X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=b9db46123c335bd5f703045adbecd9f6e0107c84;hb=8bb1df31c9d46763d2a3278d27d52ce69ba441b3;hp=d9d12db3e166a381810fafce0c885585c191337e;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index d9d12db..b9db461 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -67,8 +67,22 @@ public class SearchResults
     public Match(SequenceI seq, int start, int end)
     {
       sequence = seq;
-      this.start = start;
-      this.end = end;
+
+      /*
+       * always hold in forwards order, even if given in reverse order
+       * (such as from a mapping to a reverse strand); this avoids
+       * trouble for routines that highlight search results etc
+       */
+      if (start <= end)
+      {
+        this.start = start;
+        this.end = end;
+      }
+      else
+      {
+        this.start = end;
+        this.end = start;
+      }
     }
 
     public SequenceI getSequence()