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

Packages that use Alphabet

Package	Description
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.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.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 The biojavax packages contain a number of extensions to the core biojava interfaces.
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

Modifier and Type	Field and Description
protected Alphabet	AbstractULAlignment.alphabet

Methods in org.biojava.bio.alignment that return Alphabet

Modifier and Type	Method and Description
Alphabet	FlexibleAlignment.getAlphabet()
Alphabet	AbstractULAlignment.SubULAlignment.getAlphabet()
Alphabet	SimpleAlignment.getAlphabet()

Uses of Alphabet in org.biojava.bio.chromatogram

Methods in org.biojava.bio.chromatogram with parameters of type Alphabet

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
Alphabet	UniformDistribution.getAlphabet()
Alphabet	IndexedCount.getAlphabet()
Alphabet	TranslatedDistribution.getAlphabet()
Alphabet	SimpleDistribution.getAlphabet()
Alphabet	Distribution.getAlphabet() The alphabet from which this spectrum emits symbols.
Alphabet	Count.getAlphabet() The alphabet from which this Count is over.
Alphabet	GapDistribution.getAlphabet()
Alphabet	AbstractOrderNDistribution.getAlphabet()
Alphabet	PairDistribution.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

Modifier and Type	Method and Description
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.

Constructors in org.biojava.bio.dist with parameters of type Alphabet

Constructor and Description
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

Modifier and Type	Method and Description
Alphabet	WMAsMM.emissionAlphabet()
Alphabet	MarkovModel.emissionAlphabet() Alphabet that is emitted by the emission states.
Alphabet	SimpleMarkovModel.emissionAlphabet()
Alphabet	SimpleWeightMatrix.getAlphabet()
Alphabet	WeightMatrix.getAlphabet() The alphabet for the sequences that this weight matrix models.
Alphabet	SimpleStatePath.getAlphabet()
Alphabet	SimpleEmissionState.getMatches()

Methods in org.biojava.bio.dp with parameters of type Alphabet

Modifier and Type	Method and Description
static MagicalState	MagicalState.getMagicalState(Alphabet alphabet, int heads)

Constructors in org.biojava.bio.dp with parameters of type Alphabet

Constructor and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
Alphabet	SimpleSymbolStyle.getAlphabet()

Methods in org.biojava.bio.gui with parameters of type Alphabet

Modifier and Type	Method and Description
static Map	SimpleSymbolStyle.getStandardFillPaints(Alphabet alpha)
static Map	SimpleSymbolStyle.getStandardOutlinePaints(Alphabet alpha)

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

Fields in org.biojava.bio.program.hmmer declared as Alphabet

Modifier and Type	Field and Description
protected Alphabet	HmmerProfileParser.alph

Constructors in org.biojava.bio.program.hmmer with parameters of type Alphabet

Constructor and Description
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

Modifier and Type	Field and Description
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

Modifier and Type	Method and Description
Alphabet	SimpleAssembly.getAlphabet()
Alphabet	NewSimpleAssembly.getAlphabet()

Methods in org.biojava.bio.seq with parameters of type Alphabet

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
protected Alphabet	GenbankSequenceDB.getAlphabet()
protected Alphabet	GenpeptSequenceDB.getAlphabet()
protected Alphabet	NCBISequenceDB.getAlphabet()
protected Alphabet	SwissprotSequenceDB.getAlphabet()
protected abstract Alphabet	WebSequenceDB.getAlphabet()

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

Methods in org.biojava.bio.seq.db.biosql with parameters of type Alphabet

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
Alphabet	SimilarityPairFeature.EmptyPairwiseAlignment.getAlphabet()

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

Methods in org.biojava.bio.seq.impl that return Alphabet

Modifier and Type	Method and Description
Alphabet	NewAssembledSymbolList.getAlphabet()
Alphabet	SimpleSequence.getAlphabet()
Alphabet	DummySequence.getAlphabet()
Alphabet	SubSequence.getAlphabet()
Alphabet	ViewSequence.getAlphabet()
Alphabet	AssembledSymbolList.getAlphabet()

Constructors in org.biojava.bio.seq.impl with parameters of type Alphabet

Constructor and Description
SimpleGappedSequence(Alphabet alpha)

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

Methods in org.biojava.bio.seq.io that return Alphabet

Modifier and Type	Method and Description
Alphabet	CharacterTokenization.getAlphabet()
Alphabet	AlternateTokenization.getAlphabet()
Alphabet	WordTokenization.getAlphabet()
Alphabet	SymbolReader.getAlphabet() Find the alphabet of all symbols which may be returned by this SymbolReader.
Alphabet	SymbolTokenization.getAlphabet() The alphabet to which this tokenization applies.

Methods in org.biojava.bio.seq.io with parameters of type Alphabet

Modifier and Type	Method and Description
void	SequenceDBSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) does nothing for now.
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.
void	SmartSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
void	SimpleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
void	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	ProteinRefSeqFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.
void	SwissprotFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated. Prints out the sequences properties in order.
void	SimpleAssemblyBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
abstract void	SequenceBuilderBase.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
void	GenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) Deprecated.
void	SequenceBuilderFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
void	SeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
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.
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

Constructor and Description
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.symbol

Subinterfaces of Alphabet in org.biojava.bio.symbol

Modifier and Type	Interface and Description
interface	FiniteAlphabet An alphabet over a finite set of Symbols.

Classes in org.biojava.bio.symbol that implement Alphabet

Modifier and Type	Class and Description
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

Modifier and Type	Method and Description
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	SymbolList.getAlphabet() The alphabet that this SymbolList is over.
Alphabet	RelabeledAlignment.getAlphabet()
Alphabet	DummySymbolList.getAlphabet()
Alphabet	SimpleSymbolList.getAlphabet() Get the alphabet of this SymbolList.
Alphabet	PackedSymbolList.getAlphabet()
Alphabet	ChunkedSymbolList.getAlphabet()
Alphabet	SimpleSymbolPropertyTable.getAlphabet()
Alphabet	SimpleGappedSymbolList.getAlphabet()
Alphabet	SymbolPropertyTable.getAlphabet()
Alphabet	SoftMaskedAlphabet.CaseSensitiveTokenization.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	IntegerAlphabet.IntegerSymbol.getMatches()
Alphabet	DoubleAlphabet.DoubleSymbol.getMatches()
Alphabet	DoubleAlphabet.DoubleRange.getMatches()
Alphabet	Symbol.getMatches() The alphabet containing the symbols matched by this ambiguity symbol.
Alphabet	FundamentalAtomicSymbol.getMatches()
Alphabet	TranslationTable.getSourceAlphabet() The alphabet of Symbols that can be translated.
Alphabet	SimpleManyToOneTranslationTable.getSourceAlphabet()
Alphabet	SimpleReversibleTranslationTable.getSourceAlphabet()
abstract Alphabet	AbstractManyToOneTranslationTable.getSourceAlphabet()
abstract Alphabet	AbstractReversibleTranslationTable.getSourceAlphabet()
Alphabet	SimpleTranslationTable.getSourceAlphabet()
Alphabet	TranslationTable.getTargetAlphabet() The alphabet of Symbols that will be produced.
Alphabet	SimpleManyToOneTranslationTable.getTargetAlphabet()
Alphabet	SimpleReversibleTranslationTable.getTargetAlphabet()
abstract Alphabet	AbstractManyToOneTranslationTable.getTargetAlphabet()
abstract Alphabet	AbstractReversibleTranslationTable.getTargetAlphabet()
Alphabet	SimpleTranslationTable.getTargetAlphabet()

Methods in org.biojava.bio.symbol that return types with arguments of type Alphabet

Modifier and Type	Method and Description
List<Alphabet>	Alphabet.getAlphabets() Return an ordered List of the alphabets which make up a compound alphabet.

Methods in org.biojava.bio.symbol with parameters of type Alphabet

Modifier and Type	Method and Description
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	PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) Makes a packed SymbolList out of a list of Symbols.
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.
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

Constructor and Description
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.
SimpleGappedSymbolList(Alphabet alpha)
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

Modifier and Type	Method and Description
SymbolList	DummyCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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)

Constructors in org.biojavax.bio.seq.io with parameters of type Alphabet

Constructor and Description
HashedFastaIterator(BufferedInputStream is, Alphabet alpha, Namespace ns)