JAL-674 fix the mapping generation algorithm

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 832f519..6d8c0cd 100755 (executable)
--- 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
       {