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

Packages that use IllegalAlphabetException
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.program.ssaha SSAHA sequence searching API. 
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.homol The classes and interfaces for defining sequence similarity and honology. 
org.biojava.bio.seq.impl Standard in-memory implementations of Sequence and Feature
org.biojava.bio.seq.io Classes and interfaces for processing and producing flat-file representations of sequences. 
org.biojava.bio.symbol Representation of the Symbols that make up a sequence, and locations within them. 
org.biojava.utils.automata   
org.biojava.utils.regex This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets. 
org.biojavax.bio.db.biosql Interface between biojava and biosql databases 
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 IllegalAlphabetException in org.biojava.bio.chromatogram
 

Methods in org.biojava.bio.chromatogram that throw IllegalAlphabetException
protected  void AbstractChromatogram.setBaseCallAlignment(Alignment align)
          Provides the list of base calls.
 void SimpleChromatogram.setSymbolLists(SymbolList dna, SymbolList offsets)
          Set the DNA and OFFSETS symbol lists for the basecall alignment.
 

Uses of IllegalAlphabetException in org.biojava.bio.dist
 

Methods in org.biojava.bio.dist that throw IllegalAlphabetException
 Distribution DistributionFactory.createDistribution(Alphabet alpha)
          Generate a new Distribution as requested.
 Distribution DistributionFactory.DefaultDistributionFactory.createDistribution(Alphabet alpha)
           
 Distribution OrderNDistributionFactory.createDistribution(Alphabet alpha)
          Creates an OrderNDistribution of the appropriate type.
static Distribution[] DistributionTools.distOverAlignment(Alignment a)
          Equivalent to distOverAlignment(a, false, 0.0).
static Distribution[] DistributionTools.distOverAlignment(Alignment a, boolean countGaps)
          Creates an array of distributions, one for each column of the alignment.
static Distribution[] DistributionTools.distOverAlignment(Alignment a, boolean countGaps, double nullWeight)
          Creates an array of distributions, one for each column of the alignment.
static Distribution DistributionTools.jointDistOverAlignment(Alignment a, boolean countGaps, double nullWeight, int[] cols)
          Creates a joint distribution.
 void Count.setCounts(Count c)
          Set the counts in this Counts to be equal to the counts in c.
 void IndexedCount.setCounts(Count c)
           
 void OrderNDistribution.setDistribution(Symbol sym, Distribution dist)
          Set the distribution assocated with a symbol.
 void Distribution.setNullModel(Distribution nullDist)
          Set the null model Distribution that this Distribution recognizes.
 void PairDistribution.setNullModel(Distribution nullModel)
           
 void TranslatedDistribution.setNullModel(Distribution dist)
           
 void GapDistribution.setNullModel(Distribution nullModel)
           
 void AbstractDistribution.setNullModel(Distribution nullModel)
           
protected  void UniformDistribution.setNullModelImpl(Distribution nullModel)
          Assign a background distribution.
protected  void SimpleDistribution.setNullModelImpl(Distribution nullModel)
           
protected abstract  void AbstractDistribution.setNullModelImpl(Distribution nullModel)
          Implement this to set the null model.
 

Constructors in org.biojava.bio.dist that throw IllegalAlphabetException
AbstractOrderNDistribution(Alphabet alpha)
          Construct a new NthOrderDistribution.
SimpleDistributionTrainer(Distribution dis)
          Deprecated.  
TranslatedDistribution(ReversibleTranslationTable table, Distribution other, DistributionFactory distFact)
          Create a new TranslatedDistribution.
 

Uses of IllegalAlphabetException in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp that throw IllegalAlphabetException
 Sequence WeightMatrixAnnotator.annotate(Sequence seq)
           
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)
           
protected  void ProfileHMM.connectModel()
          This is called by constructor in setting up the allowed transitions in the model
 void SimpleStatePath.edit(Edit edit)
           
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 WeightMatrix XmlMarkovModel.readMatrix(org.w3c.dom.Element root)
           
static MarkovModel XmlMarkovModel.readModel(org.w3c.dom.Element root)
           
 void MarkovModel.setWeights(State source, Distribution dist)
          Set the probability distribution over the transitions from 'source'.
 void SimpleMarkovModel.setWeights(State source, Distribution dist)
          Use this methods to customize the transition probabilities.
protected  double BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
           
protected abstract  double AbstractTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
           
protected  double BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
           
protected  double BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType)
           
abstract  StatePath DP.viterbi(SymbolList[] symList, ScoreType scoreType)
           
 

Constructors in org.biojava.bio.dp that throw IllegalAlphabetException
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.
SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact)
           
SimpleWeightMatrix(Distribution[] columns)
           
 

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

Methods in org.biojava.bio.dp.onehead that throw IllegalAlphabetException
 double SingleDP.backward(SymbolList[] seq, ScoreType scoreType)
           
 DPMatrix SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
           
 DPMatrix SingleDP.backwardMatrix(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, ScoreType scoreType)
           
 

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

Methods in org.biojava.bio.dp.twohead that throw IllegalAlphabetException
 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)
           
 void CellCalculator.initialize(Cell[][] cells)
          Initialize the cell at [0][0] to the recursion initial parameters.
 CellCalculator DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)
           
 CellCalculator CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)
           
 StatePath PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)
           
 

Uses of IllegalAlphabetException in org.biojava.bio.gui
 

Methods in org.biojava.bio.gui that throw IllegalAlphabetException
 void DistributionLogo.setDistribution(Distribution dist)
           Set the dist to render.
 

Uses of IllegalAlphabetException in org.biojava.bio.molbio
 

Constructors in org.biojava.bio.molbio that throw IllegalAlphabetException
RestrictionEnzyme(java.lang.String name, SymbolList site, int dsForward, int dsReverse)
          Creates a new RestrictionEnzyme which cuts within or downstream of the recognition site.
RestrictionEnzyme(java.lang.String name, SymbolList site, int usForward, int usReverse, int dsForward, int dsReverse)
          Creates a new RestrictionEnzyme of the unusual type which cuts both upstream and downstream of its recognition site.
 

Uses of IllegalAlphabetException in org.biojava.bio.program
 

Constructors in org.biojava.bio.program that throw IllegalAlphabetException
Meme(java.io.InputStream is, SymbolTokenization symParser)
           
 

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

Methods in org.biojava.bio.program.abi that throw IllegalAlphabetException
static Alignment ABITools.getAlignment(SymbolList abiSeq)
           View a symbol list over the QUALITY alphabet as an alignment.
 

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

Methods in org.biojava.bio.program.hmmer that throw IllegalAlphabetException
protected  void HmmerProfileHMM.connectModel()
          This is called by constructor in setting up the allowed transitions in the model
 

Constructors in org.biojava.bio.program.hmmer that throw IllegalAlphabetException
HmmerProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, java.lang.String name)
           
 

Uses of IllegalAlphabetException in org.biojava.bio.program.phred
 

Methods in org.biojava.bio.program.phred that throw IllegalAlphabetException
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.
 

Constructors in org.biojava.bio.program.phred that throw IllegalAlphabetException
PhredSequence(SymbolList phredSequence, java.lang.String name, java.lang.String urn, Annotation anno)
          Constructs a new PhredSequence.
 

Uses of IllegalAlphabetException in org.biojava.bio.program.ssaha
 

Methods in org.biojava.bio.program.ssaha that throw IllegalAlphabetException
 DataStore MappedDataStoreFactory.buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
           
 DataStore DataStoreFactory.buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
          Build a new DataStore.
 DataStore CompactedDataStoreFactory.buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
           
 DataStore NIODataStoreFactory.buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
           
 DataStore CompactedDataStoreFactory.buildDataStore(java.io.File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold)
           
 void DataStore.search(java.lang.String id, SymbolList symList, SearchListener listener)
          Search the DataStore with a symbol list.
 

Uses of IllegalAlphabetException in org.biojava.bio.proteomics
 

Methods in org.biojava.bio.proteomics that throw IllegalAlphabetException
static double IsoelectricPointCalc.getIsoelectricPoint(SymbolList peptide)
          Static public method to compute the pI for a polypeptide in denaturating and reduced conditions with both free ends.
 double IsoelectricPointCalc.getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm)
          Computes isoelectric point of specified peptide.
 

Uses of IllegalAlphabetException in org.biojava.bio.search
 

Methods in org.biojava.bio.search that throw IllegalAlphabetException
 BioMatcher MaxMismatchPattern.matcher(SymbolList symList)
           
 BioMatcher SeqContentPattern.matcher(SymbolList symList)
           
 BioMatcher BioPattern.matcher(SymbolList symList)
          Get a matcher that will use these parameters to search a SymbolList.
 

Uses of IllegalAlphabetException in org.biojava.bio.seq
 

Methods in org.biojava.bio.seq that throw IllegalAlphabetException
 Sequence SequenceAnnotator.annotate(Sequence seq)
          Return an annotated version of a sequence.
static SymbolList RNATools.complement(SymbolList list)
          Retrieve a complement view of list.
static SymbolList DNATools.complement(SymbolList list)
          Retrieve a complement view of list.
static SymbolList NucleotideTools.complement(SymbolList list)
          Retrieve a complement view of list.
 void SimpleAssembly.edit(Edit e)
           
 void NewSimpleAssembly.edit(Edit e)
           
static SymbolList DNATools.flip(SymbolList list, StrandedFeature.Strand strand)
          Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
static Sequence SequenceTools.reverseComplement(Sequence seq)
          Reverse-complement a sequence, and flip all of its features.
static SymbolList RNATools.reverseComplement(SymbolList list)
          Retrieve a reverse-complement view of list.
static SymbolList DNATools.reverseComplement(SymbolList list)
          Retrieve a reverse-complement view of list.
static SymbolList NucleotideTools.reverseComplement(SymbolList list)
          Retrieve a reverse-complement view of list.
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end, java.lang.String name, StrandedFeature.Strand strand)
          Extract a sub-sequence from a sequence.
static SymbolList DNATools.toProtein(SymbolList syms)
          Convenience method that directly converts a DNA sequence to RNA then to protein.
static SymbolList DNATools.toProtein(SymbolList syms, int start, int end)
          Convenience method to translate a region of a DNA sequence directly into protein.
static SymbolList DNATools.toRNA(SymbolList syms)
          Converts a SymbolList from the DNA Alphabet to the RNA Alphabet.
static SymbolList RNATools.transcribe(SymbolList list)
          Deprecated. The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.
static SymbolList GeneticCodes.transcribe(SymbolList theList)
          Transcribe DNA into RNA.
static SymbolList DNATools.transcribeToRNA(SymbolList syms)
          Transcribes DNA to RNA.
static SymbolList RNATools.translate(SymbolList syms)
          Translate RNA into protein (with termination symbols).
static SymbolList GeneticCodes.translate(SymbolList theList)
          Translate RNA into protein (with termination symbols).
 

Uses of IllegalAlphabetException in org.biojava.bio.seq.homol
 

Methods in org.biojava.bio.seq.homol that throw IllegalAlphabetException
 void SimilarityPairFeature.EmptyPairwiseAlignment.edit(Edit edit)
           
 

Uses of IllegalAlphabetException in org.biojava.bio.seq.impl
 

Methods in org.biojava.bio.seq.impl that throw IllegalAlphabetException
 void DummySequence.edit(Edit edit)
           
 

Constructors in org.biojava.bio.seq.impl that throw IllegalAlphabetException
RevCompSequence(Sequence seq)
          URN, Name and Annotation are copied as is from the original Sequence, unless you use the the other contructor that sets these.
RevCompSequence(Sequence seq, java.lang.String urn, java.lang.String name, Annotation annotation)
           
SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template)
           
SimpleHomologyFeature(Sequence sourceSeq, FeatureHolder parent, HomologyFeature.Template template)
           
SimpleSimilarityPairFeature(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template)
          Creates a new SimpleSimilarityPairFeature.
 

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

Methods in org.biojava.bio.seq.io that throw IllegalAlphabetException
 void ProteinRefSeqFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Deprecated.  
 void ChunkedSymbolListFactory.addSymbols(Alphabet alfa, Symbol[] syms, int pos, int len)
          tool to construct the SymbolList by adding Symbols.
 void SimpleAssemblyBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 void SimpleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
abstract  void SequenceBuilderBase.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 void SwissprotFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Deprecated. Prints out the sequences properties in order.
 void EmblFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
          Deprecated.  
 void SmartSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 void SeqIOFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void SequenceBuilderFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void SeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void GenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
          Deprecated.  
 void SeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
          Notify the listener of symbol data.
protected  java.util.List ProteinRefSeqFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Deprecated. Converts the symbol list passed in into an array of strings.
protected  java.util.List SwissprotFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Deprecated. Converts the symbol list passed in into an array of strings.
 SymbolList ChunkedSymbolListFactory.make(SymbolReader sr)
          Method to create a Sequence with a SymbolReader.
 SymbolList ChunkedSymbolListFactory.makeSymbolList()
          Converts accumulated Symbols to a SymbolList
protected  void SwissprotFileFormer.printOutSequenceHeaderLine(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Deprecated. Prints out sequence header with only length data.
 java.lang.String CharacterTokenization.tokenizeSymbolList(SymbolList sl)
           
 java.lang.String WordTokenization.tokenizeSymbolList(SymbolList sl)
           
 java.lang.String SymbolTokenization.tokenizeSymbolList(SymbolList symList)
          Return a string representation of a list of symbols.
 java.lang.String AlternateTokenization.tokenizeSymbolList(SymbolList sl)
           
 

Uses of IllegalAlphabetException in org.biojava.bio.symbol
 

Methods in org.biojava.bio.symbol that throw IllegalAlphabetException
 void SimpleSymbolList.edit(Edit edit)
          Apply and edit to the SymbolList as specified by Edit.
 void SymbolList.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object.
 void RelabeledAlignment.edit(Edit edit)
           
 void AbstractSymbolList.edit(Edit edit)
           
static Alphabet AlphabetManager.getCrossProductAlphabet(java.util.List aList, java.lang.String name)
          Attempts to create a cross product alphabet and register it under a name.
static SoftMaskedAlphabet SoftMaskedAlphabet.getInstance(FiniteAlphabet alphaToMask)
          Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.
static SoftMaskedAlphabet SoftMaskedAlphabet.getInstance(FiniteAlphabet alphaToMask, SoftMaskedAlphabet.MaskingDetector maskingDetector)
          Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any Symbol is soft masked or not.
static Packing PackingFactory.getPacking(FiniteAlphabet alpha, boolean ambiguity)
          Get the default packing for an alphabet.
 SymbolList SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          Create a factory for SimpleSymbolLists.
 SymbolList SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          makes a SymbolList containing size Symbols from a Symbol array.
 SymbolList PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          Makes a packed SymbolList out of a list of Symbols.
static SymbolList SymbolListViews.orderNSymbolList(SymbolList source, int order)
          An n-th order view of another SymbolList.
static SymbolList SymbolListViews.translate(SymbolList symbols, TranslationTable table)
          Provides a 'translated' view of an underlying SymbolList.
 

Constructors in org.biojava.bio.symbol that throw IllegalAlphabetException
PackedSymbolList(Packing packing, Symbol[] symbols, int length, Alphabet alfa)
           Create a new PackedSymbolList from an array of Symbols.
PackedSymbolList(Packing packing, SymbolList symList)
           Create a new PackedSymbolList as a packed copy of another symbol list.
SimpleCodonPref(java.lang.String geneticCodeName, Distribution codonPref, java.lang.String name)
           
SimpleReversibleTranslationTable(FiniteAlphabet source, FiniteAlphabet target)
          Construct a new translation table.
 

Uses of IllegalAlphabetException in org.biojava.utils.automata
 

Methods in org.biojava.utils.automata that throw IllegalAlphabetException
 StateMachineFactory ArrayStateMachineToolkit.getFactory(java.lang.String factoryName, FiniteAutomaton fa)
           
 void PatternBlitz.search(SymbolList sl)
           
 

Uses of IllegalAlphabetException in org.biojava.utils.regex
 

Methods in org.biojava.utils.regex that throw IllegalAlphabetException
 void Search.addPattern(java.lang.String patternString, boolean overlap)
          add a search pattern to the searches to be conducted by this object.
 void Search.addPattern(java.lang.String label, java.lang.String patternString, boolean overlap)
          add a search pattern to the searches to be conducted by this object.
 Pattern PatternFactory.compile(java.lang.String pattern)
          Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
 Pattern PatternFactory.compile(java.lang.String pattern, java.lang.String label)
          Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
 

Uses of IllegalAlphabetException in org.biojavax.bio.db.biosql
 

Methods in org.biojavax.bio.db.biosql that throw IllegalAlphabetException
 void BioSQLRichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence as specified by the edit object.
 

Uses of IllegalAlphabetException in org.biojavax.bio.seq
 

Methods in org.biojavax.bio.seq that throw IllegalAlphabetException
 void ThinRichSequence.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object.
 void InfinitelyAmbiguousSymbolList.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object.
 void RichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence as specified by the edit object.
 void DummyRichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence as specified by the edit object.
 

Uses of IllegalAlphabetException in org.biojavax.bio.seq.io
 

Methods in org.biojavax.bio.seq.io that throw IllegalAlphabetException
 void DebuggingRichSeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void SimpleRichSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
          Notify the listener of symbol data.
 void RichSeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 

Uses of IllegalAlphabetException in org.biojavax.ga
 

Methods in org.biojavax.ga that throw IllegalAlphabetException
 void GeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria)
          Iterates the Algorithm until the stopping criteria are met.
 

Uses of IllegalAlphabetException in org.biojavax.ga.functions
 

Methods in org.biojavax.ga.functions that throw IllegalAlphabetException
 SymbolList MutationFunction.mutate(SymbolList seq)
          Produces a new SymbolList by mutation.
 SymbolList SimpleMutationFunction.mutate(SymbolList seq)
           
 SymbolList SwapMutationFunction.mutate(SymbolList seq)
           
 

Uses of IllegalAlphabetException in org.biojavax.ga.impl
 

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

Uses of IllegalAlphabetException in org.biojavax.ga.util
 

Methods in org.biojavax.ga.util that throw IllegalAlphabetException
static OrderNDistribution GATools.standardMutationDistribution(FiniteAlphabet a)
          Makes a mutation Distribution where the probability of a Symbol being mutated to itself is zero and the probability of it being changed to any other Symbol in the Alphabet a is 1.0 / (a.size() - 1.0)
static OrderNDistribution GATools.uniformMutationDistribution(FiniteAlphabet a)
          Makes a 1st order distribution which is infact uniform (equivalent to a uniform zero order distribution).