Jalview 2.6 source licence

[jalview.git] / src / jalview / gui / AnnotationLabels.java

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index bf2f152..8605f74 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -454,7 +454,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
             ap.av.setSelectionGroup(// new SequenceGroup(
                     aa[selectedRow].groupRef); // );
+            ap.av.sendSelection();
             ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
           }
           else
           {
@@ -478,6 +480,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             SequenceGroup sg = new SequenceGroup();
             sg.addSequence(aa[selectedRow].sequenceRef, false);
             ap.av.setSelectionGroup(sg);
+            ap.av.sendSelection();
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
           }
@@ -589,10 +592,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             }
           });
           pop.add(chist);
-          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+          final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
                   "Show Group Logo", aa[selectedRow].groupRef
                           .isShowSequenceLogo());
-          cprof.addActionListener(new ActionListener()
+          cprofl.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
             {
@@ -602,12 +605,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               // view
               // can be
               // updated.
-              aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
+              aaa.groupRef.setshowSequenceLogo(cprofl.getState());
               ap.repaint();
               // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
             }
           });
-          pop.add(cprof);
+          pop.add(cprofl);
         }
         else
         {