Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

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

diff --git a/test/jalview/analysis/SeqsetUtilsTest.java b/test/jalview/analysis/SeqsetUtilsTest.java
index b4d079a..9839ba0 100644 (file)
--- a/test/jalview/analysis/SeqsetUtilsTest.java
+++ b/test/jalview/analysis/SeqsetUtilsTest.java
@@ -25,10 +25,12 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 
 import java.util.Hashtable;
 
 import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 /**
@@ -37,6 +39,15 @@ import org.testng.annotations.Test;
  */
 public class SeqsetUtilsTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+
   /**
    * test for JAL-2046 bug - duplication of sequence features on reconstructed
    * alignment
@@ -51,26 +62,25 @@ public class SeqsetUtilsTest
     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));
   }
 }