## 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)`