normalised logo rendering (JAL-958)

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9b91255..94a7848 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -711,6 +711,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showGroupConservation.setSelected(av.showGroupConservation);
     showConsensusHistogram.setSelected(av.showConsensusHistogram);
     showSequenceLogo.setSelected(av.showSequenceLogo);
+    normaliseSequenceLogo.setSelected(av.normaliseSequenceLogo);
+    
     setColourSelected(ColourSchemeProperty.getColourName(av
             .getGlobalColourScheme()));
 
@@ -5041,7 +5043,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setShowSequenceLogo(showSequenceLogo.getState());
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
-
+  protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
   {
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());