From 3479ad05402df852a7758ee89b81ec1fac3301c1 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 11 Feb 2005 11:04:31 +0000
Subject: [PATCH] watch out for end of seq in findposition

---
 src/jalview/datamodel/Sequence.java |    3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

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++;
 
-- 
1.7.10.2