Uses of Interface
org.biojava.bio.program.gff.GFFDocumentHandler

Packages that use GFFDocumentHandler
org.biojava.bio.program.gff GFF manipulation. 
 

Uses of GFFDocumentHandler in org.biojava.bio.program.gff
 

Classes in org.biojava.bio.program.gff that implement GFFDocumentHandler
 class GFFFilterer
          An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others.
 class GFFWriter
          Listens to a stream of GFF events and writes the lines to a PrintWriter.
 

Methods in org.biojava.bio.program.gff that return GFFDocumentHandler
 GFFDocumentHandler GFFEntrySet.getAddHandler()
          Get the GFFDocumentHandler for adding to this set.
 

Methods in org.biojava.bio.program.gff with parameters of type GFFDocumentHandler
protected  GFFRecord GFFParser.createRecord(GFFDocumentHandler handler, java.util.List aList, java.lang.String rest, java.lang.String comment)
          Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
protected  void SequencesAsGFF.doPreProcessSequence(Sequence seq, GFFDocumentHandler handler, java.lang.String id)
          Emit any per-sequence header information.
protected  void SequencesAsGFF.doProcessFeature(Feature feature, GFFDocumentHandler handler, java.lang.String id)
          Internal method to process an individual Feature.
protected  void SequencesAsGFF.doProcessSequence(Sequence seq, GFFDocumentHandler handler, java.lang.String id)
          Internal method to process an individual Sequence.
 void GFFParser.parse(java.io.BufferedReader bReader, GFFDocumentHandler handler)
          Informs handler of each line of gff read from bReader.
 void GFFParser.parse(java.io.BufferedReader bReader, GFFDocumentHandler handler, java.lang.String locator)
          Informs handler of each line of GFF read from bReader
 void SequencesAsGFF.processDB(SequenceDB seqDB, GFFDocumentHandler handler)
          Process all Sequences within a SequenceDB, informing handler of any suitable features.
 void SequencesAsGFF.processSequence(Sequence seq, GFFDocumentHandler handler)
          Process an individual Sequence, informing handler of any suitable features.
 void GFFEntrySet.streamRecords(GFFDocumentHandler handler)
          Write all records in this set out to a handler.
 

Constructors in org.biojava.bio.program.gff with parameters of type GFFDocumentHandler
GFFFilterer(GFFDocumentHandler handler, GFFRecordFilter filter)
          Create a new GFFFilterer that will forward to handler everything that filter accepts.