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.
23 import static org.testng.Assert.assertEquals;
24 import static org.testng.Assert.assertSame;
26 import jalview.analysis.scoremodels.ScoreModels;
27 import jalview.api.analysis.ScoreModelI;
28 import jalview.bin.Cache;
30 import java.util.List;
32 import org.testng.annotations.BeforeClass;
33 import org.testng.annotations.Test;
35 public class CalculationChooserTest
37 @BeforeClass(alwaysRun = true)
40 // read-only Jalview properties
41 Cache.loadProperties("test/jalview/io/testProps.jvprops");
42 Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
43 Boolean.FALSE.toString());
46 @Test(groups = "Functional")
47 public void testGetApplicableScoreModels()
49 ScoreModels models = ScoreModels.getInstance();
50 ScoreModelI blosum62 = models.getBlosum62();
51 ScoreModelI pam250 = models.getPam250();
52 ScoreModelI dna = models.getDefaultModel(false);
55 * peptide models for PCA
57 List<ScoreModelI> filtered = CalculationChooser
58 .getApplicableScoreModels(false, true, true,false);
59 assertEquals(filtered.size(), 5);
60 assertSame(filtered.get(0), blosum62);
61 assertSame(filtered.get(1), pam250);
62 assertEquals(filtered.get(2).getName(), "PID");
63 assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
64 assertEquals(filtered.get(4).getName(), "Secondary Structure Similarity");
67 * peptide models for Tree are the same
69 filtered = CalculationChooser.getApplicableScoreModels(false, false, true,false);
70 assertEquals(filtered.size(), 5);
71 assertSame(filtered.get(0), blosum62);
72 assertSame(filtered.get(1), pam250);
73 assertEquals(filtered.get(2).getName(), "PID");
74 assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
75 assertEquals(filtered.get(4).getName(), "Secondary Structure Similarity");
78 * nucleotide models for PCA
80 filtered = CalculationChooser.getApplicableScoreModels(true, true, false,false);
81 assertEquals(filtered.size(), 3);
82 assertSame(filtered.get(0), dna);
83 assertEquals(filtered.get(1).getName(), "PID");
84 assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
87 * nucleotide models for Tree are the same
89 filtered = CalculationChooser.getApplicableScoreModels(true, false, false,false);
90 assertEquals(filtered.size(), 3);
91 assertSame(filtered.get(0), dna);
92 assertEquals(filtered.get(1).getName(), "PID");
93 assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
96 * enable inclusion of BLOSUM62 for nucleotide PCA (JAL-2962)
98 Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
99 Boolean.TRUE.toString());
102 * nucleotide models for Tree are unchanged
104 filtered = CalculationChooser.getApplicableScoreModels(true, false, true,false);
105 assertEquals(filtered.size(), 4);
106 assertSame(filtered.get(0), dna);
107 assertEquals(filtered.get(1).getName(), "PID");
108 assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
109 assertEquals(filtered.get(3).getName(), "Secondary Structure Similarity");
112 * nucleotide models for PCA add BLOSUM62 as last option
114 filtered = CalculationChooser.getApplicableScoreModels(true, true, false,false);
115 assertEquals(filtered.size(), 4);
116 assertSame(filtered.get(0), dna);
117 assertEquals(filtered.get(1).getName(), "PID");
118 assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
119 assertSame(filtered.get(3), blosum62);
121 filtered = CalculationChooser.getApplicableScoreModels(true, true, false,true);
122 assertEquals(filtered.size(), 1); // DNA matrix for DNA pasimap
123 for (int i=0; i<=8;i++)
125 boolean isDna = (i & 1) != 0,isPca = (i & 2) != 0,isSS = (i & 4) != 0;
127 assertEquals(CalculationChooser.getApplicableScoreModels(isDna,isPca,isSS,true).size(), (isDna) ? 1: 2);