X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewRenderer.java;h=1ff032bf890b296848724b8bf830bad9ab9e6aa0;hb=7cfe01e2f50e0be1965741ebde2e02cacc6aafa2;hp=f36461ac0b782ed88eb90adb16d7436b885e1859;hpb=f5c3e4c114f383442f8a551f0239415d397da2cd;p=jalview.git

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index f36461a..1ff032b 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;
@@ -78,8 +76,8 @@ public class OverviewRenderer
   private OverviewResColourFinder resColFinder;
 
   public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od,
-          AlignmentI alignment,
-          ResidueShaderI resshader, OverviewResColourFinder colFinder)
+          AlignmentI alignment, ResidueShaderI resshader,
+          OverviewResColourFinder colFinder)
   {
     finder = new FeatureColourFinder(fr);
     resColFinder = colFinder;
@@ -122,7 +120,7 @@ public class OverviewRenderer
       {
         break;
       }
-    
+
       // get details of this alignment row
       SequenceI seq = rows.getSequence(alignmentRow);
 
@@ -132,7 +130,7 @@ public class OverviewRenderer
       // calculate where this row extends to in pixels
       int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
               miniMe.getHeight() - 1);
-    
+
       int colIndex = 0;
       int pixelCol = 0;
       for (int alignmentCol : cols)
@@ -141,19 +139,19 @@ public class OverviewRenderer
         {
           break;
         }
-    
+
         // calculate where this column extends to in pixels
         int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
                 miniMe.getWidth() - 1);
-    
+
         // don't do expensive colour determination if we're not going to use it
         // NB this is important to avoid performance issues in the overview
         // panel
         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;
+    Color color = resColFinder.gapColour;
 
     if ((seq != null) && (seq.getLength() > lastcol))
     {
       color = resColFinder.getResidueColour(true, shader, allGroups, seq,
-              lastcol, fcfinder);
+              lastcol, finder);
     }
 
     return color.getRGB();
@@ -293,8 +288,8 @@ public class OverviewRenderer
     Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics();
 
     // set background to transparent
-    g2d.setComposite(AlphaComposite.Clear);
-    g2d.fillRect(0, 0, width, height);
+    // g2d.setComposite(AlphaComposite.Clear);
+    // g2d.fillRect(0, 0, width, height);
 
     // set next colour to opaque
     g2d.setComposite(AlphaComposite.Src);
@@ -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);