X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=484e05a9668224f93216b12088692bfc0c98d10e;hb=c4fe29146bd25f9b70603e62ab97422088fb71ff;hp=1a11630dce8ffbd7f98297ae24db26df8d641621;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 1a11630..484e05a 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -91,11 +91,20 @@ public class TreeCanvas extends JPanel implements MouseListener
 
       int ypos = (int)(node.ycount * chunk) + offy;
 
-      if (node.element() instanceof SequenceI) {
-          g.setColor(((SequenceI)((SequenceNode)node).element()).getColor().darker());
-      } else {
-          g.setColor(Color.black);
+      if (node.element() instanceof SequenceI)
+      {
+       if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() == Color.white)
+       {
+         g.setColor(Color.black);
+       }
+       else
+        g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().
+                   darker());
+
       }
+      else
+          g.setColor(Color.black);
+
 
       // Draw horizontal line
       g.drawLine(xstart,ypos,xend,ypos);
@@ -350,20 +359,19 @@ public class TreeCanvas extends JPanel implements MouseListener
 
               for (int i=0; i < tree.getGroups().size(); i++) {
 
-                  int tmp = i%(7);
                   Color col = new Color((int)(Math.random()*255),
                                         (int)(Math.random()*255),
                                         (int)(Math.random()*255));
-
                   setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());
 
                   // l is vector of Objects
-                  Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());
+                 // Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());
 
               }
           }
       }
 
+      PaintRefresher.Refresh(this);
       repaint();
 
   }