Package org.biojava.bio.program.gff

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.

Interface Summary

Interface	Description
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

Class	Description
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

Exception	Description
IgnoreRecordException	Ignore this record in the stream.