X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=c27289c468bdc1a396b6b78e9cd92cf410c38b3d;hb=3f12f4932226512316ec113e600695150431fd0a;hp=6bb04abee84dcec1794ed2ff47daf7cdd335fdd0;hpb=86e1bfc3ed99bee91069b3238eb291c3955338d3;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 6bb04ab..c27289c 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);
@@ -424,6 +428,12 @@ public class StructureSelectionManager
     {
       boolean infChain = true;
       final SequenceI seq = sequenceArray[s];
+      SequenceI ds = seq;
+      while (ds.getDatasetSequence() != null)
+      {
+        ds = ds.getDatasetSequence();
+      }
+
       if (targetChainIds != null && targetChainIds[s] != null)
       {
         infChain = false;
@@ -498,34 +508,89 @@ public class StructureSelectionManager
       }
 
       ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
-      if (isMapUsingSIFTs)
+      if (isMapUsingSIFTs && seq.isProtein())
       {
         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 = getStructureMapping(seq, pdbFile,
-                  targetChainId, pdb, maxChain, sqmpping, maxAlignseq);
-          seqToStrucMapping.add(mapping);
+          StructureMapping siftsMapping;
+          try
+          {
+            siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
+                    pdb, maxChain, sqmpping, maxAlignseq);
+            seqToStrucMapping.add(siftsMapping);
+            maxChain.makeExactMapping(maxAlignseq, seq);
+            maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+                                                       // "IEA:SIFTS" ?
+            maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+            ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
+          } catch (SiftsException e)
+          {
+            // fall back to NW alignment
+            System.err.println(e.getMessage());
+            StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+                    targetChainId, maxChain, pdb, maxAlignseq);
+            seqToStrucMapping.add(nwMapping);
+            maxChain.makeExactMapping(maxAlignseq, seq);
+            maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+                                                        // "IEA:Jalview" ?
+            maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+            ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+          }
         }
         else
         {
+          ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
           for (PDBChain chain : pdb.getChains())
           {
-            StructureMapping mapping = getStructureMapping(seq, pdbFile,
-                    chain.id, pdb, chain, sqmpping, maxAlignseq);
-            seqToStrucMapping.add(mapping);
+            try
+            {
+              StructureMapping siftsMapping = getStructureMapping(seq,
+                      pdbFile,
+                      chain.id, pdb, chain, sqmpping, maxAlignseq);
+              foundSiftsMappings.add(siftsMapping);
+            } catch (SiftsException e)
+            {
+              System.err.println(e.getMessage());
+            }
+          }
+          if (!foundSiftsMappings.isEmpty())
+          {
+            seqToStrucMapping.addAll(foundSiftsMappings);
+            maxChain.makeExactMapping(maxAlignseq, seq);
+            maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+                                                       // "IEA:SIFTS" ?
+            maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
+                    sqmpping);
+            ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
+          }
+          else
+          {
+            StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+                    maxChainId, maxChain, pdb, maxAlignseq);
+            seqToStrucMapping.add(nwMapping);
+            maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+                                                        // "IEA:Jalview" ?
+            maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+            ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
           }
         }
       }
       else
       {
         setProgressBar(null);
-        setProgressBar("Obtaining mapping with NW alignment");
-        seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
-                maxChain, pdb, maxAlignseq));
+        setProgressBar(MessageManager
+                .getString("status.obtaining_mapping_with_nw_alignment"));
+        StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+                maxChainId, maxChain, pdb, maxAlignseq);
+        seqToStrucMapping.add(nwMapping);
+        ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
       }
 
       if (forStructureView)
@@ -543,14 +608,25 @@ public class StructureSelectionManager
     return "cif".equalsIgnoreCase(fileExt);
   }
 
+  /**
+   * 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
+   * @return
+   * @throws SiftsException
+   */
   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
@@ -565,15 +641,6 @@ public class StructureSelectionManager
         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,
@@ -880,7 +947,10 @@ public class StructureSelectionManager
     List<AtomSpec> atoms = new ArrayList<AtomSpec>();
     for (StructureMapping sm : mappings)
     {
-      if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence())
+      if (sm.sequence == seq
+              || sm.sequence == seq.getDatasetSequence()
+              || (sm.sequence.getDatasetSequence() != null && sm.sequence
+                      .getDatasetSequence() == seq.getDatasetSequence()))
       {
         for (int index : positions)
         {
@@ -1287,6 +1357,10 @@ public class StructureSelectionManager
 
   public void setProgressBar(String message)
   {
+    if (progressIndicator == null)
+    {
+      return;
+    }
     progressIndicator.setProgressBar(message, progressSessionId);
   }