Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceOntologyLiteTest	28	18	1	0.00%	Show methods

Class SequenceOntologyLiteTest

Class SequenceOntologyLiteTest	Line # 28	Total Statements 18	Complexity 1	TOTAL Coverage 0.00%
testIsA_sequenceVariant() : void   testIsA_sequenceVariant() : void	3030	18.018	1.01	0.0 0.00%

 

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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.io.gff;
22
23		import static org.testng.AssertJUnit.assertFalse;
24		import static org.testng.AssertJUnit.assertTrue;
25
26		import org.testng.annotations.Test;
27
		0% Uncovered Elements: 19 (19) Complexity: 1 Complexity Density: 0.06
28		public class SequenceOntologyLiteTest
29		{
		0% Uncovered Elements: 18 (18) Complexity: 1 Complexity Density: 0.06 4-
30	0	@Test(groups = "Functional")...
31		public void testIsA_sequenceVariant()
32		{
33	0	SequenceOntologyI so = new SequenceOntologyLite();
34
35	0	assertFalse(so.isA("CDS", "sequence_variant"));
36	0	assertTrue(so.isA("sequence_variant", "sequence_variant"));
37
38		/*
39		* these should all be sub-types of sequence_variant
40		*/
41	0	assertTrue(so.isA("structural_variant", "sequence_variant"));
42	0	assertTrue(so.isA("feature_variant", "sequence_variant"));
43	0	assertTrue(so.isA("gene_variant", "sequence_variant"));
44	0	assertTrue(so.isA("transcript_variant", "sequence_variant"));
45	0	assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
46	0	assertTrue(so.isA("missense_variant", "sequence_variant"));
47	0	assertTrue(so.isA("synonymous_variant", "sequence_variant"));
48	0	assertTrue(so.isA("frameshift_variant", "sequence_variant"));
49	0	assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
50	0	assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
51	0	assertTrue(so.isA("stop_gained", "sequence_variant"));
52	0	assertTrue(so.isA("stop_lost", "sequence_variant"));
53	0	assertTrue(so.isA("inframe_deletion", "sequence_variant"));
54	0	assertTrue(so.isA("inframe_insertion", "sequence_variant"));
55	0	assertTrue(so.isA("splice_region_variant", "sequence_variant"));
56		}
57		}