Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
PIDModelTest	10	60	4	0	1.0100%	Show methods

Class PIDModelTest

Class PIDModelTest	Line # 10	Total Statements 60	Complexity 4	Uncovered Elements 0	TOTAL Coverage 1.0100%
testGetPairwiseScore() : void   testGetPairwiseScore() : void	1414	9.09	1.01	0.00	1.0 1.0100%
testComputePID_matchesComparisonPID() : void   testComputePID_matchesComparisonPID() : void	3232	31.031	1.01	0.00	1.0 1.0100%
testComputePID_matchShortestSequence() : void   testComputePID_matchShortestSequence() : void	9393	10.010	1.01	0.00	1.0 1.0100%
testComputePID_matchLongestSequence() : void   testComputePID_matchLongestSequence() : void	134134	10.010	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5	jalview.analysis.scoremodels.PIDModelTest.testComputePID_matchesComparisonPIDjalview.analysis.scoremodels.PIDModelTest.testComputePID_matchesComparisonPID	1PASS
	0.171875	jalview.analysis.scoremodels.PIDModelTest.testComputePID_matchShortestSequencejalview.analysis.scoremodels.PIDModelTest.testComputePID_matchShortestSequence	1PASS
	0.171875	jalview.analysis.scoremodels.PIDModelTest.testComputePID_matchLongestSequencejalview.analysis.scoremodels.PIDModelTest.testComputePID_matchLongestSequence	1PASS
	0.15625	jalview.analysis.scoremodels.PIDModelTest.testGetPairwiseScorejalview.analysis.scoremodels.PIDModelTest.testGetPairwiseScore	1PASS

 

Source view

1		package jalview.analysis.scoremodels;
2
3		import static org.testng.Assert.assertEquals;
4
5		import jalview.api.analysis.SimilarityParamsI;
6		import jalview.util.Comparison;
7
8		import org.testng.annotations.Test;
9
		100% Uncovered Elements: 0 (64) Complexity: 4 Complexity Density: 0.07
10		public class PIDModelTest
11		{
12		private static final double DELTA = 0.00001D;
13
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
14	1	@Test(groups = "Functional")...
15		public void testGetPairwiseScore()
16		{
17	1	PIDModel sm = new PIDModel();
18	1	assertEquals(sm.getPairwiseScore('A', 'A'), 1f);
19	1	assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
20	1	assertEquals(sm.getPairwiseScore('a', 'A'), 1f);
21	1	assertEquals(sm.getPairwiseScore('A', 'B'), 0f);
22	1	assertEquals(sm.getPairwiseScore('A', ' '), 0f);
23	1	assertEquals(sm.getPairwiseScore(' ', ' '), 0f);
24	1	assertEquals(sm.getPairwiseScore('.', '.'), 0f);
25	1	assertEquals(sm.getPairwiseScore('-', '-'), 0f);
26		}
27
28		/**
29		* Regression test to verify that a (suitably configured) PIDModel computes
30		* the same percentage identities as the Comparison.PID method
31		*/
		100% Uncovered Elements: 0 (31) Complexity: 1 Complexity Density: 0.03 1PASS
32	1	@Test(groups = "Functional")...
33		public void testComputePID_matchesComparisonPID()
34		{
35	1	SimilarityParamsI params = new SimilarityParams(true, true, true, true);
36
37		/*
38		* same length, no gaps
39		*/
40	1	String s1 = "ARFNQDWSGI";
41	1	String s2 = "ARKNQDQSGI";
42
43	1	new PIDModel();
44	1	double newScore = PIDModel.computePID(s1, s2, params);
45	1	double oldScore = Comparison.PID(s1, s2);
46	1	assertEquals(newScore, oldScore, DELTA);
47
48		/*
49		* same length, with gaps
50		*/
51	1	s1 = "-RFNQDWSGI";
52	1	s2 = "ARKNQ-QSGI";
53	1	new PIDModel();
54	1	newScore = PIDModel.computePID(s1, s2, params);
55	1	oldScore = Comparison.PID(s1, s2);
56	1	assertEquals(newScore, oldScore, DELTA);
57
58		/*
59		* s2 longer than s1, with gaps
60		*/
61	1	s1 = "ARK-";
62	1	s2 = "-RFNQ";
63	1	new PIDModel();
64	1	newScore = PIDModel.computePID(s1, s2, params);
65	1	oldScore = Comparison.PID(s1, s2);
66	1	assertEquals(newScore, oldScore, DELTA);
67
68		/*
69		* s1 longer than s2, with gaps
70		*/
71	1	s1 = "-RFNQ";
72	1	s2 = "ARK-";
73	1	new PIDModel();
74	1	newScore = PIDModel.computePID(s1, s2, params);
75	1	oldScore = Comparison.PID(s1, s2);
76	1	assertEquals(newScore, oldScore, DELTA);
77
78		/*
79		* same but now also with gapped columns
80		*/
81	1	s1 = "-R-F-NQ";
82	1	s2 = "AR-K--";
83	1	new PIDModel();
84	1	newScore = PIDModel.computePID(s1, s2, params);
85	1	oldScore = Comparison.PID(s1, s2);
86	1	assertEquals(newScore, oldScore, DELTA);
87		}
88
89		/**
90		* Tests for percentage identity variants where only the shorter length of two
91		* sequences is used
92		*/
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
93	1	@Test(groups = "Functional")...
94		public void testComputePID_matchShortestSequence()
95		{
96	1	String s1 = "FR-K-S";
97	1	String s2 = "FS--L";
98
99		/*
100		* match gap-gap and gap-char
101		* PID = 4/5 = 80%
102		*/
103	1	SimilarityParamsI params = new SimilarityParams(true, true, true, true);
104	1	assertEquals(PIDModel.computePID(s1, s2, params), 80d);
105
106		/*
107		* match gap-char but not gap-gap
108		* PID = 3/4 = 75%
109		*/
110	1	params = new SimilarityParams(false, true, true, true);
111	1	assertEquals(PIDModel.computePID(s1, s2, params), 75d);
112
113		/*
114		* include gaps but don't match them
115		* include gap-gap, counted as identity
116		* PID = 2/5 = 40%
117		*/
118	1	params = new SimilarityParams(true, false, true, true);
119	1	assertEquals(PIDModel.computePID(s1, s2, params), 40d);
120
121		/*
122		* include gaps but don't match them
123		* exclude gap-gap
124		* PID = 1/4 = 25%
125		*/
126	1	params = new SimilarityParams(false, false, true, true);
127	1	assertEquals(PIDModel.computePID(s1, s2, params), 25d);
128		}
129
130		/**
131		* Tests for percentage identity variants where the longer length of two
132		* sequences is used
133		*/
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
134	1	@Test(groups = "Functional")...
135		public void testComputePID_matchLongestSequence()
136		{
137	1	String s1 = "FR-K-S";
138	1	String s2 = "FS--L";
139
140		/*
141		* match gap-gap and gap-char
142		* shorter sequence treated as if with trailing gaps
143		* PID = 5/6 = 83.333...%
144		*/
145	1	SimilarityParamsI params = new SimilarityParams(true, true, true, false);
146	1	assertEquals(PIDModel.computePID(s1, s2, params), 500d / 6);
147
148		/*
149		* match gap-char but not gap-gap
150		* PID = 4/5 = 80%
151		*/
152	1	params = new SimilarityParams(false, true, true, false);
153	1	assertEquals(PIDModel.computePID(s1, s2, params), 80d);
154
155		/*
156		* include gaps but don't match them
157		* include gap-gap, counted as identity
158		* PID = 2/6 = 33.333...%
159		*/
160	1	params = new SimilarityParams(true, false, true, false);
161	1	assertEquals(PIDModel.computePID(s1, s2, params), 100d / 3);
162
163		/*
164		* include gaps but don't match them
165		* exclude gap-gap
166		* PID = 1/5 = 25%
167		*/
168	1	params = new SimilarityParams(false, false, true, false);
169	1	assertEquals(PIDModel.computePID(s1, s2, params), 20d);
170
171		/*
172		* no tests for matchGaps=true, includeGaps=false
173		* as it don't make sense
174		*/
175		}
176		}