## Uses of Interface
org.biojava.bio.symbol.Alphabet

Packages that use Alphabet
org.biojava.bio.alignment: Classes to generate and describe sequence alignments.
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.twohead
org.biojava.bio.gui: Graphical interfaces for biojava objects.
org.biojava.bio.program.das: Development client for the Distributed Annotation System.
org.biojava.bio.program.hmmer: Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.proteomics.aaindex: Classes and interfaces to load Amino Acid Index database files.
org.biojava.bio.seq: Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db: Collections of biological sequence data.
org.biojava.bio.seq.db.biosql: General purpose Sequence storage in a relational database.
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.structure: Interfaces and classes for protein structure (PDB).
org.biojava.bio.symbol: Representation of the Symbols that make up a sequence, and locations within them.
org.biojavax: The Biojava extensions packages, classes that extend the core biojava functionality
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.

Uses of Alphabet in org.biojava.bio.alignment

Fields in org.biojava.bio.alignment declared as Alphabet
`protected Alphabet` `AbstractULAlignment.alphabet`

Methods in org.biojava.bio.alignment that return Alphabet
`Alphabet` `FlexibleAlignment.getAlphabet()`
`Alphabet` `AbstractULAlignment.SubULAlignment.getAlphabet()`

Uses of Alphabet in org.biojava.bio.chromatogram

Methods in org.biojava.bio.chromatogram with parameters of type Alphabet
`protected SymbolList` `AbstractChromatogram.createImmutableSymbolList(Alphabet alpha, List syms)` A factory method for creating new symbol lists with a given alphabet.

Uses of Alphabet in org.biojava.bio.dist

Methods in org.biojava.bio.dist that return Alphabet
`Alphabet` `UniformDistribution.getAlphabet()`
`Alphabet` `TranslatedDistribution.getAlphabet()`
`Alphabet` `SimpleDistribution.getAlphabet()`
`Alphabet` `PairDistribution.getAlphabet()`
`Alphabet` `IndexedCount.getAlphabet()`
`Alphabet` `GapDistribution.getAlphabet()`
`Alphabet` `Distribution.getAlphabet()` The alphabet from which this spectrum emits symbols.
`Alphabet` `Count.getAlphabet()` The alphabet from which this Count is over.
`Alphabet` `AbstractOrderNDistribution.getAlphabet()`
`Alphabet` `OrderNDistribution.getConditionedAlphabet()` Get the conditioned alphabet.
`Alphabet` `AbstractOrderNDistribution.getConditionedAlphabet()` Get the conditioned alphabet.
`Alphabet` `OrderNDistribution.getConditioningAlphabet()` Get the conditioning alphabet of this distribution.
`Alphabet` `AbstractOrderNDistribution.getConditioningAlphabet()` Get the conditioning alphabet of this distribution.

Methods in org.biojava.bio.dist with parameters of type Alphabet
`Distribution` `OrderNDistributionFactory.createDistribution(Alphabet alpha)` Creates an OrderNDistribution of the appropriate type.
`Distribution` `DistributionFactory.createDistribution(Alphabet alpha)` Generate a new Distribution as requested.
`Distribution` `DistributionFactory.DefaultDistributionFactory.createDistribution(Alphabet alpha)`

Constructors in org.biojava.bio.dist with parameters of type Alphabet
`AbstractOrderNDistribution(Alphabet alpha)` Construct a new NthOrderDistribution.
`GapDistribution(Alphabet alpha)` Get a GapDistribution for an alphabet.

Uses of Alphabet in org.biojava.bio.dp

Methods in org.biojava.bio.dp that return Alphabet
`Alphabet` `WMAsMM.emissionAlphabet()`
`Alphabet` `SimpleMarkovModel.emissionAlphabet()`
`Alphabet` `MarkovModel.emissionAlphabet()` Alphabet that is emitted by the emission states.
`Alphabet` `WeightMatrix.getAlphabet()` The alphabet for the sequences that this weight matrix models.
`Alphabet` `SimpleWeightMatrix.getAlphabet()`
`Alphabet` `SimpleStatePath.getAlphabet()`
`Alphabet` `SimpleEmissionState.getMatches()`

Methods in org.biojava.bio.dp with parameters of type Alphabet
`static MagicalState` `MagicalState.getMagicalState(Alphabet alphabet, int heads)`

Constructors in org.biojava.bio.dp with parameters of type Alphabet
`ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory)` Deprecated.
`ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name)` Create a new ProfileHMM.
`SimpleMarkovModel(int heads, Alphabet emissionAlpha)` Deprecated.
`SimpleMarkovModel(int heads, Alphabet emissionAlpha, String name)`
`SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact)`

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

Constructors in org.biojava.bio.dp.twohead with parameters of type Alphabet
`EmissionCache(Alphabet alpha, State[] states, int dsi, ScoreType scoreType)`

Uses of Alphabet in org.biojava.bio.gui

Methods in org.biojava.bio.gui that return Alphabet
`Alphabet` `SimpleSymbolStyle.getAlphabet()`

Methods in org.biojava.bio.gui with parameters of type Alphabet
`static Map` `SimpleSymbolStyle.getStandardFillPaints(Alphabet alpha)`
`static Map` `SimpleSymbolStyle.getStandardOutlinePaints(Alphabet alpha)`

Uses of Alphabet in org.biojava.bio.program.das

Methods in org.biojava.bio.program.das that return Alphabet
`Alphabet` `DASSequence.getAlphabet()`

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

Fields in org.biojava.bio.program.hmmer declared as Alphabet
`protected Alphabet` `HmmerProfileParser.alph`

Constructors in org.biojava.bio.program.hmmer with parameters of type Alphabet
`HmmerProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name)`

Uses of Alphabet in org.biojava.bio.proteomics.aaindex

Fields in org.biojava.bio.proteomics.aaindex declared as Alphabet
`static Alphabet` `AAindex.PROTEIN_ALPHABET` The alphabet of the symbol property table, that is protein.

Uses of Alphabet in org.biojava.bio.seq

Methods in org.biojava.bio.seq that return Alphabet
`Alphabet` `SimpleAssembly.getAlphabet()`
`Alphabet` `NewSimpleAssembly.getAlphabet()`

Methods in org.biojava.bio.seq with parameters of type Alphabet
`static Sequence` `SequenceTools.createDummy(Alphabet alpha, int length, Symbol sym, String uri, String name)` Create a new Sequence that contains a single symbol repeated over and over.

Uses of Alphabet in org.biojava.bio.seq.db

Methods in org.biojava.bio.seq.db that return Alphabet
`protected abstract Alphabet` `WebSequenceDB.getAlphabet()`
`protected Alphabet` `SwissprotSequenceDB.getAlphabet()`
`protected Alphabet` `NCBISequenceDB.getAlphabet()`
`protected Alphabet` `GenpeptSequenceDB.getAlphabet()`
`protected Alphabet` `GenbankSequenceDB.getAlphabet()`

Uses of Alphabet in org.biojava.bio.seq.db.biosql

Methods in org.biojava.bio.seq.db.biosql with parameters of type Alphabet
`void` `BioSQLSequenceDB.createDummySequence(String id, Alphabet alphabet, int length)` Deprecated.

Uses of Alphabet in org.biojava.bio.seq.homol

Methods in org.biojava.bio.seq.homol that return Alphabet
`Alphabet` `SimilarityPairFeature.EmptyPairwiseAlignment.getAlphabet()`

Uses of Alphabet in org.biojava.bio.seq.impl

Methods in org.biojava.bio.seq.impl that return Alphabet
`Alphabet` `ViewSequence.getAlphabet()`
`Alphabet` `SubSequence.getAlphabet()`
`Alphabet` `SimpleSequence.getAlphabet()`
`Alphabet` `NewAssembledSymbolList.getAlphabet()`
`Alphabet` `DummySequence.getAlphabet()`
`Alphabet` `AssembledSymbolList.getAlphabet()`

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

Methods in org.biojava.bio.seq.io that return Alphabet
`Alphabet` `WordTokenization.getAlphabet()`
`Alphabet` `SymbolTokenization.getAlphabet()` The alphabet to which this tokenization applies.
`Alphabet` `SymbolReader.getAlphabet()` Find the alphabet of all symbols which may be returned by this SymbolReader.
`Alphabet` `CharacterTokenization.getAlphabet()`
`Alphabet` `AlternateTokenization.getAlphabet()`

Methods in org.biojava.bio.seq.io with parameters of type Alphabet
`void` `SwissprotFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)` Deprecated. Prints out the sequences properties in order.
`void` `SmartSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)`
`void` `SimpleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)`
`void` `SimpleAssemblyBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)`
`void` `SequenceDBSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)` does nothing for now.
`void` `SequenceBuilderFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`
`abstract void` `SequenceBuilderBase.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)`
`void` `SeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)` Notify the listener of symbol data.
`void` `SeqIOFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`
`void` `SeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`
`void` `ProteinRefSeqFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)` Deprecated.
`void` `GenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)` Deprecated.
`void` `EmblFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)` Deprecated.
`void` `ChunkedSymbolListFactory.addSymbols(Alphabet alfa, Symbol[] syms, int pos, int len)` tool to construct the SymbolList by adding Symbols.
`protected List` `SwissprotFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)` Deprecated. Converts the symbol list passed in into an array of strings.
`protected List` `ProteinRefSeqFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)` Deprecated. Converts the symbol list passed in into an array of strings.
`static SequenceBuilderFactory` `SeqIOTools.formatToFactory(SequenceFormat format, Alphabet alpha)` Deprecated. as this essentially duplicates the operation available in the method `identifyBuilderFactory`.
`protected void` `SwissprotFileFormer.printOutSequenceHeaderLine(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)` Deprecated. Prints out sequence header with only length data.
`static SequenceDB` `SeqIOTools.readFasta(InputStream seqFile, Alphabet alpha)` Deprecated. Create a sequence database from a fasta file provided as an input stream.

Constructors in org.biojava.bio.seq.io with parameters of type Alphabet
`AlternateTokenization(Alphabet alpha, boolean caseSensitive)`
`CharacterTokenization(Alphabet alpha, boolean caseSensitive)`
`CrossProductTokenization(Alphabet alpha)`
`CrossProductTokenization(Alphabet alpha, List tokenizers)`
`WordTokenization(Alphabet fab)`

Uses of Alphabet in org.biojava.bio.structure

Methods in org.biojava.bio.structure that return Alphabet
`static Alphabet` `AlphaCTools.getAlphaCarbonAngleAlphabet()` Returns a reference to the Alphabet that contains Symbols that represent PHI, PSI angles.

Uses of Alphabet in org.biojava.bio.symbol

Subinterfaces of Alphabet in org.biojava.bio.symbol
`interface` `FiniteAlphabet` An alphabet over a finite set of Symbols.

Classes in org.biojava.bio.symbol that implement Alphabet
`class` `AbstractAlphabet` An abstract implementation of `Alphabet`.
`class` `DoubleAlphabet` An efficient implementation of an Alphabet over the infinite set of double values.
`static class` `DoubleAlphabet.SubDoubleAlphabet` A class to represent a contiguous range of double symbols.
`class` `IntegerAlphabet` An efficient implementation of an Alphabet over the infinite set of integer values.
`static class` `IntegerAlphabet.SubIntegerAlphabet` A class to represent a finite contiguous subset of the infinite IntegerAlphabet
`class` `SimpleAlphabet` A simple no-frills implementation of the FiniteAlphabet interface.
`class` `SingletonAlphabet` An alphabet that contains a single atomic symbol.
`class` `SoftMaskedAlphabet` Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.

Methods in org.biojava.bio.symbol that return Alphabet
`static Alphabet` `AlphabetManager.alphabetForName(String name)` Retrieve the alphabet for a specific name.
`protected Alphabet` `SimpleAtomicSymbol.createMatches()`
`static Alphabet` `AlphabetManager.generateCrossProductAlphaFromName(String name)` Generates a new CrossProductAlphabet from the give name.
`Alphabet` `SymbolPropertyTable.getAlphabet()`
`Alphabet` `SymbolList.getAlphabet()` The alphabet that this SymbolList is over.
`Alphabet` `SoftMaskedAlphabet.CaseSensitiveTokenization.getAlphabet()`
`Alphabet` `SimpleSymbolPropertyTable.getAlphabet()`
`Alphabet` `SimpleSymbolList.getAlphabet()` Get the alphabet of this SymbolList.
`Alphabet` `SimpleGappedSymbolList.getAlphabet()`
`Alphabet` `SimpleAlignment.getAlphabet()`
`Alphabet` `RelabeledAlignment.getAlphabet()`
`Alphabet` `PackedSymbolList.getAlphabet()`
`Alphabet` `DummySymbolList.getAlphabet()`
`Alphabet` `ChunkedSymbolList.getAlphabet()`
`static Alphabet` `AlphabetManager.getCrossProductAlphabet(List aList)` Retrieve a CrossProductAlphabet instance over the alphabets in aList.
`static Alphabet` `AlphabetManager.getCrossProductAlphabet(List aList, Alphabet parent)` Retrieve a CrossProductAlphabet instance over the alphabets in aList.
`static Alphabet` `AlphabetManager.getCrossProductAlphabet(List aList, String name)` Attempts to create a cross product alphabet and register it under a name.
`Alphabet` `Symbol.getMatches()` The alphabet containing the symbols matched by this ambiguity symbol.
`Alphabet` `IntegerAlphabet.IntegerSymbol.getMatches()`
`Alphabet` `FundamentalAtomicSymbol.getMatches()`
`Alphabet` `DoubleAlphabet.DoubleSymbol.getMatches()`
`Alphabet` `DoubleAlphabet.DoubleRange.getMatches()`
`Alphabet` `TranslationTable.getSourceAlphabet()` The alphabet of Symbols that can be translated.
`Alphabet` `SimpleTranslationTable.getSourceAlphabet()`
`Alphabet` `SimpleReversibleTranslationTable.getSourceAlphabet()`
`Alphabet` `SimpleManyToOneTranslationTable.getSourceAlphabet()`
`abstract Alphabet` `AbstractReversibleTranslationTable.getSourceAlphabet()`
`abstract Alphabet` `AbstractManyToOneTranslationTable.getSourceAlphabet()`
`Alphabet` `TranslationTable.getTargetAlphabet()` The alphabet of Symbols that will be produced.
`Alphabet` `SimpleTranslationTable.getTargetAlphabet()`
`Alphabet` `SimpleReversibleTranslationTable.getTargetAlphabet()`
`Alphabet` `SimpleManyToOneTranslationTable.getTargetAlphabet()`
`abstract Alphabet` `AbstractReversibleTranslationTable.getTargetAlphabet()`
`abstract Alphabet` `AbstractManyToOneTranslationTable.getTargetAlphabet()`

Methods in org.biojava.bio.symbol with parameters of type Alphabet
`static Symbol` `AlphabetManager.createSymbol(Annotation annotation, List symList, Alphabet alpha)` Generates a new Symbol instance that represents the tuple of Symbols in symList.
`static Symbol` `AlphabetManager.createSymbol(Annotation annotation, Set symSet, Alphabet alpha)` Generates a new Symbol instance that represents the tuple of Symbols in symList.
`static Symbol` `AlphabetManager.createSymbol(char token, Annotation annotation, List symList, Alphabet alpha)` Deprecated. use the new version, without the token argument
`static Symbol` `AlphabetManager.createSymbol(char token, Annotation annotation, Set symSet, Alphabet alpha)` Deprecated. use the three-arg version of this method instead.
`static SymbolList` `SymbolListViews.emptyList(Alphabet alpha)` Get a new immutable, empty symbol list with the given alphabet.
`static List` `AlphabetManager.factorize(Alphabet alpha, Set symSet)` Return a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet.
`static Alphabet` `AlphabetManager.getCrossProductAlphabet(List aList, Alphabet parent)` Retrieve a CrossProductAlphabet instance over the alphabets in aList.
`SymbolList` `SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` makes a SymbolList containing size Symbols from a Symbol array.
`SymbolList` `SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` Create a factory for SimpleSymbolLists.
`SymbolList` `PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` Makes a packed SymbolList out of a list of Symbols.
`static void` `AlphabetManager.registerAlphabet(String[] names, Alphabet alphabet)` Register and Alphabet by more than one name.
`static void` `AlphabetManager.registerAlphabet(String name, Alphabet alphabet)` Register an alphabet by name.

Constructors in org.biojava.bio.symbol with parameters of type Alphabet
`ChunkedSymbolList(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha)`
`DummySymbolList(Alphabet alpha, int length, Symbol sym)`
`Edit(int pos, Alphabet alpha, Symbol replacement)` Convenience construtor for making single residue changes
`PackedSymbolList(Packing packing, Symbol[] symbols, int length, Alphabet alfa)` Create a new PackedSymbolList from an array of Symbols.
`SimpleSymbolList(Alphabet alpha)` Construct an empty SimpleSymbolList.
`SimpleSymbolList(Alphabet alpha, List rList)` Construct a SymbolList containing the symbols in the specified list.
`SimpleSymbolList(Symbol[] symbols, int length, Alphabet alphabet)` Construct a SimpleSymbolList given the Symbol array that backs it.
`SimpleSymbolPropertyTable(Alphabet source, String name)`
`SimpleTranslationTable(FiniteAlphabet source, Alphabet target)` Create a new translation table that will translate symbols from source to target.
`SimpleTranslationTable(FiniteAlphabet source, Alphabet target, Map transMap)` Create a new translation table that will translate symbols from source to target.

Uses of Alphabet in org.biojavax

Methods in org.biojavax with parameters of type Alphabet
`SymbolList` `DummyCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a)` Given a cross reference, return the corresponding symbol list. All responses are instances of InfinitelyAmbiguousSymbolList.
`SymbolList` `CrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a)` Given a cross reference, return the corresponding symbol list.

Uses of Alphabet in org.biojavax.bio.db.biosql

Methods in org.biojavax.bio.db.biosql with parameters of type Alphabet
`SymbolList` `BioSQLCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a)` Given a cross reference, return the corresponding symbol list.

Uses of Alphabet in org.biojavax.bio.seq

Methods in org.biojavax.bio.seq that return Alphabet
`Alphabet` `ThinRichSequence.getAlphabet()` The alphabet that this SymbolList is over.
`Alphabet` `InfinitelyAmbiguousSymbolList.getAlphabet()` The alphabet that this SymbolList is over.

Methods in org.biojavax.bio.seq with parameters of type Alphabet
`static RichSequence` `RichSequence.Tools.createRichSequence(Namespace ns, String name, String seqString, Alphabet alpha)` Create a new RichSequence in the specified namespace.
`static RichSequence` `RichSequence.Tools.createRichSequence(String name, String seqString, Alphabet alpha)` Create a new RichSequence in the default namespace.
`static RichSequence` `RichSequence.Tools.createRichSequence(String namespace, String name, String seqString, Alphabet alpha)` Create a new RichSequence in the specified namespace.

Constructors in org.biojavax.bio.seq with parameters of type Alphabet
`ThinRichSequence(Namespace ns, String name, String accession, int version, Alphabet alpha, Double seqversion)` Creates a new instance of ThinRichSequence.

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

Methods in org.biojavax.bio.seq.io with parameters of type Alphabet
`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)`
`void` `DebuggingRichSeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)`

Constructors in org.biojavax.bio.seq.io with parameters of type Alphabet
`HashedFastaIterator(BufferedInputStream is, Alphabet alpha, Namespace ns)`