X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=478706a74f6c98d7c970b36ed50552362f6dc869;hb=2c6965c96b057296981403f3394a4c180ed60ea4;hp=d36d0095cfc3746a20659488ce494be6deaacd3a;hpb=40ecea964afaaf404465d75873ec915b901117a3;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index d36d009..478706a 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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.
+ * 
+ * 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/>.
  */
 package jalview.structure;
 
@@ -259,6 +258,7 @@ public class StructureSelectionManager
 
   public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
   {
+    boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
     for (int i = 0; i < listeners.size(); i++)
     {
@@ -267,38 +267,61 @@ public class StructureSelectionManager
         if (results == null)
         {
           results = new SearchResults();
-
-          for (int j = 0; j < mappings.length; j++)
+        }
+        int indexpos;
+        for (int j = 0; j < mappings.length; j++)
+        {
+          if (mappings[j].pdbfile.equals(pdbfile)
+                  && mappings[j].pdbchain.equals(chain))
           {
-            if (mappings[j].pdbfile.equals(pdbfile)
-                    && mappings[j].pdbchain.equals(chain))
+            indexpos = mappings[j].getSeqPos(pdbResNum);
+            results.addResult(mappings[j].sequence, indexpos, indexpos);
+            // construct highlighted sequence list
+            if (seqmappings != null)
             {
-              results.addResult(mappings[j].sequence, mappings[j]
-                      .getSeqPos(pdbResNum), mappings[j]
-                      .getSeqPos(pdbResNum));
+
+              Enumeration e = seqmappings.elements();
+              while (e.hasMoreElements())
+
+              {
+                ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
+                        mappings[j].sequence, indexpos, results);
+              }
             }
           }
         }
-        if (results.getSize() > 0)
-        {
-          ((SequenceListener) listeners.elementAt(i))
-                  .highlightSequence(results);
-        }
-
+      }
+    }
+    if (results.getSize() > 0)
+    {
+      for (int i = 0; i < listeners.size(); i++)
+      {
+        Object li = listeners.elementAt(i);
+        if (li instanceof SequenceListener)
+          ((SequenceListener) li).highlightSequence(results);
       }
     }
   }
 
   Vector seqmappings = null; // should be a simpler list of mapped seuqence
 
-  // pairs
-
+  /**
+   * highlight regions associated with a position (indexpos) in seq
+   * 
+   * @param seq
+   *          the sequeence that the mouse over occured on
+   * @param indexpos
+   *          the absolute position being mouseovered in seq (0 to seq.length())
+   * @param index
+   *          the sequence position (if -1, seq.findPosition is called to
+   *          resolve the residue number)
+   */
   public void mouseOverSequence(SequenceI seq, int indexpos, int index)
   {
     boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
     SearchResults results = null;
-    if (index==-1)
-      index=seq.findPosition(indexpos);
+    if (index == -1)
+      index = seq.findPosition(indexpos);
     StructureListener sl;
     int atomNo = 0;
     for (int i = 0; i < listeners.size(); i++)
@@ -309,7 +332,8 @@ public class StructureSelectionManager
 
         for (int j = 0; j < mappings.length; j++)
         {
-          if (mappings[j].sequence == seq || mappings[j].sequence==seq.getDatasetSequence())
+          if (mappings[j].sequence == seq
+                  || mappings[j].sequence == seq.getDatasetSequence())
           {
             atomNo = mappings[j].getAtomNum(index);
 
@@ -326,9 +350,9 @@ public class StructureSelectionManager
         if (relaySeqMappings && hasSequenceListeners
                 && listeners.elementAt(i) instanceof SequenceListener)
         {
-          // DEBUG 
-          //System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
-          //  index);
+          // DEBUG
+          // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
+          // index);
 
           if (results == null)
           {
@@ -337,7 +361,7 @@ public class StructureSelectionManager
             {
               // construct highlighted sequence list
 
-              if (seqmappings!=null)
+              if (seqmappings != null)
               {
                 Enumeration e = seqmappings.elements();
                 while (e.hasMoreElements())
@@ -366,11 +390,14 @@ public class StructureSelectionManager
         else if (listeners.elementAt(i) instanceof VamsasListener
                 && !handlingVamsasMo)
         {
-          // DEBUG 
-          //System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + " " +
+          // DEBUG
+          // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
+          // " +
           // index);
-          // pass the mouse over and absolute position onto the VamsasListener(s)
-          ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, indexpos);
+          // pass the mouse over and absolute position onto the
+          // VamsasListener(s)
+          ((VamsasListener) listeners.elementAt(i))
+                  .mouseOver(seq, indexpos);
         }
       }
     }
@@ -381,23 +408,26 @@ public class StructureSelectionManager
    * handled
    */
   boolean handlingVamsasMo = false;
-  long lastmsg=0;
+
+  long lastmsg = 0;
+
   /**
    * as mouseOverSequence but only route event to SequenceListeners
    * 
    * @param sequenceI
-   * @param position in an alignment sequence
+   * @param position
+   *          in an alignment sequence
    */
   public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
   {
     handlingVamsasMo = true;
-    long msg = sequenceI.hashCode()*(1+position);
-    if (lastmsg!=msg)
+    long msg = sequenceI.hashCode() * (1 + position);
+    if (lastmsg != msg)
     {
       lastmsg = msg;
       mouseOverSequence(sequenceI, position, -1);
     }
-      handlingVamsasMo = false;
+    handlingVamsasMo = false;
   }
 
   public Annotation[] colourSequenceFromStructure(SequenceI seq,
@@ -415,9 +445,10 @@ public class StructureSelectionManager
      * 
      * for (int j = 0; j < mappings.length; j++) {
      * 
-     * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid) &&
-     * mappings[j].pdbfile.equals(sl.getPdbFile())) { System.out.println(pdbid+"
-     * "+mappings[j].getPdbId() +" "+mappings[j].pdbfile);
+     * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
+     * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
+     * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
+     * "+mappings[j].pdbfile);
      * 
      * java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
      * if(jalview.util.Comparison.isGap(seq.getCharAt(index))) continue;
@@ -554,4 +585,42 @@ public class StructureSelectionManager
   {
     modifySeqMappingList(true, codonFrames);
   }
+
+  Vector sel_listeners = new Vector();
+
+  public void addSelectionListener(SelectionListener selecter)
+  {
+    if (!sel_listeners.contains(selecter))
+    {
+      sel_listeners.addElement(selecter);
+    }
+  }
+
+  public void removeSelectionListener(SelectionListener toremove)
+  {
+    if (sel_listeners.contains(toremove))
+    {
+      sel_listeners.removeElement(toremove);
+    }
+  }
+
+  public synchronized void sendSelection(
+          jalview.datamodel.SequenceGroup selection,
+          jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+  {
+    if (sel_listeners != null && sel_listeners.size() > 0)
+    {
+      Enumeration listeners = sel_listeners.elements();
+      while (listeners.hasMoreElements())
+      {
+        SelectionListener slis = ((SelectionListener) listeners
+                .nextElement());
+        if (slis != source)
+        {
+          slis.selection(selection, colsel, source);
+        }
+        ;
+      }
+    }
+  }
 }