Uses of Class
org.biojava.bio.symbol.IllegalSymbolException
Packages that use IllegalSymbolException
Package
Description
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
Java wrappers for interacting with external bioinformatics tools.
ABI Trace Handling.
FASTQ and variants sequence format I/O.
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.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
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.
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
Classes to provide a genetic algorithm framework
GA functions
Default implementations and abstract classes.
Utility functions and helper classes
-
Uses of IllegalSymbolException in org.biojava.bio.chromatogram
Methods in org.biojava.bio.chromatogram that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionprotected SymbolList
AbstractChromatogram.createImmutableSymbolList
(Alphabet alpha, List syms) A factory method for creating new symbol lists with a given alphabet.int
AbstractChromatogram.getMax
(AtomicSymbol nucleotide) int
Chromatogram.getMax
(AtomicSymbol nucleotide) Gets the max intensity on the trace for the specified nucleotide.int[]
AbstractChromatogram.getTrace
(AtomicSymbol nucleotide) int[]
Chromatogram.getTrace
(AtomicSymbol nucleotide) Returns an array containing the intensities of the sampled waveform representing the chromatogram trace for basenucleotide
.protected final void
AbstractChromatogram.setTrace
(AtomicSymbol nuc, int[] trace, int maxVal) Provides the trace samples for a particular nucleotide.void
SimpleChromatogram.setTraceValues
(AtomicSymbol nuc, int[] trace, int maxVal) Sets the trace array for one of the DNA nucleotides. -
Uses of IllegalSymbolException in org.biojava.bio.dist
Methods in org.biojava.bio.dist that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionvoid
DistributionTrainer.addCount
(DistributionTrainerContext dtc, AtomicSymbol sym, double times) Registers that sym was counted in this state.void
DistributionTrainerContext.addCount
(Distribution dist, Symbol sym, double times) Registers that sym was counted in this state.void
IgnoreCountsTrainer.addCount
(DistributionTrainerContext dtc, AtomicSymbol sym, double times) void
SimpleDistribution.Trainer.addCount
(DistributionTrainerContext dtc, AtomicSymbol sym, double times) void
SimpleDistributionTrainer.addCount
(DistributionTrainerContext dtc, AtomicSymbol sym, double count) Deprecated.void
SimpleDistributionTrainerContext.addCount
(Distribution dist, Symbol sym, double times) double
Count.getCount
(AtomicSymbol s) Return the counts for a given Symbol.double
DistributionTrainer.getCount
(DistributionTrainerContext dtc, AtomicSymbol sym) Get the current count for 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
IgnoreCountsTrainer.getCount
(DistributionTrainerContext dtc, AtomicSymbol sym) double
IndexedCount.getCount
(AtomicSymbol s) double
SimpleDistribution.Trainer.getCount
(DistributionTrainerContext dtc, AtomicSymbol sym) double
SimpleDistributionTrainer.getCount
(DistributionTrainerContext dtc, AtomicSymbol sym) Deprecated.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
protected abstract double
AbstractDistribution.getWeightImpl
(AtomicSymbol sym) Override this method to implement getting the weight for an atomic symbol.protected double
AbstractOrderNDistribution.getWeightImpl
(AtomicSymbol sym) Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.double
SimpleDistribution.getWeightImpl
(AtomicSymbol s) protected double
UniformDistribution.getWeightImpl
(AtomicSymbol s) void
Count.increaseCount
(AtomicSymbol s, double c) Set the probability or odds that Symbol s is emitted by this state.void
IndexedCount.increaseCount
(AtomicSymbol s, double c) void
Count.setCount
(AtomicSymbol s, double c) Set the count for the Symbol s.void
IndexedCount.setCount
(AtomicSymbol s, double c) 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
protected abstract void
AbstractDistribution.setWeightImpl
(AtomicSymbol sym, double weight) Implement this to actually set the weight.void
AbstractOrderNDistribution.setWeightImpl
(AtomicSymbol sym, double w) Set a weight in one of the conditioned distributions.protected void
SimpleDistribution.setWeightImpl
(AtomicSymbol s, double w) -
Uses of IllegalSymbolException in org.biojava.bio.dp
Methods in org.biojava.bio.dp that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionvoid
Add 'count' to the transition from->to.void
Adds a state to the model.void
void
abstract double
DP.backward
(SymbolList[] symList, ScoreType scoreType) abstract DPMatrix
DP.backwardMatrix
(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrix
DP.backwardMatrix
(SymbolList[] symList, ScoreType scoreType) static int[][]
DP.backwardTransitions
(MarkovModel model, State[] states) double
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) protected void
ProfileHMM.connectModel()
This is called by constructor in setting up the allowed transitions in the modelboolean
MarkovModel.containsTransition
(State from, State to) Returns wether a transition exists or not.boolean
SimpleMarkovModel.containsTransition
(State from, State to) boolean
WMAsMM.containsTransition
(State from, State to) void
MarkovModel.createTransition
(State from, State to) Makes a transition between two states legal.void
SimpleMarkovModel.createTransition
(State from, State to) void
MarkovModel.destroyTransition
(State from, State to) Breaks a transition between two states legal.void
SimpleMarkovModel.destroyTransition
(State from, State to) static MarkovModel
DP.flatView
(MarkovModel model) abstract double
DP.forward
(SymbolList[] symList, ScoreType scoreType) abstract DPMatrix
DP.forwardMatrix
(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrix
DP.forwardMatrix
(SymbolList[] symList, ScoreType scoreType) static int[][]
DP.forwardTransitions
(MarkovModel model, State[] states) Returns a matrix for the specified States describing all valid Transitions between those States.DP.generate
(int length) Generates an alignment from a model.MarkovModel.getWeights
(State source) Get a probability Distribution over the transition from 'source'.SimpleMarkovModel.getWeights
(State source) WMAsMM.getWeights
(State source) static WeightMatrix
XmlMarkovModel.readMatrix
(Element root) static MarkovModel
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) void
MarkovModel.removeState
(State toGo) Remove a state from the model.void
SimpleMarkovModel.removeState
(State toGo) void
WMAsMM.removeState
(State toAdd) static double
DP.scoreWeightMatrix
(WeightMatrix matrix, SymbolList symList, int start) Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.static double
DP.scoreWeightMatrix
(WeightMatrix matrix, SymbolList symList, ScoreType scoreType, int start) Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType.void
MarkovModel.setWeights
(State source, Distribution dist) Set the probability distribution over the transitions from 'source'.void
SimpleMarkovModel.setWeights
(State source, Distribution dist) Use this methods to customize the transition probabilities.protected abstract double
AbstractTrainer.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList) protected double
BaumWelchSampler.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList) protected double
BaumWelchSampler.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList, ScoreType scoreType) protected double
BaumWelchTrainer.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList) State[]
DP.stateList
(MarkovModel mm) void
AbstractTrainer.train
(SequenceDB db, double nullModelWeight, StoppingCriteria stopper) Trains the sequences in db until stopper says to finnish.void
TrainingAlgorithm.train
(SequenceDB db, double nullWeight, StoppingCriteria stopper) Trains the sequences in db untill stopper says to finnish.void
TransitionTrainer.train
(double nullModel, double weight) Trains the transition, given an expected probability, and a weight for that probability.MarkovModel.transitionsFrom
(State source) Returns the FiniteAlphabet of all states that have a transition from 'source'.SimpleMarkovModel.transitionsFrom
(State from) WMAsMM.transitionsFrom
(State from) MarkovModel.transitionsTo
(State dest) Returns the FiniteAlphabet of all states that have a transition to 'dest'.SimpleMarkovModel.transitionsTo
(State to) WMAsMM.transitionsTo
(State to) abstract StatePath
DP.viterbi
(SymbolList[] symList, ScoreType scoreType) Constructors in org.biojava.bio.dp that throw IllegalSymbolExceptionModifierConstructorDescriptionProfileHMM
(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory) Deprecated.ProfileHMM
(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name) Create a new ProfileHMM.SimpleHMMTrainer
(MarkovModel model) WMAsMM
(WeightMatrix wm) -
Uses of IllegalSymbolException in org.biojava.bio.dp.onehead
Methods in org.biojava.bio.dp.onehead that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionprotected double
double
SingleDP.backward
(SymbolList[] seq, ScoreType scoreType) double
SingleDP.backward
(SymbolList[] seq, ScoreType scoreType) protected void
SingleDP.backward_initialize
(DPCursor dpCursor, ScoreType scoreType) protected void
SingleDP.backward_recurse
(DPCursor dpCursor, ScoreType scoreType) protected double
SingleDP.backward_termination
(DPCursor dpCursor, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, ScoreType scoreType) protected double
double
SingleDP.forward
(SymbolList[] seq, ScoreType scoreType) double
SingleDP.forward
(SymbolList[] seq, ScoreType scoreType) protected void
SingleDP.forward_initialize
(DPCursor dpCursor, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, ScoreType scoreType) 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.SingleDP.viterbi
(SymbolList[] symList, ScoreType scoreType) Constructors in org.biojava.bio.dp.onehead that throw IllegalSymbolException -
Uses of IllegalSymbolException in org.biojava.bio.dp.twohead
Methods in org.biojava.bio.dp.twohead that throw IllegalSymbolExceptionModifier and TypeMethodDescriptiondouble
PairwiseDP.backward
(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.backwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.backwardMatrix
(SymbolList[] seqs, ScoreType scoreType) void
Calculate the 'scores' array in the cell at cells[0][0].double
PairwiseDP.forward
(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.forwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.forwardMatrix
(SymbolList[] seqs, ScoreType scoreType) final double[]
EmissionCache.getEmissions
(List symList) final double[]
EmissionCache.getEmissions
(List symList, boolean exorcise) Retrieve the emission scores from the cache for every EmissionState for the specified symbols.void
CellCalculator.initialize
(Cell[][] cells) Initialize the cell at [0][0] to the recursion initial parameters.void
Description of the Methodvoid
retrieve the next block of cellsCellCalculatorFactory.viterbi
(ScoreType scoreType, BackPointer terminal) DPInterpreter.viterbi
(ScoreType scoreType, BackPointer terminal) PairwiseDP.viterbi
(SymbolList[] seqs, ScoreType scoreType) Constructors in org.biojava.bio.dp.twohead that throw IllegalSymbolExceptionModifierConstructorDescriptionAbstractMatrixPairDPCursor
(SymbolList seq1, SymbolList seq2, int start1, int start2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache) BackMatrixPairDPCursor
(SymbolList seq1, SymbolList seq2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache) LightPairDPCursor
(SymbolList seq1, SymbolList seq2, int depth1, int depth2, int numStates, EmissionCache eCache) Constructor for the LightPairDPCursor objectMatrixPairDPCursor
(SymbolList seq1, SymbolList seq2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache) PairwiseDP
(MarkovModel mm, CellCalculatorFactoryMaker ccfm) -
Uses of IllegalSymbolException in org.biojava.bio.gui
Methods in org.biojava.bio.gui that throw IllegalSymbolExceptionModifier 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) 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 IllegalSymbolException in org.biojava.bio.molbio
Methods in org.biojava.bio.molbio that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionvoid
Composition.setSymbolList
(SymbolList symbolList) Set theSymbolList
to calculation the composition of. -
Uses of IllegalSymbolException in org.biojava.bio.program
Constructors in org.biojava.bio.program that throw IllegalSymbolException -
Uses of IllegalSymbolException in org.biojava.bio.program.abi
Methods in org.biojava.bio.program.abi that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionstatic Symbol
ABIFParser.decodeDNAToken
(char token) Decodes a character into aSymbol
in the DNA alphabet.int[]
ABITrace.getTrace
(AtomicSymbol base) Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point. -
Uses of IllegalSymbolException in org.biojava.bio.program.fastq
Methods in org.biojava.bio.program.fastq that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionstatic SymbolList
Create and return a new DNASymbolList
from the specified FASTQ formatted sequence.static Sequence
FastqTools.createDNASequence
(Fastq fastq) Create and return a new DNASequence
from the specified FASTQ formatted sequence.static PhredSequence
FastqTools.createPhredSequence
(Fastq fastq) Create and return a newPhredSequence
from the specified FASTQ formatted sequence.static SymbolList
FastqTools.createQualityScores
(Fastq fastq) Create and return a newSymbolList
of quality scores from the specified FASTQ formatted sequence.static Distribution[]
FastqTools.createSymbolDistribution
(Fastq fastq) Create and return a new array of symbolDistribution
s from the specified FASTQ formatted sequence. -
Uses of IllegalSymbolException in org.biojava.bio.program.hmmer
Methods in org.biojava.bio.program.hmmer that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionprotected void
HmmerProfileHMM.connectModel()
This is called by constructor in setting up the allowed transitions in the modeldouble
double
HmmerProfileHMM.transScore
(State from, State to, Symbol symFrom, Symbol symTo) Constructors in org.biojava.bio.program.hmmer that throw IllegalSymbolExceptionModifierConstructorDescriptionprotected
HmmerProfileHMM
(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name) -
Uses of IllegalSymbolException in org.biojava.bio.program.phred
Methods in org.biojava.bio.program.phred that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionstatic SymbolList
PhredTools.createPhred
(SymbolList dna, SymbolList quality) Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.static 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.boolean
PhredFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) -
Uses of IllegalSymbolException in org.biojava.bio.proteomics
Methods in org.biojava.bio.proteomics that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionvoid
MassCalc.addVariableModification
(char residue, double[] masses) Add Variable modifications.void
MassCalc.addVariableModification
(Symbol residue, double[] masses) Add Variable modifications.static Protease
ProteaseManager.createProtease
(String cleaveRes, boolean endoProtease, String name) static Protease
ProteaseManager.createProtease
(String cleaveRes, boolean endoProtease, String notCleaveRes, String name) static Protease
ProteaseManager.createProtease
(SymbolList cleaveRes, boolean endoProtease, String name) static Protease
ProteaseManager.createProtease
(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) Creates and registers a new Protease.double
MassCalc.getMass
(SymbolList proteinSeq) Get the Mass of this peptide.static final double
MassCalc.getMass
(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS) getMass
calculates the mass of this peptide.static final double
MassCalc.getMolecularWeight
(SymbolList proteinSeq) Calculate the molecular weight of a protein, making estimates whenever it is possible like averaging mass values for ambiguity symbols or counting zero when gaps are encountered.double[]
MassCalc.getVariableMasses
(SymbolList peptide) Get all masses including the variable mass.boolean
MassCalc.removeVariableModifications
(char residue) Remove all variable modifications assocaited with this residue.void
MassCalc.setSymbolModification
(char symbolToken, double mass) Use this to set a post translational modification for theSymbol
represented by this character.Constructors in org.biojava.bio.proteomics that throw IllegalSymbolExceptionModifierConstructorDescriptionDeprecated.Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())Deprecated.Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())Protease
(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes) Deprecated.Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())protected
Protease
(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) -
Uses of IllegalSymbolException in org.biojava.bio.search
Methods in org.biojava.bio.search that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionint
SeqContentPattern.getMaxCounts
(AtomicSymbol as) Get the maximum counts required for a symbol.int
SeqContentPattern.getMinCounts
(AtomicSymbol as) Get the minimum counts required for a symbol.void
SeqContentPattern.setMaxCounts
(AtomicSymbol as, int count) Set the maximum counts required for a symbol.void
SeqContentPattern.setMinCounts
(AtomicSymbol as, int count) Set the minimum counts required for a symbol. -
Uses of IllegalSymbolException in org.biojava.bio.seq
Methods in org.biojava.bio.seq that throw IllegalSymbolExceptionModifier 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 SymbolList
Return a new DNA SymbolList for dna.static Sequence
DNATools.createDNASequence
(String dna, String name) Return a new DNA Sequence for dna.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 GappedSequence
DNATools.createGappedDNASequence
(String dna, String name) Get a new dna as a GappedSequencestatic GappedSequence
ProteinTools.createGappedProteinSequence
(String theProtein, String name) Get a new protein as a GappedSequencestatic SymbolList
NucleotideTools.createNucleotide
(String nucleotide) Return a new Nucleotide SymbolList for nucleotide.static Sequence
NucleotideTools.createNucleotideSequence
(String nucleotide, String name) Return a new Nucleotide Sequence for nucleotide.static SymbolList
ProteinTools.createProtein
(String theProtein) Return a new Protein SymbolList for protein.static Sequence
ProteinTools.createProteinSequence
(String protein, String name) Return a new PROTEIN Sequence for protein.static SymbolList
Return a new RNA SymbolList for rna.static Sequence
RNATools.createRNASequence
(String rna, String name) Return a new RNA Sequence for rna.static char
Get a single-character token for a DNA symbolstatic 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 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 IllegalSymbolException in org.biojava.bio.seq.io
Methods in org.biojava.bio.seq.io that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionstatic void
SeqIOTools.biojavaToFile
(int fileType, OutputStream os, Object biojava) Deprecated.Converts a Biojava object to the given filetype.static void
SeqIOTools.biojavaToFile
(String formatName, String alphabetName, OutputStream os, Object biojava) Deprecated.Writes a BiojavaSequenceIterator
,SequenceDB
,Sequence
orAligment
to anOutputStream
void
StreamParser.characters
(char[] data, int start, int len) void
StreamParser.close()
ChunkedSymbolListFactory.make
(SymbolReader sr) Method to create a Sequence with a SymbolReader.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) protected void
EmblLikeFormat.processSequenceLine
(String line, StreamParser parser) Deprecated.Dispatch symbol data from SQ-block line of an EMBL-like file.boolean
EmblLikeFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.boolean
FastaFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) Deprecated.Reads information from a flatfile to aSeqIOListener
using aSymbolTokenizer
to convert sequence strings toSymbol
objects.boolean
GenbankFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.boolean
GenbankXmlFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.boolean
SequenceFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.SymbolReader.readSymbol()
Return a single symbol from the stream.int
SymbolReader.readSymbols
(Symbol[] buffer, int start, int length) Read one or more symbols from the stream.protected List
WordTokenization.splitString
(String str) 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.SymbolTokenization.tokenizeSymbolList
(SymbolList symList) Return a string representation of a list of symbols.WordTokenization.tokenizeSymbolList
(SymbolList sl) void
FastaAlignmentFormat.write
(OutputStream os, Alignment align, int fileType) Writes out the alignment to an FASTA file.void
MSFAlignmentFormat.write
(OutputStream os, Alignment align, int fileType) void
FastaAlignmentFormat.writeDna
(OutputStream os, Alignment align) void
MSFAlignmentFormat.writeDna
(OutputStream os, Alignment align) void
FastaAlignmentFormat.writeProtein
(OutputStream os, Alignment align) void
MSFAlignmentFormat.writeProtein
(OutputStream os, Alignment align) -
Uses of IllegalSymbolException in org.biojava.bio.symbol
Methods in org.biojava.bio.symbol that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionfinal void
void
Adds a symbol to this alphabet.void
Add a new Symbol to the end of this list.protected abstract void
AbstractAlphabet.addSymbolImpl
(AtomicSymbol s) protected void
SimpleAlphabet.addSymbolImpl
(AtomicSymbol s) void
SingletonAlphabet.addSymbolImpl
(AtomicSymbol sym) void
UkkonenSuffixTree.addSymbolList
(SymbolList list, String name, boolean doNotTerminate) void
SuffixTree.addSymbols
(SymbolList sList, int window) Add a count for all motifs with length of up towindow
to this tree.static 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 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 List
Return a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet.static AlphabetIndex
AlphabetManager.getAlphabetIndex
(Symbol[] syms) Get an indexer for an array of symbols.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) IntegerAlphabet.getAmbiguity
(Set symSet) protected Symbol
AbstractAlphabet.getAmbiguityImpl
(Set syms) Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.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) final Symbol
Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.DoubleAlphabet.SubDoubleAlphabet.getSymbol
(double val) IntegerAlphabet.SubIntegerAlphabet.getSymbol
(int val) Gets the compound symbol composed of theSymbols
in the List.protected abstract AtomicSymbol
AbstractAlphabet.getSymbolImpl
(List symList) protected AtomicSymbol
IntegerAlphabet.SubIntegerAlphabet.getSymbolImpl
(List symL) protected AtomicSymbol
SimpleAlphabet.getSymbolImpl
(List symL) protected AtomicSymbol
SingletonAlphabet.getSymbolImpl
(List symList) CodonPref.getWobbleDistributionForSynonyms
(Symbol residue) returns a WobbleDistribution for a specified residue.SimpleCodonPref.getWobbleDistributionForSynonyms
(Symbol residue) int
AlphabetIndex.indexForSymbol
(Symbol s) Return the unique index for a symbol.boolean
SoftMaskedAlphabet.isMasked
(BasisSymbol s) Determines if aSymbol
is masked.static int
PackingFactory.nextWord
(SymbolList symList, int word, int offset, int wordLength, Packing packing) byte
Return a byte representing the packing of a symbol.SoftMaskedAlphabet.CaseSensitiveTokenization.parseToken
(String token) static int
PackingFactory.primeWord
(SymbolList symList, int wordLength, Packing packing) void
GappedSymbolList.removeGap
(int pos) Remove a single gap at position pos in this GappedSymbolList.void
SimpleGappedSymbolList.removeGap
(int pos) void
GappedSymbolList.removeGaps
(int pos, int length) Remove some gaps at position pos in this GappedSymbolList.void
SimpleGappedSymbolList.removeGaps
(int pos, int length) void
FiniteAlphabet.removeSymbol
(Symbol s) Remove a symbol from this alphabet.void
SimpleAlphabet.removeSymbol
(Symbol s) void
SingletonAlphabet.removeSymbol
(Symbol sym) void
SimpleSymbolPropertyTable.setDoubleProperty
(Symbol s, String value) void
SimpleManyToOneTranslationTable.setTranslation
(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.void
SimpleReversibleTranslationTable.setTranslation
(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.void
SimpleTranslationTable.setTranslation
(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbol
(Symbol s) SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbolList
(SymbolList sl) Translate a single symbol from source alphabet to the target alphabet.DNANoAmbPack.unpack
(byte b) Packing.unpack
(byte packed) Return the symbol for a packing.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
static void
CodonPrefTools.writeToXML
(CodonPref codonPref, PrintWriter writer) write out a specified CodonPref object in XML format.Constructors in org.biojava.bio.symbol that throw IllegalSymbolExceptionModifierConstructorDescriptionDummySymbolList
(Alphabet alpha, int length, Symbol sym) Convenience construtor for making single residue changesprotected
SimpleAtomicSymbol
(Annotation annotation, List syms) SimpleSymbolList
(SymbolTokenization parser, String seqString) Construct a SymbolList from a string.SimpleSymbolList
(Alphabet alpha, List rList) Construct a SymbolList containing the symbols in the specified list. -
Uses of IllegalSymbolException in org.biojava.utils.automata
Methods in org.biojava.utils.automata that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionprotected int
FiniteAutomaton.alphaIndex
(Symbol sym) protected int
Nfa.alphaIndex
(Symbol sym) -
Uses of IllegalSymbolException in org.biojava.utils.regex
Methods in org.biojava.utils.regex that throw IllegalSymbolException -
Uses of IllegalSymbolException in org.biojavax.bio.seq
Methods in org.biojavax.bio.seq that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionprotected void
SimpleRichSequence.setAlphabetName
(String alphaname) protected void
ThinRichSequence.setAlphabetName
(String alphaname) protected void
SimpleRichSequence.setStringSequence
(String seq) -
Uses of IllegalSymbolException in org.biojavax.bio.seq.io
Methods in org.biojavax.bio.seq.io that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionboolean
EMBLFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
EMBLxmlFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
FastaFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rsiol, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
GenbankFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
INSDseqFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
RichSequenceFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener listener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
UniProtFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
UniProtXMLFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
EMBLFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
EMBLxmlFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
FastaFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
GenbankFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
INSDseqFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
UniProtFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
UniProtXMLFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener. -
Uses of IllegalSymbolException in org.biojavax.ga
Methods in org.biojavax.ga that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionvoid
GeneticAlgorithm.run
(GAStoppingCriteria stoppingCriteria) Iterates the Algorithm until the stopping criteria are met. -
Uses of IllegalSymbolException in org.biojavax.ga.functions
Methods in org.biojavax.ga.functions that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionMutationFunction.mutate
(SymbolList seq) Produces a new SymbolList by mutation.SimpleMutationFunction.mutate
(SymbolList seq) SwapMutationFunction.mutate
(SymbolList seq) -
Uses of IllegalSymbolException in org.biojavax.ga.impl
Methods in org.biojavax.ga.impl that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionvoid
SimpleGeneticAlgorithm.run
(GAStoppingCriteria stoppingCriteria) -
Uses of IllegalSymbolException in org.biojavax.ga.util
Methods in org.biojavax.ga.util that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionstatic SymbolList
GATools.createBinary
(String binarySequence) Creates aSymbolList
in the GABinaryAlphabet