JAL-2375 JAL-2376 First commit of implementation for Phyre2 result browsing, template...

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 7db85ff..066a6d1 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -31,12 +31,15 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
 import jalview.gui.IProgressIndicator;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.ws.phyre2.Phyre2Client;
 import jalview.ws.sifts.SiftsClient;
 import jalview.ws.sifts.SiftsException;
 import jalview.ws.sifts.SiftsSettings;
@@ -76,6 +79,8 @@ public class StructureSelectionManager
 
   private long progressSessionId;
 
+  private boolean mappingForPhyre2Model;
+
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
@@ -321,12 +326,11 @@ public class StructureSelectionManager
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(SequenceI[] sequence,
-          String[] targetChains, String pdbFile, String protocol)
+          String[] targetChains, String pdbFile, DataSourceType protocol)
   {
     return setMapping(true, sequence, targetChains, pdbFile, protocol);
   }
 
-
   /**
    * create sequence structure mappings between each sequence and the given
    * pdbFile (retrieved via the given protocol).
@@ -341,14 +345,13 @@ public class StructureSelectionManager
    *          (may be nill, individual elements may be nill)
    * @param pdbFile
    *          - structure data resource
-   * @param protocol
+   * @param sourceType
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
-          String pdbFile,
-          String protocol)
+          String pdbFile, DataSourceType sourceType)
   {
     /*
      * There will be better ways of doing this in the future, for now we'll use
@@ -384,14 +387,16 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-        pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
-                secStructServices, pdbFile, protocol);
+      pdb = new JmolParser(pdbFile, sourceType);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
-              && AppletFormatAdapter.FILE.equals(protocol))
+              && DataSourceType.FILE == sourceType)
       {
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
+      // if PDBId is unavailable then skip SIFTS mapping execution path
+      isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -489,13 +494,13 @@ public class StructureSelectionManager
         continue;
       }
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (sourceType == DataSourceType.PASTE)
       {
         pdbFile = "INLINE" + pdb.getId();
       }
 
-      ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
-      if (isMapUsingSIFTs && seq.isProtein())
+      List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+      if (!isMappingForPhyre2Model() && isMapUsingSIFTs && seq.isProtein())
       {
         setProgressBar(null);
         setProgressBar(MessageManager
@@ -528,22 +533,27 @@ public class StructureSelectionManager
                                                         // "IEA:Jalview" ?
             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+          } catch (Exception e)
+          {
+            e.printStackTrace();
           }
         }
         else
         {
-          ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+          List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
           for (PDBChain chain : pdb.getChains())
           {
             try
             {
               StructureMapping siftsMapping = getStructureMapping(seq,
-                      pdbFile,
-                      chain.id, pdb, chain, sqmpping, maxAlignseq);
+                      pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
               foundSiftsMappings.add(siftsMapping);
             } catch (SiftsException e)
             {
               System.err.println(e.getMessage());
+            } catch (Exception e)
+            {
+              e.printStackTrace();
             }
           }
           if (!foundSiftsMappings.isEmpty())
@@ -568,6 +578,17 @@ public class StructureSelectionManager
           }
         }
       }
+      else if (isMappingForPhyre2Model())
+      {
+        setProgressBar(null);
+        setProgressBar(MessageManager
+                .getString("status.obtaining_mapping_with_phyre2_template_alignment"));
+        StructureMapping phyre2ModelMapping = new Phyre2Client(pdb)
+                .getStructureMapping(seq, pdbFile, " ");
+
+        seqToStrucMapping.add(phyre2ModelMapping);
+        ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+      }
       else
       {
         setProgressBar(null);
@@ -612,26 +633,25 @@ public class StructureSelectionManager
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
-          AlignSeq maxAlignseq) throws SiftsException
+          AlignSeq maxAlignseq) throws Exception
   {
-      StructureMapping curChainMapping = siftsClient
-              .getSiftsStructureMapping(seq, pdbFile, targetChainId);
-      try
-      {
+    StructureMapping curChainMapping = siftsClient
+            .getStructureMapping(seq, pdbFile, targetChainId);
+    try
+    {
       PDBChain chain = pdb.findChain(targetChainId);
       if (chain != null)
       {
         chain.transferResidueAnnotation(curChainMapping, sqmpping);
       }
-      } catch (Exception e)
-      {
-        e.printStackTrace();
-      }
-      return curChainMapping;
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    return curChainMapping;
   }
 
-  private StructureMapping getNWMappings(SequenceI seq,
-          String pdbFile,
+  private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
           String maxChainId, PDBChain maxChain, StructureFile pdb,
           AlignSeq maxAlignseq)
   {
@@ -806,7 +826,7 @@ public class StructureSelectionManager
       return;
     }
 
-    SearchResults results = new SearchResults();
+    SearchResultsI results = new SearchResults();
     for (AtomSpec atom : atoms)
     {
       SequenceI lastseq = null;
@@ -856,7 +876,7 @@ public class StructureSelectionManager
   {
     boolean hasSequenceListeners = handlingVamsasMo
             || !seqmappings.isEmpty();
-    SearchResults results = null;
+    SearchResultsI results = null;
     if (seqPos == -1)
     {
       seqPos = seq.findPosition(indexpos);
@@ -1356,4 +1376,15 @@ public class StructureSelectionManager
     return seqmappings;
   }
 
+  public boolean isMappingForPhyre2Model()
+  {
+    return mappingForPhyre2Model;
+  }
+
+  public void setMappingForPhyre2Model(boolean mappingForPhyre2Model)
+  {
+    this.mappingForPhyre2Model = mappingForPhyre2Model;
+  }
+
+
 }