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. 
 

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, java.util.List files)
           
SequenceStreamer.FileStreamer(SequenceFormat format, SymbolTokenization toke, java.io.File f)
           
 

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

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

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
NCBISequenceDB(java.lang.String database, SequenceFormat format)
          Parameterized constructor
NCBISequenceDB(java.lang.String server, java.lang.String CGI, java.lang.String database, SequenceFormat format)
          Parameterized constructor
EmblCDROMIndexStore(java.io.File divisionLkp, java.io.File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)
          Creates a new EmblCDROMIndexStore backed by a random access binary index.
EmblCDROMIndexStore(java.io.File pathPrefix, java.io.File divisionLkp, java.io.File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)
          Creates a new EmblCDROMIndexStore backed by a random access binary index.
TabIndexStore(java.io.File storeFile, java.io.File indexFile, java.lang.String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)
           
 

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

Classes in org.biojava.bio.seq.io that implement SequenceFormat
 class EmblLikeFormat
           Format processor for handling EMBL records and similar files.
 class FastaFormat
          Format object representing FASTA files.
 class GAMEFormat
          A rudimentary read-only GAME 1.2 Format object.
 class GenbankFormat
          Format reader for GenBank files.
 

Methods in org.biojava.bio.seq.io that return SequenceFormat
static SequenceFormat SeqIOTools.getSequenceFormat(int identifier)
          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(java.io.InputStream is, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)
           
StreamReader(java.io.BufferedReader reader, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)
           
StreamWriter(java.io.OutputStream os, SequenceFormat format)
          Generate a new StreamWriter to the stream os and using format.