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
Interface Summary Interface Description GFFDocumentHandlerThe interface for things that listen to GFF event streams. GFFErrorHandlerInterface which captures any errors which occur when parsing a GFF stream. GFFRecordA single GFF record. GFFRecordFilterA filter that will accept or reject a GFFEntry.
Class Summary Class Description GFFEntrySetA set of entries and comments as a representation of a GFF file. GFFErrorHandler.AbortErrorHandler GFFErrorHandler.SkipRecordErrorHandler GFFFiltererAn object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others. GFFParserParse a stream of GFF text into a stream of records and comments. GFFRecordFilter.AcceptAllImplementation of GFFRecordFilter that accepts everything. GFFRecordFilter.FeatureFilterImplementation of GFFRecordFilter that accepts records based upon the feature field. GFFRecordFilter.FrameFilter GFFRecordFilter.NotFilter GFFRecordFilter.SequenceFilterImplementation of GFFRecordFilter that accepts records based upon the sequence name. GFFRecordFilter.SourceFilterImplementation of GFFRecordFilter that accepts records based upon the source field. GFFRecordFilter.StrandFilter GFFTools GFFWriterListens to a stream of GFF events and writes the lines to a PrintWriter. SequencesAsGFFTurns a sequence database into a GFF event stream. SimpleGFFRecordA no-frills implementation of a GFFRecord.
Exception Summary Exception Description IgnoreRecordExceptionIgnore this record in the stream.