Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblCdsTest	43	80	7	1.0100%	Show methods

Class EnsemblCdsTest

Class EnsemblCdsTest	Line # 43	Total Statements 80	Complexity 7	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4646	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	5353	1.01	1.01	1.0 1.0100%
tearDown() : void   tearDown() : void	5959	1.01	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures() : void   testGetGenomicRangesFromFeatures() : void	6969	31.031	1.01	1.0 1.0100%
testRetainFeature() : void   testRetainFeature() : void	124124	12.012	1.01	1.0 1.0100%
testGetIdentifyingFeatures() : void   testGetIdentifyingFeatures() : void	154154	26.026	1.01	1.0 1.0100%
testIsValidReference() : void   testIsValidReference() : void	201201	7.07	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.3678161	jalview.ext.ensembl.EnsemblCdsTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblCdsTest.testGetGenomicRangesFromFeatures	1PASS
	0.31034482	jalview.ext.ensembl.EnsemblCdsTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblCdsTest.testGetIdentifyingFeatures	1PASS
	0.14942528	jalview.ext.ensembl.EnsemblCdsTest.testRetainFeaturejalview.ext.ensembl.EnsemblCdsTest.testRetainFeature	1PASS
	0.09195402	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.Sequence;
28		import jalview.datamodel.SequenceDummy;
29		import jalview.datamodel.SequenceFeature;
30		import jalview.datamodel.SequenceI;
31		import jalview.gui.JvOptionPane;
32		import jalview.io.gff.SequenceOntologyFactory;
33		import jalview.io.gff.SequenceOntologyLite;
34		import jalview.util.MapList;
35
36		import java.util.List;
37
38		import org.testng.Assert;
39		import org.testng.annotations.AfterClass;
40		import org.testng.annotations.BeforeClass;
41		import org.testng.annotations.Test;
42
		100% Uncovered Elements: 0 (87) Complexity: 7 Complexity Density: 0.09
43		public class EnsemblCdsTest
44		{
45
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
46	1	@BeforeClass(alwaysRun = true)...
47		public void setUpJvOptionPane()
48		{
49	1	JvOptionPane.setInteractiveMode(false);
50	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51		}
52
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
53	1	@BeforeClass(alwaysRun = true)...
54		public void setUp()
55		{
56	1	SequenceOntologyFactory.setSequenceOntology(new SequenceOntologyLite());
57		}
58
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
59	1	@AfterClass(alwaysRun = true)...
60		public void tearDown()
61		{
62	1	SequenceOntologyFactory.setSequenceOntology(null);
63		}
64
65		/**
66		* Test that the cdna part of genomic sequence is correctly identified by
67		* 'CDS' features (or subtypes) with the desired transcript as parent
68		*/
		100% Uncovered Elements: 0 (31) Complexity: 1 Complexity Density: 0.03 1PASS
69	1	@Test(groups = "Functional")...
70		public void testGetGenomicRangesFromFeatures()
71		{
72	1	EnsemblCds testee = new EnsemblCds();
73	1	SequenceI genomic = new SequenceDummy("chr7");
74	1	genomic.setStart(10000);
75	1	genomic.setEnd(50000);
76	1	String transcriptId = "ABC123";
77
78		// CDS at (start+10000) length 501
79	1	SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
80		null);
81	1	sf.setValue("Parent", transcriptId);
82	1	sf.setStrand("+");
83	1	genomic.addSequenceFeature(sf);
84
85		// CDS (sub-type) at (start + 10500) length 101
86	1	sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
87	1	sf.setValue("Parent", transcriptId);
88	1	sf.setStrand("+");
89	1	genomic.addSequenceFeature(sf);
90
91		// CDS belonging to a different transcript doesn't count
92	1	sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
93	1	sf.setValue("Parent", "anotherOne");
94	1	genomic.addSequenceFeature(sf);
95
96		// exon feature doesn't count
97	1	sf = new SequenceFeature("exon", "", 10000, 50000, 0f, null);
98	1	genomic.addSequenceFeature(sf);
99
100		// mRNA_region feature doesn't count (parent of CDS)
101	1	sf = new SequenceFeature("mRNA_region", "", 10000, 50000, 0f, null);
102	1	genomic.addSequenceFeature(sf);
103
104	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
105		transcriptId, 23);
106	1	List<int[]> fromRanges = ranges.getFromRanges();
107	1	assertEquals(2, fromRanges.size());
108		// from ranges should be sorted by start order
109	1	assertEquals(10500, fromRanges.get(0)[0]);
110	1	assertEquals(10600, fromRanges.get(0)[1]);
111	1	assertEquals(20000, fromRanges.get(1)[0]);
112	1	assertEquals(20500, fromRanges.get(1)[1]);
113		// to range should start from given start numbering
114	1	List<int[]> toRanges = ranges.getToRanges();
115	1	assertEquals(1, toRanges.size());
116	1	assertEquals(23, toRanges.get(0)[0]);
117	1	assertEquals(624, toRanges.get(0)[1]);
118		}
119
120		/**
121		* Test the method that retains features except for 'CDS' (or subtypes), or
122		* features with parent other than the given id
123		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
124	1	@Test(groups = "Functional")...
125		public void testRetainFeature()
126		{
127	1	String accId = "ABC123";
128	1	EnsemblCds testee = new EnsemblCds();
129
130	1	SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
131		null);
132	1	assertFalse(testee.retainFeature(sf, accId));
133
134	1	sf = new SequenceFeature("CDS_predicted", "", 20000, 20500, 0f, null);
135	1	assertFalse(testee.retainFeature(sf, accId));
136
137		// other feature with no parent is retained
138	1	sf = new SequenceFeature("anotherType", "", 20000, 20500, 0f, null);
139	1	assertTrue(testee.retainFeature(sf, accId));
140
141		// other feature with desired parent is retained
142	1	sf.setValue("Parent", accId);
143	1	assertTrue(testee.retainFeature(sf, accId));
144
145		// feature with wrong parent is not retained
146	1	sf.setValue("Parent", "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 (26) Complexity: 1 Complexity Density: 0.04 1PASS
154	1	@Test(groups = "Functional")...
155		public void testGetIdentifyingFeatures()
156		{
157	1	String accId = "ABC123";
158	1	SequenceI seq = new Sequence(accId, "MKDONS");
159
160		// cds with no parent not valid
161	1	SequenceFeature sf1 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
162	1	seq.addSequenceFeature(sf1);
163
164		// cds with wrong parent not valid
165	1	SequenceFeature sf2 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
166	1	sf2.setValue("Parent", "XYZ");
167	1	seq.addSequenceFeature(sf2);
168
169		// cds with right parent is valid
170	1	SequenceFeature sf3 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
171	1	sf3.setValue("Parent", accId);
172	1	seq.addSequenceFeature(sf3);
173
174		// cds sub-type with right parent is valid
175	1	SequenceFeature sf4 = new SequenceFeature("CDS_predicted", "", 1, 2, 0f,
176		null);
177	1	sf4.setValue("Parent", accId);
178	1	seq.addSequenceFeature(sf4);
179
180		// transcript not valid:
181	1	SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
182		null);
183	1	sf5.setValue("Parent", accId);
184	1	seq.addSequenceFeature(sf5);
185
186		// exon not valid:
187	1	SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
188	1	sf6.setValue("Parent", accId);
189	1	seq.addSequenceFeature(sf6);
190
191	1	List<SequenceFeature> sfs = new EnsemblCds().getIdentifyingFeatures(seq,
192		accId);
193	1	assertFalse(sfs.contains(sf1));
194	1	assertFalse(sfs.contains(sf2));
195	1	assertTrue(sfs.contains(sf3));
196	1	assertTrue(sfs.contains(sf4));
197	1	assertFalse(sfs.contains(sf5));
198	1	assertFalse(sfs.contains(sf6));
199		}
200
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
201	1	@Test(groups = "Functional")...
202		public void testIsValidReference() throws Exception
203		{
204	1	EnsemblSequenceFetcher esq = new EnsemblCds();
205	1	Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
206	1	Assert.assertTrue(esq.isValidReference("ENST00000288602"));
207	1	Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
208	1	Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
209	1	Assert.assertFalse(esq.isValidReference("ENST0000288602"));
210		// non-human species have a 3 character identifier included:
211	1	Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
212		}
213
214		}