X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewRenderer.java;h=e9b4de4055e1d4f67d1cccd276e2a3950d4b20e9;hb=3f308bf567cb401b0f735c8f5e9ff57eea083011;hp=f36461ac0b782ed88eb90adb16d7436b885e1859;hpb=ac91a4a9e86f896dad1dd890511913f0b000ca2e;p=jalview.git

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index f36461a..e9b4de4 100644
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -44,8 +44,6 @@ public class OverviewRenderer
   // transparency of hidden cols/seqs overlay
   private final float TRANSPARENCY = 0.5f;
 
-  private final Color HIDDEN_COLOUR = Color.DARK_GRAY.darker();
-
   public static final String UPDATE = "OverviewUpdate";
 
   private static final int MAX_PROGRESS = 100;
@@ -152,7 +150,7 @@ public class OverviewRenderer
         if (pixelCol <= endCol)
         {
           rgbcolor = getColumnColourFromSequence(allGroups, seq,
-                  alignmentCol, finder);
+                  alignmentCol);
     
           // fill in the appropriate number of pixels
           for (int row = pixelRow; row <= endRow; ++row)
@@ -216,26 +214,23 @@ public class OverviewRenderer
   }
 
   /*
-   * Find the colour of a sequence at a specified column position
+   * Find the RGB value of the colour of a sequence at a specified column position
    * 
    * @param seq
    *          sequence to get colour for
    * @param lastcol
    *          column position to get colour for
-   * @param fcfinder
-   *          FeatureColourFinder to use
    * @return colour of sequence at this position, as RGB
    */
-  private int getColumnColourFromSequence(SequenceGroup[] allGroups,
-          jalview.datamodel.SequenceI seq,
-          int lastcol, FeatureColourFinder fcfinder)
+  int getColumnColourFromSequence(SequenceGroup[] allGroups,
+          SequenceI seq, int lastcol)
   {
     Color color = resColFinder.GAP_COLOUR;
 
     if ((seq != null) && (seq.getLength() > lastcol))
     {
       color = resColFinder.getResidueColour(true, shader, allGroups, seq,
-              lastcol, fcfinder);
+              lastcol, finder);
     }
 
     return color.getRGB();
@@ -358,15 +353,13 @@ public class OverviewRenderer
    *          the graphics object to draw on
    * @param anno
    *          alignment annotation information
-   * @param charWidth
-   *          alignment character width value
    * @param y
    *          y-position for the annotation graph
    * @param cols
    *          the collection of columns used in the overview panel
    */
-  public void drawGraph(Graphics g, AlignmentAnnotation anno, int charWidth,
-          int y, AlignmentColsCollectionI cols)
+  public void drawGraph(Graphics g, AlignmentAnnotation anno, int y,
+          AlignmentColsCollectionI cols)
   {
     Annotation[] annotations = anno.annotations;
     g.setColor(Color.white);