbolList sl)
String	CharacterTokenization.tokenizeSymbolList(SymbolList sl)
String	SymbolTokenization.tokenizeSymbolList(SymbolList symList)	Return a string representation of a list of symbols.
String	WordTokenization.tokenizeSymbolList(SymbolList sl)

Constructors in org.biojava.bio.seq.io with parameters of type SymbolList

Constructor	Description
SymbolListCharSequence(SymbolList syms)	Creates a new SymbolListCharSequence wrapping a SymbolList.

Uses of SymbolList in org.biojava.bio.seq.projection

Methods in org.biojava.bio.seq.projection that return SymbolList

Modifier and Type	Method	Description
SymbolList	ProjectedFeature.getSymbols()

Uses of SymbolList in org.biojava.bio.symbol

Subinterfaces of SymbolList in org.biojava.bio.symbol

Modifier and Type	Interface	Description
interface	GappedSymbolList	This extends SymbolList with API for manipulating, inserting and deleting gaps.

Classes in org.biojava.bio.symbol that implement SymbolList

Modifier and Type	Class	Description
class	AbstractSymbolList	Abstract helper implementation of the SymbolList core interface.
class	ChunkedSymbolList	SymbolList implementation using constant-size chunks.
class	DummySymbolList	Symbol list which just consists of non-informative symbols.
class	PackedSymbolList	A SymbolList that stores symbols as bit-patterns in an array of longs.
class	RelabeledAlignment	An alignment that relabels another alignment.
class	SimpleGappedSymbolList	This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
class	SimpleSymbolList	Basic implementation of SymbolList.

Fields in org.biojava.bio.symbol declared as SymbolList

Modifier and Type	Field	Description
static SymbolList	SymbolList.EMPTY_LIST	A useful object that represents an empty symbol list, to avoid returning null.
SymbolList	Edit.replacement

Methods in org.biojava.bio.symbol that return SymbolList

Modifier and Type	Method	Description
static SymbolList	SymbolListViews.emptyList(Alphabet alpha)	Get a new immutable, empty symbol list with the given alphabet.
static SymbolList	DoubleAlphabet.fromArray(double[] dArray)	Retrieve a SymbolList view of an array of doubles.
static SymbolList	IntegerAlphabet.fromArray(int[] iArray)	Retrieve a SymbolList view of an array of integers.
SymbolList	GappedSymbolList.getSourceSymbolList()	Return the underlying (ungapped) SymbolList.
SymbolList	SimpleGappedSymbolList.getSourceSymbolList()
SymbolList	PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)	Makes a packed SymbolList out of a list of Symbols.
SymbolList	SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)	Create a factory for SimpleSymbolLists.
SymbolList	SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)	makes a SymbolList containing size Symbols from a Symbol array.
static SymbolList	SymbolListViews.orderNSymbolList(SymbolList source, int order)	An n-th order view of another SymbolList.
static SymbolList	SymbolListViews.reverse(SymbolList symbols)	A reversed view onto a SymbolList.
SymbolList	AbstractSymbolList.subList(int start, int end)
SymbolList	ChunkedSymbolList.subList(int start, int end)
SymbolList	RelabeledAlignment.subList(int min, int max)
SymbolList	SimpleSymbolList.subList(int start, int end)	create a subList of the original, this will be a view until either the original symbolList or the sublist is edited
SymbolList	SymbolList.subList(int start, int end)	Return a new SymbolList for the symbols start to end inclusive.
static SymbolList	SymbolListViews.subList(SymbolList parent, int start, int end)	View a portion of a SymbolList.
SymbolList	RelabeledAlignment.symbolListForLabel(String label)
SymbolList	AbstractLocationDecorator.symbols(SymbolList seq)
SymbolList	AbstractRangeLocation.symbols(SymbolList seq)
SymbolList	CircularLocation.symbols(SymbolList seq)
SymbolList	FuzzyPointLocation.symbols(SymbolList slist)
SymbolList	Location.symbols(SymbolList seq)	Return the symbols in a sequence that fall within this range.
static SymbolList	SymbolListViews.translate(SymbolList symbols, TranslationTable table)	Provides a 'translated' view of an underlying SymbolList.
static SymbolList	SymbolListViews.windowedSymbolList(SymbolList source, int wsize)	A view of windows onto another SymbolList.

Methods in org.biojava.bio.symbol with parameters of type SymbolList

Modifier and Type	Method	Description
void	UkkonenSuffixTree.addSymbolList(SymbolList list, String name, boolean doNotTerminate)
void	SuffixTree.addSymbols(SymbolList sList, int window)	Add a count for all motifs with length of up to window to this tree.
static Alignment	SymbolListViews.alignment(List labels, SymbolList symList)	View a SymbolList over a cross-product Alphabet as an Alignment.
static String	MotifTools.createRegex(SymbolList motif)	createRegex creates a regular expression which matches the SymbolList.
static int	PackingFactory.nextWord(SymbolList symList, int word, int offset, int wordLength, Packing packing)
static SymbolList	SymbolListViews.orderNSymbolList(SymbolList source, int order)	An n-th order view of another SymbolList.
static int	PackingFactory.primeWord(SymbolList symList, int wordLength, Packing packing)
static SymbolList	SymbolListViews.reverse(SymbolList symbols)	A reversed view onto a SymbolList.
static SymbolList	SymbolListViews.subList(SymbolList parent, int start, int end)	View a portion of a SymbolList.
SymbolList	AbstractLocationDecorator.symbols(SymbolList seq)
SymbolList	AbstractRangeLocation.symbols(SymbolList seq)
SymbolList	CircularLocation.symbols(SymbolList seq)
SymbolList	FuzzyPointLocation.symbols(SymbolList slist)
SymbolList	Location.symbols(SymbolList seq)	Return the symbols in a sequence that fall within this range.
String	SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbolList(SymbolList sl)
static SymbolList	SymbolListViews.translate(SymbolList symbols, TranslationTable table)	Provides a 'translated' view of an underlying SymbolList.
static SymbolList	SymbolListViews.windowedSymbolList(SymbolList source, int wsize)	A view of windows onto another SymbolList.

Constructors in org.biojava.bio.symbol with parameters of type SymbolList

Constructor	Description
ChunkedSymbolList(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha)
Edit(int pos, int length, SymbolList replacement)	Create a new Edit.
Edit(int pos, int length, SymbolList replacement, Map<String,Object> props)	Create a new Edit with some properties.
PackedSymbolList(Packing packing, SymbolList symList)	Create a new PackedSymbolList as a packed copy of another symbol list.
SimpleGappedSymbolList(SymbolList source)	Create a new SimpleGappedSymbolList that will view source.
SimpleSymbolList(SymbolList sl)	Construct a copy of an existing SymbolList.

Uses of SymbolList in org.biojava.utils.automata

Methods in org.biojava.utils.automata with parameters of type SymbolList

Modifier and Type	Method	Description
void	PatternBlitz.search(SymbolList sl)

Uses of SymbolList in org.biojava.utils.regex

Methods in org.biojava.utils.regex that return SymbolList

Modifier and Type	Method	Description
SymbolList	Matcher.group()	Returns the input subsequence matched by the previous match.
SymbolList	Matcher.group(int group)	Returns the input subsequence captured by the given group during the previous match operation.

Methods in org.biojava.utils.regex with parameters of type SymbolList

Modifier and Type	Method	Description
Matcher	Pattern.matcher(SymbolList sl)	Creates a matcher that will match the given input against this pattern.
boolean	Search.Listener.reportMatch(SymbolList seq, Pattern pattern, int start, int end)
Matcher	Matcher.reset(SymbolList sl)	Resets this matcher with a new input SymbolList.
void	Search.search(SymbolList seq)	search the Sequence with the patterns already registered with this object.
void	Search.search(SymbolList seq, int loLimit, int hiLimit)	search part of the SymbolList with the patterns already registered with this object.

Uses of SymbolList in org.biojavax

Methods in org.biojavax that return SymbolList

Modifier and Type	Method	Description
SymbolList	CrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a)	Given a cross reference, return the corresponding symbol list.
SymbolList	DummyCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a)	Given a cross reference, return the corresponding symbol list.

Uses of SymbolList in org.biojavax.bio.seq

Subinterfaces of SymbolList in org.biojavax.bio.seq

Modifier and Type	Interface	Description
interface	RichSequence	A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq that implement SymbolList

Modifier and Type	Class	Description
class	InfinitelyAmbiguousSymbolList	A symbol list that is Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.
class	SimpleRichSequence	A simple implementation of RichSequence.
class	ThinRichSequence	A simple implementation of RichSequence.

Methods in org.biojavax.bio.seq that return SymbolList

Modifier and Type	Method	Description
SymbolList	RichSequence.getInternalSymbolList()	A special function that returns the SymbolList that this RichSequence is based around.
SymbolList	SimpleRichSequence.getInternalSymbolList()	A special function that returns the SymbolList that this RichSequence is based around.
SymbolList	ThinRichSequence.getInternalSymbolList()	A special function that returns the SymbolList that this RichSequence is based around.
SymbolList	SimpleRichFeature.getSymbols()	Return a list of symbols that are contained in this feature.
SymbolList	DummyRichSequenceHandler.subList(RichSequence seq, int start, int end)	Return a new SymbolList for the symbols start to end inclusive.
SymbolList	InfinitelyAmbiguousSymbolList.subList(int start, int end)	Return a new SymbolList for the symbols start to end inclusive.
SymbolList	RichSequenceHandler.subList(RichSequence seq, int start, int end)	Return a new SymbolList for the symbols start to end inclusive.
SymbolList	ThinRichSequence.subList(int start, int end)	Return a new SymbolList for the symbols start to end inclusive.
SymbolList	CompoundRichLocation.symbols(SymbolList seq)	Return the symbols in a sequence that fall within this range.
SymbolList	EmptyRichLocation.symbols(SymbolList seq)	Return the symbols in a sequence that fall within this range.
SymbolList	SimpleRichLocation.symbols(SymbolList seq)	Return the symbols in a sequence that fall within this range.

Methods in org.biojavax.bio.seq with parameters of type SymbolList

Modifier and Type	Method	Description
static RichSequence	RichSequence.Tools.createRichSequence(String name, SymbolList syms)	Create a new RichSequence in the default namespace.
static RichSequence	RichSequence.Tools.createRichSequence(Namespace ns, String name, SymbolList syms)	Create a new RichSequence in the specified namespace.
SymbolList	CompoundRichLocation.symbols(SymbolList seq)	Return the symbols in a sequence that fall within this range.
SymbolList	EmptyRichLocation.symbols(SymbolList seq)	Return the symbols in a sequence that fall within this range.
SymbolList	SimpleRichLocation.symbols(SymbolList seq)	Return the symbols in a sequence that fall within this range.

Constructors in org.biojavax.bio.seq with parameters of type SymbolList

Constructor	Description
SimpleRichSequence(Namespace ns, String name, String accession, int version, SymbolList symList, Double seqversion)	Creates a new instance of SimpleRichSequence.

Uses of SymbolList in org.biojavax.ga

Methods in org.biojavax.ga that return SymbolList

Modifier and Type	Method	Description
SymbolList[]	Organism.getChromosomes()	Gets the organisms 'chromosome' sequences

Methods in org.biojavax.ga with parameters of type SymbolList

Modifier and Type	Method	Description
void	Organism.setChromosomes(SymbolList[] chromosomes)	Sets the organisms 'chromosome' sequences.

Uses of SymbolList in org.biojavax.ga.functions

Methods in org.biojavax.ga.functions that return SymbolList

Modifier and Type	Method	Description
SymbolList[]	GACross.getChromosomes()	Gets the chromosomes after the cross
SymbolList[]	GACrossResult.getChromosomes()	Gets the chromosomes after the cross
SymbolList[]	SimpleGACrossResult.getChromosomes()
SymbolList	MutationFunction.mutate(SymbolList seq)	Produces a new SymbolList by mutation.
SymbolList	MutationFunction.NoMutation.mutate(SymbolList syml)
SymbolList	SimpleMutationFunction.mutate(SymbolList seq)
SymbolList	SwapMutationFunction.mutate(SymbolList seq)

Methods in org.biojavax.ga.functions with parameters of type SymbolList

Modifier and Type	Method	Description
SymbolList	MutationFunction.mutate(SymbolList seq)	Produces a new SymbolList by mutation.
SymbolList	MutationFunction.NoMutation.mutate(SymbolList syml)
SymbolList	SimpleMutationFunction.mutate(SymbolList seq)
SymbolList	SwapMutationFunction.mutate(SymbolList seq)
GACrossResult	CrossOverFunction.NoCross.performCrossOver(SymbolList chromA, SymbolList chromB)
GACrossResult	CrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)	Performs a cross between the pair of chromosomes
GACrossResult	OrderCrossover.performCrossOver(SymbolList chromA, SymbolList chromB)
GACrossResult	SimpleCrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)

Constructors in org.biojavax.ga.functions with parameters of type SymbolList

Constructor	Description
SimpleGACrossResult(PointLocation[] crossOverPositions, SymbolList[] chromosomes)

Uses of SymbolList in org.biojavax.ga.impl

Fields in org.biojavax.ga.impl declared as SymbolList

Modifier and Type	Field	Description
protected SymbolList[]	AbstractOrganism.chromosomes

Methods in org.biojavax.ga.impl that return SymbolList

Modifier and Type	Method	Description
SymbolList[]	AbstractOrganism.getChromosomes()

Methods in org.biojavax.ga.impl with parameters of type SymbolList

Modifier and Type	Method	Description
protected abstract void	AbstractOrganism.setChromImpl(SymbolList[] chromosomes)
protected void	SimpleOrganism.setChromImpl(SymbolList[] chromosomes)
void	AbstractOrganism.setChromosomes(SymbolList[] chromosomes)

Uses of SymbolList in org.biojavax.ga.util

Methods in org.biojavax.ga.util that return SymbolList

Modifier and Type	Method	Description
static SymbolList	GATools.createBinary(String binarySequence)	Creates a SymbolList in the GABinary Alphabet