Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ComparisonTest	36	123	11	0.00%	Show methods

Class ComparisonTest

Class ComparisonTest	Line # 36	Total Statements 123	Complexity 11	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3939	2.02	1.01	0.0 0.00%
loadProperties() : void   loadProperties() : void	4646	1.01	1.01	0.0 0.00%
testIsGap() : void   testIsGap() : void	5252	7.07	1.01	0.0 0.00%
testIsNucleotide_sequences() : void   testIsNucleotide_sequences() : void	6868	34.034	1.01	0.0 0.00%
testPID_includingGaps() : void   testPID_includingGaps() : void	149149	11.011	1.01	0.0 0.00%
testIsNucleotide() : void   testIsNucleotide() : void	178178	12.012	1.01	0.0 0.00%
testIsNucleotideAmbiguity() : void   testIsNucleotideAmbiguity() : void	195195	14.014	1.01	0.0 0.00%
testPID_ungappedOnly() : void   testPID_ungappedOnly() : void	217217	5.05	1.01	0.0 0.00%
testIsNucleotideSequence() : void   testIsNucleotideSequence() : void	244244	21.021	1.01	0.0 0.00%
testIsSameResidue() : void   testIsSameResidue() : void	281281	6.06	1.01	0.0 0.00%
testNucleotideProportion() : void   testNucleotideProportion() : void	293293	10.010	1.01	0.0 0.00%

 

Contributing tests

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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.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 org.testng.annotations.BeforeClass;
28		import org.testng.annotations.BeforeMethod;
29		import org.testng.annotations.Test;
30
31		import jalview.bin.Cache;
32		import jalview.datamodel.Sequence;
33		import jalview.datamodel.SequenceI;
34		import jalview.gui.JvOptionPane;
35
		0% Uncovered Elements: 134 (134) Complexity: 11 Complexity Density: 0.09
36		public class ComparisonTest
37		{
38
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
39	0	@BeforeClass(alwaysRun = true)...
40		public void setUpJvOptionPane()
41		{
42	0	JvOptionPane.setInteractiveMode(false);
43	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
44		}
45
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
46	0	@BeforeMethod(alwaysRun = true)...
47		public void loadProperties()
48		{
49	0	Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
50		}
51
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14 4-
52	0	@Test(groups = { "Functional" })...
53		public void testIsGap()
54		{
55	0	assertTrue(Comparison.isGap('-'));
56	0	assertTrue(Comparison.isGap('.'));
57	0	assertTrue(Comparison.isGap(' '));
58	0	assertFalse(Comparison.isGap('X'));
59	0	assertFalse(Comparison.isGap('x'));
60	0	assertFalse(Comparison.isGap('*'));
61	0	assertFalse(Comparison.isGap('G'));
62		}
63
64		/**
65		* Test for isNucleotide is that sequences in a dataset are more than 85%
66		* AGCTU. Test is not case-sensitive and ignores gaps.
67		*/
		0% Uncovered Elements: 34 (34) Complexity: 1 Complexity Density: 0.03 4-
68	0	@Test(groups = { "Functional" })...
69		public void testIsNucleotide_sequences()
70		{
71	0	SequenceI seq = new Sequence("eightypercent+fivepercent", "agctuagcPV");
72	0	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
73	0	assertFalse(
74		Comparison.isNucleotide(new SequenceI[][]
75		{ new SequenceI[] { seq } }));
76
77	0	seq = new Sequence("eightyfivepercent+tenpercent",
78		"agctuagcgVagctuagcuVE");
79	0	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
80
81	0	seq = new Sequence(">nineyfivepercent+0percent",
82		"aagctuagcgEagctuagcua");
83	0	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
84
85	0	seq = new Sequence("nineyfivepercent+0percent", "agctuagcgEagctuagcua");
86	0	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
87
88	0	seq = new Sequence("nineyfivepercent+fivepercent",
89		"agctuagcgWagctuagcua");
90	0	assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
91
92	0	seq = new Sequence("nineyfivepercent+tenpercent",
93		"agctuagcgEWWctuagcua");
94	0	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
95
96	0	seq = new Sequence("eightyfivepercent+fifteenpercent",
97		"agctuagcgWWWctuagcua");
98	0	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
99
100	0	seq = new Sequence("eightyfivepercentgapped",
101		"--agc--tuA--GCPV-a---gct-uA-GC---UV");
102	0	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
103
104	0	seq = new Sequence("ninetyfivepercentgapped",
105		"ag--ct-u-a---gc---g----aag--c---tuagcuV");
106	0	assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
107
108	0	seq = new Sequence("allgap", "---------");
109	0	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
110
111	0	seq = new Sequence("DNA", "ACTugGCCAG");
112	0	SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
113		/*
114		* 90% DNA but one protein sequence - expect false
115		*/
116	0	assertFalse(
117		Comparison.isNucleotide(new SequenceI[]
118		{ seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 }));
119	0	assertFalse(
120		Comparison.isNucleotide(new SequenceI[][]
121		{ new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
122		new SequenceI[]
123		{ seq, seq, seq, seq, seq, seq2 } }));
124		/*
125		* 80% DNA but one protein sequence - Expect false
126		*/
127	0	assertFalse(
128		Comparison.isNucleotide(new SequenceI[]
129		{ seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 }));
130	0	assertFalse(
131		Comparison.isNucleotide(new SequenceI[][]
132		{ new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
133		new SequenceI[]
134		{ seq, seq, seq, seq, seq2, seq2, null } }));
135
136	0	String seqString = "aaatatatatgEcctgagtcgt";
137	0	seq = new Sequence("ShortProteinThatLooksLikeDNA", seqString);
138	0	assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
139	0	seq = new Sequence("LongProteinThatLooksLikeDNA", seqString.repeat(10));
140	0	assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
141
142	0	assertFalse(Comparison.isNucleotide((SequenceI[]) null));
143	0	assertFalse(Comparison.isNucleotide((SequenceI[][]) null));
144		}
145
146		/**
147		* Test the percentage identity calculation for two sequences
148		*/
		0% Uncovered Elements: 11 (11) Complexity: 1 Complexity Density: 0.09 4-
149	0	@Test(groups = { "Functional" })...
150		public void testPID_includingGaps()
151		{
152	0	String seq1 = "ABCDEFG"; // extra length here is ignored
153	0	String seq2 = "abcdef";
154	0	assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
155
156		// comparison range defaults to length of first sequence
157	0	seq2 = "abcdefghijklmnopqrstuvwxyz";
158	0	assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
159
160		// 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
161	0	seq1 = "a--b-cdefh";
162	0	seq2 = "a---bcdefg";
163	0	int length = seq1.length();
164
165		// match gap-residue, match gap-gap: 9/10 identical
166		// TODO should gap-gap be included in a PID score? JAL-791
167	0	assertEquals(90f, Comparison.PID(seq1, seq2, 0, length, true, false),
168		0.001f);
169		// overloaded version of the method signature above:
170	0	assertEquals(90f, Comparison.PID(seq1, seq2), 0.001f);
171
172		// don't match gap-residue, match gap-gap: 7/10 identical
173		// TODO should gap-gap be included in a PID score?
174	0	assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false),
175		0.001f);
176		}
177
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08 4-
178	0	@Test(groups = { "Functional" })...
179		public void testIsNucleotide()
180		{
181	0	assertTrue(Comparison.isNucleotide('a'));
182	0	assertTrue(Comparison.isNucleotide('A'));
183	0	assertTrue(Comparison.isNucleotide('c'));
184	0	assertTrue(Comparison.isNucleotide('C'));
185	0	assertTrue(Comparison.isNucleotide('g'));
186	0	assertTrue(Comparison.isNucleotide('G'));
187	0	assertTrue(Comparison.isNucleotide('t'));
188	0	assertTrue(Comparison.isNucleotide('T'));
189	0	assertTrue(Comparison.isNucleotide('u'));
190	0	assertTrue(Comparison.isNucleotide('U'));
191	0	assertFalse(Comparison.isNucleotide('-'));
192	0	assertFalse(Comparison.isNucleotide('P'));
193		}
194
		0% Uncovered Elements: 14 (14) Complexity: 1 Complexity Density: 0.07 4-
195	0	@Test(groups = { "Functional" })...
196		public void testIsNucleotideAmbiguity()
197		{
198	0	assertTrue(Comparison.isNucleotide('b', true));
199	0	assertTrue(Comparison.isNucleotide('B', true));
200	0	assertTrue(Comparison.isNucleotide('d', true));
201	0	assertTrue(Comparison.isNucleotide('V', true));
202	0	assertTrue(Comparison.isNucleotide('M', true));
203	0	assertTrue(Comparison.isNucleotide('s', true));
204	0	assertTrue(Comparison.isNucleotide('W', true));
205	0	assertTrue(Comparison.isNucleotide('x', true));
206	0	assertTrue(Comparison.isNucleotide('Y', true));
207	0	assertTrue(Comparison.isNucleotide('r', true));
208	0	assertTrue(Comparison.isNucleotide('i', true));
209	0	assertFalse(Comparison.isNucleotide('-', true));
210	0	assertFalse(Comparison.isNucleotide('n', true));
211	0	assertFalse(Comparison.isNucleotide('P', true));
212		}
213
214		/**
215		* Test the percentage identity calculation for two sequences
216		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2 4-
217	0	@Test(groups = { "Functional" })...
218		public void testPID_ungappedOnly()
219		{
220		// 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
221		// the extra length of seq1 is ignored
222	0	String seq1 = "a--b-cdefhr";
223	0	String seq2 = "a---bcdefg";
224	0	int length = seq1.length();
225
226		/*
227		* As currently coded, 'ungappedOnly' ignores gap-residue but counts
228		* gap-gap. Is this a bug - should gap-gap also be ignored, giving a PID of
229		* 5/6?
230		*
231		* Note also there is no variant of the calculation that penalises
232		* gap-residue i.e. counts it as a mismatch. This would give a score of 5/8
233		* (if we ignore gap-gap) or 5/10 (if we count gap-gap as a match).
234		*/
235		// match gap-residue, match gap-gap: 7/8 identical
236	0	assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, true, true),
237		0.001f);
238
239		// don't match gap-residue with 'ungapped only' - same as above
240	0	assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, false, true),
241		0.001f);
242		}
243
		0% Uncovered Elements: 21 (21) Complexity: 1 Complexity Density: 0.05 4-
244	0	@Test(groups = { "Functional" })...
245		public void testIsNucleotideSequence()
246		{
247	0	assertFalse(Comparison.isNucleotideSequence(null, true));
248	0	assertTrue(Comparison.isNucleotideSequence("", true));
249	0	assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", true));
250	0	assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", false));
251	0	assertFalse(Comparison.isNucleotideSequence("xAgGcCtTuU", false));
252	0	assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false));
253	0	assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true));
254	0	assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false));
255	0	assertFalse(Comparison.isNucleotideSequence("gatactawgataca", false));
256		// including nucleotide ambiguity
257	0	assertTrue(
258		Comparison.isNucleotideSequence("gatacaWgataca", true, true));
259	0	assertFalse(
260		Comparison.isNucleotideSequence("gatacaEgataca", true, true));
261
262		// not quite all nucleotides and ambiguity codes
263	0	Sequence seq = new Sequence("Ambiguity DNA codes", "gatacagatacabve");
264	0	assertFalse(Comparison.isNucleotide(seq));
265		// all nucleotide and nucleotide ambiguity codes
266	0	seq = new Sequence("Ambiguity DNA codes", "gatacagatacabvt");
267	0	assertFalse(Comparison.isNucleotide(seq));
268	0	seq = new Sequence("Ambiguity DNA codes", "agatacabb");
269	0	assertFalse(Comparison.isNucleotide(seq));
270		// 55% nucleotide with only Xs or Ns
271	0	assertTrue(Comparison
272		.isNucleotide(new Sequence("dnaWithXs", "gatacaXXXX")));
273	0	assertTrue(Comparison
274		.isNucleotide(new Sequence("dnaWithXs", "gatacaNNNN")));
275	0	assertFalse(Comparison
276		.isNucleotide(new Sequence("dnaWithXs", "gatacXXXXX")));
277	0	assertFalse(Comparison
278		.isNucleotide(new Sequence("dnaWithXs", "gatacNNNNN")));
279		}
280
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17 4-
281	0	@Test(groups = { "Functional" })...
282		public void testIsSameResidue()
283		{
284	0	assertTrue(Comparison.isSameResidue('a', 'a', false));
285	0	assertTrue(Comparison.isSameResidue('a', 'a', true));
286	0	assertTrue(Comparison.isSameResidue('A', 'a', false));
287	0	assertTrue(Comparison.isSameResidue('a', 'A', false));
288
289	0	assertFalse(Comparison.isSameResidue('a', 'A', true));
290	0	assertFalse(Comparison.isSameResidue('A', 'a', true));
291		}
292
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1 4-
293	0	@Test(groups = { "Functional" })...
294		public void testNucleotideProportion()
295		{
296	0	assertFalse(Comparison.myShortSequenceNucleotideProportionCount(2, 3));
297	0	assertTrue(Comparison.myShortSequenceNucleotideProportionCount(3, 3));
298	0	assertFalse(Comparison.myShortSequenceNucleotideProportionCount(2, 4));
299	0	assertTrue(Comparison.myShortSequenceNucleotideProportionCount(3, 4));
300	0	assertFalse(
301		Comparison.myShortSequenceNucleotideProportionCount(17, 20));
302	0	assertTrue(Comparison.myShortSequenceNucleotideProportionCount(18, 20));
303	0	assertFalse(
304		Comparison.myShortSequenceNucleotideProportionCount(38, 50));
305	0	assertTrue(Comparison.myShortSequenceNucleotideProportionCount(39, 50));
306	0	assertFalse(
307		Comparison.myShortSequenceNucleotideProportionCount(54, 100));
308	0	assertTrue(
309		Comparison.myShortSequenceNucleotideProportionCount(55, 100));
310		}
311		}