## 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.