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Packages that use IllegalAlphabetException | |
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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 |
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Methods in org.biojava.bio.chromatogram that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojava.bio.dist that throw IllegalAlphabetException | |
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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 | |
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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 |
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Methods in org.biojava.bio.dp that throw IllegalAlphabetException | |
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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 | |
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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)
|
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SimpleWeightMatrix(Distribution[] columns)
|
Uses of IllegalAlphabetException in org.biojava.bio.dp.onehead |
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Methods in org.biojava.bio.dp.onehead that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojava.bio.dp.twohead that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojava.bio.gui that throw IllegalAlphabetException | |
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void |
DistributionLogo.setDistribution(Distribution dist)
Set the dist to render. |
Uses of IllegalAlphabetException in org.biojava.bio.molbio |
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Constructors in org.biojava.bio.molbio that throw IllegalAlphabetException | |
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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 |
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Constructors in org.biojava.bio.program that throw IllegalAlphabetException | |
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Meme(java.io.InputStream is,
SymbolTokenization symParser)
|
Uses of IllegalAlphabetException in org.biojava.bio.program.abi |
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Methods in org.biojava.bio.program.abi that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojava.bio.program.hmmer that throw IllegalAlphabetException | |
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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 | |
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HmmerProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory,
java.lang.String name)
|
Uses of IllegalAlphabetException in org.biojava.bio.program.phred |
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Methods in org.biojava.bio.program.phred that throw IllegalAlphabetException | |
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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 | |
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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 |
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Methods in org.biojava.bio.program.ssaha that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojava.bio.proteomics that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojava.bio.search that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojava.bio.seq that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojava.bio.seq.homol that throw IllegalAlphabetException | |
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void |
SimilarityPairFeature.EmptyPairwiseAlignment.edit(Edit edit)
|
Uses of IllegalAlphabetException in org.biojava.bio.seq.impl |
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Methods in org.biojava.bio.seq.impl that throw IllegalAlphabetException | |
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void |
DummySequence.edit(Edit edit)
|
Constructors in org.biojava.bio.seq.impl that throw IllegalAlphabetException | |
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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)
|
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SimpleFramedFeature(Sequence sourceSeq,
FeatureHolder parent,
FramedFeature.Template template)
|
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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 |
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Methods in org.biojava.bio.seq.io that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojava.bio.symbol that throw IllegalAlphabetException | |
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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 | |
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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 |
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Methods in org.biojava.utils.automata that throw IllegalAlphabetException | |
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StateMachineFactory |
ArrayStateMachineToolkit.getFactory(java.lang.String factoryName,
FiniteAutomaton fa)
|
void |
PatternBlitz.search(SymbolList sl)
|
Uses of IllegalAlphabetException in org.biojava.utils.regex |
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Methods in org.biojava.utils.regex that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojavax.bio.db.biosql that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojavax.bio.seq that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojavax.bio.seq.io that throw IllegalAlphabetException | |
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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 |
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Methods in org.biojavax.ga that throw IllegalAlphabetException | |
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void |
GeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria)
Iterates the Algorithm until the stopping criteria are met. |
Uses of IllegalAlphabetException in org.biojavax.ga.functions |
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Methods in org.biojavax.ga.functions that throw IllegalAlphabetException | |
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SymbolList |
MutationFunction.mutate(SymbolList seq)
Produces a new SymbolList by mutation. |
SymbolList |
SimpleMutationFunction.mutate(SymbolList seq)
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SymbolList |
SwapMutationFunction.mutate(SymbolList seq)
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Uses of IllegalAlphabetException in org.biojavax.ga.impl |
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Methods in org.biojavax.ga.impl that throw IllegalAlphabetException | |
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void |
SimpleGeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria)
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Uses of IllegalAlphabetException in org.biojavax.ga.util |
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Methods in org.biojavax.ga.util that throw IllegalAlphabetException | |
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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). |
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