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

Packages that use Symbol

Package	Description
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.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.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

Modifier and Type	Method and Description
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	SimpleAlignment.symbolAt(int index)
Symbol	FlexibleAlignment.symbolAt(String 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(String label, int column)
Symbol	SimpleAlignment.symbolAt(String label, int column)
Symbol	Alignment.symbolAt(String label, int column) Retrieve a symbol by label and column.

Methods in org.biojava.bio.alignment with parameters of type Symbol

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Interface and Description
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

Modifier and Type	Class and Description
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

Modifier and Type	Method and Description
Symbol	SimpleStatePath.symbolAt(int col)
Symbol	SimpleStatePath.symbolAt(String label, int col)

Methods in org.biojava.bio.dp that return types with arguments of type Symbol

Modifier and Type	Method and Description
Iterator<Symbol>	SimpleStatePath.iterator()
List<Symbol>	SimpleStatePath.toList()

Methods in org.biojava.bio.dp with parameters of type Symbol

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
Symbol	DPCursor.currentRes() The current symbol.
Symbol	DPCursor.lastRes() The previous symbol.

Methods in org.biojava.bio.dp.onehead with parameters of type Symbol

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
static Symbol	ABIFParser.decodeDNAToken(char token) Decodes a character into a Symbol in the DNA alphabet.

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

Classes in org.biojava.bio.program.hmmer that implement Symbol

Modifier and Type	Class and Description
class	ProfileEmissionState A state in a HMMer model.

Methods in org.biojava.bio.program.hmmer with parameters of type Symbol

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
Symbol	SimilarityPairFeature.EmptyPairwiseAlignment.symbolAt(int index)
Symbol	SimilarityPairFeature.EmptyPairwiseAlignment.symbolAt(String label, int index)

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

Methods in org.biojava.bio.seq.impl that return Symbol

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
void	SequenceDBSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) does nothing for now.
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	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.symbol

Subinterfaces of Symbol in org.biojava.bio.symbol

Modifier and Type	Interface and Description
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

Modifier and Type	Class and Description
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

Modifier and Type	Method and Description
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	AbstractAlphabet.getAmbiguity(Set syms)
Symbol	Alphabet.getAmbiguity(Set<Symbol> syms) Get a symbol that represents the set of symbols in 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	AbstractAlphabet.getSymbol(List syms)
Symbol	Alphabet.getSymbol(List<Symbol> rl) Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
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	RelabeledAlignment.symbolAt(int pos)
Symbol	PackedSymbolList.symbolAt(int indx)
Symbol	DummySymbolList.symbolAt(int i)
Symbol	ChunkedSymbolList.symbolAt(int pos)
Symbol	RelabeledAlignment.symbolAt(String 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(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

Modifier and Type	Method and Description
Iterator<Symbol>	SymbolList.iterator() An Iterator over all Symbols in this SymbolList.
Iterator<Symbol>	FiniteAlphabet.iterator() Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.
Iterator<Symbol>	AbstractSymbolList.iterator()
List<Symbol>	SymbolList.toList() Returns a List of symbols.
List<Symbol>	AbstractSymbolList.toList()

Methods in org.biojava.bio.symbol with parameters of type Symbol

Modifier and Type	Method and Description
void	SoftMaskedAlphabet.addSymbol(Symbol s) SoftMaskedAlphabets cannot add new Symbols.
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) SoftMaskedAlphabets cannot remove Symbols.
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)

Method parameters in org.biojava.bio.symbol with type arguments of type Symbol

Modifier and Type	Method and Description
Symbol	Alphabet.getAmbiguity(Set<Symbol> syms) Get a symbol that represents the set of symbols in syms.
Symbol	Alphabet.getSymbol(List<Symbol> rl) Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.

Constructors in org.biojava.bio.symbol with parameters of type Symbol

Constructor and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
Symbol	ThinRichSequence.symbolAt(int index) Return the symbol at index, counting from 1.
Symbol	InfinitelyAmbiguousSymbolList.symbolAt(int index) Return the symbol at index, counting from 1.
Symbol	RichSequenceHandler.symbolAt(RichSequence seq, int index) Return the symbol at index, counting from 1.
Symbol	DummyRichSequenceHandler.symbolAt(RichSequence seq, int index) Return the symbol at index, counting from 1.

Methods in org.biojavax.bio.seq that return types with arguments of type Symbol

Modifier and Type	Method and Description
Iterator<Symbol>	RichSequenceHandler.iterator(RichSequence seq) An Iterator over all Symbols in this SymbolList.
Iterator<Symbol>	DummyRichSequenceHandler.iterator(RichSequence seq) An Iterator over all Symbols in this SymbolList.
List<Symbol>	RichSequenceHandler.toList(RichSequence seq) Returns a List of symbols.
List<Symbol>	DummyRichSequenceHandler.toList(RichSequence seq) Returns a List of symbols.

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

Methods in org.biojavax.bio.seq.io with parameters of type Symbol

Modifier and Type	Method and Description
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)