Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ScoreModelsTest	34	42	5	0.791666779.2%	Show methods

Class ScoreModelsTest

Class ScoreModelsTest	Line # 34	Total Statements 42	Complexity 5	TOTAL Coverage 0.791666779.2%
testConstructor() : void   testConstructor() : void	4040	37.037	1.01	1.0 1.0100%
printAllMatrices_tabDelimited() : void   printAllMatrices_tabDelimited() : void	100100	1.01	1.01	0.0 0.00%
printAllMatrices_asHtml() : void   printAllMatrices_asHtml() : void	112112	1.01	1.01	0.0 0.00%
printAllMatrices(boolean) : void   printAllMatrices(boolean) : void	123123	3.03	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.7916667	jalview.analysis.scoremodels.ScoreModelsTest.testConstructorjalview.analysis.scoremodels.ScoreModelsTest.testConstructor	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.analysis.scoremodels;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertTrue;
26
27		import jalview.api.analysis.PairwiseScoreModelI;
28		import jalview.api.analysis.ScoreModelI;
29
30		import java.util.Iterator;
31
32		import org.testng.annotations.Test;
33
		79.2% Uncovered Elements: 10 (48) Complexity: 5 Complexity Density: 0.12
34		public class ScoreModelsTest
35		{
36		/**
37		* Verify that the singleton constructor successfully loads Jalview's built-in
38		* score models
39		*/
		100% Uncovered Elements: 0 (37) Complexity: 1 Complexity Density: 0.03 1PASS
40	1	@Test(groups = "Functional")...
41		public void testConstructor()
42		{
43	1	Iterator<ScoreModelI> models = ScoreModels.getInstance().getModels()
44		.iterator();
45	1	assertTrue(models.hasNext());
46
47		/*
48		* models are served in order of addition
49		*/
50	1	ScoreModelI sm = models.next();
51	1	assertTrue(sm instanceof SimilarityScoreModel);
52	1	assertTrue(sm instanceof PairwiseScoreModelI);
53	1	assertFalse(sm instanceof DistanceScoreModel);
54	1	assertEquals(sm.getName(), "BLOSUM62");
55	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'),
56		-3f);
57
58	1	sm = models.next();
59	1	assertTrue(sm instanceof SimilarityScoreModel);
60	1	assertTrue(sm instanceof PairwiseScoreModelI);
61	1	assertFalse(sm instanceof DistanceScoreModel);
62	1	assertEquals(sm.getName(), "PAM250");
63	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'),
64		-4f);
65
66	1	sm = models.next();
67	1	assertTrue(sm instanceof SimilarityScoreModel);
68	1	assertTrue(sm instanceof PairwiseScoreModelI);
69	1	assertFalse(sm instanceof DistanceScoreModel);
70	1	assertEquals(sm.getName(), "DNA");
71	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
72
73	1	sm = models.next();
74	1	assertTrue(sm instanceof SimilarityScoreModel);
75	1	assertTrue(sm instanceof PairwiseScoreModelI);
76	1	assertFalse(sm instanceof DistanceScoreModel);
77	1	assertEquals(sm.getName(), "PID");
78	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
79	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);
80
81	1	sm = models.next();
82	1	assertFalse(sm instanceof SimilarityScoreModel);
83	1	assertFalse(sm instanceof PairwiseScoreModelI);
84	1	assertTrue(sm instanceof DistanceScoreModel);
85	1	assertEquals(sm.getName(), "Sequence Feature Similarity");
86
87	1	sm = models.next();
88	1	assertFalse(sm instanceof SimilarityScoreModel);
89	1	assertFalse(sm instanceof PairwiseScoreModelI);
90	1	assertTrue(sm instanceof DistanceScoreModel);
91	1	assertEquals(sm.getName(), "Secondary Structure Similarity");
92		}
93
94		/**
95		* 'Test' that prints out score matrices in tab-delimited format. This test is
96		* intentionally not assigned to any group so would not be run as part of a
97		* suite. It makes no assertions and is just provided as a utility method for
98		* printing out matrices. Relocated here from ScoreMatrixPrinter.
99		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 1PASS
100	0	@Test(groups = "none")...
101		public void printAllMatrices_tabDelimited()
102		{
103	0	printAllMatrices(false);
104		}
105
106		/**
107		* 'Test' that prints out score matrices in html format. This test is
108		* intentionally not assigned to any group so would not be run as part of a
109		* suite. It makes no assertions and is just provided as a utility method for
110		* printing out matrices. Relocated here from ScoreMatrixPrinter.
111		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 1PASS
112	0	@Test(groups = "none")...
113		public void printAllMatrices_asHtml()
114		{
115	0	printAllMatrices(true);
116		}
117
118		/**
119		* Print all registered ScoreMatrix as plain or html tables
120		*
121		* @param asHtml
122		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
123	0	protected void printAllMatrices(boolean asHtml)...
124		{
125	0	for (ScoreModelI sm : ScoreModels.getInstance().getModels())
126		{
127	0	if (sm instanceof ScoreMatrix)
128		{
129	0	System.out.println(((ScoreMatrix) sm).outputMatrix(asHtml));
130		}
131		}
132		}
133		}