Uses of Interface
org.biojava.bio.seq.io.SymbolTokenization
Packages that use SymbolTokenization
Package
Description
Java wrappers for interacting with external bioinformatics tools.
Parser for Phred output
SSAHA sequence searching API.
Collections of biological sequence data.
Classes and interfaces for processing and producing flat-file representations
of sequences.
Representation of the Symbols that make up a sequence, and locations within
them.
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of SymbolTokenization in org.biojava.bio.program
Constructors in org.biojava.bio.program with parameters of type SymbolTokenization -
Uses of SymbolTokenization in org.biojava.bio.program.phred
Methods in org.biojava.bio.program.phred with parameters of type SymbolTokenizationModifier and TypeMethodDescriptionboolean
PhredFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) -
Uses of SymbolTokenization in org.biojava.bio.program.ssaha
Constructors in org.biojava.bio.program.ssaha with parameters of type SymbolTokenizationModifierConstructorDescriptionFileStreamer
(SequenceFormat format, SymbolTokenization toke, File f) FileStreamer
(SequenceFormat format, SymbolTokenization toke, List files) -
Uses of SymbolTokenization in org.biojava.bio.seq.db
Methods in org.biojava.bio.seq.db that return SymbolTokenizationModifier and TypeMethodDescriptionBioIndex.getSymbolParser()
EmblCDROMIndexStore.getSymbolParser()
IndexStore.getSymbolParser()
Retrieve the symbol parser used to turn the sequence characters into Symobl objects.TabIndexStore.getSymbolParser()
Constructors in org.biojava.bio.seq.db with parameters of type SymbolTokenizationModifierConstructorDescriptionEmblCDROMIndexStore
(File pathPrefix, File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser) Creates a newEmblCDROMIndexStore
backed by a random access binary index.EmblCDROMIndexStore
(File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser) Creates a newEmblCDROMIndexStore
backed by a random access binary index.TabIndexStore
(File storeFile, File indexFile, String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser) Create a new TabIndexStore. -
Uses of SymbolTokenization in org.biojava.bio.seq.io
Classes in org.biojava.bio.seq.io that implement SymbolTokenizationModifier and TypeClassDescriptionclass
Implementation of SymbolTokenization which binds symbols to strings of characters.class
Implementation of SymbolTokenization which binds symbols to single unicode characters.class
Tokenization for cross-product alphabets.class
class
class
Simple implementation of SymbolTokenization which uses the `name' field of the symbols.class
class
Base class for tokenizations which accept whitespace-separated `words'.Methods in org.biojava.bio.seq.io with parameters of type SymbolTokenizationModifier and TypeMethodDescriptionstatic SequenceIterator
SeqIOTools.readFasta
(BufferedReader br, SymbolTokenization sTok) Deprecated.Read a fasta file.static SequenceIterator
SeqIOTools.readFasta
(BufferedReader br, SymbolTokenization sTok, SequenceBuilderFactory seqFactory) Deprecated.Read a fasta file using a custom type of SymbolList.boolean
EmblLikeFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.boolean
FastaFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) Deprecated.Reads information from a flatfile to aSeqIOListener
using aSymbolTokenizer
to convert sequence strings toSymbol
objects.boolean
GAMEFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) this version only reads annotations (no symbols)boolean
GenbankFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.boolean
GenbankXmlFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.boolean
SequenceFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.Constructors in org.biojava.bio.seq.io with parameters of type SymbolTokenizationModifierConstructorDescriptionStreamReader
(BufferedReader reader, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf) StreamReader
(InputStream is, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf) -
Uses of SymbolTokenization in org.biojava.bio.symbol
Classes in org.biojava.bio.symbol that implement SymbolTokenizationModifier and TypeClassDescriptionclass
ThisSymbolTokenizer
works with a delegate to softmask symbol tokenization as appropriate.Methods in org.biojava.bio.symbol that return SymbolTokenizationModifier and TypeMethodDescriptionAbstractAlphabet.getTokenization
(String name) Alphabet.getTokenization
(String name) Get a SymbolTokenization by name.DoubleAlphabet.getTokenization
(String name) DoubleAlphabet.SubDoubleAlphabet.getTokenization
(String name) IntegerAlphabet.getTokenization
(String name) Creates a new parser (Mark Schreiber 3 May 2001).IntegerAlphabet.SubIntegerAlphabet.getTokenization
(String name) SingletonAlphabet.getTokenization
(String name) SoftMaskedAlphabet.getTokenization
(String type) Methods in org.biojava.bio.symbol with parameters of type SymbolTokenizationModifier and TypeMethodDescriptionvoid
AbstractAlphabet.putTokenization
(String name, SymbolTokenization parser) Assigns a symbol parser to a String object.Constructors in org.biojava.bio.symbol with parameters of type SymbolTokenizationModifierConstructorDescriptionSimpleSymbolList
(SymbolTokenization parser, String seqString) Construct a SymbolList from a string. -
Uses of SymbolTokenization in org.biojavax.bio.seq
Methods in org.biojavax.bio.seq that return SymbolTokenizationModifier and TypeMethodDescriptionstatic SymbolTokenization
RichSequence.IOTools.getDNAParser()
Creates a DNA symbol tokenizer.static SymbolTokenization
RichSequence.IOTools.getNucleotideParser()
Creates a nucleotide symbol tokenizer.static SymbolTokenization
RichSequence.IOTools.getProteinParser()
Creates a protein symbol tokenizer.static SymbolTokenization
RichSequence.IOTools.getRNAParser()
Creates a RNA symbol tokenizer.Methods in org.biojavax.bio.seq with parameters of type SymbolTokenizationModifier and TypeMethodDescriptionstatic RichSequenceIterator
RichSequence.IOTools.readEMBL
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a EMBL file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readEMBLxml
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a EMBLxml file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readFasta
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a fasta file building a custom type ofRichSequence
.static RichSequenceIterator
RichSequence.IOTools.readFasta
(BufferedReader br, SymbolTokenization sTok, Namespace ns) Read a fasta file.static RichSequenceIterator
RichSequence.IOTools.readGenbank
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a GenBank file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readINSDseq
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a INSDseq file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readUniProt
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a UniProt file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readUniProtXML
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a UniProt XML file using a custom type of SymbolList. -
Uses of SymbolTokenization in org.biojavax.bio.seq.io
Methods in org.biojavax.bio.seq.io that return SymbolTokenizationModifier and TypeMethodDescriptionEMBLFormat.guessSymbolTokenization
(BufferedInputStream stream) On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.EMBLFormat.guessSymbolTokenization
(File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.EMBLxmlFormat.guessSymbolTokenization
(BufferedInputStream stream) On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.EMBLxmlFormat.guessSymbolTokenization
(File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.FastaFormat.guessSymbolTokenization
(BufferedInputStream stream) On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.FastaFormat.guessSymbolTokenization
(File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.GenbankFormat.guessSymbolTokenization
(BufferedInputStream stream) On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.GenbankFormat.guessSymbolTokenization
(File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.INSDseqFormat.guessSymbolTokenization
(BufferedInputStream stream) On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.INSDseqFormat.guessSymbolTokenization
(File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.RichSequenceFormat.BasicFormat.guessSymbolTokenization
(File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.RichSequenceFormat.guessSymbolTokenization
(BufferedInputStream stream) On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.RichSequenceFormat.guessSymbolTokenization
(File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.UniProtFormat.guessSymbolTokenization
(BufferedInputStream stream) On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.UniProtFormat.guessSymbolTokenization
(File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.UniProtXMLFormat.guessSymbolTokenization
(BufferedInputStream stream) On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.UniProtXMLFormat.guessSymbolTokenization
(File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.Methods in org.biojavax.bio.seq.io with parameters of type SymbolTokenizationModifier and TypeMethodDescriptionboolean
EMBLFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
EMBLxmlFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
FastaFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rsiol, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
GenbankFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
INSDseqFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
RichSequenceFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener listener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
UniProtFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
UniProtXMLFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.boolean
EMBLFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
EMBLxmlFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
FastaFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
GenbankFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
INSDseqFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
UniProtFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.boolean
UniProtXMLFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.Constructors in org.biojavax.bio.seq.io with parameters of type SymbolTokenizationModifierConstructorDescriptionRichStreamReader
(BufferedReader reader, RichSequenceFormat format, SymbolTokenization symParser, RichSequenceBuilderFactory sf, Namespace ns) Creates a new stream reader on the given reader, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.RichStreamReader
(InputStream is, RichSequenceFormat format, SymbolTokenization symParser, RichSequenceBuilderFactory sf, Namespace ns) Creates a new stream reader on the given input stream, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.