Uses of Interface org.biojava.bio.seq.io.SymbolTokenization (BioJava-1.5-beta API)

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

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.
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
`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
`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
`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
`SymbolTokenization` | `BioIndex.getSymbolParser()`
`SymbolTokenization` | `EmblCDROMIndexStore.getSymbolParser()`
`SymbolTokenization` | `IndexStore.getSymbolParser()` Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
`SymbolTokenization` | `TabIndexStore.getSymbolParser()`

Constructors in org.biojava.bio.seq.db with parameters of type SymbolTokenization
`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
`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
`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` | `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` | `SequenceFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Read a sequence and pass data on to a SeqIOListener.
`boolean` | `EmblLikeFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Deprecated.
`boolean` | `GenbankXmlFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Deprecated.
`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.

Constructors in org.biojava.bio.seq.io with parameters of type SymbolTokenization
`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
`class` | `SoftMaskedAlphabet.CaseSensitiveTokenization` This `SymbolTokenizer` works with a delegate to softmask symbol tokenization as appropriate.

Methods in org.biojava.bio.symbol that return SymbolTokenization
`SymbolTokenization` | `SoftMaskedAlphabet.getTokenization(String type)`
`SymbolTokenization` | `SingletonAlphabet.getTokenization(String name)`
`SymbolTokenization` | `Alphabet.getTokenization(String name)` Get a SymbolTokenization by name.
`SymbolTokenization` | `AbstractAlphabet.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)`

Methods in org.biojava.bio.symbol with parameters of type SymbolTokenization
`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
`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
`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
`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
`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. Always returns a DNA tokenizer.
`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. Returns an dna parser if the letters DNA or RNA appear in the first line of the stream.
`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. Always returns a DNA tokenizer.
`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. Always returns a protein tokenizer.
`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. Always returns a DNA tokenizer.
`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. Always returns a protein tokenizer.
`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` | `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. Returns an protein parser if the first line of sequence contains any of F/L/I/P/Q/E, otherwise returns a DNA tokenizer.
`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. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.
`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. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Returns an dna parser if the letters DNA or RNA appear in the first line of the file.
`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. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.
`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. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a protein tokenizer.
`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. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.
`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. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a protein tokenizer.
`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` | `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. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Returns an protein parser if the first line of sequence contains any of F/L/I/P/Q/E, otherwise returns a DNA tokenizer.

Methods in org.biojavax.bio.seq.io with parameters of type SymbolTokenization
`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` | `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` | `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` | `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` | `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. If namespace is null, then the namespace of the sequence in the fasta is used.
`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` | `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. If namespace is null, then the namespace of the sequence in the fasta is used.
`boolean` | `EMBLFormat.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` | `EMBLxmlFormat.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.
`boolean` | `FastaFormat.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
`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.

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