+ /**
+ * check if we need to extract secondary structure from given pdbFile and
+ * transfer to sequences
+ *
+ * @param pdbFile
+ * @param sequenceArray
+ * @return
+ */
+ private boolean isStructureFileProcessed(String pdbFile,
+ SequenceI[] sequenceArray)
+ {
+ boolean processed = false;
+ if (isPDBFileRegistered(pdbFile))
+ {
+ for (SequenceI sq : sequenceArray)
+ {
+ SequenceI ds = sq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ ;
+ if (ds.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation ala : ds.getAnnotation())
+ {
+ // false if any annotation present from this structure
+ // JBPNote this fails for jmol/chimera view because the *file* is
+ // passed, not the structure data ID -
+ if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
+ {
+ processed = true;
+ }
+ }
+ }
+ }
+ }
+ return processed;
+ }
+
+ public void addStructureMapping(StructureMapping sm)
+ {
+ if (!mappings.contains(sm))
+ {
+ mappings.add(sm);
+ }
+ }
+
+ /**
+ * retrieve a mapping for seq from SIFTs using associated DBRefEntry for
+ * uniprot or PDB
+ *
+ * @param seq
+ * @param pdbFile
+ * @param targetChainId
+ * @param pdb
+ * @param maxChain
+ * @param sqmpping
+ * @param maxAlignseq
+ * @param siftsClient
+ * client for retrieval of SIFTS mappings for this structure
+ * @return
+ * @throws SiftsException
+ */
+ private StructureMapping getStructureMapping(SequenceI seq,
+ String pdbFile, String targetChainId, StructureFile pdb,
+ PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
+ AlignSeq maxAlignseq, SiftsClient siftsClient)
+ throws SiftsException
+ {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+ try
+ {
+ PDBChain chain = pdb.findChain(targetChainId);
+ if (chain != null)
+ {
+ chain.transferResidueAnnotation(curChainMapping, null);
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return curChainMapping;
+ }
+
+ private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
+ String maxChainId, PDBChain maxChain, StructureFile pdb,