Uses of Interface
org.biojava.bio.symbol.Alphabet
Packages that use Alphabet
Package
Description
Classes to generate and describe sequence alignments.
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
Tools for working with profile Hidden Markov Models from the HMMer package.
Classes and interfaces to load Amino Acid Index database files.
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
General purpose Sequence storage in a relational database.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Representation of the Symbols that make up a sequence, and locations within
them.
The Biojava extensions packages, classes that extend the core biojava
functionality
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of Alphabet in org.biojava.bio.alignment
Fields in org.biojava.bio.alignment declared as AlphabetMethods in org.biojava.bio.alignment that return AlphabetModifier and TypeMethodDescriptionAbstractULAlignment.SubULAlignment.getAlphabet()
FlexibleAlignment.getAlphabet()
SimpleAlignment.getAlphabet()
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Uses of Alphabet in org.biojava.bio.chromatogram
Methods in org.biojava.bio.chromatogram with parameters of type AlphabetModifier and TypeMethodDescriptionprotected 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 AlphabetModifier and TypeMethodDescriptionAbstractOrderNDistribution.getAlphabet()
Count.getAlphabet()
The alphabet from which this Count is over.Distribution.getAlphabet()
The alphabet from which this spectrum emits symbols.GapDistribution.getAlphabet()
IndexedCount.getAlphabet()
PairDistribution.getAlphabet()
SimpleDistribution.getAlphabet()
TranslatedDistribution.getAlphabet()
UniformDistribution.getAlphabet()
AbstractOrderNDistribution.getConditionedAlphabet()
Get the conditioned alphabet.OrderNDistribution.getConditionedAlphabet()
Get the conditioned alphabet.AbstractOrderNDistribution.getConditioningAlphabet()
Get the conditioning alphabet of this distribution.OrderNDistribution.getConditioningAlphabet()
Get the conditioning alphabet of this distribution.Methods in org.biojava.bio.dist with parameters of type AlphabetModifier and TypeMethodDescriptionDistributionFactory.createDistribution
(Alphabet alpha) Generate a new Distribution as requested.DistributionFactory.DefaultDistributionFactory.createDistribution
(Alphabet alpha) OrderNDistributionFactory.createDistribution
(Alphabet alpha) Creates an OrderNDistribution of the appropriate type.Constructors in org.biojava.bio.dist with parameters of type AlphabetModifierConstructorDescriptionprotected
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 AlphabetModifier and TypeMethodDescriptionMarkovModel.emissionAlphabet()
Alphabet that is emitted by the emission states.SimpleMarkovModel.emissionAlphabet()
WMAsMM.emissionAlphabet()
SimpleStatePath.getAlphabet()
SimpleWeightMatrix.getAlphabet()
WeightMatrix.getAlphabet()
The alphabet for the sequences that this weight matrix models.SimpleEmissionState.getMatches()
Methods in org.biojava.bio.dp with parameters of type AlphabetModifier and TypeMethodDescriptionstatic MagicalState
MagicalState.getMagicalState
(Alphabet alphabet, int heads) Constructors in org.biojava.bio.dp with parameters of type AlphabetModifierConstructorDescriptionProfileHMM
(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 AlphabetModifierConstructorDescriptionEmissionCache
(Alphabet alpha, State[] states, int dsi, ScoreType scoreType) -
Uses of Alphabet in org.biojava.bio.gui
Methods in org.biojava.bio.gui that return AlphabetMethods in org.biojava.bio.gui with parameters of type AlphabetModifier and TypeMethodDescriptionstatic 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 AlphabetConstructors in org.biojava.bio.program.hmmer with parameters of type AlphabetModifierConstructorDescriptionprotected
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 AlphabetModifier and TypeFieldDescriptionstatic final 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 AlphabetMethods in org.biojava.bio.seq with parameters of type Alphabet -
Uses of Alphabet in org.biojava.bio.seq.db
Methods in org.biojava.bio.seq.db that return AlphabetModifier and TypeMethodDescriptionprotected Alphabet
GenbankSequenceDB.getAlphabet()
protected Alphabet
GenpeptSequenceDB.getAlphabet()
protected Alphabet
NCBISequenceDB.getAlphabet()
protected Alphabet
SwissprotSequenceDB.getAlphabet()
protected abstract Alphabet
WebSequenceDB.getAlphabet()
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Uses of Alphabet in org.biojava.bio.seq.db.biosql
Methods in org.biojava.bio.seq.db.biosql with parameters of type AlphabetModifier and TypeMethodDescriptionvoid
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 -
Uses of Alphabet in org.biojava.bio.seq.impl
Methods in org.biojava.bio.seq.impl that return AlphabetModifier and TypeMethodDescriptionAssembledSymbolList.getAlphabet()
DummySequence.getAlphabet()
NewAssembledSymbolList.getAlphabet()
SimpleSequence.getAlphabet()
SubSequence.getAlphabet()
ViewSequence.getAlphabet()
Constructors in org.biojava.bio.seq.impl with parameters of type Alphabet -
Uses of Alphabet in org.biojava.bio.seq.io
Methods in org.biojava.bio.seq.io that return AlphabetModifier and TypeMethodDescriptionAlternateTokenization.getAlphabet()
CharacterTokenization.getAlphabet()
SymbolReader.getAlphabet()
Find the alphabet of all symbols which may be returned by this SymbolReader.SymbolTokenization.getAlphabet()
The alphabet to which this tokenization applies.WordTokenization.getAlphabet()
Methods in org.biojava.bio.seq.io with parameters of type AlphabetModifier and TypeMethodDescriptionvoid
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
GenbankFileFormer.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) Deprecated.void
ProteinRefSeqFileFormer.addSymbols
(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.void
SeqIOAdapter.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) 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.abstract void
SequenceBuilderBase.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SequenceBuilderFilter.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) void
SequenceDBSequenceBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) does nothing for now.void
SimpleAssemblyBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SimpleSequenceBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SmartSequenceBuilder.addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) void
SwissprotFileFormer.addSymbols
(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated.Prints out the sequences properties in order.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.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 AlphabetModifierConstructorDescriptionAlternateTokenization
(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.symbolModifier and TypeInterfaceDescriptioninterface
An alphabet over a finite set of Symbols.Classes in org.biojava.bio.symbol that implement AlphabetModifier and TypeClassDescriptionclass
An abstract implementation ofAlphabet
.final class
An efficient implementation of an Alphabet over the infinite set of double values.static class
A class to represent a contiguous range of double symbols.final class
An efficient implementation of an Alphabet over the infinite set of integer values.static class
A class to represent a finite contiguous subset of the infinite IntegerAlphabetclass
A simple no-frills implementation of the FiniteAlphabet interface.class
An alphabet that contains a single atomic symbol.final class
Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.Fields in org.biojava.bio.symbol declared as AlphabetMethods in org.biojava.bio.symbol that return AlphabetModifier and TypeMethodDescriptionstatic 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.ChunkedSymbolList.getAlphabet()
DummySymbolList.getAlphabet()
PackedSymbolList.getAlphabet()
RelabeledAlignment.getAlphabet()
SimpleGappedSymbolList.getAlphabet()
SimpleSymbolList.getAlphabet()
Get the alphabet of this SymbolList.SimpleSymbolPropertyTable.getAlphabet()
SoftMaskedAlphabet.CaseSensitiveTokenization.getAlphabet()
SymbolList.getAlphabet()
The alphabet that this SymbolList is over.SymbolPropertyTable.getAlphabet()
static Alphabet
AlphabetManager.getCrossProductAlphabet
(List aList) 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.static Alphabet
AlphabetManager.getCrossProductAlphabet
(List aList, Alphabet parent) Retrieve a CrossProductAlphabet instance over the alphabets in aList.DoubleAlphabet.DoubleRange.getMatches()
DoubleAlphabet.DoubleSymbol.getMatches()
FundamentalAtomicSymbol.getMatches()
IntegerAlphabet.IntegerSymbol.getMatches()
Symbol.getMatches()
The alphabet containing the symbols matched by this ambiguity symbol.abstract Alphabet
AbstractManyToOneTranslationTable.getSourceAlphabet()
abstract Alphabet
AbstractReversibleTranslationTable.getSourceAlphabet()
SimpleManyToOneTranslationTable.getSourceAlphabet()
SimpleReversibleTranslationTable.getSourceAlphabet()
SimpleTranslationTable.getSourceAlphabet()
TranslationTable.getSourceAlphabet()
The alphabet of Symbols that can be translated.abstract Alphabet
AbstractManyToOneTranslationTable.getTargetAlphabet()
abstract Alphabet
AbstractReversibleTranslationTable.getTargetAlphabet()
SimpleManyToOneTranslationTable.getTargetAlphabet()
SimpleReversibleTranslationTable.getTargetAlphabet()
SimpleTranslationTable.getTargetAlphabet()
TranslationTable.getTargetAlphabet()
The alphabet of Symbols that will be produced.Methods in org.biojava.bio.symbol that return types with arguments of type AlphabetModifier and TypeMethodDescriptionAlphabet.getAlphabets()
Return an ordered List of the alphabets which make up a compound alphabet.Methods in org.biojava.bio.symbol with parameters of type AlphabetModifier and TypeMethodDescriptionstatic Symbol
AlphabetManager.createSymbol
(char token, Annotation annotation, List symList, Alphabet alpha) Deprecated.use the new version, without the token argumentstatic 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, 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 SymbolList
Get a new immutable, empty symbol list with the given alphabet.static List
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.PackedSymbolListFactory.makeSymbolList
(Symbol[] symbolArray, int size, Alphabet alfa) Makes a packed SymbolList out of a list of Symbols.SimpleSymbolListFactory.makeSymbolList
(Symbol[] symbolArray, int size, Alphabet alfa) Create a factory for SimpleSymbolLists.SymbolListFactory.makeSymbolList
(Symbol[] symbolArray, int size, Alphabet alfa) makes a SymbolList containing size Symbols from a Symbol array.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 AlphabetModifierConstructorDescriptionChunkedSymbolList
(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha) DummySymbolList
(Alphabet alpha, int length, Symbol sym) Convenience construtor for making single residue changesPackedSymbolList
(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 AlphabetModifier and TypeMethodDescriptionCrossReferenceResolver.getRemoteSymbolList
(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.DummyCrossReferenceResolver.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 AlphabetModifier and TypeMethodDescriptionBioSQLCrossReferenceResolver.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 AlphabetModifier and TypeMethodDescriptionInfinitelyAmbiguousSymbolList.getAlphabet()
The alphabet that this SymbolList is over.ThinRichSequence.getAlphabet()
The alphabet that this SymbolList is over.Methods in org.biojavax.bio.seq with parameters of type AlphabetModifier and TypeMethodDescriptionstatic RichSequence
RichSequence.Tools.createRichSequence
(String namespace, 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
(Namespace ns, 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 -
Uses of Alphabet in org.biojavax.bio.seq.io
Methods in org.biojavax.bio.seq.io with parameters of type AlphabetModifier and TypeMethodDescriptionvoid
DebuggingRichSeqIOListener.addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) void
RichSeqIOAdapter.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.Constructors in org.biojavax.bio.seq.io with parameters of type AlphabetModifierConstructorDescriptionHashedFastaIterator
(BufferedInputStream is, Alphabet alpha, Namespace ns)
identifyBuilderFactory
.