Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblGeneTest	44	138	10	13	0.912162291.2%	Show methods

Class EnsemblGeneTest

Class EnsemblGeneTest	Line # 44	Total Statements 138	Complexity 10	Uncovered Elements 13	TOTAL Coverage 0.912162291.2%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4747	2.02	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	5454	2.02	1.01	0.00	1.0 1.0100%
tearDown() : void   tearDown() : void	6161	1.01	1.01	0.00	1.0 1.0100%
testGetGenomicRangesFromFeatures() : void   testGetGenomicRangesFromFeatures() : void	7171	22.022	1.01	0.00	1.0 1.0100%
testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand() : void   testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand() : void	111111	22.022	1.01	0.00	1.0 1.0100%
testGetTranscriptFeatures() : void   testGetTranscriptFeatures() : void	153153	26.026	1.01	0.00	1.0 1.0100%
testRetainFeature() : void   testRetainFeature() : void	207207	18.018	1.01	0.00	1.0 1.0100%
testIdentifiesSequence() : void   testIdentifiesSequence() : void	242242	18.018	1.01	0.00	1.0 1.0100%
testGetFeatureColourScheme() : void   testGetFeatureColourScheme() : void	284284	15.015	1.01	0.00	1.0 1.0100%
testGetGeneIds() : void   testGetGeneIds() : void	306306	12.012	1.01	12.012	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.18243243	jalview.ext.ensembl.EnsemblGeneTest.testGetTranscriptFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetTranscriptFeatures	1PASS
	0.1554054	jalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures	1PASS
	0.1554054	jalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrandjalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand	1PASS
	0.12837838	jalview.ext.ensembl.EnsemblGeneTest.testIdentifiesSequencejalview.ext.ensembl.EnsemblGeneTest.testIdentifiesSequence	1PASS
	0.12837838	jalview.ext.ensembl.EnsemblGeneTest.testRetainFeaturejalview.ext.ensembl.EnsemblGeneTest.testRetainFeature	1PASS
	0.10810811	jalview.ext.ensembl.EnsemblGeneTest.testGetFeatureColourSchemejalview.ext.ensembl.EnsemblGeneTest.testGetFeatureColourScheme	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.api.FeatureSettingsModelI;
28		import jalview.bin.Cache;
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.awt.Color;
38		import java.util.List;
39
40		import org.testng.annotations.AfterClass;
41		import org.testng.annotations.BeforeClass;
42		import org.testng.annotations.Test;
43
		91.2% Uncovered Elements: 13 (148) Complexity: 10 Complexity Density: 0.07
44		public class EnsemblGeneTest
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 (2) Complexity: 1 Complexity Density: 0.5
54	1	@BeforeClass(alwaysRun = true)...
55		public void setUp()
56		{
57	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
58	1	SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
59		}
60
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
61	1	@AfterClass(alwaysRun = true)...
62		public void tearDown()
63		{
64	1	SequenceOntologyFactory.setInstance(null);
65		}
66
67		/**
68		* Test that the gene part of genomic sequence is uniquely identified by a
69		* 'gene' features (or subtype) with the correct gene ID
70		*/
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
71	1	@Test(groups = "Functional")...
72		public void testGetGenomicRangesFromFeatures()
73		{
74	1	EnsemblGene testee = new EnsemblGene();
75	1	SequenceI genomic = new SequenceDummy("chr7");
76	1	genomic.setStart(10000);
77	1	genomic.setEnd(50000);
78	1	String geneId = "ABC123";
79
80		// gene at (start+20000) length 501
81		// should be ignored - the first 'gene' found defines the whole range
82		// (note features are found in position order, not addition order)
83	1	SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
84		null);
85	1	sf.setValue("ID", "gene:" + geneId);
86	1	sf.setStrand("+");
87	1	genomic.addSequenceFeature(sf);
88
89		// gene at (start + 10500) length 101
90	1	sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
91	1	sf.setValue("ID", "gene:" + geneId);
92	1	sf.setStrand("+");
93	1	genomic.addSequenceFeature(sf);
94
95	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
96		23);
97	1	List<int[]> fromRanges = ranges.getFromRanges();
98	1	assertEquals(1, fromRanges.size());
99	1	assertEquals(10500, fromRanges.get(0)[0]);
100	1	assertEquals(10600, fromRanges.get(0)[1]);
101		// to range should start from given start numbering
102	1	List<int[]> toRanges = ranges.getToRanges();
103	1	assertEquals(1, toRanges.size());
104	1	assertEquals(23, toRanges.get(0)[0]);
105	1	assertEquals(123, toRanges.get(0)[1]);
106		}
107
108		/**
109		* Test variant using a sub-type of gene from the Sequence Ontology
110		*/
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
111	1	@Test(groups = "Functional")...
112		public void testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand()
113		{
114	1	EnsemblGene testee = new EnsemblGene();
115	1	SequenceI genomic = new SequenceDummy("chr7");
116	1	genomic.setStart(10000);
117	1	genomic.setEnd(50000);
118	1	String geneId = "ABC123";
119
120		// gene at (start+20000) length 501
121		// should be ignored - the first 'gene' found defines the whole range
122		// (real data would only have one such feature)
123	1	SequenceFeature sf = new SequenceFeature("ncRNA_gene", "", 20000,
124		20500, 0f, null);
125	1	sf.setValue("ID", "gene:" + geneId);
126	1	sf.setStrand("-");
127	1	genomic.addSequenceFeature(sf);
128
129		// gene at (start + 10500) length 101
130	1	sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
131	1	sf.setValue("ID", "gene:" + geneId);
132	1	sf.setStrand("+");
133	1	genomic.addSequenceFeature(sf);
134
135	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
136		23);
137	1	List<int[]> fromRanges = ranges.getFromRanges();
138	1	assertEquals(1, fromRanges.size());
139		// from range on reverse strand:
140	1	assertEquals(10500, fromRanges.get(0)[0]);
141	1	assertEquals(10600, fromRanges.get(0)[1]);
142		// to range should start from given start numbering
143	1	List<int[]> toRanges = ranges.getToRanges();
144	1	assertEquals(1, toRanges.size());
145	1	assertEquals(23, toRanges.get(0)[0]);
146	1	assertEquals(123, toRanges.get(0)[1]);
147		}
148
149		/**
150		* Test the method that extracts transcript (or subtype) features with a
151		* specified gene as parent
152		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
153	1	@Test(groups = "Functional")...
154		public void testGetTranscriptFeatures()
155		{
156	1	SequenceI genomic = new SequenceDummy("chr7");
157	1	genomic.setStart(10000);
158	1	genomic.setEnd(50000);
159	1	String geneId = "ABC123";
160
161		// transcript feature
162	1	SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
163		20500, 0f, null);
164	1	sf1.setValue("Parent", "gene:" + geneId);
165	1	sf1.setValue("transcript_id", "transcript1");
166	1	genomic.addSequenceFeature(sf1);
167
168		// transcript sub-type feature
169	1	SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
170		0f, null);
171	1	sf2.setValue("Parent", "gene:" + geneId);
172	1	sf2.setValue("transcript_id", "transcript2");
173	1	genomic.addSequenceFeature(sf2);
174
175		// NMD_transcript_variant treated like transcript in Ensembl
176	1	SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
177		22000, 22500, 0f, null);
178		// id matching should not be case-sensitive
179	1	sf3.setValue("Parent", "gene:" + geneId.toLowerCase());
180	1	sf3.setValue("transcript_id", "transcript3");
181	1	genomic.addSequenceFeature(sf3);
182
183		// transcript for a different gene - ignored
184	1	SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
185		0f, null);
186	1	sf4.setValue("Parent", "gene:XYZ");
187	1	sf4.setValue("transcript_id", "transcript4");
188	1	genomic.addSequenceFeature(sf4);
189
190	1	EnsemblGene testee = new EnsemblGene();
191
192		/*
193		* with no filter
194		*/
195	1	List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
196		genomic);
197	1	assertEquals(3, features.size());
198	1	assertTrue(features.contains(sf1));
199	1	assertTrue(features.contains(sf2));
200	1	assertTrue(features.contains(sf3));
201		}
202
203		/**
204		* Test the method that retains features except for 'gene', or 'transcript'
205		* with parent other than the given id
206		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
207	1	@Test(groups = "Functional")...
208		public void testRetainFeature()
209		{
210	1	String geneId = "ABC123";
211	1	EnsemblGene testee = new EnsemblGene();
212	1	SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
213		null);
214	1	sf.setValue("ID", "gene:" + geneId);
215	1	assertFalse(testee.retainFeature(sf, geneId));
216
217	1	sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
218	1	sf.setValue("Parent", "gene:" + geneId);
219	1	assertTrue(testee.retainFeature(sf, geneId));
220
221	1	sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
222		null);
223	1	sf.setValue("Parent", "gene:" + geneId);
224	1	assertTrue(testee.retainFeature(sf, geneId));
225
226	1	sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
227		0f, null);
228	1	sf.setValue("Parent", "gene:" + geneId);
229	1	assertTrue(testee.retainFeature(sf, geneId));
230
231	1	sf.setValue("Parent", "gene:XYZ");
232	1	assertFalse(testee.retainFeature(sf, geneId));
233
234	1	sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
235	1	assertTrue(testee.retainFeature(sf, geneId));
236		}
237
238		/**
239		* Test the method that picks out 'gene' (or subtype) features with the
240		* accession id as ID
241		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
242	1	@Test(groups = "Functional")...
243		public void testIdentifiesSequence()
244		{
245	1	String accId = "ABC123";
246	1	EnsemblGene testee = new EnsemblGene();
247
248		// gene with no ID not valid
249	1	SequenceFeature sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
250	1	assertFalse(testee.identifiesSequence(sf, accId));
251
252		// gene with wrong ID not valid
253	1	sf.setValue("ID", "gene:XYZ");
254	1	assertFalse(testee.identifiesSequence(sf, accId));
255
256		// gene with right ID is valid
257	1	sf.setValue("ID", "gene:" + accId);
258	1	assertTrue(testee.identifiesSequence(sf, accId));
259
260		// gene sub-type with right ID is valid
261	1	sf = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
262	1	sf.setValue("ID", "gene:" + accId);
263	1	assertTrue(testee.identifiesSequence(sf, accId));
264
265		// test is not case-sensitive
266	1	assertTrue(testee.identifiesSequence(sf, accId.toLowerCase()));
267
268		// transcript not valid:
269	1	sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
270	1	sf.setValue("ID", "gene:" + accId);
271	1	assertFalse(testee.identifiesSequence(sf, accId));
272
273		// exon not valid:
274	1	sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
275	1	sf.setValue("ID", "gene:" + accId);
276	1	assertFalse(testee.identifiesSequence(sf, accId));
277		}
278
279		/**
280		* Check behaviour of feature colour scheme for EnsemblGene sequences.
281		* Currently coded to display exon and sequence_variant (or sub-types) only,
282		* with sequence_variant in red above exon coloured by label.
283		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
284	1	@Test(groups = "Functional")...
285		public void testGetFeatureColourScheme()
286		{
287	1	FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
288	1	assertTrue(fc.isFeatureDisplayed("exon"));
289	1	assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
290	1	assertTrue(fc.isFeatureDisplayed("sequence_variant"));
291	1	assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
292	1	assertFalse(fc.isFeatureDisplayed("transcript"));
293	1	assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
294		.getColour());
295	1	assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
296		.getColour());
297	1	assertTrue(fc.getFeatureColour("exon").isColourByLabel());
298	1	assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
299	1	assertEquals(1, fc.compare("sequence_variant", "exon"));
300	1	assertEquals(-1, fc.compare("exon", "sequence_variant"));
301	1	assertEquals(1, fc.compare("feature_variant", "coding_exon"));
302	1	assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
303	1	assertEquals(1f, fc.getTransparency());
304		}
305
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08 1PASS
306	0	@Test(groups = "Network")...
307		public void testGetGeneIds()
308		{
309		/*
310		* ENSG00000158828 gene id PINK1 human
311		* ENST00000321556 transcript for the same gene - should not be duplicated
312		* P30419 Uniprot identifier for ENSG00000136448
313		* ENST00000592782 transcript for Uniprot gene - should not be duplicated
314		* BRAF - gene name resolvabe (at time of writing) for 6 model species
315		*/
316	0	String ids = "ENSG00000158828 ENST00000321556 P30419 ENST00000592782 BRAF";
317	0	EnsemblGene testee = new EnsemblGene();
318	0	List<String> geneIds = testee.getGeneIds(ids);
319	0	assertEquals(8, geneIds.size());
320	0	assertTrue(geneIds.contains("ENSG00000158828"));
321	0	assertTrue(geneIds.contains("ENSG00000136448"));
322	0	assertTrue(geneIds.contains("ENSG00000157764")); // BRAF human
323	0	assertTrue(geneIds.contains("ENSMUSG00000002413")); // mouse
324	0	assertTrue(geneIds.contains("ENSRNOG00000010957")); // rat
325	0	assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
326	0	assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
327	0	assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
328		}
329		}