Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblCdsTest	42	71	7	0	1.0100%	Show methods

Class EnsemblCdsTest

Class EnsemblCdsTest	Line # 42	Total Statements 71	Complexity 7	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4545	2.02	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	5252	1.01	1.01	0.00	1.0 1.0100%
tearDown() : void   tearDown() : void	5858	1.01	1.01	0.00	1.0 1.0100%
testGetGenomicRangesFromFeatures() : void   testGetGenomicRangesFromFeatures() : void	6868	31.031	1.01	0.00	1.0 1.0100%
testRetainFeature() : void   testRetainFeature() : void	123123	12.012	1.01	0.00	1.0 1.0100%
testIdentifiesSequence() : void   testIdentifiesSequence() : void	154154	17.017	1.01	0.00	1.0 1.0100%
testIsValidReference() : void   testIsValidReference() : void	188188	7.07	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.41025642	jalview.ext.ensembl.EnsemblCdsTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblCdsTest.testGetGenomicRangesFromFeatures	1PASS
	0.23076923	jalview.ext.ensembl.EnsemblCdsTest.testIdentifiesSequencejalview.ext.ensembl.EnsemblCdsTest.testIdentifiesSequence	1PASS
	0.16666667	jalview.ext.ensembl.EnsemblCdsTest.testRetainFeaturejalview.ext.ensembl.EnsemblCdsTest.testRetainFeature	1PASS
	0.102564104	jalview.ext.ensembl.EnsemblCdsTest.testIsValidReferencejalview.ext.ensembl.EnsemblCdsTest.testIsValidReference	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.ensembl;
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.SequenceDummy;
28		import jalview.datamodel.SequenceFeature;
29		import jalview.datamodel.SequenceI;
30		import jalview.gui.JvOptionPane;
31		import jalview.io.gff.SequenceOntologyFactory;
32		import jalview.io.gff.SequenceOntologyLite;
33		import jalview.util.MapList;
34
35		import java.util.List;
36
37		import org.testng.Assert;
38		import org.testng.annotations.AfterClass;
39		import org.testng.annotations.BeforeClass;
40		import org.testng.annotations.Test;
41
		100% Uncovered Elements: 0 (78) Complexity: 7 Complexity Density: 0.1
42		public class EnsemblCdsTest
43		{
44
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
45	1	@BeforeClass(alwaysRun = true)...
46		public void setUpJvOptionPane()
47		{
48	1	JvOptionPane.setInteractiveMode(false);
49	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50		}
51
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
52	1	@BeforeClass(alwaysRun = true)...
53		public void setUp()
54		{
55	1	SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
56		}
57
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
58	1	@AfterClass(alwaysRun = true)...
59		public void tearDown()
60		{
61	1	SequenceOntologyFactory.setInstance(null);
62		}
63
64		/**
65		* Test that the cdna part of genomic sequence is correctly identified by
66		* 'CDS' features (or subtypes) with the desired transcript as parent
67		*/
		100% Uncovered Elements: 0 (31) Complexity: 1 Complexity Density: 0.03 1PASS
68	1	@Test(groups = "Functional")...
69		public void testGetGenomicRangesFromFeatures()
70		{
71	1	EnsemblCds testee = new EnsemblCds();
72	1	SequenceI genomic = new SequenceDummy("chr7");
73	1	genomic.setStart(10000);
74	1	genomic.setEnd(50000);
75	1	String transcriptId = "ABC123";
76
77		// CDS at (start+10000) length 501
78	1	SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
79		null);
80	1	sf.setValue("Parent", "transcript:" + transcriptId);
81	1	sf.setStrand("+");
82	1	genomic.addSequenceFeature(sf);
83
84		// CDS (sub-type) at (start + 10500) length 101
85	1	sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
86	1	sf.setValue("Parent", "transcript:" + transcriptId);
87	1	sf.setStrand("+");
88	1	genomic.addSequenceFeature(sf);
89
90		// CDS belonging to a different transcript doesn't count
91	1	sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
92	1	sf.setValue("Parent", "transcript:anotherOne");
93	1	genomic.addSequenceFeature(sf);
94
95		// exon feature doesn't count
96	1	sf = new SequenceFeature("exon", "", 10000, 50000, 0f, null);
97	1	genomic.addSequenceFeature(sf);
98
99		// mRNA_region feature doesn't count (parent of CDS)
100	1	sf = new SequenceFeature("mRNA_region", "", 10000, 50000, 0f, null);
101	1	genomic.addSequenceFeature(sf);
102
103	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
104		transcriptId, 23);
105	1	List<int[]> fromRanges = ranges.getFromRanges();
106	1	assertEquals(2, fromRanges.size());
107		// from ranges should be sorted by start order
108	1	assertEquals(10500, fromRanges.get(0)[0]);
109	1	assertEquals(10600, fromRanges.get(0)[1]);
110	1	assertEquals(20000, fromRanges.get(1)[0]);
111	1	assertEquals(20500, fromRanges.get(1)[1]);
112		// to range should start from given start numbering
113	1	List<int[]> toRanges = ranges.getToRanges();
114	1	assertEquals(1, toRanges.size());
115	1	assertEquals(23, toRanges.get(0)[0]);
116	1	assertEquals(624, toRanges.get(0)[1]);
117		}
118
119		/**
120		* Test the method that retains features except for 'CDS' (or subtypes), or
121		* features with parent other than the given id
122		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
123	1	@Test(groups = "Functional")...
124		public void testRetainFeature()
125		{
126	1	String accId = "ABC123";
127	1	EnsemblCds testee = new EnsemblCds();
128
129	1	SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
130		null);
131	1	assertFalse(testee.retainFeature(sf, accId));
132
133	1	sf = new SequenceFeature("CDS_predicted", "", 20000, 20500, 0f, null);
134	1	assertFalse(testee.retainFeature(sf, accId));
135
136		// other feature with no parent is retained
137	1	sf = new SequenceFeature("CDS_psequence_variantredicted", "", 20000,
138		20500, 0f, null);
139	1	assertTrue(testee.retainFeature(sf, accId));
140
141		// other feature with desired parent is retained
142	1	sf.setValue("Parent", "transcript:" + accId);
143	1	assertTrue(testee.retainFeature(sf, accId));
144
145		// feature with wrong parent is not retained
146	1	sf.setValue("Parent", "transcript:XYZ");
147	1	assertFalse(testee.retainFeature(sf, accId));
148		}
149
150		/**
151		* Test the method that picks out 'CDS' (or subtype) features with the
152		* accession id as parent
153		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
154	1	@Test(groups = "Functional")...
155		public void testIdentifiesSequence()
156		{
157	1	String accId = "ABC123";
158	1	EnsemblCds testee = new EnsemblCds();
159
160		// cds with no parent not valid
161	1	SequenceFeature sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
162	1	assertFalse(testee.identifiesSequence(sf, accId));
163
164		// cds with wrong parent not valid
165	1	sf.setValue("Parent", "transcript:XYZ");
166	1	assertFalse(testee.identifiesSequence(sf, accId));
167
168		// cds with right parent is valid
169	1	sf.setValue("Parent", "transcript:" + accId);
170	1	assertTrue(testee.identifiesSequence(sf, accId));
171
172		// cds sub-type with right parent is valid
173	1	sf = new SequenceFeature("CDS_predicted", "", 1, 2, 0f, null);
174	1	sf.setValue("Parent", "transcript:" + accId);
175	1	assertTrue(testee.identifiesSequence(sf, accId));
176
177		// transcript not valid:
178	1	sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
179	1	sf.setValue("Parent", "transcript:" + accId);
180	1	assertFalse(testee.identifiesSequence(sf, accId));
181
182		// exon not valid:
183	1	sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
184	1	sf.setValue("Parent", "transcript:" + accId);
185	1	assertFalse(testee.identifiesSequence(sf, accId));
186		}
187
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
188	1	@Test(groups = "Functional")...
189		public void testIsValidReference() throws Exception
190		{
191	1	EnsemblSequenceFetcher esq = new EnsemblCds();
192	1	Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
193	1	Assert.assertTrue(esq.isValidReference("ENST00000288602"));
194	1	Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
195	1	Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
196	1	Assert.assertFalse(esq.isValidReference("ENST0000288602"));
197		// non-human species have a 3 character identifier included:
198	1	Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
199		}
200
201		}