Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / test / jalview / analysis / SeqsetUtilsTest.java

diff --git a/test/jalview/analysis/SeqsetUtilsTest.java b/test/jalview/analysis/SeqsetUtilsTest.java
index 11cb10c..0587432 100644 (file)
--- a/test/jalview/analysis/SeqsetUtilsTest.java
+++ b/test/jalview/analysis/SeqsetUtilsTest.java
@@ -47,7 +47,6 @@ public class SeqsetUtilsTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-
   /**
    * test for JAL-2046 bug - duplication of sequence features on reconstructed
    * alignment
@@ -55,33 +54,31 @@ public class SeqsetUtilsTest
   @Test(groups = { "Functional" })
   public void testSeqFeatureAddition()
   {
-    SequenceI[] sqset = new SequenceI[] {
-        new Sequence("Aseq1", "AREALSEQ"),
+    SequenceI[] sqset = new SequenceI[] { new Sequence("Aseq1", "AREALSEQ"),
         new Sequence("Aseq2", "AREALSEQ") };
 
     AlignmentI al = new Alignment(sqset);
     al.setDataset(null);
     AlignmentI ds = al.getDataset();
-    SequenceFeature sf1 = new SequenceFeature("f1", "foo", "bleh", 2, 3,
-            "far"), sf2 = new SequenceFeature("f2", "foo", "bleh", 2, 3,
-            "far");
+    SequenceFeature sf1 = new SequenceFeature("f1", "foo", 2, 3, "far");
+    SequenceFeature sf2 = new SequenceFeature("f2", "foo", 2, 3, "far");
     ds.getSequenceAt(0).addSequenceFeature(sf1);
     Hashtable unq = SeqsetUtils.uniquify(sqset, true);
     SequenceI[] sqset2 = new SequenceI[] {
         new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
         new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
-    Assert.assertTrue(sqset[0].getSequenceFeatures()[0] == sf1);
-    Assert.assertEquals(sqset2[0].getSequenceFeatures(), null);
+    Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sf1);
+    Assert.assertTrue(sqset2[0].getSequenceFeatures().isEmpty());
     ds.getSequenceAt(0).addSequenceFeature(sf2);
-    Assert.assertEquals(sqset[0].getSequenceFeatures().length, 2);
+    Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
     SeqsetUtils.deuniquify(unq, sqset2);
     // explicitly test that original sequence features still exist because they
     // are on the shared dataset sequence
-    Assert.assertEquals(sqset[0].getSequenceFeatures().length, 2);
-    Assert.assertEquals(sqset2[0].getSequenceFeatures().length, 2);
-    Assert.assertTrue(sqset[0].getSequenceFeatures()[0] == sqset2[0]
-            .getSequenceFeatures()[0]);
-    Assert.assertTrue(sqset[0].getSequenceFeatures()[1] == sqset2[0]
-            .getSequenceFeatures()[1]);
+    Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
+    Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2);
+    Assert.assertSame(sqset[0].getSequenceFeatures().get(0),
+            sqset2[0].getSequenceFeatures().get(0));
+    Assert.assertSame(sqset[0].getSequenceFeatures().get(1),
+            sqset2[0].getSequenceFeatures().get(1));
   }
 }