org.biojava.bio.program.gff
Class SequencesAsGFF

java.lang.Object
  |
  +--org.biojava.bio.program.gff.SequencesAsGFF

public class SequencesAsGFF

extends java.lang.Object

Turns a sequence database into a GFF event stream.

Author:

Matthew Pocock, Thomas Down

Constructor Summary

SequencesAsGFF()

Method Summary

protected void	doProcessSequence(Sequence seq, GFFDocumentHandler handler, java.lang.String id) Internal method to process an individual Sequence.
FeatureFilter	getFeatureFilter() Return the current FeatureFilter.
boolean	getRecurse() Return whether features will be filtered recursively or not.
void	processDB(SequenceDB seqDB, GFFDocumentHandler handler) Process all Sequences within a SequenceDB, informing handler of any suitable features.
void	processSequence(Sequence seq, GFFDocumentHandler handler) Process an individual Sequence, informing handler of any suitable features.
void	setFeatureFilter(FeatureFilter filter) Replace the current FeatureFilter with filter.
void	setRecurse(boolean recurse) Set whether features will be filtered recursively to recurse.

Methods inherited from class java.lang.Object

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

Constructor Detail

SequencesAsGFF

public SequencesAsGFF()

Method Detail

getFeatureFilter

public FeatureFilter getFeatureFilter()

Return the current FeatureFilter.

This is the object that will accept or reject individual features.

Returns:

the current FeatureFilter

setFeatureFilter

public void setFeatureFilter(FeatureFilter filter)

Replace the current FeatureFilter with filter.

Parameters:

filter - the new FeatureFilter

getRecurse

public boolean getRecurse()

Return whether features will be filtered recursively or not.

Returns:

whether or not to recurse

setRecurse

public void setRecurse(boolean recurse)

Set whether features will be filtered recursively to recurse.

Parameters:

recurse - true if you want to recurse, false otherwise

doProcessSequence

protected void doProcessSequence(Sequence seq,
                                 GFFDocumentHandler handler,
                                 java.lang.String id)
                          throws BioException,
                                 BioException

Internal method to process an individual Sequence.

Parameters:

seq - the Sequence to GFFify

handler - the GFFDocumentHandler that will receive the GFF for all suitable features within seq

id - the value of the seqName field in any GFFRecords produced

BioException

processSequence

public void processSequence(Sequence seq,
                            GFFDocumentHandler handler)
                     throws BioException,
                            BioException

Process an individual Sequence, informing handler of any suitable features.

Parameters:

seq - the Sequence to GFFify

handler - the GFFDocumentHandler that will receive the GFF for all suitable features within seq

BioException

processDB

public void processDB(SequenceDB seqDB,
                      GFFDocumentHandler handler)
               throws BioException,
                      BioException

Process all Sequences within a SequenceDB, informing handler of any suitable features.

Parameters:

seqDB - the SequenceDB to GFFify

handler - the GFFDocumentHandler that will receive the GFF for all suitable features within seqDB

BioException