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

Uses of IllegalSymbolException in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp that throw IllegalSymbolException
 void TransitionTrainer.addCount(State from, State to, double count)
          Add 'count' to the transition from->to.
 void WMAsMM.addState(State toAdd)
           
 void SimpleMarkovModel.addState(State toAdd)
           
 void MarkovModel.addState(State newState)
          Adds a state to the model.
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.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
 boolean WMAsMM.containsTransition(State from, State to)
           
 boolean SimpleMarkovModel.containsTransition(State from, State to)
           
 boolean MarkovModel.containsTransition(State from, State to)
          Returns wether a transition exists or not.
 void SimpleMarkovModel.createTransition(State from, State to)
           
 void MarkovModel.createTransition(State from, State to)
          Makes a transition between two states legal.
 void SimpleMarkovModel.destroyTransition(State from, State to)
           
 void MarkovModel.destroyTransition(State from, State to)
          Breaks a transition between two states legal.
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 WMAsMM.getWeights(State source)
           
 Distribution SimpleMarkovModel.getWeights(State source)
           
 Distribution MarkovModel.getWeights(State source)
          Get a probability Distribution over the transition from 'source'.
static WeightMatrix XmlMarkovModel.readMatrix(Element root)
           
static MarkovModel XmlMarkovModel.readModel(Element root)
           
 void SimpleHMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight)
           
 void HMMTrainer.recordEmittedSymbol(State state, Symbol symbol, double weight)
          record that the specified symbol was emitted from the specified state.
 void WMAsMM.removeState(State toAdd)
           
 void SimpleMarkovModel.removeState(State toGo)
           
 void MarkovModel.removeState(State toGo)
          Remove a state from the model.
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 SimpleMarkovModel.setWeights(State source, Distribution dist)
          Use this methods to customize the transition probabilities.
 void MarkovModel.setWeights(State source, Distribution dist)
          Set the probability distribution over the transitions from 'source'.
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)
           
protected  double BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType)
           
 State[] DP.stateList(MarkovModel mm)
           
 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.
 void AbstractTrainer.train(SequenceDB db, double nullModelWeight, StoppingCriteria stopper)
          Trains the sequences in db until stopper says to finnish.
 FiniteAlphabet WMAsMM.transitionsFrom(State from)
           
 FiniteAlphabet SimpleMarkovModel.transitionsFrom(State from)
           
 FiniteAlphabet MarkovModel.transitionsFrom(State source)
          Returns the FiniteAlphabet of all states that have a transition from 'source'.
 FiniteAlphabet WMAsMM.transitionsTo(State to)
           
 FiniteAlphabet SimpleMarkovModel.transitionsTo(State to)
           
 FiniteAlphabet MarkovModel.transitionsTo(State dest)
          Returns the FiniteAlphabet of all states that have a transition to 'dest'.
abstract  StatePath DP.viterbi(SymbolList[] symList, ScoreType scoreType)
           
 

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, 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
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)
           
protected  double SingleDP.backward(DPCursor dpCursor, ScoreType scoreType)
           
 double SingleDP.backward(SymbolList[] seq, ScoreType scoreType)
           
 double SingleDP.backward(SymbolList[] seq, 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  void SingleDP.forward_initialize(DPCursor dpCursor, ScoreType scoreType)
           
protected  double SingleDP.forward(DPCursor dpCursor, ScoreType scoreType)
           
 double SingleDP.forward(SymbolList[] seq, ScoreType scoreType)
           
 double SingleDP.forward(SymbolList[] seq, 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
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, DPMatrix d, ScoreType scoreType)
           
 DPMatrix PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
           
 CellCalculator DPInterpreter.backwards(ScoreType scoreType)
           
 CellCalculator CellCalculatorFactory.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 DPInterpreter.forwards(ScoreType scoreType)
           
 CellCalculator CellCalculatorFactory.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 PairDPCursor.next(Cell[][] cells)
          retrieve the next block of cells
 void LightPairDPCursor.next(Cell[][] cells)
          Description of the Method
 CellCalculator DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)
           
 CellCalculator CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)
           
 StatePath PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)
           
 

Constructors in org.biojava.bio.dp.twohead that throw IllegalSymbolException
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
static double DistributionLogo.entropy(Distribution dist, Symbol s)
          Calculate the information content of a symbol in bits.
 Paint SymbolStyle.fillPaint(Symbol s)
          Return the fill paint for a symbol.
 Paint SimpleSymbolStyle.fillPaint(Symbol s)
           
 Paint DNAStyle.fillPaint(Symbol s)
           
 Paint SymbolStyle.outlinePaint(Symbol s)
          Return the outline paint for a symbol.
 Paint SimpleSymbolStyle.outlinePaint(Symbol s)
           
 Paint DNAStyle.outlinePaint(Symbol s)
           
 void SimpleSymbolStyle.setFillPaint(Symbol s, Paint paint)
           
 void DNAStyle.setFillPaint(Symbol s, Paint paint)
           
 void SimpleSymbolStyle.setOutlinePaint(Symbol s, Paint paint)
           
 void DNAStyle.setOutlinePaint(Symbol s, Paint paint)
           
 

Uses of IllegalSymbolException in org.biojava.bio.molbio
 

Methods in org.biojava.bio.molbio that throw IllegalSymbolException
 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
Meme(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
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
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 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
 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
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
 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
static Symbol RNATools.complement(Symbol sym)
          Complement the symbol.
static Symbol NucleotideTools.complement(Symbol sym)
          Complement the symbol.
static Symbol DNATools.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 RNATools.forSymbol(char token)
          Retrieve the symbol for a symbol.
static Symbol NucleotideTools.forSymbol(char token)
          Retrieve the symbol for a symbol.
static Symbol DNATools.forSymbol(char token)
          Retrieve the symbol for a symbol.
static int RNATools.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 DNATools.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
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 SymbolTokenization.parseToken(String token)
          Returns the symbol for a single token.
 Symbol SubIntegerTokenization.parseToken(String seq)
           
 Symbol NameTokenization.parseToken(String token)
           
 Symbol IntegerTokenization.parseToken(String seq)
           
 Symbol DoubleTokenization.parseToken(String seq)
           
 Symbol CrossProductTokenization.parseToken(String token)
           
 Symbol CharacterTokenization.parseToken(String token)
           
 Symbol AlternateTokenization.parseToken(String token)
          Will throw an exception.
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 SequenceFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Read a sequence and pass data on to a SeqIOListener.
 boolean GenbankXmlFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Deprecated.  
 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 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 EmblLikeFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Deprecated.  
 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 SymbolTokenization.tokenizeSymbol(Symbol sym)
          Return a token representing a single symbol.
 String SubIntegerTokenization.tokenizeSymbol(Symbol sym)
           
 String NameTokenization.tokenizeSymbol(Symbol s)
           
 String IntegerTokenization.tokenizeSymbol(Symbol sym)
           
 String DoubleTokenization.tokenizeSymbol(Symbol sym)
           
 String CrossProductTokenization.tokenizeSymbol(Symbol s)
           
 String CharacterTokenization.tokenizeSymbol(Symbol s)
           
 String AlternateTokenization.tokenizeSymbol(Symbol s)
           
 String WordTokenization.tokenizeSymbolList(SymbolList sl)
           
 String SymbolTokenization.tokenizeSymbolList(SymbolList symList)
          Return a string representation of a list of symbols.
 void MSFAlignmentFormat.write(OutputStream os, Alignment align, int fileType)
           
 void FastaAlignmentFormat.write(OutputStream os, Alignment align, int fileType)
          Writes out the alignment to an FASTA file.
 void MSFAlignmentFormat.writeDna(OutputStream os, Alignment align)
           
 void FastaAlignmentFormat.writeDna(OutputStream os, Alignment align)
           
 void MSFAlignmentFormat.writeProtein(OutputStream os, Alignment align)
           
 void FastaAlignmentFormat.writeProtein(OutputStream os, Alignment align)
           
 

Uses of IllegalSymbolException in org.biojava.bio.structure
 

Methods in org.biojava.bio.structure that throw IllegalSymbolException
static Character StructureTools.convert_3code_1code(String code3)
          convert three character amino acid codes into single character e.g.
 Sequence ChainImpl.getBJSequence()
          Convert the SEQRES groups of a Chain to a Biojava Sequence object.
 Sequence Chain.getBJSequence()
          Convert the SEQRES groups of a Chain to a Biojava Sequence object.
static double AlphaCTools.getPhiAngle(Symbol phiPsiSym)
          extracts the Phi angle from a Symbol.
static Symbol AlphaCTools.getPhiPsiSymbol(double phiAngle, double psiAngle)
          Makes a Phi - Psi Symbol from the ALPHA CARBON ANGLES alphabet.
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 SimpleSymbolList.addSymbol(Symbol sym)
          Add a new Symbol to the end of this list.
 void FiniteAlphabet.addSymbol(Symbol s)
          Adds a symbol to this alphabet.
 void AbstractAlphabet.addSymbol(Symbol s)
           
 void SingletonAlphabet.addSymbolImpl(AtomicSymbol sym)
           
protected  void SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
           
protected abstract  void AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
           
 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(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.
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.
protected abstract  Symbol AbstractReversibleTranslationTable.doUntranslate(Symbol sym)
          this method is expected to reverse-translate any symbol in the source alphabet.
protected abstract  Set AbstractManyToOneTranslationTable.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 IntegerAlphabet.getAmbiguity(Set symSet)
           
 Symbol DoubleAlphabet.getAmbiguity(Set syms)
           
 Symbol Alphabet.getAmbiguity(Set syms)
           Get a symbol that represents the set of symbols in syms.
 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.
 SuffixTree.SuffixNode SuffixTree.getChild(SuffixTree.SuffixNode node, Symbol s)
          Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
 double SymbolPropertyTable.getDoubleValue(Symbol s)
           
 double SimpleSymbolPropertyTable.getDoubleValue(Symbol s)
           
 Distribution SimpleCodonPref.getFrequencyForSynonyms(Symbol residue)
           
 Distribution CodonPref.getFrequencyForSynonyms(Symbol residue)
          returns a Distribution giving the frequency of synonymous codons.
 DoubleAlphabet.DoubleSymbol DoubleAlphabet.SubDoubleAlphabet.getSymbol(double val)
           
 IntegerAlphabet.IntegerSymbol IntegerAlphabet.SubIntegerAlphabet.getSymbol(int val)
           
 Symbol SoftMaskedAlphabet.getSymbol(List l)
          Gets the compound symbol composed of the Symbols in the List.
 Symbol IntegerAlphabet.getSymbol(List symList)
           
 Symbol DoubleAlphabet.getSymbol(List symList)
           
 Symbol DoubleAlphabet.SubDoubleAlphabet.getSymbol(List rl)
           
 Symbol Alphabet.getSymbol(List rl)
           Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
 Symbol AbstractAlphabet.getSymbol(List syms)
           
protected  AtomicSymbol SingletonAlphabet.getSymbolImpl(List symList)
           
protected  AtomicSymbol SimpleAlphabet.getSymbolImpl(List symL)
           
protected  AtomicSymbol IntegerAlphabet.SubIntegerAlphabet.getSymbolImpl(List symL)
           
protected abstract  AtomicSymbol AbstractAlphabet.getSymbolImpl(List symList)
           
 WobbleDistribution SimpleCodonPref.getWobbleDistributionForSynonyms(Symbol residue)
           
 WobbleDistribution CodonPref.getWobbleDistributionForSynonyms(Symbol residue)
          returns a WobbleDistribution for a specified 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 SimpleGappedSymbolList.removeGap(int pos)
           
 void GappedSymbolList.removeGap(int pos)
          Remove a single gap at position pos in this GappedSymbolList.
 void SimpleGappedSymbolList.removeGaps(int pos, int length)
           
 void GappedSymbolList.removeGaps(int pos, int length)
          Remove some gaps at position pos in this GappedSymbolList.
 void SingletonAlphabet.removeSymbol(Symbol sym)
           
 void SimpleAlphabet.removeSymbol(Symbol s)
           
 void FiniteAlphabet.removeSymbol(Symbol s)
          Remove a symbol from this alphabet.
 void SimpleSymbolPropertyTable.setDoubleProperty(Symbol s, String value)
           
 void SimpleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to)
          Alter the translation mapping.
 void SimpleReversibleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to)
          Alter the translation mapping.
 void SimpleManyToOneTranslationTable.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 Packing.unpack(byte packed)
           Return the symbol for a packing.
 Symbol DNANoAmbPack.unpack(byte b)
           
 Symbol ReversibleTranslationTable.untranslate(Symbol sym)
          Translate a single symbol from target alphabet to the source alphabet.
 Set ManyToOneTranslationTable.untranslate(Symbol sym)
          Translate a single symbol from target alphabet to the source alphabet.
 Symbol AbstractReversibleTranslationTable.untranslate(Symbol sym)
           
 Set AbstractManyToOneTranslationTable.untranslate(Symbol sym)
          returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet.
 void SoftMaskedAlphabet.validate(Symbol s)
           
 void IntegerAlphabet.validate(Symbol s)
           
 void DoubleAlphabet.validate(Symbol s)
           
 void DoubleAlphabet.SubDoubleAlphabet.validate(Symbol sym)
           
 void Alphabet.validate(Symbol s)
           Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
 void AbstractAlphabet.validate(Symbol sym)
           
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
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(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.
 

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.
 

Uses of IllegalSymbolException in org.biojavax.bio.seq
 

Methods in org.biojavax.bio.seq that throw IllegalSymbolException
protected  void ThinRichSequence.setAlphabetName(String alphaname)
           
protected  void SimpleRichSequence.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
 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. If namespace is null, then the namespace of the sequence in the fasta is used.
 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 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 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 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 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. If namespace is null, then the namespace of the sequence in the fasta is used.
 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 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 UniProtXMLFormat.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 INSDseqFormat.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 FastaFormat.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 EMBLFormat.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
 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
 SymbolList SwapMutationFunction.mutate(SymbolList seq)
           
 SymbolList SimpleMutationFunction.mutate(SymbolList seq)
           
 SymbolList MutationFunction.mutate(SymbolList seq)
          Produces a new SymbolList by mutation.
 

Uses of IllegalSymbolException in org.biojavax.ga.impl
 

Methods in org.biojavax.ga.impl that throw IllegalSymbolException
 void SimpleGeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria)
           
 

Uses of IllegalSymbolException in org.biojavax.ga.util
 

Methods in org.biojavax.ga.util that throw IllegalSymbolException
static SymbolList GATools.createBinary(String binarySequence)
          Creates a SymbolList in the GABinary Alphabet