X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=4dda81abeb62de86984d3168b7b1b6a9e6de5718;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=d7d9ec967b97ddcd41ab58ed62fd5ff79e211895;hpb=a90e2fe3cc3b779521a81cf8de410936f3a777c1;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index d7d9ec9..4dda81a 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -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()