2.5.1 release branding

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index e12e3ab..7a5333d 100644 (file)
--- 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 2.5.1)
+ * 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;
 
@@ -134,8 +133,10 @@ public class StructureSelectionManager
 
       for (int i = 0; i < pdb.chains.size(); i++)
       {
+        
+        // TODO: correctly determine sequence type for mixed na/peptide structures
         AlignSeq as = new AlignSeq(sequence[s], ((PDBChain) pdb.chains
-                .elementAt(i)).sequence, AlignSeq.PEP);
+                .elementAt(i)).sequence, ((PDBChain)pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
         as.calcScoreMatrix();
         as.traceAlignment();
         PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
@@ -278,9 +279,9 @@ public class StructureSelectionManager
             indexpos = mappings[j].getSeqPos(pdbResNum);
             results.addResult(mappings[j].sequence, indexpos, indexpos);
             // construct highlighted sequence list
-            if (seqmappings!=null)
+            if (seqmappings != null)
             {
-              
+
               Enumeration e = seqmappings.elements();
               while (e.hasMoreElements())
 
@@ -310,13 +311,12 @@ public class StructureSelectionManager
    * highlight regions associated with a position (indexpos) in seq
    * 
    * @param seq
-   *                the sequeence that the mouse over occured on
+   *          the sequeence that the mouse over occured on
    * @param indexpos
-   *                the absolute position being mouseovered in seq (0 to
-   *                seq.length())
+   *          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)
+   *          the sequence position (if -1, seq.findPosition is called to
+   *          resolve the residue number)
    */
   public void mouseOverSequence(SequenceI seq, int indexpos, int index)
   {
@@ -418,7 +418,7 @@ public class StructureSelectionManager
    * 
    * @param sequenceI
    * @param position
-   *                in an alignment sequence
+   *          in an alignment sequence
    */
   public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
   {
@@ -447,9 +447,10 @@ 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;
@@ -586,4 +587,42 @@ 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);
+        }
+        ;
+      }
+    }
+  }
 }