3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertFalse;
5 import static org.testng.AssertJUnit.assertTrue;
7 import jalview.datamodel.Alignment;
8 import jalview.datamodel.AlignmentI;
9 import jalview.datamodel.Sequence;
10 import jalview.datamodel.SequenceFeature;
11 import jalview.datamodel.SequenceI;
13 import java.util.List;
15 import org.testng.annotations.Test;
17 public class AlignFrameTest
21 public void testHideFeatureColumns()
23 SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
24 SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
25 seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5,
27 seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10,
29 seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
31 seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
33 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
34 AlignFrame af = new AlignFrame(al, al.getWidth(), al.getHeight());
37 * hiding a feature not present does nothing
39 assertFalse(af.hideFeatureColumns("exon", true));
40 assertTrue(af.getViewport().getColumnSelection().isEmpty());
41 assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
43 assertFalse(af.hideFeatureColumns("exon", false));
44 assertTrue(af.getViewport().getColumnSelection().isEmpty());
45 assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
49 * hiding a feature in all columns does nothing
51 assertFalse(af.hideFeatureColumns("Metal", true));
52 assertTrue(af.getViewport().getColumnSelection().isEmpty());
53 List<int[]> hidden = af.getViewport().getColumnSelection()
55 assertTrue(hidden.isEmpty());
58 * hide a feature present in some columns
59 * sequence positions [2-4], [7-9] are column positions
60 * [1-3], [6-8] base zero
62 assertTrue(af.hideFeatureColumns("Turn", true));
63 hidden = af.getViewport().getColumnSelection()
65 assertEquals(2, hidden.size());
66 assertEquals(1, hidden.get(0)[0]);
67 assertEquals(3, hidden.get(0)[1]);
68 assertEquals(6, hidden.get(1)[0]);
69 assertEquals(8, hidden.get(1)[1]);