Merge branch 'develop' into features/JAL-2094_colourInterface

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index a5d9736..7b103be 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -32,6 +32,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
 import jalview.gui.IProgressIndicator;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.StructureFile;
@@ -384,17 +385,7 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-
-      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);
-      }
+      pdb = new JmolParser(pdbFile, protocol);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && AppletFormatAdapter.FILE.equals(protocol))
@@ -424,6 +415,12 @@ 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 +495,89 @@ 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 +595,25 @@ 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 +628,6 @@ 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,