X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=95c32615120b246b38c52c3689e56a6fef4f9a2d;hb=7c9fbca0e2d9be5fd05e1c89f24f81d558bf6849;hp=dc8aad4787f1055a16252c848db226c25dc2984e;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index dc8aad4..95c3261 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,7 +23,8 @@ package jalview.gui;
 import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -92,12 +93,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     {
       if (currentSequenceGroup.getDisplayBoxes())
       {
-        getBoxColour(currentSequenceGroup.cs, seq, i);
+        getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
       }
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.getGlobalColourScheme(), seq, i);
+      getBoxColour(av.getResidueShading(), seq, i);
     }
 
     return resBoxColour;
@@ -131,21 +132,21 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   /**
    * DOCUMENT ME!
    * 
-   * @param cs
+   * @param shader
    *          DOCUMENT ME!
    * @param seq
    *          DOCUMENT ME!
    * @param i
    *          DOCUMENT ME!
    */
-  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    if (cs != null)
+    if (shader != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
+      resBoxColour = shader.findColour(seq.getCharAt(i),
+              i, seq);
     }
-    else if (forOverview
-            && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
     {
       resBoxColour = Color.lightGray;
     }
@@ -234,14 +235,14 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         {
           if (currentSequenceGroup.getDisplayBoxes())
           {
-            getBoxColour(currentSequenceGroup.cs, seq, i);
+            getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+                    i);
           }
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
         }
-
       }
 
       if (resBoxColour != tempColour)
@@ -345,7 +346,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
                   || currentSequenceGroup.getColourText())
           {
             getboxColour = true;
-            getBoxColour(currentSequenceGroup.cs, seq, i);
+            getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+                    i);
 
             if (currentSequenceGroup.getColourText())
             {
@@ -385,7 +387,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (av.getColourText())
           {
             getboxColour = true;
-            getBoxColour(av.getGlobalColourScheme(), seq, i);
+            getBoxColour(av.getResidueShading(), seq, i);
 
             if (av.getShowBoxes())
             {
@@ -401,7 +403,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             if (!getboxColour)
             {
-              getBoxColour(av.getGlobalColourScheme(), seq, i);
+              getBoxColour(av.getResidueShading(), seq, i);
             }
 
             if (resBoxColour.getRed() + resBoxColour.getBlue()