X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=cb638dda875a1e6ef53157f53921785fb50051e2;hb=14bad6b2390493bb6ad030c6f3ea7cde4cba1b53;hp=92ee3a2b79f32926e1492b8ba46379bda2e736dd;hpb=645c2b050820af4a0cefd91ccb1db62bccb084c2;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 92ee3a2..cb638dd 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -206,8 +206,6 @@ 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))
@@ -389,8 +387,8 @@ public class AnnotationPanel
                           y + iconOffset + 3);
                   }
                   else if (((row.annotations[j - 1] == null) ||
-                          (row.annotations[j].displayCharacter != row.annotations[j -
-                          1].displayCharacter)))
+                          (!row.annotations[j].displayCharacter.equals(
+                           row.annotations[j - 1].displayCharacter))))
                   {
                       g.drawString(row.annotations[j].displayCharacter, x+charOffset,
                           y + iconOffset + 3);
@@ -582,13 +580,6 @@ public class AnnotationPanel
     g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
 
 
-    if(aa.threshold!=null)
-    {
-        g.setColor(aa.threshold.colour);
-        y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
-        g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
-    }
-
     for (int j = sRes; j < eRes; j++)
     {
       if(aa.annotations[j]==null || aa.annotations[j-1]==null)
@@ -602,6 +593,15 @@ public class AnnotationPanel
         g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
         x += av.charWidth;
      }
+
+
+     if(aa.threshold!=null)
+     {
+         g.setColor(aa.threshold.colour);
+         y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
+         g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+     }
+
   }
 
   public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
@@ -619,13 +619,6 @@ public class AnnotationPanel
 
     float range = max - min;
 
-    if(aa.threshold!=null)
-    {
-        g.setColor(aa.threshold.colour);
-        y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
-        g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
-    }
-
     y1 = y2 = y;
 
     if(min<0)
@@ -633,7 +626,7 @@ public class AnnotationPanel
 
     g.setColor(Color.gray);
 
-    g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2);
+    g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
 
     for (int j = sRes; j < eRes; j++)
     {
@@ -655,6 +648,15 @@ public class AnnotationPanel
         x += av.charWidth;
     }
 
+
+    if(aa.threshold!=null)
+    {
+        g.setColor(aa.threshold.colour);
+        y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
+        g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+    }
+
+
   }
 
   // used by overview window