X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=d6188091491f83d54bfe6e4f4460883c91b44d40;hb=b41c6db8eab0dc6c71ae65037c271e0305691d69;hp=5d58d423cd8b73ef0edab08c0761ee139cc3d120;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 5d58d42..d618809 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -210,10 +210,7 @@ public class ClustalFile extends AlignFile
     {
       String tmp = printId(s[i], jvsuffix);
 
-      if (s[i].getSequence().length > max)
-      {
-        max = s[i].getSequence().length;
-      }
+      max = Math.max(max, s[i].getLength());
 
       if (tmp.length() > maxid)
       {
@@ -245,14 +242,14 @@ public class ClustalFile extends AlignFile
         int start = i * len;
         int end = start + len;
 
-        if ((end < s[j].getSequence().length)
-                && (start < s[j].getSequence().length))
+        int length = s[j].getLength();
+        if ((end < length) && (start < length))
         {
           out.append(s[j].getSequenceAsString(start, end));
         }
         else
         {
-          if (start < s[j].getSequence().length)
+          if (start < length)
           {
             out.append(s[j].getSequenceAsString().substring(start));
           }