X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=0434aac9b8ca38fae132e7133286f8e3af6c967a;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=35e0ea528872ec706ed2384ce077ea3ad6c71e5a;hpb=d98019da2b9c4babbd0d981579a90adf11e9911a;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 35e0ea5..0434aac 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,64 +1,203 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.structure;
 
-import java.io.*;
-import java.util.*;
-
-import MCview.*;
-import jalview.analysis.*;
-import jalview.api.AlignmentViewPanel;
+import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MessageManager;
+
+import java.io.PrintStream;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.IdentityHashMap;
+import java.util.Vector;
+
+import MCview.Atom;
+import MCview.PDBChain;
 
 public class StructureSelectionManager
 {
-  static IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager> instances;
+  static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
 
   StructureMapping[] mappings;
 
+  private boolean processSecondaryStructure = false,
+          secStructServices = false, addTempFacAnnot = false;
+
+  /**
+   * @return true if will try to use external services for processing secondary
+   *         structure
+   */
+  public boolean isSecStructServices()
+  {
+    return secStructServices;
+  }
+
+  /**
+   * control use of external services for processing secondary structure
+   * 
+   * @param secStructServices
+   */
+  public void setSecStructServices(boolean secStructServices)
+  {
+    this.secStructServices = secStructServices;
+  }
+
+  /**
+   * flag controlling addition of any kind of structural annotation
+   * 
+   * @return true if temperature factor annotation will be added
+   */
+  public boolean isAddTempFacAnnot()
+  {
+    return addTempFacAnnot;
+  }
+
+  /**
+   * set flag controlling addition of structural annotation
+   * 
+   * @param addTempFacAnnot
+   */
+  public void setAddTempFacAnnot(boolean addTempFacAnnot)
+  {
+    this.addTempFacAnnot = addTempFacAnnot;
+  }
+
+  /**
+   * 
+   * @return if true, the structure manager will attempt to add secondary
+   *         structure lines for unannotated sequences
+   */
+
+  public boolean isProcessSecondaryStructure()
+  {
+    return processSecondaryStructure;
+  }
+
+  /**
+   * Control whether structure manager will try to annotate mapped sequences
+   * with secondary structure from PDB data.
+   * 
+   * @param enable
+   */
+  public void setProcessSecondaryStructure(boolean enable)
+  {
+    processSecondaryStructure = enable;
+  }
+
   /**
    * debug function - write all mappings to stdout
    */
-  public void reportMapping() {
-    if (mappings==null)
-    {
-      System.err.println("reportMapping: No PDB/Sequence mappings.");
-    }else{
-      System.err.println("reportMapping: There are "+mappings.length+" mappings.");
-      for (int m=0;m<mappings.length;m++)
-      {
-        System.err.println("mapping "+m+" : "+mappings[m].pdbfile);
-      }
-    }
-  }
-  Hashtable mappingData = new Hashtable();
-
-  public static StructureSelectionManager getStructureSelectionManager(StructureSelectionManagerProvider context)
+  public void reportMapping()
+  {
+    if (mappings == null)
+    {
+      System.err.println("reportMapping: No PDB/Sequence mappings.");
+    }
+    else
+    {
+      System.err.println("reportMapping: There are " + mappings.length
+              + " mappings.");
+      for (int m = 0; m < mappings.length; m++)
+      {
+        System.err.println("mapping " + m + " : " + mappings[m].pdbfile);
+      }
+    }
+  }
+
+  /**
+   * map between the PDB IDs (or structure identifiers) used by Jalview and the
+   * absolute filenames for PDB data that corresponds to it
+   */
+  HashMap<String, String> pdbIdFileName = new HashMap<String, String>(),
+          pdbFileNameId = new HashMap<String, String>();
+
+  public void registerPDBFile(String idForFile, String absoluteFile)
+  {
+    pdbIdFileName.put(idForFile, absoluteFile);
+    pdbFileNameId.put(absoluteFile, idForFile);
+  }
+
+  public String findIdForPDBFile(String idOrFile)
+  {
+    String id = pdbFileNameId.get(idOrFile);
+    return id;
+  }
+
+  public String findFileForPDBId(String idOrFile)
+  {
+    String id = pdbIdFileName.get(idOrFile);
+    return id;
+  }
+
+  public boolean isPDBFileRegistered(String idOrFile)
   {
+    return pdbFileNameId.containsKey(idOrFile)
+            || pdbIdFileName.containsKey(idOrFile);
+  }
+
+  private static StructureSelectionManager nullProvider = null;
+
+  public static StructureSelectionManager getStructureSelectionManager(
+          StructureSelectionManagerProvider context)
+  {
+    if (context == null)
+    {
+      if (nullProvider == null)
+      {
+        if (instances != null)
+        {
+          throw new Error(MessageManager.getString("error.implementation_error_structure_selection_manager_null"),
+                  new NullPointerException(MessageManager.getString("exception.ssm_context_is_null")));
+        }
+        else
+        {
+          nullProvider = new StructureSelectionManager();
+        }
+        return nullProvider;
+      }
+    }
     if (instances == null)
     {
-      instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager>();
+      instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
     }
-    StructureSelectionManager instance=instances.get(context);
-    if (instance==null)
+    StructureSelectionManager instance = instances.get(context);
+    if (instance == null)
     {
-      instances.put(context, instance=new StructureSelectionManager());
+      if (nullProvider != null)
+      {
+        instance = nullProvider;
+      }
+      else
+      {
+        instance = new StructureSelectionManager();
+      }
+      instances.put(context, instance);
     }
     return instance;
   }
@@ -96,6 +235,7 @@ public class StructureSelectionManager
 
   /**
    * register a listener for alignment sequence mouseover events
+   * 
    * @param svl
    */
   public void addStructureViewerListener(Object svl)
@@ -122,9 +262,33 @@ public class StructureSelectionManager
   }
 
   /**
+   * Import structure data and register a structure mapping for broadcasting
+   * colouring, mouseovers and selection events (convenience wrapper).
+   * 
+   * @param sequence
+   *          - one or more sequences to be mapped to pdbFile
+   * @param targetChains
+   *          - optional chain specification for mapping each sequence to pdb
+   *          (may be nill, individual elements may be nill)
+   * @param pdbFile
+   *          - structure data resource
+   * @param protocol
+   *          - how to resolve data from resource
+   * @return null or the structure data parsed as a pdb file
+   */
+  synchronized public MCview.PDBfile 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).
    * 
+   * @param forStructureView
+   *          when true, record the mapping for use in mouseOvers
+   * 
    * @param sequence
    *          - one or more sequences to be mapped to pdbFile
    * @param targetChains
@@ -136,7 +300,8 @@ public class StructureSelectionManager
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
-  synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
+  synchronized public MCview.PDBfile setMapping(boolean forStructureView,
+          SequenceI[] sequence,
           String[] targetChains, String pdbFile, String protocol)
   {
     /*
@@ -144,15 +309,48 @@ public class StructureSelectionManager
      * the tried and tested MCview pdb mapping
      */
     MCview.PDBfile pdb = null;
+    boolean parseSecStr = processSecondaryStructure;
+    if (isPDBFileRegistered(pdbFile))
+    {
+      for (SequenceI sq : sequence)
+      {
+        SequenceI ds = sq;
+        while (ds.getDatasetSequence() != null)
+        {
+          ds = ds.getDatasetSequence();
+        }
+        ;
+        if (ds.getAnnotation() != null)
+        {
+          for (AlignmentAnnotation ala : ds.getAnnotation())
+          {
+            // false if any annotation present from this structure
+            // JBPNote this fails for jmol/chimera view because the *file* is
+            // passed, not the structure data ID -
+            if (MCview.PDBfile.isCalcIdForFile(ala,
+                    findIdForPDBFile(pdbFile)))
+            {
+              parseSecStr = false;
+            }
+          }
+        }
+      }
+    }
     try
     {
-      pdb = new MCview.PDBfile(pdbFile, protocol);
+      pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr,
+              secStructServices, pdbFile, protocol);
+      if (pdb.id != null && pdb.id.trim().length() > 0
+              && AppletFormatAdapter.FILE.equals(protocol))
+      {
+        registerPDBFile(pdb.id.trim(), pdbFile);
+      }
     } catch (Exception ex)
     {
       ex.printStackTrace();
       return null;
     }
-    
+
     String targetChain;
     for (int s = 0; s < sequence.length; s++)
     {
@@ -180,7 +378,9 @@ public class StructureSelectionManager
         }
       }
       else
+      {
         targetChain = "";
+      }
 
       int max = -10;
       AlignSeq maxAlignseq = null;
@@ -189,16 +389,17 @@ public class StructureSelectionManager
       boolean first = true;
       for (int i = 0; i < pdb.chains.size(); i++)
       {
-        PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
-        if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain)
+        PDBChain chain = (pdb.chains.elementAt(i));
+        if (targetChain.length() > 0 && !targetChain.equals(chain.id)
+                && !infChain)
         {
           continue; // don't try to map chains don't match.
         }
         // TODO: correctly determine sequence type for mixed na/peptide
         // structures
         AlignSeq as = new AlignSeq(sequence[s],
-                ((PDBChain) pdb.chains.elementAt(i)).sequence,
-                ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+                pdb.chains.elementAt(i).sequence,
+                pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
                         : AlignSeq.PEP);
         as.calcScoreMatrix();
         as.traceAlignment();
@@ -224,11 +425,13 @@ public class StructureSelectionManager
               + maxChain.residues.size() + "\n\n");
       PrintStream ps = new PrintStream(System.out)
       {
+        @Override
         public void print(String x)
         {
           mappingDetails.append(x);
         }
 
+        @Override
         public void println()
         {
           mappingDetails.append("\n");
@@ -244,12 +447,16 @@ public class StructureSelectionManager
               + (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
 
       maxChain.makeExactMapping(maxAlignseq, sequence[s]);
-
+      jalview.datamodel.Mapping sqmpping = maxAlignseq
+              .getMappingFromS1(false);
+      jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
+              sqmpping.getMap().getInverse());
       maxChain.transferRESNUMFeatures(sequence[s], null);
 
       // allocate enough slots to store the mapping from positions in
       // sequence[s] to the associated chain
-      int[][] mapping = new int[sequence[s].findPosition(sequence[s].getLength()) + 2][2];
+      int[][] mapping = new int[sequence[s].findPosition(sequence[s]
+              .getLength()) + 2][2];
       int resNum = -10000;
       int index = 0;
 
@@ -266,24 +473,30 @@ public class StructureSelectionManager
         index++;
       } while (index < maxChain.atoms.size());
 
-      if (mappings == null)
+      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
       {
-        mappings = new StructureMapping[1];
+        pdbFile = "INLINE" + pdb.id;
       }
-      else
+      StructureMapping newMapping = new StructureMapping(sequence[s],
+              pdbFile, pdb.id, maxChainId, mapping,
+              mappingDetails.toString());
+      if (forStructureView)
       {
-        StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
-        System.arraycopy(mappings, 0, tmp, 0, mappings.length);
-        mappings = tmp;
-      }
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
-        pdbFile = "INLINE" + pdb.id;
+        if (mappings == null)
+        {
+          mappings = new StructureMapping[1];
+        }
+        else
+        {
+          StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
+          System.arraycopy(mappings, 0, tmp, 0, mappings.length);
+          mappings = tmp;
+        }
 
-      mappings[mappings.length - 1] = new StructureMapping(sequence[s],
-              pdbFile, pdb.id, maxChainId, mapping,
-              mappingDetails.toString());
-      maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
+        mappings[mappings.length - 1] = newMapping;
+      }
+      maxChain.transferResidueAnnotation(newMapping, sqmpping);
     }
     // ///////
 
@@ -295,24 +508,26 @@ public class StructureSelectionManager
     listeners.removeElement(svl);
     if (svl instanceof SequenceListener)
     {
-      for (int i=0;i<listeners.size();i++)
+      for (int i = 0; i < listeners.size(); i++)
       {
         if (listeners.elementAt(i) instanceof StructureListener)
         {
-          ((StructureListener)listeners.elementAt(i)).releaseReferences(svl);
+          ((StructureListener) listeners.elementAt(i))
+                  .releaseReferences(svl);
         }
       }
     }
-      
+
     if (pdbfiles == null)
     {
       return;
     }
-    boolean removeMapping = true;
     String[] handlepdbs;
     Vector pdbs = new Vector();
     for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
+    {
       ;
+    }
     StructureListener sl;
     for (int i = 0; i < listeners.size(); i++)
     {
@@ -349,7 +564,7 @@ public class StructureSelectionManager
 
   public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
   {
-    if (listeners==null)
+    if (listeners == null)
     {
       // old or prematurely sent event
       return;
@@ -398,13 +613,15 @@ public class StructureSelectionManager
         }
       }
     }
-    if (results!=null)
+    if (results != null)
     {
       for (int i = 0; i < listeners.size(); i++)
       {
         Object li = listeners.elementAt(i);
         if (li instanceof SequenceListener)
+        {
           ((SequenceListener) li).highlightSequence(results);
+        }
       }
     }
   }
@@ -428,13 +645,15 @@ public class StructureSelectionManager
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
     if (index == -1)
+    {
       index = seq.findPosition(indexpos);
+    }
     StructureListener sl;
     int atomNo = 0;
     for (int i = 0; i < listeners.size(); i++)
     {
-      Object listener=listeners.elementAt(i);
-      if (listener==source)
+      Object listener = listeners.elementAt(i);
+      if (listener == source)
       {
         continue;
       }
@@ -498,12 +717,10 @@ public class StructureSelectionManager
           }
           if (hasSequenceListeners)
           {
-            ((SequenceListener) listener)
-                    .highlightSequence(results);
+            ((SequenceListener) listener).highlightSequence(results);
           }
         }
-        else if (listener instanceof VamsasListener
-                && !handlingVamsasMo)
+        else if (listener instanceof VamsasListener && !handlingVamsasMo)
         {
           // DEBUG
           // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
@@ -511,11 +728,12 @@ public class StructureSelectionManager
           // index);
           // pass the mouse over and absolute position onto the
           // VamsasListener(s)
-          ((VamsasListener) listener).mouseOver(seq,
-                  indexpos, source);
+          ((VamsasListener) listener).mouseOver(seq, indexpos, source);
         }
-        else if(listener instanceof SecondaryStructureListener){
-        	((SecondaryStructureListener) listener).mouseOverSequence(seq,indexpos);
+        else if (listener instanceof SecondaryStructureListener)
+        {
+          ((SecondaryStructureListener) listener).mouseOverSequence(seq,
+                  indexpos);
         }
       }
     }
@@ -647,9 +865,13 @@ public class StructureSelectionManager
           AlignedCodonFrame[] codonFrames)
   {
     if (!add && (seqmappings == null || seqmappings.size() == 0))
+    {
       return;
+    }
     if (seqmappings == null)
+    {
       seqmappings = new Vector();
+    }
     if (codonFrames != null && codonFrames.length > 0)
     {
       for (int cf = 0; cf < codonFrames.length; cf++)
@@ -687,8 +909,10 @@ public class StructureSelectionManager
             int[] nsr = new int[(seqmappingrefs == null) ? 1
                     : seqmappingrefs.length + 1];
             if (seqmappingrefs != null && seqmappingrefs.length > 0)
+            {
               System.arraycopy(seqmappingrefs, 0, nsr, 0,
                       seqmappingrefs.length);
+            }
             nsr[(seqmappingrefs == null) ? 0 : seqmappingrefs.length] = 1;
             seqmappingrefs = nsr;
           }
@@ -744,19 +968,21 @@ public class StructureSelectionManager
       }
     }
   }
-  
-  Vector<AlignmentViewPanelListener> view_listeners=new Vector<AlignmentViewPanelListener>();
-  public synchronized void sendViewPosition(jalview.api.AlignmentViewPanel source, int startRes,
-          int endRes, int startSeq, int endSeq)
+
+  Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
+
+  public synchronized void sendViewPosition(
+          jalview.api.AlignmentViewPanel source, int startRes, int endRes,
+          int startSeq, int endSeq)
   {
 
     if (view_listeners != null && view_listeners.size() > 0)
     {
-      Enumeration<AlignmentViewPanelListener> listeners = view_listeners.elements();
+      Enumeration<AlignmentViewPanelListener> listeners = view_listeners
+              .elements();
       while (listeners.hasMoreElements())
       {
-        AlignmentViewPanelListener slis = listeners
-                .nextElement();
+        AlignmentViewPanelListener slis = listeners.nextElement();
         if (slis != source)
         {
           slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
@@ -765,39 +991,41 @@ public class StructureSelectionManager
       }
     }
   }
-  
 
-  public void finalize() throws Throwable {
-    if (listeners!=null) {
+  public void finalize() throws Throwable
+  {
+    if (listeners != null)
+    {
       listeners.clear();
-      listeners=null;
+      listeners = null;
     }
-    if (mappingData!=null)
+    if (pdbIdFileName != null)
     {
-      mappingData.clear();
-      mappingData=null;
+      pdbIdFileName.clear();
+      pdbIdFileName = null;
     }
-    if (sel_listeners!=null)
+    if (sel_listeners != null)
     {
       sel_listeners.clear();
-      sel_listeners=null;
+      sel_listeners = null;
     }
-    if (view_listeners!=null)
+    if (view_listeners != null)
     {
       view_listeners.clear();
-      view_listeners=null;
+      view_listeners = null;
     }
-    mappings=null;
-    seqmappingrefs=null;
+    mappings = null;
+    seqmappingrefs = null;
   }
 
   /**
    * release all references associated with this manager provider
+   * 
    * @param jalviewLite
    */
   public static void release(StructureSelectionManagerProvider jalviewLite)
   {
-//    synchronized (instances)
+    // synchronized (instances)
     {
       if (instances == null)
       {
@@ -818,4 +1046,13 @@ public class StructureSelectionManager
     }
   }
 
+  public void registerPDBEntry(PDBEntry pdbentry)
+  {
+    if (pdbentry.getFile() != null
+            && pdbentry.getFile().trim().length() > 0)
+    {
+      registerPDBFile(pdbentry.getId(), pdbentry.getFile());
+    }
+  }
+
 }