X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=40ab6bbe5693623afdc133f60a2d07c2c6463a8e;hb=06ce849ffedc7ab10a3c54cda96b9a7dec58c136;hp=514d486dc746582ae78b676c7d0d4d42ca1429f8;hpb=ca0a70b02a67f842a195319414d241ffa336656b;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 514d486..40ab6bb 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -845,7 +845,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showReverse.setVisible(nucleotide);
     showReverseComplement.setVisible(nucleotide);
     conservationMenuItem.setEnabled(!nucleotide);
-    modifyConservation.setEnabled(!nucleotide);
+    modifyConservation.setEnabled(!nucleotide
+            && conservationMenuItem.isSelected());
     showGroupConservation.setEnabled(!nucleotide);
 
     showComplementMenuItem.setText(nucleotide ? MessageManager
@@ -876,7 +877,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     padGapsMenuitem.setSelected(av.isPadGaps());
     colourTextMenuItem.setSelected(av.isShowColourText());
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+    modifyPID.setEnabled(abovePIDThreshold.isSelected());
     conservationMenuItem.setSelected(av.getConservationSelected());
+    modifyConservation.setEnabled(conservationMenuItem.isSelected());
     seqLimits.setSelected(av.getShowJVSuffix());
     idRightAlign.setSelected(av.isRightAlignIds());
     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
@@ -3400,41 +3403,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on selecting or deselecting (Colour) By Conservation
    */
   @Override
   protected void conservationMenuItem_actionPerformed()
   {
-    viewport.setConservationSelected(conservationMenuItem.isSelected());
-
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setSelected(false);
+    boolean selected = conservationMenuItem.isSelected();
+    modifyConservation.setEnabled(selected);
+    viewport.setConservationSelected(selected);
 
     changeColour(viewport.getGlobalColourScheme());
-
-    modifyConservation_actionPerformed();
+    if (selected)
+    {
+      modifyConservation_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hideConservationSlider();
+    }
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on selecting or deselecting (Colour) Above PID Threshold
    */
   @Override
   public void abovePIDThreshold_actionPerformed()
   {
-    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
-    conservationMenuItem.setSelected(false);
-    viewport.setConservationSelected(false);
+    boolean selected = abovePIDThreshold.isSelected();
+    modifyPID.setEnabled(selected);
+    viewport.setAbovePIDThreshold(selected);
 
     changeColour(viewport.getGlobalColourScheme());
-
-    modifyPID_actionPerformed();
+    if (selected)
+    {
+      modifyPID_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hidePIDSlider();
+    }
   }
 
   /**