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

Packages that use SymbolList

org.biojava.bio.alignment	Implementation of the Alignment interface.
org.biojava.bio.chromatogram	Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
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.gui.sequence	Graphical displays of biological sequences and associated annotations.
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.abi	ABI Trace Handling.
org.biojava.bio.program.das	Development client for the Distributed Annotation System.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.scf	Support for the SCF chromatogram format.
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.

Uses of SymbolList in org.biojava.bio.alignment

Subinterfaces of SymbolList in org.biojava.bio.alignment

interface	ARAlignment ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
interface	UnequalLengthAlignment UnequalLengthAlignment has the following behavior.

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

class	AbstractULAlignment
class	AbstractULAlignment.SubULAlignment
class	FlexibleAlignment FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment.

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

protected SymbolList

SimpleAlignmentElement.seq

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

SymbolList	SimpleAlignmentElement.getSymbolList()
SymbolList	FlexibleAlignment.symbolListForLabel(Object label)
SymbolList	AlignmentElement.getSymbolList()
SymbolList	AbstractULAlignment.SubULAlignment.symbolListForLabel(Object label)

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

protected boolean

FlexibleAlignment.allGaps(SymbolList seq, int start, int end) make sure that all Symbols in this range are gaps

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

SimpleAlignmentElement(Object label, SymbolList seq, Location loc)

Uses of SymbolList in org.biojava.bio.chromatogram

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

static SymbolList	ChromatogramTools.getDNASequence(Chromatogram chromat) Get the called DNA sequence from a chromatogram.
static SymbolList	ChromatogramTools.getTraceOffsets(Chromatogram chromat) Get the peak offsets for the called bases of a chromatogram.
protected SymbolList	AbstractChromatogram.reverseComplementBaseCallList(Object label) Return a symbol list containing the reverse complement of the base call data for the given label.
protected SymbolList	AbstractChromatogram.createImmutableSymbolList(Alphabet alpha, List syms) A factory method for creating new symbol lists with a given alphabet.

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

void	SimpleChromatogram.setSymbolLists(SymbolList dna, SymbolList offsets) Set the DNA and OFFSETS symbol lists for the basecall alignment.
static int	ChromatogramTools.getIntFromSymbolList(SymbolList list, int which) Retrieves, unwraps, and returns an int from a SymbolList containing IntegerAlphabet.IntegerSymbols.

Uses of SymbolList in org.biojava.bio.dist

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

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

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

class

SimpleStatePath A no-frills implementation of StatePath.

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

SymbolList	SimpleStatePath.symbolListForLabel(Object label)
SymbolList	SimpleStatePath.subList(int start, int end)
SymbolList[]	DPMatrix.symList()

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

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.
abstract double	DP.forward(SymbolList[] symList, ScoreType scoreType)
abstract double	DP.backward(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.forwardMatrix(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.backwardMatrix(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.forwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)
abstract DPMatrix	DP.backwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)
abstract StatePath	DP.viterbi(SymbolList[] symList, ScoreType scoreType)
DPMatrix	DP.forwardsBackwards(SymbolList[] symList, ScoreType scoreType)
protected double	BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected double	BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected abstract double	AbstractTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)

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

SimpleStatePath(double score, SymbolList sequence, SymbolList states, SymbolList scores)

DP.ReverseIterator(SymbolList sym)

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

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

SymbolList[]

SingleDPMatrix.symList()

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

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

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

SingleDPMatrix(DP dp, SymbolList symList)

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

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

protected SymbolList[]

AbstractMatrixPairDPCursor.seqs

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

SymbolList[]

PairDPMatrix.symList()

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

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

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

PairDPMatrix(DP dp, SymbolList seq0, SymbolList seq1)

MatrixPairDPCursor(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

BackMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)

AbstractMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int start1, int start2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)

Uses of SymbolList in org.biojava.bio.gui.sequence

Methods in org.biojava.bio.gui.sequence that return SymbolList

SymbolList	TranslatedSequencePanel.getSequence() getSequence returns the entire Sequence currently being rendered.
SymbolList	TranslatedSequencePanel.getSymbols() getSymbols returns all of the Symbols belonging to the currently rendered Sequence.
SymbolList	SubSequenceRenderContext.getSymbols()
SymbolList	SubPairwiseRenderContext.getSymbols()
SymbolList	SubPairwiseRenderContext.getSecondarySymbols()
SymbolList	SubCircularRendererContext.getSymbols()
SymbolList	SequenceRenderContext.getSymbols() The SymbolList that is currently rendered by this SequenceRenderContext.
SymbolList	SequencePoster.getSymbols() Deprecated. Retrieve the currently rendered SymbolList
SymbolList	SequencePanel.getSequence()
SymbolList	SequencePanel.getSymbols() Retrieve the currently rendered SymbolList
SymbolList	PairwiseSequencePanel.getSymbols() getSymbols returns all of the Symbols belonging to the currently rendered Sequence.
SymbolList	PairwiseSequencePanel.getSecondarySymbols() getSecondarySymbols returns all of the Symbols belonging to the currently rendered secondary Sequence.
SymbolList	PairwiseRenderContext.getSecondarySymbols() getSecondarySymbols returns the symbols of the secondary sequence.
SymbolList	HeadlessRenderContext.getSymbols()
SymbolList	CircularRendererPanel.getSequence()
SymbolList	CircularRendererContext.getSymbols() The SymbolList that is currently rendered by this context.

Methods in org.biojava.bio.gui.sequence with parameters of type SymbolList

void	TranslatedSequencePanel.setSequence(SymbolList sequence) setSequence sets the Sequence to be rendered.
void	SequencePanel.setSequence(SymbolList s) Set the SymboList to be rendered.
void	CircularRendererPanel.setSequence(SymbolList symList)

Constructors in org.biojava.bio.gui.sequence with parameters of type SymbolList

SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range)

SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range, int symOffset)

SubPairwiseRenderContext(PairwiseRenderContext context, SymbolList symbols, SymbolList secondarySymbols, FeatureHolder features, FeatureHolder secondaryFeatures, RangeLocation range, RangeLocation secondaryRange)
Creates a new SubPairwiseRenderContext.

SubCircularRendererContext(CircularRendererContext delegate, SymbolList symbols, FeatureHolder features, double radius)
Create a new sub context.

Uses of SymbolList in org.biojava.bio.molbio

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

protected SymbolList

RestrictionEnzyme.site

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

SymbolList

RestrictionEnzyme.getRecognitionSite() getRecognitionSite returns the forward strand of the recognition site.

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

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.abi

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

SymbolList

ABITrace.getSequence() Returns the original programatically determined (unedited) sequence as a SymbolList.

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

static Alignment

ABITools.getAlignment(SymbolList abiSeq) View a symbol list over the QUALITY alphabet as an alignment.

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

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

SymbolList	DASSequence.subList(int start, int end)
protected SymbolList	DASSequence.getSymbols()

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

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

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

SymbolList	Qualitative.getQuality() Retreives the list of quality symbols from the underlying object.
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.getQuality() Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.
SymbolList	PhredSequence.getDNA() Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList

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

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

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

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

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

protected SymbolList

SCF.reverseComplementBaseCallList(Object label) Overrides AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object) to support the 7 quality values from the SCF.

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

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

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

Uses of SymbolList in org.biojava.bio.proteomics

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

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

static Protease	ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) Creates and registers a new Protease.
static Protease	ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, String name)
static double	MassCalc.getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS) getMass calculates the mass of this peptide.
double	MassCalc.getMass(SymbolList proteinSeq) Get the Mass of this peptide.
double[]	MassCalc.getVariableMasses(SymbolList peptide) Get all masses including the variable mass.
double	IsoelectricPointCalc.getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm) Computes isoelectric point of specified peptide.

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

Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name)

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

Uses of SymbolList in org.biojava.bio.search

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

SymbolList	MaxMissmatchPattern.getPattern()
SymbolList	KnuthMorrisPrattSearch.getPattern()
SymbolList	BioMatcher.group() Get the matching region as a SymbolList.

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

SeqSimilaritySearchResult	SeqSimilaritySearcher.search(SymbolList querySeq, SequenceDB db, Map searchParameters) Using this sequence similarity searcher, search with the given sequence against the given sequence database.
BioMatcher	SeqContentPattern.matcher(SymbolList symList)
void	MaxMissmatchPattern.setPattern(SymbolList pattern)
BioMatcher	MaxMissmatchPattern.matcher(SymbolList symList)
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.

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

MaxMissmatchPattern(SymbolList pattern, int missmatches)

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

Uses of SymbolList in org.biojava.bio.seq

Subinterfaces of SymbolList in org.biojava.bio.seq

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

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

SymbolList	StrandedFeature.getSymbols() Return a list of symbols that are contained in this feature.
SymbolList	SimpleAssembly.subList(int start, int end)
static SymbolList	RNATools.createRNA(String rna) Return a new RNA SymbolList for rna.
static SymbolList	RNATools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	RNATools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
static SymbolList	RNATools.transcribe(SymbolList list) Transcribe DNA into RNA.
static SymbolList	RNATools.translate(SymbolList syms) Translate RNA into protein (with termination symbols).
static SymbolList	ProteinTools.createProtein(String theProtein) Return a new Protein SymbolList for protein.
static SymbolList	NucleotideTools.createNucleotide(String nucleotide) Return a new Nucleotide SymbolList for nucleotide.
static SymbolList	NucleotideTools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	NucleotideTools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
SymbolList	NewSimpleAssembly.subList(int start, int end)
static SymbolList	GeneticCodes.transcribe(SymbolList theList) Transcribe DNA into RNA.
static SymbolList	GeneticCodes.translate(SymbolList theList) Translate RNA into protein (with termination symbols).
SymbolList	Feature.getSymbols() Return a list of symbols that are contained in this feature.
static SymbolList	DNATools.createDNA(String dna) Return a new DNA SymbolList for dna.
static SymbolList	DNATools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	DNATools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
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	CircularView.subList(int start, int end) Over rides ViewSequence.

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

static Sequence	SequenceTools.createSequence(SymbolList syms, String uri, String name, Annotation ann)
Sequence	SequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation) Creates a sequence using these parameters.
static SymbolList	RNATools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	RNATools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
static SymbolList	RNATools.transcribe(SymbolList list) Transcribe DNA into RNA.
static SymbolList	RNATools.translate(SymbolList syms) Translate RNA into protein (with termination symbols).
static SymbolList	NucleotideTools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	NucleotideTools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
static SymbolList	GeneticCodes.transcribe(SymbolList theList) Transcribe DNA into RNA.
static SymbolList	GeneticCodes.translate(SymbolList theList) Translate RNA into protein (with termination symbols).
static SymbolList	DNATools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	DNATools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
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.

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

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

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

SymbolList	SimilarityPairFeature.EmptyPairwiseAlignment.symbolListForLabel(Object label)
SymbolList	SimilarityPairFeature.EmptyPairwiseAlignment.subList(int index1, int index2)

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

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

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

SymbolList	ViewSequence.subList(int start, int end)
SymbolList	SubSequence.subList(int start, int end)
SymbolList	SimpleStrandedFeature.getSymbols()
SymbolList	SimpleSequence.subList(int start, int end)
SymbolList	SimpleFeature.getSymbols()
SymbolList	NewAssembledSymbolList.subList(int start, int end)
SymbolList	DummySequence.subList(int start, int end)
SymbolList	AssembledSymbolList.subList(int start, int end)

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

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

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

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

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

String	WordTokenization.tokenizeSymbolList(SymbolList sl)
String	SymbolTokenization.tokenizeSymbolList(SymbolList symList) Return a string representation of a list of symbols.
String	CharacterTokenization.tokenizeSymbolList(SymbolList sl)

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

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

SymbolList

ProjectedFeature.getSymbols()

Uses of SymbolList in org.biojava.bio.symbol

Subinterfaces of SymbolList in org.biojava.bio.symbol

interface	Alignment An alignment containing multiple SymbolLists.
interface	GappedSymbolList This extends SymbolList with API for manipulating, inserting and deleting gaps.

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

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	SimpleAlignment A simple implementation of an 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

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

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

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

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

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

SimpleSymbolList(SymbolList sl)
Construct a copy of an existing SymbolList.

SimpleGappedSymbolList(SymbolList source)
Create a new SimpleGappedSymbolList that will view source.

PackedSymbolList(Packing packing, SymbolList symList)
Create a new PackedSymbolList as a packed copy of another symbol list.

Edit(int pos, int length, SymbolList replacement)
Create a new Edit.

ChunkedSymbolList(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha)

Uses of SymbolList in org.biojava.utils.automata

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

void	PatternBlitz.search(SymbolList sl)

Uses of SymbolList in org.biojava.utils.regex

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

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

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.
boolean	Search.Listener.reportMatch(SymbolList seq, Pattern pattern, int start, int end)
Matcher	Pattern.matcher(SymbolList sl) Creates a matcher that will match the given input against this pattern.
Matcher	Matcher.reset(SymbolList sl) Resets this matcher with a new input SymbolList.