X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=ebdff92bb896cd11255b7c8dd8959fa0d2b48339;hb=cd1ded4a9a6f3478f3b704c9c97fd323ac5dbdd7;hp=cf578c03bd47a17cd599db6df57f43f7cfa5a3ac;hpb=8fd0b8182a10ed77b078160fffccca67f7ecb118;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cf578c0..ebdff92 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -184,10 +184,9 @@ public class Sequence implements SequenceI
     int j   = 0;
     int pos = start;
 
-    while (j < i)
+    while (j < i && j<sequence.length())
     {
       char c = sequence.charAt(j);
-
       if (!jalview.util.Comparison.isGap((c)))
         pos++;