- int resNum = Integer.valueOf(residue.getDbResNum());
- mapping[currSeqIndex][PDB_RES_POS] = Integer.valueOf(resNum);
+ int resNum;
+ try
+ {
+ resNum = (pdbRefDb == null) ? Integer.valueOf(residue
+ .getDbResNum()) : Integer.valueOf(pdbRefDb.getDbResNum());
+ } catch (NumberFormatException nfe)
+ {
+ resNum = (pdbRefDb == null) ? Integer.valueOf(residue
+ .getDbResNum()) : Integer.valueOf(pdbRefDb
+ .getDbResNum().split("[a-zA-Z]")[0]);
+ }
+ try
+ {
+ mapping[currSeqIndex][PDB_RES_POS] = Integer.valueOf(resNum);
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ // do nothing..
+ }