Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblCdnaTest	43	117	9	0	1.0100%	Show methods

Class EnsemblCdnaTest

Class EnsemblCdnaTest	Line # 43	Total Statements 117	Complexity 9	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4646	2.02	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	5353	1.01	1.01	0.00	1.0 1.0100%
tearDown() : void   tearDown() : void	5959	1.01	1.01	0.00	1.0 1.0100%
testGetGenomicRangesFromFeatures_reverseStrand() : void   testGetGenomicRangesFromFeatures_reverseStrand() : void	6969	29.029	1.01	0.00	1.0 1.0100%
testGetGenomicRangesFromFeatures() : void   testGetGenomicRangesFromFeatures() : void	124124	30.030	1.01	0.00	1.0 1.0100%
testGetGenomicRangesFromFeatures_mixedStrand() : void   testGetGenomicRangesFromFeatures_mixedStrand() : void	176176	15.015	1.01	0.00	1.0 1.0100%
testRetainFeature() : void   testRetainFeature() : void	205205	15.015	1.01	0.00	1.0 1.0100%
testIdentifiesSequence() : void   testIdentifiesSequence() : void	243243	17.017	1.01	0.00	1.0 1.0100%
testIsValidReference() : void   testIsValidReference() : void	277277	7.07	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.24603175	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures	1PASS
	0.23809524	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrand	1PASS
	0.14285715	jalview.ext.ensembl.EnsemblCdnaTest.testIdentifiesSequencejalview.ext.ensembl.EnsemblCdnaTest.testIdentifiesSequence	1PASS
	0.12698413	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_mixedStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_mixedStrand	1PASS
	0.12698413	jalview.ext.ensembl.EnsemblCdnaTest.testRetainFeaturejalview.ext.ensembl.EnsemblCdnaTest.testRetainFeature	1PASS
	0.06349207	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.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 (126) Complexity: 9 Complexity Density: 0.08
43		public class EnsemblCdnaTest
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.setInstance(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.setInstance(null);
63		}
64
65		/**
66		* Test that the cdna part of genomic sequence is correctly identified by
67		* 'exon' features (or subtypes) - reverse strand case.
68		*/
		100% Uncovered Elements: 0 (29) Complexity: 1 Complexity Density: 0.03 1PASS
69	1	@Test(groups = "Functional")...
70		public void testGetGenomicRangesFromFeatures_reverseStrand()
71		{
72	1	EnsemblCdna testee = new EnsemblCdna();
73	1	SequenceI genomic = new SequenceDummy("chr7");
74	1	genomic.setStart(10000);
75	1	genomic.setEnd(50000);
76	1	String transcriptId = "ABC123";
77
78		// exon at (start+10000) length 501
79	1	SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
80		null);
81	1	sf.setValue("Parent", "transcript:" + transcriptId);
82	1	sf.setStrand("-");
83	1	genomic.addSequenceFeature(sf);
84
85		// exon (sub-type) at (start + exon_variant) length 101
86	1	sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
87	1	sf.setValue("Parent", "transcript:" + transcriptId);
88	1	sf.setStrand("-");
89	1	genomic.addSequenceFeature(sf);
90
91		// exon belonging to a different transcript doesn't count
92	1	sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
93	1	sf.setValue("Parent", "transcript:anotherOne");
94	1	genomic.addSequenceFeature(sf);
95
96		// transcript feature doesn't count
97	1	sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
98	1	genomic.addSequenceFeature(sf);
99
100	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
101		transcriptId, 23);
102	1	List<int[]> fromRanges = ranges.getFromRanges();
103	1	assertEquals(2, fromRanges.size());
104
105		/*
106		* from ranges should be sorted by start order descending
107		* and hold mappings from reverse strand sense
108		*/
109	1	assertEquals(20500, fromRanges.get(0)[0]);
110	1	assertEquals(20000, fromRanges.get(0)[1]);
111	1	assertEquals(10600, fromRanges.get(1)[0]);
112	1	assertEquals(10500, 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 that the cdna part of genomic sequence is correctly identified by
122		* 'exon' features (or subtypes) with the desired transcript as parent
123		*/
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
124	1	@Test(groups = "Functional")...
125		public void testGetGenomicRangesFromFeatures()
126		{
127	1	EnsemblCdna testee = new EnsemblCdna();
128	1	SequenceI genomic = new SequenceDummy("chr7");
129	1	genomic.setStart(10000);
130	1	genomic.setEnd(50000);
131	1	String transcriptId = "ABC123";
132
133		// exon at (start+10000) length 501
134	1	SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
135		null);
136	1	sf.setValue("Parent", "transcript:" + transcriptId);
137	1	sf.setStrand("+");
138	1	genomic.addSequenceFeature(sf);
139
140		// exon (sub-type) at (start + exon_variant) length 101
141	1	sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
142	1	sf.setValue("Parent", "transcript:" + transcriptId);
143	1	sf.setStrand("+");
144	1	genomic.addSequenceFeature(sf);
145
146		// exon belonging to a different transcript doesn't count
147	1	sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
148	1	sf.setValue("Parent", "transcript:anotherOne");
149	1	genomic.addSequenceFeature(sf);
150
151		// transcript feature doesn't count
152	1	sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
153	1	sf.setStrand("-"); // weird but ignored
154	1	genomic.addSequenceFeature(sf);
155
156	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
157		transcriptId, 23);
158	1	List<int[]> fromRanges = ranges.getFromRanges();
159	1	assertEquals(2, fromRanges.size());
160		// from ranges should be sorted by start order
161	1	assertEquals(10500, fromRanges.get(0)[0]);
162	1	assertEquals(10600, fromRanges.get(0)[1]);
163	1	assertEquals(20000, fromRanges.get(1)[0]);
164	1	assertEquals(20500, fromRanges.get(1)[1]);
165		// to range should start from given start numbering
166	1	List<int[]> toRanges = ranges.getToRanges();
167	1	assertEquals(1, toRanges.size());
168	1	assertEquals(23, toRanges.get(0)[0]);
169	1	assertEquals(624, toRanges.get(0)[1]);
170		}
171
172		/**
173		* The method under test should give up and return null if both forward and
174		* reverse strands are present in the features of interest
175		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
176	1	@Test(groups = "Functional")...
177		public void testGetGenomicRangesFromFeatures_mixedStrand()
178		{
179	1	EnsemblCdna testee = new EnsemblCdna();
180	1	SequenceI genomic = new SequenceDummy("chr7");
181	1	genomic.setStart(10000);
182	1	genomic.setEnd(50000);
183	1	String transcriptId = "ABC123";
184
185	1	SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
186		null);
187	1	sf.setValue("Parent", "transcript:" + transcriptId);
188	1	sf.setStrand("-");
189	1	genomic.addSequenceFeature(sf);
190
191	1	sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
192	1	sf.setValue("Parent", "transcript:" + transcriptId);
193	1	sf.setStrand("+");
194	1	genomic.addSequenceFeature(sf);
195
196	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
197		transcriptId, 23);
198	1	assertNull(ranges);
199		}
200
201		/**
202		* Test the method that retains features except for 'transcript' (or
203		* subtypes), or features with parent other than the given id
204		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
205	1	@Test(groups = "Functional")...
206		public void testRetainFeature()
207		{
208	1	String accId = "ABC123";
209	1	EnsemblCdna testee = new EnsemblCdna();
210
211	1	SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
212		20500, 0f, null);
213	1	assertFalse(testee.retainFeature(sf, accId));
214
215	1	sf = new SequenceFeature("aberrant_processed_transcript", "", 20000,
216		20500, 0f, null);
217	1	assertFalse(testee.retainFeature(sf, accId));
218
219	1	sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
220		0f, null);
221	1	assertFalse(testee.retainFeature(sf, accId));
222
223		// other feature with no parent is retained
224	1	sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f, null);
225	1	assertTrue(testee.retainFeature(sf, accId));
226
227		// other feature with desired parent is retained
228	1	sf.setValue("Parent", "transcript:" + accId);
229	1	assertTrue(testee.retainFeature(sf, accId));
230
231		// test is not case-sensitive
232	1	assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
233
234		// feature with wrong parent is not retained
235	1	sf.setValue("Parent", "transcript:XYZ");
236	1	assertFalse(testee.retainFeature(sf, accId));
237		}
238
239		/**
240		* Test the method that picks out 'exon' (or subtype) features with the
241		* accession id as parent
242		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
243	1	@Test(groups = "Functional")...
244		public void testIdentifiesSequence()
245		{
246	1	String accId = "ABC123";
247	1	EnsemblCdna testee = new EnsemblCdna();
248
249		// exon with no parent not valid
250	1	SequenceFeature sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
251	1	assertFalse(testee.identifiesSequence(sf, accId));
252
253		// exon with wrong parent not valid
254	1	sf.setValue("Parent", "transcript:XYZ");
255	1	assertFalse(testee.identifiesSequence(sf, accId));
256
257		// exon with right parent is valid
258	1	sf.setValue("Parent", "transcript:" + accId);
259	1	assertTrue(testee.identifiesSequence(sf, accId));
260
261		// exon sub-type with right parent is valid
262	1	sf = new SequenceFeature("coding_exon", "", 1, 2, 0f, null);
263	1	sf.setValue("Parent", "transcript:" + accId);
264	1	assertTrue(testee.identifiesSequence(sf, accId));
265
266		// transcript not valid:
267	1	sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
268	1	sf.setValue("Parent", "transcript:" + accId);
269	1	assertFalse(testee.identifiesSequence(sf, accId));
270
271		// CDS not valid:
272	1	sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
273	1	sf.setValue("Parent", "transcript:" + accId);
274	1	assertFalse(testee.identifiesSequence(sf, accId));
275		}
276
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
277	1	@Test(groups = "Functional")...
278		public void testIsValidReference() throws Exception
279		{
280	1	EnsemblSequenceFetcher esq = new EnsemblCdna();
281	1	Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
282	1	Assert.assertTrue(esq.isValidReference("ENST00000288602"));
283	1	Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
284	1	Assert.assertFalse(esq.isValidReference("ENSP00000288602"));
285	1	Assert.assertFalse(esq.isValidReference("ENST0000288602"));
286		// non-human species having a 3 character identifier included:
287	1	Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
288		}
289		}