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.structure	Interfaces and classes for molecular structure.
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.

Uses of Symbol in org.biojava.bio.alignment

Methods in org.biojava.bio.alignment that return Symbol

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.symbolAt(int index) this will return the ambiguity symbol associated with all symbols in that column
Symbol	AbstractULAlignment.SubULAlignment.symbolAt(Object label, int column)
Symbol	AbstractULAlignment.SubULAlignment.symbolAt(int column)

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

double	TranslatedDistribution.getWeight(Symbol sym)
void	TranslatedDistribution.setWeight(Symbol sym, double weight)
void	SimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)
double	SimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym)
double	PairDistribution.getWeight(Symbol sym)
void	PairDistribution.setWeight(Symbol sym, double weight)
void	OrderNDistribution.setDistribution(Symbol sym, Distribution dist) Set the distribution assocated with a symbol.
Distribution	OrderNDistribution.getDistribution(Symbol sym)
double	GapDistribution.getWeight(Symbol sym)
void	GapDistribution.setWeight(Symbol s, double w)
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	Distribution.getWeight(Symbol s) Return the probability that Symbol s is emitted by this spectrum.
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.
double	AbstractDistribution.getWeight(Symbol sym) Retrieve the weight for 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

void	SimpleHMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight)
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.

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

Paint	SymbolStyle.outlinePaint(Symbol s) Return the outline paint for a symbol.
Paint	SymbolStyle.fillPaint(Symbol s) Return the fill paint for a symbol.
Paint	SimpleSymbolStyle.outlinePaint(Symbol s)
Paint	SimpleSymbolStyle.fillPaint(Symbol s)
void	SimpleSymbolStyle.setOutlinePaint(Symbol s, Paint paint)
void	SimpleSymbolStyle.setFillPaint(Symbol s, Paint paint)
Paint	PlainStyle.outlinePaint(Symbol s)
Paint	PlainStyle.fillPaint(Symbol s)
Paint	DNAStyle.outlinePaint(Symbol s)
Paint	DNAStyle.fillPaint(Symbol s)
void	DNAStyle.setOutlinePaint(Symbol s, Paint paint)
void	DNAStyle.setFillPaint(Symbol s, Paint paint)
static double	DistributionLogo.entropy(Distribution dist, Symbol s) Calculate the information content of a symbol in bits.

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

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

Symbol	SimpleAssembly.symbolAt(int pos)
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.
Symbol	NewSimpleAssembly.symbolAt(int pos)
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	CircularView.symbolAt(int index) Over rides ViewSequence.

Methods in org.biojava.bio.seq with parameters of type 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 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(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	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[]	WordTokenization.parseString(String s)
Symbol	SymbolTokenization.parseToken(String token) Returns the symbol for a single token.
Symbol	SymbolReader.readSymbol() Return a single symbol from the stream.
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)
protected Symbol[]	CharacterTokenization.getTokenTable()
protected Symbol	CharacterTokenization.parseTokenChar(char c)

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

String	SymbolTokenization.tokenizeSymbol(Symbol sym) Return a token representing a single symbol.
int	SymbolReader.readSymbols(Symbol[] buffer, int start, int length) Read one or more symbols from the stream.
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 List	SwissprotFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Converts the symbol list passed in into an array of strings.
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)
protected List	ProteinRefSeqFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Converts the symbol list passed in into an array of strings.
String	NameTokenization.tokenizeSymbol(Symbol s)
String	IntegerTokenization.tokenizeSymbol(Symbol sym)
void	GenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
void	EmblFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
String	DoubleTokenization.tokenizeSymbol(Symbol sym)
String	CrossProductTokenization.tokenizeSymbol(Symbol s)
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.
String	CharacterTokenization.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

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

Methods in org.biojava.bio.symbol that return Symbol

Symbol	WobbleDistribution.getResidue() returns the residue encoded by this WobbleDistribution
Symbol	TranslationTable.translate(Symbol sym) Translate a single symbol from source alphabet to the target alphabet.
Symbol	SymbolList.symbolAt(int index) Return the symbol at index, counting from 1.
Symbol	SoftMaskedAlphabet.getSymbol(List l)
Symbol	SoftMaskedAlphabet.getAmbiguity(Set s)
Symbol	SoftMaskedAlphabet.getGapSymbol()
Symbol	SoftMaskedAlphabet.CaseSensitiveTokenization.parseToken(String token)
Symbol	SimpleTranslationTable.doTranslate(Symbol sym)
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.
protected Symbol	SimpleReversibleTranslationTable.doTranslate(Symbol sym)
protected Symbol	SimpleReversibleTranslationTable.doUntranslate(Symbol sym)
protected Symbol	SimpleManyToOneTranslationTable.doTranslate(Symbol sym)
Symbol	SimpleGappedSymbolList.symbolAt(int indx)
Symbol	SimpleAlignment.symbolAt(int index)
Symbol	SimpleAlignment.symbolAt(Object label, int column)
Symbol	ReversibleTranslationTable.untranslate(Symbol sym) Translate a single symbol from target alphabet to the source alphabet.
Symbol	RelabeledAlignment.symbolAt(Object label, int column)
Symbol	RelabeledAlignment.symbolAt(int pos)
Symbol	Packing.unpack(byte packed) Return the symbol for a packing.
Symbol	PackedSymbolList.symbolAt(int indx)
Symbol	IntegerAlphabet.getGapSymbol()
Symbol	IntegerAlphabet.getSymbol(List symList)
Symbol	IntegerAlphabet.getAmbiguity(Set symSet)
Symbol	IllegalSymbolException.getSymbol() Retrieve the symbol that caused this exception, or null.
Symbol	DummySymbolList.symbolAt(int i)
Symbol	DoubleAlphabet.getGapSymbol()
Symbol	DoubleAlphabet.getAmbiguity(Set syms)
Symbol	DoubleAlphabet.getSymbol(List symList)
Symbol	DoubleAlphabet.SubDoubleAlphabet.getSymbol(List rl)
Symbol	DoubleAlphabet.SubDoubleAlphabet.getAmbiguity(Set syms)
Symbol	DoubleAlphabet.SubDoubleAlphabet.getGapSymbol()
Symbol	DNANoAmbPack.unpack(byte b)
Symbol	DNAAmbPack.unpack(byte b)
Symbol	ChunkedSymbolList.symbolAt(int pos)
static Symbol	AlphabetManager.getAllAmbiguitySymbol(FiniteAlphabet alpha) Return the ambiguity symbol which matches all symbols in a given alphabet.
static Symbol	AlphabetManager.symbolForName(String name) Deprecated. use symbolForLifeScienceID() instead
static Symbol	AlphabetManager.symbolForLifeScienceID(LifeScienceIdentifier lsid) Retreives the Symbol for the LSID
static Symbol	AlphabetManager.getGapSymbol() Get the special `gap' Symbol.
static Symbol	AlphabetManager.getGapSymbol(List alphas) Get the gap symbol appropriate to this list of alphabets.
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(Annotation annotation, 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, Set symSet, Alphabet alpha) Deprecated. use the three-arg version of this method instead.
static Symbol	AlphabetManager.createSymbol(Annotation annotation, Set symSet, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.
Symbol	AlphabetIndex.symbolForIndex(int i) Retrieve the symbol for an index.
Symbol	Alphabet.getSymbol(List rl) Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
Symbol	Alphabet.getAmbiguity(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	Alignment.symbolAt(Object label, int column) Retrieve a symbol by label and column.
protected abstract Symbol	AbstractReversibleTranslationTable.doUntranslate(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.
Symbol	AbstractReversibleTranslationTable.untranslate(Symbol sym)
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	AbstractAlphabet.getSymbol(List syms)
Symbol	AbstractAlphabet.getGapSymbol()

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

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.
Symbol	TranslationTable.translate(Symbol sym) Translate a single symbol from source alphabet to the target alphabet.
double	SymbolPropertyTable.getDoubleValue(Symbol s)
SymbolList	SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) makes a SymbolList containing size Symbols from a Symbol array.
SuffixTree.SuffixNode	SuffixTree.getChild(SuffixTree.SuffixNode node, Symbol s) Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
boolean	SoftMaskedAlphabet.contains(Symbol s)
void	SoftMaskedAlphabet.validate(Symbol s)
void	SoftMaskedAlphabet.addSymbol(Symbol s) SoftMaskedAlphabets cannot add new Symbols.
void	SoftMaskedAlphabet.removeSymbol(Symbol s) SoftMaskedAlphabets cannot remove Symbols.
String	SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbol(Symbol s)
void	SingletonAlphabet.removeSymbol(Symbol sym)
Symbol	SimpleTranslationTable.doTranslate(Symbol sym)
void	SimpleSymbolPropertyTable.setDoubleProperty(Symbol s, String value)
double	SimpleSymbolPropertyTable.getDoubleValue(Symbol s)
SymbolList	SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) Create a factory for SimpleSymbolLists.
void	SimpleSymbolList.addSymbol(Symbol sym) Add a new Symbol to the end of this list.
protected Symbol	SimpleReversibleTranslationTable.doTranslate(Symbol sym)
protected Symbol	SimpleReversibleTranslationTable.doUntranslate(Symbol sym)
protected Symbol	SimpleManyToOneTranslationTable.doTranslate(Symbol sym)
protected Set	SimpleManyToOneTranslationTable.doUntranslate(Symbol sym)
Distribution	SimpleCodonPref.getFrequencyForSynonyms(Symbol residue)
WobbleDistribution	SimpleCodonPref.getWobbleDistributionForSynonyms(Symbol residue)
void	SimpleAlphabet.removeSymbol(Symbol s)
Symbol	ReversibleTranslationTable.untranslate(Symbol sym) Translate a single symbol from target alphabet to the source alphabet.
byte	Packing.pack(Symbol sym) Return a byte representing the packing of a symbol.
SymbolList	PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) Makes a packed SymbolList out of a list of Symbols.
Set	ManyToOneTranslationTable.untranslate(Symbol sym) Translate a single symbol from target alphabet to the source alphabet.
boolean	IntegerAlphabet.contains(Symbol s)
void	IntegerAlphabet.validate(Symbol s)
void	IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)
void	FiniteAlphabet.addSymbol(Symbol s) Adds a symbol to this alphabet.
void	FiniteAlphabet.removeSymbol(Symbol s) Remove a symbol from this alphabet.
boolean	DoubleAlphabet.contains(Symbol s)
void	DoubleAlphabet.validate(Symbol s)
boolean	DoubleAlphabet.SubDoubleAlphabet.contains(Symbol s)
void	DoubleAlphabet.SubDoubleAlphabet.validate(Symbol sym)
byte	DNANoAmbPack.pack(Symbol sym)
byte	DNAAmbPack.pack(Symbol sym)
Distribution	CodonPref.getFrequencyForSynonyms(Symbol residue) returns a Distribution giving the frequency of synonymous codons.
WobbleDistribution	CodonPref.getWobbleDistributionForSynonyms(Symbol residue) returns a WobbleDistribution for a specified residue.
static AlphabetIndex	AlphabetManager.getAlphabetIndex(Symbol[] syms) Get an indexer for an array of symbols.
int	AlphabetIndex.indexForSymbol(Symbol s) Return the unique index for a symbol.
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.
protected abstract Symbol	AbstractReversibleTranslationTable.doUntranslate(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.
Symbol	AbstractReversibleTranslationTable.untranslate(Symbol sym)
protected abstract Set	AbstractManyToOneTranslationTable.doUntranslate(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.
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	AbstractAlphabet.addSymbol(Symbol s)
boolean	AbstractAlphabet.contains(Symbol sym)
void	AbstractAlphabet.validate(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.

PackedSymbolList(Packing packing, Symbol[] symbols, int length, Alphabet alfa)
Create a new PackedSymbolList from an array of Symbols.

IllegalSymbolException(Symbol sym, String message)
Make the exception with a message and a symbol.

IllegalSymbolException(Throwable cause, Symbol sym, String message)

Edit(int pos, Alphabet alpha, Symbol replacement)
Convenience construtor for making single residue changes

DummySymbolList(Alphabet alpha, int length, Symbol sym)

DNANoAmbPack(Symbol placeHolderSymbol)
Construct a new packing which translates unknown symbols into the specified symbol.

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)
protected int	Nfa.alphaIndex(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	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.