* final count of chain mappings discovered
*/
int chainmaps = 0;
+ // JBPNote: JAL-2693 - this should be a list of chain mappings per
+ // [pdbentry][sequence]
String[][] newchains = new String[pdbEntry.length][];
int pe = 0;
for (PDBEntry pdb : pdbEntry)
String chain = (chains != null && chains[pe] != null)
? chains[pe][se]
: null;
- SequenceI sq = asq.getDatasetSequence();
+ SequenceI sq = (asq.getDatasetSequence() == null) ? asq
+ : asq.getDatasetSequence();
if (sq.getAllPDBEntries() != null)
{
for (PDBEntry pdbentry : sq.getAllPDBEntries())