## 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

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` `AbstractULAlignment.SubULAlignment.symbolAt(java.lang.Object label, 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

Methods in org.biojava.bio.alignment with parameters of type Symbol
`int` `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` `AbstractDistribution.sampleSymbol()`
`Symbol` `GapDistribution.sampleSymbol()`
`Symbol` `Distribution.sampleSymbol()` Sample a symbol from this state's probability distribution.
`Symbol` `TranslatedDistribution.sampleSymbol()`
`Symbol` `PairDistribution.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` `AbstractDistribution.getWeight(Symbol sym)` Retrieve the weight for this distribution.
`double` `GapDistribution.getWeight(Symbol sym)`
`double` `Distribution.getWeight(Symbol s)` Return the probability that Symbol s is emitted by this spectrum.
`double` `TranslatedDistribution.getWeight(Symbol sym)`
`double` `PairDistribution.getWeight(Symbol sym)`
`void` `OrderNDistribution.setDistribution(Symbol sym, Distribution dist)` Set the distribution assocated with a symbol.
`void` `AbstractDistribution.setWeight(Symbol sym, double weight)` Set the weight of a given symbol in this distribution.
`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` `TranslatedDistribution.setWeight(Symbol sym, double weight)`
`void` `PairDistribution.setWeight(Symbol sym, double weight)`

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` `HMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight)` record that the specified symbol was emitted from the specified state.
`void` `SimpleHMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight)`

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` `PlainStyle.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` `DNAStyle.fillPaint(Symbol s)`
`java.awt.Paint` `PlainStyle.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` `DNAStyle.outlinePaint(Symbol s)`
`void` `SimpleSymbolStyle.setFillPaint(Symbol s, java.awt.Paint paint)`
`void` `DNAStyle.setFillPaint(Symbol s, java.awt.Paint paint)`
`void` `SimpleSymbolStyle.setOutlinePaint(Symbol s, java.awt.Paint paint)`
`void` `DNAStyle.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` `PhredSequence.getQualityAt(int index)`
`Symbol` `Qualitative.getQualityAt(int index)` Retreives the quality symbol for the specified 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.complement(Symbol sym)` Complement the symbol.
`static Symbol` `NucleotideTools.complement(Symbol sym)` Complement the symbol.
`static Symbol` `RNATools.complement(Symbol sym)` Complement the symbol.
`static Symbol` `NucleotideTools.d()`
`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.forIndex(int index)` Return the symbol for an index - compatible with index.
`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` `RNATools.forSymbol(char token)` Retrieve the symbol for a symbol.
`static Symbol` `NucleotideTools.h()`
`static Symbol` `NucleotideTools.k()`
`static Symbol` `NucleotideTools.m()`
`static Symbol` `DNATools.n()`
`static Symbol` `NucleotideTools.n()`
`static Symbol` `RNATools.n()`
`static Symbol` `NucleotideTools.r()`
`static Symbol` `NucleotideTools.s()`
`Symbol` `SimpleAssembly.symbolAt(int pos)`
`Symbol` `CircularView.symbolAt(int index)` Over rides ViewSequence.
`Symbol` `NewSimpleAssembly.symbolAt(int pos)`
`static Symbol` `NucleotideTools.v()`
`static Symbol` `NucleotideTools.w()`
`static Symbol` `NucleotideTools.y()`

Methods in org.biojava.bio.seq with parameters of type Symbol
`static Symbol` `DNATools.complement(Symbol sym)` Complement the symbol.
`static Symbol` `NucleotideTools.complement(Symbol sym)` Complement the symbol.
`static Symbol` `RNATools.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` `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 int` `RNATools.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` `SimpleSequence.symbolAt(int index)`
`Symbol` `DummySequence.symbolAt(int index)`
`Symbol` `ViewSequence.symbolAt(int indx)`
`Symbol` `AssembledSymbolList.symbolAt(int pos)`
`Symbol` `NewAssembledSymbolList.symbolAt(int pos)`
`Symbol` `SubSequence.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(java.lang.String s)`
`Symbol` `SymbolTokenization.parseToken(java.lang.String token)` Returns the symbol for a single token.
`Symbol` `SubIntegerTokenization.parseToken(java.lang.String seq)`
`Symbol` `DoubleTokenization.parseToken(java.lang.String seq)`
`Symbol` `CrossProductTokenization.parseToken(java.lang.String token)`
`Symbol` `CharacterTokenization.parseToken(java.lang.String token)`
`Symbol` `NameTokenization.parseToken(java.lang.String token)`
`Symbol` `IntegerTokenization.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` `SequenceBuilderFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`
`void` `SeqIOFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`
`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` `GenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)` Deprecated.
`void` `SmartSequenceBuilder.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` `SimpleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)`
`void` `EmblFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)` Deprecated.
`void` `SimpleAssemblyBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)`
`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` `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` `CharacterTokenization.bindSymbol(Symbol s, char c)` Bind a Symbol to a character.
`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 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 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` `SymbolTokenization.tokenizeSymbol(Symbol sym)` Return a token representing a single symbol.
`java.lang.String` `SubIntegerTokenization.tokenizeSymbol(Symbol sym)`
`java.lang.String` `DoubleTokenization.tokenizeSymbol(Symbol sym)`
`java.lang.String` `CrossProductTokenization.tokenizeSymbol(Symbol s)`
`java.lang.String` `CharacterTokenization.tokenizeSymbol(Symbol s)`
`java.lang.String` `NameTokenization.tokenizeSymbol(Symbol s)`
`java.lang.String` `IntegerTokenization.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` `SimpleReversibleTranslationTable.doTranslate(Symbol sym)`
`protected Symbol` `SimpleManyToOneTranslationTable.doTranslate(Symbol sym)`
`Symbol` `SimpleTranslationTable.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(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` `AbstractAlphabet.getAmbiguity(java.util.Set syms)`
`Symbol` `IntegerAlphabet.getAmbiguity(java.util.Set symSet)`
`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.
`static Symbol` `AlphabetManager.getGapSymbol()` Get the special `gap' Symbol.
`Symbol` `SoftMaskedAlphabet.getGapSymbol()`
`Symbol` `Alphabet.getGapSymbol()` Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
`Symbol` `AbstractAlphabet.getGapSymbol()`
`Symbol` `IntegerAlphabet.getGapSymbol()`
`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` `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` `AbstractAlphabet.getSymbol(java.util.List syms)`
`Symbol` `IntegerAlphabet.getSymbol(java.util.List symList)`
`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` `SimpleGappedSymbolList.symbolAt(int indx)`
`Symbol` `DummySymbolList.symbolAt(int i)`
`Symbol` `RelabeledAlignment.symbolAt(int pos)`
`Symbol` `PackedSymbolList.symbolAt(int indx)`
`Symbol` `SymbolList.symbolAt(int index)` Return the symbol at index, counting from 1.
`Symbol` `SimpleAlignment.symbolAt(int index)`
`Symbol` `SimpleSymbolList.symbolAt(int pos)` Find a symbol at a specified offset in the SymbolList.
`Symbol` `ChunkedSymbolList.symbolAt(int pos)`
`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` `SimpleAlignment.symbolAt(java.lang.Object label, int 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` `DNANoAmbPack.unpack(byte b)`
`Symbol` `DNAAmbPack.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 with parameters of type Symbol
`void` `SoftMaskedAlphabet.addSymbol(Symbol s)` `SoftMaskedAlphabet`s cannot add new `Symbol`s.
`void` `AbstractAlphabet.addSymbol(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.
`boolean` `SoftMaskedAlphabet.contains(Symbol s)`
`boolean` `Alphabet.contains(Symbol s)` Returns whether or not this Alphabet contains the symbol.
`boolean` `AbstractAlphabet.contains(Symbol sym)`
`boolean` `IntegerAlphabet.contains(Symbol s)`
`boolean` `DoubleAlphabet.contains(Symbol s)`
`boolean` `DoubleAlphabet.SubDoubleAlphabet.contains(Symbol s)`
`protected Symbol` `SimpleReversibleTranslationTable.doTranslate(Symbol sym)`
`protected Symbol` `SimpleManyToOneTranslationTable.doTranslate(Symbol sym)`
`Symbol` `SimpleTranslationTable.doTranslate(Symbol sym)`
`protected Symbol` `SimpleReversibleTranslationTable.doUntranslate(Symbol sym)`
`protected java.util.Set` `SimpleManyToOneTranslationTable.doUntranslate(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.
`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` `CodonPref.getFrequencyForSynonyms(Symbol residue)` returns a Distribution giving the frequency of synonymous codons.
`Distribution` `SimpleCodonPref.getFrequencyForSynonyms(Symbol residue)`
`WobbleDistribution` `CodonPref.getWobbleDistributionForSynonyms(Symbol residue)` returns a WobbleDistribution for a specified residue.
`WobbleDistribution` `SimpleCodonPref.getWobbleDistributionForSynonyms(Symbol 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` `DNANoAmbPack.pack(Symbol sym)`
`byte` `DNAAmbPack.pack(Symbol sym)`
`byte` `Packing.pack(Symbol sym)` Return a byte representing the packing of a symbol.
`void` `SoftMaskedAlphabet.removeSymbol(Symbol s)` `SoftMaskedAlphabet`s cannot remove `Symbol`s.
`void` `SingletonAlphabet.removeSymbol(Symbol sym)`
`void` `IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)`
`void` `SimpleAlphabet.removeSymbol(Symbol s)`
`void` `FiniteAlphabet.removeSymbol(Symbol s)` Remove a symbol from this alphabet.
`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.
`java.util.Set` `ManyToOneTranslationTable.untranslate(Symbol sym)` Translate a single symbol from target alphabet to the source alphabet.
`Symbol` `AbstractReversibleTranslationTable.untranslate(Symbol sym)`
`Symbol` `ReversibleTranslationTable.untranslate(Symbol sym)` Translate a single symbol from target alphabet to the source alphabet.
`void` `SoftMaskedAlphabet.validate(Symbol s)`
`void` `Alphabet.validate(Symbol s)` Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
`void` `AbstractAlphabet.validate(Symbol sym)`
`void` `IntegerAlphabet.validate(Symbol s)`
`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` `NfaSubModel.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` `NfaBuilder.addTransition(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym)`
`protected int` `FiniteAutomaton.alphaIndex(Symbol sym)`
`protected int` `Nfa.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` `DebuggingRichSeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`
`void` `RichSeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`