Package org.biojava.bio.program.gff
Class SequencesAsGFF
java.lang.Object
org.biojava.bio.program.gff.SequencesAsGFF
Turns a sequence database into a GFF event stream.
- Author:
- Matthew Pocock, Thomas Down, Len Trigg
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected 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.Return the current FeatureFilter.boolean
Discover if per-sequence header lines will be generated.boolean
Return whether features will be filtered recursively or not.boolean
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.
-
Constructor Details
-
SequencesAsGFF
public SequencesAsGFF()
-
-
Method Details
-
setShatter
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
Determine if features with non-contiguous locations will be broken into multiple GFF records.- Since:
- 1.4
-
setGenerateSequenceHeader
Specify whether a per-sequence header line, giving the length of the sequence, should be generated.- Since:
- 1.4
-
getGenerateSequenceHeader
Discover if per-sequence header lines will be generated.- Since:
- 1.4
-
getFeatureFilter
Return the current FeatureFilter.This is the object that will accept or reject individual features.
- Returns:
- the current FeatureFilter
-
setFeatureFilter
Replace the current FeatureFilter with filter.- Parameters:
filter
- the new FeatureFilter
-
getRecurse
Return whether features will be filtered recursively or not.- Returns:
- whether or not to recurse
-
setRecurse
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 GFFifyhandler
- the GFFDocumentHandler that will receive the GFF for all suitable features within seqid
- 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 GFFifyhandler
- the GFFDocumentHandler that will receive the GFF for this featureid
- the value of the seqName field in any GFFRecords produced- Throws:
BioException
-
createGFFRecord
Internal method to create a GFFRecord from an individual Feature.- Parameters:
feature
- the Feature to GFFifyid
- the value of the seqName field in any GFFRecords produced- Throws:
BioException
-
processSequence
Process an individual Sequence, informing handler of any suitable features.- Parameters:
seq
- the Sequence to GFFifyhandler
- the GFFDocumentHandler that will receive the GFF for all suitable features within seq- Throws:
BioException
-
processDB
Process all Sequences within a SequenceDB, informing handler of any suitable features.- Parameters:
seqDB
- the SequenceDB to GFFifyhandler
- the GFFDocumentHandler that will receive the GFF for all suitable features within seqDB- Throws:
BioException
-