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

Packages that use Symbol
org.biojava.bio.alignment Implementation of the Alignment interface. 
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.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 Symbol in org.biojava.bio.alignment
 

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(java.lang.Object label, int 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
 

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 TranslatedDistribution.sampleSymbol()
           
 Symbol GapDistribution.sampleSymbol()
           
 Symbol PairDistribution.sampleSymbol()
           
 Symbol AbstractDistribution.sampleSymbol()
           
 Symbol Distribution.sampleSymbol()
          Sample a symbol from this state's probability distribution.
 

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

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)
           
 

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

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 SimpleSymbolStyle.outlinePaint(Symbol s)
           
 java.awt.Paint SimpleSymbolStyle.fillPaint(Symbol s)
           
 void SimpleSymbolStyle.setOutlinePaint(Symbol s, java.awt.Paint paint)
           
 void SimpleSymbolStyle.setFillPaint(Symbol s, java.awt.Paint paint)
           
 java.awt.Paint DNAStyle.outlinePaint(Symbol s)
           
 java.awt.Paint DNAStyle.fillPaint(Symbol s)
           
 void DNAStyle.setOutlinePaint(Symbol s, java.awt.Paint paint)
           
 void DNAStyle.setFillPaint(Symbol s, java.awt.Paint paint)
           
 java.awt.Paint SymbolStyle.outlinePaint(Symbol s)
          Return the outline paint for a symbol.
 java.awt.Paint SymbolStyle.fillPaint(Symbol s)
          Return the fill paint for a symbol.
 java.awt.Paint PlainStyle.outlinePaint(Symbol s)
           
 java.awt.Paint PlainStyle.fillPaint(Symbol s)
           
 

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 HmmerProfileHMM.transScore(State from, State to, Symbol symFrom, Symbol symTo)
           
 double ProfileEmissionState.logProb(Symbol sym)
           
 

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

Methods in org.biojava.bio.program.phred that return Symbol
 Symbol Qualitative.getQualityAt(int index)
          Retreives the quality symbol for the specified index.
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).
 Symbol PhredSequence.getQualityAt(int index)
           
 Symbol PhredSequence.getDNAAt(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 IntegerAlphabet.IntegerSymbol PhredTools.integerSymbolFromPhred(Symbol phredSym)
          Retrives the IntegerSymbol 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).
 

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 RNATools.n()
           
static Symbol RNATools.forIndex(int index)
          Return the symbol for an index - compatible with index.
static Symbol RNATools.complement(Symbol sym)
          Complement the symbol.
static Symbol RNATools.forSymbol(char token)
          Retrieve the symbol for a symbol.
static Symbol NucleotideTools.r()
           
static Symbol NucleotideTools.y()
           
static Symbol NucleotideTools.m()
           
static Symbol NucleotideTools.k()
           
static Symbol NucleotideTools.s()
           
static Symbol NucleotideTools.w()
           
static Symbol NucleotideTools.b()
           
static Symbol NucleotideTools.d()
           
static Symbol NucleotideTools.h()
           
static Symbol NucleotideTools.v()
           
static Symbol NucleotideTools.n()
           
static Symbol NucleotideTools.forIndex(int index)
          Return the symbol for an index - compatible with index.
static Symbol NucleotideTools.complement(Symbol sym)
          Complement the symbol.
static Symbol NucleotideTools.forSymbol(char token)
          Retrieve the symbol for a symbol.
static Symbol DNATools.n()
           
static Symbol DNATools.forIndex(int index)
          Return the symbol for an index - compatible with index.
static Symbol DNATools.complement(Symbol sym)
          Complement the symbol.
static Symbol DNATools.forSymbol(char token)
          Retrieve the symbol for a symbol.
 Symbol ViewSequence.symbolAt(int indx)
           
 Symbol CircularView.symbolAt(int index)
           Over rides ViewSequence.
 Symbol SimpleAssembly.symbolAt(int pos)
           
 Symbol SubSequence.symbolAt(int pos)
           
 Symbol DummySequence.symbolAt(int index)
           
 

Methods in org.biojava.bio.seq with parameters of type Symbol
static int RNATools.index(Symbol sym)
          Return an integer index for a symbol - compatible with forIndex.
static Symbol RNATools.complement(Symbol sym)
          Complement the symbol.
static int NucleotideTools.index(Symbol sym)
          Return an integer index for a symbol - compatible with forIndex.
static Symbol NucleotideTools.complement(Symbol sym)
          Complement the symbol.
static char NucleotideTools.nucleotideToken(Symbol sym)
          Get a single-character token for a Nucleotide symbol
static int DNATools.index(Symbol sym)
          Return an integer index for a symbol - compatible with forIndex.
static Symbol DNATools.complement(Symbol sym)
          Complement the symbol.
static char DNATools.dnaToken(Symbol sym)
          Get a single-character token for a DNA symbol
 

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

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

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

Methods in org.biojava.bio.seq.impl that return Symbol
 Symbol AssembledSymbolList.symbolAt(int pos)
           
 Symbol SimpleSequence.symbolAt(int index)
           
 

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

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

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

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

Methods in org.biojava.bio.seq.ragbag with parameters of type Symbol
 void RagbagIdleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 

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.
(package private)  class org.biojava.bio.symbol.SimpleBasisSymbol
          A basic implementation of BasisSymbol.
(package private)  class org.biojava.bio.symbol.SimpleSymbol
          A basic implementation of Symbol.
 

Methods in org.biojava.bio.symbol that return Symbol
 Symbol TranslationTable.translate(Symbol sym)
          Translate a single symbol from source alphabet to the target alphabet.
 Symbol SimpleAlignment.symbolAt(int index)
           
 Symbol SimpleAlignment.symbolAt(java.lang.Object label, int column)
           
 Symbol SimpleSymbolList.symbolAt(int pos)
          Find a symbol at a specified offset in the SymbolList.
 Symbol[] SimpleSymbolList.getSymbolArray()
          Return the Java Symbol[] array that backs this object.
 Symbol SymbolList.symbolAt(int index)
          Return the symbol at index, counting from 1.
 Symbol SymbolList.EmptySymbolList.symbolAt(int index)
           
 Symbol Packing.unpack(byte packed)
           Return the symbol for a packing.
 Symbol RelabeledAlignment.symbolAt(java.lang.Object label, int column)
           
 Symbol RelabeledAlignment.symbolAt(int pos)
           
 Symbol SimpleReversibleTranslationTable.untranslate(Symbol sym)
           
 Symbol AbstractAlphabet.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 AbstractAlphabet.getSymbol(java.util.List syms)
           
 Symbol AbstractAlphabet.getGapSymbol()
           
static Symbol AlphabetManager.getAllAmbiguitySymbol(FiniteAlphabet alpha)
          Return the ambiguity symbol which matches all symbols in a given alphabet.
static Symbol AlphabetManager.symbolForName(java.lang.String name)
          Retrieve the symbol represented a String object
static Symbol AlphabetManager.getGapSymbol()
           Get the special `gap' Symbol.
static Symbol AlphabetManager.getGapSymbol(java.util.List alphas)
           Get the gap symbol appropriate to this list of alphabets.
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(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(char token, Annotation annotation, java.util.Set symSet, Alphabet alpha)
          Deprecated. use the three-arg version of this method instead.
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.
 Symbol SimpleTranslationTable.translate(Symbol sym)
           
 Symbol DNANoAmbPack.unpack(byte b)
           
 Symbol Alphabet.getSymbol(java.util.List rl)
           Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
 Symbol Alphabet.getAmbiguity(java.util.Set syms)
           Get a symbol that represents the set of symbols in syms.
 Symbol Alphabet.getGapSymbol()
           Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
 Symbol ReversibleTranslationTable.untranslate(Symbol sym)
          Translate a single symbol from target alphabet to the source alphabet.
 Symbol AlphabetIndex.symbolForIndex(int i)
          Retrieve the symbol for an index.
 Symbol DoubleAlphabet.getGapSymbol()
           
 Symbol DoubleAlphabet.getAmbiguity(java.util.Set syms)
           
 Symbol DoubleAlphabet.getSymbol(java.util.List symList)
           
 Symbol DoubleAlphabet.SubDoubleAlphabet.getSymbol(java.util.List rl)
           
 Symbol DoubleAlphabet.SubDoubleAlphabet.getAmbiguity(java.util.Set syms)
           
 Symbol DoubleAlphabet.SubDoubleAlphabet.getGapSymbol()
           
 Symbol SimpleGappedSymbolList.symbolAt(int indx)
           
 Symbol Alignment.symbolAt(java.lang.Object label, int column)
          Retrieve a symbol by label and column.
 Symbol DummySymbolList.symbolAt(int i)
           
 Symbol PackedSymbolList.symbolAt(int indx)
           
 Symbol PackedDnaSymbolList.symbolAt(int index)
           
 Symbol DNAAmbPack.unpack(byte b)
           
 Symbol IllegalSymbolException.getSymbol()
          Retrieve the symbol that caused this exception, or null.
 Symbol IntegerAlphabet.getGapSymbol()
           
 Symbol IntegerAlphabet.getSymbol(java.util.List symList)
           
 Symbol IntegerAlphabet.getAmbiguity(java.util.Set symSet)
           
 

Methods in org.biojava.bio.symbol with parameters of type Symbol
 Symbol TranslationTable.translate(Symbol sym)
          Translate a single symbol from source alphabet to the target alphabet.
 void SimpleSymbolList.addSymbol(Symbol sym)
          Add a new Symbol to the end of this list.
 void SimpleSymbolPropertyTable.setDoubleProperty(Symbol s, java.lang.String value)
           
 double SimpleSymbolPropertyTable.getDoubleValue(Symbol s)
           
 double SymbolPropertyTable.getDoubleValue(Symbol s)
           
 SymbolList SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          makes a SymbolList containing size Symbols from a Symbol array.
 byte Packing.pack(Symbol sym)
           Return a byte representing the packing of a symbol.
 void SingletonAlphabet.removeSymbol(Symbol sym)
           
 Symbol SimpleReversibleTranslationTable.untranslate(Symbol sym)
           
 void FiniteAlphabet.addSymbol(Symbol s)
          Adds a symbol to this alphabet.
 void FiniteAlphabet.removeSymbol(Symbol s)
          Remove a symbol from this alphabet.
 void AbstractAlphabet.addSymbol(Symbol s)
           
 boolean AbstractAlphabet.contains(Symbol sym)
           
 void AbstractAlphabet.validate(Symbol sym)
           
static AlphabetIndex AlphabetManager.getAlphabetIndex(Symbol[] syms)
          Get an indexer for an array of symbols.
 Symbol SimpleTranslationTable.translate(Symbol sym)
           
 SymbolList PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
           
 byte DNANoAmbPack.pack(Symbol sym)
           
 boolean Alphabet.contains(Symbol s)
           Returns whether or not this Alphabet contains the symbol.
 void Alphabet.validate(Symbol s)
           Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
 Symbol ReversibleTranslationTable.untranslate(Symbol sym)
          Translate a single symbol from target alphabet to the source alphabet.
 int AlphabetIndex.indexForSymbol(Symbol s)
          Return the unique index for a symbol.
 boolean DoubleAlphabet.contains(Symbol s)
           
 void DoubleAlphabet.validate(Symbol s)
           
 boolean DoubleAlphabet.SubDoubleAlphabet.contains(Symbol s)
           
 void DoubleAlphabet.SubDoubleAlphabet.validate(Symbol sym)
           
 SymbolList SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          Create a factory for SimpleSymbolLists.
 byte DNAAmbPack.pack(Symbol sym)
           
 void SimpleAlphabet.removeSymbol(Symbol s)
           
 SuffixTree.SuffixNode SuffixTree.getChild(SuffixTree.SuffixNode node, Symbol s)
          Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
 boolean IntegerAlphabet.contains(Symbol s)
           
 void IntegerAlphabet.validate(Symbol s)
           
 void IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)
           
 

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