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

Packages that use Alphabet

org.biojava.bio.alignment	Implementation of the Alignment interface.
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.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 molecular structure.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.

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	OrderNDistribution.getConditioningAlphabet() Get the conditioning alphabet of this distribution.
Alphabet	OrderNDistribution.getConditionedAlphabet() Get the conditioned alphabet.
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.getConditioningAlphabet() Get the conditioning alphabet of this distribution.
Alphabet	AbstractOrderNDistribution.getConditionedAlphabet() Get the conditioned alphabet.
Alphabet	AbstractOrderNDistribution.getAlphabet()

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

GapDistribution(Alphabet alpha)
Get a GapDistribution for an alphabet.

AbstractOrderNDistribution(Alphabet alpha)
Construct a new NthOrderDistribution.

Uses of Alphabet in org.biojava.bio.dp

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

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

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

SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact)

SimpleMarkovModel(int heads, Alphabet emissionAlpha, String name)

SimpleMarkovModel(int heads, Alphabet emissionAlpha)
Deprecated.

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.

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.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)

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()

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

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 List	SwissprotFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Converts the symbol list passed in into an array of strings.
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)
static SequenceDB	SeqIOTools.readFasta(InputStream seqFile, Alphabet alpha) Create a sequence database from a fasta file provided as an input stream.
static SequenceBuilderFactory	SeqIOTools.formatToFactory(SequenceFormat format, Alphabet alpha) Deprecated. as this essentially duplicates the operation available in the method identifyBuilderFactory.
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)
protected List	ProteinRefSeqFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Converts the symbol list passed in into an array of strings.
void	GenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
void	EmblFileFormer.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.

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

WordTokenization(Alphabet fab)

CrossProductTokenization(Alphabet alpha)

CrossProductTokenization(Alphabet alpha, List tokenizers)

CharacterTokenization(Alphabet alpha, boolean caseSensitive)

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

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

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

static SymbolList	SymbolListViews.emptyList(Alphabet alpha) Get a new immutable, empty symbol list with the given alphabet.
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 name, Alphabet alphabet) Register an alphabet by name.
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(Annotation annotation, List symList, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.
static Symbol	AlphabetManager.createSymbol(char token, Annotation annotation, Set symSet, Alphabet alpha) Deprecated. use the three-arg version of this method instead.
static Symbol	AlphabetManager.createSymbol(Annotation annotation, Set symSet, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.
static Alphabet	AlphabetManager.getCrossProductAlphabet(List aList, Alphabet parent) Retrieve a CrossProductAlphabet instance over the alphabets in aList.
static List	AlphabetManager.factorize(Alphabet alpha, Set symSet) Return a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet.

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

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.

SimpleSymbolPropertyTable(Alphabet source, String name)

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.

PackedSymbolList(Packing packing, Symbol[] symbols, int length, Alphabet alfa)
Create a new PackedSymbolList from an array of Symbols.

Edit(int pos, Alphabet alpha, Symbol replacement)
Convenience construtor for making single residue changes

DummySymbolList(Alphabet alpha, int length, Symbol sym)

ChunkedSymbolList(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha)