X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=78ed4a3fe35ccded29e7141cfd7e8c6697597970;hb=c437fc72420baf7b045d417fb6cabcebe87987c5;hp=4d9d37cf233515b92ecc7248d7ab35914e73b273;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 4d9d37c..78ed4a3 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.schemes.CollectionColourSchemeI;
+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;
@@ -96,31 +95,29 @@ 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(CollectionColourSchemeI collectionColourSchemeI,
-          SequenceI seq, int i)
+  void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    if (collectionColourSchemeI != null)
+    if (shader != null)
     {
-      resBoxColour = collectionColourSchemeI.findColour(seq.getCharAt(i),
-              i, seq);
+      resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@ -184,7 +181,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.getViewportColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
         }
       }
 
@@ -274,7 +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());