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.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;
38 import java.awt.Color;
39 import java.util.List;
41 import org.testng.annotations.AfterClass;
42 import org.testng.annotations.BeforeClass;
43 import org.testng.annotations.Test;
45 public class EnsemblGeneTest
48 @BeforeClass(alwaysRun = true)
49 public void setUpJvOptionPane()
51 JvOptionPane.setInteractiveMode(false);
52 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55 @BeforeClass(alwaysRun = true)
58 Cache.loadProperties("test/jalview/io/testProps.jvprops");
59 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
62 @AfterClass(alwaysRun = true)
63 public void tearDown()
65 SequenceOntologyFactory.setInstance(null);
69 * Test that the gene part of genomic sequence is uniquely identified by a
70 * 'gene' features (or subtype) with the correct gene ID
72 @Test(groups = "Functional")
73 public void testGetGenomicRangesFromFeatures()
75 EnsemblGene testee = new EnsemblGene();
76 SequenceI genomic = new SequenceDummy("chr7");
77 genomic.setStart(10000);
78 genomic.setEnd(50000);
79 String geneId = "ABC123";
81 // gene at (start + 10500) length 101
82 SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
84 sf.setValue("id", geneId);
86 genomic.addSequenceFeature(sf);
88 MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
90 List<int[]> fromRanges = ranges.getFromRanges();
91 assertEquals(1, fromRanges.size());
92 assertEquals(10500, fromRanges.get(0)[0]);
93 assertEquals(10600, fromRanges.get(0)[1]);
94 // to range should start from given start numbering
95 List<int[]> toRanges = ranges.getToRanges();
96 assertEquals(1, toRanges.size());
97 assertEquals(23, toRanges.get(0)[0]);
98 assertEquals(123, toRanges.get(0)[1]);
102 * Test variant using a sub-type of gene from the Sequence Ontology
104 @Test(groups = "Functional")
105 public void testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand()
107 EnsemblGene testee = new EnsemblGene();
108 SequenceI genomic = new SequenceDummy("chr7");
109 genomic.setStart(10000);
110 genomic.setEnd(50000);
111 String geneId = "ABC123";
113 // gene at (start + 10500) length 101
114 SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
116 sf.setValue("id", geneId);
118 genomic.addSequenceFeature(sf);
120 MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
122 List<int[]> fromRanges = ranges.getFromRanges();
123 assertEquals(1, fromRanges.size());
124 // from range on reverse strand:
125 assertEquals(10500, fromRanges.get(0)[0]);
126 assertEquals(10600, fromRanges.get(0)[1]);
127 // to range should start from given start numbering
128 List<int[]> toRanges = ranges.getToRanges();
129 assertEquals(1, toRanges.size());
130 assertEquals(23, toRanges.get(0)[0]);
131 assertEquals(123, toRanges.get(0)[1]);
135 * Test the method that extracts transcript (or subtype) features with a
136 * specified gene as parent
138 @Test(groups = "Functional")
139 public void testGetTranscriptFeatures()
141 SequenceI genomic = new SequenceDummy("chr7");
142 genomic.setStart(10000);
143 genomic.setEnd(50000);
144 String geneId = "ABC123";
146 // transcript feature
147 SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
149 sf1.setValue("Parent", geneId);
150 sf1.setValue("id", "transcript1");
151 genomic.addSequenceFeature(sf1);
153 // transcript sub-type feature
154 SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
156 sf2.setValue("Parent", geneId);
157 sf2.setValue("id", "transcript2");
158 genomic.addSequenceFeature(sf2);
160 // NMD_transcript_variant treated like transcript in Ensembl
161 SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
162 22000, 22500, 0f, null);
163 // id matching should not be case-sensitive
164 sf3.setValue("Parent", geneId.toLowerCase());
165 sf3.setValue("id", "transcript3");
166 genomic.addSequenceFeature(sf3);
168 // transcript for a different gene - ignored
169 SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
171 sf4.setValue("Parent", "XYZ");
172 sf4.setValue("id", "transcript4");
173 genomic.addSequenceFeature(sf4);
175 EnsemblGene testee = new EnsemblGene();
180 List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
182 assertEquals(3, features.size());
183 assertTrue(features.contains(sf1));
184 assertTrue(features.contains(sf2));
185 assertTrue(features.contains(sf3));
189 * Test the method that retains features except for 'gene', or 'transcript'
190 * with parent other than the given id
192 @Test(groups = "Functional")
193 public void testRetainFeature()
195 String geneId = "ABC123";
196 EnsemblGene testee = new EnsemblGene();
197 SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
199 sf.setValue("id", geneId);
200 assertFalse(testee.retainFeature(sf, geneId));
202 sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
203 sf.setValue("Parent", geneId);
204 assertTrue(testee.retainFeature(sf, geneId));
206 sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
208 sf.setValue("Parent", geneId);
209 assertTrue(testee.retainFeature(sf, geneId));
211 sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
213 sf.setValue("Parent", geneId);
214 assertTrue(testee.retainFeature(sf, geneId));
216 sf.setValue("Parent", "ßXYZ");
217 assertFalse(testee.retainFeature(sf, geneId));
219 sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
220 assertTrue(testee.retainFeature(sf, geneId));
224 * Test the method that picks out 'gene' (or subtype) features with the
227 @Test(groups = "Functional")
228 public void testGetIdentifyingFeatures()
230 String accId = "ABC123";
231 SequenceI seq = new Sequence(accId, "HIBEES");
233 // gene with no ID not valid
234 SequenceFeature sf1 = new SequenceFeature("gene", "", 1, 2, 0f, null);
235 seq.addSequenceFeature(sf1);
237 // gene with wrong ID not valid
238 SequenceFeature sf2 = new SequenceFeature("gene", "a", 1, 2, 0f, null);
239 sf2.setValue("id", "XYZ");
240 seq.addSequenceFeature(sf2);
242 // gene with right ID is valid
243 SequenceFeature sf3 = new SequenceFeature("gene", "b", 1, 2, 0f, null);
244 sf3.setValue("id", accId);
245 seq.addSequenceFeature(sf3);
247 // gene sub-type with right ID is valid
248 SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
249 sf4.setValue("id", accId);
250 seq.addSequenceFeature(sf4);
252 // transcript not valid:
253 SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
254 sf5.setValue("id", accId);
255 seq.addSequenceFeature(sf5);
258 SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
259 sf6.setValue("id", accId);
260 seq.addSequenceFeature(sf6);
262 List<SequenceFeature> sfs = new EnsemblGene()
263 .getIdentifyingFeatures(seq, accId);
264 assertFalse(sfs.contains(sf1));
265 assertFalse(sfs.contains(sf2));
266 assertTrue(sfs.contains(sf3));
267 assertTrue(sfs.contains(sf4));
268 assertFalse(sfs.contains(sf5));
269 assertFalse(sfs.contains(sf6));
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.
277 @Test(groups = "Functional")
278 public void testGetFeatureColourScheme()
280 FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
281 assertTrue(fc.isFeatureDisplayed("exon"));
282 assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
283 assertTrue(fc.isFeatureDisplayed("sequence_variant"));
284 assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
285 assertFalse(fc.isFeatureDisplayed("transcript"));
286 assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
288 assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
290 assertTrue(fc.getFeatureColour("exon").isColourByLabel());
291 assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
292 assertEquals(1, fc.compare("sequence_variant", "exon"));
293 assertEquals(-1, fc.compare("exon", "sequence_variant"));
294 assertEquals(1, fc.compare("feature_variant", "coding_exon"));
295 assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
296 assertEquals(1f, fc.getTransparency());
299 @Test(groups = "Network")
300 public void testGetGeneIds()
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
309 String ids = "ENSG00000158828 ENST00000321556 P30419 ENST00000592782 BRAF";
310 EnsemblGene testee = new EnsemblGene();
311 List<String> geneIds = testee.getGeneIds(ids);
312 assertEquals(8, geneIds.size());
313 assertTrue(geneIds.contains("ENSG00000158828"));
314 assertTrue(geneIds.contains("ENSG00000136448"));
315 assertTrue(geneIds.contains("ENSG00000157764")); // BRAF human
316 assertTrue(geneIds.contains("ENSMUSG00000002413")); // mouse
317 assertTrue(geneIds.contains("ENSRNOG00000010957")); // rat
318 assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
319 assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
320 assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken