Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblCdnaTest	46	126	9	1.0100%	Show methods

Class EnsemblCdnaTest

Class EnsemblCdnaTest	Line # 46	Total Statements 126	Complexity 9	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4949	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	5656	1.01	1.01	1.0 1.0100%
tearDown() : void   tearDown() : void	6262	1.01	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures_reverseStrand() : void   testGetGenomicRangesFromFeatures_reverseStrand() : void	7272	29.029	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures() : void   testGetGenomicRangesFromFeatures() : void	127127	30.030	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures_mixedStrand() : void   testGetGenomicRangesFromFeatures_mixedStrand() : void	179179	15.015	1.01	1.0 1.0100%
testRetainFeature() : void   testRetainFeature() : void	208208	15.015	1.01	1.0 1.0100%
testGetIdentifyingFeatures() : void   testGetIdentifyingFeatures() : void	247247	26.026	1.01	1.0 1.0100%
testIsValidReference() : void   testIsValidReference() : void	295295	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.testGetGenomicRangesFromFeatures_mixedStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_mixedStrand	1PASS
	0.11851852	jalview.ext.ensembl.EnsemblCdnaTest.testRetainFeaturejalview.ext.ensembl.EnsemblCdnaTest.testRetainFeature	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 java.util.Locale;
24
25		import static org.testng.AssertJUnit.assertEquals;
26		import static org.testng.AssertJUnit.assertFalse;
27		import static org.testng.AssertJUnit.assertNull;
28		import static org.testng.AssertJUnit.assertTrue;
29
30		import jalview.datamodel.Sequence;
31		import jalview.datamodel.SequenceDummy;
32		import jalview.datamodel.SequenceFeature;
33		import jalview.datamodel.SequenceI;
34		import jalview.gui.JvOptionPane;
35		import jalview.io.gff.SequenceOntologyFactory;
36		import jalview.io.gff.SequenceOntologyLite;
37		import jalview.util.MapList;
38
39		import java.util.List;
40
41		import org.testng.Assert;
42		import org.testng.annotations.AfterClass;
43		import org.testng.annotations.BeforeClass;
44		import org.testng.annotations.Test;
45
		100% Uncovered Elements: 0 (135) Complexity: 9 Complexity Density: 0.07
46		public class EnsemblCdnaTest
47		{
48
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
49	1	@BeforeClass(alwaysRun = true)...
50		public void setUpJvOptionPane()
51		{
52	1	JvOptionPane.setInteractiveMode(false);
53	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54		}
55
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
56	1	@BeforeClass(alwaysRun = true)...
57		public void setUp()
58		{
59	1	SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
60		}
61
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
62	1	@AfterClass(alwaysRun = true)...
63		public void tearDown()
64		{
65	1	SequenceOntologyFactory.setInstance(null);
66		}
67
68		/**
69		* Test that the cdna part of genomic sequence is correctly identified by
70		* 'exon' features (or subtypes) - reverse strand case.
71		*/
		100% Uncovered Elements: 0 (29) Complexity: 1 Complexity Density: 0.03 1PASS
72	1	@Test(groups = "Functional")...
73		public void testGetGenomicRangesFromFeatures_reverseStrand()
74		{
75	1	EnsemblCdna testee = new EnsemblCdna();
76	1	SequenceI genomic = new SequenceDummy("chr7");
77	1	genomic.setStart(10000);
78	1	genomic.setEnd(50000);
79	1	String transcriptId = "ABC123";
80
81		// exon at (start+10000) length 501
82	1	SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
83		null);
84	1	sf.setValue("Parent", transcriptId);
85	1	sf.setStrand("-");
86	1	genomic.addSequenceFeature(sf);
87
88		// exon (sub-type) at (start + exon_variant) length 101
89	1	sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
90	1	sf.setValue("Parent", transcriptId);
91	1	sf.setStrand("-");
92	1	genomic.addSequenceFeature(sf);
93
94		// exon belonging to a different transcript doesn't count
95	1	sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
96	1	sf.setValue("Parent", "anotherOne");
97	1	genomic.addSequenceFeature(sf);
98
99		// transcript feature doesn't count
100	1	sf = new SequenceFeature("transcript", "", 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
108		/*
109		* from ranges should be sorted by start order descending
110		* and hold mappings from reverse strand sense
111		*/
112	1	assertEquals(20500, fromRanges.get(0)[0]);
113	1	assertEquals(20000, fromRanges.get(0)[1]);
114	1	assertEquals(10600, fromRanges.get(1)[0]);
115	1	assertEquals(10500, fromRanges.get(1)[1]);
116		// to range should start from given start numbering
117	1	List<int[]> toRanges = ranges.getToRanges();
118	1	assertEquals(1, toRanges.size());
119	1	assertEquals(23, toRanges.get(0)[0]);
120	1	assertEquals(624, toRanges.get(0)[1]);
121		}
122
123		/**
124		* Test that the cdna part of genomic sequence is correctly identified by
125		* 'exon' features (or subtypes) with the desired transcript as parent
126		*/
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
127	1	@Test(groups = "Functional")...
128		public void testGetGenomicRangesFromFeatures()
129		{
130	1	EnsemblCdna testee = new EnsemblCdna();
131	1	SequenceI genomic = new SequenceDummy("chr7");
132	1	genomic.setStart(10000);
133	1	genomic.setEnd(50000);
134	1	String transcriptId = "ABC123";
135
136		// exon at (start+10000) length 501
137	1	SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
138		null);
139	1	sf.setValue("Parent", transcriptId);
140	1	sf.setStrand("+");
141	1	genomic.addSequenceFeature(sf);
142
143		// exon (sub-type) at (start + exon_variant) length 101
144	1	sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
145	1	sf.setValue("Parent", transcriptId);
146	1	sf.setStrand("+");
147	1	genomic.addSequenceFeature(sf);
148
149		// exon belonging to a different transcript doesn't count
150	1	sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
151	1	sf.setValue("Parent", "anotherOne");
152	1	genomic.addSequenceFeature(sf);
153
154		// transcript feature doesn't count
155	1	sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
156	1	sf.setStrand("-"); // weird but ignored
157	1	genomic.addSequenceFeature(sf);
158
159	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
160		transcriptId, 23);
161	1	List<int[]> fromRanges = ranges.getFromRanges();
162	1	assertEquals(2, fromRanges.size());
163		// from ranges should be sorted by start order
164	1	assertEquals(10500, fromRanges.get(0)[0]);
165	1	assertEquals(10600, fromRanges.get(0)[1]);
166	1	assertEquals(20000, fromRanges.get(1)[0]);
167	1	assertEquals(20500, fromRanges.get(1)[1]);
168		// to range should start from given start numbering
169	1	List<int[]> toRanges = ranges.getToRanges();
170	1	assertEquals(1, toRanges.size());
171	1	assertEquals(23, toRanges.get(0)[0]);
172	1	assertEquals(624, toRanges.get(0)[1]);
173		}
174
175		/**
176		* The method under test should give up and return null if both forward and
177		* reverse strands are present in the features of interest
178		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
179	1	@Test(groups = "Functional")...
180		public void testGetGenomicRangesFromFeatures_mixedStrand()
181		{
182	1	EnsemblCdna testee = new EnsemblCdna();
183	1	SequenceI genomic = new SequenceDummy("chr7");
184	1	genomic.setStart(10000);
185	1	genomic.setEnd(50000);
186	1	String transcriptId = "ABC123";
187
188	1	SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
189		null);
190	1	sf.setValue("Parent", "transcript:" + transcriptId);
191	1	sf.setStrand("-");
192	1	genomic.addSequenceFeature(sf);
193
194	1	sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
195	1	sf.setValue("Parent", "transcript:" + transcriptId);
196	1	sf.setStrand("+");
197	1	genomic.addSequenceFeature(sf);
198
199	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
200		transcriptId, 23);
201	1	assertNull(ranges);
202		}
203
204		/**
205		* Test the method that retains features except for 'transcript' (or
206		* subtypes), or features with parent other than the given id
207		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
208	1	@Test(groups = "Functional")...
209		public void testRetainFeature()
210		{
211	1	String accId = "ABC123";
212	1	EnsemblCdna testee = new EnsemblCdna();
213
214	1	SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
215		0f, null);
216	1	assertFalse(testee.retainFeature(sf, accId));
217
218	1	sf = new SequenceFeature("aberrant_processed_transcript", "", 20000,
219		20500, 0f, null);
220	1	assertFalse(testee.retainFeature(sf, accId));
221
222	1	sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
223		null);
224	1	assertFalse(testee.retainFeature(sf, accId));
225
226		// other feature with no parent is retained
227	1	sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f,
228		null);
229	1	assertTrue(testee.retainFeature(sf, accId));
230
231		// other feature with desired parent is retained
232	1	sf.setValue("Parent", accId);
233	1	assertTrue(testee.retainFeature(sf, accId));
234
235		// test is not case-sensitive
236	1	assertTrue(testee.retainFeature(sf, accId.toLowerCase(Locale.ROOT)));
237
238		// feature with wrong parent is not retained
239	1	sf.setValue("Parent", "XYZ");
240	1	assertFalse(testee.retainFeature(sf, accId));
241		}
242
243		/**
244		* Test the method that picks out 'exon' (or subtype) features with the
245		* accession id as parent
246		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
247	1	@Test(groups = "Functional")...
248		public void testGetIdentifyingFeatures()
249		{
250	1	String accId = "ABC123";
251	1	SequenceI seq = new Sequence(accId, "MKLNFRQIE");
252
253		// exon with no parent: not valid
254	1	SequenceFeature sf1 = new SequenceFeature("exon", "", 1, 2, 0f, null);
255	1	seq.addSequenceFeature(sf1);
256
257		// exon with wrong parent: not valid
258	1	SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
259	1	sf2.setValue("Parent", "XYZ");
260	1	seq.addSequenceFeature(sf2);
261
262		// exon with right parent is valid
263	1	SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
264	1	sf3.setValue("Parent", accId);
265	1	seq.addSequenceFeature(sf3);
266
267		// exon sub-type with right parent is valid
268	1	SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f,
269		null);
270	1	sf4.setValue("Parent", accId);
271	1	seq.addSequenceFeature(sf4);
272
273		// transcript not valid:
274	1	SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
275		null);
276	1	sf5.setValue("Parent", accId);
277	1	seq.addSequenceFeature(sf5);
278
279		// CDS not valid:
280	1	SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
281		null);
282	1	sf6.setValue("Parent", accId);
283	1	seq.addSequenceFeature(sf6);
284
285	1	List<SequenceFeature> sfs = new EnsemblCdna()
286		.getIdentifyingFeatures(seq, accId);
287	1	assertFalse(sfs.contains(sf1));
288	1	assertFalse(sfs.contains(sf2));
289	1	assertTrue(sfs.contains(sf3));
290	1	assertTrue(sfs.contains(sf4));
291	1	assertFalse(sfs.contains(sf5));
292	1	assertFalse(sfs.contains(sf6));
293		}
294
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
295	1	@Test(groups = "Functional")...
296		public void testIsValidReference() throws Exception
297		{
298	1	EnsemblSequenceFetcher esq = new EnsemblCdna();
299	1	Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
300	1	Assert.assertTrue(esq.isValidReference("ENST00000288602"));
301	1	Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
302	1	Assert.assertFalse(esq.isValidReference("ENSP00000288602"));
303	1	Assert.assertFalse(esq.isValidReference("ENST0000288602"));
304		// non-human species having a 3 character identifier included:
305	1	Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
306		}
307		}