Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblGeneTest	47	143	10	0.915032791.5%	Show methods

Class EnsemblGeneTest

Class EnsemblGeneTest	Line # 47	Total Statements 143	Complexity 10	TOTAL Coverage 0.915032791.5%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	5757	2.02	1.01	1.0 1.0100%
tearDown() : void   tearDown() : void	6464	1.01	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures() : void   testGetGenomicRangesFromFeatures() : void	7474	18.018	1.01	1.0 1.0100%
testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand() : void   testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand() : void	106106	18.018	1.01	1.0 1.0100%
testGetTranscriptFeatures() : void   testGetTranscriptFeatures() : void	140140	26.026	1.01	1.0 1.0100%
testRetainFeature() : void   testRetainFeature() : void	194194	18.018	1.01	1.0 1.0100%
testGetIdentifyingFeatures() : void   testGetIdentifyingFeatures() : void	229229	26.026	1.01	1.0 1.0100%
testGetFeatureColourScheme() : void   testGetFeatureColourScheme() : void	281281	20.020	1.01	1.0 1.0100%
testGetGeneIds() : void   testGetGeneIds() : void	309309	12.012	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.1764706	jalview.ext.ensembl.EnsemblGeneTest.testGetTranscriptFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetTranscriptFeatures	1PASS
	0.1764706	jalview.ext.ensembl.EnsemblGeneTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetIdentifyingFeatures	1PASS
	0.13725491	jalview.ext.ensembl.EnsemblGeneTest.testGetFeatureColourSchemejalview.ext.ensembl.EnsemblGeneTest.testGetFeatureColourScheme	1PASS
	0.12418301	jalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrandjalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand	1PASS
	0.12418301	jalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures	1PASS
	0.12418301	jalview.ext.ensembl.EnsemblGeneTest.testRetainFeaturejalview.ext.ensembl.EnsemblGeneTest.testRetainFeature	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.assertTrue;
28
29		import jalview.api.FeatureSettingsModelI;
30		import jalview.bin.Cache;
31		import jalview.datamodel.Sequence;
32		import jalview.datamodel.SequenceDummy;
33		import jalview.datamodel.SequenceFeature;
34		import jalview.datamodel.SequenceI;
35		import jalview.gui.JvOptionPane;
36		import jalview.io.gff.SequenceOntologyFactory;
37		import jalview.io.gff.SequenceOntologyLite;
38		import jalview.util.MapList;
39
40		import java.awt.Color;
41		import java.util.List;
42
43		import org.testng.annotations.AfterClass;
44		import org.testng.annotations.BeforeClass;
45		import org.testng.annotations.Test;
46
		91.5% Uncovered Elements: 13 (153) Complexity: 10 Complexity Density: 0.07
47		public class EnsemblGeneTest
48		{
49
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
50	1	@BeforeClass(alwaysRun = true)...
51		public void setUpJvOptionPane()
52		{
53	1	JvOptionPane.setInteractiveMode(false);
54	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55		}
56
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
57	1	@BeforeClass(alwaysRun = true)...
58		public void setUp()
59		{
60	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
61	1	SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
62		}
63
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
64	1	@AfterClass(alwaysRun = true)...
65		public void tearDown()
66		{
67	1	SequenceOntologyFactory.setInstance(null);
68		}
69
70		/**
71		* Test that the gene part of genomic sequence is uniquely identified by a
72		* 'gene' features (or subtype) with the correct gene ID
73		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
74	1	@Test(groups = "Functional")...
75		public void testGetGenomicRangesFromFeatures()
76		{
77	1	EnsemblGene testee = new EnsemblGene();
78	1	SequenceI genomic = new SequenceDummy("chr7");
79	1	genomic.setStart(10000);
80	1	genomic.setEnd(50000);
81	1	String geneId = "ABC123";
82
83		// gene at (start + 10500) length 101
84	1	SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
85		null);
86	1	sf.setValue("id", geneId);
87	1	sf.setStrand("+");
88	1	genomic.addSequenceFeature(sf);
89
90	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
91		23);
92	1	List<int[]> fromRanges = ranges.getFromRanges();
93	1	assertEquals(1, fromRanges.size());
94	1	assertEquals(10500, fromRanges.get(0)[0]);
95	1	assertEquals(10600, fromRanges.get(0)[1]);
96		// to range should start from given start numbering
97	1	List<int[]> toRanges = ranges.getToRanges();
98	1	assertEquals(1, toRanges.size());
99	1	assertEquals(23, toRanges.get(0)[0]);
100	1	assertEquals(123, toRanges.get(0)[1]);
101		}
102
103		/**
104		* Test variant using a sub-type of gene from the Sequence Ontology
105		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
106	1	@Test(groups = "Functional")...
107		public void testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand()
108		{
109	1	EnsemblGene testee = new EnsemblGene();
110	1	SequenceI genomic = new SequenceDummy("chr7");
111	1	genomic.setStart(10000);
112	1	genomic.setEnd(50000);
113	1	String geneId = "ABC123";
114
115		// gene at (start + 10500) length 101
116	1	SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
117		null);
118	1	sf.setValue("id", geneId);
119	1	sf.setStrand("+");
120	1	genomic.addSequenceFeature(sf);
121
122	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
123		23);
124	1	List<int[]> fromRanges = ranges.getFromRanges();
125	1	assertEquals(1, fromRanges.size());
126		// from range on reverse strand:
127	1	assertEquals(10500, fromRanges.get(0)[0]);
128	1	assertEquals(10600, fromRanges.get(0)[1]);
129		// to range should start from given start numbering
130	1	List<int[]> toRanges = ranges.getToRanges();
131	1	assertEquals(1, toRanges.size());
132	1	assertEquals(23, toRanges.get(0)[0]);
133	1	assertEquals(123, toRanges.get(0)[1]);
134		}
135
136		/**
137		* Test the method that extracts transcript (or subtype) features with a
138		* specified gene as parent
139		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
140	1	@Test(groups = "Functional")...
141		public void testGetTranscriptFeatures()
142		{
143	1	SequenceI genomic = new SequenceDummy("chr7");
144	1	genomic.setStart(10000);
145	1	genomic.setEnd(50000);
146	1	String geneId = "ABC123";
147
148		// transcript feature
149	1	SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
150		20500, 0f, null);
151	1	sf1.setValue("Parent", geneId);
152	1	sf1.setValue("id", "transcript1");
153	1	genomic.addSequenceFeature(sf1);
154
155		// transcript sub-type feature
156	1	SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500, 0f,
157		null);
158	1	sf2.setValue("Parent", geneId);
159	1	sf2.setValue("id", "transcript2");
160	1	genomic.addSequenceFeature(sf2);
161
162		// NMD_transcript_variant treated like transcript in Ensembl
163	1	SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
164		22000, 22500, 0f, null);
165		// id matching should not be case-sensitive
166	1	sf3.setValue("Parent", geneId.toLowerCase(Locale.ROOT));
167	1	sf3.setValue("id", "transcript3");
168	1	genomic.addSequenceFeature(sf3);
169
170		// transcript for a different gene - ignored
171	1	SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500, 0f,
172		null);
173	1	sf4.setValue("Parent", "XYZ");
174	1	sf4.setValue("id", "transcript4");
175	1	genomic.addSequenceFeature(sf4);
176
177	1	EnsemblGene testee = new EnsemblGene();
178
179		/*
180		* with no filter
181		*/
182	1	List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
183		genomic);
184	1	assertEquals(3, features.size());
185	1	assertTrue(features.contains(sf1));
186	1	assertTrue(features.contains(sf2));
187	1	assertTrue(features.contains(sf3));
188		}
189
190		/**
191		* Test the method that retains features except for 'gene', or 'transcript'
192		* with parent other than the given id
193		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
194	1	@Test(groups = "Functional")...
195		public void testRetainFeature()
196		{
197	1	String geneId = "ABC123";
198	1	EnsemblGene testee = new EnsemblGene();
199	1	SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
200		null);
201	1	sf.setValue("id", geneId);
202	1	assertFalse(testee.retainFeature(sf, geneId));
203
204	1	sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
205	1	sf.setValue("Parent", geneId);
206	1	assertTrue(testee.retainFeature(sf, geneId));
207
208	1	sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
209		null);
210	1	sf.setValue("Parent", geneId);
211	1	assertTrue(testee.retainFeature(sf, geneId));
212
213	1	sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
214		null);
215	1	sf.setValue("Parent", geneId);
216	1	assertTrue(testee.retainFeature(sf, geneId));
217
218	1	sf.setValue("Parent", "ßXYZ");
219	1	assertFalse(testee.retainFeature(sf, geneId));
220
221	1	sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
222	1	assertTrue(testee.retainFeature(sf, geneId));
223		}
224
225		/**
226		* Test the method that picks out 'gene' (or subtype) features with the
227		* accession id as ID
228		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
229	1	@Test(groups = "Functional")...
230		public void testGetIdentifyingFeatures()
231		{
232	1	String accId = "ABC123";
233	1	SequenceI seq = new Sequence(accId, "HIBEES");
234
235		// gene with no ID not valid
236	1	SequenceFeature sf1 = new SequenceFeature("gene", "", 1, 2, 0f, null);
237	1	seq.addSequenceFeature(sf1);
238
239		// gene with wrong ID not valid
240	1	SequenceFeature sf2 = new SequenceFeature("gene", "a", 1, 2, 0f, null);
241	1	sf2.setValue("id", "XYZ");
242	1	seq.addSequenceFeature(sf2);
243
244		// gene with right ID is valid
245	1	SequenceFeature sf3 = new SequenceFeature("gene", "b", 1, 2, 0f, null);
246	1	sf3.setValue("id", accId);
247	1	seq.addSequenceFeature(sf3);
248
249		// gene sub-type with right ID is valid
250	1	SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f,
251		null);
252	1	sf4.setValue("id", accId);
253	1	seq.addSequenceFeature(sf4);
254
255		// transcript not valid:
256	1	SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
257		null);
258	1	sf5.setValue("id", accId);
259	1	seq.addSequenceFeature(sf5);
260
261		// exon not valid:
262	1	SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
263	1	sf6.setValue("id", accId);
264	1	seq.addSequenceFeature(sf6);
265
266	1	List<SequenceFeature> sfs = new EnsemblGene()
267		.getIdentifyingFeatures(seq, accId);
268	1	assertFalse(sfs.contains(sf1));
269	1	assertFalse(sfs.contains(sf2));
270	1	assertTrue(sfs.contains(sf3));
271	1	assertTrue(sfs.contains(sf4));
272	1	assertFalse(sfs.contains(sf5));
273	1	assertFalse(sfs.contains(sf6));
274		}
275
276		/**
277		* Check behaviour of feature colour scheme for EnsemblGene sequences.
278		* Currently coded to hide all except exon and sequence_variant (or sub-types)
279		* only, with sequence_variant in red above exon coloured by label.
280		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
281	1	@Test(groups = "Functional")...
282		public void testGetFeatureColourScheme()
283		{
284	1	FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
285	1	assertFalse(fc.isFeatureDisplayed("exon"));
286	1	assertFalse(fc.isFeatureHidden("exon"));
287	1	assertFalse(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
288	1	assertFalse(fc.isFeatureHidden("coding_exon")); // subtype of exon
289	1	assertFalse(fc.isFeatureDisplayed("sequence_variant"));
290	1	assertFalse(fc.isFeatureHidden("sequence_variant"));
291	1	assertFalse(fc.isFeatureDisplayed("feature_variant")); // subtype
292	1	assertFalse(fc.isFeatureHidden("feature_variant")); // subtype
293	1	assertTrue(fc.isFeatureHidden("transcript"));
294	1	assertTrue(fc.isFeatureHidden("CDS"));
295
296	1	assertEquals(Color.RED,
297		fc.getFeatureColour("sequence_variant").getColour());
298	1	assertEquals(Color.RED,
299		fc.getFeatureColour("feature_variant").getColour());
300	1	assertTrue(fc.getFeatureColour("exon").isColourByLabel());
301	1	assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
302	1	assertEquals(1, fc.compare("sequence_variant", "exon"));
303	1	assertEquals(-1, fc.compare("exon", "sequence_variant"));
304	1	assertEquals(1, fc.compare("feature_variant", "coding_exon"));
305	1	assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
306	1	assertEquals(1f, fc.getTransparency());
307		}
308
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08 1PASS
309	0	@Test(groups = "Network")...
310		public void testGetGeneIds()
311		{
312		/*
313		* ENSG00000158828 gene id PINK1 human
314		* ENST00000321556 transcript for the same gene - should not be duplicated
315		* P30419 Uniprot identifier for ENSG00000136448
316		* ENST00000592782 transcript for Uniprot gene - should not be duplicated
317		* BRAF - gene name resolvabe (at time of writing) for 6 model species
318		*/
319	0	String ids = "ENSG00000158828 ENST00000321556 P30419 ENST00000592782 BRAF";
320	0	EnsemblGene testee = new EnsemblGene();
321	0	List<String> geneIds = testee.getGeneIds(ids);
322	0	assertTrue(geneIds.contains("ENSG00000158828"));
323	0	assertTrue(geneIds.contains("ENSG00000136448"));
324	0	assertTrue(geneIds.contains("ENSG00000157764")); // BRAF human
325	0	assertTrue(geneIds.contains("ENSMUSG00000002413")); // mouse
326	0	assertTrue(geneIds.contains("ENSRNOG00000010957")); // rat
327	0	assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
328	0	assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
329		// was ENSGALG00000012865 - which is still the canonical uniprot BRAF cross
330		// reference via GRCg6a
331	0	assertTrue(geneIds.contains("ENSGALG00010013466")); // chicken BRAF
332		// bGalGal1.mat.broiler.GRCg7b
333	0	assertEquals(8, geneIds.size());
334
335		}
336		}