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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
Gff3Helper.java
diff --git
a/src/jalview/io/gff/Gff3Helper.java
b/src/jalview/io/gff/Gff3Helper.java
index
594040a
..
c7e1d7a
100644
(file)
--- a/
src/jalview/io/gff/Gff3Helper.java
+++ b/
src/jalview/io/gff/Gff3Helper.java
@@
-311,10
+311,9
@@
public class Gff3Helper extends GffHelperBase
* give the mapped sequence a copy of the sequence feature, with
* start/end range adjusted
*/
* give the mapped sequence a copy of the sequence feature, with
* start/end range adjusted
*/
- SequenceFeature sf2 = new SequenceFeature(sf);
- sf2.setBegin(1);
int sequenceFeatureLength = 1 + sf.getEnd() - sf.getBegin();
int sequenceFeatureLength = 1 + sf.getEnd() - sf.getBegin();
- sf2.setEnd(sequenceFeatureLength);
+ SequenceFeature sf2 = new SequenceFeature(sf, 1,
+ sequenceFeatureLength, sf.getFeatureGroup(), sf.getScore());
mappedSequence.addSequenceFeature(sf2);
/*
mappedSequence.addSequenceFeature(sf2);
/*
@@
-363,9
+362,11
@@
public class Gff3Helper extends GffHelperBase
*/
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
*/
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
+ int typeColumn, String group,
Map<String, List<String>> attributes)
{
Map<String, List<String>> attributes)
{
- SequenceFeature sf = super.buildSequenceFeature(gff, attributes);
+ SequenceFeature sf = super.buildSequenceFeature(gff, typeColumn, group,
+ attributes);
String desc = getDescription(sf, attributes);
if (desc != null)
{
String desc = getDescription(sf, attributes);
if (desc != null)
{