X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=38031e4e43f27e2afeb17b871e1d89e4de7a8762;hb=1499d3297cf70ff34df05362449dbf36873c5bc1;hp=1c7c4ce85c32ad89ab7b32d6d2f562078a88a437;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 1c7c4ce..38031e4 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -20,10 +20,10 @@
  */
 package jalview.appletgui;
 
-import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -69,8 +69,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     this.renderGaps = renderGaps;
   }
 
-  @Override
-  public Color getResidueBoxColour(SequenceI seq, int i)
+  protected Color getResidueBoxColour(SequenceI seq, int i)
   {
     allGroups = av.getAlignment().findAllGroups(seq);
 
@@ -83,7 +82,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.getViewportColourScheme(), seq, i);
+      getBoxColour(av.getResidueShading(), seq, i);
     }
 
     return resBoxColour;
@@ -96,27 +95,27 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * 
    * @param seq
    * @param position
-   * @param fr
+   * @param finder
    * @return
    */
   @Override
   public Color getResidueColour(final SequenceI seq, int position,
-          FeatureRenderer fr)
+          FeatureColourFinder finder)
   {
     // TODO replace 8 or so code duplications with calls to this method
     // (refactored as needed)
     Color col = getResidueBoxColour(seq, position);
 
-    if (fr != null)
+    if (finder != null)
     {
-      col = fr.findFeatureColour(col, seq, position);
+      col = finder.findFeatureColour(col, seq, position);
     }
     return col;
   }
 
   void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    if (shader != null)
+    if (shader.getColourScheme() != null)
     {
       resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
     }
@@ -182,7 +181,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.getViewportColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
         }
       }
 
@@ -272,7 +271,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
         if (av.getColourText())
         {
-          getBoxColour(av.getViewportColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
           if (av.getShowBoxes())
           {
             graphics.setColor(resBoxColour.darker());