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.datamodel.Sequence;
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.util.List;
38 import org.testng.annotations.AfterClass;
39 import org.testng.annotations.BeforeClass;
40 import org.testng.annotations.Test;
42 public class EnsemblGenomeTest
45 @BeforeClass(alwaysRun = true)
46 public void setUpJvOptionPane()
48 JvOptionPane.setInteractiveMode(false);
49 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52 @BeforeClass(alwaysRun = true)
55 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
58 @AfterClass(alwaysRun = true)
59 public void tearDown()
61 SequenceOntologyFactory.setInstance(null);
65 * Test that the genomic sequence part of genomic sequence is correctly
66 * identified by 'transcript' features (or subtypes) with the correct gene ID
68 @Test(groups = "Functional")
69 public void testGetGenomicRangesFromFeatures()
71 EnsemblGenome testee = new EnsemblGenome();
72 SequenceI genomic = new SequenceDummy("chr7");
73 genomic.setStart(10000);
74 genomic.setEnd(50000);
75 String transcriptId = "ABC123";
77 // transcript at (start+10000) length 501
78 SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
80 sf.setValue("ID", "transcript:" + transcriptId);
82 genomic.addSequenceFeature(sf);
84 // transcript (sub-type) at (start + 10500) length 101
85 sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
86 sf.setValue("ID", "transcript:" + transcriptId);
88 genomic.addSequenceFeature(sf);
90 // Ensembl treats NMD_transcript_variant as if transcript
91 // although strictly it is a sequence_variant in SO
92 sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
94 sf.setValue("ID", "transcript:" + transcriptId);
96 genomic.addSequenceFeature(sf);
98 // transcript with a different ID doesn't count
99 sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
100 sf.setValue("ID", "transcript:anotherOne");
101 genomic.addSequenceFeature(sf);
103 // parent of transcript feature doesn't count
104 sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
106 genomic.addSequenceFeature(sf);
108 MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
110 List<int[]> fromRanges = ranges.getFromRanges();
111 assertEquals(3, fromRanges.size());
112 // from ranges should be sorted by start order
113 assertEquals(10500, fromRanges.get(0)[0]);
114 assertEquals(10600, fromRanges.get(0)[1]);
115 assertEquals(11000, fromRanges.get(1)[0]);
116 assertEquals(12000, fromRanges.get(1)[1]);
117 assertEquals(20000, fromRanges.get(2)[0]);
118 assertEquals(20500, fromRanges.get(2)[1]);
119 // to range should start from given start numbering
120 List<int[]> toRanges = ranges.getToRanges();
121 assertEquals(1, toRanges.size());
122 assertEquals(23, toRanges.get(0)[0]);
123 assertEquals(1625, toRanges.get(0)[1]);
127 * Test the method that retains features except for 'transcript' (or
128 * sub-type), or those with parent other than the given id
130 @Test(groups = "Functional")
131 public void testRetainFeature()
133 String accId = "ABC123";
134 EnsemblGenome testee = new EnsemblGenome();
136 SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
138 assertFalse(testee.retainFeature(sf, accId));
140 sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
142 assertFalse(testee.retainFeature(sf, accId));
144 sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
146 assertFalse(testee.retainFeature(sf, accId));
148 // other feature with no parent is kept
149 sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
150 assertTrue(testee.retainFeature(sf, accId));
152 // other feature with correct parent is kept
153 sf.setValue("Parent", "transcript:" + accId);
154 assertTrue(testee.retainFeature(sf, accId));
156 // other feature with wrong parent is not kept
157 sf.setValue("Parent", "transcript:XYZ");
158 assertFalse(testee.retainFeature(sf, accId));
162 * Test the method that picks out 'transcript' (or subtype) features with the
165 @Test(groups = "Functional")
166 public void testGetIdentifyingFeatures()
168 String accId = "ABC123";
169 SequenceI seq = new Sequence(accId, "HEARTS");
171 // transcript with no ID not valid
172 SequenceFeature sf1 = new SequenceFeature("transcript", "", 1, 2, 0f,
174 seq.addSequenceFeature(sf1);
176 // transcript with wrong ID not valid
177 SequenceFeature sf2 = new SequenceFeature("transcript", "", 1, 2, 0f,
179 sf2.setValue("ID", "transcript");
180 seq.addSequenceFeature(sf2);
182 // transcript with right ID is valid
183 SequenceFeature sf3 = new SequenceFeature("transcript", "", 1, 2, 0f,
185 sf3.setValue("ID", "transcript:" + accId);
186 seq.addSequenceFeature(sf3);
188 // transcript sub-type with right ID is valid
189 SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
190 sf4.setValue("ID", "transcript:" + accId);
191 seq.addSequenceFeature(sf4);
193 // Ensembl treats NMD_transcript_variant as if a transcript
194 SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
196 sf5.setValue("ID", "transcript:" + accId);
197 seq.addSequenceFeature(sf5);
200 SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
201 sf6.setValue("ID", "transcript:" + accId);
202 seq.addSequenceFeature(sf6);
205 SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
206 sf7.setValue("ID", "transcript:" + accId);
207 seq.addSequenceFeature(sf7);
209 List<SequenceFeature> sfs = new EnsemblGenome()
210 .getIdentifyingFeatures(seq, accId);
211 assertFalse(sfs.contains(sf1));
212 assertFalse(sfs.contains(sf2));
213 assertTrue(sfs.contains(sf3));
214 assertTrue(sfs.contains(sf4));
215 assertTrue(sfs.contains(sf5));
216 assertFalse(sfs.contains(sf6));
217 assertFalse(sfs.contains(sf7));