X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=2ef1c766fd3603ec72fdfbb6845b9d56c1a17fdd;hb=fecc0f8bab5ea8327eb8602fce11a3177ecfd38e;hp=c546310dd50ede5f5d74ae83d813096cd2ace242;hpb=8fc03b5f923a6b80e2a7fc22f6fdd2c5c7ad9de9;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index c546310..2ef1c76 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;
@@ -1146,9 +1153,10 @@ public class AlignSeq
               ap++;
             }
           }
-          if (sq.getAnnotation() != null)
+          if (sq.getAnnotation() != null && sq.getAnnotation().length > 0)
           {
-            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+            annotations.addAll(inspos == -1 ? annotations.size() : inspos,
+                    Arrays.asList(sq.getAnnotation()));
           }
         }
       }