Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PIDModelTest	30	73	4	1.0100%	Show methods

Class PIDModelTest

Class PIDModelTest	Line # 30	Total Statements 73	Complexity 4	TOTAL Coverage 1.0100%
testGetPairwiseScore() : void   testGetPairwiseScore() : void	3434	9.09	1.01	1.0 1.0100%
testComputePID_matchesComparisonPID() : void   testComputePID_matchesComparisonPID() : void	5252	36.036	1.01	1.0 1.0100%
testComputePID_matchShortestSequence() : void   testComputePID_matchShortestSequence() : void	119119	14.014	1.01	1.0 1.0100%
testComputePID_matchLongestSequence() : void   testComputePID_matchLongestSequence() : void	164164	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_matchLongestSequencejalview.analysis.scoremodels.PIDModelTest.testComputePID_matchLongestSequence	1PASS
	0.19480519	jalview.analysis.scoremodels.PIDModelTest.testComputePID_matchShortestSequencejalview.analysis.scoremodels.PIDModelTest.testComputePID_matchShortestSequence	1PASS
	0.12987013	jalview.analysis.scoremodels.PIDModelTest.testGetPairwiseScorejalview.analysis.scoremodels.PIDModelTest.testGetPairwiseScore	1PASS

 

Source view

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
25		import jalview.api.analysis.SimilarityParamsI;
26		import jalview.util.Comparison;
27
28		import org.testng.annotations.Test;
29
		100% Uncovered Elements: 0 (77) Complexity: 4 Complexity Density: 0.05
30		public class PIDModelTest
31		{
32		private static final double DELTA = 0.00001D;
33
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
34	1	@Test(groups = "Functional")...
35		public void testGetPairwiseScore()
36		{
37	1	PIDModel sm = new PIDModel();
38	1	assertEquals(sm.getPairwiseScore('A', 'A'), 1f);
39	1	assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
40	1	assertEquals(sm.getPairwiseScore('a', 'A'), 1f);
41	1	assertEquals(sm.getPairwiseScore('A', 'B'), 0f);
42	1	assertEquals(sm.getPairwiseScore('A', ' '), 0f);
43	1	assertEquals(sm.getPairwiseScore(' ', ' '), 0f);
44	1	assertEquals(sm.getPairwiseScore('.', '.'), 0f);
45	1	assertEquals(sm.getPairwiseScore('-', '-'), 0f);
46		}
47
48		/**
49		* Regression test to verify that a (suitably configured) PIDModel computes
50		* the same percentage identities as the Comparison.PID method
51		*/
		100% Uncovered Elements: 0 (36) Complexity: 1 Complexity Density: 0.03 1PASS
52	1	@Test(groups = "Functional")...
53		public void testComputePID_matchesComparisonPID()
54		{
55	1	SimilarityParamsI params = new SimilarityParams(true, true, true, true);
56
57		/*
58		* same length, no gaps
59		*/
60	1	String s1 = "ARFNQDWSGI";
61	1	String s2 = "ARKNQDQSGI";
62
63	1	new PIDModel();
64	1	double newScore = PIDModel.computePID(s1, s2, params);
65	1	double oldScore = Comparison.PID(s1, s2);
66	1	assertEquals(newScore, oldScore, DELTA);
67		// and verify PIDModel calculation is symmetric
68	1	assertEquals(newScore, PIDModel.computePID(s2, s1, params));
69
70		/*
71		* same length, with gaps
72		*/
73	1	s1 = "-RFNQDWSGI";
74	1	s2 = "ARKNQ-QSGI";
75	1	new PIDModel();
76	1	newScore = PIDModel.computePID(s1, s2, params);
77	1	oldScore = Comparison.PID(s1, s2);
78	1	assertEquals(newScore, oldScore, DELTA);
79	1	assertEquals(newScore, PIDModel.computePID(s2, s1, params));
80
81		/*
82		* s2 longer than s1, with gaps
83		*/
84	1	s1 = "ARK-";
85	1	s2 = "-RFNQ";
86	1	new PIDModel();
87	1	newScore = PIDModel.computePID(s1, s2, params);
88	1	oldScore = Comparison.PID(s1, s2);
89	1	assertEquals(newScore, oldScore, DELTA);
90	1	assertEquals(newScore, PIDModel.computePID(s2, s1, params));
91
92		/*
93		* s1 longer than s2, with gaps
94		*/
95	1	s1 = "-RFNQ";
96	1	s2 = "ARK-";
97	1	new PIDModel();
98	1	newScore = PIDModel.computePID(s1, s2, params);
99	1	oldScore = Comparison.PID(s1, s2);
100	1	assertEquals(newScore, oldScore, DELTA);
101	1	assertEquals(newScore, PIDModel.computePID(s2, s1, params));
102
103		/*
104		* same but now also with gapped columns
105		*/
106	1	s1 = "-R-F-NQ";
107	1	s2 = "AR-K--";
108	1	new PIDModel();
109	1	newScore = PIDModel.computePID(s1, s2, params);
110	1	oldScore = Comparison.PID(s1, s2);
111	1	assertEquals(newScore, oldScore, DELTA);
112	1	assertEquals(newScore, PIDModel.computePID(s2, s1, params));
113		}
114
115		/**
116		* Tests for percentage identity variants where only the shorter length of two
117		* sequences is used
118		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
119	1	@Test(groups = "Functional")...
120		public void testComputePID_matchShortestSequence()
121		{
122	1	String s1 = "FR-K-S";
123	1	String s2 = "FS--L";
124
125		/*
126		* match gap-gap and gap-char
127		* PID = 4/5 = 80%
128		*/
129	1	SimilarityParamsI params = new SimilarityParams(true, true, true, true);
130	1	assertEquals(PIDModel.computePID(s1, s2, params), 80d);
131	1	assertEquals(PIDModel.computePID(s2, s1, params), 80d);
132
133		/*
134		* match gap-char but not gap-gap
135		* PID = 3/4 = 75%
136		*/
137	1	params = new SimilarityParams(false, true, true, true);
138	1	assertEquals(PIDModel.computePID(s1, s2, params), 75d);
139	1	assertEquals(PIDModel.computePID(s2, s1, params), 75d);
140
141		/*
142		* include gaps but don't match them
143		* include gap-gap, counted as identity
144		* PID = 2/5 = 40%
145		*/
146	1	params = new SimilarityParams(true, false, true, true);
147	1	assertEquals(PIDModel.computePID(s1, s2, params), 40d);
148	1	assertEquals(PIDModel.computePID(s2, s1, params), 40d);
149
150		/*
151		* include gaps but don't match them
152		* exclude gap-gap
153		* PID = 1/4 = 25%
154		*/
155	1	params = new SimilarityParams(false, false, true, true);
156	1	assertEquals(PIDModel.computePID(s1, s2, params), 25d);
157	1	assertEquals(PIDModel.computePID(s2, s1, params), 25d);
158		}
159
160		/**
161		* Tests for percentage identity variants where the longer length of two
162		* sequences is used
163		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
164	1	@Test(groups = "Functional")...
165		public void testComputePID_matchLongestSequence()
166		{
167	1	String s1 = "FR-K-S";
168	1	String s2 = "FS--L";
169
170		/*
171		* match gap-gap and gap-char
172		* shorter sequence treated as if with trailing gaps
173		* PID = 5/6 = 83.333...%
174		*/
175	1	SimilarityParamsI params = new SimilarityParams(true, true, true,
176		false);
177	1	assertEquals(PIDModel.computePID(s1, s2, params), 500d / 6);
178	1	assertEquals(PIDModel.computePID(s2, s1, params), 500d / 6);
179
180		/*
181		* match gap-char but not gap-gap
182		* PID = 4/5 = 80%
183		*/
184	1	params = new SimilarityParams(false, true, true, false);
185	1	assertEquals(PIDModel.computePID(s1, s2, params), 80d);
186	1	assertEquals(PIDModel.computePID(s2, s1, params), 80d);
187
188		/*
189		* include gaps but don't match them
190		* include gap-gap, counted as identity
191		* PID = 2/6 = 33.333...%
192		*/
193	1	params = new SimilarityParams(true, false, true, false);
194	1	assertEquals(PIDModel.computePID(s1, s2, params), 100d / 3);
195	1	assertEquals(PIDModel.computePID(s2, s1, params), 100d / 3);
196
197		/*
198		* include gaps but don't match them
199		* exclude gap-gap
200		* PID = 1/5 = 25%
201		*/
202	1	params = new SimilarityParams(false, false, true, false);
203	1	assertEquals(PIDModel.computePID(s1, s2, params), 20d);
204	1	assertEquals(PIDModel.computePID(s2, s1, params), 20d);
205
206		/*
207		* no tests for matchGaps=true, includeGaps=false
208		* as it don't make sense
209		*/
210		}
211		}