2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ext.ensembl;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.api.FeatureSettingsModelI;
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;
36 import java.awt.Color;
37 import java.util.List;
39 import org.testng.annotations.AfterClass;
40 import org.testng.annotations.BeforeClass;
41 import org.testng.annotations.Test;
43 public class EnsemblGeneTest
46 @BeforeClass(alwaysRun = true)
47 public void setUpJvOptionPane()
49 JvOptionPane.setInteractiveMode(false);
50 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53 @BeforeClass(alwaysRun = true)
56 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
59 @AfterClass(alwaysRun = true)
60 public void tearDown()
62 SequenceOntologyFactory.setInstance(null);
66 * Test that the gene part of genomic sequence is uniquely identified by a
67 * 'gene' features (or subtype) with the correct gene ID
69 @Test(groups = "Functional")
70 public void testGetGenomicRangesFromFeatures()
72 EnsemblGene testee = new EnsemblGene();
73 SequenceI genomic = new SequenceDummy("chr7");
74 genomic.setStart(10000);
75 genomic.setEnd(50000);
76 String geneId = "ABC123";
78 // gene at (start+20000) length 501
79 // should be ignored - the first 'gene' found defines the whole range
80 // (note features are found in position order, not addition order)
81 SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
83 sf.setValue("ID", "gene:" + geneId);
85 genomic.addSequenceFeature(sf);
87 // gene at (start + 10500) length 101
88 sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
89 sf.setValue("ID", "gene:" + geneId);
91 genomic.addSequenceFeature(sf);
93 MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
95 List<int[]> fromRanges = ranges.getFromRanges();
96 assertEquals(1, fromRanges.size());
97 assertEquals(10500, fromRanges.get(0)[0]);
98 assertEquals(10600, fromRanges.get(0)[1]);
99 // to range should start from given start numbering
100 List<int[]> toRanges = ranges.getToRanges();
101 assertEquals(1, toRanges.size());
102 assertEquals(23, toRanges.get(0)[0]);
103 assertEquals(123, toRanges.get(0)[1]);
107 * Test variant using a sub-type of gene from the Sequence Ontology
109 @Test(groups = "Functional")
110 public void testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand()
112 EnsemblGene testee = new EnsemblGene();
113 SequenceI genomic = new SequenceDummy("chr7");
114 genomic.setStart(10000);
115 genomic.setEnd(50000);
116 String geneId = "ABC123";
118 // gene at (start+20000) length 501
119 // should be ignored - the first 'gene' found defines the whole range
120 // (real data would only have one such feature)
121 SequenceFeature sf = new SequenceFeature("ncRNA_gene", "", 20000,
123 sf.setValue("ID", "gene:" + geneId);
125 genomic.addSequenceFeature(sf);
127 // gene at (start + 10500) length 101
128 sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
129 sf.setValue("ID", "gene:" + geneId);
131 genomic.addSequenceFeature(sf);
133 MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
135 List<int[]> fromRanges = ranges.getFromRanges();
136 assertEquals(1, fromRanges.size());
137 // from range on reverse strand:
138 assertEquals(10500, fromRanges.get(0)[0]);
139 assertEquals(10600, fromRanges.get(0)[1]);
140 // to range should start from given start numbering
141 List<int[]> toRanges = ranges.getToRanges();
142 assertEquals(1, toRanges.size());
143 assertEquals(23, toRanges.get(0)[0]);
144 assertEquals(123, toRanges.get(0)[1]);
148 * Test the method that extracts transcript (or subtype) features with a
149 * specified gene as parent
151 @Test(groups = "Functional")
152 public void testGetTranscriptFeatures()
154 SequenceI genomic = new SequenceDummy("chr7");
155 genomic.setStart(10000);
156 genomic.setEnd(50000);
157 String geneId = "ABC123";
159 // transcript feature
160 SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
162 sf1.setValue("Parent", "gene:" + geneId);
163 sf1.setValue("transcript_id", "transcript1");
164 genomic.addSequenceFeature(sf1);
166 // transcript sub-type feature
167 SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
169 sf2.setValue("Parent", "gene:" + geneId);
170 sf2.setValue("transcript_id", "transcript2");
171 genomic.addSequenceFeature(sf2);
173 // NMD_transcript_variant treated like transcript in Ensembl
174 SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
175 22000, 22500, 0f, null);
176 sf3.setValue("Parent", "gene:" + geneId);
177 sf3.setValue("transcript_id", "transcript3");
178 genomic.addSequenceFeature(sf3);
180 // transcript for a different gene - ignored
181 SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
183 sf4.setValue("Parent", "gene:XYZ");
184 sf4.setValue("transcript_id", "transcript4");
185 genomic.addSequenceFeature(sf4);
187 EnsemblGene testee = new EnsemblGene();
192 List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
194 assertEquals(3, features.size());
195 assertTrue(features.contains(sf1));
196 assertTrue(features.contains(sf2));
197 assertTrue(features.contains(sf3));
201 * Test the method that retains features except for 'gene', or 'transcript'
202 * with parent other than the given id
204 @Test(groups = "Functional")
205 public void testRetainFeature()
207 String geneId = "ABC123";
208 EnsemblGene testee = new EnsemblGene();
209 SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
211 sf.setValue("ID", "gene:" + geneId);
212 assertFalse(testee.retainFeature(sf, geneId));
214 sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
215 sf.setValue("Parent", "gene:" + geneId);
216 assertTrue(testee.retainFeature(sf, geneId));
218 sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
220 sf.setValue("Parent", "gene:" + geneId);
221 assertTrue(testee.retainFeature(sf, geneId));
223 sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
225 sf.setValue("Parent", "gene:" + geneId);
226 assertTrue(testee.retainFeature(sf, geneId));
228 sf.setValue("Parent", "gene:XYZ");
229 assertFalse(testee.retainFeature(sf, geneId));
231 sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
232 assertTrue(testee.retainFeature(sf, geneId));
236 * Test the method that picks out 'gene' (or subtype) features with the
239 @Test(groups = "Functional")
240 public void testIdentifiesSequence()
242 String accId = "ABC123";
243 EnsemblGene testee = new EnsemblGene();
245 // gene with no ID not valid
246 SequenceFeature sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
247 assertFalse(testee.identifiesSequence(sf, accId));
249 // gene with wrong ID not valid
250 sf.setValue("ID", "gene:XYZ");
251 assertFalse(testee.identifiesSequence(sf, accId));
253 // gene with right ID is valid
254 sf.setValue("ID", "gene:" + accId);
255 assertTrue(testee.identifiesSequence(sf, accId));
257 // gene sub-type with right ID is valid
258 sf = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
259 sf.setValue("ID", "gene:" + accId);
260 assertTrue(testee.identifiesSequence(sf, accId));
262 // transcript not valid:
263 sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
264 sf.setValue("ID", "gene:" + accId);
265 assertFalse(testee.identifiesSequence(sf, accId));
268 sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
269 sf.setValue("ID", "gene:" + accId);
270 assertFalse(testee.identifiesSequence(sf, accId));
274 * Check behaviour of feature colour scheme for EnsemblGene sequences.
275 * Currently coded to display exon and sequence_variant (or sub-types) only,
276 * with sequence_variant in red above exon coloured by label.
278 @Test(groups = "Functional")
279 public void testGetFeatureColourScheme()
281 FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
282 assertTrue(fc.isFeatureDisplayed("exon"));
283 assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
284 assertTrue(fc.isFeatureDisplayed("sequence_variant"));
285 assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
286 assertFalse(fc.isFeatureDisplayed("transcript"));
287 assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
289 assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
291 assertTrue(fc.getFeatureColour("exon").isColourByLabel());
292 assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
293 assertEquals(1, fc.compare("sequence_variant", "exon"));
294 assertEquals(-1, fc.compare("exon", "sequence_variant"));
295 assertEquals(1, fc.compare("feature_variant", "coding_exon"));
296 assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
297 assertEquals(1f, fc.getTransparency());
300 @Test(groups = "Network")
301 public void testGetGeneIds()
304 * ENSG00000158828 gene id PINK1 human
305 * ENST00000321556 transcript for the same gene - should not be duplicated
306 * P30419 Uniprot identifier for ENSG00000136448
307 * ENST00000592782 transcript for Uniprot gene - should not be duplicated
308 * BRAF - gene name resolvabe (at time of writing) for 6 model species
310 String ids = "ENSG00000158828 ENST00000321556 P30419 ENST00000592782 BRAF";
311 EnsemblGene testee = new EnsemblGene();
312 List<String> geneIds = testee.getGeneIds(ids);
313 assertEquals(8, geneIds.size());
314 assertTrue(geneIds.contains("ENSG00000158828"));
315 assertTrue(geneIds.contains("ENSG00000136448"));
316 assertTrue(geneIds.contains("ENSG00000157764")); // BRAF human
317 assertTrue(geneIds.contains("ENSMUSG00000002413")); // mouse
318 assertTrue(geneIds.contains("ENSRNOG00000010957")); // rat
319 assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
320 assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
321 assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken