From 7dc7404ce7a339c600130e9828e3efc05b1e3270 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 19 May 2020 18:27:40 +0100
Subject: [PATCH] JAL-3621 corrected sequence feature sort and test

---
 .../datamodel/features/SequenceFeaturesTest.java   |   38 ++++++++++++++------
 1 file changed, 27 insertions(+), 11 deletions(-)

diff --git a/test/jalview/datamodel/features/SequenceFeaturesTest.java b/test/jalview/datamodel/features/SequenceFeaturesTest.java
index 4198a37..56512cd 100644
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -5,8 +5,6 @@ import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
-import jalview.datamodel.SequenceFeature;
-
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -15,6 +13,7 @@ import java.util.Set;
 
 import org.testng.annotations.Test;
 
+import jalview.datamodel.SequenceFeature;
 import junit.extensions.PA;
 
 public class SequenceFeaturesTest
@@ -1052,7 +1051,8 @@ public class SequenceFeaturesTest
   public void testSortFeatures()
   {
     List<SequenceFeature> sfs = new ArrayList<>();
-    SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 80,
+    SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30,
+            60,
             Float.NaN, null);
     sfs.add(sf1);
     SequenceFeature sf2 = new SequenceFeature("Rfam", "desc", 40, 50,
@@ -1061,18 +1061,34 @@ public class SequenceFeaturesTest
     SequenceFeature sf3 = new SequenceFeature("Rfam", "desc", 50, 60,
             Float.NaN, null);
     sfs.add(sf3);
+    SequenceFeature sf4 = new SequenceFeature("Xfam", "desc", 30,
+            80,
+            Float.NaN, null);
+    sfs.add(sf4);
+    SequenceFeature sf5 = new SequenceFeature("Xfam", "desc", 30,
+            90,
+            Float.NaN, null);
+    sfs.add(sf5);
 
-    // sort by end position descending
+    /*
+     * sort by end position descending, order unchanged if matched
+     */
     SequenceFeatures.sortFeatures(sfs, false);
-    assertSame(sfs.get(0), sf1);
-    assertSame(sfs.get(1), sf3);
-    assertSame(sfs.get(2), sf2);
+    assertSame(sfs.get(0), sf5); // end 90
+    assertSame(sfs.get(1), sf4); // end 80
+    assertSame(sfs.get(2), sf1); // end 60, start 50
+    assertSame(sfs.get(3), sf3); // end 60, start 30
+    assertSame(sfs.get(4), sf2); // end 50
 
-    // sort by start position ascending
+    /*
+     * resort {5, 4, 1, 3, 2} by start position ascending, end descending
+     */
     SequenceFeatures.sortFeatures(sfs, true);
-    assertSame(sfs.get(0), sf1);
-    assertSame(sfs.get(1), sf2);
-    assertSame(sfs.get(2), sf3);
+    assertSame(sfs.get(0), sf5); // start 30, end 90
+    assertSame(sfs.get(1), sf4); // start 30, end 80
+    assertSame(sfs.get(2), sf1); // start 30, end 60
+    assertSame(sfs.get(3), sf2); // start 40
+    assertSame(sfs.get(4), sf3); // start 50
   }
 
   @Test(groups = "Functional")
-- 
1.7.10.2