- SequenceFeature tx = new SequenceFeature(features[i]);
- tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
- .elementAt(0).alignmentMapping);
- tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
- .elementAt(0).alignmentMapping);
+ int newBegin = 1 + residues.elementAt(features[i].getBegin()
+ - offset).atoms
+ .elementAt(0).alignmentMapping;
+ int newEnd = 1 + residues.elementAt(features[i].getEnd() - offset).atoms
+ .elementAt(0).alignmentMapping;
+ SequenceFeature tx = new SequenceFeature(features[i], newBegin,
+ newEnd, features[i].getFeatureGroup());