Uses of Interface
org.biojava.bio.seq.io.SymbolTokenization

Packages that use SymbolTokenization

Package	Description
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.
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 SymbolTokenization in org.biojava.bio.program

Constructors in org.biojava.bio.program with parameters of type SymbolTokenization

Constructor and Description
Meme(InputStream is, SymbolTokenization symParser)

Uses of SymbolTokenization in org.biojava.bio.program.phred

Methods in org.biojava.bio.program.phred with parameters of type SymbolTokenization

Modifier and Type	Method and Description
boolean	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 SymbolTokenization

Constructor and Description
SequenceStreamer.FileStreamer(SequenceFormat format, SymbolTokenization toke, File f)
SequenceStreamer.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 SymbolTokenization

Modifier and Type	Method and Description
SymbolTokenization	TabIndexStore.getSymbolParser()
SymbolTokenization	IndexStore.getSymbolParser() Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
SymbolTokenization	EmblCDROMIndexStore.getSymbolParser()
SymbolTokenization	BioIndex.getSymbolParser()

Constructors in org.biojava.bio.seq.db with parameters of type SymbolTokenization

Constructor and Description
EmblCDROMIndexStore(File pathPrefix, File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser) Creates a new EmblCDROMIndexStore backed by a random access binary index.
EmblCDROMIndexStore(File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser) Creates a new EmblCDROMIndexStore 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 SymbolTokenization

Modifier and Type	Class and Description
class	AlternateTokenization Implementation of SymbolTokenization which binds symbols to strings of characters.
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	SubIntegerTokenization
class	WordTokenization Base class for tokenizations which accept whitespace-separated `words'.

Methods in org.biojava.bio.seq.io with parameters of type SymbolTokenization

Modifier and Type	Method and Description
static 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	SequenceFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.
boolean	GenbankXmlFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.
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	GAMEFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) this version only reads annotations (no symbols)
boolean	FastaFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) Deprecated. Reads information from a flatfile to a SeqIOListener using a SymbolTokenizer to convert sequence strings to Symbol objects.
boolean	EmblLikeFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.

Constructors in org.biojava.bio.seq.io with parameters of type SymbolTokenization

Constructor and Description
StreamReader(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 SymbolTokenization

Modifier and Type	Class and Description
class	SoftMaskedAlphabet.CaseSensitiveTokenization This SymbolTokenizer works with a delegate to softmask symbol tokenization as appropriate.

Methods in org.biojava.bio.symbol that return SymbolTokenization

Modifier and Type	Method and Description
SymbolTokenization	SoftMaskedAlphabet.getTokenization(String type)
SymbolTokenization	SingletonAlphabet.getTokenization(String name)
SymbolTokenization	IntegerAlphabet.getTokenization(String name) Creates a new parser (Mark Schreiber 3 May 2001).
SymbolTokenization	IntegerAlphabet.SubIntegerAlphabet.getTokenization(String name)
SymbolTokenization	DoubleAlphabet.getTokenization(String name)
SymbolTokenization	DoubleAlphabet.SubDoubleAlphabet.getTokenization(String name)
SymbolTokenization	Alphabet.getTokenization(String name) Get a SymbolTokenization by name.
SymbolTokenization	AbstractAlphabet.getTokenization(String name)

Methods in org.biojava.bio.symbol with parameters of type SymbolTokenization

Modifier and Type	Method and Description
void	AbstractAlphabet.putTokenization(String name, SymbolTokenization parser) Assigns a symbol parser to a String object.

Constructors in org.biojava.bio.symbol with parameters of type SymbolTokenization

Constructor and Description
SimpleSymbolList(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 SymbolTokenization

Modifier and Type	Method and Description
static 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 SymbolTokenization

Modifier and Type	Method and Description
static 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, Namespace ns) Read a fasta file.
static RichSequenceIterator	RichSequence.IOTools.readFasta(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a fasta file building a custom type of RichSequence .
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 SymbolTokenization

Modifier and Type	Method and Description
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	EMBLFormat.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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.
SymbolTokenization	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.

Methods in org.biojavax.bio.seq.io with parameters of type SymbolTokenization

Modifier and Type	Method and Description
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	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	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	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	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	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	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	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	UniProtXMLFormat.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	INSDseqFormat.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	FastaFormat.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	EMBLFormat.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 SymbolTokenization

Constructor and Description
RichStreamReader(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.