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.assertSame;
26 import static org.testng.AssertJUnit.assertTrue;
28 import jalview.api.FeatureSettingsModelI;
29 import jalview.datamodel.SequenceDummy;
30 import jalview.datamodel.SequenceFeature;
31 import jalview.datamodel.SequenceI;
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
45 @BeforeClass(alwaysRun = true)
48 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
51 @AfterClass(alwaysRun = true)
52 public void tearDown()
54 SequenceOntologyFactory.setInstance(null);
58 * Test that the gene part of genomic sequence is uniquely identified by a
59 * 'gene' features (or subtype) with the correct gene ID
61 @Test(groups = "Functional")
62 public void testGetGenomicRangesFromFeatures()
64 EnsemblGene testee = new EnsemblGene();
65 SequenceI genomic = new SequenceDummy("chr7");
66 genomic.setStart(10000);
67 genomic.setEnd(50000);
68 String geneId = "ABC123";
70 // gene at (start+10000) length 501
71 SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
73 sf.setValue("ID", "gene:" + geneId);
75 genomic.addSequenceFeature(sf);
77 // gene at (start + 10500) length 101
78 // should be ignored - the first 'gene' found defines the whole range
79 sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
80 sf.setValue("ID", "gene:" + geneId);
82 genomic.addSequenceFeature(sf);
84 MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
86 List<int[]> fromRanges = ranges.getFromRanges();
87 assertEquals(1, fromRanges.size());
88 assertEquals(20000, fromRanges.get(0)[0]);
89 assertEquals(20500, fromRanges.get(0)[1]);
90 // to range should start from given start numbering
91 List<int[]> toRanges = ranges.getToRanges();
92 assertEquals(1, toRanges.size());
93 assertEquals(23, toRanges.get(0)[0]);
94 assertEquals(523, toRanges.get(0)[1]);
98 * Test variant using a sub-type of gene from the Sequence Ontology
100 @Test(groups = "Functional")
101 public void testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand()
103 EnsemblGene testee = new EnsemblGene();
104 SequenceI genomic = new SequenceDummy("chr7");
105 genomic.setStart(10000);
106 genomic.setEnd(50000);
107 String geneId = "ABC123";
109 // gene at (start+10000) length 501
110 SequenceFeature sf = new SequenceFeature("ncRNA_gene", "", 20000,
112 sf.setValue("ID", "gene:" + geneId);
114 genomic.addSequenceFeature(sf);
116 // gene at (start + 10500) length 101
117 // should be ignored - the first 'gene' found defines the whole range
118 // (real data would only have one such feature)
119 sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
120 sf.setValue("ID", "gene:" + geneId);
122 genomic.addSequenceFeature(sf);
124 MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
126 List<int[]> fromRanges = ranges.getFromRanges();
127 assertEquals(1, fromRanges.size());
128 // from range on reverse strand:
129 assertEquals(20500, fromRanges.get(0)[0]);
130 assertEquals(20000, fromRanges.get(0)[1]);
131 // to range should start from given start numbering
132 List<int[]> toRanges = ranges.getToRanges();
133 assertEquals(1, toRanges.size());
134 assertEquals(23, toRanges.get(0)[0]);
135 assertEquals(523, toRanges.get(0)[1]);
139 * Test the method that extracts transcript (or subtype) features with a
140 * specified gene as parent
142 @Test(groups = "Functional")
143 public void testGetTranscriptFeatures()
145 SequenceI genomic = new SequenceDummy("chr7");
146 genomic.setStart(10000);
147 genomic.setEnd(50000);
148 String geneId = "ABC123";
150 // transcript feature
151 SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
153 sf1.setValue("Parent", "gene:" + geneId);
154 sf1.setValue("transcript_id", "transcript1");
155 genomic.addSequenceFeature(sf1);
157 // transcript sub-type feature
158 SequenceFeature sf2 = new SequenceFeature("snRNA", "", 20000, 20500,
160 sf2.setValue("Parent", "gene:" + geneId);
161 sf2.setValue("transcript_id", "transcript2");
162 genomic.addSequenceFeature(sf2);
164 // NMD_transcript_variant treated like transcript in Ensembl
165 SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
166 20000, 20500, 0f, null);
167 sf3.setValue("Parent", "gene:" + geneId);
168 sf3.setValue("transcript_id", "transcript3");
169 genomic.addSequenceFeature(sf3);
171 // transcript for a different gene - ignored
172 SequenceFeature sf4 = new SequenceFeature("snRNA", "", 20000, 20500,
174 sf4.setValue("Parent", "gene:XYZ");
175 sf4.setValue("transcript_id", "transcript4");
176 genomic.addSequenceFeature(sf4);
178 EnsemblGene testee = new EnsemblGene();
183 List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
185 assertEquals(3, features.size());
186 assertSame(sf1, features.get(0));
187 assertSame(sf2, features.get(1));
188 assertSame(sf3, features.get(2));
192 * Test the method that retains features except for 'gene', or 'transcript'
193 * with parent other than the given id
195 @Test(groups = "Functional")
196 public void testRetainFeature()
198 String geneId = "ABC123";
199 EnsemblGene testee = new EnsemblGene();
200 SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
202 sf.setValue("ID", "gene:" + geneId);
203 assertFalse(testee.retainFeature(sf, geneId));
205 sf.setType("transcript");
206 sf.setValue("Parent", "gene:" + geneId);
207 assertTrue(testee.retainFeature(sf, geneId));
209 sf.setType("mature_transcript");
210 sf.setValue("Parent", "gene:" + geneId);
211 assertTrue(testee.retainFeature(sf, geneId));
213 sf.setType("NMD_transcript_variant");
214 sf.setValue("Parent", "gene:" + geneId);
215 assertTrue(testee.retainFeature(sf, geneId));
217 sf.setValue("Parent", "gene:XYZ");
218 assertFalse(testee.retainFeature(sf, geneId));
220 sf.setType("anything");
221 assertTrue(testee.retainFeature(sf, geneId));
225 * Test the method that picks out 'gene' (or subtype) features with the
228 @Test(groups = "Functional")
229 public void testIdentifiesSequence()
231 String accId = "ABC123";
232 EnsemblGene testee = new EnsemblGene();
234 // gene with no ID not valid
235 SequenceFeature sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
236 assertFalse(testee.identifiesSequence(sf, accId));
238 // gene with wrong ID not valid
239 sf.setValue("ID", "gene:XYZ");
240 assertFalse(testee.identifiesSequence(sf, accId));
242 // gene with right ID is valid
243 sf.setValue("ID", "gene:" + accId);
244 assertTrue(testee.identifiesSequence(sf, accId));
246 // gene sub-type with right ID is valid
247 sf.setType("snRNA_gene");
248 assertTrue(testee.identifiesSequence(sf, accId));
250 // transcript not valid:
251 sf.setType("transcript");
252 assertFalse(testee.identifiesSequence(sf, accId));
256 assertFalse(testee.identifiesSequence(sf, accId));
260 * Check behaviour of feature colour scheme for EnsemblGene sequences.
261 * Currently coded to display exon and sequence_variant (or sub-types) only,
262 * with sequence_variant in red above exon coloured by label.
264 @Test(groups = "Functional")
265 public void testGetFeatureColourScheme()
267 FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
268 assertTrue(fc.isFeatureDisplayed("exon"));
269 assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
270 assertTrue(fc.isFeatureDisplayed("sequence_variant"));
271 assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
272 assertFalse(fc.isFeatureDisplayed("transcript"));
273 assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
275 assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
277 assertTrue(fc.getFeatureColour("exon").isColourByLabel());
278 assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
279 assertEquals(1, fc.compare("sequence_variant", "exon"));
280 assertEquals(-1, fc.compare("exon", "sequence_variant"));
281 assertEquals(1, fc.compare("feature_variant", "coding_exon"));
282 assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
283 assertEquals(1f, fc.getTransparency());