X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;fp=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=307a06fa7e728beff858393adb92c98a6f140521;hb=49a7daf06cb98b45ce2d33ea25b15172c4204dda;hp=c546310dd50ede5f5d74ae83d813096cd2ace242;hpb=227ee1c1c69c228b67d408a0a83ae51bf5811272;p=jalview.git

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;