+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ {
+ // no mapping to gaps in sequence
+ continue;
+ }
+ int t = asp.findPosition(r); // sequence position
+ int apos = mapping[m].getAtomNum(t);
+ int pos = mapping[m].getPDBResNum(t);
+
+ if (pos < 1 || pos == lastPos)
+ {
+ // can't align unmapped sequence
+ continue;
+ }
+ matched[r] = true; // this is a good ite
+ lastPos = pos;
+ // just record this residue position
+ commonrpositions[pdbfnum][r] = pos;
+ }
+ // create model selection suffix
+ isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";
+ if (mapping[m].getChain() == null
+ || mapping[m].getChain().trim().length() == 0)