From a31403382672ec59acdf56e095d6d0136199fb44 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 3 Dec 2015 16:26:51 +0000
Subject: [PATCH] JAL-653 handle reverse strand mapping in SearchResults
 matches

---
 src/jalview/datamodel/SearchResults.java      |   18 ++++++++++++++++--
 test/jalview/datamodel/SearchResultsTest.java |   23 +++++++++++++++++++++++
 2 files changed, 39 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index ad0e472..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()
diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index 3838ac8..ffcaa26 100644
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -22,8 +22,11 @@ package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.SearchResults.Match;
+
 import org.testng.annotations.Test;
 
 public class SearchResultsTest
@@ -166,4 +169,24 @@ public class SearchResultsTest
     sr2.addResult(seq1, 6, 8);
     assertEquals(sr1.hashCode(), sr2.hashCode());
   }
+  
+  /**
+   * Verify that SearchResults$Match constructor normalises start/end to the
+   * 'forwards' direction
+   */
+  @Test(groups = { "Functional" })
+  public void testMatchConstructor()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    Match m = new SearchResults().new Match(seq1, 2, 5);
+    assertSame(seq1, m.getSequence());
+    assertEquals(2, m.getStart());
+    assertEquals(5, m.getEnd());
+
+    // now a reverse mapping:
+    m = new SearchResults().new Match(seq1, 5, 2);
+    assertSame(seq1, m.getSequence());
+    assertEquals(2, m.getStart());
+    assertEquals(5, m.getEnd());
+  }
 }
-- 
1.7.10.2