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Packages that use SymbolTokenization | |
org.biojava.bio.program | Java wrappers for interacting with external bioinformatics tools. |
org.biojava.bio.program.phred | Parser for Phred output |
org.biojava.bio.program.ssaha | SSAHA sequence searching API. |
org.biojava.bio.seq.db | Collections of biological sequence data. |
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 SymbolTokenization in org.biojava.bio.program |
Constructors in org.biojava.bio.program with parameters of type SymbolTokenization | |
Meme(java.io.InputStream is,
SymbolTokenization symParser)
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Uses of SymbolTokenization in org.biojava.bio.program.phred |
Methods in org.biojava.bio.program.phred with parameters of type SymbolTokenization | |
boolean |
PhredFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
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Uses of SymbolTokenization in org.biojava.bio.program.ssaha |
Constructors in org.biojava.bio.program.ssaha with parameters of type SymbolTokenization | |
SequenceStreamer.FileStreamer(SequenceFormat format,
SymbolTokenization toke,
java.util.List files)
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SequenceStreamer.FileStreamer(SequenceFormat format,
SymbolTokenization toke,
java.io.File f)
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Uses of SymbolTokenization in org.biojava.bio.seq.db |
Methods in org.biojava.bio.seq.db that return SymbolTokenization | |
SymbolTokenization |
BioIndex.getSymbolParser()
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SymbolTokenization |
IndexStore.getSymbolParser()
Retrieve the symbol parser used to turn the sequence characters into Symobl objects. |
SymbolTokenization |
EmblCDROMIndexStore.getSymbolParser()
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SymbolTokenization |
TabIndexStore.getSymbolParser()
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Constructors in org.biojava.bio.seq.db with parameters of type SymbolTokenization | |
EmblCDROMIndexStore(java.io.File divisionLkp,
java.io.File entryNamIdx,
SequenceFormat format,
SequenceBuilderFactory factory,
SymbolTokenization parser)
Creates a new EmblCDROMIndexStore backed by a
random access binary index. |
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EmblCDROMIndexStore(java.io.File pathPrefix,
java.io.File divisionLkp,
java.io.File entryNamIdx,
SequenceFormat format,
SequenceBuilderFactory factory,
SymbolTokenization parser)
Creates a new EmblCDROMIndexStore backed by a
random access binary index. |
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TabIndexStore(java.io.File storeFile,
java.io.File indexFile,
java.lang.String name,
SequenceFormat format,
SequenceBuilderFactory sbFactory,
SymbolTokenization symbolParser)
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Uses of SymbolTokenization in org.biojava.bio.seq.io |
Classes in org.biojava.bio.seq.io that implement SymbolTokenization | |
class |
CharacterTokenization
Implementation of SymbolTokenization which binds symbols to single unicode characters. |
class |
CrossProductTokenization
Tokenization for cross-product alphabets. |
class |
DoubleTokenization
|
class |
IntegerTokenization
|
class |
NameTokenization
Simple implementation of SymbolTokenization which uses the `name' field of the symbols. |
class |
WordTokenization
Base class for tokenizations which accept whitespace-separated `words'. |
Methods in org.biojava.bio.seq.io with parameters of type SymbolTokenization | |
boolean |
SequenceFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
FastaFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
|
boolean |
GAMEFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
this version only reads annotations (no symbols) |
boolean |
EmblLikeFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
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boolean |
GenbankFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided. |
Constructors in org.biojava.bio.seq.io with parameters of type SymbolTokenization | |
StreamReader(java.io.InputStream is,
SequenceFormat format,
SymbolTokenization symParser,
SequenceBuilderFactory sf)
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StreamReader(java.io.BufferedReader reader,
SequenceFormat format,
SymbolTokenization symParser,
SequenceBuilderFactory sf)
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Uses of SymbolTokenization in org.biojava.bio.symbol |
Methods in org.biojava.bio.symbol that return SymbolTokenization | |
SymbolTokenization |
IntegerAlphabet.getTokenization(java.lang.String name)
Creates a new parser (Mark Schreiber 3 May 2001). |
SymbolTokenization |
IntegerAlphabet.SubIntegerAlphabet.getTokenization(java.lang.String name)
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SymbolTokenization |
AbstractAlphabet.getTokenization(java.lang.String name)
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SymbolTokenization |
DoubleAlphabet.getTokenization(java.lang.String name)
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SymbolTokenization |
DoubleAlphabet.SubDoubleAlphabet.getTokenization(java.lang.String name)
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SymbolTokenization |
SingletonAlphabet.getTokenization(java.lang.String name)
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SymbolTokenization |
Alphabet.getTokenization(java.lang.String name)
Get a SymbolTokenization by name. |
Methods in org.biojava.bio.symbol with parameters of type SymbolTokenization | |
void |
AbstractAlphabet.putTokenization(java.lang.String name,
SymbolTokenization parser)
Assigns a symbol parser to a String object. |
Constructors in org.biojava.bio.symbol with parameters of type SymbolTokenization | |
SimpleSymbolList(SymbolTokenization parser,
java.lang.String seqString)
Construct a SymbolList from a string. |
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