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 java.util.Locale;
25 import static org.testng.AssertJUnit.assertEquals;
26 import static org.testng.AssertJUnit.assertFalse;
27 import static org.testng.AssertJUnit.assertTrue;
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;
40 import java.awt.Color;
41 import java.util.List;
43 import org.testng.annotations.AfterClass;
44 import org.testng.annotations.BeforeClass;
45 import org.testng.annotations.Test;
47 public class EnsemblGeneTest
50 @BeforeClass(alwaysRun = true)
51 public void setUpJvOptionPane()
53 JvOptionPane.setInteractiveMode(false);
54 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57 @BeforeClass(alwaysRun = true)
60 Cache.loadProperties("test/jalview/io/testProps.jvprops");
61 SequenceOntologyFactory.setSequenceOntology(new SequenceOntologyLite());
64 @AfterClass(alwaysRun = true)
65 public void tearDown()
67 SequenceOntologyFactory.setSequenceOntology(null);
71 * Test that the gene part of genomic sequence is uniquely identified by a
72 * 'gene' features (or subtype) with the correct gene ID
74 @Test(groups = "Functional")
75 public void testGetGenomicRangesFromFeatures()
77 EnsemblGene testee = new EnsemblGene();
78 SequenceI genomic = new SequenceDummy("chr7");
79 genomic.setStart(10000);
80 genomic.setEnd(50000);
81 String geneId = "ABC123";
83 // gene at (start + 10500) length 101
84 SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
86 sf.setValue("id", geneId);
88 genomic.addSequenceFeature(sf);
90 MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
92 List<int[]> fromRanges = ranges.getFromRanges();
93 assertEquals(1, fromRanges.size());
94 assertEquals(10500, fromRanges.get(0)[0]);
95 assertEquals(10600, fromRanges.get(0)[1]);
96 // to range should start from given start numbering
97 List<int[]> toRanges = ranges.getToRanges();
98 assertEquals(1, toRanges.size());
99 assertEquals(23, toRanges.get(0)[0]);
100 assertEquals(123, toRanges.get(0)[1]);
104 * Test variant using a sub-type of gene from the Sequence Ontology
106 @Test(groups = "Functional")
107 public void testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand()
109 EnsemblGene testee = new EnsemblGene();
110 SequenceI genomic = new SequenceDummy("chr7");
111 genomic.setStart(10000);
112 genomic.setEnd(50000);
113 String geneId = "ABC123";
115 // gene at (start + 10500) length 101
116 SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
118 sf.setValue("id", geneId);
120 genomic.addSequenceFeature(sf);
122 MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
124 List<int[]> fromRanges = ranges.getFromRanges();
125 assertEquals(1, fromRanges.size());
126 // from range on reverse strand:
127 assertEquals(10500, fromRanges.get(0)[0]);
128 assertEquals(10600, fromRanges.get(0)[1]);
129 // to range should start from given start numbering
130 List<int[]> toRanges = ranges.getToRanges();
131 assertEquals(1, toRanges.size());
132 assertEquals(23, toRanges.get(0)[0]);
133 assertEquals(123, toRanges.get(0)[1]);
137 * Test the method that extracts transcript (or subtype) features with a
138 * specified gene as parent
140 @Test(groups = "Functional")
141 public void testGetTranscriptFeatures()
143 SequenceI genomic = new SequenceDummy("chr7");
144 genomic.setStart(10000);
145 genomic.setEnd(50000);
146 String geneId = "ABC123";
148 // transcript feature
149 SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
151 sf1.setValue("Parent", geneId);
152 sf1.setValue("id", "transcript1");
153 genomic.addSequenceFeature(sf1);
155 // transcript sub-type feature
156 SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500, 0f,
158 sf2.setValue("Parent", geneId);
159 sf2.setValue("id", "transcript2");
160 genomic.addSequenceFeature(sf2);
162 // NMD_transcript_variant treated like transcript in Ensembl
163 SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
164 22000, 22500, 0f, null);
165 // id matching should not be case-sensitive
166 sf3.setValue("Parent", geneId.toLowerCase(Locale.ROOT));
167 sf3.setValue("id", "transcript3");
168 genomic.addSequenceFeature(sf3);
170 // transcript for a different gene - ignored
171 SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500, 0f,
173 sf4.setValue("Parent", "XYZ");
174 sf4.setValue("id", "transcript4");
175 genomic.addSequenceFeature(sf4);
177 EnsemblGene testee = new EnsemblGene();
182 List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
184 assertEquals(3, features.size());
185 assertTrue(features.contains(sf1));
186 assertTrue(features.contains(sf2));
187 assertTrue(features.contains(sf3));
191 * Test the method that retains features except for 'gene', or 'transcript'
192 * with parent other than the given id
194 @Test(groups = "Functional")
195 public void testRetainFeature()
197 String geneId = "ABC123";
198 EnsemblGene testee = new EnsemblGene();
199 SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
201 sf.setValue("id", geneId);
202 assertFalse(testee.retainFeature(sf, geneId));
204 sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
205 sf.setValue("Parent", geneId);
206 assertTrue(testee.retainFeature(sf, geneId));
208 sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
210 sf.setValue("Parent", geneId);
211 assertTrue(testee.retainFeature(sf, geneId));
213 sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
215 sf.setValue("Parent", geneId);
216 assertTrue(testee.retainFeature(sf, geneId));
218 sf.setValue("Parent", "ßXYZ");
219 assertFalse(testee.retainFeature(sf, geneId));
221 sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
222 assertTrue(testee.retainFeature(sf, geneId));
226 * Test the method that picks out 'gene' (or subtype) features with the
229 @Test(groups = "Functional")
230 public void testGetIdentifyingFeatures()
232 String accId = "ABC123";
233 SequenceI seq = new Sequence(accId, "HIBEES");
235 // gene with no ID not valid
236 SequenceFeature sf1 = new SequenceFeature("gene", "", 1, 2, 0f, null);
237 seq.addSequenceFeature(sf1);
239 // gene with wrong ID not valid
240 SequenceFeature sf2 = new SequenceFeature("gene", "a", 1, 2, 0f, null);
241 sf2.setValue("id", "XYZ");
242 seq.addSequenceFeature(sf2);
244 // gene with right ID is valid
245 SequenceFeature sf3 = new SequenceFeature("gene", "b", 1, 2, 0f, null);
246 sf3.setValue("id", accId);
247 seq.addSequenceFeature(sf3);
249 // gene sub-type with right ID is valid
250 SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f,
252 sf4.setValue("id", accId);
253 seq.addSequenceFeature(sf4);
255 // transcript not valid:
256 SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
258 sf5.setValue("id", accId);
259 seq.addSequenceFeature(sf5);
262 SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
263 sf6.setValue("id", accId);
264 seq.addSequenceFeature(sf6);
266 List<SequenceFeature> sfs = new EnsemblGene()
267 .getIdentifyingFeatures(seq, accId);
268 assertFalse(sfs.contains(sf1));
269 assertFalse(sfs.contains(sf2));
270 assertTrue(sfs.contains(sf3));
271 assertTrue(sfs.contains(sf4));
272 assertFalse(sfs.contains(sf5));
273 assertFalse(sfs.contains(sf6));
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.
281 @Test(groups = "Functional")
282 public void testGetFeatureColourScheme()
284 FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
285 assertFalse(fc.isFeatureDisplayed("exon"));
286 assertFalse(fc.isFeatureHidden("exon"));
287 assertFalse(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
288 assertFalse(fc.isFeatureHidden("coding_exon")); // subtype of exon
289 assertFalse(fc.isFeatureDisplayed("sequence_variant"));
290 assertFalse(fc.isFeatureHidden("sequence_variant"));
291 assertFalse(fc.isFeatureDisplayed("feature_variant")); // subtype
292 assertFalse(fc.isFeatureHidden("feature_variant")); // subtype
293 assertTrue(fc.isFeatureHidden("transcript"));
294 assertTrue(fc.isFeatureHidden("CDS"));
296 assertEquals(Color.RED,
297 fc.getFeatureColour("sequence_variant").getColour());
298 assertEquals(Color.RED,
299 fc.getFeatureColour("feature_variant").getColour());
300 assertTrue(fc.getFeatureColour("exon").isColourByLabel());
301 assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
302 assertEquals(1, fc.compare("sequence_variant", "exon"));
303 assertEquals(-1, fc.compare("exon", "sequence_variant"));
304 assertEquals(1, fc.compare("feature_variant", "coding_exon"));
305 assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
306 assertEquals(1f, fc.getTransparency());
309 @Test(groups = "Network")
310 public void testGetGeneIds()
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
319 String ids = "ENSG00000158828 ENST00000321556 P30419 ENST00000592782 BRAF";
320 EnsemblGene testee = new EnsemblGene();
321 List<String> geneIds = testee.getGeneIds(ids);
322 assertTrue(geneIds.contains("ENSG00000158828"));
323 assertTrue(geneIds.contains("ENSG00000136448"));
324 assertTrue(geneIds.contains("ENSG00000157764")); // BRAF human
325 assertTrue(geneIds.contains("ENSMUSG00000002413")); // mouse
326 assertTrue(geneIds.contains("ENSRNOG00000010957")); // rat
327 assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
328 assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
329 assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
330 assertEquals(8, geneIds.size());