Package org.biojava.bio.program.gff

Class SequencesAsGFF

java.lang.Object

org.biojava.bio.program.gff.SequencesAsGFF

public class SequencesAsGFF
extends Object

Turns a sequence database into a GFF event stream.

Author:

Matthew Pocock, Thomas Down, Len Trigg

Constructor Summary

Constructors

Constructor	Description
SequencesAsGFF()

Method Summary

Modifier and Type	Method	Description
protected SimpleGFFRecord	createGFFRecord(Feature feature, String id)	Internal method to create a GFFRecord from an individual Feature.
protected void	doPreProcessSequence(Sequence seq, GFFDocumentHandler handler, String id)	Emit any per-sequence header information.
protected void	doProcessFeature(Feature feature, GFFDocumentHandler handler, String id)	Internal method to process an individual Feature.
protected void	doProcessSequence(Sequence seq, GFFDocumentHandler handler, String id)	Internal method to process an individual Sequence.
FeatureFilter	getFeatureFilter()	Return the current FeatureFilter.
boolean	getGenerateSequenceHeader()	Discover if per-sequence header lines will be generated.
boolean	getRecurse()	Return whether features will be filtered recursively or not.
boolean	getShatter()	Determine if features with non-contiguous locations will be broken into multiple GFF records.
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	setGenerateSequenceHeader(boolean b)	Specify whether a per-sequence header line, giving the length of the sequence, should be generated.
void	setRecurse(boolean recurse)	Set whether features will be filtered recursively to recurse.
void	setShatter(boolean b)	Specify whether features with non-contiguous locations should be broken up such that a GFF feature line is emitted for each contiguous block.

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

setShatter

public void setShatter(boolean b)

Specify whether features with non-contiguous locations should be broken up such that a GFF feature line is emitted for each contiguous block.

Parameters:

b -

Since:

1.4

getShatter

public boolean getShatter()

Determine if features with non-contiguous locations will be broken into multiple GFF records.

Since:

1.4

setGenerateSequenceHeader

public void setGenerateSequenceHeader(boolean b)

Specify whether a per-sequence header line, giving the length of the sequence, should be generated.

Since:

1.4

getGenerateSequenceHeader

public boolean getGenerateSequenceHeader()

Discover if per-sequence header lines will be generated.

Since:

1.4

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

doPreProcessSequence

protected void doPreProcessSequence(Sequence seq,
                                    GFFDocumentHandler handler,
                                    String id)
                             throws BioException

Emit any per-sequence header information. The default implementation emits sequence-region comment lines.

Throws:

BioException

Since:

1.4

doProcessSequence

protected void doProcessSequence(Sequence seq,
                                 GFFDocumentHandler handler,
                                 String id)
                          throws 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

Throws:

BioException

doProcessFeature

protected void doProcessFeature(Feature feature,
                                GFFDocumentHandler handler,
                                String id)
                         throws BioException

Internal method to process an individual Feature.

Parameters:

feature - the Feature to GFFify

handler - the GFFDocumentHandler that will receive the GFF for this feature

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

Throws:

BioException

createGFFRecord

protected SimpleGFFRecord createGFFRecord(Feature feature,
                                          String id)
                                   throws BioException

Internal method to create a GFFRecord from an individual Feature.

Parameters:

feature - the Feature to GFFify

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

Throws:

BioException

processSequence

public void processSequence(Sequence seq,
                            GFFDocumentHandler handler)
                     throws 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

Throws:

BioException

processDB

public void processDB(SequenceDB seqDB,
                      GFFDocumentHandler handler)
               throws 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

Throws:

BioException