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.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
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 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, java.util.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 OrderNDistribution.getConditioningAlphabet()
          Get the conditioning alphabet of this distribution.
 Alphabet OrderNDistribution.getConditionedAlphabet()
          Get the conditioned alphabet.
 Alphabet UniformDistribution.getAlphabet()
           
 Alphabet Count.getAlphabet()
          The alphabet from which this Count is over.
 Alphabet TranslatedDistribution.getAlphabet()
           
 Alphabet SimpleDistribution.getAlphabet()
           
 Alphabet IndexedCount.getAlphabet()
           
 Alphabet AbstractOrderNDistribution.getConditioningAlphabet()
          Get the conditioning alphabet of this distribution.
 Alphabet AbstractOrderNDistribution.getConditionedAlphabet()
          Get the conditioned alphabet.
 Alphabet AbstractOrderNDistribution.getAlphabet()
           
 Alphabet PairDistribution.getAlphabet()
           
 Alphabet Distribution.getAlphabet()
          The alphabet from which this spectrum emits symbols.
 Alphabet GapDistribution.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
AbstractOrderNDistribution(Alphabet alpha)
          Construct a new NthOrderDistribution.
GapDistribution(Alphabet alpha)
           
 

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 SimpleEmissionState.getMatches()
           
 Alphabet WeightMatrix.getAlphabet()
          The alphabet for the sequences that this weight matrix models.
 Alphabet SimpleWeightMatrix.getAlphabet()
           
 Alphabet SimpleStatePath.getAlphabet()
           
 Alphabet WMAsMM.emissionAlphabet()
           
 

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
SimpleMarkovModel(int heads, Alphabet emissionAlpha, java.lang.String name)
           
SimpleMarkovModel(int heads, Alphabet emissionAlpha)
          Deprecated.  
SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact)
           
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory)
          Deprecated.  
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, java.lang.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 java.util.Map SimpleSymbolStyle.getStandardFillPaints(Alphabet alpha)
           
static java.util.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, java.lang.String name)
           
 

Uses of Alphabet in org.biojava.bio.seq
 

Methods in org.biojava.bio.seq that return Alphabet
 Alphabet SubSequence.getAlphabet()
           
 Alphabet ViewSequence.getAlphabet()
           
 Alphabet DummySequence.getAlphabet()
           
 Alphabet SimpleAssembly.getAlphabet()
           
 

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

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

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

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

Methods in org.biojava.bio.seq.io with parameters of type Alphabet
 void SeqIOFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void SimpleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 void SeqIOAdapter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void SequenceBuilderFilter.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void GenbankFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void SmartSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 void SequenceDBSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
          does nothing for now.
abstract  void SequenceBuilderBase.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 void SimpleAssemblyBuilder.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 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  java.util.List SwissprotFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Converts the symbol list passed in into an array of strings.
 void ChunkedSymbolListBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
static SequenceDB SeqIOTools.readFasta(java.io.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 EmblFileFormer.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
           
 void ProteinRefSeqFileFormer.addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
           
protected  java.util.List ProteinRefSeqFileFormer.breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength)
          Converts the symbol list passed in into an array of strings.
 void SeqIOListener.addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
          Notify the listener of symbol data.
 

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

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

Methods in org.biojava.bio.seq.ragbag with parameters of type Alphabet
 void RagbagIdleSequenceBuilder.addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
           
 

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.
 

Fields in org.biojava.bio.symbol declared as Alphabet
static Alphabet Alphabet.EMPTY_ALPHABET
          A really useful static alphabet that is always empty.
 

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

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

Constructors in org.biojava.bio.symbol with parameters of type Alphabet
PackedSymbolList(Packing packing, Symbol[] symbols, int length, Alphabet alfa)
           Create a new PackedSymbolList from an array of Symbols.
SimpleTranslationTable(FiniteAlphabet source, Alphabet target)
          Create a new translation table that will translate symbols from source to target.
SimpleTranslationTable(FiniteAlphabet source, Alphabet target, java.util.Map transMap)
          Create a new translation table that will translate symbols from source to target.
SimpleSymbolPropertyTable(Alphabet source, java.lang.String name)
           
Edit(int pos, Alphabet alpha, Symbol replacement)
          Convenience construtor for making single residue changes
SimpleSymbolList(Alphabet alpha)
          Construct an empty SimpleSymbolList.
SimpleSymbolList(Alphabet alpha, java.util.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.