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.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 into alternate coordinate systems. 
org.biojava.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
org.biojava.bio.symbol Representation of the Symbols that make up a sequence, and locations within them. 
 

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

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(java.lang.Object label, SymbolList seq, Location loc)
           
 

Uses of SymbolList in org.biojava.bio.chromatogram
 

Methods in org.biojava.bio.chromatogram that return SymbolList
protected  SymbolList AbstractChromatogram.reverseComplementBaseCallList(java.lang.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, java.util.List syms)
          A factory method for creating new symbol lists with a given alphabet.
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.
 

Methods in org.biojava.bio.chromatogram with parameters of type SymbolList
static int ChromatogramTools.getIntFromSymbolList(SymbolList list, int which)
          Retrieves, unwraps, and returns an int from a SymbolList containing IntegerAlphabet.IntegerSymbols.
 void SimpleChromatogram.setSymbolLists(SymbolList dna, SymbolList offsets)
          Set the DNA and OFFSETS symbol lists for the basecall alignment.
 

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

Methods in org.biojava.bio.dp with parameters of type SymbolList
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)
           
static double DP.scoreWeightMatrix(WeightMatrix matrix, SymbolList symList, int start)
          Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.
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)
           
 

Constructors in org.biojava.bio.dp with parameters of type SymbolList
DP.ReverseIterator(SymbolList sym)
           
SimpleStatePath(double score, SymbolList sequence, SymbolList states, SymbolList scores)
           
 

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
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)
           
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 SequenceRenderContext.getSymbols()
          The SymbolList that is currently rendered by this SequenceRenderContext.
 SymbolList TranslatedSequencePanel.getSymbols()
          getSymbols returns all of the Symbols belonging to the currently rendered Sequence.
 SymbolList HeadlessRenderContext.getSymbols()
           
 SymbolList SubPairwiseRenderContext.getSymbols()
           
 SymbolList SubPairwiseRenderContext.getSecondarySymbols()
           
 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 SequencePoster.getSymbols()
          Retrieve the currently rendered SymbolList
 SymbolList PairwiseRenderContext.getSecondarySymbols()
          getSecondarySymbols returns the symbols of the secondary sequence.
 SymbolList SubSequenceRenderContext.getSymbols()
           
 SymbolList SequencePanel.getSymbols()
          Retrieve the currently rendered SymbolList
 

Constructors in org.biojava.bio.gui.sequence with parameters of type SymbolList
SubPairwiseRenderContext(PairwiseRenderContext context, SymbolList symbols, SymbolList secondarySymbols, FeatureHolder features, FeatureHolder secondaryFeatures, RangeLocation range, RangeLocation secondaryRange)
          Creates a new SubPairwiseRenderContext.
SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range)
           
 

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(java.lang.String name, SymbolList site, int dsForward, int dsReverse)
          Creates a new RestrictionEnzyme which cuts within or downstream of the recognition site.
RestrictionEnzyme(java.lang.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 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
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 Qualitative.getQuality()
          Retreives the list of quality symbols from the underlying object.
 

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, java.lang.String name, java.lang.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(java.lang.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 CompactedDataStore.search(java.lang.String seqID, SymbolList symList, SearchListener listener)
           
 void DataStore.search(java.lang.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
 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, java.lang.String name)
          Creates and registers a new Protease.
static Protease ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, java.lang.String name)
           
 double IsoelectricPointCalc.getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm)
          Computes isoelectric point of specified peptide.
static double MassCalc.getMass(SymbolList proteinSeq, java.lang.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.
 

Constructors in org.biojava.bio.proteomics with parameters of type SymbolList
Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, java.lang.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 KnuthMorrisPrattSearch.getPattern()
           
 

Methods in org.biojava.bio.search with parameters of type SymbolList
 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).
 SeqSimilaritySearchResult SeqSimilaritySearcher.search(SymbolList querySeq, SequenceDB db, java.util.Map searchParameters)
          Using this sequence similarity searcher, search with the given sequence against the given sequence database.
 

Constructors in org.biojava.bio.search with parameters of type SymbolList
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 DummySequence
           
 class SimpleAssembly
          A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
 class SimpleGappedSequence
          Simple implementation of GappedSequence.
 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 that return SymbolList
 SymbolList SubSequence.subList(int start, int end)
           
static SymbolList NucleotideTools.createNucleotide(java.lang.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.
static SymbolList RNATools.createRNA(java.lang.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 DNATools.createDNA(java.lang.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.
 SymbolList ViewSequence.subList(int start, int end)
           
 SymbolList CircularView.subList(int start, int end)
           Over rides ViewSequence.
 SymbolList StrandedFeature.getSymbols()
          Return a list of symbols that are contained in this feature.
static SymbolList GeneticCodes.transcribe(SymbolList theList)
          Transcribe DNA into RNA.
static SymbolList GeneticCodes.translate(SymbolList theList)
          Translate RNA into protein (with termination symbols).
 SymbolList DummySequence.subList(int start, int end)
           
 SymbolList Feature.getSymbols()
          Return a list of symbols that are contained in this feature.
 SymbolList SimpleAssembly.subList(int start, int end)
           
static SymbolList ProteinTools.createProtein(java.lang.String theProtein)
          Return a new Protein SymbolList for protein.
 

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

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(java.lang.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 RevCompSequence
          A reverse complement view onto Sequence interface.
 class SimpleSequence
          A basic implementation of the Sequence interface.
 

Methods in org.biojava.bio.seq.impl that return SymbolList
 SymbolList SimpleFeature.getSymbols()
           
 SymbolList AssembledSymbolList.subList(int start, int end)
           
 SymbolList SimpleSequence.subList(int start, int end)
           
 SymbolList SimpleStrandedFeature.getSymbols()
           
 

Methods in org.biojava.bio.seq.impl with parameters of type SymbolList
 void AssembledSymbolList.putComponent(Location l, SymbolList sl)
           
 Sequence SimpleSequenceFactory.createSequence(SymbolList symList, java.lang.String uri, java.lang.String name, Annotation annotation)
           
 

Constructors in org.biojava.bio.seq.impl with parameters of type SymbolList
SimpleSequence(SymbolList sym, java.lang.String urn, java.lang.String name, Annotation annotation)
          Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed.
SimpleSequence(SymbolList sym, java.lang.String urn, java.lang.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.
 SymbolList ChunkedSymbolListBuilder.makeSymbolList()
           
 

Methods in org.biojava.bio.seq.io with parameters of type SymbolList
 java.lang.String WordTokenization.tokenizeSymbolList(SymbolList sl)
           
 java.lang.String SymbolTokenization.tokenizeSymbolList(SymbolList sl)
          Return a string representation of a list of symbols.
 java.lang.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 ProjectedStrandedFeature.getSymbols()
           
 SymbolList ProjectedFeature.getSymbols()
           
 

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

Classes in org.biojava.bio.seq.ragbag that implement SymbolList
(package private)  class org.biojava.bio.seq.ragbag.RagbagAbstractSequence
          object that instantiates a sequence in Ragbag.
 class RagbagAssembly
          object that instantiates a sequence when given a Ragbag directory.
 

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 DummySymbolList
          Symbol list which just consists of non-informative symbols.
 class PackedDnaSymbolList
          a class that implements storage of symbols in packed form (2 symbols per byte).
 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.
static class SymbolList.EmptySymbolList
          The empty immutable implementation.
 

Fields in org.biojava.bio.symbol declared as SymbolList
 SymbolList Edit.replacement
           
static SymbolList SymbolList.EMPTY_LIST
          A useful object that represents an empty symbol list, to avoid returning null.
 

Methods in org.biojava.bio.symbol that return SymbolList
static SymbolList IntegerAlphabet.fromArray(int[] iArray)
          Retrieve a SymbolList view of an array of integers.
 SymbolList RelabeledAlignment.symbolListForLabel(java.lang.Object label)
           
 SymbolList RelabeledAlignment.subList(int min, int max)
           
 SymbolList AbstractRangeLocation.symbols(SymbolList seq)
           
 SymbolList SimpleAlignment.symbolListForLabel(java.lang.Object label)
           
 SymbolList PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
           
 SymbolList FuzzyPointLocation.symbols(SymbolList slist)
           
 SymbolList UkkonenSuffixTree.stringToSymbolList(java.lang.String string)
          Converts a string that came from symbolListToString back to a SymbolList.
 SymbolList Location.symbols(SymbolList seq)
          Return the symbols in a sequence that fall within this range.
 SymbolList SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          Create a factory for SimpleSymbolLists.
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 DoubleAlphabet.fromArray(double[] dArray)
           Retrieve a SymbolList view of an array of doubles.
 SymbolList AbstractSymbolList.subList(int start, int end)
           
 SymbolList SimpleGappedSymbolList.getSourceSymbolList()
          Return the underlying (ungapped) SymbolList.
 SymbolList Alignment.symbolListForLabel(java.lang.Object label)
          Retrieve a single row of the alignment by label.
 SymbolList SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          makes a SymbolList containing size Symbols from a Symbol array.
 SymbolList AbstractLocationDecorator.symbols(SymbolList seq)
           
 SymbolList CircularLocation.symbols(SymbolList seq)
           
 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.
 SymbolList SymbolList.EmptySymbolList.subList(int start, int end)
           
 SymbolList GappedSymbolList.getSourceSymbolList()
          Return the underlying (ungapped) SymbolList.
 

Methods in org.biojava.bio.symbol with parameters of type SymbolList
 SymbolList AbstractRangeLocation.symbols(SymbolList seq)
           
static int PackingFactory.primeWord(SymbolList symList, int wordLength, Packing packing)
           
static int PackingFactory.nextWord(SymbolList symList, int word, int offset, int wordLength, Packing packing)
           
 SymbolList FuzzyPointLocation.symbols(SymbolList slist)
           
 java.lang.String UkkonenSuffixTree.symbolListToString(SymbolList list)
          Makes a string out of a SymbolList, this string should only be used for internal or testing purposes, as it will necessarily consist of visible characters.
 void UkkonenSuffixTree.addSymbolList(SymbolList list, java.lang.String name, boolean doNotTerminate)
           
 SymbolList Location.symbols(SymbolList seq)
          Return the symbols in a sequence that fall within this range.
 void SuffixTree.addSymbols(SymbolList sList, int window)
          Add a count for all motifs with length of up to window to this tree.
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(java.util.List labels, SymbolList symList)
          View a SymbolList over a cross-product Alphabet as an Alignment.
static java.lang.String MotifTools.createRegex(SymbolList motif)
          createRegex creates a regular expression which matches the SymbolList.
 SymbolList AbstractLocationDecorator.symbols(SymbolList seq)
           
 SymbolList CircularLocation.symbols(SymbolList seq)
           
 

Constructors in org.biojava.bio.symbol with parameters of type SymbolList
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.
Edit(int pos, int length, SymbolList replacement)
          Create a new Edit.
SimpleSymbolList(SymbolList sl)
          Construct a copy of an existing SymbolList.
PackedDnaSymbolList(SymbolList symList)
          constructor taking another symbol list.