X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewRenderer.java;h=1b5d5da4bb677d3f4ba3584ef1227f3a400958f4;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=e9b4de4055e1d4f67d1cccd276e2a3950d4b20e9;hpb=3f308bf567cb401b0f735c8f5e9ff57eea083011;p=jalview.git

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index e9b4de4..1b5d5da 100644
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -76,8 +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;
@@ -120,7 +120,7 @@ public class OverviewRenderer
       {
         break;
       }
-    
+
       // get details of this alignment row
       SequenceI seq = rows.getSequence(alignmentRow);
 
@@ -130,7 +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)
@@ -139,11 +139,11 @@ 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
@@ -151,7 +151,7 @@ public class OverviewRenderer
         {
           rgbcolor = getColumnColourFromSequence(allGroups, seq,
                   alignmentCol);
-    
+
           // fill in the appropriate number of pixels
           for (int row = pixelRow; row <= endRow; ++row)
           {
@@ -222,8 +222,8 @@ public class OverviewRenderer
    *          column position to get colour for
    * @return colour of sequence at this position, as RGB
    */
-  int getColumnColourFromSequence(SequenceGroup[] allGroups,
-          SequenceI seq, int lastcol)
+  int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq,
+          int lastcol)
   {
     Color color = resColFinder.GAP_COLOUR;
 
@@ -288,8 +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);