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

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 53d118b..35a87d4 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -41,6 +41,8 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.CollectionColourScheme;
+import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.CommandListener;
@@ -61,7 +63,6 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 
 /**
  * DOCUMENT ME!
@@ -292,14 +293,15 @@ public class AlignViewport extends AlignmentViewport implements
     }
     if (propertyValue != null)
     {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-              propertyValue);
+      ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
+              alignment, propertyValue);
+      globalColourScheme = new CollectionColourScheme(colourScheme);
 
-      if (globalColourScheme instanceof UserColourScheme)
+      if (colourScheme instanceof UserColourScheme)
       {
-        globalColourScheme = UserDefinedColours.loadDefaultColours();
-        ((UserColourScheme) globalColourScheme).setThreshold(0,
-                isIgnoreGapsConsensus());
+        globalColourScheme = new CollectionColourScheme(
+                UserDefinedColours.loadDefaultColours());
+        globalColourScheme.setThreshold(0, isIgnoreGapsConsensus());
       }
 
       if (globalColourScheme != null)