Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CalculationChooserTest	35	48	4	1.0100%	Show methods

Class CalculationChooserTest

Class CalculationChooserTest	Line # 35	Total Statements 48	Complexity 4	TOTAL Coverage 1.0100%
setUp() : void   setUp() : void	3737	2.02	1.01	1.0 1.0100%
testGetApplicableScoreModels() : void   testGetApplicableScoreModels() : void	4646	46.046	3.03	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.9444444	jalview.gui.CalculationChooserTest.testGetApplicableScoreModelsjalview.gui.CalculationChooserTest.testGetApplicableScoreModels	1PASS

 

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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
		100% Uncovered Elements: 0 (54) Complexity: 4 Complexity Density: 0.08
35		public class CalculationChooserTest
36		{
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
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
		100% Uncovered Elements: 0 (50) Complexity: 3 Complexity Density: 0.07 1PASS
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		}