X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAMSAFile.java;h=e7e6d97bf3b1d74ab9cb982525f1112239e555cd;hb=390461d621255f960721a8370ee8fb06ba20aec9;hp=1f3fca08349ac3e54bb463f0e74cbc9cbf038871;hpb=1d282590b622a5c8bbf8a294e76f8f12bdee50e8;p=jalview.git

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 1f3fca0..e7e6d97 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -45,9 +45,12 @@ public class AMSAFile
     AlignmentAnnotation aa;
     if (al.getAlignmentAnnotation() != null)
     {
+
       for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
       {
         aa = al.getAlignmentAnnotation()[i];
+
+
         if (aa.autoCalculated || !aa.visible)
         {
           continue;
@@ -61,7 +64,8 @@ public class AMSAFile
 
         out.append("\n");
 
-        int nochunks = (aa.annotations.length / len) + 1;
+        int nochunks = Math.min(aa.annotations.length, al.getWidth())
+                        / len + 1;
 
         for (int j = 0; j < nochunks; j++)
         {