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 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
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 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
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
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 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
 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 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 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 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. 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 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 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 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 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 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 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. 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 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.
 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 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.
 

Methods in org.biojavax.bio.seq.io with parameters of type SymbolTokenization
 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 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. If namespace is null, then the namespace of the sequence in the fasta is used.
 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
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.