Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PIDModelTest	10	73	4	1.0100%	Show methods

Class PIDModelTest

Class PIDModelTest	Line # 10	Total Statements 73	Complexity 4	TOTAL Coverage 1.0100%
testGetPairwiseScore() : void   testGetPairwiseScore() : void	1414	9.09	1.01	1.0 1.0100%
testComputePID_matchesComparisonPID() : void   testComputePID_matchesComparisonPID() : void	3232	36.036	1.01	1.0 1.0100%
testComputePID_matchShortestSequence() : void   testComputePID_matchShortestSequence() : void	9999	14.014	1.01	1.0 1.0100%
testComputePID_matchLongestSequence() : void   testComputePID_matchLongestSequence() : void	144144	14.014	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.48051947	jalview.analysis.scoremodels.PIDModelTest.testComputePID_matchesComparisonPIDjalview.analysis.scoremodels.PIDModelTest.testComputePID_matchesComparisonPID	1PASS
	0.19480519	jalview.analysis.scoremodels.PIDModelTest.testComputePID_matchShortestSequencejalview.analysis.scoremodels.PIDModelTest.testComputePID_matchShortestSequence	1PASS
	0.19480519	jalview.analysis.scoremodels.PIDModelTest.testComputePID_matchLongestSequencejalview.analysis.scoremodels.PIDModelTest.testComputePID_matchLongestSequence	1PASS
	0.12987013	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 (77) Complexity: 4 Complexity Density: 0.05
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 (36) 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		// and verify PIDModel calculation is symmetric
48	1	assertEquals(newScore, PIDModel.computePID(s2, s1, params));
49
50		/*
51		* same length, with gaps
52		*/
53	1	s1 = "-RFNQDWSGI";
54	1	s2 = "ARKNQ-QSGI";
55	1	new PIDModel();
56	1	newScore = PIDModel.computePID(s1, s2, params);
57	1	oldScore = Comparison.PID(s1, s2);
58	1	assertEquals(newScore, oldScore, DELTA);
59	1	assertEquals(newScore, PIDModel.computePID(s2, s1, params));
60
61		/*
62		* s2 longer than s1, with gaps
63		*/
64	1	s1 = "ARK-";
65	1	s2 = "-RFNQ";
66	1	new PIDModel();
67	1	newScore = PIDModel.computePID(s1, s2, params);
68	1	oldScore = Comparison.PID(s1, s2);
69	1	assertEquals(newScore, oldScore, DELTA);
70	1	assertEquals(newScore, PIDModel.computePID(s2, s1, params));
71
72		/*
73		* s1 longer than s2, with gaps
74		*/
75	1	s1 = "-RFNQ";
76	1	s2 = "ARK-";
77	1	new PIDModel();
78	1	newScore = PIDModel.computePID(s1, s2, params);
79	1	oldScore = Comparison.PID(s1, s2);
80	1	assertEquals(newScore, oldScore, DELTA);
81	1	assertEquals(newScore, PIDModel.computePID(s2, s1, params));
82
83		/*
84		* same but now also with gapped columns
85		*/
86	1	s1 = "-R-F-NQ";
87	1	s2 = "AR-K--";
88	1	new PIDModel();
89	1	newScore = PIDModel.computePID(s1, s2, params);
90	1	oldScore = Comparison.PID(s1, s2);
91	1	assertEquals(newScore, oldScore, DELTA);
92	1	assertEquals(newScore, PIDModel.computePID(s2, s1, params));
93		}
94
95		/**
96		* Tests for percentage identity variants where only the shorter length of two
97		* sequences is used
98		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
99	1	@Test(groups = "Functional")...
100		public void testComputePID_matchShortestSequence()
101		{
102	1	String s1 = "FR-K-S";
103	1	String s2 = "FS--L";
104
105		/*
106		* match gap-gap and gap-char
107		* PID = 4/5 = 80%
108		*/
109	1	SimilarityParamsI params = new SimilarityParams(true, true, true, true);
110	1	assertEquals(PIDModel.computePID(s1, s2, params), 80d);
111	1	assertEquals(PIDModel.computePID(s2, s1, params), 80d);
112
113		/*
114		* match gap-char but not gap-gap
115		* PID = 3/4 = 75%
116		*/
117	1	params = new SimilarityParams(false, true, true, true);
118	1	assertEquals(PIDModel.computePID(s1, s2, params), 75d);
119	1	assertEquals(PIDModel.computePID(s2, s1, params), 75d);
120
121		/*
122		* include gaps but don't match them
123		* include gap-gap, counted as identity
124		* PID = 2/5 = 40%
125		*/
126	1	params = new SimilarityParams(true, false, true, true);
127	1	assertEquals(PIDModel.computePID(s1, s2, params), 40d);
128	1	assertEquals(PIDModel.computePID(s2, s1, params), 40d);
129
130		/*
131		* include gaps but don't match them
132		* exclude gap-gap
133		* PID = 1/4 = 25%
134		*/
135	1	params = new SimilarityParams(false, false, true, true);
136	1	assertEquals(PIDModel.computePID(s1, s2, params), 25d);
137	1	assertEquals(PIDModel.computePID(s2, s1, params), 25d);
138		}
139
140		/**
141		* Tests for percentage identity variants where the longer length of two
142		* sequences is used
143		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
144	1	@Test(groups = "Functional")...
145		public void testComputePID_matchLongestSequence()
146		{
147	1	String s1 = "FR-K-S";
148	1	String s2 = "FS--L";
149
150		/*
151		* match gap-gap and gap-char
152		* shorter sequence treated as if with trailing gaps
153		* PID = 5/6 = 83.333...%
154		*/
155	1	SimilarityParamsI params = new SimilarityParams(true, true, true, false);
156	1	assertEquals(PIDModel.computePID(s1, s2, params), 500d / 6);
157	1	assertEquals(PIDModel.computePID(s2, s1, params), 500d / 6);
158
159		/*
160		* match gap-char but not gap-gap
161		* PID = 4/5 = 80%
162		*/
163	1	params = new SimilarityParams(false, true, true, false);
164	1	assertEquals(PIDModel.computePID(s1, s2, params), 80d);
165	1	assertEquals(PIDModel.computePID(s2, s1, params), 80d);
166
167		/*
168		* include gaps but don't match them
169		* include gap-gap, counted as identity
170		* PID = 2/6 = 33.333...%
171		*/
172	1	params = new SimilarityParams(true, false, true, false);
173	1	assertEquals(PIDModel.computePID(s1, s2, params), 100d / 3);
174	1	assertEquals(PIDModel.computePID(s2, s1, params), 100d / 3);
175
176		/*
177		* include gaps but don't match them
178		* exclude gap-gap
179		* PID = 1/5 = 25%
180		*/
181	1	params = new SimilarityParams(false, false, true, false);
182	1	assertEquals(PIDModel.computePID(s1, s2, params), 20d);
183	1	assertEquals(PIDModel.computePID(s2, s1, params), 20d);
184
185		/*
186		* no tests for matchGaps=true, includeGaps=false
187		* as it don't make sense
188		*/
189		}
190		}