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 TypeMethodDescriptionshort
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 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.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 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 TypeMethodDescriptionvoid
DistributionTrainerContext.addCount
(Distribution dist, Symbol sym, double times) Registers that sym was counted in this state.void
SimpleDistributionTrainerContext.addCount
(Distribution dist, Symbol sym, double times) double
DistributionTrainerContext.getCount
(Distribution dist, Symbol sym) Return the number of counts of a particular symbol which will be used to train the specified distribution.double
SimpleDistributionTrainerContext.getCount
(Distribution dist, Symbol sym) OrderNDistribution.getDistribution
(Symbol sym) final double
Retrieve the weight for this distribution.double
Return the probability that Symbol s is emitted by this spectrum.double
double
double
void
OrderNDistribution.setDistribution
(Symbol sym, Distribution dist) Set the distribution assocated with a symbol.final void
Set the weight of a given symbol in this distribution.void
Set the probability or odds that Symbol s is emitted by this state.void
void
void
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Uses of Symbol in org.biojava.bio.dp
Subinterfaces of Symbol in org.biojava.bio.dpModifier and TypeInterfaceDescriptioninterface
A Dot state.interface
A state in a markov process that has an emission spectrum.interface
A state that contains an entire sub-model.interface
A state in a markov process.Classes in org.biojava.bio.dp that implement SymbolModifier and TypeClassDescriptionfinal class
Start/end state for HMMs.class
A Dot state that you can make and use.class
class
Methods 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 TypeMethodDescriptiondouble
ScoreType.calculateScore
(Distribution dist, Symbol sym) Calculates the score associated with a distribution and a symbol.double
ScoreType.NullModel.calculateScore
(Distribution dist, Symbol sym) double
ScoreType.Odds.calculateScore
(Distribution dist, Symbol sym) double
ScoreType.Probability.calculateScore
(Distribution dist, Symbol sym) void
HMMTrainer.recordEmittedSymbol
(State state, Symbol symbol, double weight) record that the specified symbol was emitted from the specified state.void
SimpleHMMTrainer.recordEmittedSymbol
(State state, Symbol symbol, double weight) -
Uses of Symbol in org.biojava.bio.dp.onehead
Methods in org.biojava.bio.dp.onehead that return 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 double
DistributionLogo.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.void
DNAStyle.setFillPaint
(Symbol s, Paint paint) void
SimpleSymbolStyle.setFillPaint
(Symbol s, Paint paint) void
DNAStyle.setOutlinePaint
(Symbol s, Paint paint) void
SimpleSymbolStyle.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 Symbol
ABIFParser.decodeDNAToken
(char token) Decodes a character into aSymbol
in 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 Symbol
PhredTools.dnaSymbolFromPhred
(Symbol phredSym) Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.PhredSequence.getDNAAt
(int index) static final 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).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 Symbol
PhredTools.dnaSymbolFromPhred
(Symbol phredSym) Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.static final 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 final 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 SymbolModifier and TypeMethodDescriptionvoid
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 SymbolModifier and TypeMethodDescriptionstatic Symbol
DNATools.b()
static Symbol
NucleotideTools.b()
static Symbol
DNATools.complement
(Symbol sym) Complement the symbol.static Symbol
NucleotideTools.complement
(Symbol sym) Complement the symbol.static Symbol
RNATools.complement
(Symbol sym) Complement the symbol.static Symbol
DNATools.d()
static Symbol
NucleotideTools.d()
static Symbol
DNATools.forIndex
(int index) Return the symbol for an index - compatible withindex
.static Symbol
NucleotideTools.forIndex
(int index) Return the symbol for an index - compatible withindex
.static Symbol
RNATools.forIndex
(int index) Return the symbol for an index - compatible with index.static Symbol
DNATools.forSymbol
(char token) Retrieve the symbol for a symbol.static Symbol
NucleotideTools.forSymbol
(char token) Retrieve the symbol for a symbol.static Symbol
RNATools.forSymbol
(char token) Retrieve the symbol for a symbol.static Symbol
DNATools.h()
static Symbol
NucleotideTools.h()
static Symbol
DNATools.k()
static Symbol
NucleotideTools.k()
static Symbol
DNATools.m()
static Symbol
NucleotideTools.m()
static Symbol
DNATools.n()
static Symbol
NucleotideTools.n()
static Symbol
RNATools.n()
static Symbol
DNATools.r()
static Symbol
NucleotideTools.r()
static Symbol
DNATools.s()
static Symbol
NucleotideTools.s()
CircularView.symbolAt
(int index) Over rides ViewSequence.NewSimpleAssembly.symbolAt
(int pos) SimpleAssembly.symbolAt
(int pos) static Symbol
DNATools.v()
static Symbol
NucleotideTools.v()
static Symbol
DNATools.w()
static Symbol
NucleotideTools.w()
static Symbol
DNATools.y()
static Symbol
NucleotideTools.y()
Methods in org.biojava.bio.seq with parameters of type SymbolModifier and TypeMethodDescriptionstatic Symbol
DNATools.complement
(Symbol sym) Complement the symbol.static Symbol
NucleotideTools.complement
(Symbol sym) Complement the symbol.static Symbol
RNATools.complement
(Symbol sym) Complement the symbol.static Sequence
SequenceTools.createDummy
(Alphabet alpha, int length, Symbol sym, String uri, String name) Create a new Sequence that contains a single symbol repeated over and over.static char
Get a single-character token for a DNA symbolstatic int
Return an integer index for a symbol - compatible withforIndex
.static int
Return an integer index for a symbol - compatible withforIndex
.static int
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 -
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 Symbol
CharacterTokenization.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 TypeMethodDescriptionvoid
ChunkedSymbolListFactory.addSymbols
(Alphabet alfa, Symbol[] syms, int pos, int len) tool to construct the SymbolList by adding Symbols.void
EmblFileFormer.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) Deprecated.void
GenbankFileFormer.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) Deprecated.void
ProteinRefSeqFileFormer.addSymbols
(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.void
SeqIOAdapter.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) void
SeqIOFilter.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) void
SeqIOListener.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) Notify the listener of symbol data.abstract void
SequenceBuilderBase.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SequenceBuilderFilter.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) void
SequenceDBSequenceBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) does nothing for now.void
SimpleAssemblyBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SimpleSequenceBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SmartSequenceBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SwissprotFileFormer.addSymbols
(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.Prints out the sequences properties in order.void
AlternateTokenization.bindSymbol
(Symbol s, String str) Bind a Symbol to a string.void
CharacterTokenization.bindSymbol
(Symbol s, char c) Bind a Symbol to a character.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 List
SwissprotFileFormer.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.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 TypeInterfaceDescriptioninterface
A symbol that is not ambiguous.interface
A symbol that can be represented as a string of Symbols.Classes in org.biojava.bio.symbol that implement SymbolModifier and TypeClassDescriptionclass
The base-class for Symbol implementations.static class
A range of double values.static class
A single double value.class
An atomic symbol consisting only of itself.static class
A single int value.class
A basic implementation of AtomicSymbol.Methods in org.biojava.bio.symbol that return SymbolModifier and TypeMethodDescriptionstatic Symbol
AlphabetManager.createSymbol
(char token, Annotation annotation, List symList, Alphabet alpha) Deprecated.use the new version, without the token argumentstatic 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, 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.protected Symbol
SimpleManyToOneTranslationTable.doTranslate
(Symbol sym) protected Symbol
SimpleReversibleTranslationTable.doTranslate
(Symbol sym) SimpleTranslationTable.doTranslate
(Symbol sym) protected abstract Symbol
AbstractReversibleTranslationTable.doUntranslate
(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.protected Symbol
SimpleReversibleTranslationTable.doUntranslate
(Symbol sym) static Symbol
AlphabetManager.getAllAmbiguitySymbol
(FiniteAlphabet alpha) Return the ambiguity symbol which matches all symbols in a given alphabet.final Symbol
AbstractAlphabet.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 Symbol
AbstractAlphabet.getAmbiguityImpl
(Set syms) Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.final Symbol
AbstractAlphabet.getGapSymbol()
Alphabet.getGapSymbol()
Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.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.DoubleAlphabet.getGapSymbol()
DoubleAlphabet.SubDoubleAlphabet.getGapSymbol()
IntegerAlphabet.getGapSymbol()
SoftMaskedAlphabet.getGapSymbol()
WobbleDistribution.getResidue()
returns the residue encoded by this WobbleDistributionfinal Symbol
Get 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 theSymbols
in 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 Symbol
AlphabetManager.symbolForLifeScienceID
(LifeScienceIdentifier lsid) Retreives the Symbol for the LSIDstatic Symbol
AlphabetManager.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 void
void
Adds a symbol to this alphabet.void
Add a new Symbol to the end of this list.void
SoftMaskedAlphabet
s cannot add newSymbol
s.final boolean
boolean
Returns whether or not this Alphabet contains the symbol.boolean
boolean
boolean
boolean
protected Symbol
SimpleManyToOneTranslationTable.doTranslate
(Symbol sym) protected Symbol
SimpleReversibleTranslationTable.doTranslate
(Symbol sym) SimpleTranslationTable.doTranslate
(Symbol sym) protected abstract Set
AbstractManyToOneTranslationTable.doUntranslate
(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.protected abstract Symbol
AbstractReversibleTranslationTable.doUntranslate
(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.protected Set
SimpleManyToOneTranslationTable.doUntranslate
(Symbol sym) protected Symbol
SimpleReversibleTranslationTable.doUntranslate
(Symbol sym) static AlphabetIndex
AlphabetManager.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.double
SimpleSymbolPropertyTable.getDoubleValue
(Symbol s) double
SymbolPropertyTable.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.int
AlphabetIndex.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.byte
byte
byte
Return a byte representing the packing of a symbol.void
FiniteAlphabet.removeSymbol
(Symbol s) Remove a symbol from this alphabet.void
IntegerAlphabet.SubIntegerAlphabet.removeSymbol
(Symbol sym) void
SimpleAlphabet.removeSymbol
(Symbol s) void
SingletonAlphabet.removeSymbol
(Symbol sym) void
SoftMaskedAlphabet.removeSymbol
(Symbol s) SoftMaskedAlphabet
s cannot removeSymbol
s.void
SimpleSymbolPropertyTable.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 void
void
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.void
void
void
void
Method 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.Transition
FiniteAutomaton.addTransition
(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym) org.biojava.utils.automata.FiniteAutomaton.Transition
NfaBuilder.addTransition
(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym) org.biojava.utils.automata.FiniteAutomaton.Transition
NfaSubModel.addTransition
(org.biojava.utils.automata.FiniteAutomaton.Node start, org.biojava.utils.automata.FiniteAutomaton.Node end, Symbol sym) protected int
FiniteAutomaton.alphaIndex
(Symbol sym) protected int
Nfa.alphaIndex
(Symbol sym) -
Uses of Symbol in org.biojava.utils.regex
Methods in org.biojava.utils.regex with parameters of type Symbol -
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 TypeMethodDescriptionvoid
DebuggingRichSeqIOListener.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) void
RichSeqIOAdapter.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) void
SimpleRichSequenceBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) Notify the listener of symbol data.