Uses of Interface
org.biojava.bio.symbol.Symbol
Packages that use Symbol
Package
Description
Classes to generate and describe sequence alignments.
Tools for displaying chromatograms.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
ABI Trace Handling.
Tools for working with profile Hidden Markov Models from the HMMer package.
Parser for Phred output
Utilities to aid in performing various physical analysis of proteins.
Classes and interfaces for defining biological sequences and informatics
objects.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence and
Feature.Classes and interfaces for processing and producing flat-file representations
of sequences.
Representation of the Symbols that make up a sequence, and locations within
them.
This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of Symbol in org.biojava.bio.alignment
Methods in org.biojava.bio.alignment that return SymbolModifier and TypeMethodDescriptionAbstractULAlignment.SubULAlignment.symbolAt(int column) AbstractULAlignment.symbolAt(int index) this will return the ambiguity symbol associated with all symbols in that columnRetrieve a symbol by label and 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 nullSimpleAlignment.symbolAt(int index) Methods in org.biojava.bio.alignment with parameters of type SymbolModifier and TypeMethodDescriptionshortSubstitutionMatrix.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 SymbolModifier and TypeMethodDescriptionChromatogramGraphic.getBaseColor(Symbol b) Returns the color that will be used to draw the trace for the given DNA symbol.ChromatogramGraphic.getBaseFillColor(Symbol b) Returns the color that will be used to fill in the callboxes for calls with the given symbol.voidChromatogramGraphic.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 SymbolModifier and TypeMethodDescriptionAbstractDistribution.sampleSymbol()Distribution.sampleSymbol()Sample a symbol from this state's probability distribution.GapDistribution.sampleSymbol()PairDistribution.sampleSymbol()TranslatedDistribution.sampleSymbol()Methods in org.biojava.bio.dist with parameters of type SymbolModifier and TypeMethodDescriptionvoidDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times) Registers that sym was counted in this state.voidSimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times) doubleDistributionTrainerContext.getCount(Distribution dist, Symbol sym) Return the number of counts of a particular symbol which will be used to train the specified distribution.doubleSimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym) OrderNDistribution.getDistribution(Symbol sym) final doubleRetrieve the weight for this distribution.doubleReturn the probability that Symbol s is emitted by this spectrum.doubledoubledoublevoidOrderNDistribution.setDistribution(Symbol sym, Distribution dist) Set the distribution assocated with a symbol.final voidSet the weight of a given symbol in this distribution.voidSet the probability or odds that Symbol s is emitted by this state.voidvoidvoid -
Uses of Symbol in org.biojava.bio.dp
Subinterfaces of Symbol in org.biojava.bio.dpModifier and TypeInterfaceDescriptioninterfaceA Dot state.interfaceA state in a markov process that has an emission spectrum.interfaceA state that contains an entire sub-model.interfaceA state in a markov process.Classes in org.biojava.bio.dp that implement SymbolModifier and TypeClassDescriptionfinal classStart/end state for HMMs.classA Dot state that you can make and use.classclassMethods in org.biojava.bio.dp that return SymbolMethods in org.biojava.bio.dp that return types with arguments of type SymbolMethods in org.biojava.bio.dp with parameters of type SymbolModifier and TypeMethodDescriptiondoubleScoreType.calculateScore(Distribution dist, Symbol sym) Calculates the score associated with a distribution and a symbol.doubleScoreType.NullModel.calculateScore(Distribution dist, Symbol sym) doubleScoreType.Odds.calculateScore(Distribution dist, Symbol sym) doubleScoreType.Probability.calculateScore(Distribution dist, Symbol sym) voidHMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight) record that the specified symbol was emitted from the specified state.voidSimpleHMMTrainer.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 SymbolModifier and TypeMethodDescriptionDPCursor.currentRes()The current symbol.DPCursor.lastRes()The previous symbol.Methods in org.biojava.bio.dp.onehead with parameters of type SymbolModifier and TypeMethodDescriptiondouble[]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 SymbolModifier and TypeMethodDescriptionstatic doubleDistributionLogo.entropy(Distribution dist, Symbol s) Calculate the information content of a symbol in bits.Return the fill paint for a symbol.DNAStyle.outlinePaint(Symbol s) PlainStyle.outlinePaint(Symbol s) SimpleSymbolStyle.outlinePaint(Symbol s) SymbolStyle.outlinePaint(Symbol s) Return the outline paint for a symbol.voidDNAStyle.setFillPaint(Symbol s, Paint paint) voidSimpleSymbolStyle.setFillPaint(Symbol s, Paint paint) voidDNAStyle.setOutlinePaint(Symbol s, Paint paint) voidSimpleSymbolStyle.setOutlinePaint(Symbol s, Paint paint) -
Uses of Symbol in org.biojava.bio.program.abi
Methods in org.biojava.bio.program.abi that return SymbolModifier and TypeMethodDescriptionstatic SymbolABIFParser.decodeDNAToken(char token) Decodes a character into aSymbolin the DNA alphabet. -
Uses of Symbol in org.biojava.bio.program.hmmer
Classes in org.biojava.bio.program.hmmer that implement SymbolMethods in org.biojava.bio.program.hmmer with parameters of type Symbol -
Uses of Symbol in org.biojava.bio.program.phred
Methods in org.biojava.bio.program.phred that return SymbolModifier and TypeMethodDescriptionstatic final SymbolPhredTools.dnaSymbolFromPhred(Symbol phredSym) Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.PhredSequence.getDNAAt(int index) static final SymbolPhredTools.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).PhredSequence.getQualityAt(int index) Qualitative.getQualityAt(int index) Retreives the quality symbol for the specified index.Methods in org.biojava.bio.program.phred with parameters of type SymbolModifier and TypeMethodDescriptionstatic final SymbolPhredTools.dnaSymbolFromPhred(Symbol phredSym) Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.static final SymbolPhredTools.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 final IntegerAlphabet.IntegerSymbolPhredTools.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 SymbolModifier and TypeMethodDescriptionvoidMassCalc.addVariableModification(Symbol residue, double[] masses) Add Variable modifications.booleanMassCalc.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 SymbolModifier and TypeMethodDescriptionstatic SymbolDNATools.b()static SymbolNucleotideTools.b()static SymbolDNATools.complement(Symbol sym) Complement the symbol.static SymbolNucleotideTools.complement(Symbol sym) Complement the symbol.static SymbolRNATools.complement(Symbol sym) Complement the symbol.static SymbolDNATools.d()static SymbolNucleotideTools.d()static SymbolDNATools.forIndex(int index) Return the symbol for an index - compatible withindex.static SymbolNucleotideTools.forIndex(int index) Return the symbol for an index - compatible withindex.static SymbolRNATools.forIndex(int index) Return the symbol for an index - compatible with index.static SymbolDNATools.forSymbol(char token) Retrieve the symbol for a symbol.static SymbolNucleotideTools.forSymbol(char token) Retrieve the symbol for a symbol.static SymbolRNATools.forSymbol(char token) Retrieve the symbol for a symbol.static SymbolDNATools.h()static SymbolNucleotideTools.h()static SymbolDNATools.k()static SymbolNucleotideTools.k()static SymbolDNATools.m()static SymbolNucleotideTools.m()static SymbolDNATools.n()static SymbolNucleotideTools.n()static SymbolRNATools.n()static SymbolDNATools.r()static SymbolNucleotideTools.r()static SymbolDNATools.s()static SymbolNucleotideTools.s()CircularView.symbolAt(int index) Over rides ViewSequence.NewSimpleAssembly.symbolAt(int pos) SimpleAssembly.symbolAt(int pos) static SymbolDNATools.v()static SymbolNucleotideTools.v()static SymbolDNATools.w()static SymbolNucleotideTools.w()static SymbolDNATools.y()static SymbolNucleotideTools.y()Methods in org.biojava.bio.seq with parameters of type SymbolModifier and TypeMethodDescriptionstatic SymbolDNATools.complement(Symbol sym) Complement the symbol.static SymbolNucleotideTools.complement(Symbol sym) Complement the symbol.static SymbolRNATools.complement(Symbol sym) Complement the symbol.static SequenceSequenceTools.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 charGet a single-character token for a DNA symbolstatic intReturn an integer index for a symbol - compatible withforIndex.static intReturn an integer index for a symbol - compatible withforIndex.static intReturn an integer index for a symbol - compatible with forIndex.static charNucleotideTools.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 -
Uses of Symbol in org.biojava.bio.seq.impl
Methods in org.biojava.bio.seq.impl that return Symbol -
Uses of Symbol in org.biojava.bio.seq.io
Methods in org.biojava.bio.seq.io that return SymbolModifier and TypeMethodDescriptionprotected Symbol[]CharacterTokenization.getTokenTable()protected Symbol[]WordTokenization.parseString(String s) AlternateTokenization.parseToken(String token) Will throw an exception.CharacterTokenization.parseToken(String token) CrossProductTokenization.parseToken(String token) DoubleTokenization.parseToken(String seq) IntegerTokenization.parseToken(String seq) NameTokenization.parseToken(String token) SubIntegerTokenization.parseToken(String seq) SymbolTokenization.parseToken(String token) Returns the symbol for a single token.protected SymbolCharacterTokenization.parseTokenChar(char c) SymbolReader.readSymbol()Return a single symbol from the stream.Methods in org.biojava.bio.seq.io with parameters of type SymbolModifier and TypeMethodDescriptionvoidChunkedSymbolListFactory.addSymbols(Alphabet alfa, Symbol[] syms, int pos, int len) tool to construct the SymbolList by adding Symbols.voidEmblFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) Deprecated.voidGenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) Deprecated.voidProteinRefSeqFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.voidSeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) voidSeqIOFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) voidSeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) Notify the listener of symbol data.abstract voidSequenceBuilderBase.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) voidSequenceBuilderFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) voidSequenceDBSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) does nothing for now.voidSimpleAssemblyBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) voidSimpleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) voidSmartSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) voidSwissprotFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.Prints out the sequences properties in order.voidAlternateTokenization.bindSymbol(Symbol s, String str) Bind a Symbol to a string.voidCharacterTokenization.bindSymbol(Symbol s, char c) Bind a Symbol to a character.protected ListProteinRefSeqFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.Converts the symbol list passed in into an array of strings.protected ListSwissprotFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.Converts the symbol list passed in into an array of strings.protected voidSwissprotFileFormer.printOutSequenceHeaderLine(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.Prints out sequence header with only length data.intSymbolReader.readSymbols(Symbol[] buffer, int start, int length) Read one or more symbols from the stream.AlternateTokenization.tokenizeSymbol(Symbol s) CharacterTokenization.tokenizeSymbol(Symbol s) CrossProductTokenization.tokenizeSymbol(Symbol s) DoubleTokenization.tokenizeSymbol(Symbol sym) IntegerTokenization.tokenizeSymbol(Symbol sym) NameTokenization.tokenizeSymbol(Symbol s) SubIntegerTokenization.tokenizeSymbol(Symbol sym) SymbolTokenization.tokenizeSymbol(Symbol sym) Return a token representing a single symbol. -
Uses of Symbol in org.biojava.bio.symbol
Subinterfaces of Symbol in org.biojava.bio.symbolModifier and TypeInterfaceDescriptioninterfaceA symbol that is not ambiguous.interfaceA symbol that can be represented as a string of Symbols.Classes in org.biojava.bio.symbol that implement SymbolModifier and TypeClassDescriptionclassThe base-class for Symbol implementations.static classA range of double values.static classA single double value.classAn atomic symbol consisting only of itself.static classA single int value.classA basic implementation of AtomicSymbol.Methods in org.biojava.bio.symbol that return SymbolModifier and TypeMethodDescriptionstatic SymbolAlphabetManager.createSymbol(char token, Annotation annotation, List symList, Alphabet alpha) Deprecated.use the new version, without the token argumentstatic SymbolAlphabetManager.createSymbol(char token, Annotation annotation, Set symSet, Alphabet alpha) Deprecated.use the three-arg version of this method instead.static SymbolAlphabetManager.createSymbol(Annotation annotation, List symList, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.static SymbolAlphabetManager.createSymbol(Annotation annotation, Set symSet, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.protected SymbolSimpleManyToOneTranslationTable.doTranslate(Symbol sym) protected SymbolSimpleReversibleTranslationTable.doTranslate(Symbol sym) SimpleTranslationTable.doTranslate(Symbol sym) protected abstract SymbolAbstractReversibleTranslationTable.doUntranslate(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.protected SymbolSimpleReversibleTranslationTable.doUntranslate(Symbol sym) static SymbolAlphabetManager.getAllAmbiguitySymbol(FiniteAlphabet alpha) Return the ambiguity symbol which matches all symbols in a given alphabet.final SymbolAbstractAlphabet.getAmbiguity(Set syms) Alphabet.getAmbiguity(Set<Symbol> syms) Get a symbol that represents the set of symbols in syms.DoubleAlphabet.getAmbiguity(Set syms) DoubleAlphabet.SubDoubleAlphabet.getAmbiguity(Set syms) IntegerAlphabet.getAmbiguity(Set symSet) SoftMaskedAlphabet.getAmbiguity(Set s) This is not supported.protected SymbolAbstractAlphabet.getAmbiguityImpl(Set syms) Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.final SymbolAbstractAlphabet.getGapSymbol()Alphabet.getGapSymbol()Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.static SymbolAlphabetManager.getGapSymbol()Get the special `gap' Symbol.static SymbolAlphabetManager.getGapSymbol(List alphas) Get the gap symbol appropriate to this list of alphabets.DoubleAlphabet.getGapSymbol()DoubleAlphabet.SubDoubleAlphabet.getGapSymbol()IntegerAlphabet.getGapSymbol()SoftMaskedAlphabet.getGapSymbol()WobbleDistribution.getResidue()returns the residue encoded by this WobbleDistributionfinal SymbolGet a symbol from the Alphabet which corresponds to the specified ordered list of symbols.IllegalSymbolException.getSymbol()Retrieve the symbol that caused this exception, or null.Gets the compound symbol composed of theSymbolsin the List.Symbol[]SimpleSymbolList.getSymbolArray()Return the Java Symbol[] array that backs this object.SoftMaskedAlphabet.CaseSensitiveTokenization.parseToken(String token) ChunkedSymbolList.symbolAt(int pos) DummySymbolList.symbolAt(int i) PackedSymbolList.symbolAt(int indx) RelabeledAlignment.symbolAt(int pos) SimpleGappedSymbolList.symbolAt(int indx) SimpleSymbolList.symbolAt(int pos) Find a symbol at a specified offset in the SymbolList.SymbolList.symbolAt(int index) Return the symbol at index, counting from 1.AlphabetIndex.symbolForIndex(int i) Retrieve the symbol for an index.static SymbolAlphabetManager.symbolForLifeScienceID(LifeScienceIdentifier lsid) Retreives the Symbol for the LSIDstatic SymbolAlphabetManager.symbolForName(String name) Deprecated.use symbolForLifeScienceID() insteadTranslate a single symbol from source alphabet to the target alphabet.DNAAmbPack.unpack(byte b) DNANoAmbPack.unpack(byte b) Packing.unpack(byte packed) Return the symbol for a packing.AbstractReversibleTranslationTable.untranslate(Symbol sym) ReversibleTranslationTable.untranslate(Symbol sym) Translate a single symbol from target alphabet to the source alphabet.Methods in org.biojava.bio.symbol that return types with arguments of type SymbolModifier and TypeMethodDescriptionAbstractSymbolList.iterator()FiniteAlphabet.iterator()Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.SymbolList.iterator()An Iterator over all Symbols in this SymbolList.AbstractSymbolList.toList()SymbolList.toList()Returns a List of symbols.Methods in org.biojava.bio.symbol with parameters of type SymbolModifier and TypeMethodDescriptionfinal voidvoidAdds a symbol to this alphabet.voidAdd a new Symbol to the end of this list.voidSoftMaskedAlphabets cannot add newSymbols.final booleanbooleanReturns whether or not this Alphabet contains the symbol.booleanbooleanbooleanbooleanprotected SymbolSimpleManyToOneTranslationTable.doTranslate(Symbol sym) protected SymbolSimpleReversibleTranslationTable.doTranslate(Symbol sym) SimpleTranslationTable.doTranslate(Symbol sym) protected abstract SetAbstractManyToOneTranslationTable.doUntranslate(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.protected abstract SymbolAbstractReversibleTranslationTable.doUntranslate(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.protected SetSimpleManyToOneTranslationTable.doUntranslate(Symbol sym) protected SymbolSimpleReversibleTranslationTable.doUntranslate(Symbol sym) static AlphabetIndexAlphabetManager.getAlphabetIndex(Symbol[] syms) Get an indexer for an array of symbols.SuffixTree.getChild(SuffixTree.SuffixNode node, Symbol s) Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.doubleSimpleSymbolPropertyTable.getDoubleValue(Symbol s) doubleSymbolPropertyTable.getDoubleValue(Symbol s) CodonPref.getFrequencyForSynonyms(Symbol residue) returns a Distribution giving the frequency of synonymous codons.SimpleCodonPref.getFrequencyForSynonyms(Symbol residue) CodonPref.getWobbleDistributionForSynonyms(Symbol residue) returns a WobbleDistribution for a specified residue.SimpleCodonPref.getWobbleDistributionForSynonyms(Symbol residue) 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.intAlphabetIndex.indexForSymbol(Symbol s) Return the unique index for a symbol.PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) Makes a packed SymbolList out of a list of Symbols.SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) Create a factory for SimpleSymbolLists.SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) makes a SymbolList containing size Symbols from a Symbol array.bytebytebyteReturn a byte representing the packing of a symbol.voidFiniteAlphabet.removeSymbol(Symbol s) Remove a symbol from this alphabet.voidIntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym) voidSimpleAlphabet.removeSymbol(Symbol s) voidSingletonAlphabet.removeSymbol(Symbol sym) voidSoftMaskedAlphabet.removeSymbol(Symbol s) SoftMaskedAlphabets cannot removeSymbols.voidSimpleSymbolPropertyTable.setDoubleProperty(Symbol s, String value) SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbol(Symbol s) Translate a single symbol from source alphabet to the target alphabet.AbstractManyToOneTranslationTable.untranslate(Symbol sym) returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet.AbstractReversibleTranslationTable.untranslate(Symbol sym) ManyToOneTranslationTable.untranslate(Symbol sym) Translate a single symbol from target alphabet to the source alphabet.ReversibleTranslationTable.untranslate(Symbol sym) Translate a single symbol from target alphabet to the source alphabet.final voidvoidThrows a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.voidvoidvoidvoidMethod parameters in org.biojava.bio.symbol with type arguments of type SymbolModifier and TypeMethodDescriptionAlphabet.getAmbiguity(Set<Symbol> syms) Get a symbol that represents the set of symbols in syms.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 SymbolModifierConstructorDescriptionDNANoAmbPack(Symbol placeHolderSymbol) Construct a new packing which translates unknown symbols into the specified symbol.DummySymbolList(Alphabet alpha, int length, Symbol sym) Convenience construtor for making single residue changesIllegalSymbolException(Throwable cause, Symbol sym, String message) IllegalSymbolException(Symbol sym, String message) Make the exception with a message and a symbol.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 SymbolModifier and TypeMethodDescriptionorg.biojava.utils.automata.FiniteAutomaton.TransitionFiniteAutomaton.addTransition(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym) org.biojava.utils.automata.FiniteAutomaton.TransitionNfaBuilder.addTransition(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym) org.biojava.utils.automata.FiniteAutomaton.TransitionNfaSubModel.addTransition(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym) protected intFiniteAutomaton.alphaIndex(Symbol sym) protected intNfa.alphaIndex(Symbol sym) -
Uses of Symbol in org.biojava.utils.regex
Methods in org.biojava.utils.regex with parameters of type Symbol -
Uses of Symbol in org.biojavax.bio.db.biosql
Methods in org.biojavax.bio.db.biosql that return SymbolModifier and TypeMethodDescriptionBioSQLRichSequenceHandler.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 SymbolModifier and TypeMethodDescriptionDummyRichSequenceHandler.symbolAt(RichSequence seq, int index) Return the symbol at index, counting from 1.InfinitelyAmbiguousSymbolList.symbolAt(int index) Return the symbol at index, counting from 1.RichSequenceHandler.symbolAt(RichSequence seq, int index) Return the symbol at index, counting from 1.ThinRichSequence.symbolAt(int index) Return the symbol at index, counting from 1.Methods in org.biojavax.bio.seq that return types with arguments of type SymbolModifier and TypeMethodDescriptionDummyRichSequenceHandler.iterator(RichSequence seq) An Iterator over all Symbols in this SymbolList.RichSequenceHandler.iterator(RichSequence seq) An Iterator over all Symbols in this SymbolList.DummyRichSequenceHandler.toList(RichSequence seq) Returns a List of symbols.RichSequenceHandler.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 SymbolModifier and TypeMethodDescriptionvoidDebuggingRichSeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) voidRichSeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) voidSimpleRichSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) Notify the listener of symbol data.