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MappingTest | 37 | 26 | 4 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
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. | |
11 | * | |
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. | |
16 | * | |
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. | |
20 | */ | |
21 | package jalview.datamodel; | |
22 | ||
23 | import static org.testng.AssertJUnit.assertEquals; | |
24 | import static org.testng.AssertJUnit.assertSame; | |
25 | ||
26 | import jalview.gui.JvOptionPane; | |
27 | import jalview.util.MapList; | |
28 | ||
29 | import java.util.Arrays; | |
30 | ||
31 | import org.testng.annotations.BeforeClass; | |
32 | import org.testng.annotations.Test; | |
33 | ||
34 | /** | |
35 | * Test class refactored from main method | |
36 | */ | |
37 | public class MappingTest | |
38 | { | |
39 | ||
40 | 1 | @BeforeClass(alwaysRun = true) |
41 | public void setUpJvOptionPane() | |
42 | { | |
43 | 1 | JvOptionPane.setInteractiveMode(false); |
44 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
45 | } | |
46 | ||
47 | /** | |
48 | * trite test of the intersectVisContigs method for a simple DNA -> Protein | |
49 | * exon map and a range of visContigs | |
50 | */ | |
51 | 1 | @Test(groups = { "Functional" }) |
52 | public void testIntersectVisContigs() | |
53 | { | |
54 | 1 | MapList fk = new MapList(new int[] { 1, 6, 8, 13, 15, 23 }, |
55 | new int[] | |
56 | { 1, 7 }, 3, 1); | |
57 | 1 | Mapping m = new Mapping(fk); |
58 | 1 | Mapping m_1 = m |
59 | .intersectVisContigs(new int[] | |
60 | { fk.getFromLowest(), fk.getFromHighest() }); | |
61 | 1 | Mapping m_2 = m.intersectVisContigs(new int[] { 1, 7, 11, 20 }); |
62 | ||
63 | // assertions from output values 'as is', not checked for correctness | |
64 | 1 | String result = Arrays.deepToString(m_1.map.getFromRanges().toArray()); |
65 | 1 | System.out.println(result); |
66 | 1 | assertEquals("[[1, 6], [8, 13], [15, 23]]", result); |
67 | ||
68 | 1 | result = Arrays.deepToString(m_2.map.getFromRanges().toArray()); |
69 | 1 | System.out.println(result); |
70 | 1 | assertEquals("[[1, 6], [11, 13], [15, 20]]", result); |
71 | } | |
72 | ||
73 | 1 | @Test(groups = { "Functional" }) |
74 | public void testToString() | |
75 | { | |
76 | /* | |
77 | * with no sequence | |
78 | */ | |
79 | 1 | MapList fk = new MapList(new int[] { 1, 6, 8, 13 }, new int[] { 4, 7 }, |
80 | 3, 1); | |
81 | 1 | Mapping m = new Mapping(fk); |
82 | 1 | assertEquals("[ [1, 6] [8, 13] ] 3:1 to [ [4, 7] ] ", m.toString()); |
83 | ||
84 | /* | |
85 | * with a sequence | |
86 | */ | |
87 | 1 | SequenceI seq = new Sequence("Seq1", ""); |
88 | 1 | m = new Mapping(seq, fk); |
89 | 1 | assertEquals("[ [1, 6] [8, 13] ] 3:1 to [ [4, 7] ] Seq1", m.toString()); |
90 | } | |
91 | ||
92 | 1 | @Test(groups = { "Functional" }) |
93 | public void testCopyConstructor() | |
94 | { | |
95 | 1 | MapList ml = new MapList(new int[] { 1, 6, 8, 13 }, new int[] { 4, 7 }, |
96 | 3, 1); | |
97 | 1 | SequenceI seq = new Sequence("seq1", "agtacg"); |
98 | 1 | Mapping m = new Mapping(seq, ml); |
99 | 1 | m.setMappedFromId("abc"); |
100 | 1 | Mapping copy = new Mapping(m); |
101 | 1 | assertEquals("abc", copy.getMappedFromId()); |
102 | 1 | assertEquals(ml, copy.getMap()); |
103 | 1 | assertSame(seq, copy.getTo()); |
104 | } | |
105 | } |