Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceOntologyTest	32	53	6	0.965517296.6%	Show methods

Class SequenceOntologyTest

Class SequenceOntologyTest	Line # 32	Total Statements 53	Complexity 6	TOTAL Coverage 0.965517296.6%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3535	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	4444	7.07	2.02	0.71428573 0.7142857371.4%
testIsA() : void   testIsA() : void	6161	20.020	1.01	1.0 1.0100%
testIsCDS() : void   testIsCDS() : void	9898	8.08	1.01	1.0 1.0100%
testIsSequenceVariant() : void   testIsSequenceVariant() : void	111111	16.016	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.36206895	jalview.ext.so.SequenceOntologyTest.testIsAjalview.ext.so.SequenceOntologyTest.testIsA	1PASS
	0.29310346	jalview.ext.so.SequenceOntologyTest.testIsSequenceVariantjalview.ext.so.SequenceOntologyTest.testIsSequenceVariant	1PASS
	0.15517241	jalview.ext.so.SequenceOntologyTest.testIsCDSjalview.ext.so.SequenceOntologyTest.testIsCDS	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.ext.so;
22
23		import static org.testng.AssertJUnit.assertFalse;
24		import static org.testng.AssertJUnit.assertTrue;
25
26		import jalview.gui.JvOptionPane;
27		import jalview.io.gff.SequenceOntologyI;
28
29		import org.testng.annotations.BeforeClass;
30		import org.testng.annotations.Test;
31
		96.6% Uncovered Elements: 2 (58) Complexity: 6 Complexity Density: 0.11
32		public class SequenceOntologyTest
33		{
34
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
35	1	@BeforeClass(alwaysRun = true)...
36		public void setUpJvOptionPane()
37		{
38	1	JvOptionPane.setInteractiveMode(false);
39	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
40		}
41
42		private SequenceOntologyI so;
43
		71.4% Uncovered Elements: 2 (7) Complexity: 2 Complexity Density: 0.29
44	1	@BeforeClass(alwaysRun = true)...
45		public void setUp()
46		{
47	1	long now = System.currentTimeMillis();
48	1	try
49		{
50	1	so = new SequenceOntology();
51		} catch (Throwable t)
52		{
53	0	System.out.println("SOTest error ");
54	0	t.printStackTrace(System.err);
55		}
56	1	long elapsed = System.currentTimeMillis() - now;
57	1	System.out.println("Load and cache of Sequence Ontology took "
58		+ elapsed + "ms");
59		}
60
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
61	1	@Test(groups = "Functional")...
62		public void testIsA()
63		{
64	1	assertFalse(so.isA(null, null));
65	1	assertFalse(so.isA(null, "SO:0000087"));
66	1	assertFalse(so.isA("SO:0000087", null));
67	1	assertFalse(so.isA("complete", "garbage"));
68
69	1	assertTrue(so.isA("SO:0000087", "SO:0000704"));
70	1	assertFalse(so.isA("SO:0000704", "SO:0000087"));
71	1	assertTrue(so.isA("SO:0000736", "SO:0000735"));
72
73		// same thing:
74	1	assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
75		// direct parent:
76	1	assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
77		// grandparent:
78	1	assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
79		// great-grandparent:
80	1	assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
81
82		// same thing by name / description:
83	1	assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
84	1	assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
85	1	assertTrue(so.isA("SO:0000084", "SO:0000084"));
86
87		// SO name to description:
88	1	assertTrue(so.isA("SO:0000084", "organelle_sequence"));
89	1	assertTrue(so.isA("SO:0000084", "sequence_location"));
90	1	assertTrue(so.isA("SO:0000084", "sequence_attribute"));
91
92		// description to SO name:
93	1	assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
94	1	assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
95	1	assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
96		}
97
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
98	1	@Test(groups = "Functional")...
99		public void testIsCDS()
100		{
101	1	assertTrue(so.isA("CDS", "CDS"));
102	1	assertTrue(so.isA("CDS_predicted", "CDS"));
103	1	assertTrue(so.isA("transposable_element_CDS", "CDS"));
104	1	assertTrue(so.isA("edited_CDS", "CDS"));
105	1	assertTrue(so.isA("CDS_independently_known", "CDS"));
106	1	assertTrue(so.isA("CDS_fragment", "CDS"));
107	1	assertFalse(so.isA("CDS_region", "CDS"));// part_of
108	1	assertFalse(so.isA("polypeptide", "CDS")); // derives_from
109		}
110
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
111	1	@Test(groups = "Functional")...
112		public void testIsSequenceVariant()
113		{
114	1	assertFalse(so.isA("CDS", "sequence_variant"));
115	1	assertTrue(so.isA("sequence_variant", "sequence_variant"));
116
117		/*
118		* these should all be sub-types of sequence_variant
119		*/
120	1	assertTrue(so.isA("structural_variant", "sequence_variant"));
121	1	assertTrue(so.isA("feature_variant", "sequence_variant"));
122	1	assertTrue(so.isA("gene_variant", "sequence_variant"));
123	1	assertTrue(so.isA("transcript_variant", "sequence_variant"));
124	1	assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
125	1	assertTrue(so.isA("missense_variant", "sequence_variant"));
126	1	assertTrue(so.isA("synonymous_variant", "sequence_variant"));
127	1	assertTrue(so.isA("frameshift_variant", "sequence_variant"));
128	1	assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
129	1	assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
130	1	assertTrue(so.isA("stop_gained", "sequence_variant"));
131	1	assertTrue(so.isA("stop_lost", "sequence_variant"));
132	1	assertTrue(so.isA("inframe_deletion", "sequence_variant"));
133	1	assertTrue(so.isA("inframe_insertion", "sequence_variant"));
134		}
135		}