+ private StructureMapping getStructureMapping(SequenceI seq,
+ String pdbFile, String targetChainId, PDBfile pdb,
+ PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
+ AlignSeq maxAlignseq)
+ {
+ String maxChainId = targetChainId;
+ try
+ {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+ PDBChain chain = pdb.findChain(targetChainId);
+ if (chain != null)
+ {
+ chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ }
+ 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,
+ String pdbFile,