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Packages that use Alphabet | |
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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 |
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Fields in org.biojava.bio.alignment declared as Alphabet | |
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protected Alphabet |
AbstractULAlignment.alphabet
|
Methods in org.biojava.bio.alignment that return Alphabet | |
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Alphabet |
FlexibleAlignment.getAlphabet()
|
Alphabet |
AbstractULAlignment.SubULAlignment.getAlphabet()
|
Uses of Alphabet in org.biojava.bio.chromatogram |
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Methods in org.biojava.bio.chromatogram with parameters of type Alphabet | |
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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 |
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Methods in org.biojava.bio.dist that return Alphabet | |
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Alphabet |
UniformDistribution.getAlphabet()
|
Alphabet |
TranslatedDistribution.getAlphabet()
|
Alphabet |
SimpleDistribution.getAlphabet()
|
Alphabet |
PairDistribution.getAlphabet()
|
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.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 | |
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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 | |
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AbstractOrderNDistribution(Alphabet alpha)
Construct a new NthOrderDistribution. |
|
GapDistribution(Alphabet alpha)
Get a GapDistribution for an alphabet. |
Uses of Alphabet in org.biojava.bio.dp |
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Methods in org.biojava.bio.dp that return Alphabet | |
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Alphabet |
WMAsMM.emissionAlphabet()
|
Alphabet |
SimpleMarkovModel.emissionAlphabet()
|
Alphabet |
MarkovModel.emissionAlphabet()
Alphabet that is emitted by the emission states. |
Alphabet |
WeightMatrix.getAlphabet()
The alphabet for the sequences that this weight matrix models. |
Alphabet |
SimpleWeightMatrix.getAlphabet()
|
Alphabet |
SimpleStatePath.getAlphabet()
|
Alphabet |
SimpleEmissionState.getMatches()
|
Methods in org.biojava.bio.dp with parameters of type Alphabet | |
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static MagicalState |
MagicalState.getMagicalState(Alphabet alphabet,
int heads)
|
Constructors in org.biojava.bio.dp with parameters of type Alphabet | |
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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)
|
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SimpleWeightMatrix(Alphabet alpha,
int columns,
DistributionFactory dFact)
|
Uses of Alphabet in org.biojava.bio.dp.twohead |
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Constructors in org.biojava.bio.dp.twohead with parameters of type Alphabet | |
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EmissionCache(Alphabet alpha,
State[] states,
int dsi,
ScoreType scoreType)
|
Uses of Alphabet in org.biojava.bio.gui |
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Methods in org.biojava.bio.gui that return Alphabet | |
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Alphabet |
SimpleSymbolStyle.getAlphabet()
|
Methods in org.biojava.bio.gui with parameters of type Alphabet | |
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static Map |
SimpleSymbolStyle.getStandardFillPaints(Alphabet alpha)
|
static Map |
SimpleSymbolStyle.getStandardOutlinePaints(Alphabet alpha)
|
Uses of Alphabet in org.biojava.bio.program.das |
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Methods in org.biojava.bio.program.das that return Alphabet | |
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Alphabet |
DASSequence.getAlphabet()
|
Uses of Alphabet in org.biojava.bio.program.hmmer |
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Fields in org.biojava.bio.program.hmmer declared as Alphabet | |
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protected Alphabet |
HmmerProfileParser.alph
|
Constructors in org.biojava.bio.program.hmmer with parameters of type Alphabet | |
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HmmerProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory,
String name)
|
Uses of Alphabet in org.biojava.bio.proteomics.aaindex |
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Fields in org.biojava.bio.proteomics.aaindex declared as Alphabet | |
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static Alphabet |
AAindex.PROTEIN_ALPHABET
The alphabet of the symbol property table, that is protein. |
Uses of Alphabet in org.biojava.bio.seq |
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Methods in org.biojava.bio.seq that return Alphabet | |
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Alphabet |
SimpleAssembly.getAlphabet()
|
Alphabet |
NewSimpleAssembly.getAlphabet()
|
Methods in org.biojava.bio.seq with parameters of type Alphabet | |
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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 |
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Methods in org.biojava.bio.seq.db that return Alphabet | |
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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 |
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Methods in org.biojava.bio.seq.db.biosql with parameters of type Alphabet | |
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void |
BioSQLSequenceDB.createDummySequence(String id,
Alphabet alphabet,
int length)
Deprecated. |
Uses of Alphabet in org.biojava.bio.seq.homol |
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Methods in org.biojava.bio.seq.homol that return Alphabet | |
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Alphabet |
SimilarityPairFeature.EmptyPairwiseAlignment.getAlphabet()
|
Uses of Alphabet in org.biojava.bio.seq.impl |
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Methods in org.biojava.bio.seq.impl that return Alphabet | |
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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 |
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Methods in org.biojava.bio.seq.io that return Alphabet | |
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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()
|
Alphabet |
AlternateTokenization.getAlphabet()
|
Methods in org.biojava.bio.seq.io with parameters of type Alphabet | |
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void |
SwissprotFileFormer.addSymbols(Alphabet theAlphabet,
Symbol[] theSymbols,
int theStart,
int theLength)
Deprecated. Prints out the sequences properties in order. |
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)
|
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)
Deprecated. |
void |
GenbankFileFormer.addSymbols(Alphabet alpha,
Symbol[] syms,
int start,
int length)
Deprecated. |
void |
EmblFileFormer.addSymbols(Alphabet alpha,
Symbol[] syms,
int start,
int length)
Deprecated. |
void |
ChunkedSymbolListFactory.addSymbols(Alphabet alfa,
Symbol[] syms,
int pos,
int len)
tool to construct the SymbolList by adding Symbols. |
protected List |
SwissprotFileFormer.breakSymbolArray(Alphabet theAlphabet,
Symbol[] theSymbols,
int theStart,
int theLength)
Deprecated. Converts the symbol list passed in into an array of strings. |
protected List |
ProteinRefSeqFileFormer.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 | |
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AlternateTokenization(Alphabet alpha,
boolean caseSensitive)
|
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CharacterTokenization(Alphabet alpha,
boolean caseSensitive)
|
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CrossProductTokenization(Alphabet alpha)
|
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CrossProductTokenization(Alphabet alpha,
List tokenizers)
|
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WordTokenization(Alphabet fab)
|
Uses of Alphabet in org.biojava.bio.structure |
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Methods in org.biojava.bio.structure that return Alphabet | |
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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 |
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Subinterfaces of Alphabet in org.biojava.bio.symbol | |
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interface |
FiniteAlphabet
An alphabet over a finite set of Symbols. |
Classes in org.biojava.bio.symbol that implement Alphabet | |
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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 | |
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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 |
SymbolPropertyTable.getAlphabet()
|
Alphabet |
SymbolList.getAlphabet()
The alphabet that this SymbolList is over. |
Alphabet |
SoftMaskedAlphabet.CaseSensitiveTokenization.getAlphabet()
|
Alphabet |
SimpleSymbolPropertyTable.getAlphabet()
|
Alphabet |
SimpleSymbolList.getAlphabet()
Get the alphabet of this SymbolList. |
Alphabet |
SimpleGappedSymbolList.getAlphabet()
|
Alphabet |
SimpleAlignment.getAlphabet()
|
Alphabet |
RelabeledAlignment.getAlphabet()
|
Alphabet |
PackedSymbolList.getAlphabet()
|
Alphabet |
DummySymbolList.getAlphabet()
|
Alphabet |
ChunkedSymbolList.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 |
Symbol.getMatches()
The alphabet containing the symbols matched by this ambiguity symbol. |
Alphabet |
IntegerAlphabet.IntegerSymbol.getMatches()
|
Alphabet |
FundamentalAtomicSymbol.getMatches()
|
Alphabet |
DoubleAlphabet.DoubleSymbol.getMatches()
|
Alphabet |
DoubleAlphabet.DoubleRange.getMatches()
|
Alphabet |
TranslationTable.getSourceAlphabet()
The alphabet of Symbols that can be translated. |
Alphabet |
SimpleTranslationTable.getSourceAlphabet()
|
Alphabet |
SimpleReversibleTranslationTable.getSourceAlphabet()
|
Alphabet |
SimpleManyToOneTranslationTable.getSourceAlphabet()
|
abstract Alphabet |
AbstractReversibleTranslationTable.getSourceAlphabet()
|
abstract Alphabet |
AbstractManyToOneTranslationTable.getSourceAlphabet()
|
Alphabet |
TranslationTable.getTargetAlphabet()
The alphabet of Symbols that will be produced. |
Alphabet |
SimpleTranslationTable.getTargetAlphabet()
|
Alphabet |
SimpleReversibleTranslationTable.getTargetAlphabet()
|
Alphabet |
SimpleManyToOneTranslationTable.getTargetAlphabet()
|
abstract Alphabet |
AbstractReversibleTranslationTable.getTargetAlphabet()
|
abstract Alphabet |
AbstractManyToOneTranslationTable.getTargetAlphabet()
|
Methods in org.biojava.bio.symbol with parameters of type Alphabet | |
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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 |
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[] 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 | |
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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. |
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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)
|
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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 |
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Methods in org.biojavax with parameters of type Alphabet | |
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SymbolList |
DummyCrossReferenceResolver.getRemoteSymbolList(CrossRef cr,
Alphabet a)
Given a cross reference, return the corresponding symbol list. All responses are instances of InfinitelyAmbiguousSymbolList. |
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 |
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Methods in org.biojavax.bio.db.biosql with parameters of type Alphabet | |
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SymbolList |
BioSQLCrossReferenceResolver.getRemoteSymbolList(CrossRef cr,
Alphabet a)
Given a cross reference, return the corresponding symbol list. |
Uses of Alphabet in org.biojavax.bio.seq |
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Methods in org.biojavax.bio.seq that return Alphabet | |
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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 | |
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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 | |
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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 |
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Methods in org.biojavax.bio.seq.io with parameters of type Alphabet | |
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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)
|
void |
DebuggingRichSeqIOListener.addSymbols(Alphabet alpha,
Symbol[] syms,
int start,
int length)
|
Constructors in org.biojavax.bio.seq.io with parameters of type Alphabet | |
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HashedFastaIterator(BufferedInputStream is,
Alphabet alpha,
Namespace ns)
|
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