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Packages that use GFFDocumentHandler | |
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 | |
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 | |
GFFDocumentHandler |
GFFEntrySet.getAddHandler()
Get the GFFDocumentHandler for adding to this set. |
Methods in org.biojava.bio.program.gff with parameters of type GFFDocumentHandler | |
void |
GFFParser.parse(java.io.BufferedReader bReader,
GFFDocumentHandler handler)
Informs handler of each line of gff read from bReader. |
void |
GFFParser.parse(java.io.BufferedReader bReader,
GFFDocumentHandler handler,
java.lang.String locator)
Informs handler of each line of GFF read from bReader |
protected GFFRecord |
GFFParser.createRecord(GFFDocumentHandler handler,
java.util.List aList,
java.lang.String rest,
java.lang.String comment)
Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler. |
void |
GFFEntrySet.streamRecords(GFFDocumentHandler handler)
Write all records in this set out to a handler. |
protected void |
SequencesAsGFF.doProcessSequence(Sequence seq,
GFFDocumentHandler handler,
java.lang.String id)
Internal method to process an individual Sequence. |
void |
SequencesAsGFF.processSequence(Sequence seq,
GFFDocumentHandler handler)
Process an individual Sequence, informing handler of any suitable features. |
void |
SequencesAsGFF.processDB(SequenceDB seqDB,
GFFDocumentHandler handler)
Process all Sequences within a SequenceDB, informing handler of any suitable features. |
Constructors in org.biojava.bio.program.gff with parameters of type GFFDocumentHandler | |
GFFFilterer(GFFDocumentHandler handler,
GFFRecordFilter filter)
Create a new GFFFilterer that will forward to handler everything that filter accepts. |
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