Uses of Class
org.biojava.bio.symbol.IllegalAlphabetException
Packages that use IllegalAlphabetException
Package
Description
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
Java wrappers for interacting with external bioinformatics tools.
ABI Trace Handling.
FASTQ and variants sequence format I/O.
Tools for working with profile Hidden Markov Models from the HMMer package.
Parser for Phred output
SSAHA sequence searching API.
Utilities to aid in performing various physical analysis of proteins.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Representation of the Symbols that make up a sequence, and locations within
them.
This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
Classes to provide a genetic algorithm framework
GA functions
Default implementations and abstract classes.
Utility functions and helper classes
-
Uses of IllegalAlphabetException in org.biojava.bio.chromatogram
Methods in org.biojava.bio.chromatogram that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionprotected final 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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionDistributionFactory.createDistribution
(Alphabet alpha) Generate a new Distribution as requested.DistributionFactory.DefaultDistributionFactory.createDistribution
(Alphabet alpha) 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 final Distribution[]
DistributionTools.distOverAlignment
(Alignment a, boolean countGaps) Creates an array of distributions, one for each column of the alignment.static final Distribution[]
DistributionTools.distOverAlignment
(Alignment a, boolean countGaps, double nullWeight) Creates an array of distributions, one for each column of the alignment.static final Distribution
DistributionTools.jointDistOverAlignment
(Alignment a, boolean countGaps, double nullWeight, int[] cols) Creates a joint distribution.void
Set the counts in this Counts to be equal to the counts in c.void
void
OrderNDistribution.setDistribution
(Symbol sym, Distribution dist) Set the distribution assocated with a symbol.final void
AbstractDistribution.setNullModel
(Distribution nullModel) 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
TranslatedDistribution.setNullModel
(Distribution dist) protected abstract void
AbstractDistribution.setNullModelImpl
(Distribution nullModel) Implement this to set the null model.protected void
SimpleDistribution.setNullModelImpl
(Distribution nullModel) protected void
UniformDistribution.setNullModelImpl
(Distribution nullModel) Assign a background distribution.Constructors in org.biojava.bio.dist that throw IllegalAlphabetExceptionModifierConstructorDescriptionprotected
Construct a new NthOrderDistribution.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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionabstract 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 modelvoid
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
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 abstract double
AbstractTrainer.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList) protected double
BaumWelchSampler.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList) protected double
BaumWelchSampler.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList, ScoreType scoreType) protected double
BaumWelchTrainer.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList) abstract StatePath
DP.viterbi
(SymbolList[] symList, ScoreType scoreType) Constructors in org.biojava.bio.dp that throw IllegalAlphabetExceptionModifierConstructorDescriptionProfileHMM
(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
(Distribution[] columns) SimpleWeightMatrix
(Alphabet alpha, int columns, DistributionFactory dFact) -
Uses of IllegalAlphabetException in org.biojava.bio.dp.onehead
Methods in org.biojava.bio.dp.onehead that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptiondouble
SingleDP.backward
(SymbolList[] seq, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, ScoreType scoreType) double
SingleDP.forward
(SymbolList[] seq, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, ScoreType scoreType) -
Uses of IllegalAlphabetException in org.biojava.bio.dp.twohead
Methods in org.biojava.bio.dp.twohead that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptiondouble
PairwiseDP.backward
(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.backwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.backwardMatrix
(SymbolList[] seqs, ScoreType scoreType) void
Calculate the 'scores' array in the cell at cells[0][0].double
PairwiseDP.forward
(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.forwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.forwardMatrix
(SymbolList[] seqs, ScoreType scoreType) void
CellCalculator.initialize
(Cell[][] cells) Initialize the cell at [0][0] to the recursion initial parameters.CellCalculatorFactory.viterbi
(ScoreType scoreType, BackPointer terminal) DPInterpreter.viterbi
(ScoreType scoreType, BackPointer terminal) PairwiseDP.viterbi
(SymbolList[] seqs, ScoreType scoreType) -
Uses of IllegalAlphabetException in org.biojava.bio.gui
Methods in org.biojava.bio.gui that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionvoid
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 IllegalAlphabetExceptionModifierConstructorDescriptionRestrictionEnzyme
(String name, SymbolList site, int dsForward, int dsReverse) Creates a newRestrictionEnzyme
which cuts within or downstream of the recognition site.RestrictionEnzyme
(String name, SymbolList site, int usForward, int usReverse, int dsForward, int dsReverse) Creates a newRestrictionEnzyme
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 -
Uses of IllegalAlphabetException in org.biojava.bio.program.abi
Methods in org.biojava.bio.program.abi that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionstatic 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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionstatic PhredSequence
FastqTools.createPhredSequence
(Fastq fastq) Create and return a newPhredSequence
from the specified FASTQ formatted sequence.static Distribution[]
FastqTools.createSymbolDistribution
(Fastq fastq) Create and return a new array of symbolDistribution
s from the specified FASTQ formatted sequence. -
Uses of IllegalAlphabetException in org.biojava.bio.program.hmmer
Methods in org.biojava.bio.program.hmmer that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionprotected void
HmmerProfileHMM.connectModel()
This is called by constructor in setting up the allowed transitions in the modelConstructors in org.biojava.bio.program.hmmer that throw IllegalAlphabetExceptionModifierConstructorDescriptionprotected
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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionstatic 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 IllegalAlphabetExceptionModifierConstructorDescriptionPhredSequence
(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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionCompactedDataStoreFactory.buildDataStore
(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold) CompactedDataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) DataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) Build a new DataStore.MappedDataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) NIODataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, 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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionstatic 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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionBioPattern.matcher
(SymbolList symList) Get a matcher that will use these parameters to search a SymbolList.MaxMismatchPattern.matcher
(SymbolList symList) SeqContentPattern.matcher
(SymbolList symList) -
Uses of IllegalAlphabetException in org.biojava.bio.seq
Methods in org.biojava.bio.seq that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionReturn an annotated version of a sequence.static SymbolList
DNATools.complement
(SymbolList list) Retrieve a complement view of list.static SymbolList
NucleotideTools.complement
(SymbolList list) Retrieve a complement view of list.static SymbolList
RNATools.complement
(SymbolList list) Retrieve a complement view of list.void
void
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 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 SymbolList
RNATools.reverseComplement
(SymbolList list) Retrieve a reverse-complement view of list.static Sequence
SequenceTools.reverseComplement
(Sequence seq) Reverse-complement a sequence, and flip all of its features.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 aSymbolList
from the DNAAlphabet
to the RNAAlphabet
.static SymbolList
GeneticCodes.transcribe
(SymbolList theList) Transcribe DNA into RNA.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
DNATools.transcribeToRNA
(SymbolList syms) Transcribes DNA to RNA.static SymbolList
GeneticCodes.translate
(SymbolList theList) Translate RNA into protein (with termination symbols).static SymbolList
RNATools.translate
(SymbolList syms) 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 -
Uses of IllegalAlphabetException in org.biojava.bio.seq.impl
Methods in org.biojava.bio.seq.impl that throw IllegalAlphabetExceptionConstructors in org.biojava.bio.seq.impl that throw IllegalAlphabetExceptionModifierConstructorDescriptionRevCompSequence
(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 newSimpleSimilarityPairFeature
. -
Uses of IllegalAlphabetException in org.biojava.bio.seq.io
Methods in org.biojava.bio.seq.io that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionvoid
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
GenbankFileFormer.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) Deprecated.void
ProteinRefSeqFileFormer.addSymbols
(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.void
SeqIOAdapter.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) 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.abstract void
SequenceBuilderBase.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SequenceBuilderFilter.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) void
SimpleAssemblyBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SimpleSequenceBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SmartSequenceBuilder.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.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.ChunkedSymbolListFactory.make
(SymbolReader sr) Method to create a Sequence with a SymbolReader.ChunkedSymbolListFactory.makeSymbolList()
Converts accumulated Symbols to a SymbolListprotected void
SwissprotFileFormer.printOutSequenceHeaderLine
(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.Prints out sequence header with only length data.AlternateTokenization.tokenizeSymbolList
(SymbolList sl) CharacterTokenization.tokenizeSymbolList
(SymbolList sl) SymbolTokenization.tokenizeSymbolList
(SymbolList symList) Return a string representation of a list of symbols.WordTokenization.tokenizeSymbolList
(SymbolList sl) -
Uses of IllegalAlphabetException in org.biojava.bio.symbol
Methods in org.biojava.bio.symbol that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionvoid
void
void
void
Apply and edit to the SymbolList as specified by Edit.void
Apply an edit to the SymbolList as specified by the edit object.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 anySymbol
is soft masked or not.static Packing
PackingFactory.getPacking
(FiniteAlphabet alpha, boolean ambiguity) Get the default packing for an alphabet.PackedSymbolListFactory.makeSymbolList
(Symbol[] symbolArray, int size, Alphabet alfa) Makes a packed SymbolList out of a list of Symbols.SimpleSymbolListFactory.makeSymbolList
(Symbol[] symbolArray, int size, Alphabet alfa) Create a factory for SimpleSymbolLists.SymbolListFactory.makeSymbolList
(Symbol[] symbolArray, int size, Alphabet alfa) makes a SymbolList containing size Symbols from a Symbol array.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 IllegalAlphabetExceptionModifierConstructorDescriptionPackedSymbolList
(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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionArrayStateMachineToolkit.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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionvoid
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.Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionvoid
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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionvoid
DummyRichSequenceHandler.edit
(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.void
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
Apply an edit to the SymbolList as specified by the edit object. -
Uses of IllegalAlphabetException in org.biojavax.bio.seq.io
Methods in org.biojavax.bio.seq.io that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionvoid
DebuggingRichSeqIOListener.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) void
RichSeqIOAdapter.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. -
Uses of IllegalAlphabetException in org.biojavax.ga
Methods in org.biojavax.ga that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionvoid
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 IllegalAlphabetExceptionModifier and TypeMethodDescriptionMutationFunction.mutate
(SymbolList seq) Produces a new SymbolList by mutation.SimpleMutationFunction.mutate
(SymbolList seq) SwapMutationFunction.mutate
(SymbolList seq) -
Uses of IllegalAlphabetException in org.biojavax.ga.impl
Methods in org.biojavax.ga.impl that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionvoid
SimpleGeneticAlgorithm.run
(GAStoppingCriteria stoppingCriteria) -
Uses of IllegalAlphabetException in org.biojavax.ga.util
Methods in org.biojavax.ga.util that throw IllegalAlphabetExceptionModifier and TypeMethodDescriptionstatic OrderNDistribution
GATools.standardMutationDistribution
(FiniteAlphabet a) Makes a mutationDistribution
where the probability of aSymbol
being mutated to itself is zero and the probability of it being changed to any otherSymbol
in theAlphabet a
is1.0 / (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).