X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=c27289c468bdc1a396b6b78e9cd92cf410c38b3d;hb=3f12f4932226512316ec113e600695150431fd0a;hp=be042e6b6476a7491dc7494d89a138d6771662d9;hpb=ccc31f21ed36c2e43b5a1b450846284151c680bb;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index be042e6..c27289c 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -428,6 +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;
@@ -502,7 +508,7 @@ public class StructureSelectionManager
       }
 
       ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
-      if (isMapUsingSIFTs)
+      if (isMapUsingSIFTs && seq.isProtein())
       {
         setProgressBar(null);
         setProgressBar(MessageManager
@@ -518,8 +524,11 @@ public class StructureSelectionManager
                     pdb, maxChain, sqmpping, maxAlignseq);
             seqToStrucMapping.add(siftsMapping);
             maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, null);
+            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
@@ -527,6 +536,11 @@ public class StructureSelectionManager
             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
@@ -549,15 +563,21 @@ public class StructureSelectionManager
           {
             seqToStrucMapping.addAll(foundSiftsMappings);
             maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, null);
+            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));
           }
         }
       }
@@ -566,8 +586,11 @@ public class StructureSelectionManager
         setProgressBar(null);
         setProgressBar(MessageManager
                 .getString("status.obtaining_mapping_with_nw_alignment"));
-        seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
-                maxChain, pdb, maxAlignseq));
+        StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+                maxChainId, maxChain, pdb, maxAlignseq);
+        seqToStrucMapping.add(nwMapping);
+        ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
       }
 
       if (forStructureView)
@@ -585,6 +608,20 @@ 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,