X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=fb96b2218eb06e0db036eae5bbe9798009128f41;hb=4eb1ed22600411fe5b6e9ac93084b45429ccfad6;hp=2f81ec4786ef3a07876ab8d5f36a33c03365d45c;hpb=c926361b2442081210826ee47b6f223a9e19434a;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 2f81ec4..fb96b22 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -34,6 +34,7 @@ import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
 import jalview.gui.IProgressIndicator;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.ws.sifts.SiftsClient;
@@ -319,12 +320,13 @@ public class StructureSelectionManager
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
-  synchronized public PDBfile setMapping(SequenceI[] sequence,
+  synchronized public StructureFile setMapping(SequenceI[] sequence,
           String[] targetChains, String pdbFile, String protocol)
   {
     return setMapping(true, sequence, targetChains, pdbFile, protocol);
   }
 
+
   /**
    * create sequence structure mappings between each sequence and the given
    * pdbFile (retrieved via the given protocol).
@@ -343,7 +345,7 @@ public class StructureSelectionManager
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
-  synchronized public PDBfile setMapping(boolean forStructureView,
+  synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
           String pdbFile,
           String protocol)
@@ -378,17 +380,26 @@ public class StructureSelectionManager
         }
       }
     }
-    PDBfile pdb = null;
+    StructureFile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-      pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
-              pdbFile, protocol);
 
-      if (pdb.id != null && pdb.id.trim().length() > 0
+      if (pdbFile != null && isCIFFile(pdbFile))
+      {
+        pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
+                secStructServices, pdbFile, protocol);
+      }
+      else
+      {
+        pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
+                pdbFile, protocol);
+      }
+
+      if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && AppletFormatAdapter.FILE.equals(protocol))
       {
-        registerPDBFile(pdb.id.trim(), pdbFile);
+        registerPDBFile(pdb.getId().trim(), pdbFile);
       }
     } catch (Exception ex)
     {
@@ -449,7 +460,7 @@ public class StructureSelectionManager
       String maxChainId = " ";
       PDBChain maxChain = null;
       boolean first = true;
-      for (PDBChain chain : pdb.chains)
+      for (PDBChain chain : pdb.getChains())
       {
         if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
                 && !infChain)
@@ -483,36 +494,74 @@ public class StructureSelectionManager
 
       if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
       {
-        pdbFile = "INLINE" + pdb.id;
+        pdbFile = "INLINE" + pdb.getId();
       }
 
       ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
       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 = 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);
+            maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+          } 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);
+          }
         }
         else
         {
-          for (PDBChain chain : pdb.chains)
+          ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+          for (PDBChain chain : pdb.getChains())
+          {
+            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())
           {
-            StructureMapping mapping = getStructureMapping(seq, pdbFile,
-                    chain.id, pdb, chain, sqmpping, maxAlignseq);
-            seqToStrucMapping.add(mapping);
+            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));
       }
@@ -525,36 +574,37 @@ public class StructureSelectionManager
     return pdb;
   }
 
+  private boolean isCIFFile(String filename)
+  {
+    String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
+            filename.length());
+    return "cif".equalsIgnoreCase(fileExt);
+  }
+
   private StructureMapping getStructureMapping(SequenceI seq,
-          String pdbFile, String targetChainId, PDBfile pdb,
+          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
+      {
       PDBChain chain = pdb.findChain(targetChainId);
       if (chain != null)
       {
         chain.transferResidueAnnotation(curChainMapping, sqmpping);
       }
+      } catch (Exception e)
+      {
+        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,
           String pdbFile,
-          String maxChainId, PDBChain maxChain, PDBfile pdb,
+          String maxChainId, PDBChain maxChain, StructureFile pdb,
           AlignSeq maxAlignseq)
   {
     final StringBuilder mappingDetails = new StringBuilder(128);
@@ -626,7 +676,7 @@ public class StructureSelectionManager
     } while (index < maxChain.atoms.size());
 
     StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
-            pdb.id, maxChainId, mapping, mappingDetails.toString());
+            pdb.getId(), maxChainId, mapping, mappingDetails.toString());
     maxChain.transferResidueAnnotation(nwMapping, sqmpping);
     return nwMapping;
   }
@@ -856,7 +906,10 @@ 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)
         {
@@ -1263,6 +1316,10 @@ public class StructureSelectionManager
 
   public void setProgressBar(String message)
   {
+    if (progressIndicator == null)
+    {
+      return;
+    }
     progressIndicator.setProgressBar(message, progressSessionId);
   }