Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ScoreModelsTest	14	37	5	10	0.7674418776.7%	Show methods

Class ScoreModelsTest

Class ScoreModelsTest	Line # 14	Total Statements 37	Complexity 5	Uncovered Elements 10	TOTAL Coverage 0.7674418776.7%
testConstructor() : void   testConstructor() : void	2020	32.032	1.01	0.00	1.0 1.0100%
printAllMatrices_tabDelimited() : void   printAllMatrices_tabDelimited() : void	7272	1.01	1.01	1.01	0.0 0.00%
printAllMatrices_asHtml() : void   printAllMatrices_asHtml() : void	8484	1.01	1.01	1.01	0.0 0.00%
printAllMatrices(boolean) : void   printAllMatrices(boolean) : void	9595	3.03	2.02	5.05	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.76744187	jalview.analysis.scoremodels.ScoreModelsTest.testConstructorjalview.analysis.scoremodels.ScoreModelsTest.testConstructor	1PASS

 

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1		package jalview.analysis.scoremodels;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertFalse;
5		import static org.testng.Assert.assertTrue;
6
7		import jalview.api.analysis.PairwiseScoreModelI;
8		import jalview.api.analysis.ScoreModelI;
9
10		import java.util.Iterator;
11
12		import org.testng.annotations.Test;
13
		76.7% Uncovered Elements: 10 (43) Complexity: 5 Complexity Density: 0.14
14		public class ScoreModelsTest
15		{
16		/**
17		* Verify that the singleton constructor successfully loads Jalview's built-in
18		* score models
19		*/
		100% Uncovered Elements: 0 (32) Complexity: 1 Complexity Density: 0.03 1PASS
20	1	@Test(groups = "Functional")...
21		public void testConstructor()
22		{
23	1	Iterator<ScoreModelI> models = ScoreModels.getInstance().getModels()
24		.iterator();
25	1	assertTrue(models.hasNext());
26
27		/*
28		* models are served in order of addition
29		*/
30	1	ScoreModelI sm = models.next();
31	1	assertTrue(sm instanceof SimilarityScoreModel);
32	1	assertTrue(sm instanceof PairwiseScoreModelI);
33	1	assertFalse(sm instanceof DistanceScoreModel);
34	1	assertEquals(sm.getName(), "BLOSUM62");
35	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'), -3f);
36
37	1	sm = models.next();
38	1	assertTrue(sm instanceof SimilarityScoreModel);
39	1	assertTrue(sm instanceof PairwiseScoreModelI);
40	1	assertFalse(sm instanceof DistanceScoreModel);
41	1	assertEquals(sm.getName(), "PAM250");
42	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), -4f);
43
44	1	sm = models.next();
45	1	assertTrue(sm instanceof SimilarityScoreModel);
46	1	assertTrue(sm instanceof PairwiseScoreModelI);
47	1	assertFalse(sm instanceof DistanceScoreModel);
48	1	assertEquals(sm.getName(), "PID");
49	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
50	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);
51
52	1	sm = models.next();
53	1	assertTrue(sm instanceof SimilarityScoreModel);
54	1	assertTrue(sm instanceof PairwiseScoreModelI);
55	1	assertFalse(sm instanceof DistanceScoreModel);
56	1	assertEquals(sm.getName(), "DNA");
57	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
58
59	1	sm = models.next();
60	1	assertFalse(sm instanceof SimilarityScoreModel);
61	1	assertFalse(sm instanceof PairwiseScoreModelI);
62	1	assertTrue(sm instanceof DistanceScoreModel);
63	1	assertEquals(sm.getName(), "Sequence Feature Similarity");
64		}
65
66		/**
67		* 'Test' that prints out score matrices in tab-delimited format. This test is
68		* intentionally not assigned to any group so would not be run as part of a
69		* suite. It makes no assertions and is just provided as a utility method for
70		* printing out matrices. Relocated here from ScoreMatrixPrinter.
71		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 1PASS
72	0	@Test(groups = "none")...
73		public void printAllMatrices_tabDelimited()
74		{
75	0	printAllMatrices(false);
76		}
77
78		/**
79		* 'Test' that prints out score matrices in html format. This test is
80		* intentionally not assigned to any group so would not be run as part of a
81		* suite. It makes no assertions and is just provided as a utility method for
82		* printing out matrices. Relocated here from ScoreMatrixPrinter.
83		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 1PASS
84	0	@Test(groups = "none")...
85		public void printAllMatrices_asHtml()
86		{
87	0	printAllMatrices(true);
88		}
89
90		/**
91		* Print all registered ScoreMatrix as plain or html tables
92		*
93		* @param asHtml
94		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
95	0	protected void printAllMatrices(boolean asHtml)...
96		{
97	0	for (ScoreModelI sm : ScoreModels.getInstance().getModels())
98		{
99	0	if (sm instanceof ScoreMatrix)
100		{
101	0	System.out.println(((ScoreMatrix) sm).outputMatrix(asHtml));
102		}
103		}
104		}
105		}