Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ScoreModelsTest	34	49	5	0.818181881.8%	Show methods

Class ScoreModelsTest

Class ScoreModelsTest	Line # 34	Total Statements 49	Complexity 5	TOTAL Coverage 0.818181881.8%
testConstructor() : void   testConstructor() : void	4040	44.044	1.01	1.0 1.0100%
printAllMatrices_tabDelimited() : void   printAllMatrices_tabDelimited() : void	108108	1.01	1.01	0.0 0.00%
printAllMatrices_asHtml() : void   printAllMatrices_asHtml() : void	120120	1.01	1.01	0.0 0.00%
printAllMatrices(boolean) : void   printAllMatrices(boolean) : void	131131	3.03	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.8181818	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
		81.8% Uncovered Elements: 10 (55) Complexity: 5 Complexity Density: 0.1
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 (44) Complexity: 1 Complexity Density: 0.02 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(), "Mat3di");
78	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), -1f);
79	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 6f);
80
81	1	sm = models.next();
82	1	assertTrue(sm instanceof SimilarityScoreModel);
83	1	assertTrue(sm instanceof PairwiseScoreModelI);
84	1	assertFalse(sm instanceof DistanceScoreModel);
85	1	assertEquals(sm.getName(), "PID");
86	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
87	1	assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);
88
89	1	sm = models.next();
90	1	assertFalse(sm instanceof SimilarityScoreModel);
91	1	assertFalse(sm instanceof PairwiseScoreModelI);
92	1	assertTrue(sm instanceof DistanceScoreModel);
93	1	assertEquals(sm.getName(), "Sequence Feature Similarity");
94
95	1	sm = models.next();
96	1	assertFalse(sm instanceof SimilarityScoreModel);
97	1	assertFalse(sm instanceof PairwiseScoreModelI);
98	1	assertTrue(sm instanceof DistanceScoreModel);
99	1	assertEquals(sm.getName(), "Secondary Structure Similarity");
100		}
101
102		/**
103		* 'Test' that prints out score matrices in tab-delimited format. This test is
104		* intentionally not assigned to any group so would not be run as part of a
105		* suite. It makes no assertions and is just provided as a utility method for
106		* printing out matrices. Relocated here from ScoreMatrixPrinter.
107		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 1PASS
108	0	@Test(groups = "none")...
109		public void printAllMatrices_tabDelimited()
110		{
111	0	printAllMatrices(false);
112		}
113
114		/**
115		* 'Test' that prints out score matrices in html format. This test is
116		* intentionally not assigned to any group so would not be run as part of a
117		* suite. It makes no assertions and is just provided as a utility method for
118		* printing out matrices. Relocated here from ScoreMatrixPrinter.
119		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 1PASS
120	0	@Test(groups = "none")...
121		public void printAllMatrices_asHtml()
122		{
123	0	printAllMatrices(true);
124		}
125
126		/**
127		* Print all registered ScoreMatrix as plain or html tables
128		*
129		* @param asHtml
130		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
131	0	protected void printAllMatrices(boolean asHtml)...
132		{
133	0	for (ScoreModelI sm : ScoreModels.getInstance().getModels())
134		{
135	0	if (sm instanceof ScoreMatrix)
136		{
137	0	System.out.println(((ScoreMatrix) sm).outputMatrix(asHtml));
138		}
139		}
140		}
141		}