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CalculationChooserTest | 35 | 48 | 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.gui; | |
22 | ||
23 | import static org.testng.Assert.assertEquals; | |
24 | import static org.testng.Assert.assertSame; | |
25 | ||
26 | import jalview.analysis.scoremodels.ScoreModels; | |
27 | import jalview.api.analysis.ScoreModelI; | |
28 | import jalview.bin.Cache; | |
29 | ||
30 | import java.util.List; | |
31 | ||
32 | import org.testng.annotations.BeforeClass; | |
33 | import org.testng.annotations.Test; | |
34 | ||
35 | public class CalculationChooserTest | |
36 | { | |
37 | 1 | @BeforeClass(alwaysRun = true) |
38 | public void setUp() | |
39 | { | |
40 | // read-only Jalview properties | |
41 | 1 | Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
42 | 1 | Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE", |
43 | Boolean.FALSE.toString()); | |
44 | } | |
45 | ||
46 | 1 | @Test(groups = "Functional") |
47 | public void testGetApplicableScoreModels() | |
48 | { | |
49 | 1 | ScoreModels models = ScoreModels.getInstance(); |
50 | 1 | ScoreModelI blosum62 = models.getBlosum62(); |
51 | 1 | ScoreModelI pam250 = models.getPam250(); |
52 | 1 | ScoreModelI dna = models.getDefaultModel(false); |
53 | ||
54 | /* | |
55 | * peptide models for PCA | |
56 | */ | |
57 | 1 | List<ScoreModelI> filtered = CalculationChooser |
58 | .getApplicableScoreModels(false, true, true, false); | |
59 | 1 | assertEquals(filtered.size(), 5); |
60 | 1 | assertSame(filtered.get(0), blosum62); |
61 | 1 | assertSame(filtered.get(1), pam250); |
62 | 1 | assertEquals(filtered.get(2).getName(), "PID"); |
63 | 1 | assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity"); |
64 | 1 | assertEquals(filtered.get(4).getName(), |
65 | "Secondary Structure Similarity"); | |
66 | ||
67 | /* | |
68 | * peptide models for Tree are the same | |
69 | */ | |
70 | 1 | filtered = CalculationChooser.getApplicableScoreModels(false, false, |
71 | true, false); | |
72 | 1 | assertEquals(filtered.size(), 5); |
73 | 1 | assertSame(filtered.get(0), blosum62); |
74 | 1 | assertSame(filtered.get(1), pam250); |
75 | 1 | assertEquals(filtered.get(2).getName(), "PID"); |
76 | 1 | assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity"); |
77 | 1 | assertEquals(filtered.get(4).getName(), |
78 | "Secondary Structure Similarity"); | |
79 | ||
80 | /* | |
81 | * nucleotide models for PCA | |
82 | */ | |
83 | 1 | filtered = CalculationChooser.getApplicableScoreModels(true, true, |
84 | false, false); | |
85 | 1 | assertEquals(filtered.size(), 3); |
86 | 1 | assertSame(filtered.get(0), dna); |
87 | 1 | assertEquals(filtered.get(1).getName(), "PID"); |
88 | 1 | assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity"); |
89 | ||
90 | /* | |
91 | * nucleotide models for Tree are the same | |
92 | */ | |
93 | 1 | filtered = CalculationChooser.getApplicableScoreModels(true, false, |
94 | false, false); | |
95 | 1 | assertEquals(filtered.size(), 3); |
96 | 1 | assertSame(filtered.get(0), dna); |
97 | 1 | assertEquals(filtered.get(1).getName(), "PID"); |
98 | 1 | assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity"); |
99 | ||
100 | /* | |
101 | * enable inclusion of BLOSUM62 for nucleotide PCA (JAL-2962) | |
102 | */ | |
103 | 1 | Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE", |
104 | Boolean.TRUE.toString()); | |
105 | ||
106 | /* | |
107 | * nucleotide models for Tree are unchanged | |
108 | */ | |
109 | 1 | filtered = CalculationChooser.getApplicableScoreModels(true, false, |
110 | true, false); | |
111 | 1 | assertEquals(filtered.size(), 4); |
112 | 1 | assertSame(filtered.get(0), dna); |
113 | 1 | assertEquals(filtered.get(1).getName(), "PID"); |
114 | 1 | assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity"); |
115 | 1 | assertEquals(filtered.get(3).getName(), |
116 | "Secondary Structure Similarity"); | |
117 | ||
118 | /* | |
119 | * nucleotide models for PCA add BLOSUM62 as last option | |
120 | */ | |
121 | 1 | filtered = CalculationChooser.getApplicableScoreModels(true, true, |
122 | false, false); | |
123 | 1 | assertEquals(filtered.size(), 4); |
124 | 1 | assertSame(filtered.get(0), dna); |
125 | 1 | assertEquals(filtered.get(1).getName(), "PID"); |
126 | 1 | assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity"); |
127 | 1 | assertSame(filtered.get(3), blosum62); |
128 | ||
129 | 1 | filtered = CalculationChooser.getApplicableScoreModels(true, true, |
130 | false, true); | |
131 | 1 | assertEquals(filtered.size(), 1); // DNA matrix for DNA pasimap |
132 | 10 | for (int i = 0; i <= 8; i++) |
133 | { | |
134 | 9 | boolean isDna = (i & 1) != 0, isPca = (i & 2) != 0, |
135 | isSS = (i & 4) != 0; | |
136 | ||
137 | 9 | assertEquals(CalculationChooser |
138 | .getApplicableScoreModels(isDna, isPca, isSS, true).size(), | |
139 | 9 | (isDna) ? 1 : 2); |
140 | } | |
141 | } | |
142 | } |