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Packages that use Symbol | |
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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.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 protein structure (PDB). |
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 |
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Fields in org.biojava.bio.alignment with type parameters of type Symbol | |
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protected Map<Symbol,Integer> |
SubstitutionMatrix.colSymbols
|
protected Map<Symbol,Integer> |
SubstitutionMatrix.rowSymbols
|
Methods in org.biojava.bio.alignment that return Symbol | |
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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 |
AbstractULAlignment.SubULAlignment.symbolAt(Object label,
int column)
|
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 |
Methods in org.biojava.bio.alignment with parameters of type Symbol | |
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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 |
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Methods in org.biojava.bio.chromatogram.graphic with parameters of type Symbol | |
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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 |
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Methods in org.biojava.bio.dist that return Symbol | |
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Symbol |
AbstractDistribution.sampleSymbol()
|
Symbol |
TranslatedDistribution.sampleSymbol()
|
Symbol |
GapDistribution.sampleSymbol()
|
Symbol |
Distribution.sampleSymbol()
Sample a symbol from this state's probability distribution. |
Symbol |
PairDistribution.sampleSymbol()
|
Methods in org.biojava.bio.dist with parameters of type Symbol | |
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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 |
AbstractDistribution.getWeight(Symbol sym)
Retrieve the weight for this distribution. |
double |
TranslatedDistribution.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 |
PairDistribution.getWeight(Symbol sym)
|
void |
OrderNDistribution.setDistribution(Symbol sym,
Distribution dist)
Set the distribution assocated with a symbol. |
void |
AbstractDistribution.setWeight(Symbol sym,
double weight)
Set the weight of a given symbol in this distribution. |
void |
TranslatedDistribution.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 |
PairDistribution.setWeight(Symbol sym,
double weight)
|
Uses of Symbol in org.biojava.bio.dp |
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Subinterfaces of Symbol in org.biojava.bio.dp | |
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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 | |
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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 | |
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Symbol |
SimpleStatePath.symbolAt(int col)
|
Symbol |
SimpleStatePath.symbolAt(Object label,
int col)
|
Methods in org.biojava.bio.dp with parameters of type Symbol | |
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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. |
void |
SimpleHMMTrainer.recordEmittedSymbol(State state,
Symbol symbol,
double weight)
|
Uses of Symbol in org.biojava.bio.dp.onehead |
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Methods in org.biojava.bio.dp.onehead that return Symbol | |
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Symbol |
DPCursor.currentRes()
The current symbol. |
Symbol |
DPCursor.lastRes()
The previous symbol. |
Methods in org.biojava.bio.dp.onehead with parameters of type Symbol | |
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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 |
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Methods in org.biojava.bio.gui with parameters of type Symbol | |
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static double |
DistributionLogo.entropy(Distribution dist,
Symbol s)
Calculate the information content of a symbol in bits. |
Paint |
DNAStyle.fillPaint(Symbol s)
|
Paint |
SimpleSymbolStyle.fillPaint(Symbol s)
|
Paint |
SymbolStyle.fillPaint(Symbol s)
Return the fill paint for a symbol. |
Paint |
PlainStyle.fillPaint(Symbol s)
|
Paint |
DNAStyle.outlinePaint(Symbol s)
|
Paint |
SimpleSymbolStyle.outlinePaint(Symbol s)
|
Paint |
SymbolStyle.outlinePaint(Symbol s)
Return the outline paint for a symbol. |
Paint |
PlainStyle.outlinePaint(Symbol s)
|
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 |
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Methods in org.biojava.bio.program.abi that return Symbol | |
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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 |
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Methods in org.biojava.bio.program.das that return Symbol | |
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Symbol |
DASSequence.symbolAt(int pos)
|
Uses of Symbol in org.biojava.bio.program.hmmer |
---|
Classes in org.biojava.bio.program.hmmer that implement Symbol | |
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class |
ProfileEmissionState
A state in a HMMer model. |
Methods in org.biojava.bio.program.hmmer with parameters of type Symbol | |
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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 |
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Methods in org.biojava.bio.program.phred that return Symbol | |
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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 |
PhredSequence.getQualityAt(int index)
|
Symbol |
Qualitative.getQualityAt(int index)
Retreives the quality symbol for the specified 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 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 |
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Methods in org.biojava.bio.proteomics with parameters of type Symbol | |
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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 |
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Methods in org.biojava.bio.seq that return Symbol | |
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static Symbol |
NucleotideTools.b()
|
static Symbol |
DNATools.b()
|
static Symbol |
NucleotideTools.complement(Symbol sym)
Complement the symbol. |
static Symbol |
RNATools.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 |
NucleotideTools.forIndex(int index)
Return the symbol for an index - compatible with index . |
static Symbol |
RNATools.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 |
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.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 |
NucleotideTools.n()
|
static Symbol |
RNATools.n()
|
static Symbol |
DNATools.n()
|
static Symbol |
NucleotideTools.r()
|
static Symbol |
DNATools.r()
|
static Symbol |
NucleotideTools.s()
|
static Symbol |
DNATools.s()
|
Symbol |
NewSimpleAssembly.symbolAt(int pos)
|
Symbol |
CircularView.symbolAt(int index)
Over rides ViewSequence. |
Symbol |
SimpleAssembly.symbolAt(int pos)
|
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 | |
---|---|
static Symbol |
NucleotideTools.complement(Symbol sym)
Complement the symbol. |
static Symbol |
RNATools.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 |
NucleotideTools.index(Symbol sym)
Return an integer index for a symbol - compatible with forIndex . |
static int |
RNATools.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 |
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Methods in org.biojava.bio.seq.homol that return Symbol | |
---|---|
Symbol |
SimilarityPairFeature.EmptyPairwiseAlignment.symbolAt(int index)
|
Symbol |
SimilarityPairFeature.EmptyPairwiseAlignment.symbolAt(Object label,
int index)
|
Uses of Symbol in org.biojava.bio.seq.impl |
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Methods in org.biojava.bio.seq.impl that return Symbol | |
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Symbol |
ViewSequence.symbolAt(int indx)
|
Symbol |
SimpleSequence.symbolAt(int index)
|
Symbol |
AssembledSymbolList.symbolAt(int pos)
|
Symbol |
NewAssembledSymbolList.symbolAt(int pos)
|
Symbol |
SubSequence.symbolAt(int pos)
|
Symbol |
DummySequence.symbolAt(int index)
|
Uses of Symbol in org.biojava.bio.seq.io |
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Methods in org.biojava.bio.seq.io that return Symbol | |
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protected Symbol[] |
CharacterTokenization.getTokenTable()
|
protected Symbol[] |
WordTokenization.parseString(String s)
|
Symbol |
SymbolTokenization.parseToken(String token)
Returns the symbol for a single token. |
Symbol |
IntegerTokenization.parseToken(String seq)
|
Symbol |
SubIntegerTokenization.parseToken(String seq)
|
Symbol |
CrossProductTokenization.parseToken(String token)
|
Symbol |
DoubleTokenization.parseToken(String seq)
|
Symbol |
CharacterTokenization.parseToken(String token)
|
Symbol |
NameTokenization.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 | |
---|---|
void |
GenbankFileFormer.addSymbols(Alphabet alpha,
Symbol[] syms,
int start,
int length)
Deprecated. |
void |
SeqIOAdapter.addSymbols(Alphabet alpha,
Symbol[] syms,
int start,
int length)
|
void |
SequenceBuilderFilter.addSymbols(Alphabet alpha,
Symbol[] syms,
int start,
int length)
|
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 |
SimpleAssemblyBuilder.addSymbols(Alphabet alpha,
Symbol[] syms,
int pos,
int len)
|
void |
SeqIOFilter.addSymbols(Alphabet alpha,
Symbol[] syms,
int start,
int length)
|
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 |
ProteinRefSeqFileFormer.addSymbols(Alphabet theAlphabet,
Symbol[] theSymbols,
int theStart,
int theLength)
Deprecated. |
void |
SeqIOListener.addSymbols(Alphabet alpha,
Symbol[] syms,
int start,
int length)
Notify the listener of symbol data. |
void |
SimpleSequenceBuilder.addSymbols(Alphabet alpha,
Symbol[] syms,
int pos,
int len)
|
abstract void |
SequenceBuilderBase.addSymbols(Alphabet alpha,
Symbol[] syms,
int pos,
int len)
|
void |
SequenceDBSequenceBuilder.addSymbols(Alphabet alpha,
Symbol[] syms,
int pos,
int len)
does nothing for now. |
void |
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 |
IntegerTokenization.tokenizeSymbol(Symbol sym)
|
String |
SubIntegerTokenization.tokenizeSymbol(Symbol sym)
|
String |
CrossProductTokenization.tokenizeSymbol(Symbol s)
|
String |
DoubleTokenization.tokenizeSymbol(Symbol sym)
|
String |
CharacterTokenization.tokenizeSymbol(Symbol s)
|
String |
NameTokenization.tokenizeSymbol(Symbol s)
|
String |
AlternateTokenization.tokenizeSymbol(Symbol s)
|
Uses of Symbol in org.biojava.bio.structure |
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Methods in org.biojava.bio.structure that return Symbol | |
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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 |
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Subinterfaces of Symbol in org.biojava.bio.symbol | |
---|---|
interface |
AtomicSymbol
A symbol that is not ambiguous. |
interface |
BasisSymbol
A symbol that can be represented as a string of Symbols. |
Classes in org.biojava.bio.symbol that implement Symbol | |
---|---|
class |
AbstractSymbol
The base-class for Symbol implementations. |
static class |
DoubleAlphabet.DoubleRange
A range of double values. |
static class |
DoubleAlphabet.DoubleSymbol
A single double value. |
class |
FundamentalAtomicSymbol
An atomic symbol consisting only of itself. |
static class |
IntegerAlphabet.IntegerSymbol
A single int value. |
class |
SimpleAtomicSymbol
A basic implementation of AtomicSymbol. |
Methods in org.biojava.bio.symbol that return Symbol | |
---|---|
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. |
protected Symbol |
SimpleReversibleTranslationTable.doTranslate(Symbol sym)
|
protected Symbol |
SimpleManyToOneTranslationTable.doTranslate(Symbol sym)
|
Symbol |
SimpleTranslationTable.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 |
DoubleAlphabet.getAmbiguity(Set syms)
|
Symbol |
DoubleAlphabet.SubDoubleAlphabet.getAmbiguity(Set syms)
|
Symbol |
IntegerAlphabet.getAmbiguity(Set symSet)
|
Symbol |
SoftMaskedAlphabet.getAmbiguity(Set s)
This is not supported. |
Symbol |
Alphabet.getAmbiguity(Set syms)
Get a symbol that represents the set of symbols in syms. |
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 |
DoubleAlphabet.getGapSymbol()
|
Symbol |
DoubleAlphabet.SubDoubleAlphabet.getGapSymbol()
|
Symbol |
IntegerAlphabet.getGapSymbol()
|
Symbol |
SoftMaskedAlphabet.getGapSymbol()
|
Symbol |
Alphabet.getGapSymbol()
Get the 'gap' ambiguity symbol that is most appropriate for this alphabet. |
static Symbol |
AlphabetManager.getGapSymbol()
Get the special `gap' Symbol. |
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 |
DoubleAlphabet.getSymbol(List symList)
|
Symbol |
DoubleAlphabet.SubDoubleAlphabet.getSymbol(List rl)
|
Symbol |
IntegerAlphabet.getSymbol(List symList)
|
Symbol |
SoftMaskedAlphabet.getSymbol(List l)
Gets the compound symbol composed of the Symbols in the List. |
Symbol |
Alphabet.getSymbol(List rl)
Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols. |
Symbol |
AbstractAlphabet.getSymbol(List syms)
|
Symbol[] |
SimpleSymbolList.getSymbolArray()
Return the Java Symbol[] array that backs this object. |
Symbol |
SoftMaskedAlphabet.CaseSensitiveTokenization.parseToken(String token)
|
Symbol |
PackedSymbolList.symbolAt(int indx)
|
Symbol |
ChunkedSymbolList.symbolAt(int pos)
|
Symbol |
SimpleSymbolList.symbolAt(int pos)
Find a symbol at a specified offset in the SymbolList. |
Symbol |
DummySymbolList.symbolAt(int i)
|
Symbol |
RelabeledAlignment.symbolAt(int pos)
|
Symbol |
SymbolList.symbolAt(int index)
Return the symbol at index, counting from 1. |
Symbol |
SimpleAlignment.symbolAt(int index)
|
Symbol |
SimpleGappedSymbolList.symbolAt(int indx)
|
Symbol |
Alignment.symbolAt(Object label,
int column)
Retrieve a symbol by label and column. |
Symbol |
RelabeledAlignment.symbolAt(Object label,
int column)
|
Symbol |
SimpleAlignment.symbolAt(Object 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 |
DNANoAmbPack.unpack(byte b)
|
Symbol |
Packing.unpack(byte packed)
Return the symbol for a packing. |
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 | |
---|---|
Iterator<Symbol> |
FiniteAlphabet.iterator()
Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet. |
Methods in org.biojava.bio.symbol with parameters of type Symbol | |
---|---|
void |
FiniteAlphabet.addSymbol(Symbol s)
Adds a symbol to this alphabet. |
void |
SimpleSymbolList.addSymbol(Symbol sym)
Add a new Symbol to the end of this list. |
void |
SoftMaskedAlphabet.addSymbol(Symbol s)
SoftMaskedAlphabet s cannot add new Symbol s. |
void |
AbstractAlphabet.addSymbol(Symbol s)
|
boolean |
DoubleAlphabet.contains(Symbol s)
|
boolean |
DoubleAlphabet.SubDoubleAlphabet.contains(Symbol s)
|
boolean |
IntegerAlphabet.contains(Symbol s)
|
boolean |
SoftMaskedAlphabet.contains(Symbol s)
|
boolean |
Alphabet.contains(Symbol s)
Returns whether or not this Alphabet contains the symbol. |
boolean |
AbstractAlphabet.contains(Symbol sym)
|
protected Symbol |
SimpleReversibleTranslationTable.doTranslate(Symbol sym)
|
protected Symbol |
SimpleManyToOneTranslationTable.doTranslate(Symbol sym)
|
Symbol |
SimpleTranslationTable.doTranslate(Symbol sym)
|
protected Symbol |
SimpleReversibleTranslationTable.doUntranslate(Symbol sym)
|
protected Set |
SimpleManyToOneTranslationTable.doUntranslate(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. |
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 |
SimpleSymbolPropertyTable.getDoubleValue(Symbol s)
|
double |
SymbolPropertyTable.getDoubleValue(Symbol s)
|
Distribution |
CodonPref.getFrequencyForSynonyms(Symbol residue)
returns a Distribution giving the frequency of synonymous codons. |
Distribution |
SimpleCodonPref.getFrequencyForSynonyms(Symbol residue)
|
WobbleDistribution |
CodonPref.getWobbleDistributionForSynonyms(Symbol residue)
returns a WobbleDistribution for a specified residue. |
WobbleDistribution |
SimpleCodonPref.getWobbleDistributionForSynonyms(Symbol 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 |
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. |
SymbolList |
SymbolListFactory.makeSymbolList(Symbol[] symbolArray,
int size,
Alphabet alfa)
makes a SymbolList containing size Symbols from a Symbol array. |
byte |
DNANoAmbPack.pack(Symbol sym)
|
byte |
Packing.pack(Symbol sym)
Return a byte representing the packing of a symbol. |
byte |
DNAAmbPack.pack(Symbol sym)
|
void |
FiniteAlphabet.removeSymbol(Symbol s)
Remove a symbol from this alphabet. |
void |
SimpleAlphabet.removeSymbol(Symbol s)
|
void |
IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)
|
void |
SoftMaskedAlphabet.removeSymbol(Symbol s)
SoftMaskedAlphabet s cannot remove Symbol s. |
void |
SingletonAlphabet.removeSymbol(Symbol sym)
|
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. |
Set |
AbstractManyToOneTranslationTable.untranslate(Symbol sym)
returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet. |
Symbol |
AbstractReversibleTranslationTable.untranslate(Symbol sym)
|
void |
DoubleAlphabet.validate(Symbol s)
|
void |
DoubleAlphabet.SubDoubleAlphabet.validate(Symbol sym)
|
void |
IntegerAlphabet.validate(Symbol s)
|
void |
SoftMaskedAlphabet.validate(Symbol s)
|
void |
Alphabet.validate(Symbol s)
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet. |
void |
AbstractAlphabet.validate(Symbol sym)
|
Constructors in org.biojava.bio.symbol with parameters of type Symbol | |
---|---|
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 | |
---|---|
org.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 |
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 |
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 | |
---|---|
char |
PatternFactory.charValue(Symbol sym)
Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for. |
char |
Search.charValue(Symbol sym)
|
Uses of Symbol in org.biojavax.bio.db.biosql |
---|
Methods in org.biojavax.bio.db.biosql that return Symbol | |
---|---|
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 | |
---|---|
Symbol |
InfinitelyAmbiguousSymbolList.symbolAt(int index)
Return the symbol at index, counting from 1. |
Symbol |
ThinRichSequence.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. |
Uses of Symbol in org.biojavax.bio.seq.io |
---|
Methods in org.biojavax.bio.seq.io with parameters of type Symbol | |
---|---|
void |
RichSeqIOAdapter.addSymbols(Alphabet alpha,
Symbol[] syms,
int start,
int length)
|
void |
DebuggingRichSeqIOListener.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. |
|
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