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

Packages that use SymbolList
org.biojava.bio.alignment Classes to generate and describe sequence alignments. 
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. 
org.biojavax The Biojava extensions packages, classes that extend the core biojava functionality 
org.biojavax.bio.db.biosql Interface between biojava and biosql databases 
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
 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 AlignmentElement.getSymbolList()
           
 SymbolList AbstractULAlignment.SubULAlignment.symbolListForLabel(Object label)
           
 SymbolList FlexibleAlignment.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
protected  SymbolList AbstractChromatogram.createImmutableSymbolList(Alphabet alpha, 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.
protected  SymbolList AbstractChromatogram.reverseComplementBaseCallList(Object label)
          Return a symbol list containing the reverse complement of the base call data for the given label.
 

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

Methods in org.biojava.bio.dp with parameters of type SymbolList
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 BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
           
protected  double BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType)
           
abstract  StatePath DP.viterbi(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
 

Fields in org.biojava.bio.dp.onehead declared as SymbolList
protected  SymbolList[] SingleDPMatrix.symList
           
 

Methods in org.biojava.bio.dp.onehead that return SymbolList
 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
 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
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
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, 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
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.gui.sequence
 

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

Methods in org.biojava.bio.gui.sequence with parameters of type SymbolList
 void CircularRendererPanel.setSequence(SymbolList symList)
           
 void SequencePanel.setSequence(SymbolList s)
          Set the SymboList to be rendered.
 void TranslatedSequencePanel.setSequence(SymbolList sequence)
          setSequence sets the Sequence to be rendered.
 

Constructors in org.biojava.bio.gui.sequence with parameters of type SymbolList
SubCircularRendererContext(CircularRendererContext delegate, SymbolList symbols, FeatureHolder features, double radius)
          Create a new sub context.
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)
           
SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range, int symOffset)
           
 

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

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
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
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 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
 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, String name)
           
static Protease ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name)
          Creates and registers a new Protease.
 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.
 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
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
 SymbolList MaxMismatchPattern.getPattern()
           
 SymbolList KnuthMorrisPrattSearch.getPattern()
           
 SymbolList MaxMismatchMatcher.group()
           
 SymbolList BioMatcher.group()
          Get the matching region as a SymbolList.
 

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).
 BioMatcher MaxMismatchPattern.matcher(SymbolList symList)
           
 BioMatcher SeqContentPattern.matcher(SymbolList symList)
           
 BioMatcher BioPattern.matcher(SymbolList symList)
          Get a matcher that will use these parameters to search a 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.
 void MaxMismatchPattern.setPattern(SymbolList pattern)
           
 

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.
MaxMismatchPattern(SymbolList pattern, int mismatches)
           
 

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
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 StrandedFeature.getSymbols()
          Return a list of symbols that are contained in this feature.
 SymbolList Feature.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 SimpleAssembly.subList(int start, int end)
           
 SymbolList CircularView.subList(int start, int end)
           Over rides ViewSequence.
 SymbolList NewSimpleAssembly.subList(int start, int end)
           
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
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.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
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.subList(int index1, int index2)
           
 SymbolList SimilarityPairFeature.EmptyPairwiseAlignment.symbolListForLabel(Object label)
           
 

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 SimpleFeature.getSymbols()
           
 SymbolList SimpleStrandedFeature.getSymbols()
           
 SymbolList SimpleSequence.subList(int start, int end)
           
 SymbolList DummySequence.subList(int start, int end)
           
 SymbolList ViewSequence.subList(int start, int end)
           
 SymbolList AssembledSymbolList.subList(int start, int end)
           
 SymbolList NewAssembledSymbolList.subList(int start, int end)
           
 SymbolList SubSequence.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.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
 String SymbolTokenization.tokenizeSymbolList(SymbolList symList)
          Return a string representation of a list of symbols.
 String WordTokenization.tokenizeSymbolList(SymbolList sl)
           
 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.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 SimpleGappedSymbolList.getSourceSymbolList()
           
 SymbolList GappedSymbolList.getSourceSymbolList()
          Return the underlying (ungapped) SymbolList.
 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.
 SymbolList PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          Makes a packed SymbolList out of a list of Symbols.
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 RelabeledAlignment.subList(int min, int max)
           
 SymbolList SymbolList.subList(int start, int end)
          Return a new SymbolList for the symbols start to end inclusive.
 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 ChunkedSymbolList.subList(int start, int end)
           
static SymbolList SymbolListViews.subList(SymbolList parent, int start, int end)
          View a portion of a SymbolList.
 SymbolList RelabeledAlignment.symbolListForLabel(Object label)
           
 SymbolList Alignment.symbolListForLabel(Object label)
          Retrieve a single row of the alignment by label.
 SymbolList SimpleAlignment.symbolListForLabel(Object label)
           
 SymbolList CircularLocation.symbols(SymbolList seq)
           
 SymbolList FuzzyPointLocation.symbols(SymbolList slist)
           
 SymbolList AbstractRangeLocation.symbols(SymbolList seq)
           
 SymbolList AbstractLocationDecorator.symbols(SymbolList seq)
           
 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
 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 CircularLocation.symbols(SymbolList seq)
           
 SymbolList FuzzyPointLocation.symbols(SymbolList slist)
           
 SymbolList AbstractRangeLocation.symbols(SymbolList seq)
           
 SymbolList AbstractLocationDecorator.symbols(SymbolList seq)
           
 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
ChunkedSymbolList(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha)
           
Edit(int pos, int length, SymbolList replacement)
          Create a new Edit.
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
 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
 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
 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. All responses are instances of InfinitelyAmbiguousSymbolList.
 

Uses of SymbolList in org.biojavax.bio.db.biosql
 

Methods in org.biojavax.bio.db.biosql that return SymbolList
 SymbolList BioSQLCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a)
          Given a cross reference, return the corresponding symbol list.
 SymbolList BioSQLRichSequenceHandler.subList(RichSequence seq, int start, int end)
          Return a new SymbolList for the symbols start to end inclusive.

The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.

 

Uses of SymbolList in org.biojavax.bio.seq
 

Subinterfaces of SymbolList in org.biojavax.bio.seq
 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
 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
 SymbolList SimpleRichSequence.getInternalSymbolList()
          A special function that returns the SymbolList that this RichSequence is based around. This should _not_ be the RichSequence object itself, as this function is used to perform actions on the symbol list without referring to the RichSequence object directly.
 SymbolList ThinRichSequence.getInternalSymbolList()
          A special function that returns the SymbolList that this RichSequence is based around.
 SymbolList RichSequence.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 ThinRichSequence.subList(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. ALWAYS RETURNS SELF
 SymbolList RichSequenceHandler.subList(RichSequence seq, int start, int end)
          Return a new SymbolList for the symbols start to end inclusive.
 SymbolList DummyRichSequenceHandler.subList(RichSequence seq, int start, int end)
          Return a new SymbolList for the symbols start to end inclusive.
 SymbolList SimpleRichLocation.symbols(SymbolList seq)
          Return the symbols in a sequence that fall within this range. If the location is circular but the sequence is not, or they are both circular but of different circular lengths, an exception is thrown.
 SymbolList EmptyRichLocation.symbols(SymbolList seq)
          Return the symbols in a sequence that fall within this range. ALWAYS RETURNS THE EMPTY SYMBOL LIST
 SymbolList CompoundRichLocation.symbols(SymbolList seq)
          Return the symbols in a sequence that fall within this range. If the location is circular but the sequence is not, or they are both circular but of different circular lengths, an exception is thrown. This function concatenates the symbols of all its child locations.
 

Methods in org.biojavax.bio.seq with parameters of type SymbolList
static RichSequence RichSequence.Tools.createRichSequence(Namespace ns, String name, SymbolList syms)
          Create a new RichSequence in the specified namespace.
static RichSequence RichSequence.Tools.createRichSequence(String name, SymbolList syms)
          Create a new RichSequence in the default namespace.
 SymbolList SimpleRichLocation.symbols(SymbolList seq)
          Return the symbols in a sequence that fall within this range. If the location is circular but the sequence is not, or they are both circular but of different circular lengths, an exception is thrown.
 SymbolList EmptyRichLocation.symbols(SymbolList seq)
          Return the symbols in a sequence that fall within this range. ALWAYS RETURNS THE EMPTY SYMBOL LIST
 SymbolList CompoundRichLocation.symbols(SymbolList seq)
          Return the symbols in a sequence that fall within this range. If the location is circular but the sequence is not, or they are both circular but of different circular lengths, an exception is thrown. This function concatenates the symbols of all its child locations.
 

Constructors in org.biojavax.bio.seq with parameters of type SymbolList
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
 SymbolList[] Organism.getChromosomes()
          Gets the organisms 'chromosome' sequences
 

Methods in org.biojavax.ga with parameters of type SymbolList
 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
 SymbolList[] GACrossResult.getChromosomes()
          Gets the chromosomes after the cross
 SymbolList[] GACross.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)
           
 

Methods in org.biojavax.ga.functions with parameters of type SymbolList
 SymbolList MutationFunction.mutate(SymbolList seq)
          Produces a new SymbolList by mutation.
 SymbolList MutationFunction.NoMutation.mutate(SymbolList syml)
           
 SymbolList SimpleMutationFunction.mutate(SymbolList seq)
           
 GACrossResult SimpleCrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)
           
 GACrossResult CrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)
          Performs a cross between the pair of chromosomes
 GACrossResult CrossOverFunction.NoCross.performCrossOver(SymbolList chromA, SymbolList chromB)
           
 

Constructors in org.biojavax.ga.functions with parameters of type SymbolList
SimpleGACrossResult(PointLocation[] crossOverPositions, SymbolList[] chromosomes)
           
 

Uses of SymbolList in org.biojavax.ga.impl
 

Methods in org.biojavax.ga.impl that return SymbolList
 SymbolList[] AbstractOrganism.getChromosomes()
           
 

Methods in org.biojavax.ga.impl with parameters of type SymbolList
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
static SymbolList GATools.createBinary(String binarySequence)
          Creates a SymbolList in the GABinary Alphabet