Uses of Class
org.biojava.bio.symbol.IllegalSymbolException

Packages that use IllegalSymbolException

Package	Description
org.biojava.bio.chromatogram	Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
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.dp.twohead
org.biojava.bio.gui	Graphical interfaces for biojava objects.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program	Java wrappers for interacting with external bioinformatics tools.
org.biojava.bio.program.abi	ABI Trace Handling.
org.biojava.bio.program.fastq	FASTQ and variants sequence format I/O.
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.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
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.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.
org.biojavax.ga	Classes to provide a genetic algorithm framework
org.biojavax.ga.functions	GA functions
org.biojavax.ga.impl	Default implementations and abstract classes.
org.biojavax.ga.util	Utility functions and helper classes

Uses of IllegalSymbolException in org.biojava.bio.chromatogram

Methods in org.biojava.bio.chromatogram that throw IllegalSymbolException

Modifier and Type	Method	Description
protected 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 base nucleotide.
protected 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 IllegalSymbolException

Modifier and Type	Method	Description
void	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)
Distribution	OrderNDistribution.getDistribution(Symbol sym)
double	AbstractDistribution.getWeight(Symbol sym)	Retrieve the weight for this distribution.
double	Distribution.getWeight(Symbol s)	Return the probability that Symbol s is emitted by this spectrum.
double	GapDistribution.getWeight(Symbol sym)
double	PairDistribution.getWeight(Symbol sym)
double	TranslatedDistribution.getWeight(Symbol sym)
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.
void	AbstractDistribution.setWeight(Symbol sym, double weight)	Set the weight of a given symbol in this distribution.
void	Distribution.setWeight(Symbol s, double w)	Set the probability or odds that Symbol s is emitted by this state.
void	GapDistribution.setWeight(Symbol s, double w)
void	TranslatedDistribution.setWeight(Symbol sym, double weight)
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 IllegalSymbolException

Modifier and Type	Method	Description
void	TransitionTrainer.addCount(State from, State to, double count)	Add 'count' to the transition from->to.
void	MarkovModel.addState(State newState)	Adds a state to the model.
void	SimpleMarkovModel.addState(State toAdd)
void	WMAsMM.addState(State toAdd)
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 model
boolean	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.
StatePath	DP.generate(int length)	Generates an alignment from a model.
Distribution	MarkovModel.getWeights(State source)	Get a probability Distribution over the transition from 'source'.
Distribution	SimpleMarkovModel.getWeights(State source)
Distribution	WMAsMM.getWeights(State source)
static WeightMatrix	XmlMarkovModel.readMatrix(Element root)
static MarkovModel	XmlMarkovModel.readModel(Element root)
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.
FiniteAlphabet	MarkovModel.transitionsFrom(State source)	Returns the FiniteAlphabet of all states that have a transition from 'source'.
FiniteAlphabet	SimpleMarkovModel.transitionsFrom(State from)
FiniteAlphabet	WMAsMM.transitionsFrom(State from)
FiniteAlphabet	MarkovModel.transitionsTo(State dest)	Returns the FiniteAlphabet of all states that have a transition to 'dest'.
FiniteAlphabet	SimpleMarkovModel.transitionsTo(State to)
FiniteAlphabet	WMAsMM.transitionsTo(State to)
abstract StatePath	DP.viterbi(SymbolList[] symList, ScoreType scoreType)

Constructors in org.biojava.bio.dp that throw IllegalSymbolException

Constructor	Description
ProfileHMM(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 IllegalSymbolException

Modifier and Type	Method	Description
protected double	SingleDP.backward(DPCursor dpCursor, ScoreType scoreType)
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)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)
protected double	SingleDP.forward(DPCursor dpCursor, ScoreType scoreType)
double	SingleDP.forward(SymbolList[] seq, ScoreType scoreType)
double	SingleDP.forward(SymbolList[] seq, ScoreType scoreType)
protected void	SingleDP.forward_initialize(DPCursor dpCursor, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, ScoreType scoreType)
DPMatrix	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.
StatePath	SingleDP.viterbi(SymbolList[] symList, ScoreType scoreType)

Constructors in org.biojava.bio.dp.onehead that throw IllegalSymbolException

Constructor	Description
SingleDP(MarkovModel model)

Uses of IllegalSymbolException in org.biojava.bio.dp.twohead

Methods in org.biojava.bio.dp.twohead that throw IllegalSymbolException

Modifier and Type	Method	Description
double	PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
CellCalculator	CellCalculatorFactory.backwards(ScoreType scoreType)
CellCalculator	DPInterpreter.backwards(ScoreType scoreType)
void	CellCalculator.calcCell(Cell[][] cells)	Calculate the 'scores' array in the cell at cells[0][0].
double	PairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType)
CellCalculator	CellCalculatorFactory.forwards(ScoreType scoreType)
CellCalculator	DPInterpreter.forwards(ScoreType scoreType)
double[]	EmissionCache.getEmissions(List symList)
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	LightPairDPCursor.next(Cell[][] cells)	Description of the Method
void	PairDPCursor.next(Cell[][] cells)	retrieve the next block of cells
CellCalculator	CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)
CellCalculator	DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)
StatePath	PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)

Constructors in org.biojava.bio.dp.twohead that throw IllegalSymbolException

Constructor	Description
AbstractMatrixPairDPCursor(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 object
MatrixPairDPCursor(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 IllegalSymbolException

Modifier and Type	Method	Description
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	DNAStyle.outlinePaint(Symbol s)
Paint	SimpleSymbolStyle.outlinePaint(Symbol s)
Paint	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 IllegalSymbolException

Modifier and Type	Method	Description
void	Composition.setSymbolList(SymbolList symbolList)	Set the SymbolList to calculation the composition of.

Uses of IllegalSymbolException in org.biojava.bio.program

Constructors in org.biojava.bio.program that throw IllegalSymbolException

Constructor	Description
Meme(InputStream is, SymbolTokenization symParser)

Uses of IllegalSymbolException in org.biojava.bio.program.abi

Methods in org.biojava.bio.program.abi that throw IllegalSymbolException

Modifier and Type	Method	Description
static Symbol	ABIFParser.decodeDNAToken(char token)	Decodes a character into a Symbol 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 IllegalSymbolException

Modifier and Type	Method	Description
static SymbolList	FastqTools.createDNA(Fastq fastq)	Create and return a new DNA SymbolList from the specified FASTQ formatted sequence.
static Sequence	FastqTools.createDNASequence(Fastq fastq)	Create and return a new DNA Sequence from the specified FASTQ formatted sequence.
static PhredSequence	FastqTools.createPhredSequence(Fastq fastq)	Create and return a new PhredSequence from the specified FASTQ formatted sequence.
static SymbolList	FastqTools.createQualityScores(Fastq fastq)	Create and return a new SymbolList of quality scores from the specified FASTQ formatted sequence.
static Distribution[]	FastqTools.createSymbolDistribution(Fastq fastq)	Create and return a new array of symbol Distributions from the specified FASTQ formatted sequence.

Uses of IllegalSymbolException in org.biojava.bio.program.hmmer

Methods in org.biojava.bio.program.hmmer that throw IllegalSymbolException

Modifier and Type	Method	Description
protected void	HmmerProfileHMM.connectModel()	This is called by constructor in setting up the allowed transitions in the model
double	ProfileEmissionState.logProb(Symbol sym)
double	HmmerProfileHMM.transScore(State from, State to, Symbol symFrom, Symbol symTo)

Constructors in org.biojava.bio.program.hmmer that throw IllegalSymbolException

Constructor	Description
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 IllegalSymbolException

Modifier and Type	Method	Description
static 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 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.
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 IllegalSymbolException

Modifier and Type	Method	Description
void	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 double	MassCalc.getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS)	getMass calculates the mass of this peptide.
static 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 the Symbol represented by this character.

Constructors in org.biojava.bio.proteomics that throw IllegalSymbolException

Constructor	Description
Protease(String cleavageRes, boolean endoProtease)	Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
Protease(String cleaveRes, boolean endoProtease, String notCleaveRes)	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())
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 IllegalSymbolException

Modifier and Type	Method	Description
int	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 IllegalSymbolException

Modifier and Type	Method	Description
static Symbol	DNATools.complement(Symbol sym)	Complement the symbol.
static Symbol	NucleotideTools.complement(Symbol sym)	Complement the symbol.
static Symbol	RNATools.complement(Symbol sym)	Complement the symbol.
static SymbolList	DNATools.createDNA(String dna)	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 GappedSequence
static GappedSequence	ProteinTools.createGappedProteinSequence(String theProtein, String name)	Get a new protein as a GappedSequence
static 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	RNATools.createRNA(String rna)	Return a new RNA SymbolList for rna.
static Sequence	RNATools.createRNASequence(String rna, String name)	Return a new RNA Sequence for rna.
static char	DNATools.dnaToken(Symbol sym)	Get a single-character token for a DNA symbol
static Symbol	DNATools.forSymbol(char token)	Retrieve the symbol for a symbol.
static Symbol	NucleotideTools.forSymbol(char token)	Retrieve the symbol for a symbol.
static Symbol	RNATools.forSymbol(char token)	Retrieve the symbol for a symbol.
static int	DNATools.index(Symbol sym)	Return an integer index for a symbol - compatible with forIndex.
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 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 IllegalSymbolException

Modifier and Type	Method	Description
static 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 Biojava SequenceIterator, SequenceDB, Sequence or Aligment to an OutputStream
void	StreamParser.characters(char[] data, int start, int len)
void	StreamParser.close()
SymbolList	ChunkedSymbolListFactory.make(SymbolReader sr)	Method to create a Sequence with a SymbolReader.
protected Symbol[]	WordTokenization.parseString(String s)
Symbol	AlternateTokenization.parseToken(String token)	Will throw an exception.
Symbol	CharacterTokenization.parseToken(String token)
Symbol	CrossProductTokenization.parseToken(String token)
Symbol	DoubleTokenization.parseToken(String seq)
Symbol	IntegerTokenization.parseToken(String seq)
Symbol	NameTokenization.parseToken(String token)
Symbol	SubIntegerTokenization.parseToken(String seq)
Symbol	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 a SeqIOListener using a SymbolTokenizer to convert sequence strings to Symbol 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.
Symbol	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)
String	AlternateTokenization.tokenizeSymbol(Symbol s)
String	CharacterTokenization.tokenizeSymbol(Symbol s)
String	CrossProductTokenization.tokenizeSymbol(Symbol s)
String	DoubleTokenization.tokenizeSymbol(Symbol sym)
String	IntegerTokenization.tokenizeSymbol(Symbol sym)
String	NameTokenization.tokenizeSymbol(Symbol s)
String	SubIntegerTokenization.tokenizeSymbol(Symbol sym)
String	SymbolTokenization.tokenizeSymbol(Symbol sym)	Return a token representing a single symbol.
String	SymbolTokenization.tokenizeSymbolList(SymbolList symList)	Return a string representation of a list of symbols.
String	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 IllegalSymbolException

Modifier and Type	Method	Description
void	AbstractAlphabet.addSymbol(Symbol s)
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.
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 to window to this tree.
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.
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	AlphabetManager.factorize(Alphabet alpha, Set symSet)	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.
Symbol	AbstractAlphabet.getAmbiguity(Set syms)
Symbol	Alphabet.getAmbiguity(Set<Symbol> syms)	Get a symbol that represents the set of symbols in syms.
Symbol	DoubleAlphabet.getAmbiguity(Set syms)
Symbol	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.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)
Symbol	AbstractAlphabet.getSymbol(List syms)
Symbol	Alphabet.getSymbol(List<Symbol> rl)	Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
Symbol	DoubleAlphabet.getSymbol(List symList)
DoubleAlphabet.DoubleSymbol	DoubleAlphabet.SubDoubleAlphabet.getSymbol(double val)
Symbol	DoubleAlphabet.SubDoubleAlphabet.getSymbol(List rl)
Symbol	IntegerAlphabet.getSymbol(List symList)
IntegerAlphabet.IntegerSymbol	IntegerAlphabet.SubIntegerAlphabet.getSymbol(int val)
Symbol	SoftMaskedAlphabet.getSymbol(List l)	Gets the compound symbol composed of the Symbols 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)
WobbleDistribution	CodonPref.getWobbleDistributionForSynonyms(Symbol residue)	returns a WobbleDistribution for a specified residue.
WobbleDistribution	SimpleCodonPref.getWobbleDistributionForSynonyms(Symbol residue)
int	AlphabetIndex.indexForSymbol(Symbol s)	Return the unique index for a symbol.
boolean	SoftMaskedAlphabet.isMasked(BasisSymbol s)	Determines if a Symbol is masked.
static int	PackingFactory.nextWord(SymbolList symList, int word, int offset, int wordLength, Packing packing)
byte	Packing.pack(Symbol sym)	Return a byte representing the packing of a symbol.
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.
String	SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbol(Symbol s)
String	SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbolList(SymbolList sl)
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.
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)
Set	ManyToOneTranslationTable.untranslate(Symbol sym)	Translate a single symbol from target alphabet to the source alphabet.
Symbol	ReversibleTranslationTable.untranslate(Symbol sym)	Translate a single symbol from target alphabet to the source alphabet.
void	AbstractAlphabet.validate(Symbol sym)
void	Alphabet.validate(Symbol s)	Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
void	DoubleAlphabet.SubDoubleAlphabet.validate(Symbol sym)
void	DoubleAlphabet.validate(Symbol s)
void	IntegerAlphabet.validate(Symbol s)
void	SoftMaskedAlphabet.validate(Symbol s)
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 IllegalSymbolException

Constructor	Description
DummySymbolList(Alphabet alpha, int length, Symbol sym)
Edit(int pos, Alphabet alpha, Symbol replacement)	Convenience construtor for making single residue changes
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 IllegalSymbolException

Modifier and Type	Method	Description
protected 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

Modifier and Type	Method	Description
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 IllegalSymbolException in org.biojavax.bio.seq

Methods in org.biojavax.bio.seq that throw IllegalSymbolException

Modifier and Type	Method	Description
protected 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 IllegalSymbolException

Modifier and Type	Method	Description
boolean	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 IllegalSymbolException

Modifier and Type	Method	Description
void	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 IllegalSymbolException

Modifier and Type	Method	Description
SymbolList	MutationFunction.mutate(SymbolList seq)	Produces a new SymbolList by mutation.
SymbolList	SimpleMutationFunction.mutate(SymbolList seq)
SymbolList	SwapMutationFunction.mutate(SymbolList seq)

Uses of IllegalSymbolException in org.biojavax.ga.impl

Methods in org.biojavax.ga.impl that throw IllegalSymbolException

Modifier and Type	Method	Description
void	SimpleGeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria)

Uses of IllegalSymbolException in org.biojavax.ga.util

Methods in org.biojavax.ga.util that throw IllegalSymbolException

Modifier and Type	Method	Description
static SymbolList	GATools.createBinary(String binarySequence)	Creates a SymbolList in the GABinary Alphabet