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", "-a-MMMaaaaaaaaaaaaaaaa");
41 SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
42 SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
43 SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
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,
56 // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
57 seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", 8, 12,
61 * select the first five columns --> Metal in seq1 cols 4-5
63 SequenceGroup sg = new SequenceGroup();
64 sg.setStartRes(0); // base 0
66 sg.addSequence(seq1, false);
67 sg.addSequence(seq2, false);
68 sg.addSequence(seq3, false);
69 sg.addSequence(seq4, false);
71 BitSet bs = new BitSet();
72 int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
74 assertEquals(1, seqCount);
75 assertEquals(2, bs.cardinality());
76 assertTrue(bs.get(3)); // base 0
77 assertTrue(bs.get(4));
80 * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7
84 seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
85 assertEquals(2, seqCount);
86 assertEquals(4, bs.cardinality());
87 assertTrue(bs.get(3));
88 assertTrue(bs.get(4));
89 assertTrue(bs.get(5));
90 assertTrue(bs.get(6));
93 * select column 14: Metal in seq3 only
98 seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
99 assertEquals(1, seqCount);
100 assertEquals(1, bs.cardinality());
101 assertTrue(bs.get(13));
104 * select columns 18-20: no Metal feature
109 seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
110 assertEquals(0, seqCount);
111 assertEquals(0, bs.cardinality());
114 * columns 11-13 should not match disulfide bond at 8/12
119 seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
121 assertEquals(0, seqCount);
122 assertEquals(0, bs.cardinality());
125 * columns 6-18 should match disulfide bond at columns 9, 14
130 seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
132 assertEquals(1, seqCount);
133 assertEquals(2, bs.cardinality());
134 assertTrue(bs.get(8));
135 assertTrue(bs.get(13));
138 * look for a feature that isn't there
143 seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
144 assertEquals(0, seqCount);
145 assertEquals(0, bs.cardinality());