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.
21 package jalview.controller;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertTrue;
26 import jalview.datamodel.Sequence;
27 import jalview.datamodel.SequenceFeature;
28 import jalview.datamodel.SequenceGroup;
29 import jalview.datamodel.SequenceI;
31 import java.util.BitSet;
33 import org.testng.annotations.Test;
35 public class AlignViewControllerTest
37 @Test(groups = "Functional")
38 public void testFindColumnsWithFeature()
40 SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
41 SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
42 SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
43 SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
46 * features start/end are base 1
48 seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
50 seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
52 seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f,
54 seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
58 * select the first three columns --> Metal in seq1 2-3
60 SequenceGroup sg = new SequenceGroup();
61 sg.setStartRes(0); // base 0
63 sg.addSequence(seq1, false);
64 sg.addSequence(seq2, false);
65 sg.addSequence(seq3, false);
66 sg.addSequence(seq4, false);
68 BitSet bs = new BitSet();
69 int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
71 assertEquals(1, seqCount);
72 assertEquals(2, bs.cardinality());
73 assertTrue(bs.get(1));
74 assertTrue(bs.get(2));
77 * select the first four columns: Metal in seq1 2:4, seq2 4:4
81 seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
82 assertEquals(2, seqCount);
83 assertEquals(3, bs.cardinality());
84 assertTrue(bs.get(1));
85 assertTrue(bs.get(2));
86 assertTrue(bs.get(3));
89 * select column 11: Metal in seq3 only
94 seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
95 assertEquals(1, seqCount);
96 assertEquals(1, bs.cardinality());
97 assertTrue(bs.get(10));
100 * select columns 16-20: no Metal feature
105 seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
106 assertEquals(0, seqCount);
107 assertEquals(0, bs.cardinality());
110 * look for a feature that isn't there
115 seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
116 assertEquals(0, seqCount);
117 assertEquals(0, bs.cardinality());