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

Packages that use Symbol
org.biojava.bio.alignment Classes to generate and describe sequence alignments. 
org.biojava.bio.chromatogram.graphic Tools for displaying chromatograms. 
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.gui Graphical interfaces for biojava objects. 
org.biojava.bio.program.abi ABI Trace Handling. 
org.biojava.bio.program.das Development client for the Distributed Annotation System. 
org.biojava.bio.program.hmmer Tools for working with profile Hidden Markov Models from the HMMer package. 
org.biojava.bio.program.phred Parser for Phred output 
org.biojava.bio.proteomics Utilities to aid in performing various physical analysis of proteins. 
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.structure Interfaces and classes for protein structure (PDB). 
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.bio.db.biosql Interface between biojava and biosql databases 
org.biojavax.bio.seq Rich implementations of Sequences, Locations and Features. 
org.biojavax.bio.seq.io Classes to support the I/O of RichSequence and Bioentry objects. 
 

Uses of Symbol in org.biojava.bio.alignment
 

Fields in org.biojava.bio.alignment with type parameters of type Symbol
protected  java.util.Map<Symbol,java.lang.Integer> SubstitutionMatrix.colSymbols
           
protected  java.util.Map<Symbol,java.lang.Integer> SubstitutionMatrix.rowSymbols
           
 

Methods in org.biojava.bio.alignment that return Symbol
 Symbol AbstractULAlignment.symbolAt(int index)
          this will return the ambiguity symbol associated with all symbols in that column
 Symbol AbstractULAlignment.SubULAlignment.symbolAt(int column)
           
 Symbol FlexibleAlignment.symbolAt(java.lang.Object label, int column)
          This gets the symbol for an individual sequence at position in the overall alignment If the sequence is not aligned at that location it returns null
 Symbol AbstractULAlignment.SubULAlignment.symbolAt(java.lang.Object label, int column)
           
 

Methods in org.biojava.bio.alignment with parameters of type Symbol
 short SubstitutionMatrix.getValueAt(Symbol row, Symbol col)
          There are some substitution matrices containing more columns than lines.
 

Uses of Symbol in org.biojava.bio.chromatogram.graphic
 

Methods in org.biojava.bio.chromatogram.graphic with parameters of type Symbol
 java.awt.Color ChromatogramGraphic.getBaseColor(Symbol b)
          Returns the color that will be used to draw the trace for the given DNA symbol.
 java.awt.Color ChromatogramGraphic.getBaseFillColor(Symbol b)
          Returns the color that will be used to fill in the callboxes for calls with the given symbol.
 void ChromatogramGraphic.setBaseColor(Symbol b, java.awt.Color c)
          Maps a color to a DNA symbol.
 

Uses of Symbol in org.biojava.bio.dist
 

Methods in org.biojava.bio.dist that return Symbol
 Symbol Distribution.sampleSymbol()
          Sample a symbol from this state's probability distribution.
 Symbol PairDistribution.sampleSymbol()
           
 Symbol TranslatedDistribution.sampleSymbol()
           
 Symbol GapDistribution.sampleSymbol()
           
 Symbol AbstractDistribution.sampleSymbol()
           
 

Methods in org.biojava.bio.dist with parameters of type Symbol
 void DistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)
           Registers that sym was counted in this state.
 void SimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)
           
 double DistributionTrainerContext.getCount(Distribution dist, Symbol sym)
          Return the number of counts of a particular symbol which will be used to train the specified distribution.
 double SimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym)
           
 Distribution OrderNDistribution.getDistribution(Symbol sym)
           
 double Distribution.getWeight(Symbol s)
           Return the probability that Symbol s is emitted by this spectrum.
 double PairDistribution.getWeight(Symbol sym)
           
 double TranslatedDistribution.getWeight(Symbol sym)
           
 double GapDistribution.getWeight(Symbol sym)
           
 double AbstractDistribution.getWeight(Symbol sym)
          Retrieve the weight for this distribution.
 void OrderNDistribution.setDistribution(Symbol sym, Distribution dist)
          Set the distribution assocated with a symbol.
 void Distribution.setWeight(Symbol s, double w)
          Set the probability or odds that Symbol s is emitted by this state.
 void PairDistribution.setWeight(Symbol sym, double weight)
           
 void TranslatedDistribution.setWeight(Symbol sym, double weight)
           
 void GapDistribution.setWeight(Symbol s, double w)
           
 void AbstractDistribution.setWeight(Symbol sym, double weight)
          Set the weight of a given symbol in this distribution.
 

Uses of Symbol in org.biojava.bio.dp
 

Subinterfaces of Symbol in org.biojava.bio.dp
 interface DotState
           A Dot state.
 interface EmissionState
           A state in a markov process that has an emission spectrum.
 interface ModelInState
          A state that contains an entire sub-model.
 interface State
          A state in a markov process.
 

Classes in org.biojava.bio.dp that implement Symbol
 class MagicalState
          Start/end state for HMMs.
 class SimpleDotState
          A Dot state that you can make and use.
 class SimpleEmissionState
           
 class SimpleModelInState
           
 

Methods in org.biojava.bio.dp that return Symbol
 Symbol SimpleStatePath.symbolAt(int col)
           
 Symbol SimpleStatePath.symbolAt(java.lang.Object label, int col)
           
 

Methods in org.biojava.bio.dp with parameters of type Symbol
 double ScoreType.calculateScore(Distribution dist, Symbol sym)
          Calculates the score associated with a distribution and a symbol.
 double ScoreType.Probability.calculateScore(Distribution dist, Symbol sym)
           
 double ScoreType.Odds.calculateScore(Distribution dist, Symbol sym)
           
 double ScoreType.NullModel.calculateScore(Distribution dist, Symbol sym)
           
 void SimpleHMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight)
           
 void HMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight)
          record that the specified symbol was emitted from the specified state.
 

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

Methods in org.biojava.bio.dp.onehead that return Symbol
 Symbol DPCursor.currentRes()
          The current symbol.
 Symbol DPCursor.lastRes()
          The previous symbol.
 

Methods in org.biojava.bio.dp.onehead with parameters of type Symbol
 double[] SingleDP.getEmission(Symbol sym, ScoreType scoreType)
          This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache.
 

Uses of Symbol in org.biojava.bio.gui
 

Methods in org.biojava.bio.gui with parameters of type Symbol
static double DistributionLogo.entropy(Distribution dist, Symbol s)
          Calculate the information content of a symbol in bits.
 java.awt.Paint DNAStyle.fillPaint(Symbol s)
           
 java.awt.Paint SimpleSymbolStyle.fillPaint(Symbol s)
           
 java.awt.Paint SymbolStyle.fillPaint(Symbol s)
          Return the fill paint for a symbol.
 java.awt.Paint PlainStyle.fillPaint(Symbol s)
           
 java.awt.Paint DNAStyle.outlinePaint(Symbol s)
           
 java.awt.Paint SimpleSymbolStyle.outlinePaint(Symbol s)
           
 java.awt.Paint SymbolStyle.outlinePaint(Symbol s)
          Return the outline paint for a symbol.
 java.awt.Paint PlainStyle.outlinePaint(Symbol s)
           
 void DNAStyle.setFillPaint(Symbol s, java.awt.Paint paint)
           
 void SimpleSymbolStyle.setFillPaint(Symbol s, java.awt.Paint paint)
           
 void DNAStyle.setOutlinePaint(Symbol s, java.awt.Paint paint)
           
 void SimpleSymbolStyle.setOutlinePaint(Symbol s, java.awt.Paint paint)
           
 

Uses of Symbol in org.biojava.bio.program.abi
 

Methods in org.biojava.bio.program.abi that return Symbol
static Symbol ABIFParser.decodeDNAToken(char token)
          Decodes a character into a Symbol in the DNA alphabet.
 

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

Methods in org.biojava.bio.program.das that return Symbol
 Symbol DASSequence.symbolAt(int pos)
           
 

Uses of Symbol in org.biojava.bio.program.hmmer
 

Classes in org.biojava.bio.program.hmmer that implement Symbol
 class ProfileEmissionState
          A state in a HMMer model.
 

Methods in org.biojava.bio.program.hmmer with parameters of type Symbol
 double ProfileEmissionState.logProb(Symbol sym)
           
 double HmmerProfileHMM.transScore(State from, State to, Symbol symFrom, Symbol symTo)
           
 

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

Methods in org.biojava.bio.program.phred that return Symbol
static Symbol PhredTools.dnaSymbolFromPhred(Symbol phredSym)
          Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
 Symbol PhredSequence.getDNAAt(int index)
           
static Symbol PhredTools.getPhredSymbol(Symbol dna, Symbol integer)
          Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
 Symbol Qualitative.getQualityAt(int index)
          Retreives the quality symbol for the specified index.
 Symbol PhredSequence.getQualityAt(int index)
           
 

Methods in org.biojava.bio.program.phred with parameters of type Symbol
static Symbol PhredTools.dnaSymbolFromPhred(Symbol phredSym)
          Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
static Symbol PhredTools.getPhredSymbol(Symbol dna, Symbol integer)
          Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
static IntegerAlphabet.IntegerSymbol PhredTools.integerSymbolFromPhred(Symbol phredSym)
          Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.
 

Uses of Symbol in org.biojava.bio.proteomics
 

Methods in org.biojava.bio.proteomics with parameters of type Symbol
 void MassCalc.addVariableModification(Symbol residue, double[] masses)
          Add Variable modifications.
 boolean MassCalc.removeVariableModifications(Symbol residue)
          Remove all variable modifications assocaited with this residue.
 

Uses of Symbol in org.biojava.bio.seq
 

Methods in org.biojava.bio.seq that return Symbol
static Symbol DNATools.b()
           
static Symbol NucleotideTools.b()
           
static Symbol RNATools.complement(Symbol sym)
          Complement the symbol.
static Symbol DNATools.complement(Symbol sym)
          Complement the symbol.
static Symbol NucleotideTools.complement(Symbol sym)
          Complement the symbol.
static Symbol DNATools.d()
           
static Symbol NucleotideTools.d()
           
static Symbol RNATools.forIndex(int index)
          Return the symbol for an index - compatible with index.
static Symbol DNATools.forIndex(int index)
          Return the symbol for an index - compatible with index.
static Symbol NucleotideTools.forIndex(int index)
          Return the symbol for an index - compatible with index.
static Symbol RNATools.forSymbol(char token)
          Retrieve the symbol for a symbol.
static Symbol DNATools.forSymbol(char token)
          Retrieve the symbol for a symbol.
static Symbol NucleotideTools.forSymbol(char token)
          Retrieve the symbol for a symbol.
static Symbol DNATools.h()
           
static Symbol NucleotideTools.h()
           
static Symbol DNATools.k()
           
static Symbol NucleotideTools.k()
           
static Symbol DNATools.m()
           
static Symbol NucleotideTools.m()
           
static Symbol RNATools.n()
           
static Symbol DNATools.n()
           
static Symbol NucleotideTools.n()
           
static Symbol DNATools.r()
           
static Symbol NucleotideTools.r()
           
static Symbol DNATools.s()
           
static Symbol NucleotideTools.s()
           
 Symbol SimpleAssembly.symbolAt(int pos)
           
 Symbol CircularView.symbolAt(int index)
           Over rides ViewSequence.
 Symbol NewSimpleAssembly.symbolAt(int pos)
           
static Symbol DNATools.v()
           
static Symbol NucleotideTools.v()
           
static Symbol DNATools.w()
           
static Symbol NucleotideTools.w()
           
static Symbol DNATools.y()
           
static Symbol NucleotideTools.y()
           
 

Methods in org.biojava.bio.seq with parameters of type Symbol
static Symbol RNATools.complement(Symbol sym)
          Complement the symbol.
static Symbol DNATools.complement(Symbol sym)
          Complement the symbol.
static Symbol NucleotideTools.complement(Symbol sym)
          Complement the symbol.
static Sequence SequenceTools.createDummy(Alphabet alpha, int length, Symbol sym, java.lang.String uri, java.lang.String name)
          Create a new Sequence that contains a single symbol repeated over and over.
static char DNATools.dnaToken(Symbol sym)
          Get a single-character token for a DNA symbol
static int RNATools.index(Symbol sym)
          Return an integer index for a symbol - compatible with forIndex.
static int DNATools.index(Symbol sym)
          Return an integer index for a symbol - compatible with forIndex.
static int NucleotideTools.index(Symbol sym)
          Return an integer index for a symbol - compatible with forIndex.
static char NucleotideTools.nucleotideToken(Symbol sym)
          Get a single-character token for a Nucleotide symbol
 

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

Methods in org.biojava.bio.seq.homol that return Symbol
 Symbol SimilarityPairFeature.EmptyPairwiseAlignment.symbolAt(int index)
           
 Symbol SimilarityPairFeature.EmptyPairwiseAlignment.symbolAt(java.lang.Object label, int index)
           
 

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

Methods in org.biojava.bio.seq.impl that return Symbol
 Symbol SubSequence.symbolAt(int pos)
           
 Symbol SimpleSequence.symbolAt(int index)
           
 Symbol AssembledSymbolList.symbolAt(int pos)
           
 Symbol NewAssembledSymbolList.symbolAt(int pos)
           
 Symbol ViewSequence.symbolAt(int indx)
           
 Symbol DummySequence.symbolAt(int index)
           
 

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

Methods in org.biojava.bio.seq.io that return Symbol
protected  Symbol[] CharacterTokenization.getTokenTable()
           
protected  Symbol[] WordTokenization.parseString(java.lang.String s)
           
 Symbol CharacterTokenization.parseToken(java.lang.String token)
           
 Symbol IntegerTokenization.parseToken(java.lang.String seq)
           
 Symbol SymbolTokenization.parseToken(java.lang.String token)
          Returns the symbol for a single token.
 Symbol CrossProductTokenization.parseToken(java.lang.String token)
           
 Symbol AlternateTokenization.parseToken(java.lang.String token)
          Will throw an exception.
 Symbol DoubleTokenization.parseToken(java.lang.String seq)
           
 Symbol NameTokenization.parseToken(java.lang.String token)
           
 Symbol SubIntegerTokenization.parseToken(java.lang.String seq)
           
protected  Symbol CharacterTokenization.parseTokenChar(char c)
           
 Symbol SymbolReader.readSymbol()
          Return a single symbol from the stream.
 

Methods in org.biojava.bio.seq.io with parameters of type Symbol
 void ProteinRefSeqFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Deprecated.  
 void ChunkedSymbolListFactory.addSymbols(Alphabet alfa, Symbol[] syms, int pos, int len)
          tool to construct the SymbolList by adding Symbols.
 void SimpleAssemblyBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 void SimpleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
abstract  void SequenceBuilderBase.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 void SwissprotFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Deprecated. Prints out the sequences properties in order.
 void EmblFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
          Deprecated.  
 void SmartSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 void SeqIOFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void SequenceBuilderFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void SeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void SequenceDBSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
          does nothing for now.
 void GenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
          Deprecated.  
 void SeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
          Notify the listener of symbol data.
 void CharacterTokenization.bindSymbol(Symbol s, char c)
           Bind a Symbol to a character.
 void AlternateTokenization.bindSymbol(Symbol s, java.lang.String str)
          Bind a Symbol to a string.
protected  java.util.List ProteinRefSeqFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Deprecated. Converts the symbol list passed in into an array of strings.
protected  java.util.List SwissprotFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Deprecated. Converts the symbol list passed in into an array of strings.
protected  void SwissprotFileFormer.printOutSequenceHeaderLine(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Deprecated. Prints out sequence header with only length data.
 int SymbolReader.readSymbols(Symbol[] buffer, int start, int length)
          Read one or more symbols from the stream.
 java.lang.String CharacterTokenization.tokenizeSymbol(Symbol s)
           
 java.lang.String IntegerTokenization.tokenizeSymbol(Symbol sym)
           
 java.lang.String SymbolTokenization.tokenizeSymbol(Symbol sym)
          Return a token representing a single symbol.
 java.lang.String CrossProductTokenization.tokenizeSymbol(Symbol s)
           
 java.lang.String AlternateTokenization.tokenizeSymbol(Symbol s)
           
 java.lang.String DoubleTokenization.tokenizeSymbol(Symbol sym)
           
 java.lang.String NameTokenization.tokenizeSymbol(Symbol s)
           
 java.lang.String SubIntegerTokenization.tokenizeSymbol(Symbol sym)
           
 

Uses of Symbol in org.biojava.bio.structure
 

Methods in org.biojava.bio.structure that return Symbol
static Symbol AlphaCTools.getPhiPsiSymbol(double phiAngle, double psiAngle)
          Makes a Phi - Psi Symbol from the ALPHA CARBON ANGLES alphabet.
 

Methods in org.biojava.bio.structure with parameters of type Symbol
static double AlphaCTools.getPhiAngle(Symbol phiPsiSym)
          extracts the Phi angle from a Symbol.
static double AlphaCTools.getPsiAngle(Symbol phiPsiSym)
          extracts the Psi angle from a Symbol.
 

Uses of Symbol in org.biojava.bio.symbol
 

Subinterfaces of Symbol in org.biojava.bio.symbol
 interface AtomicSymbol
           A symbol that is not ambiguous.
 interface BasisSymbol
           A symbol that can be represented as a string of Symbols.
 

Classes in org.biojava.bio.symbol that implement Symbol
 class AbstractSymbol
          The base-class for Symbol implementations.
static class DoubleAlphabet.DoubleRange
          A range of double values.
static class DoubleAlphabet.DoubleSymbol
          A single double value.
 class FundamentalAtomicSymbol
          An atomic symbol consisting only of itself.
static class IntegerAlphabet.IntegerSymbol
          A single int value.
 class SimpleAtomicSymbol
          A basic implementation of AtomicSymbol.
 

Methods in org.biojava.bio.symbol that return Symbol
static Symbol AlphabetManager.createSymbol(Annotation annotation, java.util.List symList, Alphabet alpha)
           Generates a new Symbol instance that represents the tuple of Symbols in symList.
static Symbol AlphabetManager.createSymbol(Annotation annotation, java.util.Set symSet, Alphabet alpha)
           Generates a new Symbol instance that represents the tuple of Symbols in symList.
static Symbol AlphabetManager.createSymbol(char token, Annotation annotation, java.util.List symList, Alphabet alpha)
          Deprecated. use the new version, without the token argument
static Symbol AlphabetManager.createSymbol(char token, Annotation annotation, java.util.Set symSet, Alphabet alpha)
          Deprecated. use the three-arg version of this method instead.
protected  Symbol SimpleManyToOneTranslationTable.doTranslate(Symbol sym)
           
 Symbol SimpleTranslationTable.doTranslate(Symbol sym)
           
protected  Symbol SimpleReversibleTranslationTable.doTranslate(Symbol sym)
           
protected abstract  Symbol AbstractReversibleTranslationTable.doUntranslate(Symbol sym)
          this method is expected to reverse-translate any symbol in the source alphabet.
protected  Symbol SimpleReversibleTranslationTable.doUntranslate(Symbol sym)
           
static Symbol AlphabetManager.getAllAmbiguitySymbol(FiniteAlphabet alpha)
          Return the ambiguity symbol which matches all symbols in a given alphabet.
 Symbol IntegerAlphabet.getAmbiguity(java.util.Set symSet)
           
 Symbol AbstractAlphabet.getAmbiguity(java.util.Set syms)
           
 Symbol SoftMaskedAlphabet.getAmbiguity(java.util.Set s)
          This is not supported.
 Symbol Alphabet.getAmbiguity(java.util.Set syms)
           Get a symbol that represents the set of symbols in syms.
 Symbol DoubleAlphabet.getAmbiguity(java.util.Set syms)
           
 Symbol DoubleAlphabet.SubDoubleAlphabet.getAmbiguity(java.util.Set syms)
           
protected  Symbol AbstractAlphabet.getAmbiguityImpl(java.util.Set syms)
          Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
 Symbol IntegerAlphabet.getGapSymbol()
           
 Symbol AbstractAlphabet.getGapSymbol()
           
 Symbol SoftMaskedAlphabet.getGapSymbol()
           
 Symbol Alphabet.getGapSymbol()
           Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
static Symbol AlphabetManager.getGapSymbol()
           Get the special `gap' Symbol.
 Symbol DoubleAlphabet.getGapSymbol()
           
 Symbol DoubleAlphabet.SubDoubleAlphabet.getGapSymbol()
           
static Symbol AlphabetManager.getGapSymbol(java.util.List alphas)
           Get the gap symbol appropriate to this list of alphabets.
 Symbol WobbleDistribution.getResidue()
          returns the residue encoded by this WobbleDistribution
 Symbol IllegalSymbolException.getSymbol()
          Retrieve the symbol that caused this exception, or null.
 Symbol IntegerAlphabet.getSymbol(java.util.List symList)
           
 Symbol AbstractAlphabet.getSymbol(java.util.List syms)
           
 Symbol SoftMaskedAlphabet.getSymbol(java.util.List l)
          Gets the compound symbol composed of the Symbols in the List.
 Symbol Alphabet.getSymbol(java.util.List rl)
           Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
 Symbol DoubleAlphabet.getSymbol(java.util.List symList)
           
 Symbol DoubleAlphabet.SubDoubleAlphabet.getSymbol(java.util.List rl)
           
 Symbol[] SimpleSymbolList.getSymbolArray()
          Return the Java Symbol[] array that backs this object.
 Symbol SoftMaskedAlphabet.CaseSensitiveTokenization.parseToken(java.lang.String token)
           
 Symbol SimpleSymbolList.symbolAt(int pos)
          Find a symbol at a specified offset in the SymbolList.
 Symbol SimpleGappedSymbolList.symbolAt(int indx)
           
 Symbol PackedSymbolList.symbolAt(int indx)
           
 Symbol ChunkedSymbolList.symbolAt(int pos)
           
 Symbol SimpleAlignment.symbolAt(int index)
           
 Symbol DummySymbolList.symbolAt(int i)
           
 Symbol SymbolList.symbolAt(int index)
          Return the symbol at index, counting from 1.
 Symbol RelabeledAlignment.symbolAt(int pos)
           
 Symbol SimpleAlignment.symbolAt(java.lang.Object label, int column)
           
 Symbol RelabeledAlignment.symbolAt(java.lang.Object label, int column)
           
 Symbol Alignment.symbolAt(java.lang.Object label, int column)
          Retrieve a symbol by label and column.
 Symbol AlphabetIndex.symbolForIndex(int i)
          Retrieve the symbol for an index.
static Symbol AlphabetManager.symbolForLifeScienceID(LifeScienceIdentifier lsid)
          Retreives the Symbol for the LSID
static Symbol AlphabetManager.symbolForName(java.lang.String name)
          Deprecated. use symbolForLifeScienceID() instead
 Symbol TranslationTable.translate(Symbol sym)
          Translate a single symbol from source alphabet to the target alphabet.
 Symbol DNAAmbPack.unpack(byte b)
           
 Symbol DNANoAmbPack.unpack(byte b)
           
 Symbol Packing.unpack(byte packed)
           Return the symbol for a packing.
 Symbol AbstractReversibleTranslationTable.untranslate(Symbol sym)
           
 Symbol ReversibleTranslationTable.untranslate(Symbol sym)
          Translate a single symbol from target alphabet to the source alphabet.
 

Methods in org.biojava.bio.symbol that return types with arguments of type Symbol
 java.util.Iterator<Symbol> FiniteAlphabet.iterator()
          Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.
 

Methods in org.biojava.bio.symbol with parameters of type Symbol
 void SimpleSymbolList.addSymbol(Symbol sym)
          Add a new Symbol to the end of this list.
 void FiniteAlphabet.addSymbol(Symbol s)
          Adds a symbol to this alphabet.
 void AbstractAlphabet.addSymbol(Symbol s)
           
 void SoftMaskedAlphabet.addSymbol(Symbol s)
          SoftMaskedAlphabets cannot add new Symbols.
 boolean IntegerAlphabet.contains(Symbol s)
           
 boolean AbstractAlphabet.contains(Symbol sym)
           
 boolean SoftMaskedAlphabet.contains(Symbol s)
           
 boolean Alphabet.contains(Symbol s)
           Returns whether or not this Alphabet contains the symbol.
 boolean DoubleAlphabet.contains(Symbol s)
           
 boolean DoubleAlphabet.SubDoubleAlphabet.contains(Symbol s)
           
protected  Symbol SimpleManyToOneTranslationTable.doTranslate(Symbol sym)
           
 Symbol SimpleTranslationTable.doTranslate(Symbol sym)
           
protected  Symbol SimpleReversibleTranslationTable.doTranslate(Symbol sym)
           
protected abstract  java.util.Set AbstractManyToOneTranslationTable.doUntranslate(Symbol sym)
          this method is expected to reverse-translate any symbol in the source alphabet.
protected abstract  Symbol AbstractReversibleTranslationTable.doUntranslate(Symbol sym)
          this method is expected to reverse-translate any symbol in the source alphabet.
protected  java.util.Set SimpleManyToOneTranslationTable.doUntranslate(Symbol sym)
           
protected  Symbol SimpleReversibleTranslationTable.doUntranslate(Symbol sym)
           
static AlphabetIndex AlphabetManager.getAlphabetIndex(Symbol[] syms)
          Get an indexer for an array of symbols.
 SuffixTree.SuffixNode SuffixTree.getChild(SuffixTree.SuffixNode node, Symbol s)
          Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
 double SymbolPropertyTable.getDoubleValue(Symbol s)
           
 double SimpleSymbolPropertyTable.getDoubleValue(Symbol s)
           
 Distribution SimpleCodonPref.getFrequencyForSynonyms(Symbol residue)
           
 Distribution CodonPref.getFrequencyForSynonyms(Symbol residue)
          returns a Distribution giving the frequency of synonymous codons.
 WobbleDistribution SimpleCodonPref.getWobbleDistributionForSynonyms(Symbol residue)
           
 WobbleDistribution CodonPref.getWobbleDistributionForSynonyms(Symbol residue)
          returns a WobbleDistribution for a specified residue.
 Distribution WobbleDistribution.getWobbleFrequency(Symbol nonWobbleBases)
          returns the frequency of a specific wobble base in a set of synonymous codons that start with the same two bases.
 int AlphabetIndex.indexForSymbol(Symbol s)
          Return the unique index for a symbol.
 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.
 byte DNAAmbPack.pack(Symbol sym)
           
 byte DNANoAmbPack.pack(Symbol sym)
           
 byte Packing.pack(Symbol sym)
           Return a byte representing the packing of a symbol.
 void FiniteAlphabet.removeSymbol(Symbol s)
          Remove a symbol from this alphabet.
 void SimpleAlphabet.removeSymbol(Symbol s)
           
 void IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)
           
 void SingletonAlphabet.removeSymbol(Symbol sym)
           
 void SoftMaskedAlphabet.removeSymbol(Symbol s)
          SoftMaskedAlphabets cannot remove Symbols.
 void SimpleSymbolPropertyTable.setDoubleProperty(Symbol s, java.lang.String value)
           
 java.lang.String SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbol(Symbol s)
           
 Symbol TranslationTable.translate(Symbol sym)
          Translate a single symbol from source alphabet to the target alphabet.
 java.util.Set AbstractManyToOneTranslationTable.untranslate(Symbol sym)
          returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet.
 Symbol AbstractReversibleTranslationTable.untranslate(Symbol sym)
           
 java.util.Set ManyToOneTranslationTable.untranslate(Symbol sym)
          Translate a single symbol from target alphabet to the source alphabet.
 Symbol ReversibleTranslationTable.untranslate(Symbol sym)
          Translate a single symbol from target alphabet to the source alphabet.
 void IntegerAlphabet.validate(Symbol s)
           
 void AbstractAlphabet.validate(Symbol sym)
           
 void SoftMaskedAlphabet.validate(Symbol s)
           
 void Alphabet.validate(Symbol s)
           Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
 void DoubleAlphabet.validate(Symbol s)
           
 void DoubleAlphabet.SubDoubleAlphabet.validate(Symbol sym)
           
 

Constructors in org.biojava.bio.symbol with parameters of type Symbol
DNANoAmbPack(Symbol placeHolderSymbol)
          Construct a new packing which translates unknown symbols into the specified symbol.
DummySymbolList(Alphabet alpha, int length, Symbol sym)
           
Edit(int pos, Alphabet alpha, Symbol replacement)
          Convenience construtor for making single residue changes
IllegalSymbolException(Symbol sym, java.lang.String message)
          Make the exception with a message and a symbol.
IllegalSymbolException(java.lang.Throwable cause, Symbol sym, java.lang.String message)
           
PackedSymbolList(Packing packing, Symbol[] symbols, int length, Alphabet alfa)
           Create a new PackedSymbolList from an array of Symbols.
SimpleSymbolList(Symbol[] symbols, int length, Alphabet alphabet)
          Construct a SimpleSymbolList given the Symbol array that backs it.
 

Uses of Symbol in org.biojava.utils.automata
 

Methods in org.biojava.utils.automata with parameters of type Symbol
 org.biojava.utils.automata.FiniteAutomaton.Transition NfaBuilder.addTransition(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym)
           
 org.biojava.utils.automata.FiniteAutomaton.Transition FiniteAutomaton.addTransition(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym)
           
 org.biojava.utils.automata.FiniteAutomaton.Transition NfaSubModel.addTransition(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym)
           
protected  int Nfa.alphaIndex(Symbol sym)
           
protected  int FiniteAutomaton.alphaIndex(Symbol sym)
           
 

Uses of Symbol in org.biojava.utils.regex
 

Methods in org.biojava.utils.regex with parameters of type Symbol
 char Search.charValue(Symbol sym)
           
 char PatternFactory.charValue(Symbol sym)
          Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for.
 

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

Methods in org.biojavax.bio.db.biosql that return Symbol
 Symbol BioSQLRichSequenceHandler.symbolAt(RichSequence seq, int index)
          Return the symbol at index, counting from 1.
 

Uses of Symbol in org.biojavax.bio.seq
 

Methods in org.biojavax.bio.seq that return Symbol
 Symbol ThinRichSequence.symbolAt(int index)
          Return the symbol at index, counting from 1.
 Symbol InfinitelyAmbiguousSymbolList.symbolAt(int index)
          Return the symbol at index, counting from 1.
 Symbol RichSequenceHandler.symbolAt(RichSequence seq, int index)
          Return the symbol at index, counting from 1.
 Symbol DummyRichSequenceHandler.symbolAt(RichSequence seq, int index)
          Return the symbol at index, counting from 1.
 

Uses of Symbol in org.biojavax.bio.seq.io
 

Methods in org.biojavax.bio.seq.io with parameters of type Symbol
 void DebuggingRichSeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void SimpleRichSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
          Notify the listener of symbol data.
 void RichSeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)