}
/**
- * copy over the RESNUM seqfeatures from the internal chain sequence to the
+ * Copies over the RESNUM seqfeatures from the internal chain sequence to the
* mapped sequence
*
* @param seq
* @param status
* The Status of the transferred annotation
- * @return the features added to sq (or its dataset)
*/
- public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
+ public void transferRESNUMFeatures(SequenceI seq,
String status)
{
SequenceI sq = seq;
sq = sq.getDatasetSequence();
if (sq == sequence)
{
- return null;
+ return;
}
}
- /**
+
+ /*
* Remove any existing features for this chain if they exist ?
* SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
* totfeat=seqsfeatures.length; // Remove any features for this exact chain
{
status = PDBChain.IEASTATUS;
}
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (features == null)
- {
- return null;
- }
- for (int i = 0; i < features.length; i++)
+
+ List<SequenceFeature> features = sequence.getSequenceFeatures();
+ for (SequenceFeature feature : features)
{
- if (features[i].getFeatureGroup() != null
- && features[i].getFeatureGroup().equals(pdbid))
+ if (feature.getFeatureGroup() != null
+ && feature.getFeatureGroup().equals(pdbid))
{
- int newBegin = 1 + residues.elementAt(features[i].getBegin()
- - offset).atoms
+ int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms
.elementAt(0).alignmentMapping;
- int newEnd = 1 + residues.elementAt(features[i].getEnd() - offset).atoms
+ int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
.elementAt(0).alignmentMapping;
- SequenceFeature tx = new SequenceFeature(features[i], newBegin,
- newEnd, features[i].getFeatureGroup());
+ SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
+ feature.getFeatureGroup(), feature.getScore());
tx.setStatus(status
+ ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
: ":" + tx.getStatus()));
}
}
}
- return features;
}
/**
&& !residues.isEmpty()
&& residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber)
{
- SequenceFeature sf = new SequenceFeature("INSERTION",
- currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid
- + id, "", offset + count - 1, offset + count - 1,
- "PDB_INS");
+ String desc = currAtom.resName + ":" + currAtom.resNumIns + " "
+ + pdbid + id;
+ SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset
+ + count - 1, offset + count - 1, "PDB_INS");
resFeatures.addElement(sf);
residues.lastElement().atoms.addAll(resAtoms);
}
else
{
-
// Make a new Residue object with the new atoms vector
residues.addElement(new Residue(resAtoms, resNumber - 1, count));
Residue tmpres = residues.lastElement();
Atom tmpat = tmpres.atoms.get(0);
// Make A new SequenceFeature for the current residue numbering
- SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, tmpat.resName
- + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
- + count, offset + count, pdbid);
+ String desc = tmpat.resName
+ + ":" + tmpat.resNumIns + " " + pdbid + id;
+ SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
+ offset + count, offset + count, pdbid);
resFeatures.addElement(sf);
resAnnotation.addElement(new Annotation(tmpat.tfactor));
// Keep totting up the sequence