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

Packages that use IllegalAlphabetException

Package	Description
org.biojava.bio.chromatogram	Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead
org.biojava.bio.dp.twohead
org.biojava.bio.gui	Graphical interfaces for biojava objects.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program	Java wrappers for interacting with external bioinformatics tools.
org.biojava.bio.program.abi	ABI Trace Handling.
org.biojava.bio.program.fastq	FASTQ and variants sequence format I/O.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.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 A genetic algorithm requires a number of 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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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	IndexedCount.setCounts(Count c)
void	Count.setCounts(Count c) Set the counts in this Counts to be equal to the counts in c.
void	OrderNDistribution.setDistribution(Symbol sym, Distribution dist) Set the distribution assocated with a symbol.
void	TranslatedDistribution.setNullModel(Distribution dist)
void	Distribution.setNullModel(Distribution nullDist) Set the null model Distribution that this Distribution recognizes.
void	GapDistribution.setNullModel(Distribution nullModel)
void	PairDistribution.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

Constructor and Description
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

Modifier and Type	Method and Description
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(Element root)
static MarkovModel	XmlMarkovModel.readModel(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 double	BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected abstract double	AbstractTrainer.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

Constructor and Description
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory) Deprecated.
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name) Create a new ProfileHMM.
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

Modifier and Type	Method and Description
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

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

Modifier and Type	Method and Description
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

Constructor and Description
RestrictionEnzyme(String name, SymbolList site, int dsForward, int dsReverse) Creates a new RestrictionEnzyme which cuts within or downstream of the recognition site.
RestrictionEnzyme(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

Constructor and Description
Meme(InputStream is, SymbolTokenization symParser)

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

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

Modifier and Type	Method and Description
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.fastq

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

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

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

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

Modifier and Type	Method and Description
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

Constructor and Description
HmmerProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name)

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

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

Modifier and Type	Method and Description
static SymbolList	PhredTools.createPhred(SymbolList dna, SymbolList quality) Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.

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

Constructor and Description
PhredSequence(SymbolList phredSequence, String name, 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

Modifier and Type	Method and Description
DataStore	NIODataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	DataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) Build a new DataStore.
DataStore	MappedDataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	CompactedDataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	CompactedDataStoreFactory.buildDataStore(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold)
void	DataStore.search(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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
BioMatcher	MaxMismatchPattern.matcher(SymbolList symList)
BioMatcher	BioPattern.matcher(SymbolList symList) Get a matcher that will use these parameters to search a SymbolList.
BioMatcher	SeqContentPattern.matcher(SymbolList symList)

Uses of IllegalAlphabetException in org.biojava.bio.seq

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

Modifier and Type	Method and Description
Sequence	SequenceAnnotator.annotate(Sequence seq) Return an annotated version of a sequence.
static SymbolList	NucleotideTools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	DNATools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	RNATools.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	NucleotideTools.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	RNATools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
static Sequence	SequenceTools.subSequence(Sequence seq, int start, int end, 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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
void	DummySequence.edit(Edit edit)

Constructors in org.biojava.bio.seq.impl that throw IllegalAlphabetException

Constructor and Description
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, String urn, 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

Modifier and Type	Method and Description
void	SeqIOFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
void	SeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) Notify the listener of symbol data.
void	SmartSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
void	SimpleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
void	ChunkedSymbolListFactory.addSymbols(Alphabet alfa, Symbol[] syms, int pos, int len) tool to construct the SymbolList by adding Symbols.
void	EmblFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) Deprecated.
void	ProteinRefSeqFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.
void	SwissprotFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated. Prints out the sequences properties in order.
void	SimpleAssemblyBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
abstract void	SequenceBuilderBase.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
void	GenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) Deprecated.
void	SequenceBuilderFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
void	SeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
protected List	ProteinRefSeqFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated. Converts the symbol list passed in into an array of strings.
protected 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.
String	CharacterTokenization.tokenizeSymbolList(SymbolList sl)
String	AlternateTokenization.tokenizeSymbolList(SymbolList sl)
String	WordTokenization.tokenizeSymbolList(SymbolList sl)
String	SymbolTokenization.tokenizeSymbolList(SymbolList symList) Return a string representation of a list of symbols.

Uses of IllegalAlphabetException in org.biojava.bio.symbol

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

Modifier and Type	Method and Description
void	SymbolList.edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
void	RelabeledAlignment.edit(Edit edit)
void	SimpleSymbolList.edit(Edit edit) Apply and edit to the SymbolList as specified by Edit.
void	ChunkedSymbolList.edit(Edit edit)
void	AbstractSymbolList.edit(Edit edit)
static Alphabet	AlphabetManager.getCrossProductAlphabet(List aList, 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	PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) Makes a packed SymbolList out of a list of Symbols.
SymbolList	SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) makes a SymbolList containing size Symbols from a Symbol array.
SymbolList	SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) Create a factory for SimpleSymbolLists.
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

Constructor and Description
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(String geneticCodeName, Distribution codonPref, 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

Modifier and Type	Method and Description
StateMachineFactory	ArrayStateMachineToolkit.getFactory(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

Modifier and Type	Method and Description
void	Search.addPattern(String patternString, boolean overlap) add a search pattern to the searches to be conducted by this object.
void	Search.addPattern(String label, String patternString, boolean overlap) add a search pattern to the searches to be conducted by this object.
Pattern	PatternFactory.compile(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(String pattern, 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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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	DummyRichSequenceHandler.edit(RichSequence seq, Edit edit) Apply an edit to the Sequence 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.

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

Methods in org.biojavax.bio.seq.io that throw IllegalAlphabetException

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

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

Uses of IllegalAlphabetException in org.biojavax.ga.impl

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

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

Uses of IllegalAlphabetException in org.biojavax.ga.util

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

Modifier and Type	Method and Description
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).