Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblGeneTest	45	138	10	0.912162291.2%	Show methods

Class EnsemblGeneTest

Class EnsemblGeneTest	Line # 45	Total Statements 138	Complexity 10	TOTAL Coverage 0.912162291.2%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4848	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	5555	2.02	1.01	1.0 1.0100%
tearDown() : void   tearDown() : void	6262	1.01	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures() : void   testGetGenomicRangesFromFeatures() : void	7272	18.018	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand() : void   testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand() : void	104104	18.018	1.01	1.0 1.0100%
testGetTranscriptFeatures() : void   testGetTranscriptFeatures() : void	138138	26.026	1.01	1.0 1.0100%
testRetainFeature() : void   testRetainFeature() : void	192192	18.018	1.01	1.0 1.0100%
testGetIdentifyingFeatures() : void   testGetIdentifyingFeatures() : void	227227	26.026	1.01	1.0 1.0100%
testGetFeatureColourScheme() : void   testGetFeatureColourScheme() : void	277277	15.015	1.01	1.0 1.0100%
testGetGeneIds() : void   testGetGeneIds() : void	299299	12.012	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.18243243	jalview.ext.ensembl.EnsemblGeneTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetIdentifyingFeatures	1PASS
	0.18243243	jalview.ext.ensembl.EnsemblGeneTest.testGetTranscriptFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetTranscriptFeatures	1PASS
	0.12837838	jalview.ext.ensembl.EnsemblGeneTest.testRetainFeaturejalview.ext.ensembl.EnsemblGeneTest.testRetainFeature	1PASS
	0.12837838	jalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrandjalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand	1PASS
	0.12837838	jalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures	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.Sequence;
30		import jalview.datamodel.SequenceDummy;
31		import jalview.datamodel.SequenceFeature;
32		import jalview.datamodel.SequenceI;
33		import jalview.gui.JvOptionPane;
34		import jalview.io.gff.SequenceOntologyFactory;
35		import jalview.io.gff.SequenceOntologyLite;
36		import jalview.util.MapList;
37
38		import java.awt.Color;
39		import java.util.List;
40
41		import org.testng.annotations.AfterClass;
42		import org.testng.annotations.BeforeClass;
43		import org.testng.annotations.Test;
44
		91.2% Uncovered Elements: 13 (148) Complexity: 10 Complexity Density: 0.07
45		public class EnsemblGeneTest
46		{
47
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
48	1	@BeforeClass(alwaysRun = true)...
49		public void setUpJvOptionPane()
50		{
51	1	JvOptionPane.setInteractiveMode(false);
52	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53		}
54
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
55	1	@BeforeClass(alwaysRun = true)...
56		public void setUp()
57		{
58	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
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 gene part of genomic sequence is uniquely identified by a
70		* 'gene' features (or subtype) with the correct gene ID
71		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
72	1	@Test(groups = "Functional")...
73		public void testGetGenomicRangesFromFeatures()
74		{
75	1	EnsemblGene testee = new EnsemblGene();
76	1	SequenceI genomic = new SequenceDummy("chr7");
77	1	genomic.setStart(10000);
78	1	genomic.setEnd(50000);
79	1	String geneId = "ABC123";
80
81		// gene at (start + 10500) length 101
82	1	SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
83		null);
84	1	sf.setValue("id", geneId);
85	1	sf.setStrand("+");
86	1	genomic.addSequenceFeature(sf);
87
88	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
89		23);
90	1	List<int[]> fromRanges = ranges.getFromRanges();
91	1	assertEquals(1, fromRanges.size());
92	1	assertEquals(10500, fromRanges.get(0)[0]);
93	1	assertEquals(10600, fromRanges.get(0)[1]);
94		// to range should start from given start numbering
95	1	List<int[]> toRanges = ranges.getToRanges();
96	1	assertEquals(1, toRanges.size());
97	1	assertEquals(23, toRanges.get(0)[0]);
98	1	assertEquals(123, toRanges.get(0)[1]);
99		}
100
101		/**
102		* Test variant using a sub-type of gene from the Sequence Ontology
103		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
104	1	@Test(groups = "Functional")...
105		public void testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand()
106		{
107	1	EnsemblGene testee = new EnsemblGene();
108	1	SequenceI genomic = new SequenceDummy("chr7");
109	1	genomic.setStart(10000);
110	1	genomic.setEnd(50000);
111	1	String geneId = "ABC123";
112
113		// gene at (start + 10500) length 101
114	1	SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
115		null);
116	1	sf.setValue("id", geneId);
117	1	sf.setStrand("+");
118	1	genomic.addSequenceFeature(sf);
119
120	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
121		23);
122	1	List<int[]> fromRanges = ranges.getFromRanges();
123	1	assertEquals(1, fromRanges.size());
124		// from range on reverse strand:
125	1	assertEquals(10500, fromRanges.get(0)[0]);
126	1	assertEquals(10600, fromRanges.get(0)[1]);
127		// to range should start from given start numbering
128	1	List<int[]> toRanges = ranges.getToRanges();
129	1	assertEquals(1, toRanges.size());
130	1	assertEquals(23, toRanges.get(0)[0]);
131	1	assertEquals(123, toRanges.get(0)[1]);
132		}
133
134		/**
135		* Test the method that extracts transcript (or subtype) features with a
136		* specified gene as parent
137		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
138	1	@Test(groups = "Functional")...
139		public void testGetTranscriptFeatures()
140		{
141	1	SequenceI genomic = new SequenceDummy("chr7");
142	1	genomic.setStart(10000);
143	1	genomic.setEnd(50000);
144	1	String geneId = "ABC123";
145
146		// transcript feature
147	1	SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
148		20500, 0f, null);
149	1	sf1.setValue("Parent", geneId);
150	1	sf1.setValue("id", "transcript1");
151	1	genomic.addSequenceFeature(sf1);
152
153		// transcript sub-type feature
154	1	SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
155		0f, null);
156	1	sf2.setValue("Parent", geneId);
157	1	sf2.setValue("id", "transcript2");
158	1	genomic.addSequenceFeature(sf2);
159
160		// NMD_transcript_variant treated like transcript in Ensembl
161	1	SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
162		22000, 22500, 0f, null);
163		// id matching should not be case-sensitive
164	1	sf3.setValue("Parent", geneId.toLowerCase());
165	1	sf3.setValue("id", "transcript3");
166	1	genomic.addSequenceFeature(sf3);
167
168		// transcript for a different gene - ignored
169	1	SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
170		0f, null);
171	1	sf4.setValue("Parent", "XYZ");
172	1	sf4.setValue("id", "transcript4");
173	1	genomic.addSequenceFeature(sf4);
174
175	1	EnsemblGene testee = new EnsemblGene();
176
177		/*
178		* with no filter
179		*/
180	1	List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
181		genomic);
182	1	assertEquals(3, features.size());
183	1	assertTrue(features.contains(sf1));
184	1	assertTrue(features.contains(sf2));
185	1	assertTrue(features.contains(sf3));
186		}
187
188		/**
189		* Test the method that retains features except for 'gene', or 'transcript'
190		* with parent other than the given id
191		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
192	1	@Test(groups = "Functional")...
193		public void testRetainFeature()
194		{
195	1	String geneId = "ABC123";
196	1	EnsemblGene testee = new EnsemblGene();
197	1	SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
198		null);
199	1	sf.setValue("id", geneId);
200	1	assertFalse(testee.retainFeature(sf, geneId));
201
202	1	sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
203	1	sf.setValue("Parent", geneId);
204	1	assertTrue(testee.retainFeature(sf, geneId));
205
206	1	sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
207		null);
208	1	sf.setValue("Parent", geneId);
209	1	assertTrue(testee.retainFeature(sf, geneId));
210
211	1	sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
212		0f, null);
213	1	sf.setValue("Parent", geneId);
214	1	assertTrue(testee.retainFeature(sf, geneId));
215
216	1	sf.setValue("Parent", "ßXYZ");
217	1	assertFalse(testee.retainFeature(sf, geneId));
218
219	1	sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
220	1	assertTrue(testee.retainFeature(sf, geneId));
221		}
222
223		/**
224		* Test the method that picks out 'gene' (or subtype) features with the
225		* accession id as ID
226		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
227	1	@Test(groups = "Functional")...
228		public void testGetIdentifyingFeatures()
229		{
230	1	String accId = "ABC123";
231	1	SequenceI seq = new Sequence(accId, "HIBEES");
232
233		// gene with no ID not valid
234	1	SequenceFeature sf1 = new SequenceFeature("gene", "", 1, 2, 0f, null);
235	1	seq.addSequenceFeature(sf1);
236
237		// gene with wrong ID not valid
238	1	SequenceFeature sf2 = new SequenceFeature("gene", "a", 1, 2, 0f, null);
239	1	sf2.setValue("id", "XYZ");
240	1	seq.addSequenceFeature(sf2);
241
242		// gene with right ID is valid
243	1	SequenceFeature sf3 = new SequenceFeature("gene", "b", 1, 2, 0f, null);
244	1	sf3.setValue("id", accId);
245	1	seq.addSequenceFeature(sf3);
246
247		// gene sub-type with right ID is valid
248	1	SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
249	1	sf4.setValue("id", accId);
250	1	seq.addSequenceFeature(sf4);
251
252		// transcript not valid:
253	1	SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
254	1	sf5.setValue("id", accId);
255	1	seq.addSequenceFeature(sf5);
256
257		// exon not valid:
258	1	SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
259	1	sf6.setValue("id", accId);
260	1	seq.addSequenceFeature(sf6);
261
262	1	List<SequenceFeature> sfs = new EnsemblGene()
263		.getIdentifyingFeatures(seq, accId);
264	1	assertFalse(sfs.contains(sf1));
265	1	assertFalse(sfs.contains(sf2));
266	1	assertTrue(sfs.contains(sf3));
267	1	assertTrue(sfs.contains(sf4));
268	1	assertFalse(sfs.contains(sf5));
269	1	assertFalse(sfs.contains(sf6));
270		}
271
272		/**
273		* Check behaviour of feature colour scheme for EnsemblGene sequences.
274		* Currently coded to display exon and sequence_variant (or sub-types) only,
275		* with sequence_variant in red above exon coloured by label.
276		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
277	1	@Test(groups = "Functional")...
278		public void testGetFeatureColourScheme()
279		{
280	1	FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
281	1	assertTrue(fc.isFeatureDisplayed("exon"));
282	1	assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
283	1	assertTrue(fc.isFeatureDisplayed("sequence_variant"));
284	1	assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
285	1	assertFalse(fc.isFeatureDisplayed("transcript"));
286	1	assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
287		.getColour());
288	1	assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
289		.getColour());
290	1	assertTrue(fc.getFeatureColour("exon").isColourByLabel());
291	1	assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
292	1	assertEquals(1, fc.compare("sequence_variant", "exon"));
293	1	assertEquals(-1, fc.compare("exon", "sequence_variant"));
294	1	assertEquals(1, fc.compare("feature_variant", "coding_exon"));
295	1	assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
296	1	assertEquals(1f, fc.getTransparency());
297		}
298
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08 1PASS
299	0	@Test(groups = "Network")...
300		public void testGetGeneIds()
301		{
302		/*
303		* ENSG00000158828 gene id PINK1 human
304		* ENST00000321556 transcript for the same gene - should not be duplicated
305		* P30419 Uniprot identifier for ENSG00000136448
306		* ENST00000592782 transcript for Uniprot gene - should not be duplicated
307		* BRAF - gene name resolvabe (at time of writing) for 6 model species
308		*/
309	0	String ids = "ENSG00000158828 ENST00000321556 P30419 ENST00000592782 BRAF";
310	0	EnsemblGene testee = new EnsemblGene();
311	0	List<String> geneIds = testee.getGeneIds(ids);
312	0	assertEquals(8, geneIds.size());
313	0	assertTrue(geneIds.contains("ENSG00000158828"));
314	0	assertTrue(geneIds.contains("ENSG00000136448"));
315	0	assertTrue(geneIds.contains("ENSG00000157764")); // BRAF human
316	0	assertTrue(geneIds.contains("ENSMUSG00000002413")); // mouse
317	0	assertTrue(geneIds.contains("ENSRNOG00000010957")); // rat
318	0	assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
319	0	assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
320	0	assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
321		}
322		}