Uses of Interface
org.biojava.bio.program.gff.GFFDocumentHandler
Packages that use GFFDocumentHandler
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Uses of GFFDocumentHandler in org.biojava.bio.program.gff
Classes in org.biojava.bio.program.gff that implement GFFDocumentHandlerModifier and TypeClassDescriptionclass
An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others.class
Listens to a stream of GFF events and writes the lines to a PrintWriter.Methods in org.biojava.bio.program.gff that return GFFDocumentHandlerModifier and TypeMethodDescriptionGFFEntrySet.getAddHandler()
Get the GFFDocumentHandler for adding to this set.Methods in org.biojava.bio.program.gff with parameters of type GFFDocumentHandlerModifier and TypeMethodDescriptionprotected GFFRecord
GFFParser.createRecord
(GFFDocumentHandler handler, List aList, String rest, String comment) Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.protected void
SequencesAsGFF.doPreProcessSequence
(Sequence seq, GFFDocumentHandler handler, String id) Emit any per-sequence header information.protected void
SequencesAsGFF.doProcessFeature
(Feature feature, GFFDocumentHandler handler, String id) Internal method to process an individual Feature.protected void
SequencesAsGFF.doProcessSequence
(Sequence seq, GFFDocumentHandler handler, String id) Internal method to process an individual Sequence.void
GFFParser.parse
(BufferedReader bReader, GFFDocumentHandler handler) Informs handler of each line of gff read from bReader.void
GFFParser.parse
(BufferedReader bReader, GFFDocumentHandler handler, String locator) Informs handler of each line of GFF read from bReadervoid
SequencesAsGFF.processDB
(SequenceDB seqDB, GFFDocumentHandler handler) Process all Sequences within a SequenceDB, informing handler of any suitable features.void
SequencesAsGFF.processSequence
(Sequence seq, GFFDocumentHandler handler) Process an individual Sequence, informing handler of any suitable features.void
GFFEntrySet.streamRecords
(GFFDocumentHandler handler) Write all records in this set out to a handler.Constructors in org.biojava.bio.program.gff with parameters of type GFFDocumentHandlerModifierConstructorDescriptionGFFFilterer
(GFFDocumentHandler handler, GFFRecordFilter filter) Create a new GFFFilterer that will forward to handler everything that filter accepts.