X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=8a873a22607c4854a2ebb52d3f7241a2186c6e48;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=56e70acffb17f92dbdba210db100dfd0cc1f6d1e;hpb=f3bc67915e61855d87866b4a614fe7a953813408;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 56e70ac..8a873a2 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -418,7 +418,16 @@ public class SeqCanvas extends JComponent
     String getMask()
     {
       String mask = "00";
-      for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+      int maxWidth = 0;
+      int tmp;
+      for(int i=0; i<av.alignment.getHeight(); i++)
+      {
+        tmp = av.alignment.getSequenceAt(i).getEnd();
+        if(tmp>maxWidth)
+          maxWidth = tmp;
+      }
+
+      for (int i = maxWidth; i > 0; i /= 10)
       {
         mask += "0";
       }
@@ -554,14 +563,12 @@ public class SeqCanvas extends JComponent
                 annotations = new AnnotationPanel(av);
 
               annotations.drawComponent( (Graphics2D) g, startRes, endx+1);
-              g.translate(0, -cHeight - ypos);
+              g.translate(0, -cHeight - ypos -3);
             }
             g.setClip(clip);
             g.translate(-LABEL_WEST, 0);
 
             ypos += cHeight+getAnnotationHeight()+hgap;
-            if(av.showAnnotation)
-              ypos -= 3;
 
             startRes += cWidth;
         }