X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;fp=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=1c0420d5f3088f615bb5d27a15635316ddae8df9;hb=d5bcc3830eab04e6db816e1c2ad8fce1dc189612;hp=95c32615120b246b38c52c3689e56a6fef4f9a2d;hpb=3ebdd4e28382e38a181aae1eed71549f603f9025;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 95c3261..1c0420d 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -20,10 +20,10 @@
  */
 package jalview.gui;
 
-import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.util.Comparison;
 
 import java.awt.Color;
@@ -53,14 +53,13 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   boolean forOverview = false;
 
   /**
-   * Creates a new SequenceRenderer object.
+   * Creates a new SequenceRenderer object
    * 
-   * @param av
-   *          DOCUMENT ME!
+   * @param viewport
    */
-  public SequenceRenderer(AlignViewport av)
+  public SequenceRenderer(AlignViewport viewport)
   {
-    this.av = av;
+    this.av = viewport;
   }
 
   /**
@@ -83,8 +82,7 @@ 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)
   {
     // rate limiting step when rendering overview for lots of groups
     allGroups = av.getAlignment().findAllGroups(seq);
@@ -111,20 +109,18 @@ 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;
   }