2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.Sequence;
30 import jalview.datamodel.SequenceFeature;
31 import jalview.datamodel.SequenceI;
33 import java.util.List;
35 import org.testng.annotations.Test;
37 public class AlignFrameTest
40 @Test(groups = "Functional")
41 public void testHideFeatureColumns()
43 SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
44 SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
45 seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5,
47 seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10,
49 seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
51 seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
53 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
54 AlignFrame af = new AlignFrame(al, al.getWidth(), al.getHeight());
57 * hiding a feature not present does nothing
59 assertFalse(af.hideFeatureColumns("exon", true));
60 assertTrue(af.getViewport().getColumnSelection().isEmpty());
61 assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
63 assertFalse(af.hideFeatureColumns("exon", false));
64 assertTrue(af.getViewport().getColumnSelection().isEmpty());
65 assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
69 * hiding a feature in all columns does nothing
71 assertFalse(af.hideFeatureColumns("Metal", true));
72 assertTrue(af.getViewport().getColumnSelection().isEmpty());
73 List<int[]> hidden = af.getViewport().getColumnSelection()
75 assertTrue(hidden.isEmpty());
78 * hide a feature present in some columns
79 * sequence positions [2-4], [7-9] are column positions
80 * [1-3], [6-8] base zero
82 assertTrue(af.hideFeatureColumns("Turn", true));
83 hidden = af.getViewport().getColumnSelection().getHiddenColumns();
84 assertEquals(2, hidden.size());
85 assertEquals(1, hidden.get(0)[0]);
86 assertEquals(3, hidden.get(0)[1]);
87 assertEquals(6, hidden.get(1)[0]);
88 assertEquals(8, hidden.get(1)[1]);