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 AbstractULAlignment.SubULAlignment.getAlphabet()
           
 Alphabet FlexibleAlignment.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 AbstractOrderNDistribution.getAlphabet()
           
 Alphabet Count.getAlphabet()
          The alphabet from which this Count is over.
 Alphabet Distribution.getAlphabet()
          The alphabet from which this spectrum emits symbols.
 Alphabet GapDistribution.getAlphabet()
           
 Alphabet IndexedCount.getAlphabet()
           
 Alphabet PairDistribution.getAlphabet()
           
 Alphabet SimpleDistribution.getAlphabet()
           
 Alphabet TranslatedDistribution.getAlphabet()
           
 Alphabet UniformDistribution.getAlphabet()
           
 Alphabet AbstractOrderNDistribution.getConditionedAlphabet()
          Get the conditioned alphabet.
 Alphabet OrderNDistribution.getConditionedAlphabet()
          Get the conditioned alphabet.
 Alphabet AbstractOrderNDistribution.getConditioningAlphabet()
          Get the conditioning alphabet of this distribution.
 Alphabet OrderNDistribution.getConditioningAlphabet()
          Get the conditioning alphabet of this distribution.
 

Methods in org.biojava.bio.dist with parameters of type Alphabet
 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
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 MarkovModel.emissionAlphabet()
          Alphabet that is emitted by the emission states.
 Alphabet SimpleMarkovModel.emissionAlphabet()
           
 Alphabet WMAsMM.emissionAlphabet()
           
 Alphabet SimpleStatePath.getAlphabet()
           
 Alphabet SimpleWeightMatrix.getAlphabet()
           
 Alphabet WeightMatrix.getAlphabet()
          The alphabet for the sequences that this weight matrix models.
 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 NewSimpleAssembly.getAlphabet()
           
 Alphabet SimpleAssembly.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  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
 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 AssembledSymbolList.getAlphabet()
           
 Alphabet DummySequence.getAlphabet()
           
 Alphabet NewAssembledSymbolList.getAlphabet()
           
 Alphabet SimpleSequence.getAlphabet()
           
 Alphabet SubSequence.getAlphabet()
           
 Alphabet ViewSequence.getAlphabet()
           
 

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

Methods in org.biojava.bio.seq.io that return Alphabet
 Alphabet AlternateTokenization.getAlphabet()
           
 Alphabet CharacterTokenization.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.
 Alphabet WordTokenization.getAlphabet()
           
 

Methods in org.biojava.bio.seq.io with parameters of type Alphabet
 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 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. 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 ChunkedSymbolList.getAlphabet()
           
 Alphabet DummySymbolList.getAlphabet()
           
 Alphabet PackedSymbolList.getAlphabet()
           
 Alphabet RelabeledAlignment.getAlphabet()
           
 Alphabet SimpleAlignment.getAlphabet()
           
 Alphabet SimpleGappedSymbolList.getAlphabet()
           
 Alphabet SimpleSymbolList.getAlphabet()
          Get the alphabet of this SymbolList.
 Alphabet SimpleSymbolPropertyTable.getAlphabet()
           
 Alphabet SoftMaskedAlphabet.CaseSensitiveTokenization.getAlphabet()
           
 Alphabet SymbolList.getAlphabet()
          The alphabet that this SymbolList is over.
 Alphabet SymbolPropertyTable.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 DoubleAlphabet.DoubleSymbol.getMatches()
           
 Alphabet DoubleAlphabet.DoubleRange.getMatches()
           
 Alphabet FundamentalAtomicSymbol.getMatches()
           
 Alphabet IntegerAlphabet.IntegerSymbol.getMatches()
           
 Alphabet Symbol.getMatches()
          The alphabet containing the symbols matched by this ambiguity symbol.
abstract  Alphabet AbstractManyToOneTranslationTable.getSourceAlphabet()
           
abstract  Alphabet AbstractReversibleTranslationTable.getSourceAlphabet()
           
 Alphabet SimpleManyToOneTranslationTable.getSourceAlphabet()
           
 Alphabet SimpleReversibleTranslationTable.getSourceAlphabet()
           
 Alphabet SimpleTranslationTable.getSourceAlphabet()
           
 Alphabet TranslationTable.getSourceAlphabet()
          The alphabet of Symbols that can be translated.
abstract  Alphabet AbstractManyToOneTranslationTable.getTargetAlphabet()
           
abstract  Alphabet AbstractReversibleTranslationTable.getTargetAlphabet()
           
 Alphabet SimpleManyToOneTranslationTable.getTargetAlphabet()
           
 Alphabet SimpleReversibleTranslationTable.getTargetAlphabet()
           
 Alphabet SimpleTranslationTable.getTargetAlphabet()
           
 Alphabet TranslationTable.getTargetAlphabet()
          The alphabet of Symbols that will be produced.
 

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 PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          Makes a packed SymbolList out of a list of Symbols.
 SymbolList SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)
          Create a factory for SimpleSymbolLists.
 SymbolList 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 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 CrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a)
          Given a cross reference, return the corresponding symbol list.
 SymbolList 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 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 InfinitelyAmbiguousSymbolList.getAlphabet()
          The alphabet that this SymbolList is over.
 Alphabet ThinRichSequence.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 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 Alphabet
HashedFastaIterator(BufferedInputStream is, Alphabet alpha, Namespace ns)