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
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Uses of IllegalSymbolException in org.biojava.bio.chromatogram
Methods in org.biojava.bio.chromatogram that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionprotected SymbolListAbstractChromatogram.createImmutableSymbolList(Alphabet alpha, List syms) A factory method for creating new symbol lists with a given alphabet.intAbstractChromatogram.getMax(AtomicSymbol nucleotide) intChromatogram.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 voidAbstractChromatogram.setTrace(AtomicSymbol nuc, int[] trace, int maxVal) Provides the trace samples for a particular nucleotide.voidSimpleChromatogram.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 TypeMethodDescriptionvoidDistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times) Registers that sym was counted in this state.voidDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times) Registers that sym was counted in this state.voidIgnoreCountsTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times) voidSimpleDistribution.Trainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times) voidSimpleDistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double count) Deprecated.voidSimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times) doubleCount.getCount(AtomicSymbol s) Return the counts for a given Symbol.doubleDistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) Get the current count for this state.doubleDistributionTrainerContext.getCount(Distribution dist, Symbol sym) Return the number of counts of a particular symbol which will be used to train the specified distribution.doubleIgnoreCountsTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) doubleIndexedCount.getCount(AtomicSymbol s) doubleSimpleDistribution.Trainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) doubleSimpleDistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) Deprecated.doubleSimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym) OrderNDistribution.getDistribution(Symbol sym) final doubleRetrieve the weight for this distribution.doubleReturn the probability that Symbol s is emitted by this spectrum.doubledoubledoubleprotected abstract doubleAbstractDistribution.getWeightImpl(AtomicSymbol sym) Override this method to implement getting the weight for an atomic symbol.protected doubleAbstractOrderNDistribution.getWeightImpl(AtomicSymbol sym) Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.doubleSimpleDistribution.getWeightImpl(AtomicSymbol s) protected doubleUniformDistribution.getWeightImpl(AtomicSymbol s) voidCount.increaseCount(AtomicSymbol s, double c) Set the probability or odds that Symbol s is emitted by this state.voidIndexedCount.increaseCount(AtomicSymbol s, double c) voidCount.setCount(AtomicSymbol s, double c) Set the count for the Symbol s.voidIndexedCount.setCount(AtomicSymbol s, double c) voidOrderNDistribution.setDistribution(Symbol sym, Distribution dist) Set the distribution assocated with a symbol.final voidSet the weight of a given symbol in this distribution.voidSet the probability or odds that Symbol s is emitted by this state.voidvoidprotected abstract voidAbstractDistribution.setWeightImpl(AtomicSymbol sym, double weight) Implement this to actually set the weight.voidAbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym, double w) Set a weight in one of the conditioned distributions.protected voidSimpleDistribution.setWeightImpl(AtomicSymbol s, double w) -
Uses of IllegalSymbolException in org.biojava.bio.dp
Methods in org.biojava.bio.dp that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionvoidAdd 'count' to the transition from->to.voidAdds a state to the model.voidvoidabstract doubleDP.backward(SymbolList[] symList, ScoreType scoreType) abstract DPMatrixDP.backwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrixDP.backwardMatrix(SymbolList[] symList, ScoreType scoreType) static int[][]DP.backwardTransitions(MarkovModel model, State[] states) doubleScoreType.calculateScore(Distribution dist, Symbol sym) Calculates the score associated with a distribution and a symbol.doubleScoreType.NullModel.calculateScore(Distribution dist, Symbol sym) doubleScoreType.Odds.calculateScore(Distribution dist, Symbol sym) doubleScoreType.Probability.calculateScore(Distribution dist, Symbol sym) protected voidProfileHMM.connectModel()This is called by constructor in setting up the allowed transitions in the modelbooleanMarkovModel.containsTransition(State from, State to) Returns wether a transition exists or not.booleanSimpleMarkovModel.containsTransition(State from, State to) booleanWMAsMM.containsTransition(State from, State to) voidMarkovModel.createTransition(State from, State to) Makes a transition between two states legal.voidSimpleMarkovModel.createTransition(State from, State to) voidMarkovModel.destroyTransition(State from, State to) Breaks a transition between two states legal.voidSimpleMarkovModel.destroyTransition(State from, State to) static MarkovModelDP.flatView(MarkovModel model) abstract doubleDP.forward(SymbolList[] symList, ScoreType scoreType) abstract DPMatrixDP.forwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrixDP.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 WeightMatrixXmlMarkovModel.readMatrix(Element root) static MarkovModelvoidHMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight) record that the specified symbol was emitted from the specified state.voidSimpleHMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight) voidMarkovModel.removeState(State toGo) Remove a state from the model.voidSimpleMarkovModel.removeState(State toGo) voidWMAsMM.removeState(State toAdd) static doubleDP.scoreWeightMatrix(WeightMatrix matrix, SymbolList symList, int start) Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.static doubleDP.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.voidMarkovModel.setWeights(State source, Distribution dist) Set the probability distribution over the transitions from 'source'.voidSimpleMarkovModel.setWeights(State source, Distribution dist) Use this methods to customize the transition probabilities.protected abstract doubleAbstractTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList) protected doubleBaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList) protected doubleBaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType) protected doubleBaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList) State[]DP.stateList(MarkovModel mm) voidAbstractTrainer.train(SequenceDB db, double nullModelWeight, StoppingCriteria stopper) Trains the sequences in db until stopper says to finnish.voidTrainingAlgorithm.train(SequenceDB db, double nullWeight, StoppingCriteria stopper) Trains the sequences in db untill stopper says to finnish.voidTransitionTrainer.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 StatePathDP.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 doubledoubleSingleDP.backward(SymbolList[] seq, ScoreType scoreType) doubleSingleDP.backward(SymbolList[] seq, ScoreType scoreType) protected voidSingleDP.backward_initialize(DPCursor dpCursor, ScoreType scoreType) protected voidSingleDP.backward_recurse(DPCursor dpCursor, ScoreType scoreType) protected doubleSingleDP.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 doubledoubleSingleDP.forward(SymbolList[] seq, ScoreType scoreType) doubleSingleDP.forward(SymbolList[] seq, ScoreType scoreType) protected voidSingleDP.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 TypeMethodDescriptiondoublePairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType) voidCalculate the 'scores' array in the cell at cells[0][0].doublePairwiseDP.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.voidCellCalculator.initialize(Cell[][] cells) Initialize the cell at [0][0] to the recursion initial parameters.voidDescription of the Methodvoidretrieve 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 doubleDistributionLogo.entropy(Distribution dist, Symbol s) Calculate the information content of a symbol in bits.Return the fill paint for a symbol.DNAStyle.outlinePaint(Symbol s) SimpleSymbolStyle.outlinePaint(Symbol s) SymbolStyle.outlinePaint(Symbol s) Return the outline paint for a symbol.voidDNAStyle.setFillPaint(Symbol s, Paint paint) voidSimpleSymbolStyle.setFillPaint(Symbol s, Paint paint) voidDNAStyle.setOutlinePaint(Symbol s, Paint paint) voidSimpleSymbolStyle.setOutlinePaint(Symbol s, Paint paint) -
Uses of IllegalSymbolException in org.biojava.bio.molbio
Methods in org.biojava.bio.molbio that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionvoidComposition.setSymbolList(SymbolList symbolList) Set theSymbolListto 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 SymbolABIFParser.decodeDNAToken(char token) Decodes a character into aSymbolin 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 SymbolListCreate and return a new DNASymbolListfrom the specified FASTQ formatted sequence.static SequenceFastqTools.createDNASequence(Fastq fastq) Create and return a new DNASequencefrom the specified FASTQ formatted sequence.static PhredSequenceFastqTools.createPhredSequence(Fastq fastq) Create and return a newPhredSequencefrom the specified FASTQ formatted sequence.static SymbolListFastqTools.createQualityScores(Fastq fastq) Create and return a newSymbolListof quality scores from the specified FASTQ formatted sequence.static Distribution[]FastqTools.createSymbolDistribution(Fastq fastq) Create and return a new array of symbolDistributions 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 voidHmmerProfileHMM.connectModel()This is called by constructor in setting up the allowed transitions in the modeldoubledoubleHmmerProfileHMM.transScore(State from, State to, Symbol symFrom, Symbol symTo) Constructors in org.biojava.bio.program.hmmer that throw IllegalSymbolExceptionModifierConstructorDescriptionprotectedHmmerProfileHMM(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 SymbolListPhredTools.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 SymbolPhredTools.dnaSymbolFromPhred(Symbol phredSym) Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.static final SymbolPhredTools.getPhredSymbol(Symbol dna, Symbol integer) Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).static final IntegerAlphabet.IntegerSymbolPhredTools.integerSymbolFromPhred(Symbol phredSym) Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.booleanPhredFormat.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 TypeMethodDescriptionvoidMassCalc.addVariableModification(char residue, double[] masses) Add Variable modifications.voidMassCalc.addVariableModification(Symbol residue, double[] masses) Add Variable modifications.static ProteaseProteaseManager.createProtease(String cleaveRes, boolean endoProtease, String name) static ProteaseProteaseManager.createProtease(String cleaveRes, boolean endoProtease, String notCleaveRes, String name) static ProteaseProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, String name) static ProteaseProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) Creates and registers a new Protease.doubleMassCalc.getMass(SymbolList proteinSeq) Get the Mass of this peptide.static final doubleMassCalc.getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS) getMasscalculates the mass of this peptide.static final doubleMassCalc.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.booleanMassCalc.removeVariableModifications(char residue) Remove all variable modifications assocaited with this residue.voidMassCalc.setSymbolModification(char symbolToken, double mass) Use this to set a post translational modification for theSymbolrepresented 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())protectedProtease(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 TypeMethodDescriptionintSeqContentPattern.getMaxCounts(AtomicSymbol as) Get the maximum counts required for a symbol.intSeqContentPattern.getMinCounts(AtomicSymbol as) Get the minimum counts required for a symbol.voidSeqContentPattern.setMaxCounts(AtomicSymbol as, int count) Set the maximum counts required for a symbol.voidSeqContentPattern.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 SymbolDNATools.complement(Symbol sym) Complement the symbol.static SymbolNucleotideTools.complement(Symbol sym) Complement the symbol.static SymbolRNATools.complement(Symbol sym) Complement the symbol.static SymbolListReturn a new DNA SymbolList for dna.static SequenceDNATools.createDNASequence(String dna, String name) Return a new DNA Sequence for dna.static SequenceSequenceTools.createDummy(Alphabet alpha, int length, Symbol sym, String uri, String name) Create a new Sequence that contains a single symbol repeated over and over.static GappedSequenceDNATools.createGappedDNASequence(String dna, String name) Get a new dna as a GappedSequencestatic GappedSequenceProteinTools.createGappedProteinSequence(String theProtein, String name) Get a new protein as a GappedSequencestatic SymbolListNucleotideTools.createNucleotide(String nucleotide) Return a new Nucleotide SymbolList for nucleotide.static SequenceNucleotideTools.createNucleotideSequence(String nucleotide, String name) Return a new Nucleotide Sequence for nucleotide.static SymbolListProteinTools.createProtein(String theProtein) Return a new Protein SymbolList for protein.static SequenceProteinTools.createProteinSequence(String protein, String name) Return a new PROTEIN Sequence for protein.static SymbolListReturn a new RNA SymbolList for rna.static SequenceRNATools.createRNASequence(String rna, String name) Return a new RNA Sequence for rna.static charGet a single-character token for a DNA symbolstatic SymbolDNATools.forSymbol(char token) Retrieve the symbol for a symbol.static SymbolNucleotideTools.forSymbol(char token) Retrieve the symbol for a symbol.static SymbolRNATools.forSymbol(char token) Retrieve the symbol for a symbol.static intReturn an integer index for a symbol - compatible withforIndex.static intReturn an integer index for a symbol - compatible withforIndex.static intReturn an integer index for a symbol - compatible with forIndex.static charNucleotideTools.nucleotideToken(Symbol sym) Get a single-character token for a Nucleotide symbol -
Uses of IllegalSymbolException in org.biojava.bio.seq.io
Methods in org.biojava.bio.seq.io that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionstatic voidSeqIOTools.biojavaToFile(int fileType, OutputStream os, Object biojava) Deprecated.Converts a Biojava object to the given filetype.static voidSeqIOTools.biojavaToFile(String formatName, String alphabetName, OutputStream os, Object biojava) Deprecated.Writes a BiojavaSequenceIterator,SequenceDB,SequenceorAligmentto anOutputStreamvoidStreamParser.characters(char[] data, int start, int len) voidStreamParser.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 SymbolCharacterTokenization.parseTokenChar(char c) protected voidEmblLikeFormat.processSequenceLine(String line, StreamParser parser) Deprecated.Dispatch symbol data from SQ-block line of an EMBL-like file.booleanEmblLikeFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.booleanFastaFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) Deprecated.Reads information from a flatfile to aSeqIOListenerusing aSymbolTokenizerto convert sequence strings toSymbolobjects.booleanGenbankFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.booleanGenbankXmlFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.booleanSequenceFormat.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.intSymbolReader.readSymbols(Symbol[] buffer, int start, int length) Read one or more symbols from the stream.protected ListWordTokenization.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) voidFastaAlignmentFormat.write(OutputStream os, Alignment align, int fileType) Writes out the alignment to an FASTA file.voidMSFAlignmentFormat.write(OutputStream os, Alignment align, int fileType) voidFastaAlignmentFormat.writeDna(OutputStream os, Alignment align) voidMSFAlignmentFormat.writeDna(OutputStream os, Alignment align) voidFastaAlignmentFormat.writeProtein(OutputStream os, Alignment align) voidMSFAlignmentFormat.writeProtein(OutputStream os, Alignment align) -
Uses of IllegalSymbolException in org.biojava.bio.symbol
Methods in org.biojava.bio.symbol that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionfinal voidvoidAdds a symbol to this alphabet.voidAdd a new Symbol to the end of this list.protected abstract voidAbstractAlphabet.addSymbolImpl(AtomicSymbol s) protected voidSimpleAlphabet.addSymbolImpl(AtomicSymbol s) voidSingletonAlphabet.addSymbolImpl(AtomicSymbol sym) voidUkkonenSuffixTree.addSymbolList(SymbolList list, String name, boolean doNotTerminate) voidSuffixTree.addSymbols(SymbolList sList, int window) Add a count for all motifs with length of up towindowto this tree.static SymbolAlphabetManager.createSymbol(char token, Annotation annotation, List symList, Alphabet alpha) Deprecated.use the new version, without the token argumentstatic SymbolAlphabetManager.createSymbol(char token, Annotation annotation, Set symSet, Alphabet alpha) Deprecated.use the three-arg version of this method instead.static SymbolAlphabetManager.createSymbol(Annotation annotation, List symList, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.static SymbolAlphabetManager.createSymbol(Annotation annotation, Set symSet, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.protected abstract SetAbstractManyToOneTranslationTable.doUntranslate(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.protected abstract SymbolAbstractReversibleTranslationTable.doUntranslate(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.static ListReturn a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet.static AlphabetIndexAlphabetManager.getAlphabetIndex(Symbol[] syms) Get an indexer for an array of symbols.final SymbolAbstractAlphabet.getAmbiguity(Set syms) Alphabet.getAmbiguity(Set<Symbol> syms) Get a symbol that represents the set of symbols in syms.DoubleAlphabet.getAmbiguity(Set syms) IntegerAlphabet.getAmbiguity(Set symSet) protected SymbolAbstractAlphabet.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.doubleSimpleSymbolPropertyTable.getDoubleValue(Symbol s) doubleSymbolPropertyTable.getDoubleValue(Symbol s) CodonPref.getFrequencyForSynonyms(Symbol residue) returns a Distribution giving the frequency of synonymous codons.SimpleCodonPref.getFrequencyForSynonyms(Symbol residue) final SymbolGet 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 theSymbolsin the List.protected abstract AtomicSymbolAbstractAlphabet.getSymbolImpl(List symList) protected AtomicSymbolIntegerAlphabet.SubIntegerAlphabet.getSymbolImpl(List symL) protected AtomicSymbolSimpleAlphabet.getSymbolImpl(List symL) protected AtomicSymbolSingletonAlphabet.getSymbolImpl(List symList) CodonPref.getWobbleDistributionForSynonyms(Symbol residue) returns a WobbleDistribution for a specified residue.SimpleCodonPref.getWobbleDistributionForSynonyms(Symbol residue) intAlphabetIndex.indexForSymbol(Symbol s) Return the unique index for a symbol.booleanSoftMaskedAlphabet.isMasked(BasisSymbol s) Determines if aSymbolis masked.static intPackingFactory.nextWord(SymbolList symList, int word, int offset, int wordLength, Packing packing) byteReturn a byte representing the packing of a symbol.SoftMaskedAlphabet.CaseSensitiveTokenization.parseToken(String token) static intPackingFactory.primeWord(SymbolList symList, int wordLength, Packing packing) voidGappedSymbolList.removeGap(int pos) Remove a single gap at position pos in this GappedSymbolList.voidSimpleGappedSymbolList.removeGap(int pos) voidGappedSymbolList.removeGaps(int pos, int length) Remove some gaps at position pos in this GappedSymbolList.voidSimpleGappedSymbolList.removeGaps(int pos, int length) voidFiniteAlphabet.removeSymbol(Symbol s) Remove a symbol from this alphabet.voidSimpleAlphabet.removeSymbol(Symbol s) voidSingletonAlphabet.removeSymbol(Symbol sym) voidSimpleSymbolPropertyTable.setDoubleProperty(Symbol s, String value) voidSimpleManyToOneTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.voidSimpleReversibleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.voidSimpleTranslationTable.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 voidvoidThrows a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.voidvoidvoidvoidstatic voidCodonPrefTools.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 changesprotectedSimpleAtomicSymbol(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 intFiniteAutomaton.alphaIndex(Symbol sym) protected intNfa.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 voidSimpleRichSequence.setAlphabetName(String alphaname) protected voidThinRichSequence.setAlphabetName(String alphaname) protected voidSimpleRichSequence.setStringSequence(String seq) -
Uses of IllegalSymbolException in org.biojavax.bio.seq.io
Methods in org.biojavax.bio.seq.io that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionbooleanEMBLFormat.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.booleanEMBLxmlFormat.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.booleanFastaFormat.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.booleanGenbankFormat.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.booleanINSDseqFormat.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.booleanRichSequenceFormat.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.booleanUniProtFormat.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.booleanUniProtXMLFormat.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.booleanEMBLFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanEMBLxmlFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanFastaFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanGenbankFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanINSDseqFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanUniProtFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanUniProtXMLFormat.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 TypeMethodDescriptionvoidGeneticAlgorithm.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 TypeMethodDescriptionvoidSimpleGeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria) -
Uses of IllegalSymbolException in org.biojavax.ga.util
Methods in org.biojavax.ga.util that throw IllegalSymbolExceptionModifier and TypeMethodDescriptionstatic SymbolListGATools.createBinary(String binarySequence) Creates aSymbolListin the GABinaryAlphabet