X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=8a873a22607c4854a2ebb52d3f7241a2186c6e48;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=aa98e76cdef6b2c32069cea96d313b2c5a9992be;hpb=987c0089ccb8885a1bf768d74ee3858859b489f5;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index aa98e76..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";
       }
@@ -560,8 +569,6 @@ public class SeqCanvas extends JComponent
             g.translate(-LABEL_WEST, 0);
 
             ypos += cHeight+getAnnotationHeight()+hgap;
-            if(av.showAnnotation)
-              ypos -= 3;
 
             startRes += cWidth;
         }