From 006110e029b12f863d4d97f0141f8f1573422090 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 18 Jun 2013 17:28:50 +0100
Subject: [PATCH] JAL-674 fix the mapping generation algorithm

---
 src/jalview/analysis/AlignSeq.java |   10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 832f519..6d8c0cd 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -969,17 +969,13 @@ public class AlignSeq
       {
         lastmatch = true;
         // extend mapping interval.
-        if (lp1 + 1 != alignpos)
+        if (lp1 + 1 != alignpos || lp2+1 !=pdbpos)
         {
           as1.add(Integer.valueOf(alignpos));
-          lp1 = alignpos;
-        }
-
-        if (lp2 + 1 != pdbpos)
-        {
           as2.add(Integer.valueOf(pdbpos));
-          lp2 = pdbpos;
         }
+        lp1 = alignpos;
+        lp2 = pdbpos;
       }
       else
       {
-- 
1.7.10.2