Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblCdnaTest	44	126	9	1.0100%	Show methods

Class EnsemblCdnaTest

Class EnsemblCdnaTest	Line # 44	Total Statements 126	Complexity 9	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4747	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	5454	1.01	1.01	1.0 1.0100%
tearDown() : void   tearDown() : void	6060	1.01	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures_reverseStrand() : void   testGetGenomicRangesFromFeatures_reverseStrand() : void	7070	29.029	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures() : void   testGetGenomicRangesFromFeatures() : void	125125	30.030	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures_mixedStrand() : void   testGetGenomicRangesFromFeatures_mixedStrand() : void	177177	15.015	1.01	1.0 1.0100%
testRetainFeature() : void   testRetainFeature() : void	206206	15.015	1.01	1.0 1.0100%
testGetIdentifyingFeatures() : void   testGetIdentifyingFeatures() : void	244244	26.026	1.01	1.0 1.0100%
testIsValidReference() : void   testIsValidReference() : void	292292	7.07	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.22962964	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures	1PASS
	0.22222222	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrand	1PASS
	0.2	jalview.ext.ensembl.EnsemblCdnaTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblCdnaTest.testGetIdentifyingFeatures	1PASS
	0.11851852	jalview.ext.ensembl.EnsemblCdnaTest.testRetainFeaturejalview.ext.ensembl.EnsemblCdnaTest.testRetainFeature	1PASS
	0.11851852	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_mixedStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_mixedStrand	1PASS
	0.05925926	jalview.ext.ensembl.EnsemblCdnaTest.testIsValidReferencejalview.ext.ensembl.EnsemblCdnaTest.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.assertNull;
26		import static org.testng.AssertJUnit.assertTrue;
27
28		import jalview.datamodel.Sequence;
29		import jalview.datamodel.SequenceDummy;
30		import jalview.datamodel.SequenceFeature;
31		import jalview.datamodel.SequenceI;
32		import jalview.gui.JvOptionPane;
33		import jalview.io.gff.SequenceOntologyFactory;
34		import jalview.io.gff.SequenceOntologyLite;
35		import jalview.util.MapList;
36
37		import java.util.List;
38
39		import org.testng.Assert;
40		import org.testng.annotations.AfterClass;
41		import org.testng.annotations.BeforeClass;
42		import org.testng.annotations.Test;
43
		100% Uncovered Elements: 0 (135) Complexity: 9 Complexity Density: 0.07
44		public class EnsemblCdnaTest
45		{
46
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
47	1	@BeforeClass(alwaysRun = true)...
48		public void setUpJvOptionPane()
49		{
50	1	JvOptionPane.setInteractiveMode(false);
51	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52		}
53
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
54	1	@BeforeClass(alwaysRun = true)...
55		public void setUp()
56		{
57	1	SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
58		}
59
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
60	1	@AfterClass(alwaysRun = true)...
61		public void tearDown()
62		{
63	1	SequenceOntologyFactory.setInstance(null);
64		}
65
66		/**
67		* Test that the cdna part of genomic sequence is correctly identified by
68		* 'exon' features (or subtypes) - reverse strand case.
69		*/
		100% Uncovered Elements: 0 (29) Complexity: 1 Complexity Density: 0.03 1PASS
70	1	@Test(groups = "Functional")...
71		public void testGetGenomicRangesFromFeatures_reverseStrand()
72		{
73	1	EnsemblCdna testee = new EnsemblCdna();
74	1	SequenceI genomic = new SequenceDummy("chr7");
75	1	genomic.setStart(10000);
76	1	genomic.setEnd(50000);
77	1	String transcriptId = "ABC123";
78
79		// exon at (start+10000) length 501
80	1	SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
81		null);
82	1	sf.setValue("Parent", transcriptId);
83	1	sf.setStrand("-");
84	1	genomic.addSequenceFeature(sf);
85
86		// exon (sub-type) at (start + exon_variant) length 101
87	1	sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
88	1	sf.setValue("Parent", transcriptId);
89	1	sf.setStrand("-");
90	1	genomic.addSequenceFeature(sf);
91
92		// exon belonging to a different transcript doesn't count
93	1	sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
94	1	sf.setValue("Parent", "anotherOne");
95	1	genomic.addSequenceFeature(sf);
96
97		// transcript feature doesn't count
98	1	sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
99	1	genomic.addSequenceFeature(sf);
100
101	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
102		transcriptId, 23);
103	1	List<int[]> fromRanges = ranges.getFromRanges();
104	1	assertEquals(2, fromRanges.size());
105
106		/*
107		* from ranges should be sorted by start order descending
108		* and hold mappings from reverse strand sense
109		*/
110	1	assertEquals(20500, fromRanges.get(0)[0]);
111	1	assertEquals(20000, fromRanges.get(0)[1]);
112	1	assertEquals(10600, fromRanges.get(1)[0]);
113	1	assertEquals(10500, fromRanges.get(1)[1]);
114		// to range should start from given start numbering
115	1	List<int[]> toRanges = ranges.getToRanges();
116	1	assertEquals(1, toRanges.size());
117	1	assertEquals(23, toRanges.get(0)[0]);
118	1	assertEquals(624, toRanges.get(0)[1]);
119		}
120
121		/**
122		* Test that the cdna part of genomic sequence is correctly identified by
123		* 'exon' features (or subtypes) with the desired transcript as parent
124		*/
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
125	1	@Test(groups = "Functional")...
126		public void testGetGenomicRangesFromFeatures()
127		{
128	1	EnsemblCdna testee = new EnsemblCdna();
129	1	SequenceI genomic = new SequenceDummy("chr7");
130	1	genomic.setStart(10000);
131	1	genomic.setEnd(50000);
132	1	String transcriptId = "ABC123";
133
134		// exon at (start+10000) length 501
135	1	SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
136		null);
137	1	sf.setValue("Parent", transcriptId);
138	1	sf.setStrand("+");
139	1	genomic.addSequenceFeature(sf);
140
141		// exon (sub-type) at (start + exon_variant) length 101
142	1	sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
143	1	sf.setValue("Parent", transcriptId);
144	1	sf.setStrand("+");
145	1	genomic.addSequenceFeature(sf);
146
147		// exon belonging to a different transcript doesn't count
148	1	sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
149	1	sf.setValue("Parent", "anotherOne");
150	1	genomic.addSequenceFeature(sf);
151
152		// transcript feature doesn't count
153	1	sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
154	1	sf.setStrand("-"); // weird but ignored
155	1	genomic.addSequenceFeature(sf);
156
157	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
158		transcriptId, 23);
159	1	List<int[]> fromRanges = ranges.getFromRanges();
160	1	assertEquals(2, fromRanges.size());
161		// from ranges should be sorted by start order
162	1	assertEquals(10500, fromRanges.get(0)[0]);
163	1	assertEquals(10600, fromRanges.get(0)[1]);
164	1	assertEquals(20000, fromRanges.get(1)[0]);
165	1	assertEquals(20500, fromRanges.get(1)[1]);
166		// to range should start from given start numbering
167	1	List<int[]> toRanges = ranges.getToRanges();
168	1	assertEquals(1, toRanges.size());
169	1	assertEquals(23, toRanges.get(0)[0]);
170	1	assertEquals(624, toRanges.get(0)[1]);
171		}
172
173		/**
174		* The method under test should give up and return null if both forward and
175		* reverse strands are present in the features of interest
176		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
177	1	@Test(groups = "Functional")...
178		public void testGetGenomicRangesFromFeatures_mixedStrand()
179		{
180	1	EnsemblCdna testee = new EnsemblCdna();
181	1	SequenceI genomic = new SequenceDummy("chr7");
182	1	genomic.setStart(10000);
183	1	genomic.setEnd(50000);
184	1	String transcriptId = "ABC123";
185
186	1	SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
187		null);
188	1	sf.setValue("Parent", "transcript:" + transcriptId);
189	1	sf.setStrand("-");
190	1	genomic.addSequenceFeature(sf);
191
192	1	sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
193	1	sf.setValue("Parent", "transcript:" + transcriptId);
194	1	sf.setStrand("+");
195	1	genomic.addSequenceFeature(sf);
196
197	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
198		transcriptId, 23);
199	1	assertNull(ranges);
200		}
201
202		/**
203		* Test the method that retains features except for 'transcript' (or
204		* subtypes), or features with parent other than the given id
205		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
206	1	@Test(groups = "Functional")...
207		public void testRetainFeature()
208		{
209	1	String accId = "ABC123";
210	1	EnsemblCdna testee = new EnsemblCdna();
211
212	1	SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
213		20500, 0f, null);
214	1	assertFalse(testee.retainFeature(sf, accId));
215
216	1	sf = new SequenceFeature("aberrant_processed_transcript", "", 20000,
217		20500, 0f, null);
218	1	assertFalse(testee.retainFeature(sf, accId));
219
220	1	sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
221		0f, null);
222	1	assertFalse(testee.retainFeature(sf, accId));
223
224		// other feature with no parent is retained
225	1	sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f, null);
226	1	assertTrue(testee.retainFeature(sf, accId));
227
228		// other feature with desired parent is retained
229	1	sf.setValue("Parent", accId);
230	1	assertTrue(testee.retainFeature(sf, accId));
231
232		// test is not case-sensitive
233	1	assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
234
235		// feature with wrong parent is not retained
236	1	sf.setValue("Parent", "XYZ");
237	1	assertFalse(testee.retainFeature(sf, accId));
238		}
239
240		/**
241		* Test the method that picks out 'exon' (or subtype) features with the
242		* accession id as parent
243		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
244	1	@Test(groups = "Functional")...
245		public void testGetIdentifyingFeatures()
246		{
247	1	String accId = "ABC123";
248	1	SequenceI seq = new Sequence(accId, "MKLNFRQIE");
249
250		// exon with no parent: not valid
251	1	SequenceFeature sf1 = new SequenceFeature("exon", "", 1, 2, 0f, null);
252	1	seq.addSequenceFeature(sf1);
253
254		// exon with wrong parent: not valid
255	1	SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
256	1	sf2.setValue("Parent", "XYZ");
257	1	seq.addSequenceFeature(sf2);
258
259		// exon with right parent is valid
260	1	SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
261	1	sf3.setValue("Parent", accId);
262	1	seq.addSequenceFeature(sf3);
263
264		// exon sub-type with right parent is valid
265	1	SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f,
266		null);
267	1	sf4.setValue("Parent", accId);
268	1	seq.addSequenceFeature(sf4);
269
270		// transcript not valid:
271	1	SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
272		null);
273	1	sf5.setValue("Parent", accId);
274	1	seq.addSequenceFeature(sf5);
275
276		// CDS not valid:
277	1	SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
278		null);
279	1	sf6.setValue("Parent", accId);
280	1	seq.addSequenceFeature(sf6);
281
282	1	List<SequenceFeature> sfs = new EnsemblCdna()
283		.getIdentifyingFeatures(seq, accId);
284	1	assertFalse(sfs.contains(sf1));
285	1	assertFalse(sfs.contains(sf2));
286	1	assertTrue(sfs.contains(sf3));
287	1	assertTrue(sfs.contains(sf4));
288	1	assertFalse(sfs.contains(sf5));
289	1	assertFalse(sfs.contains(sf6));
290		}
291
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
292	1	@Test(groups = "Functional")...
293		public void testIsValidReference() throws Exception
294		{
295	1	EnsemblSequenceFetcher esq = new EnsemblCdna();
296	1	Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
297	1	Assert.assertTrue(esq.isValidReference("ENST00000288602"));
298	1	Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
299	1	Assert.assertFalse(esq.isValidReference("ENSP00000288602"));
300	1	Assert.assertFalse(esq.isValidReference("ENST0000288602"));
301		// non-human species having a 3 character identifier included:
302	1	Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
303		}
304		}