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Packages that use FiniteAlphabet | |
org.biojava.bio.dist | Probability distributions over Alphabets. |
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.gui | Graphical interfaces for biojava objects. |
org.biojava.bio.program.abi | ABI Trace Handling. |
org.biojava.bio.program.phred | Parser for Phred output |
org.biojava.bio.program.ssaha | SSAHA sequence searching API. |
org.biojava.bio.program.ssbind | Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. |
org.biojava.bio.program.xff | Event-driven parsing system for the Extensible Feature Format (XFF). |
org.biojava.bio.proteomics | Utilities to aid in performing various physical analysis of proteins. |
org.biojava.bio.seq | Classes and interfaces for defining biological sequences and informatics objects. |
org.biojava.bio.seq.io | Classes and interfaces for processing and producing flat-file representations of sequences. |
org.biojava.bio.symbol | Representation of the Symbols that make up a sequence, and locations within them. |
Uses of FiniteAlphabet in org.biojava.bio.dist |
Constructors in org.biojava.bio.dist with parameters of type FiniteAlphabet | |
UniformDistribution(FiniteAlphabet alphabet)
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SimpleDistribution(FiniteAlphabet alphabet)
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IndexedCount(FiniteAlphabet fa)
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UntrainableDistribution(FiniteAlphabet alpha)
Construct a new untrainable distribution over the specified alphabet |
Uses of FiniteAlphabet in org.biojava.bio.dp |
Methods in org.biojava.bio.dp that return FiniteAlphabet | |
FiniteAlphabet |
MarkovModel.stateAlphabet()
FiniteAlphabet of the states. |
FiniteAlphabet |
MarkovModel.transitionsFrom(State source)
Returns the FiniteAlphabet of all states that have a transition from 'source'. |
FiniteAlphabet |
MarkovModel.transitionsTo(State dest)
Returns the FiniteAlphabet of all states that have a transition to 'dest'. |
FiniteAlphabet |
SimpleMarkovModel.stateAlphabet()
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FiniteAlphabet |
SimpleMarkovModel.transitionsFrom(State from)
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FiniteAlphabet |
SimpleMarkovModel.transitionsTo(State to)
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FiniteAlphabet |
WMAsMM.stateAlphabet()
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FiniteAlphabet |
WMAsMM.transitionsFrom(State from)
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FiniteAlphabet |
WMAsMM.transitionsTo(State to)
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Uses of FiniteAlphabet in org.biojava.bio.gui |
Constructors in org.biojava.bio.gui with parameters of type FiniteAlphabet | |
SimpleSymbolStyle(FiniteAlphabet alphabet)
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Uses of FiniteAlphabet in org.biojava.bio.program.abi |
Fields in org.biojava.bio.program.abi declared as FiniteAlphabet | |
static FiniteAlphabet |
ABITools.QUALITY
The quality alphabet. |
Uses of FiniteAlphabet in org.biojava.bio.program.phred |
Methods in org.biojava.bio.program.phred that return FiniteAlphabet | |
static FiniteAlphabet |
PhredTools.getPhredAlphabet()
Retrieves the PHRED alphabet from the AlphabetManager. |
Uses of FiniteAlphabet in org.biojava.bio.program.ssaha |
Methods in org.biojava.bio.program.ssaha that return FiniteAlphabet | |
FiniteAlphabet |
CompactedDataStore.getAlphabet()
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FiniteAlphabet |
DataStore.getAlphabet()
The alphabet of symbol lists that can be searched against this DataStore. |
Uses of FiniteAlphabet in org.biojava.bio.program.ssbind |
Methods in org.biojava.bio.program.ssbind that return FiniteAlphabet | |
static FiniteAlphabet |
AlphabetResolver.resolveAlphabet(java.lang.String identifier)
resolveAlphabet returns an appropriate
Alphabet for an arbitrary identifier. |
Uses of FiniteAlphabet in org.biojava.bio.program.xff |
Methods in org.biojava.bio.program.xff with parameters of type FiniteAlphabet | |
static Sequence |
XFFTools.readXFF(java.io.File xffFile,
java.lang.String seqID,
FiniteAlphabet alpha)
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Uses of FiniteAlphabet in org.biojava.bio.proteomics |
Methods in org.biojava.bio.proteomics that return FiniteAlphabet | |
FiniteAlphabet |
StructureTools.getStructure()
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Uses of FiniteAlphabet in org.biojava.bio.seq |
Methods in org.biojava.bio.seq that return FiniteAlphabet | |
static FiniteAlphabet |
NucleotideTools.getNucleotide()
Return the Nucleotide alphabet. |
static FiniteAlphabet |
RNATools.getRNA()
Return the RNA alphabet. |
static FiniteAlphabet |
RNATools.getCodonAlphabet()
Gets the (RNA x RNA x RNA) Alphabet |
static FiniteAlphabet |
DNATools.getDNA()
Return the DNA alphabet. |
static FiniteAlphabet |
DNATools.getCodonAlphabet()
Gets the (DNA x DNA x DNA) Alphabet |
static FiniteAlphabet |
ProteinTools.getAlphabet()
Gets the protein alphabet |
static FiniteAlphabet |
ProteinTools.getTAlphabet()
Gets the protein alphabet including the translation termination symbols |
Uses of FiniteAlphabet in org.biojava.bio.seq.io |
Methods in org.biojava.bio.seq.io that return FiniteAlphabet | |
static FiniteAlphabet |
SeqIOTools.getAlphabet(int identifier)
getAlphabet accepts a value which represents a
sequence format and returns the relevant
FiniteAlphabet object. |
Constructors in org.biojava.bio.seq.io with parameters of type FiniteAlphabet | |
NameTokenization(FiniteAlphabet fab,
boolean caseSensitive)
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NameTokenization(FiniteAlphabet fab)
Construct a new NameTokenization, defaulting to case-insensitive. |
Uses of FiniteAlphabet in org.biojava.bio.symbol |
Classes in org.biojava.bio.symbol that implement FiniteAlphabet | |
class |
AbstractAlphabet
An abstract implementation of Alphabet . |
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. |
Methods in org.biojava.bio.symbol that return FiniteAlphabet | |
FiniteAlphabet |
Packing.getAlphabet()
The FiniteAlphabet this packing is for. |
FiniteAlphabet |
AlphabetIndex.getAlphabet()
Retrieve the alphabet that this indexes. |
FiniteAlphabet |
DNANoAmbPack.getAlphabet()
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FiniteAlphabet |
DNAAmbPack.getAlphabet()
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FiniteAlphabet |
SuffixTree.getAlphabet()
Return the Alphabet containing all Symbols which might be found in this SuffixTree. |
Methods in org.biojava.bio.symbol with parameters of type FiniteAlphabet | |
static Packing |
PackingFactory.getPacking(FiniteAlphabet alpha,
boolean ambiguity)
Get the default packing for an alphabet. |
static Symbol |
AlphabetManager.getAllAmbiguitySymbol(FiniteAlphabet alpha)
Return the ambiguity symbol which matches all symbols in a given alphabet. |
static java.util.Set |
AlphabetManager.getAllSymbols(FiniteAlphabet alpha)
Return a set containing all possible symbols which can be considered members of a given alphabet, including ambiguous symbols. |
static AlphabetIndex |
AlphabetManager.getAlphabetIndex(FiniteAlphabet alpha)
Get an indexer for a specified alphabet. |
Constructors in org.biojava.bio.symbol with parameters of type FiniteAlphabet | |
SimpleReversibleTranslationTable(FiniteAlphabet source,
FiniteAlphabet target)
Construct a new translation table. |
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UkkonenSuffixTree(FiniteAlphabet alpha)
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SimpleTranslationTable(FiniteAlphabet source,
Alphabet target)
Create a new translation table that will translate symbols from source to target. |
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SimpleTranslationTable(FiniteAlphabet source,
Alphabet target,
java.util.Map transMap)
Create a new translation table that will translate symbols from source to target. |
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SuffixTree(FiniteAlphabet alphabet)
Construct a new SuffixTree to contain motifs over the specified alphabet. |
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DummySymbolList(FiniteAlphabet alpha,
int length)
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