X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=86d1f98e51ec53f834954274fc85672769b8150d;hb=bc096ecbcd3cf4bbf17a24f9e9df88806789d688;hp=970d20e751ebc98b32e4c93d16c686519fd3bf20;hpb=b935f11dfb481b022ffa261f4d8ee672d3b06c0c;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 970d20e..86d1f98 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -23,7 +23,7 @@ package jalview.appletgui;
 import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -78,12 +78,12 @@ 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;
@@ -114,11 +114,11 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     return col;
   }
 
-  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)))
@@ -176,12 +176,13 @@ 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);
         }
       }
 
@@ -254,7 +255,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
         if (currentSequenceGroup.getColourText())
         {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
+          getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
           graphics.setColor(resBoxColour.darker());
         }
         if (currentSequenceGroup.getShowNonconserved())
@@ -271,7 +272,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
         if (av.getColourText())
         {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
           if (av.getShowBoxes())
           {
             graphics.setColor(resBoxColour.darker());