resolved merge conflict

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 7b103be..59f37d9 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -31,13 +31,15 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 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.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.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;
 import jalview.ws.sifts.SiftsClient;
 import jalview.ws.sifts.SiftsException;
 import jalview.ws.sifts.SiftsSettings;

@@ -48,6 +50,7 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;

+import java.util.Hashtable;

 import java.util.IdentityHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.IdentityHashMap;
 import java.util.List;
 import java.util.Map;

@@ -77,6 +80,7 @@ public class StructureSelectionManager
 
   private long progressSessionId;
 
 
   private long progressSessionId;
 

+

   /*
    * Set of any registered mappings between (dataset) sequences.
    */
   /*
    * Set of any registered mappings between (dataset) sequences.
    */

@@ -86,6 +90,8 @@ public class StructureSelectionManager
 
   private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
 
 
   private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
 

+  private Map<String, String> phyre2ModelTemplates = new Hashtable<String, String>();
+

   /**
    * @return true if will try to use external services for processing secondary
    *         structure
   /**
    * @return true if will try to use external services for processing secondary
    *         structure

@@ -322,9 +328,11 @@ public class StructureSelectionManager
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(SequenceI[] sequence,
    * @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,
+          IProgressIndicator progress)

   {
   {

-    return setMapping(true, sequence, targetChains, pdbFile, protocol);
+    return computeMapping(true, sequence, targetChains, pdbFile, protocol,
+            progress);

   }
 
 
   }
 
 

@@ -339,7 +347,7 @@ public class StructureSelectionManager
    *          - one or more sequences to be mapped to pdbFile
    * @param targetChainIds
    *          - optional chain specification for mapping each sequence to pdb
    *          - one or more sequences to be mapped to pdbFile
    * @param targetChainIds
    *          - optional chain specification for mapping each sequence to pdb

-   *          (may be nill, individual elements may be nill)
+   *          (may be null, individual elements may be null)

    * @param pdbFile
    *          - structure data resource
    * @param protocol
    * @param pdbFile
    *          - structure data resource
    * @param protocol

@@ -348,9 +356,18 @@ public class StructureSelectionManager
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,

-          String pdbFile,
-          String protocol)
+          String pdbFile, DataSourceType protocol)

   {
   {

+    return computeMapping(forStructureView, sequenceArray, targetChainIds,
+            pdbFile, protocol, null);
+  }
+
+  synchronized public StructureFile computeMapping(
+          boolean forStructureView, SequenceI[] sequenceArray,
+          String[] targetChainIds, String pdbFile, DataSourceType protocol,
+          IProgressIndicator progress)
+  {
+    long progressSessionId = System.currentTimeMillis() * 3;

     /*
      * There will be better ways of doing this in the future, for now we'll use
      * the tried and tested MCview pdb mapping
     /*
      * There will be better ways of doing this in the future, for now we'll use
      * the tried and tested MCview pdb mapping

@@ -388,10 +405,13 @@ public class StructureSelectionManager
       pdb = new JmolParser(pdbFile, protocol);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
       pdb = new JmolParser(pdbFile, protocol);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0

-              && AppletFormatAdapter.FILE.equals(protocol))
+              && DataSourceType.FILE == protocol)

       {
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
       {
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }

+      // if PDBId is unavailable then skip SIFTS mapping execution path
+      isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+

     } catch (Exception ex)
     {
       ex.printStackTrace();
     } catch (Exception ex)
     {
       ex.printStackTrace();

@@ -434,7 +454,7 @@ public class StructureSelectionManager
         {
           if (targetChainId.trim().length() == 0)
           {
         {
           if (targetChainId.trim().length() == 0)
           {

-            targetChainId = " ";
+            targetChainId = StructureMapping.NO_CHAIN;

           }
           else
           {
           }
           else
           {

@@ -454,7 +474,7 @@ public class StructureSelectionManager
        */
       int max = -10;
       AlignSeq maxAlignseq = null;
        */
       int max = -10;
       AlignSeq maxAlignseq = null;

-      String maxChainId = " ";
+      String maxChainId = StructureMapping.NO_CHAIN; // space

       PDBChain maxChain = null;
       boolean first = true;
       for (PDBChain chain : pdb.getChains())
       PDBChain maxChain = null;
       boolean first = true;
       for (PDBChain chain : pdb.getChains())

@@ -489,17 +509,19 @@ public class StructureSelectionManager
         continue;
       }
 
         continue;
       }
 

-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (protocol.equals(DataSourceType.PASTE))

       {
         pdbFile = "INLINE" + pdb.getId();
       }
       {
         pdbFile = "INLINE" + pdb.getId();
       }

-
-      ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
-      if (isMapUsingSIFTs && seq.isProtein())
+      boolean phyre2Template = isPhyre2Template(pdbFile);
+      List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+      if (!phyre2Template && isMapUsingSIFTs && seq.isProtein())

       {
       {

-        setProgressBar(null);
-        setProgressBar(MessageManager
-                .getString("status.obtaining_mapping_with_sifts"));
+        if (progress!=null) {
+          progress.setProgressBar(MessageManager
+                .getString("status.obtaining_mapping_with_sifts"),
+                  progressSessionId);
+        }

         jalview.datamodel.Mapping sqmpping = maxAlignseq
                 .getMappingFromS1(false);
         if (targetChainId != null && !targetChainId.trim().isEmpty())
         jalview.datamodel.Mapping sqmpping = maxAlignseq
                 .getMappingFromS1(false);
         if (targetChainId != null && !targetChainId.trim().isEmpty())

@@ -528,22 +550,27 @@ public class StructureSelectionManager
                                                         // "IEA:Jalview" ?
             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
                                                         // "IEA:Jalview" ?
             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));

+          } catch (Exception e)
+          {
+            e.printStackTrace();

           }
         }
         else
         {
           }
         }
         else
         {

-          ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+          List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();

           for (PDBChain chain : pdb.getChains())
           {
             try
             {
               StructureMapping siftsMapping = getStructureMapping(seq,
           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());
               foundSiftsMappings.add(siftsMapping);
             } catch (SiftsException e)
             {
               System.err.println(e.getMessage());

+            } catch (Exception e)
+            {
+              e.printStackTrace();

             }
           }
           if (!foundSiftsMappings.isEmpty())
             }
           }
           if (!foundSiftsMappings.isEmpty())

@@ -568,11 +595,31 @@ public class StructureSelectionManager
           }
         }
       }
           }
         }
       }

-      else
+      else if (phyre2Template)

       {
         setProgressBar(null);
         setProgressBar(MessageManager
       {
         setProgressBar(null);
         setProgressBar(MessageManager

-                .getString("status.obtaining_mapping_with_nw_alignment"));
+                .getString("status.obtaining_mapping_with_phyre2_template_alignment"));
+        String fastaFile = getPhyre2FastaFileFor(pdbFile);
+        StructureMapping phyre2ModelMapping = new Phyre2Client(pdb)
+                .getStructureMapping(seq, pdbFile, fastaFile,
+                        StructureMapping.NO_CHAIN);
+        seqToStrucMapping.add(phyre2ModelMapping);
+        maxChain.makeExactMapping(maxAlignseq, seq);
+        maxChain.transferRESNUMFeatures(seq, null);
+        jalview.datamodel.Mapping sqmpping = maxAlignseq
+                .getMappingFromS1(false);
+        maxChain.transferResidueAnnotation(phyre2ModelMapping, sqmpping);
+        ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+      }
+      else
+      {
+        if (progress != null)
+        {
+          progress.setProgressBar(MessageManager
+                                  .getString("status.obtaining_mapping_with_nw_alignment"),
+                  progressSessionId);
+        }

         StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                 maxChainId, maxChain, pdb, maxAlignseq);
         seqToStrucMapping.add(nwMapping);
         StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                 maxChainId, maxChain, pdb, maxAlignseq);
         seqToStrucMapping.add(nwMapping);

@@ -588,11 +635,10 @@ public class StructureSelectionManager
     return pdb;
   }
 
     return pdb;
   }
 

-  private boolean isCIFFile(String filename)
+  public void registerPhyre2Template(String phyre2Template,
+          String fastaMappingFile)

   {
   {

-    String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
-            filename.length());
-    return "cif".equalsIgnoreCase(fileExt);
+    phyre2ModelTemplates.put(phyre2Template, fastaMappingFile);

   }
 
   /**
   }
 
   /**

@@ -612,26 +658,25 @@ public class StructureSelectionManager
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
   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);
       }
       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)
   {
           String maxChainId, PDBChain maxChain, StructureFile pdb,
           AlignSeq maxAlignseq)
   {

@@ -741,7 +786,7 @@ public class StructureSelectionManager
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);

-        for (String pdbfile : sl.getPdbFile())
+        for (String pdbfile : sl.getStructureFiles())

         {
           pdbs.remove(pdbfile);
         }
         {
           pdbs.remove(pdbfile);
         }

@@ -806,7 +851,28 @@ public class StructureSelectionManager
       return;
     }
 
       return;
     }
 

-    SearchResults results = new SearchResults();
+    SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms);
+    for (Object li : listeners)
+    {
+      if (li instanceof SequenceListener)
+      {
+        ((SequenceListener) li).highlightSequence(results);
+      }
+    }
+  }
+
+  /**
+   * Constructs a SearchResults object holding regions (if any) in the Jalview
+   * alignment which have a mapping to the structure viewer positions in the
+   * supplied list
+   * 
+   * @param atoms
+   * @return
+   */
+  public SearchResultsI findAlignmentPositionsForStructurePositions(
+          List<AtomSpec> atoms)
+  {
+    SearchResultsI results = new SearchResults();

     for (AtomSpec atom : atoms)
     {
       SequenceI lastseq = null;
     for (AtomSpec atom : atoms)
     {
       SequenceI lastseq = null;

@@ -817,7 +883,7 @@ public class StructureSelectionManager
                 && sm.pdbchain.equals(atom.getChain()))
         {
           int indexpos = sm.getSeqPos(atom.getPdbResNum());
                 && sm.pdbchain.equals(atom.getChain()))
         {
           int indexpos = sm.getSeqPos(atom.getPdbResNum());

-          if (lastipos != indexpos && lastseq != sm.sequence)
+          if (lastipos != indexpos || lastseq != sm.sequence)

           {
             results.addResult(sm.sequence, indexpos, indexpos);
             lastipos = indexpos;
           {
             results.addResult(sm.sequence, indexpos, indexpos);
             lastipos = indexpos;

@@ -831,13 +897,7 @@ public class StructureSelectionManager
         }
       }
     }
         }
       }
     }

-    for (Object li : listeners)
-    {
-      if (li instanceof SequenceListener)
-      {
-        ((SequenceListener) li).highlightSequence(results);
-      }
-    }
+    return results;

   }
 
   /**
   }
 
   /**

@@ -856,7 +916,7 @@ public class StructureSelectionManager
   {
     boolean hasSequenceListeners = handlingVamsasMo
             || !seqmappings.isEmpty();
   {
     boolean hasSequenceListeners = handlingVamsasMo
             || !seqmappings.isEmpty();

-    SearchResults results = null;
+    SearchResultsI results = null;

     if (seqPos == -1)
     {
       seqPos = seq.findPosition(indexpos);
     if (seqPos == -1)
     {
       seqPos = seq.findPosition(indexpos);

@@ -1356,4 +1416,31 @@ public class StructureSelectionManager
     return seqmappings;
   }
 
     return seqmappings;
   }
 

+  public boolean isPhyre2Template(String structureFile)
+  {
+    if (structureFile == null || phyre2ModelTemplates == null
+            || phyre2ModelTemplates.isEmpty())
+    {
+      return false;
+    }
+    return phyre2ModelTemplates.get(structureFile) != null
+            && !phyre2ModelTemplates.get(structureFile).isEmpty();
+  }
+
+  public String getPhyre2FastaFileFor(String structureFile)
+  {
+    return phyre2ModelTemplates.get(structureFile);
+  }
+
+
+  public static StructureSelectionManager getStructureSelectionManager()
+  {
+    return instances.values().iterator().next();
+  }
+
+  public void addStructureMapping(StructureMapping smapping)
+  {
+    mappings.add(smapping);
+  }
+

 }
 }