X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=be042e6b6476a7491dc7494d89a138d6771662d9;hb=134291d04042b3d7252598a9f73753f40da08a18;hp=4dff04dff9c90000176f7ce51f7804f27e165c8e;hpb=4316d20b437d529be1d9ddafc0118fadd1b6a4ce;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 4dff04d..be042e6 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -385,7 +385,11 @@ public class StructureSelectionManager
     try
     {
 
-      if (pdbFile != null && isCIFFile(pdbFile))
+      boolean isParseWithJMOL = StructureImportSettings
+              .getDefaultPDBFileParser().equalsIgnoreCase(
+                      StructureImportSettings.StructureParser.JMOL_PARSER
+                              .toString());
+      if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile)))
       {
         pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
                 secStructServices, pdbFile, protocol);
@@ -501,53 +505,67 @@ public class StructureSelectionManager
       if (isMapUsingSIFTs)
       {
         setProgressBar(null);
-        setProgressBar("Obtaining mapping with SIFTS");
+        setProgressBar(MessageManager
+                .getString("status.obtaining_mapping_with_sifts"));
         jalview.datamodel.Mapping sqmpping = maxAlignseq
                 .getMappingFromS1(false);
         if (targetChainId != null && !targetChainId.trim().isEmpty())
         {
-          StructureMapping mapping;
+          StructureMapping siftsMapping;
           try
           {
-            mapping = getStructureMapping(seq, pdbFile, targetChainId, pdb,
-                    maxChain, sqmpping, maxAlignseq);
-            seqToStrucMapping.add(mapping);
+            siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
+                    pdb, maxChain, sqmpping, maxAlignseq);
+            seqToStrucMapping.add(siftsMapping);
+            maxChain.makeExactMapping(maxAlignseq, seq);
+            maxChain.transferRESNUMFeatures(seq, null);
+            maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
           } catch (SiftsException e)
           {
-            // e.printStackTrace();
             // fall back to NW alignment
             System.err.println(e.getMessage());
-            seqToStrucMapping.add(getNWMappings(seq, pdbFile,
-                    targetChainId,
-                    maxChain, pdb, maxAlignseq));
+            StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+                    targetChainId, maxChain, pdb, maxAlignseq);
+            seqToStrucMapping.add(nwMapping);
           }
         }
         else
         {
-          try
+          ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+          for (PDBChain chain : pdb.getChains())
           {
-            ArrayList<StructureMapping> tempMapping = new ArrayList<StructureMapping>();
-            for (PDBChain chain : pdb.getChains())
+            try
             {
-              StructureMapping mapping = getStructureMapping(seq, pdbFile,
+              StructureMapping siftsMapping = getStructureMapping(seq,
+                      pdbFile,
                       chain.id, pdb, chain, sqmpping, maxAlignseq);
-              tempMapping.add(mapping);
+              foundSiftsMappings.add(siftsMapping);
+            } catch (SiftsException e)
+            {
+              System.err.println(e.getMessage());
             }
-            seqToStrucMapping.addAll(tempMapping);
-          } catch (SiftsException e)
+          }
+          if (!foundSiftsMappings.isEmpty())
           {
-            // e.printStackTrace();
-            // fall back to NW alignment
-            System.err.println(e.getMessage());
-            seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
-                    maxChain, pdb, maxAlignseq));
+            seqToStrucMapping.addAll(foundSiftsMappings);
+            maxChain.makeExactMapping(maxAlignseq, seq);
+            maxChain.transferRESNUMFeatures(seq, null);
+            maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
+                    sqmpping);
+          }
+          else
+          {
+            StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+                    maxChainId, maxChain, pdb, maxAlignseq);
+            seqToStrucMapping.add(nwMapping);
           }
         }
       }
       else
       {
         setProgressBar(null);
-        setProgressBar("Obtaining mapping with NW alignment");
+        setProgressBar(MessageManager
+                .getString("status.obtaining_mapping_with_nw_alignment"));
         seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
                 maxChain, pdb, maxAlignseq));
       }