Package org.biojava.bio.program.gff

GFF manipulation.

See:
          Description

Interface Summary
GFFDocumentHandler The interface for things that listen to GFF event streams.
GFFErrorHandler Interface which captures any errors which occur when parsing a GFF stream.
GFFRecord A single GFF record.
GFFRecordFilter A filter that will accept or reject a GFFEntry.
 

Class Summary
GFFEntrySet A set of entries and comments as a representation of a GFF file.
GFFErrorHandler.AbortErrorHandler  
GFFErrorHandler.SkipRecordErrorHandler  
GFFFilterer An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others.
GFFParser Parse a stream of GFF text into a stream of records and comments.
GFFRecordFilter.AcceptAll Implementation of GFFRecordFilter that accepts everything.
GFFRecordFilter.FeatureFilter Implementation of GFFRecordFilter that accepts records based upon the feature field.
GFFRecordFilter.FrameFilter  
GFFRecordFilter.NotFilter  
GFFRecordFilter.SequenceFilter Implementation of GFFRecordFilter that accepts records based upon the sequence name.
GFFRecordFilter.SourceFilter Implementation of GFFRecordFilter that accepts records based upon the source field.
GFFRecordFilter.StrandFilter  
GFFTools  
GFFWriter Listens to a stream of GFF events and writes the lines to a PrintWriter.
SequencesAsGFF Turns a sequence database into a GFF event stream.
SimpleGFFRecord A no-frills implementation of a GFFRecord.
 

Exception Summary
IgnoreRecordException Ignore this record in the stream.
 

Package org.biojava.bio.program.gff Description

GFF manipulation.

GFF is a text-file format for specifying features within sequences. For up-to-date information, go to the GFF home page. Using this package, you can load GFF from a stream, create Features on Sequences, generate GFF from Features and write GFF to file.

Nearly all of the API uses the concept of a GFF stream that 'pushes' GFF from some source to a recipient. Recipients implement the GFFDocumentHandler interface.

There should be some demonstration programs in the biojava-live/demos/gff directory.