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

Packages that use IllegalSymbolException

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.program	Java wrappers for interacting with external bioinformatics tools.
org.biojava.bio.program.abi	ABI Trace Handling.
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.structure	Interfaces and classes for molecular structure.
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.

Uses of IllegalSymbolException in org.biojava.bio.chromatogram

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

void	SimpleChromatogram.setTraceValues(AtomicSymbol nuc, int[] trace, int maxVal) Sets the trace array for one of the DNA nucleotides.
int	Chromatogram.getMax(AtomicSymbol nucleotide) Gets the max intensity on the trace for the specified nucleotide.
int[]	Chromatogram.getTrace(AtomicSymbol nucleotide) Returns an array containing the intensities of the sampled waveform representing the chromatogram trace for base nucleotide.
int[]	AbstractChromatogram.getTrace(AtomicSymbol nucleotide)
int	AbstractChromatogram.getMax(AtomicSymbol nucleotide)
protected void	AbstractChromatogram.setTrace(AtomicSymbol nuc, int[] trace, int maxVal) Provides the trace samples for a particular nucleotide.
protected SymbolList	AbstractChromatogram.createImmutableSymbolList(Alphabet alpha, List syms) A factory method for creating new symbol lists with a given alphabet.

Uses of IllegalSymbolException in org.biojava.bio.dist

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

protected double	UniformDistribution.getWeightImpl(AtomicSymbol s)
double	TranslatedDistribution.getWeight(Symbol sym)
void	TranslatedDistribution.setWeight(Symbol sym, double weight)
void	SimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)
double	SimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym)
void	SimpleDistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double count) Deprecated.
double	SimpleDistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) Deprecated.
double	SimpleDistribution.getWeightImpl(AtomicSymbol s)
protected void	SimpleDistribution.setWeightImpl(AtomicSymbol s, double w)
void	SimpleDistribution.Trainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
double	SimpleDistribution.Trainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
double	PairDistribution.getWeight(Symbol sym)
void	OrderNDistribution.setDistribution(Symbol sym, Distribution dist) Set the distribution assocated with a symbol.
Distribution	OrderNDistribution.getDistribution(Symbol sym)
double	IndexedCount.getCount(AtomicSymbol s)
void	IndexedCount.setCount(AtomicSymbol s, double c)
void	IndexedCount.increaseCount(AtomicSymbol s, double c)
void	IgnoreCountsTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
double	IgnoreCountsTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
double	GapDistribution.getWeight(Symbol sym)
void	GapDistribution.setWeight(Symbol s, double w)
void	DistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times) Registers that sym was counted in 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.
void	DistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times) Registers that sym was counted in this state.
double	DistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) Get the current count for this state.
double	Distribution.getWeight(Symbol s) Return the probability that Symbol s is emitted by this spectrum.
void	Distribution.setWeight(Symbol s, double w) Set the probability or odds that Symbol s is emitted by this state.
double	Count.getCount(AtomicSymbol s) Return the counts for a given Symbol.
void	Count.setCount(AtomicSymbol s, double c) Set the count for the Symbol s.
void	Count.increaseCount(AtomicSymbol s, double c) Set the probability or odds that Symbol s is emitted by this state.
protected double	AbstractOrderNDistribution.getWeightImpl(AtomicSymbol sym) Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.
void	AbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym, double w) Set a weight in one of the conditioned distributions.
protected abstract void	AbstractDistribution.setWeightImpl(AtomicSymbol sym, double weight) Implement this to actually set the weight.
void	AbstractDistribution.setWeight(Symbol sym, double weight) Set the weight of a given symbol in this distribution.
double	AbstractDistribution.getWeight(Symbol sym) Retrieve the weight for this distribution.
protected abstract double	AbstractDistribution.getWeightImpl(AtomicSymbol sym) Override this method to implement getting the weight for an atomic symbol.

Uses of IllegalSymbolException in org.biojava.bio.dp

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

static WeightMatrix	XmlMarkovModel.readMatrix(Element root)
static MarkovModel	XmlMarkovModel.readModel(Element root)
Distribution	WMAsMM.getWeights(State source)
FiniteAlphabet	WMAsMM.transitionsFrom(State from)
FiniteAlphabet	WMAsMM.transitionsTo(State to)
void	WMAsMM.addState(State toAdd)
void	WMAsMM.removeState(State toAdd)
boolean	WMAsMM.containsTransition(State from, State to)
void	TransitionTrainer.addCount(State from, State to, double count) Add 'count' to the transition from->to.
void	TransitionTrainer.train(double nullModel, double weight) Trains the transition, given an expected probability, and a weight for that probability.
void	TrainingAlgorithm.train(SequenceDB db, double nullWeight, StoppingCriteria stopper) Trains the sequences in db untill stopper says to finnish.
Distribution	SimpleMarkovModel.getWeights(State source)
void	SimpleMarkovModel.setWeights(State source, Distribution dist) Use this methods to customize the transition probabilities.
void	SimpleMarkovModel.createTransition(State from, State to)
void	SimpleMarkovModel.destroyTransition(State from, State to)
boolean	SimpleMarkovModel.containsTransition(State from, State to)
FiniteAlphabet	SimpleMarkovModel.transitionsFrom(State from)
FiniteAlphabet	SimpleMarkovModel.transitionsTo(State to)
void	SimpleMarkovModel.addState(State toAdd)
void	SimpleMarkovModel.removeState(State toGo)
void	SimpleHMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight)
double	ScoreType.calculateScore(Distribution dist, Symbol sym) Calculates the score associated with a distribution and a symbol.
double	ScoreType.Probability.calculateScore(Distribution dist, Symbol sym)
double	ScoreType.Odds.calculateScore(Distribution dist, Symbol sym)
double	ScoreType.NullModel.calculateScore(Distribution dist, Symbol sym)
protected void	ProfileHMM.connectModel() This is called by constructor in setting up the allowed transitions in the model
Distribution	MarkovModel.getWeights(State source) Get a probability Distribution over the transition from 'source'.
void	MarkovModel.setWeights(State source, Distribution dist) Set the probability distribution over the transitions from 'source'.
FiniteAlphabet	MarkovModel.transitionsFrom(State source) Returns the FiniteAlphabet of all states that have a transition from 'source'.
FiniteAlphabet	MarkovModel.transitionsTo(State dest) Returns the FiniteAlphabet of all states that have a transition to 'dest'.
boolean	MarkovModel.containsTransition(State from, State to) Returns wether a transition exists or not.
void	MarkovModel.createTransition(State from, State to) Makes a transition between two states legal.
void	MarkovModel.destroyTransition(State from, State to) Breaks a transition between two states legal.
void	MarkovModel.addState(State newState) Adds a state to the model.
void	MarkovModel.removeState(State toGo) Remove a state from the model.
void	HMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight) record that the specified symbol was emitted from the specified state.
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.
static MarkovModel	DP.flatView(MarkovModel model)
State[]	DP.stateList(MarkovModel mm)
static int[][]	DP.forwardTransitions(MarkovModel model, State[] states) Returns a matrix for the specified States describing all valid Transitions between those States.
static int[][]	DP.backwardTransitions(MarkovModel model, State[] states)
abstract double	DP.forward(SymbolList[] symList, ScoreType scoreType)
abstract double	DP.backward(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.forwardMatrix(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.backwardMatrix(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.forwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)
abstract DPMatrix	DP.backwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)
abstract StatePath	DP.viterbi(SymbolList[] symList, ScoreType scoreType)
StatePath	DP.generate(int length) Generates an alignment from a model.
protected double	BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected double	BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected abstract double	AbstractTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
void	AbstractTrainer.train(SequenceDB db, double nullModelWeight, StoppingCriteria stopper) Trains the sequences in db until stopper says to finnish.

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

WMAsMM(WeightMatrix wm)

SimpleHMMTrainer(MarkovModel model)

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.

DP(MarkovModel model)

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

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

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.
double	SingleDP.forward(SymbolList[] seq, ScoreType scoreType)
double	SingleDP.forward(SymbolList[] seq, ScoreType scoreType)
double	SingleDP.backward(SymbolList[] seq, ScoreType scoreType)
double	SingleDP.backward(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
StatePath	SingleDP.viterbi(SymbolList[] symList, ScoreType scoreType)

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

SingleDP(MarkovModel model)

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

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

double	PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
double	PairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
StatePath	PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)
void	PairDPCursor.next(Cell[][] cells) retrieve the next block of cells
void	LightPairDPCursor.next(Cell[][] cells) Description of the Method
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.
CellCalculator	DPInterpreter.forwards(ScoreType scoreType)
CellCalculator	DPInterpreter.backwards(ScoreType scoreType)
CellCalculator	DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)
CellCalculator	CellCalculatorFactory.forwards(ScoreType scoreType)
CellCalculator	CellCalculatorFactory.backwards(ScoreType scoreType)
CellCalculator	CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)
void	CellCalculator.initialize(Cell[][] cells) Initialize the cell at [0][0] to the recursion initial parameters.
void	CellCalculator.calcCell(Cell[][] cells) Calculate the 'scores' array in the cell at cells[0][0].

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

PairwiseDP(MarkovModel mm, CellCalculatorFactoryMaker ccfm)

MatrixPairDPCursor(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

BackMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)

AbstractMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int start1, int start2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)

Uses of IllegalSymbolException in org.biojava.bio.gui

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

Paint	SymbolStyle.outlinePaint(Symbol s) Return the outline paint for a symbol.
Paint	SymbolStyle.fillPaint(Symbol s) Return the fill paint for a symbol.
Paint	SimpleSymbolStyle.outlinePaint(Symbol s)
Paint	SimpleSymbolStyle.fillPaint(Symbol s)
void	SimpleSymbolStyle.setOutlinePaint(Symbol s, Paint paint)
void	SimpleSymbolStyle.setFillPaint(Symbol s, Paint paint)
Paint	DNAStyle.outlinePaint(Symbol s)
Paint	DNAStyle.fillPaint(Symbol s)
void	DNAStyle.setOutlinePaint(Symbol s, Paint paint)
void	DNAStyle.setFillPaint(Symbol s, Paint paint)
static double	DistributionLogo.entropy(Distribution dist, Symbol s) Calculate the information content of a symbol in bits.

Uses of IllegalSymbolException in org.biojava.bio.program

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

Meme(InputStream is, SymbolTokenization symParser)

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

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

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.
static Symbol	ABIFParser.decodeDNAToken(char token) Decodes a character into a Symbol in the DNA alphabet.

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

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

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

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

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

static Symbol	PhredTools.dnaSymbolFromPhred(Symbol phredSym) Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
static IntegerAlphabet.IntegerSymbol	PhredTools.integerSymbolFromPhred(Symbol phredSym) Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.
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.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).
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

static Protease	ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) Creates and registers a new Protease.
static Protease	ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, String name)
static Protease	ProteaseManager.createProtease(String cleaveRes, boolean endoProtease, String notCleaveRes, String name)
static Protease	ProteaseManager.createProtease(String cleaveRes, boolean endoProtease, String name)
void	MassCalc.setSymbolModification(char symbolToken, double mass) Use this to set a post translational modification for the Symbol represented by this character.
void	MassCalc.addVariableModification(char residue, double[] masses) Add Variable modifications.
void	MassCalc.addVariableModification(Symbol residue, double[] masses) Add Variable modifications.
boolean	MassCalc.removeVariableModifications(char residue) Remove all variable modifications assocaited with this residue.
static double	MassCalc.getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS) getMass calculates the mass of this peptide.
double	MassCalc.getMass(SymbolList proteinSeq) Get the Mass of this peptide.
double[]	MassCalc.getVariableMasses(SymbolList peptide) Get all masses including the variable mass.

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

Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name)

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

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

Uses of IllegalSymbolException in org.biojava.bio.search

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

void	SeqContentPattern.setMinCounts(AtomicSymbol as, int count) Set the minimum 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.
int	SeqContentPattern.getMaxCounts(AtomicSymbol as) Get the maximum counts required for a symbol.

Uses of IllegalSymbolException in org.biojava.bio.seq

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

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 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 int	RNATools.index(Symbol sym) Return an integer index for a symbol - compatible with forIndex.
static Symbol	RNATools.complement(Symbol sym) Complement the symbol.
static Symbol	RNATools.forSymbol(char token) Retrieve the symbol for a symbol.
static SymbolList	ProteinTools.createProtein(String theProtein) Return a new Protein SymbolList for protein.
static GappedSequence	ProteinTools.createGappedProteinSequence(String theProtein, String name) Get a new protein as a GappedSequence
static Sequence	ProteinTools.createProteinSequence(String protein, String name) Return a new PROTEIN Sequence for protein.
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 int	NucleotideTools.index(Symbol sym) Return an integer index for a symbol - compatible with forIndex.
static Symbol	NucleotideTools.complement(Symbol sym) Complement the symbol.
static Symbol	NucleotideTools.forSymbol(char token) Retrieve the symbol for a symbol.
static char	NucleotideTools.nucleotideToken(Symbol sym) Get a single-character token for a Nucleotide 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 GappedSequence	DNATools.createGappedDNASequence(String dna, String name) Get a new dna as a GappedSequence
static int	DNATools.index(Symbol sym) Return an integer index for a symbol - compatible with forIndex.
static Symbol	DNATools.complement(Symbol sym) Complement the symbol.
static Symbol	DNATools.forSymbol(char token) Retrieve the symbol for a symbol.
static char	DNATools.dnaToken(Symbol sym) Get a single-character token for a DNA symbol

Uses of IllegalSymbolException in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io that throw IllegalSymbolException

String	WordTokenization.tokenizeSymbolList(SymbolList sl)
protected List	WordTokenization.splitString(String str)
protected Symbol[]	WordTokenization.parseString(String s)
Symbol	SymbolTokenization.parseToken(String token) Returns the symbol for a single token.
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.
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.
void	StreamParser.characters(char[] data, int start, int len)
void	StreamParser.close()
boolean	SequenceFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.
static void	SeqIOTools.biojavaToFile(String formatName, String alphabetName, OutputStream os, Object biojava) Writes a Biojava SequenceIterator, SequenceDB, Sequence or Aligment to an OutputStream
static void	SeqIOTools.biojavaToFile(int fileType, OutputStream os, Object biojava) Converts a Biojava object to the given filetype.
Symbol	NameTokenization.parseToken(String token)
String	NameTokenization.tokenizeSymbol(Symbol s)
void	MSFAlignmentFormat.write(OutputStream os, Alignment align, int fileType)
void	MSFAlignmentFormat.writeDna(OutputStream os, Alignment align)
void	MSFAlignmentFormat.writeProtein(OutputStream os, Alignment align)
Symbol	IntegerTokenization.parseToken(String seq)
String	IntegerTokenization.tokenizeSymbol(Symbol sym)
boolean	GenbankFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.
boolean	FastaFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)
void	FastaAlignmentFormat.write(OutputStream os, Alignment align, int fileType) Writes out the alignment to an FASTA file.
void	FastaAlignmentFormat.writeDna(OutputStream os, Alignment align)
void	FastaAlignmentFormat.writeProtein(OutputStream os, Alignment align)
boolean	EmblLikeFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
protected void	EmblLikeFormat.processSequenceLine(String line, StreamParser parser) Dispatch symbol data from SQ-block line of an EMBL-like file.
Symbol	DoubleTokenization.parseToken(String seq)
String	DoubleTokenization.tokenizeSymbol(Symbol sym)
Symbol	CrossProductTokenization.parseToken(String token)
String	CrossProductTokenization.tokenizeSymbol(Symbol s)
SymbolList	ChunkedSymbolListFactory.make(SymbolReader sr) Method to create a Sequence with a SymbolReader.
Symbol	CharacterTokenization.parseToken(String token)
protected Symbol	CharacterTokenization.parseTokenChar(char c)
String	CharacterTokenization.tokenizeSymbol(Symbol s)

Uses of IllegalSymbolException in org.biojava.bio.structure

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

static Symbol	AlphaCTools.getPhiPsiSymbol(double phiAngle, double psiAngle) Makes a Phi - Psi Symbol from the ALPHA CARBON ANGLES alphabet
static double	AlphaCTools.getPhiAngle(Symbol phiPsiSym) extracts the Phi angle from a Symbol
static double	AlphaCTools.getPsiAngle(Symbol phiPsiSym) extracts the Psi angle from a Symbol

Uses of IllegalSymbolException in org.biojava.bio.symbol

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

void	UkkonenSuffixTree.addSymbolList(SymbolList list, String name, boolean doNotTerminate)
Symbol	TranslationTable.translate(Symbol sym) Translate a single symbol from source alphabet to the target alphabet.
double	SymbolPropertyTable.getDoubleValue(Symbol s)
SuffixTree.SuffixNode	SuffixTree.getChild(SuffixTree.SuffixNode node, Symbol s) Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
void	SuffixTree.addSymbols(SymbolList sList, int window) Add a count for all motifs with length of up to window to this tree.
Symbol	SoftMaskedAlphabet.getSymbol(List l)
void	SoftMaskedAlphabet.validate(Symbol s)
boolean	SoftMaskedAlphabet.isMasked(AtomicSymbol s)
Symbol	SoftMaskedAlphabet.CaseSensitiveTokenization.parseToken(String token)
String	SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbolList(SymbolList sl)
String	SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbol(Symbol s)
void	SingletonAlphabet.addSymbolImpl(AtomicSymbol sym)
void	SingletonAlphabet.removeSymbol(Symbol sym)
protected AtomicSymbol	SingletonAlphabet.getSymbolImpl(List symList)
void	SimpleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.
void	SimpleSymbolPropertyTable.setDoubleProperty(Symbol s, String value)
double	SimpleSymbolPropertyTable.getDoubleValue(Symbol s)
void	SimpleSymbolList.addSymbol(Symbol sym) Add a new Symbol to the end of this list.
void	SimpleReversibleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.
void	SimpleManyToOneTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.
void	SimpleGappedSymbolList.removeGap(int pos)
void	SimpleGappedSymbolList.removeGaps(int pos, int length)
Distribution	SimpleCodonPref.getFrequencyForSynonyms(Symbol residue)
WobbleDistribution	SimpleCodonPref.getWobbleDistributionForSynonyms(Symbol residue)
protected void	SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
void	SimpleAlphabet.removeSymbol(Symbol s)
protected AtomicSymbol	SimpleAlphabet.getSymbolImpl(List symL)
Symbol	ReversibleTranslationTable.untranslate(Symbol sym) Translate a single symbol from target alphabet to the source alphabet.
static int	PackingFactory.primeWord(SymbolList symList, int wordLength, Packing packing)
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	Packing.unpack(byte packed) Return the symbol for a packing.
Set	ManyToOneTranslationTable.untranslate(Symbol sym) Translate a single symbol from target alphabet to the source alphabet.
Symbol	IntegerAlphabet.getSymbol(List symList)
Symbol	IntegerAlphabet.getAmbiguity(Set symSet)
void	IntegerAlphabet.validate(Symbol s)
IntegerAlphabet.IntegerSymbol	IntegerAlphabet.SubIntegerAlphabet.getSymbol(int val)
protected AtomicSymbol	IntegerAlphabet.SubIntegerAlphabet.getSymbolImpl(List symL)
void	GappedSymbolList.removeGap(int pos) Remove a single gap at position pos in this GappedSymbolList.
void	GappedSymbolList.removeGaps(int pos, int length) Remove some gaps at position pos in this GappedSymbolList.
void	FiniteAlphabet.addSymbol(Symbol s) Adds a symbol to this alphabet.
void	FiniteAlphabet.removeSymbol(Symbol s) Remove a symbol from this alphabet.
void	DoubleAlphabet.validate(Symbol s)
Symbol	DoubleAlphabet.getAmbiguity(Set syms)
Symbol	DoubleAlphabet.getSymbol(List symList)
Symbol	DoubleAlphabet.SubDoubleAlphabet.getSymbol(List rl)
DoubleAlphabet.DoubleSymbol	DoubleAlphabet.SubDoubleAlphabet.getSymbol(double val)
void	DoubleAlphabet.SubDoubleAlphabet.validate(Symbol sym)
Symbol	DNANoAmbPack.unpack(byte b)
static void	CodonPrefTools.writeToXML(CodonPref codonPref, PrintWriter writer) write out a specified CodonPref object in XML format.
Distribution	CodonPref.getFrequencyForSynonyms(Symbol residue) returns a Distribution giving the frequency of synonymous codons.
WobbleDistribution	CodonPref.getWobbleDistributionForSynonyms(Symbol residue) returns a WobbleDistribution for a specified residue.
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(Annotation annotation, List symList, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.
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, Set symSet, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.
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.
int	AlphabetIndex.indexForSymbol(Symbol s) Return the unique index for a symbol.
Symbol	Alphabet.getSymbol(List rl) Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
Symbol	Alphabet.getAmbiguity(Set syms) Get a symbol that represents the set of symbols in syms.
void	Alphabet.validate(Symbol s) Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
protected abstract Symbol	AbstractReversibleTranslationTable.doUntranslate(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.
Symbol	AbstractReversibleTranslationTable.untranslate(Symbol sym)
protected abstract Set	AbstractManyToOneTranslationTable.doUntranslate(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.
Set	AbstractManyToOneTranslationTable.untranslate(Symbol sym) returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet.
Symbol	AbstractAlphabet.getAmbiguity(Set syms)
protected Symbol	AbstractAlphabet.getAmbiguityImpl(Set syms) Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
Symbol	AbstractAlphabet.getSymbol(List syms)
protected abstract AtomicSymbol	AbstractAlphabet.getSymbolImpl(List symList)
protected abstract void	AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
void	AbstractAlphabet.addSymbol(Symbol s)
void	AbstractAlphabet.validate(Symbol sym)

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

SimpleSymbolList(Alphabet alpha, List rList)
Construct a SymbolList containing the symbols in the specified list.

SimpleSymbolList(SymbolTokenization parser, String seqString)
Construct a SymbolList from a string.

SimpleAtomicSymbol(Annotation annotation, List syms)

Edit(int pos, Alphabet alpha, Symbol replacement)
Convenience construtor for making single residue changes

DummySymbolList(Alphabet alpha, int length, Symbol sym)

Uses of IllegalSymbolException in org.biojava.utils.automata

Methods in org.biojava.utils.automata that throw IllegalSymbolException

protected int	Nfa.alphaIndex(Symbol sym)
protected int	FiniteAutomaton.alphaIndex(Symbol sym)

Uses of IllegalSymbolException in org.biojava.utils.regex

Methods in org.biojava.utils.regex that throw IllegalSymbolException

char	Search.charValue(Symbol sym)
char	PatternFactory.charValue(Symbol sym) Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for.