Merge branch 'features/JAL-2371collectionColourScheme' into develop

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 53d118b..69f155b 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.renderer.ResidueShader;
+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!
@@ -292,19 +293,20 @@ public class AlignViewport extends AlignmentViewport implements
     }
     if (propertyValue != null)
     {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-              propertyValue);
+      ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
+              alignment, propertyValue);
+      residueShading = new ResidueShader(colourScheme);
 
-      if (globalColourScheme instanceof UserColourScheme)
+      if (colourScheme instanceof UserColourScheme)
       {
-        globalColourScheme = UserDefinedColours.loadDefaultColours();
-        ((UserColourScheme) globalColourScheme).setThreshold(0,
-                isIgnoreGapsConsensus());
+        residueShading = new ResidueShader(
+                UserDefinedColours.loadDefaultColours());
+        residueShading.setThreshold(0, isIgnoreGapsConsensus());
       }
 
-      if (globalColourScheme != null)
+      if (residueShading != null)
       {
-        globalColourScheme.setConsensus(hconsensus);
+        residueShading.setConsensus(hconsensus);
       }
     }
   }
@@ -383,7 +385,11 @@ public class AlignViewport extends AlignmentViewport implements
     super.setViewStyle(settingsForView);
     setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
             viewStyle.getFontSize()), false);
-
+    if (residueShading != null)
+    {
+      residueShading.setConservationApplied(settingsForView
+              .isConservationColourSelected());
+    }
   }
 
   /**