X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=6399b1c5f63cc7d72c2243a47245aa50d3f63baf;hb=8da7acff9214ddaf0e6d28e76219ab51bd38e62d;hp=ad4aeb80703f34c597cc168b60fb80ad719ea21a;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index ad4aeb8..6399b1c 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -192,6 +192,8 @@ public class AnnotationPanel
 
   public void paint(Graphics g)
   {
+    g.setColor(Color.white);
+    g.fillRect(0,0, getSize().width, getSize().height);
     imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
     if (image == null || imgWidth != image.getWidth(this))
@@ -336,13 +338,13 @@ public class AnnotationPanel
                             fm.charWidth(row.annotations[j].displayCharacter.
                                          charAt(0))) / 2;
           g.setColor(row.annotations[j].colour);
-          if (j == 0)
+          if (j == 0 || row.isGraph)
           {
             if (row.annotations[0].secondaryStructure == 'H'
                 || row.annotations[0].secondaryStructure == 'E')
             {
               g.drawString(row.annotations[j].displayCharacter, x,
-                           y + iconOffset + 2);
+                           y + iconOffset + 3);
             }
           }
           else if ( (row.annotations[j].secondaryStructure == 'H'
@@ -353,13 +355,13 @@ public class AnnotationPanel
           {
 
             g.drawString(row.annotations[j].displayCharacter, x + charOffset,
-                         y + iconOffset + 2);
+                         y + iconOffset + 3);
           }
 
           if (!row.hasIcons)
           {
             g.drawString(row.annotations[j].displayCharacter, x + charOffset,
-                         y + iconOffset + 2);
+                         y + iconOffset + 3);
           }
         }