single-click highlights, double click selectes th associated group or sequence for...

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 0e766c4..a34f8f5 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -419,12 +419,47 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void mouseClicked(MouseEvent evt)
   {
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    if (SwingUtilities.isLeftMouseButton(evt))
+    {
+      if (selectedRow < aa.length)
+        {
+        if (aa[selectedRow].groupRef!=null)
+        {
+          ap.seqPanel.ap.idPanel.highlightSearchResults(aa[selectedRow].groupRef.getSequences(null));
+          if (evt.getClickCount()>=2)
+          {
+            // todo: make the ap scroll to the selection
+            ap.av.setSelectionGroup(new SequenceGroup(aa[selectedRow].groupRef));
+            ap.paintAlignment(false);
+          }
+          return;
+        } else 
+        if (aa[selectedRow].sequenceRef!=null){
+          Vector sr = new Vector();
+          sr.addElement(aa[selectedRow].sequenceRef);
+          if (evt.getClickCount()==1)
+          {
+          ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+          } else
+            if (evt.getClickCount()>=2)
+          {
+              ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+              SequenceGroup sg = new SequenceGroup();
+            sg.addSequence(aa[selectedRow].sequenceRef,false);
+            ap.av.setSelectionGroup(sg);
+            ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+          }
+          
+        }
+      }
+    }
     if (!SwingUtilities.isRightMouseButton(evt))
     {
       return;
     }
 
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
     JPopupMenu pop = new JPopupMenu("Annotations");
     JMenuItem item = new JMenuItem(ADDNEW);
@@ -461,7 +496,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       pop.addSeparator();
       // av and sequencegroup need to implement same interface for 
       final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-              "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
+              "Ignore Gaps In Consensus", (aa[selectedRow].groupRef!=null) ? aa[selectedRow].groupRef.getIgnoreGapsConsensus() : ap.av.getIgnoreGapsConsensus());
       final AlignmentAnnotation aaa = aa[selectedRow];
       cbmi.addActionListener(new ActionListener()
       {
@@ -469,12 +504,28 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         {
           if (aaa.groupRef!=null)
           {
-            aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+            aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); // TODO: pass on reference to ap so the view can be updated.
+            ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+          } else {
+            ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
           }
-          ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
         }
       });
       pop.add(cbmi);
+      // av and sequencegroup need to implement same interface for 
+      if (aaa.groupRef!=null) {
+        final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+                "Show Full Profile", aa[selectedRow].groupRef.isIncludeAllConsSymbols());
+        cprof.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            aaa.groupRef.setIncludeAllConsSymbols(cprof.getState()); // TODO: pass on reference to ap so the view can be updated.
+            ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+          }
+        });
+        pop.add(cprof);
+      }
       final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
       consclipbrd.addActionListener(this);
       pop.add(consclipbrd);