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

Packages that use SequenceFormat
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.biojavax.bio.seq.io Classes to support the I/O of RichSequence and Bioentry objects. 
 

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

Classes in org.biojava.bio.program.phred that implement SequenceFormat
 class PhredFormat
          Format object representing Phred Quality files.
 

Uses of SequenceFormat in org.biojava.bio.program.ssaha
 

Constructors in org.biojava.bio.program.ssaha with parameters of type SequenceFormat
SequenceStreamer.FileStreamer(SequenceFormat format, SymbolTokenization toke, File f)
           
SequenceStreamer.FileStreamer(SequenceFormat format, SymbolTokenization toke, List files)
           
 

Uses of SequenceFormat in org.biojava.bio.seq.db
 

Methods in org.biojava.bio.seq.db that return SequenceFormat
 SequenceFormat IndexStore.getFormat()
          Retrieve the format of the index file.
 SequenceFormat BioIndex.getFormat()
           
 SequenceFormat TabIndexStore.getFormat()
           
 SequenceFormat EmblCDROMIndexStore.getFormat()
           
 SequenceFormat NCBISequenceDB.getSequenceFormat()
           
protected abstract  SequenceFormat WebSequenceDB.getSequenceFormat()
           
protected  SequenceFormat SwissprotSequenceDB.getSequenceFormat()
           
protected  SequenceFormat GenpeptSequenceDB.getSequenceFormat()
           
protected  SequenceFormat GenbankSequenceDB.getSequenceFormat()
           
 

Methods in org.biojava.bio.seq.db with parameters of type SequenceFormat
 void NCBISequenceDB.setSequenceFormat(SequenceFormat format)
           
 

Constructors in org.biojava.bio.seq.db with parameters of type SequenceFormat
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.
NCBISequenceDB(String database, SequenceFormat format)
          Parameterized constructor
NCBISequenceDB(String server, String CGI, String database, SequenceFormat format)
          Parameterized constructor
TabIndexStore(File storeFile, File indexFile, String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)
          Create a new TabIndexStore.
 

Uses of SequenceFormat in org.biojava.bio.seq.io
 

Classes in org.biojava.bio.seq.io that implement SequenceFormat
 class EmblLikeFormat
          Deprecated. Use org.biojavax.bio.seq.io.EMBLFormat instead
 class FastaFormat
          Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
 class GAMEFormat
          A rudimentary read-only GAME 1.2 Format object.
 class GenbankFormat
          Deprecated. Use org.biojavax.bio.seq.io.GenbankFormat
 class GenbankXmlFormat
          Deprecated. Use org.biojavax.bio.seq.io.INSDseqFormat
 class GenpeptFormat
          Deprecated. Use org.biojavax.bio.seq.io framework instead
 

Methods in org.biojava.bio.seq.io that return SequenceFormat
static SequenceFormat SeqIOTools.getSequenceFormat(int identifier)
          Deprecated. getSequenceFormat accepts a value which represents a sequence format and returns the relevant SequenceFormat object.
 

Methods in org.biojava.bio.seq.io with parameters of type SequenceFormat
static SequenceBuilderFactory SeqIOTools.formatToFactory(SequenceFormat format, Alphabet alpha)
          Deprecated. as this essentially duplicates the operation available in the method identifyBuilderFactory.
 

Constructors in org.biojava.bio.seq.io with parameters of type SequenceFormat
StreamReader(BufferedReader reader, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)
           
StreamReader(InputStream is, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)
           
StreamWriter(OutputStream os, SequenceFormat format)
          Generate a new StreamWriter to the stream os and using format.
 

Uses of SequenceFormat in org.biojavax.bio.seq.io
 

Subinterfaces of SequenceFormat in org.biojavax.bio.seq.io
 interface RichSequenceFormat
          Allows a file format to be read/written as RichSequences.
 

Classes in org.biojavax.bio.seq.io that implement SequenceFormat
 class EMBLFormat
          Format reader for EMBL files.
 class EMBLxmlFormat
          Format reader for EMBLxml files.
 class INSDseqFormat
          Format reader for INSDseq files.
static class RichSequenceFormat.BasicFormat
          Provides a basic format with simple things like line-widths precoded.
static class RichSequenceFormat.HeaderlessFormat
          Provides the basic implementation required for simple header/footer-less files such as Genbank.
 class UniProtFormat
          Format reader for UniProt files.
 class UniProtXMLFormat
          Format reader for UniProtXML files.