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.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.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
org.biojava.bio.symbol Representation of the Symbols that make up a sequence, and locations within them. 
 

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

Constructors in org.biojava.bio.dist that throw IllegalAlphabetException
TranslatedDistribution(ReversibleTranslationTable table, Distribution other, DistributionFactory distFact)
          Users should make these thigs via getDistribuiton.
SimpleDistributionTrainer(Distribution dis)
           
AbstractOrderNDistribution(Alphabet alpha)
          Construct a new NthOrderDistribution.
 

Uses of IllegalAlphabetException in org.biojava.bio.dp
 

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

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.forward(SymbolList[] seq, ScoreType scoreType)
           
 double SingleDP.backward(SymbolList[] seq, ScoreType scoreType)
           
 DPMatrix SingleDP.forwardMatrix(SymbolList[] seq, ScoreType scoreType)
           
 DPMatrix SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)
           
 DPMatrix SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
           
 DPMatrix SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
           
 

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

Methods in org.biojava.bio.dp.twohead that throw IllegalAlphabetException
 CellCalculator DPInterpreter.forwards(ScoreType scoreType)
           
 CellCalculator DPInterpreter.backwards(ScoreType scoreType)
           
 CellCalculator DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)
           
 void CellCalculator.initialize(Cell[][] cells)
          Initialize the cell at [0][0] to the recursion initial parameters.
 void CellCalculator.calcCell(Cell[][] cells)
           Calculate the 'scores' array in the cell at cells[0][0].
 CellCalculator CellCalculatorFactory.forwards(ScoreType scoreType)
           
 CellCalculator CellCalculatorFactory.backwards(ScoreType scoreType)
           
 CellCalculator CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)
           
 double PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)
           
 DPMatrix PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
           
 DPMatrix PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
           
 double PairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType)
           
 DPMatrix PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType)
           
 DPMatrix PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
           
 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 CompactedDataStoreFactory.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.
 DataStore DataStoreFactory.buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
          Build a new DataStore.
 DataStore NIODataStoreFactory.buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
           
 DataStore MappedDataStoreFactory.buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
           
 

Uses of IllegalAlphabetException in org.biojava.bio.proteomics
 

Methods in org.biojava.bio.proteomics that throw IllegalAlphabetException
 double IsoelectricPointCalc.getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm)
          Computes isoelectric point of specified peptide.
 

Uses of IllegalAlphabetException in org.biojava.bio.seq
 

Methods in org.biojava.bio.seq that throw IllegalAlphabetException
static SymbolList RNATools.complement(SymbolList list)
          Retrieve a complement view of list.
static SymbolList RNATools.reverseComplement(SymbolList list)
          Retrieve a reverse-complement view of list.
static SymbolList RNATools.transcribe(SymbolList list)
          Transcribe DNA into RNA.
static SymbolList RNATools.translate(SymbolList syms)
          Translate RNA into protein (with termination symbols).
static SymbolList NucleotideTools.complement(SymbolList list)
          Retrieve a complement view of list.
static SymbolList NucleotideTools.reverseComplement(SymbolList list)
          Retrieve a reverse-complement view of list.
static SymbolList DNATools.complement(SymbolList list)
          Retrieve a complement view of list.
static SymbolList DNATools.reverseComplement(SymbolList list)
          Retrieve a reverse-complement view of list.
 Sequence SequenceAnnotator.annotate(Sequence seq)
          Return an annotated version of a sequence.
 void SimpleAssembly.edit(Edit e)
           
static SymbolList GeneticCodes.transcribe(SymbolList theList)
          Transcribe DNA into RNA.
static SymbolList GeneticCodes.translate(SymbolList theList)
          Translate RNA into protein (with termination symbols).
static Sequence SequenceTools.reverseComplement(Sequence seq)
           
 void DummySequence.edit(Edit edit)
           
 

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
 

Constructors in org.biojava.bio.seq.impl that throw IllegalAlphabetException
SimpleHomologyFeature(Sequence sourceSeq, FeatureHolder parent, HomologyFeature.Template template)
           
SimpleSimilarityPairFeature(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template)
          Creates a new SimpleSimilarityPairFeature.
SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template)
           
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)
           
 

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

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

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

Methods in org.biojava.bio.seq.ragbag that throw IllegalAlphabetException
 void RagbagIdleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 

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.
 SymbolList SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          makes a SymbolList containing size Symbols from a Symbol array.
 void RelabeledAlignment.edit(Edit edit)
           
static Packing PackingFactory.getPacking(FiniteAlphabet alpha, boolean ambiguity)
          Get the default packing for an alphabet.
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.
static Alphabet AlphabetManager.getCrossProductAlphabet(java.util.List aList, java.lang.String name)
           
 SymbolList PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
           
 void AbstractSymbolList.edit(Edit edit)
           
 SymbolList SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          Create a factory for SimpleSymbolLists.
 

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