X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=b9db46123c335bd5f703045adbecd9f6e0107c84;hb=0673686a4ceda776a64350afd35ecff18e74e575;hp=33294318ed89a3c0c87042bfb4a6cf27a24d8dac;hpb=07e95212532922e9a7966b81724b5a54e26b51a8;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 3329431..b9db461 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()
@@ -232,8 +246,7 @@ public class SearchResults
 
           if (result == null)
           {
-            result = new int[]
-            { matchStart, matchEnd };
+            result = new int[] { matchStart, matchEnd };
           }
           else
           {