JAL-958 normalise logo menu options in applet

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

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 5393b07..03b4ed1 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -505,7 +505,27 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
                 }
               });
+              
               popup.add(cprofl);
+              final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+                      "Normalise Group Logo", aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+              cprofn.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  aaa.groupRef.setshowSequenceLogo(true);
+                  aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(cprofn);
             }
             else
             {
@@ -522,6 +542,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // can be
                   // updated.
                   av.setShowConsensusHistogram(chist.getState());
+                  ap.alignFrame.showConsensusHistogram.setState(chist.getState()); // TODO: implement ap.updateGUI()/alignFrame.updateGUI for applet
                   ap.repaint();
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
                 }
@@ -540,11 +561,32 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // can be
                   // updated.
                   av.setShowSequenceLogo(cprof.getState());
+                  ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO: implement ap.updateGUI()/alignFrame.updateGUI for applet
                   ap.repaint();
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
                 }
               });
               popup.add(cprof);
+              final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+                      "Normalise Logo", av.isNormaliseSequenceLogo());
+              cprofn.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  av.setShowSequenceLogo(true);
+                  ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO: implement ap.updateGUI()/alignFrame.updateGUI for applet
+                  av.setNormaliseSequenceLogo(cprofn.getState());
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(cprofn);
             }
 
             item = new MenuItem(COPYCONS_SEQ);