Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 31d049a..4c4c84f 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2631,30 +2631,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   @Override
   public void changeColour(ColourSchemeI cs)
   {
-    // FIXME threshold, conservation, increment belong inside
-    // AlignmentColourScheme and/or ViewStyleI, not ColourSchemeI
-    if (cs != null)
-    {
-      if (viewport.getAbovePIDThreshold())
-      {
-        viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
-                viewport.getViewportColourScheme(), "Background"));
-      }
-
-      if (viewport.getConservationSelected())
-      {
-        // cs.setConservationApplied(true);
-        viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
-                viewport.getViewportColourScheme(), "Background"));
-      }
-      // else
-      // {
-      // cs.setConservationApplied(false);
-      // }
-    }
     viewport.setGlobalColourScheme(cs);
-    viewport.getViewportColourScheme().setConservationApplied(
-            viewport.getConservationSelected());
 
     alignPanel.paintAlignment(true);
   }
@@ -2683,26 +2660,43 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   protected void conservationMenuItem_actionPerformed()
   {
-    viewport.setConservationSelected(conservationMenuItem.getState());
+    boolean selected = conservationMenuItem.getState();
+    modifyConservation.setEnabled(selected);
+    viewport.setConservationSelected(selected);
 
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setState(false);
+    // viewport.setAbovePIDThreshold(false);
+    // abovePIDThreshold.setState(false);
 
     changeColour(viewport.getGlobalColourScheme());
 
-    modifyConservation_actionPerformed();
+    if (selected)
+    {
+      modifyConservation_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hideConservationSlider();
+    }
   }
 
   public void abovePIDThreshold_actionPerformed()
   {
-    viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
-
-    conservationMenuItem.setState(false);
-    viewport.setConservationSelected(false);
+    boolean selected = abovePIDThreshold.getState();
+    modifyPID.setEnabled(selected);
+    viewport.setAbovePIDThreshold(selected);
+    // conservationMenuItem.setState(false);
+    // viewport.setConservationSelected(false);
 
     changeColour(viewport.getGlobalColourScheme());
 
-    modifyPID_actionPerformed();
+    if (selected)
+    {
+      modifyPID_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hidePIDSlider();
+    }
   }
 
   public void sortPairwiseMenuItem_actionPerformed()
@@ -3530,9 +3524,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     nucleotideColour.addActionListener(this);
     modifyPID.setLabel(MessageManager
             .getString("label.modify_identity_threshold"));
+    modifyPID.setEnabled(abovePIDThreshold.getState());
     modifyPID.addActionListener(this);
     modifyConservation.setLabel(MessageManager
             .getString("label.modify_conservation_threshold"));
+    modifyConservation.setEnabled(conservationMenuItem.getState());
     modifyConservation.addActionListener(this);
     annotationColour.setLabel(MessageManager
             .getString("action.by_annotation"));