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.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. 
 

Uses of IllegalSymbolException in org.biojava.bio.chromatogram
 

Methods in org.biojava.bio.chromatogram that throw IllegalSymbolException
 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, java.util.List syms)
          A factory method for creating new symbol lists with a given alphabet.
 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.
 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
 void OrderNDistribution.setDistribution(Symbol sym, Distribution dist)
           
 Distribution OrderNDistribution.getDistribution(Symbol sym)
           
 void SimpleDistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double count)
           
 double SimpleDistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
           
protected  double UniformDistribution.getWeightImpl(AtomicSymbol s)
           
 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 emited by this state.
 void IgnoreCountsTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
           
 double IgnoreCountsTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
           
 double TranslatedDistribution.getWeight(Symbol sym)
           
 void TranslatedDistribution.setWeight(Symbol sym, double weight)
           
 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 IndexedCount.getCount(AtomicSymbol s)
           
 void IndexedCount.setCount(AtomicSymbol s, double c)
           
 void IndexedCount.increaseCount(AtomicSymbol s, double c)
           
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.
 void SimpleDistributionTrainerContext.addCount(Distribution dist, Symbol sym, double times)
           
 double SimpleDistributionTrainerContext.getCount(Distribution dist, Symbol sym)
           
protected abstract  void AbstractDistribution.setWeightImpl(AtomicSymbol sym, double 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)
           
 double PairDistribution.getWeight(Symbol sym)
           
 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.
 double Distribution.getWeight(Symbol s)
           Return the probability that Symbol s is emited by this spectrum.
 void Distribution.setWeight(Symbol s, double w)
          Set the probability or odds that Symbol s is emited by this state.
 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 GapDistribution.getWeight(Symbol sym)
           
 void GapDistribution.setWeight(Symbol s, double w)
           
 

Uses of IllegalSymbolException in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp that throw IllegalSymbolException
 void TrainingAlgorithm.train(SequenceDB db, double nullWeight, StoppingCriteria stopper)
          Trains the sequences in db untill stopper says to finnish.
 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.
protected  double BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
           
 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)
           
 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)
           
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.
static WeightMatrix XmlMarkovModel.readMatrix(org.w3c.dom.Element root)
           
static MarkovModel XmlMarkovModel.readModel(org.w3c.dom.Element root)
           
protected  void ProfileHMM.connectModel()
          This is called by constructor in setting up the allowed transitions in the model
 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.
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 MarkovModel DP.flatView(MarkovModel model)
           
static State[] DP.stateList(MarkovModel mm)
           
static int[][] DP.forwardTransitions(MarkovModel model, State[] states)
           
static double[][] DP.forwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType)
           
static int[][] DP.backwardTransitions(MarkovModel model, State[] states)
           
static double[][] DP.backwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType)
           
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.
 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)
           
 

Constructors in org.biojava.bio.dp that throw IllegalSymbolException
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory)
          Deprecated.  
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, java.lang.String name)
          Create a new ProfileHMM.
DP(MarkovModel model)
           
WMAsMM(WeightMatrix wm)
           
 

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
 void LightPairDPCursor.next(Cell[][] cells)
          Description of the Method
 CellCalculator CellCalculatorFactory.forwards(ScoreType scoreType)
           
 CellCalculator CellCalculatorFactory.backwards(ScoreType scoreType)
           
 CellCalculator CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)
           
 void PairDPCursor.next(Cell[][] cells)
          retrieve the next block of cells
 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].
 CellCalculator DPInterpreter.forwards(ScoreType scoreType)
           
 CellCalculator DPInterpreter.backwards(ScoreType scoreType)
           
 CellCalculator DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)
           
 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)
           
 double[] EmissionCache.getEmissions(java.util.List symList)
           
 

Constructors in org.biojava.bio.dp.twohead that throw IllegalSymbolException
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)
           
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
 java.awt.Paint SimpleSymbolStyle.outlinePaint(Symbol s)
           
 java.awt.Paint SimpleSymbolStyle.fillPaint(Symbol s)
           
 void SimpleSymbolStyle.setOutlinePaint(Symbol s, java.awt.Paint paint)
           
 void SimpleSymbolStyle.setFillPaint(Symbol s, java.awt.Paint paint)
           
 java.awt.Paint DNAStyle.outlinePaint(Symbol s)
           
 java.awt.Paint DNAStyle.fillPaint(Symbol s)
           
 void DNAStyle.setOutlinePaint(Symbol s, java.awt.Paint paint)
           
 void DNAStyle.setFillPaint(Symbol s, java.awt.Paint paint)
           
 java.awt.Paint SymbolStyle.outlinePaint(Symbol s)
          Return the outline paint for a symbol.
 java.awt.Paint SymbolStyle.fillPaint(Symbol s)
          Return the fill paint for a symbol.
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(java.io.InputStream is, SymbolTokenization symParser)
           
 

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

Methods in org.biojava.bio.program.abi that throw IllegalSymbolException
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.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, java.lang.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(java.io.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, java.lang.String name)
          Creates and registers a new Protease.
static Protease ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, java.lang.String name)
           
static Protease ProteaseManager.createProtease(java.lang.String cleaveRes, boolean endoProtease, java.lang.String notCleaveRes, java.lang.String name)
           
static Protease ProteaseManager.createProtease(java.lang.String cleaveRes, boolean endoProtease, java.lang.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, java.lang.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, java.lang.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(java.lang.String cleaveRes, boolean endoProtease, java.lang.String notCleaveRes)
          Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
Protease(java.lang.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.seq
 

Methods in org.biojava.bio.seq that throw IllegalSymbolException
static SymbolList NucleotideTools.createNucleotide(java.lang.String nucleotide)
          Return a new Nucleotide SymbolList for nucleotide.
static Sequence NucleotideTools.createNucleotideSequence(java.lang.String nucleotide, java.lang.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 RNATools.createRNA(java.lang.String rna)
          Return a new RNA SymbolList for rna.
static Sequence RNATools.createRNASequence(java.lang.String rna, java.lang.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 DNATools.createDNA(java.lang.String dna)
          Return a new DNA SymbolList for dna.
static Sequence DNATools.createDNASequence(java.lang.String dna, java.lang.String name)
          Return a new DNA Sequence for dna.
static GappedSequence DNATools.createGappedDNASequence(java.lang.String dna, java.lang.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
static SymbolList ProteinTools.createProtein(java.lang.String theProtein)
          Return a new Protein SymbolList for protein.
static GappedSequence ProteinTools.createGappedProteinSequence(java.lang.String theProtein, java.lang.String name)
          Get a new protein as a GappedSequence
static Sequence ProteinTools.createProteinSequence(java.lang.String protein, java.lang.String name)
          Return a new PROTEIN Sequence for protein.
 

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

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

Uses of IllegalSymbolException in org.biojava.bio.symbol
 

Methods in org.biojava.bio.symbol that throw IllegalSymbolException
 Symbol IntegerAlphabet.getSymbol(java.util.List symList)
           
 Symbol IntegerAlphabet.getAmbiguity(java.util.Set symSet)
           
 void IntegerAlphabet.validate(Symbol s)
           
 IntegerAlphabet.IntegerSymbol IntegerAlphabet.SubIntegerAlphabet.getSymbol(int val)
           
protected  AtomicSymbol IntegerAlphabet.SubIntegerAlphabet.getSymbolImpl(java.util.List symL)
           
 Symbol AbstractAlphabet.getAmbiguity(java.util.Set syms)
           
protected  Symbol AbstractAlphabet.getAmbiguityImpl(java.util.Set syms)
          Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
 Symbol AbstractAlphabet.getSymbol(java.util.List syms)
           
protected abstract  AtomicSymbol AbstractAlphabet.getSymbolImpl(java.util.List symList)
           
protected abstract  void AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
           
 void AbstractAlphabet.addSymbol(Symbol s)
           
 void AbstractAlphabet.validate(Symbol sym)
           
 void SimpleReversibleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to)
           
 Symbol SimpleReversibleTranslationTable.untranslate(Symbol sym)
           
static int PackingFactory.primeWord(SymbolList symList, int wordLength, Packing packing)
           
static int PackingFactory.nextWord(SymbolList symList, int word, int offset, int wordLength, Packing packing)
           
 void FiniteAlphabet.addSymbol(Symbol s)
          Adds a symbol to this alphabet.
 void FiniteAlphabet.removeSymbol(Symbol s)
          Remove a symbol from this alphabet.
 java.lang.String UkkonenSuffixTree.symbolListToString(SymbolList list)
          Makes a string out of a SymbolList, this string should only be used for internal or testing purposes, as it will necessarily consist of visible characters.
 void UkkonenSuffixTree.addSymbolList(SymbolList list, java.lang.String name, boolean doNotTerminate)
           
 double SymbolPropertyTable.getDoubleValue(Symbol s)
           
 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.
 Symbol SimpleTranslationTable.translate(Symbol sym)
           
 void SimpleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to)
          Alter the translation mapping.
 int AlphabetIndex.indexForSymbol(Symbol s)
          Return the unique index for a symbol.
 Symbol DNANoAmbPack.unpack(byte b)
           
 void SimpleSymbolPropertyTable.setDoubleProperty(Symbol s, java.lang.String value)
           
 double SimpleSymbolPropertyTable.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.
 void DoubleAlphabet.validate(Symbol s)
           
 Symbol DoubleAlphabet.getAmbiguity(java.util.Set syms)
           
 Symbol DoubleAlphabet.getSymbol(java.util.List symList)
           
 Symbol DoubleAlphabet.SubDoubleAlphabet.getSymbol(java.util.List rl)
           
 DoubleAlphabet.DoubleSymbol DoubleAlphabet.SubDoubleAlphabet.getSymbol(double val)
           
 void DoubleAlphabet.SubDoubleAlphabet.validate(Symbol sym)
           
 void SingletonAlphabet.addSymbolImpl(AtomicSymbol sym)
           
 void SingletonAlphabet.removeSymbol(Symbol sym)
           
protected  AtomicSymbol SingletonAlphabet.getSymbolImpl(java.util.List symList)
           
 Symbol ReversibleTranslationTable.untranslate(Symbol sym)
          Translate a single symbol from target alphabet to the source alphabet.
 void SimpleGappedSymbolList.removeGap(int pos)
           
 void SimpleGappedSymbolList.removeGaps(int pos, int length)
           
static Symbol AlphabetManager.createSymbol(char token, Annotation annotation, java.util.List symList, Alphabet alpha)
          Deprecated. use the new version, without the token argument
static Symbol AlphabetManager.createSymbol(Annotation annotation, java.util.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, java.util.Set symSet, Alphabet alpha)
          Deprecated. use the three-arg version of this method instead.
static Symbol AlphabetManager.createSymbol(Annotation annotation, java.util.Set symSet, Alphabet alpha)
           Generates a new Symbol instance that represents the tuple of Symbols in symList.
static java.util.List AlphabetManager.factorize(Alphabet alpha, java.util.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 TranslationTable.translate(Symbol sym)
          Translate a single symbol from source alphabet to the target alphabet.
protected  void SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
           
 void SimpleAlphabet.removeSymbol(Symbol s)
           
protected  AtomicSymbol SimpleAlphabet.getSymbolImpl(java.util.List symL)
           
 void SimpleSymbolList.addSymbol(Symbol sym)
          Add a new Symbol to the end of this list.
 Symbol Alphabet.getSymbol(java.util.List rl)
           Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
 Symbol Alphabet.getAmbiguity(java.util.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.
 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.
 

Constructors in org.biojava.bio.symbol that throw IllegalSymbolException
SimpleAtomicSymbol(Annotation annotation, java.util.List syms)
           
Edit(int pos, Alphabet alpha, Symbol replacement)
          Convenience construtor for making single residue changes
SimpleSymbolList(Alphabet alpha, java.util.List rList)
          Construct a SymbolList containing the symbols in the specified list.
SimpleSymbolList(SymbolTokenization parser, java.lang.String seqString)
          Construct a SymbolList from a string.