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Packages that use FiniteAlphabet | |
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org.biojava.bio.alignment | Classes to generate and describe sequence alignments. |
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.search | Interfaces and classes for representing sequence similarity search results. |
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.structure.io | Input and Output of Structures |
org.biojava.bio.symbol | Representation of the Symbols that make up a sequence, and locations within them. |
org.biojava.utils.automata | |
org.biojava.utils.regex | This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets. |
org.biojavax.bio.seq | Rich implementations of Sequences, Locations and Features. |
org.biojavax.ga.util | Utility functions and helper classes |
Uses of FiniteAlphabet in org.biojava.bio.alignment |
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Fields in org.biojava.bio.alignment declared as FiniteAlphabet | |
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protected FiniteAlphabet |
SubstitutionMatrix.alphabet
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Methods in org.biojava.bio.alignment that return FiniteAlphabet | |
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FiniteAlphabet |
SubstitutionMatrix.getAlphabet()
Gives the alphabet used by this matrix. |
Constructors in org.biojava.bio.alignment with parameters of type FiniteAlphabet | |
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SubstitutionMatrix(FiniteAlphabet alpha,
File matrixFile)
This constructs a SubstitutionMatrix object that contains
two Map data structures having BioJava symbols as keys and
the value being the index of the matrix containing the substitution score. |
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SubstitutionMatrix(FiniteAlphabet alpha,
short match,
short replace)
Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters. |
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SubstitutionMatrix(FiniteAlphabet alpha,
String matrixString,
String name)
With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file. |
Uses of FiniteAlphabet in org.biojava.bio.dist |
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Constructors in org.biojava.bio.dist with parameters of type FiniteAlphabet | |
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IndexedCount(FiniteAlphabet fa)
Get a new IdexedCount for an alphabet using the default indexer. |
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SimpleDistribution(FiniteAlphabet alphabet)
make an instance of SimpleDistribution for the specified Alphabet. |
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UniformDistribution(FiniteAlphabet alphabet)
Create a new UniformDistribution. |
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UntrainableDistribution(FiniteAlphabet alpha)
Construct a new untrainable distribution over the specified alphabet. |
Uses of FiniteAlphabet in org.biojava.bio.dp |
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Methods in org.biojava.bio.dp that return FiniteAlphabet | |
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FiniteAlphabet |
MarkovModel.stateAlphabet()
FiniteAlphabet of the states. |
FiniteAlphabet |
SimpleMarkovModel.stateAlphabet()
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FiniteAlphabet |
WMAsMM.stateAlphabet()
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FiniteAlphabet |
MarkovModel.transitionsFrom(State source)
Returns the FiniteAlphabet of all states that have a transition from 'source'. |
FiniteAlphabet |
SimpleMarkovModel.transitionsFrom(State from)
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FiniteAlphabet |
WMAsMM.transitionsFrom(State from)
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FiniteAlphabet |
MarkovModel.transitionsTo(State dest)
Returns the FiniteAlphabet of all states that have a transition to 'dest'. |
FiniteAlphabet |
SimpleMarkovModel.transitionsTo(State to)
|
FiniteAlphabet |
WMAsMM.transitionsTo(State to)
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Uses of FiniteAlphabet in org.biojava.bio.gui |
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Constructors in org.biojava.bio.gui with parameters of type FiniteAlphabet | |
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SimpleSymbolStyle(FiniteAlphabet alphabet)
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Uses of FiniteAlphabet in org.biojava.bio.program.abi |
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Fields in org.biojava.bio.program.abi declared as FiniteAlphabet | |
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static FiniteAlphabet |
ABITools.QUALITY
The quality alphabet. |
Uses of FiniteAlphabet in org.biojava.bio.program.phred |
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Methods in org.biojava.bio.program.phred that return FiniteAlphabet | |
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static FiniteAlphabet |
PhredTools.getPhredAlphabet()
Retrieves the PHRED alphabet from the AlphabetManager. |
Uses of FiniteAlphabet in org.biojava.bio.program.ssaha |
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Methods in org.biojava.bio.program.ssaha that return FiniteAlphabet | |
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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 |
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Methods in org.biojava.bio.program.ssbind that return FiniteAlphabet | |
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static FiniteAlphabet |
AlphabetResolver.resolveAlphabet(String identifier)
resolveAlphabet returns an appropriate
Alphabet for an arbitrary identifier. |
Uses of FiniteAlphabet in org.biojava.bio.program.xff |
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Methods in org.biojava.bio.program.xff with parameters of type FiniteAlphabet | |
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static Sequence |
XFFTools.readXFF(File xffFile,
String seqID,
FiniteAlphabet alpha)
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Uses of FiniteAlphabet in org.biojava.bio.proteomics |
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Methods in org.biojava.bio.proteomics that return FiniteAlphabet | |
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FiniteAlphabet |
StructureTools.getStructure()
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Uses of FiniteAlphabet in org.biojava.bio.search |
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Constructors in org.biojava.bio.search with parameters of type FiniteAlphabet | |
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SeqContentPattern(FiniteAlphabet alpha)
Create a new SeqContentPattern over an alphabet. |
Uses of FiniteAlphabet in org.biojava.bio.seq |
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Methods in org.biojava.bio.seq that return FiniteAlphabet | |
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static FiniteAlphabet |
ProteinTools.getAlphabet()
Gets the protein alphabet |
static FiniteAlphabet |
DNATools.getCodonAlphabet()
Gets the (DNA x DNA x DNA) Alphabet |
static FiniteAlphabet |
RNATools.getCodonAlphabet()
Gets the (RNA x RNA x RNA) Alphabet |
static FiniteAlphabet |
DNATools.getDNA()
Return the DNA alphabet. |
static FiniteAlphabet |
DNATools.getDNAxDNA()
Gets the (DNA x DNA) Alphabet |
static FiniteAlphabet |
NucleotideTools.getNucleotide()
Return the Nucleotide alphabet. |
static FiniteAlphabet |
RNATools.getRNA()
Return the RNA alphabet. |
static FiniteAlphabet |
ProteinTools.getTAlphabet()
Gets the protein alphabet including the translation termination symbols |
Uses of FiniteAlphabet in org.biojava.bio.seq.io |
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Methods in org.biojava.bio.seq.io that return FiniteAlphabet | |
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static FiniteAlphabet |
SeqIOTools.getAlphabet(int identifier)
Deprecated. 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 | |
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NameTokenization(FiniteAlphabet fab)
Construct a new NameTokenization, defaulting to case-insensitive. |
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NameTokenization(FiniteAlphabet fab,
boolean caseSensitive)
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Uses of FiniteAlphabet in org.biojava.bio.structure.io |
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Methods in org.biojava.bio.structure.io with parameters of type FiniteAlphabet | |
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static SubstitutionMatrix |
SeqRes2AtomAligner.getSubstitutionMatrix(FiniteAlphabet alphabet)
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Uses of FiniteAlphabet in org.biojava.bio.symbol |
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Classes in org.biojava.bio.symbol that implement FiniteAlphabet | |
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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. |
class |
SoftMaskedAlphabet
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 FiniteAlphabet | |
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static FiniteAlphabet |
Alphabet.EMPTY_ALPHABET
A really useful static alphabet that is always empty. |
Methods in org.biojava.bio.symbol that return FiniteAlphabet | |
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FiniteAlphabet |
AlphabetIndex.getAlphabet()
Retrieve the alphabet that this indexes. |
FiniteAlphabet |
DNAAmbPack.getAlphabet()
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FiniteAlphabet |
DNANoAmbPack.getAlphabet()
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FiniteAlphabet |
Packing.getAlphabet()
The FiniteAlphabet this packing is for. |
FiniteAlphabet |
SuffixTree.getAlphabet()
Return the Alphabet containing all Symbols which might be found in this SuffixTree. |
protected FiniteAlphabet |
SoftMaskedAlphabet.getDelegate()
The compound alpha that holds the symbols used by this wrapper |
static FiniteAlphabet |
CodonPrefTools.getDinucleotideAlphabet()
returns an RNA dinucleotide alphabet. |
FiniteAlphabet |
SoftMaskedAlphabet.getMaskedAlphabet()
Gets the Alphabet upon which masking is being applied |
Methods in org.biojava.bio.symbol with parameters of type FiniteAlphabet | |
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static Symbol |
AlphabetManager.getAllAmbiguitySymbol(FiniteAlphabet alpha)
Return the ambiguity symbol which matches all symbols in a given alphabet. |
static 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. |
static SoftMaskedAlphabet |
SoftMaskedAlphabet.getInstance(FiniteAlphabet alphaToMask)
Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked. |
static SoftMaskedAlphabet |
SoftMaskedAlphabet.getInstance(FiniteAlphabet alphaToMask,
SoftMaskedAlphabet.MaskingDetector maskingDetector)
Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any Symbol is soft masked or not. |
static Packing |
PackingFactory.getPacking(FiniteAlphabet alpha,
boolean ambiguity)
Get the default packing for an alphabet. |
Constructors in org.biojava.bio.symbol with parameters of type FiniteAlphabet | |
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DummySymbolList(FiniteAlphabet alpha,
int length)
|
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SimpleGeneticCodeTable(FiniteAlphabet source,
FiniteAlphabet target)
Creates a new instance of SimpleGeneticCodeTable |
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SimpleManyToOneTranslationTable(FiniteAlphabet source,
FiniteAlphabet target)
Construct a new translation table. |
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SimpleReversibleTranslationTable(FiniteAlphabet source,
FiniteAlphabet target)
Construct a new translation table. |
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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,
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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UkkonenSuffixTree(FiniteAlphabet alpha)
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Uses of FiniteAlphabet in org.biojava.utils.automata |
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Constructors in org.biojava.utils.automata with parameters of type FiniteAlphabet | |
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Nfa(String name,
FiniteAlphabet alfa)
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PatternBlitz(FiniteAlphabet alfa,
org.biojava.utils.automata.StateMachineToolkit factory)
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Uses of FiniteAlphabet in org.biojava.utils.regex |
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Methods in org.biojava.utils.regex that return FiniteAlphabet | |
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FiniteAlphabet |
Pattern.getAlphabet()
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Methods in org.biojava.utils.regex with parameters of type FiniteAlphabet | |
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static PatternFactory |
PatternFactory.makeFactory(FiniteAlphabet alfa)
Returns a factory for Patterns in the specified Alphabet. |
Constructors in org.biojava.utils.regex with parameters of type FiniteAlphabet | |
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Search(FiniteAlphabet alfa)
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Uses of FiniteAlphabet in org.biojavax.bio.seq |
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Constructors in org.biojavax.bio.seq with parameters of type FiniteAlphabet | |
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InfinitelyAmbiguousSymbolList(FiniteAlphabet fa)
Creates a new instance of InfinitelyAmbiguousSymbolList |
Uses of FiniteAlphabet in org.biojavax.ga.util |
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Methods in org.biojavax.ga.util that return FiniteAlphabet | |
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static FiniteAlphabet |
GATools.getBinaryAlphabet()
Gets a Reference to the FlyWeight GA_Binary Alphabet . |
Methods in org.biojavax.ga.util with parameters of type FiniteAlphabet | |
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static OrderNDistribution |
GATools.standardMutationDistribution(FiniteAlphabet a)
Makes a mutation Distribution where the probability
of a Symbol being mutated to itself is zero and the
probability of it being changed to any other Symbol in
the Alphabet a is 1.0 / (a.size() - 1.0) |
static OrderNDistribution |
GATools.uniformMutationDistribution(FiniteAlphabet a)
Makes a 1st order distribution which is infact uniform (equivalent to a uniform zero order distribution). |
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