JAL-2385 more tests/bug fixes mostly for gui.SliderPanel and some

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 35a87d4..ea9eb21 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -41,7 +41,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourScheme;
+import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
@@ -295,11 +295,11 @@ public class AlignViewport extends AlignmentViewport implements
     {
       ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
               alignment, propertyValue);
-      globalColourScheme = new CollectionColourScheme(colourScheme);
+      globalColourScheme = new ResidueShader(colourScheme);
 
       if (colourScheme instanceof UserColourScheme)
       {
-        globalColourScheme = new CollectionColourScheme(
+        globalColourScheme = new ResidueShader(
                 UserDefinedColours.loadDefaultColours());
         globalColourScheme.setThreshold(0, isIgnoreGapsConsensus());
       }
@@ -385,7 +385,11 @@ public class AlignViewport extends AlignmentViewport implements
     super.setViewStyle(settingsForView);
     setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
             viewStyle.getFontSize()), false);
-
+    if (globalColourScheme != null)
+    {
+      globalColourScheme.setConservationApplied(settingsForView
+              .isConservationColourSelected());
+    }
   }
 
   /**