Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ComparisonTest	34	74	8	0	1.0100%	Show methods

Class ComparisonTest

Class ComparisonTest	Line # 34	Total Statements 74	Complexity 8	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3737	2.02	1.01	0.00	1.0 1.0100%
testIsGap() : void   testIsGap() : void	4444	7.07	1.01	0.00	1.0 1.0100%
testIsNucleotide_sequences() : void   testIsNucleotide_sequences() : void	6060	23.023	1.01	0.00	1.0 1.0100%
testPID_includingGaps() : void   testPID_includingGaps() : void	115115	11.011	1.01	0.00	1.0 1.0100%
testIsNucleotide() : void   testIsNucleotide() : void	144144	12.012	1.01	0.00	1.0 1.0100%
testPID_ungappedOnly() : void   testPID_ungappedOnly() : void	164164	5.05	1.01	0.00	1.0 1.0100%
testIsNucleotideSequence() : void   testIsNucleotideSequence() : void	191191	8.08	1.01	0.00	1.0 1.0100%
testIsSameResidue() : void   testIsSameResidue() : void	204204	6.06	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.29268292	jalview.util.ComparisonTest.testIsNucleotide_sequencesjalview.util.ComparisonTest.testIsNucleotide_sequences	1PASS
	0.15853658	jalview.util.ComparisonTest.testIsNucleotidejalview.util.ComparisonTest.testIsNucleotide	1PASS
	0.14634146	jalview.util.ComparisonTest.testPID_includingGapsjalview.util.ComparisonTest.testPID_includingGaps	1PASS
	0.1097561	jalview.util.ComparisonTest.testIsNucleotideSequencejalview.util.ComparisonTest.testIsNucleotideSequence	1PASS
	0.09756097	jalview.util.ComparisonTest.testIsGapjalview.util.ComparisonTest.testIsGap	1PASS
	0.085365854	jalview.util.ComparisonTest.testIsSameResiduejalview.util.ComparisonTest.testIsSameResidue	1PASS
	0.07317073	jalview.util.ComparisonTest.testPID_ungappedOnlyjalview.util.ComparisonTest.testPID_ungappedOnly	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.util;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import jalview.datamodel.Sequence;
28		import jalview.datamodel.SequenceI;
29		import jalview.gui.JvOptionPane;
30
31		import org.testng.annotations.BeforeClass;
32		import org.testng.annotations.Test;
33
		100% Uncovered Elements: 0 (82) Complexity: 8 Complexity Density: 0.11
34		public class ComparisonTest
35		{
36
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
37	1	@BeforeClass(alwaysRun = true)...
38		public void setUpJvOptionPane()
39		{
40	1	JvOptionPane.setInteractiveMode(false);
41	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
42		}
43
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
44	1	@Test(groups = { "Functional" })...
45		public void testIsGap()
46		{
47	1	assertTrue(Comparison.isGap('-'));
48	1	assertTrue(Comparison.isGap('.'));
49	1	assertTrue(Comparison.isGap(' '));
50	1	assertFalse(Comparison.isGap('X'));
51	1	assertFalse(Comparison.isGap('x'));
52	1	assertFalse(Comparison.isGap('*'));
53	1	assertFalse(Comparison.isGap('G'));
54		}
55
56		/**
57		* Test for isNucleotide is that sequences in a dataset are more than 85%
58		* AGCTU. Test is not case-sensitive and ignores gaps.
59		*/
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
60	1	@Test(groups = { "Functional" })...
61		public void testIsNucleotide_sequences()
62		{
63	1	SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
64	1	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
65	1	assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
66		{ seq } }));
67
68	1	seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
69	1	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
70
71	1	seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
72	1	assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
73
74	1	seq = new Sequence("eightyfivepercentgapped",
75		"--agc--tuA--GCPV-a---gct-uA-GC---UV");
76	1	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
77
78	1	seq = new Sequence("nineypercentgapped",
79		"ag--ct-u-A---GC---g----Vag--c---tuAGCUV");
80	1	assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
81
82	1	seq = new Sequence("allgap", "---------");
83	1	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
84
85	1	seq = new Sequence("DNA", "ACTugGCCAG");
86	1	SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
87		/*
88		* 90% DNA:
89		*/
90	1	assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
91		seq, seq, seq, seq, seq, seq, seq2 }));
92	1	assertTrue(Comparison.isNucleotide(new SequenceI[][] {
93		new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
94		new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
95		/*
96		* 80% DNA:
97		*/
98	1	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
99		seq, seq, seq, seq, seq, seq2, seq2 }));
100	1	assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
101		{ seq }, new SequenceI[] { seq, seq, seq },
102		new SequenceI[] { seq, seq, seq, seq, seq2, seq2, null } }));
103
104	1	seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
105		// 12/14 = 85.7%
106	1	assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
107
108	1	assertFalse(Comparison.isNucleotide((SequenceI[]) null));
109	1	assertFalse(Comparison.isNucleotide((SequenceI[][]) null));
110		}
111
112		/**
113		* Test the percentage identity calculation for two sequences
114		*/
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
115	1	@Test(groups = { "Functional" })...
116		public void testPID_includingGaps()
117		{
118	1	String seq1 = "ABCDEFG"; // extra length here is ignored
119	1	String seq2 = "abcdef";
120	1	assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
121
122		// comparison range defaults to length of first sequence
123	1	seq2 = "abcdefghijklmnopqrstuvwxyz";
124	1	assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
125
126		// 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
127	1	seq1 = "a--b-cdefh";
128	1	seq2 = "a---bcdefg";
129	1	int length = seq1.length();
130
131		// match gap-residue, match gap-gap: 9/10 identical
132		// TODO should gap-gap be included in a PID score? JAL-791
133	1	assertEquals(90f, Comparison.PID(seq1, seq2, 0, length, true, false),
134		0.001f);
135		// overloaded version of the method signature above:
136	1	assertEquals(90f, Comparison.PID(seq1, seq2), 0.001f);
137
138		// don't match gap-residue, match gap-gap: 7/10 identical
139		// TODO should gap-gap be included in a PID score?
140	1	assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false),
141		0.001f);
142		}
143
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
144	1	@Test(groups = { "Functional" })...
145		public void testIsNucleotide()
146		{
147	1	assertTrue(Comparison.isNucleotide('a'));
148	1	assertTrue(Comparison.isNucleotide('A'));
149	1	assertTrue(Comparison.isNucleotide('c'));
150	1	assertTrue(Comparison.isNucleotide('C'));
151	1	assertTrue(Comparison.isNucleotide('g'));
152	1	assertTrue(Comparison.isNucleotide('G'));
153	1	assertTrue(Comparison.isNucleotide('t'));
154	1	assertTrue(Comparison.isNucleotide('T'));
155	1	assertTrue(Comparison.isNucleotide('u'));
156	1	assertTrue(Comparison.isNucleotide('U'));
157	1	assertFalse(Comparison.isNucleotide('-'));
158	1	assertFalse(Comparison.isNucleotide('P'));
159		}
160
161		/**
162		* Test the percentage identity calculation for two sequences
163		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
164	1	@Test(groups = { "Functional" })...
165		public void testPID_ungappedOnly()
166		{
167		// 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
168		// the extra length of seq1 is ignored
169	1	String seq1 = "a--b-cdefhr";
170	1	String seq2 = "a---bcdefg";
171	1	int length = seq1.length();
172
173		/*
174		* As currently coded, 'ungappedOnly' ignores gap-residue but counts
175		* gap-gap. Is this a bug - should gap-gap also be ignored, giving a PID of
176		* 5/6?
177		*
178		* Note also there is no variant of the calculation that penalises
179		* gap-residue i.e. counts it as a mismatch. This would give a score of 5/8
180		* (if we ignore gap-gap) or 5/10 (if we count gap-gap as a match).
181		*/
182		// match gap-residue, match gap-gap: 7/8 identical
183	1	assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, true, true),
184		0.001f);
185
186		// don't match gap-residue with 'ungapped only' - same as above
187	1	assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, false, true),
188		0.001f);
189		}
190
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
191	1	@Test(groups = { "Functional" })...
192		public void testIsNucleotideSequence()
193		{
194	1	assertFalse(Comparison.isNucleotideSequence(null, true));
195	1	assertTrue(Comparison.isNucleotideSequence("", true));
196	1	assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", true));
197	1	assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", false));
198	1	assertFalse(Comparison.isNucleotideSequence("xAgGcCtTuU", false));
199	1	assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false));
200	1	assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true));
201	1	assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false));
202		}
203
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
204	1	@Test(groups = { "Functional" })...
205		public void testIsSameResidue()
206		{
207	1	assertTrue(Comparison.isSameResidue('a', 'a', false));
208	1	assertTrue(Comparison.isSameResidue('a', 'a', true));
209	1	assertTrue(Comparison.isSameResidue('A', 'a', false));
210	1	assertTrue(Comparison.isSameResidue('a', 'A', false));
211
212	1	assertFalse(Comparison.isSameResidue('a', 'A', true));
213	1	assertFalse(Comparison.isSameResidue('A', 'a', true));
214		}
215		}