* 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();
- sf2.setEnd(sequenceFeatureLength);
+ SequenceFeature sf2 = new SequenceFeature(sf, 1,
+ sequenceFeatureLength, sf.getFeatureGroup(), sf.getScore());
mappedSequence.addSequenceFeature(sf2);
/*
*/
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
+ int typeColumn, String group,
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)
{