- if (status==null)
- status = "IEA:jalview";
- SequenceFeature[] features = sequence.getSequenceFeatures();
- for (int i=0; i<features.length; i++) {
- if (features[i].getFeatureGroup().equals(PDBChain.PDBFILEFEATURE)) {
- SequenceFeature tx = new SequenceFeature(features[i]);
- tx.setBegin(1+((Atom)((Residue)residues.elementAt(tx.getBegin()-offset)).atoms.elementAt(0)).alignmentMapping);
- tx.setEnd(1+((Atom)((Residue)residues.elementAt(tx.getEnd()-offset)).atoms.elementAt(0)).alignmentMapping);
- tx.setStatus(status+((tx.getStatus()==null || tx.getStatus().length()==0) ? "" : ":"+tx.getStatus()));
- seq.getDatasetSequence().addSequenceFeature(tx);
- }
+ if (status==null)
+ status = PDBChain.IEASTATUS;
+ SequenceFeature[] features = sequence.getSequenceFeatures();
+ for (int i=0; i<features.length; i++) {
+ if (features[i].getFeatureGroup().equals(PDBChain.PDBFILEFEATURE)) {
+ SequenceFeature tx = new SequenceFeature(features[i]);
+ tx.setBegin(1+((Atom)((Residue)residues.elementAt(tx.getBegin()-offset)).atoms.elementAt(0)).alignmentMapping);
+ tx.setEnd(1+((Atom)((Residue)residues.elementAt(tx.getEnd()-offset)).atoms.elementAt(0)).alignmentMapping);
+ tx.setStatus(status+((tx.getStatus()==null || tx.getStatus().length()==0) ? "" : ":"+tx.getStatus()));
+ seq.addSequenceFeature(tx);