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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. |
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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