Use propertyListener for alignment edits

[jalview.git] / src / jalview / appletgui / AnnotationPanel.java

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