Package org.biojava.bio.program.gff
Class GFFFilterer
java.lang.Object
org.biojava.bio.program.gff.GFFFilterer
- All Implemented Interfaces:
GFFDocumentHandler
An object that filters a stream of GFF, forwarding some
GFFRecords to a
listening GFFDocumentHandler, and dropping others.
The choice to forward or drop is made by a GFFRecordFilter.
Unless otherwise stated, all methods forward to the listening handler without altering the arguments in any way.
- Author:
- Matthew Pocock
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Constructor Summary
ConstructorsConstructorDescriptionGFFFilterer
(GFFDocumentHandler handler, GFFRecordFilter filter) Create a new GFFFilterer that will forward to handler everything that filter accepts. -
Method Summary
Modifier and TypeMethodDescriptionvoid
commentLine
(String comment) A comment line has been encountered.void
Indicates that the current GFF document has now ended.void
recordLine
(GFFRecord record) Only forward the GFFRecords that match a filter.void
startDocument
(String locator) Indicates that a new GFF document has been started.
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Constructor Details
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GFFFilterer
Create a new GFFFilterer that will forward to handler everything that filter accepts.- Parameters:
handler
- the listening GFFDocumentHandlerfilter
- the GFFRecordFilter that decides what is forwarded to handler
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Method Details
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startDocument
Description copied from interface:GFFDocumentHandler
Indicates that a new GFF document has been started. This gives you a hook to set up per-document resources.- Specified by:
startDocument
in interfaceGFFDocumentHandler
- Parameters:
locator
- A URI for the stream being parsed.
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endDocument
Description copied from interface:GFFDocumentHandler
Indicates that the current GFF document has now ended.This gives you the chance to flush results, or do calculations if you wish.
- Specified by:
endDocument
in interfaceGFFDocumentHandler
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commentLine
Description copied from interface:GFFDocumentHandler
A comment line has been encountered.comment has already had the leading '
#
' removed, and may have had leading-and-trailing whitespace trimmed.- Specified by:
commentLine
in interfaceGFFDocumentHandler
- Parameters:
comment
- the comment String
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recordLine
Only forward the GFFRecords that match a filter.- Specified by:
recordLine
in interfaceGFFDocumentHandler
- Parameters:
record
- the GFFRecord containing all the info
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