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CigarArrayTest | 30 | 59 | 2 |
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.Assert.assertEquals; | |
24 | ||
25 | import jalview.gui.JvOptionPane; | |
26 | ||
27 | import org.testng.annotations.BeforeClass; | |
28 | import org.testng.annotations.Test; | |
29 | ||
30 | public class CigarArrayTest | |
31 | { | |
32 | 1 | @BeforeClass(alwaysRun = true) |
33 | public void setUpJvOptionPane() | |
34 | { | |
35 | 1 | JvOptionPane.setInteractiveMode(false); |
36 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
37 | } | |
38 | ||
39 | 1 | @Test(groups = "Functional") |
40 | public void testConstructor() | |
41 | { | |
42 | 1 | SequenceI seq1 = new Sequence("sq1", |
43 | "ASFDDABACBACBACBACBACBACBABCABCBACBABCAB"); | |
44 | 1 | Sequence seq2 = new Sequence("sq2", |
45 | "TTTTTTACBCBABCABCABCABCBACBACBABCABCABCBA"); | |
46 | ||
47 | // construct alignment | |
48 | 1 | AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); |
49 | ||
50 | // hide columns | |
51 | 1 | HiddenColumns hc = new HiddenColumns(); |
52 | 1 | hc.hideColumns(3, 6); |
53 | 1 | hc.hideColumns(16, 20); |
54 | ||
55 | // select group | |
56 | 1 | SequenceGroup sg1 = new SequenceGroup(); |
57 | 1 | sg1.addSequence(seq1, false); |
58 | 1 | sg1.setStartRes(2); |
59 | 1 | sg1.setEndRes(23); |
60 | ||
61 | // Cigar array meanings: | |
62 | // M = match | |
63 | // D = deletion | |
64 | // I = insertion | |
65 | // number preceding M/D/I is the number of residues which | |
66 | // match/are deleted/are inserted | |
67 | // In the CigarArray constructor only matches or deletions are created, as | |
68 | // we are comparing a sequence to its own subsequence (the group) + hidden | |
69 | // columns. | |
70 | ||
71 | // no hidden columns case | |
72 | 1 | CigarArray cig = new CigarArray(al, null, sg1); |
73 | 1 | String result = cig.getCigarstring(); |
74 | 1 | assertEquals(result, "22M"); |
75 | ||
76 | 1 | cig = new CigarArray(al, hc, sg1); |
77 | 1 | result = cig.getCigarstring(); |
78 | 1 | assertEquals(result, "1M4D9M5D3M"); |
79 | ||
80 | // group starts at hidden cols | |
81 | 1 | sg1.setStartRes(3); |
82 | 1 | cig = new CigarArray(al, hc, sg1); |
83 | 1 | result = cig.getCigarstring(); |
84 | 1 | assertEquals(result, "4D9M5D3M"); |
85 | ||
86 | // group starts at last but 1 hidden col | |
87 | 1 | sg1.setStartRes(5); |
88 | 1 | cig = new CigarArray(al, hc, sg1); |
89 | 1 | result = cig.getCigarstring(); |
90 | 1 | assertEquals(result, "2D9M5D3M"); |
91 | ||
92 | // group starts at last hidden col | |
93 | 1 | sg1.setStartRes(6); |
94 | 1 | cig = new CigarArray(al, hc, sg1); |
95 | 1 | result = cig.getCigarstring(); |
96 | 1 | assertEquals(result, "1D9M5D3M"); |
97 | ||
98 | // group starts just after hidden region | |
99 | 1 | sg1.setStartRes(7); |
100 | 1 | cig = new CigarArray(al, hc, sg1); |
101 | 1 | result = cig.getCigarstring(); |
102 | 1 | assertEquals(result, "9M5D3M"); |
103 | ||
104 | // group ends just before start of hidden region | |
105 | 1 | sg1.setStartRes(5); |
106 | 1 | sg1.setEndRes(15); |
107 | 1 | cig = new CigarArray(al, hc, sg1); |
108 | 1 | result = cig.getCigarstring(); |
109 | 1 | assertEquals(result, "2D9M"); |
110 | ||
111 | // group ends at start of hidden region | |
112 | 1 | sg1.setEndRes(16); |
113 | 1 | cig = new CigarArray(al, hc, sg1); |
114 | 1 | result = cig.getCigarstring(); |
115 | 1 | assertEquals(result, "2D9M1D"); |
116 | ||
117 | // group ends 1 after start of hidden region | |
118 | 1 | sg1.setEndRes(17); |
119 | 1 | cig = new CigarArray(al, hc, sg1); |
120 | 1 | result = cig.getCigarstring(); |
121 | 1 | assertEquals(result, "2D9M2D"); |
122 | ||
123 | // group ends at end of hidden region | |
124 | 1 | sg1.setEndRes(20); |
125 | 1 | cig = new CigarArray(al, hc, sg1); |
126 | 1 | result = cig.getCigarstring(); |
127 | 1 | assertEquals(result, "2D9M5D"); |
128 | ||
129 | // group ends just after end of hidden region | |
130 | 1 | sg1.setEndRes(21); |
131 | 1 | cig = new CigarArray(al, hc, sg1); |
132 | 1 | result = cig.getCigarstring(); |
133 | 1 | assertEquals(result, "2D9M5D1M"); |
134 | ||
135 | // group ends 2 after end of hidden region | |
136 | 1 | sg1.setEndRes(22); |
137 | 1 | cig = new CigarArray(al, hc, sg1); |
138 | 1 | result = cig.getCigarstring(); |
139 | 1 | assertEquals(result, "2D9M5D2M"); |
140 | } | |
141 | } |