X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;fp=src%2Fjalview%2Fgui%2FSliderPanel.java;h=ec53e93e1e96e0db1b879ff24b694a46a8674ac6;hb=d065bc916cb63af83cdab7319f5177a855724aba;hp=0c4e03e89f57b538279384c4f4eb2fb462f2d466;hpb=d346ed81a91c4fbed1836379bb794ed908cd9a11;p=jalview.git

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 0c4e03e..ec53e93 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.Conservation;
 import jalview.datamodel.SequenceGroup;
 import jalview.jbgui.GSliderPanel;
 import jalview.renderer.ResidueShaderI;
@@ -28,6 +29,7 @@ import jalview.util.MessageManager;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.beans.PropertyVetoException;
+import java.util.List;
 
 import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
@@ -170,7 +172,8 @@ public class SliderPanel extends GSliderPanel
             "label.conservation_colour_increment",
             new String[] { source == null ? BACKGROUND : source }));
 
-    if (ap.av.getAlignment().getGroups() != null)
+    List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+    if (groups != null && !groups.isEmpty())
     {
       sliderPanel.setAllGroupsCheckEnabled(true);
     }
@@ -331,13 +334,14 @@ public class SliderPanel extends GSliderPanel
     {
       ap.av.setThreshold(percent);
     }
-    updateColourScheme(percent, cs);
+    updateColourScheme(percent, cs, null);
 
     if (allGroupsCheck.isSelected())
     {
-      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+      for (SequenceGroup sg : groups)
       {
-        updateColourScheme(percent, sg.getGroupColourScheme());
+        updateColourScheme(percent, sg.getGroupColourScheme(), sg);
       }
     }
 
@@ -350,8 +354,10 @@ public class SliderPanel extends GSliderPanel
    * 
    * @param percent
    * @param scheme
+   * @param sg
    */
-  protected void updateColourScheme(int percent, ResidueShaderI scheme)
+  protected void updateColourScheme(int percent, ResidueShaderI scheme,
+          SequenceGroup sg)
   {
     if (scheme == null)
     {
@@ -359,6 +365,20 @@ public class SliderPanel extends GSliderPanel
     }
     if (forConservation)
     {
+      if (!scheme.conservationApplied())
+      {
+        /*
+         * first time the colour scheme has had Conservation shading applied
+         * - compute conservation
+         */
+        Conservation c = new Conservation("Group", sg.getSequences(null),
+                sg.getStartRes(), sg.getEndRes());
+        c.calculate();
+        c.verdict(false, ap.av.getConsPercGaps());
+        sg.cs.setConservation(c);
+
+      }
+      scheme.setConservationApplied(true);
       scheme.setConservationInc(percent);
     }
     else
@@ -376,6 +396,7 @@ public class SliderPanel extends GSliderPanel
   public void setAllGroupsCheckEnabled(boolean b)
   {
     allGroupsCheck.setEnabled(b);
+    allGroupsCheck.setSelected(ap.av.getColourAppliesToAllGroups());
   }
 
   /**