Package org.biojava.bio.program.gff

Class GFFFilterer

java.lang.Object

org.biojava.bio.program.gff.GFFFilterer

All Implemented Interfaces:

GFFDocumentHandler

public class GFFFilterer
extends Object
implements 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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	commentLine(String comment)	A comment line has been encountered.
void	endDocument()	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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GFFFilterer

public GFFFilterer(GFFDocumentHandler handler,
                   GFFRecordFilter filter)

Create a new GFFFilterer that will forward to handler everything that filter accepts.

Parameters:

handler - the listening GFFDocumentHandler

filter - the GFFRecordFilter that decides what is forwarded to handler

Method Detail

startDocument

public void startDocument(String locator)

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 interface GFFDocumentHandler

Parameters:

locator - A URI for the stream being parsed.

endDocument

public void 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 interface GFFDocumentHandler

commentLine

public void commentLine(String comment)

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 interface GFFDocumentHandler

Parameters:

comment - the comment String

recordLine

public void recordLine(GFFRecord record)

Only forward the GFFRecords that match a filter.

Specified by:

recordLine in interface GFFDocumentHandler

Parameters:

record - the GFFRecord containing all the info