Uses of Interface
org.biojava.bio.program.gff.GFFDocumentHandler

Packages that use GFFDocumentHandler

Package	Description
org.biojava.bio.program.gff	GFF manipulation.

Uses of GFFDocumentHandler in org.biojava.bio.program.gff

Classes in org.biojava.bio.program.gff that implement GFFDocumentHandler

Modifier and Type	Class and Description
class	GFFFilterer An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others.
class	GFFWriter Listens to a stream of GFF events and writes the lines to a PrintWriter.

Methods in org.biojava.bio.program.gff that return GFFDocumentHandler

Modifier and Type	Method and Description
GFFDocumentHandler	GFFEntrySet.getAddHandler() Get the GFFDocumentHandler for adding to this set.

Methods in org.biojava.bio.program.gff with parameters of type GFFDocumentHandler

Modifier and Type	Method and Description
protected 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 bReader
void	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 GFFDocumentHandler

Constructor and Description
GFFFilterer(GFFDocumentHandler handler, GFFRecordFilter filter) Create a new GFFFilterer that will forward to handler everything that filter accepts.