## 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 Map<Symbol,Integer>` `SubstitutionMatrix.colSymbols`
`protected Map<Symbol,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(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(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
`Color` `ChromatogramGraphic.getBaseColor(Symbol b)` Returns the color that will be used to draw the trace for the given DNA symbol.
`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, 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` `PairDistribution.sampleSymbol()`
`Symbol` `GapDistribution.sampleSymbol()`
`Symbol` `Distribution.sampleSymbol()` Sample a symbol from this state's probability distribution.
`Symbol` `AbstractDistribution.sampleSymbol()`

Methods in org.biojava.bio.dist with parameters of type Symbol
`void` `SimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)`
`void` `DistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)` Registers that sym was counted in this state.
`double` `SimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym)`
`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.
`Distribution` `OrderNDistribution.getDistribution(Symbol sym)`
`double` `TranslatedDistribution.getWeight(Symbol sym)`
`double` `PairDistribution.getWeight(Symbol sym)`
`double` `GapDistribution.getWeight(Symbol sym)`
`double` `Distribution.getWeight(Symbol s)` Return the probability that Symbol s is emitted by this spectrum.
`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` `TranslatedDistribution.setWeight(Symbol sym, double weight)`
`void` `PairDistribution.setWeight(Symbol sym, double weight)`
`void` `GapDistribution.setWeight(Symbol s, double w)`
`void` `Distribution.setWeight(Symbol s, double w)` Set the probability or odds that Symbol s is emitted by this state.
`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(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.
`Paint` `SymbolStyle.fillPaint(Symbol s)` Return the fill paint for a symbol.
`Paint` `SimpleSymbolStyle.fillPaint(Symbol s)`
`Paint` `PlainStyle.fillPaint(Symbol s)`
`Paint` `DNAStyle.fillPaint(Symbol s)`
`Paint` `SymbolStyle.outlinePaint(Symbol s)` Return the outline paint for a symbol.
`Paint` `SimpleSymbolStyle.outlinePaint(Symbol s)`
`Paint` `PlainStyle.outlinePaint(Symbol s)`
`Paint` `DNAStyle.outlinePaint(Symbol s)`
`void` `SimpleSymbolStyle.setFillPaint(Symbol s, Paint paint)`
`void` `DNAStyle.setFillPaint(Symbol s, Paint paint)`
`void` `SimpleSymbolStyle.setOutlinePaint(Symbol s, Paint paint)`
`void` `DNAStyle.setOutlinePaint(Symbol s, 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` `NucleotideTools.b()`
`static Symbol` `DNATools.b()`
`static Symbol` `RNATools.complement(Symbol sym)` Complement the symbol.
`static Symbol` `NucleotideTools.complement(Symbol sym)` Complement the symbol.
`static Symbol` `DNATools.complement(Symbol sym)` Complement the symbol.
`static Symbol` `NucleotideTools.d()`
`static Symbol` `DNATools.d()`
`static Symbol` `RNATools.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` `DNATools.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` `NucleotideTools.forSymbol(char token)` Retrieve the symbol for a symbol.
`static Symbol` `DNATools.forSymbol(char token)` Retrieve the symbol for a symbol.
`static Symbol` `NucleotideTools.h()`
`static Symbol` `DNATools.h()`
`static Symbol` `NucleotideTools.k()`
`static Symbol` `DNATools.k()`
`static Symbol` `NucleotideTools.m()`
`static Symbol` `DNATools.m()`
`static Symbol` `RNATools.n()`
`static Symbol` `NucleotideTools.n()`
`static Symbol` `DNATools.n()`
`static Symbol` `NucleotideTools.r()`
`static Symbol` `DNATools.r()`
`static Symbol` `NucleotideTools.s()`
`static Symbol` `DNATools.s()`
`Symbol` `SimpleAssembly.symbolAt(int pos)`
`Symbol` `NewSimpleAssembly.symbolAt(int pos)`
`Symbol` `CircularView.symbolAt(int index)` Over rides ViewSequence.
`static Symbol` `NucleotideTools.v()`
`static Symbol` `DNATools.v()`
`static Symbol` `NucleotideTools.w()`
`static Symbol` `DNATools.w()`
`static Symbol` `NucleotideTools.y()`
`static Symbol` `DNATools.y()`

Methods in org.biojava.bio.seq with parameters of type Symbol
`static Symbol` `RNATools.complement(Symbol sym)` Complement the symbol.
`static Symbol` `NucleotideTools.complement(Symbol sym)` Complement the symbol.
`static Symbol` `DNATools.complement(Symbol sym)` Complement the symbol.
`static Sequence` `SequenceTools.createDummy(Alphabet alpha, int length, Symbol sym, String uri, 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` `NucleotideTools.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 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(Object label, int index)`

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

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

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(String s)`
`Symbol` `SymbolTokenization.parseToken(String token)` Returns the symbol for a single token.
`Symbol` `SubIntegerTokenization.parseToken(String seq)`
`Symbol` `NameTokenization.parseToken(String token)`
`Symbol` `IntegerTokenization.parseToken(String seq)`
`Symbol` `DoubleTokenization.parseToken(String seq)`
`Symbol` `CrossProductTokenization.parseToken(String token)`
`Symbol` `CharacterTokenization.parseToken(String token)`
`Symbol` `AlternateTokenization.parseToken(String token)` Will throw an exception.
`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` `SwissprotFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)` Deprecated. Prints out the sequences properties in order.
`void` `SmartSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)`
`void` `SimpleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)`
`void` `SimpleAssemblyBuilder.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` `SequenceBuilderFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`
`abstract void` `SequenceBuilderBase.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)`
`void` `SeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)` Notify the listener of symbol data.
`void` `SeqIOFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`
`void` `SeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`
`void` `ProteinRefSeqFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)` Deprecated.
`void` `GenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)` Deprecated.
`void` `EmblFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)` Deprecated.
`void` `ChunkedSymbolListFactory.addSymbols(Alphabet alfa, Symbol[] syms, int pos, int len)` tool to construct the SymbolList by adding Symbols.
`void` `CharacterTokenization.bindSymbol(Symbol s, char c)` Bind a Symbol to a character.
`void` `AlternateTokenization.bindSymbol(Symbol s, String str)` Bind a Symbol to a string.
`protected List` `SwissprotFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)` Deprecated. Converts the symbol list passed in into an array of strings.
`protected List` `ProteinRefSeqFileFormer.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.
`String` `SymbolTokenization.tokenizeSymbol(Symbol sym)` Return a token representing a single symbol.
`String` `SubIntegerTokenization.tokenizeSymbol(Symbol sym)`
`String` `NameTokenization.tokenizeSymbol(Symbol s)`
`String` `IntegerTokenization.tokenizeSymbol(Symbol sym)`
`String` `DoubleTokenization.tokenizeSymbol(Symbol sym)`
`String` `CrossProductTokenization.tokenizeSymbol(Symbol s)`
`String` `CharacterTokenization.tokenizeSymbol(Symbol s)`
`String` `AlternateTokenization.tokenizeSymbol(Symbol s)`

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

Methods in org.biojava.bio.symbol that return types with arguments of type Symbol
`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` `SoftMaskedAlphabet.addSymbol(Symbol s)` `SoftMaskedAlphabet`s cannot add new `Symbol`s.
`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)`
`boolean` `SoftMaskedAlphabet.contains(Symbol s)`
`boolean` `IntegerAlphabet.contains(Symbol s)`
`boolean` `DoubleAlphabet.contains(Symbol s)`
`boolean` `DoubleAlphabet.SubDoubleAlphabet.contains(Symbol s)`
`boolean` `Alphabet.contains(Symbol s)` Returns whether or not this Alphabet contains the symbol.
`boolean` `AbstractAlphabet.contains(Symbol sym)`
`Symbol` `SimpleTranslationTable.doTranslate(Symbol sym)`
`protected Symbol` `SimpleReversibleTranslationTable.doTranslate(Symbol sym)`
`protected Symbol` `SimpleManyToOneTranslationTable.doTranslate(Symbol sym)`
`protected Symbol` `SimpleReversibleTranslationTable.doUntranslate(Symbol sym)`
`protected Set` `SimpleManyToOneTranslationTable.doUntranslate(Symbol sym)`
`protected abstract Symbol` `AbstractReversibleTranslationTable.doUntranslate(Symbol sym)` this method is expected to reverse-translate any symbol in the source alphabet.
`protected abstract Set` `AbstractManyToOneTranslationTable.doUntranslate(Symbol sym)` this method is expected to reverse-translate any symbol in the source alphabet.
`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` `SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` makes a SymbolList containing size Symbols from a Symbol array.
`SymbolList` `SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` Create a factory for SimpleSymbolLists.
`SymbolList` `PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` Makes a packed SymbolList out of a list of Symbols.
`byte` `Packing.pack(Symbol sym)` Return a byte representing the packing of a symbol.
`byte` `DNANoAmbPack.pack(Symbol sym)`
`byte` `DNAAmbPack.pack(Symbol sym)`
`void` `SoftMaskedAlphabet.removeSymbol(Symbol s)` `SoftMaskedAlphabet`s cannot remove `Symbol`s.
`void` `SingletonAlphabet.removeSymbol(Symbol sym)`
`void` `SimpleAlphabet.removeSymbol(Symbol s)`
`void` `IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)`
`void` `FiniteAlphabet.removeSymbol(Symbol s)` Remove a symbol from this alphabet.
`void` `SimpleSymbolPropertyTable.setDoubleProperty(Symbol s, String value)`
`String` `SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbol(Symbol s)`
`Symbol` `TranslationTable.translate(Symbol sym)` Translate a single symbol from source alphabet to the target alphabet.
`Symbol` `ReversibleTranslationTable.untranslate(Symbol sym)` Translate a single symbol from target alphabet to the source alphabet.
`Set` `ManyToOneTranslationTable.untranslate(Symbol sym)` Translate a single symbol from target alphabet to the source alphabet.
`Symbol` `AbstractReversibleTranslationTable.untranslate(Symbol sym)`
`Set` `AbstractManyToOneTranslationTable.untranslate(Symbol sym)` returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet.
`void` `SoftMaskedAlphabet.validate(Symbol s)`
`void` `IntegerAlphabet.validate(Symbol s)`
`void` `DoubleAlphabet.validate(Symbol s)`
`void` `DoubleAlphabet.SubDoubleAlphabet.validate(Symbol sym)`
`void` `Alphabet.validate(Symbol s)` Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
`void` `AbstractAlphabet.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, String message)` Make the exception with a message and a symbol.
`IllegalSymbolException(Throwable cause, Symbol sym, 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` `NfaSubModel.addTransition(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym)`
`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)`
`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. ALWAYS RETURNS THE AMBIGUITY SYMBOL
`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` `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)`
`void` `DebuggingRichSeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`