From 99b68710784bd85a781b5d157f34691fc7beacce Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 12 Nov 2014 12:39:50 +0000
Subject: [PATCH] JAL-674 patch broken getMapping function

---
 src/jalview/analysis/AlignSeq.java |   11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index c546310..307a06f 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1020,22 +1020,29 @@ public class AlignSeq
 
       if (allowmismatch || c1 == c2)
       {
-        lastmatch = true;
-        // extend mapping interval.
+        // extend mapping interval
         if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
         {
           as1.add(Integer.valueOf(alignpos));
           as2.add(Integer.valueOf(pdbpos));
         }
+        lastmatch = true;
         lp1 = alignpos;
         lp2 = pdbpos;
       }
       else
       {
+        // extend mapping interval
+        if (lastmatch)
+        {
+          as1.add(Integer.valueOf(lp1));
+          as2.add(Integer.valueOf(lp2));
+        }
         lastmatch = false;
       }
     }
     // construct range pairs
+
     int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
             .size() + (lastmatch ? 1 : 0)];
     int i = 0;
-- 
1.7.10.2