X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cf6a901ec488015e62f8b67884740b7bccb97f81;hb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;hp=266cbcb4c79792b46fbff69ea03f2be9d81247c0;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 266cbcb..cf6a901 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3301,7 +3301,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param selected
    */
   @Override
-  protected void applyToAllGroups_actionPerformed(boolean selected)
+  public void applyToAllGroups_actionPerformed(boolean selected)
   {
     viewport.setColourAppliesToAllGroups(selected);
   }
@@ -3359,7 +3359,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void modifyPID_actionPerformed()
   {
     SliderPanel.setPIDSliderSource(alignPanel,
-            viewport.getViewportColourScheme(), "Background");
+            viewport.getViewportColourScheme(), alignPanel.getViewName());
     SliderPanel.showPIDSlider();
   }
 
@@ -3370,7 +3370,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void modifyConservation_actionPerformed()
   {
     SliderPanel.setConservationSlider(alignPanel,
-            viewport.getViewportColourScheme(), "Background");
+            viewport.getViewportColourScheme(), alignPanel.getViewName());
     SliderPanel.showConservationSlider();
   }
 
@@ -3378,7 +3378,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Action on selecting or deselecting (Colour) By Conservation
    */
   @Override
-  protected void conservationMenuItem_actionPerformed(boolean selected)
+  public void conservationMenuItem_actionPerformed(boolean selected)
   {
     modifyConservation.setEnabled(selected);
     viewport.setConservationSelected(selected);
@@ -3403,6 +3403,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     modifyPID.setEnabled(selected);
     viewport.setAbovePIDThreshold(selected);
+    if (!selected)
+    {
+      viewport.getViewportColourScheme().setThreshold(0,
+              viewport.isIgnoreGapsConsensus());
+    }
 
     changeColour(viewport.getGlobalColourScheme());
     if (selected)
@@ -4828,6 +4833,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     /*
+     * 'focus' any colour slider that is open to the selected viewport
+     */
+    if (viewport.getConservationSelected())
+    {
+      SliderPanel.setConservationSlider(alignPanel,
+              viewport.getViewportColourScheme(), alignPanel.getViewName());
+    }
+    else
+    {
+      SliderPanel.hideConservationSlider();
+    }
+    if (viewport.getAbovePIDThreshold())
+    {
+      SliderPanel.setPIDSliderSource(alignPanel,
+              viewport.getViewportColourScheme(), alignPanel.getViewName());
+    }
+    else
+    {
+      SliderPanel.hidePIDSlider();
+    }
+
+    /*
      * If there is a frame linked to this one in a SplitPane, switch it to the
      * same view tab index. No infinite recursion of calls should happen, since
      * tabSelectionChanged() should not get invoked on setting the selected