org.biojava.bio.program.gff (BioJava-1.5-beta API)
Keywords: org.biojava.bio.program.gff package

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## 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.

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