.getMappingFromS1(false);
if (targetChainId != null && !targetChainId.trim().isEmpty())
{
- StructureMapping mapping = getStructureMapping(seq, pdbFile,
- targetChainId, pdb, maxChain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(mapping);
+ StructureMapping mapping;
+ try
+ {
+ mapping = getStructureMapping(seq, pdbFile, targetChainId, pdb,
+ maxChain, sqmpping, maxAlignseq);
+ seqToStrucMapping.add(mapping);
+ } catch (SiftsException e)
+ {
+ // e.printStackTrace();
+ // fall back to NW alignment
+ System.err.println(e.getMessage());
+ seqToStrucMapping.add(getNWMappings(seq, pdbFile,
+ targetChainId,
+ maxChain, pdb, maxAlignseq));
+ }
}
else
{
- for (PDBChain chain : pdb.getChains())
+ try
{
- StructureMapping mapping = getStructureMapping(seq, pdbFile,
- chain.id, pdb, chain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(mapping);
+ ArrayList<StructureMapping> tempMapping = new ArrayList<StructureMapping>();
+ for (PDBChain chain : pdb.getChains())
+ {
+ StructureMapping mapping = getStructureMapping(seq, pdbFile,
+ chain.id, pdb, chain, sqmpping, maxAlignseq);
+ tempMapping.add(mapping);
+ }
+ seqToStrucMapping.addAll(tempMapping);
+ } catch (SiftsException e)
+ {
+ // e.printStackTrace();
+ // fall back to NW alignment
+ System.err.println(e.getMessage());
+ seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
+ maxChain, pdb, maxAlignseq));
}
}
}
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq)
+ AlignSeq maxAlignseq) throws SiftsException
{
- String maxChainId = targetChainId;
- try
- {
StructureMapping curChainMapping = siftsClient
.getSiftsStructureMapping(seq, pdbFile, targetChainId);
try
e.printStackTrace();
}
return curChainMapping;
- } catch (SiftsException e)
- {
- System.err.println(e.getMessage());
- System.err.println(">>> Now switching mapping with NW alignment...");
- setProgressBar(null);
- setProgressBar(">>> Now switching mapping with NW alignment...");
- return getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb,
- maxAlignseq);
- }
}
private StructureMapping getNWMappings(SequenceI seq,