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.Assert;
39 import org.testng.annotations.AfterClass;
40 import org.testng.annotations.BeforeClass;
41 import org.testng.annotations.Test;
43 public class EnsemblCdsTest
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 cdna part of genomic sequence is correctly identified by
67 * 'CDS' features (or subtypes) with the desired transcript as parent
69 @Test(groups = "Functional")
70 public void testGetGenomicRangesFromFeatures()
72 EnsemblCds testee = new EnsemblCds();
73 SequenceI genomic = new SequenceDummy("chr7");
74 genomic.setStart(10000);
75 genomic.setEnd(50000);
76 String transcriptId = "ABC123";
78 // CDS at (start+10000) length 501
79 SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
81 sf.setValue("Parent", transcriptId);
83 genomic.addSequenceFeature(sf);
85 // CDS (sub-type) at (start + 10500) length 101
86 sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
87 sf.setValue("Parent", transcriptId);
89 genomic.addSequenceFeature(sf);
91 // CDS belonging to a different transcript doesn't count
92 sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
93 sf.setValue("Parent", "anotherOne");
94 genomic.addSequenceFeature(sf);
96 // exon feature doesn't count
97 sf = new SequenceFeature("exon", "", 10000, 50000, 0f, null);
98 genomic.addSequenceFeature(sf);
100 // mRNA_region feature doesn't count (parent of CDS)
101 sf = new SequenceFeature("mRNA_region", "", 10000, 50000, 0f, null);
102 genomic.addSequenceFeature(sf);
104 MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
106 List<int[]> fromRanges = ranges.getFromRanges();
107 assertEquals(2, fromRanges.size());
108 // from ranges should be sorted by start order
109 assertEquals(10500, fromRanges.get(0)[0]);
110 assertEquals(10600, fromRanges.get(0)[1]);
111 assertEquals(20000, fromRanges.get(1)[0]);
112 assertEquals(20500, fromRanges.get(1)[1]);
113 // to range should start from given start numbering
114 List<int[]> toRanges = ranges.getToRanges();
115 assertEquals(1, toRanges.size());
116 assertEquals(23, toRanges.get(0)[0]);
117 assertEquals(624, toRanges.get(0)[1]);
121 * Test the method that retains features except for 'CDS' (or subtypes), or
122 * features with parent other than the given id
124 @Test(groups = "Functional")
125 public void testRetainFeature()
127 String accId = "ABC123";
128 EnsemblCds testee = new EnsemblCds();
130 SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
132 assertFalse(testee.retainFeature(sf, accId));
134 sf = new SequenceFeature("CDS_predicted", "", 20000, 20500, 0f, null);
135 assertFalse(testee.retainFeature(sf, accId));
137 // other feature with no parent is retained
138 sf = new SequenceFeature("anotherType", "", 20000, 20500, 0f, null);
139 assertTrue(testee.retainFeature(sf, accId));
141 // other feature with desired parent is retained
142 sf.setValue("Parent", accId);
143 assertTrue(testee.retainFeature(sf, accId));
145 // feature with wrong parent is not retained
146 sf.setValue("Parent", "XYZ");
147 assertFalse(testee.retainFeature(sf, accId));
151 * Test the method that picks out 'CDS' (or subtype) features with the
152 * accession id as parent
154 @Test(groups = "Functional")
155 public void testGetIdentifyingFeatures()
157 String accId = "ABC123";
158 SequenceI seq = new Sequence(accId, "MKDONS");
160 // cds with no parent not valid
161 SequenceFeature sf1 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
162 seq.addSequenceFeature(sf1);
164 // cds with wrong parent not valid
165 SequenceFeature sf2 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
166 sf2.setValue("Parent", "XYZ");
167 seq.addSequenceFeature(sf2);
169 // cds with right parent is valid
170 SequenceFeature sf3 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
171 sf3.setValue("Parent", accId);
172 seq.addSequenceFeature(sf3);
174 // cds sub-type with right parent is valid
175 SequenceFeature sf4 = new SequenceFeature("CDS_predicted", "", 1, 2, 0f,
177 sf4.setValue("Parent", accId);
178 seq.addSequenceFeature(sf4);
180 // transcript not valid:
181 SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
183 sf5.setValue("Parent", accId);
184 seq.addSequenceFeature(sf5);
187 SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
188 sf6.setValue("Parent", accId);
189 seq.addSequenceFeature(sf6);
191 List<SequenceFeature> sfs = new EnsemblCds().getIdentifyingFeatures(seq,
193 assertFalse(sfs.contains(sf1));
194 assertFalse(sfs.contains(sf2));
195 assertTrue(sfs.contains(sf3));
196 assertTrue(sfs.contains(sf4));
197 assertFalse(sfs.contains(sf5));
198 assertFalse(sfs.contains(sf6));
201 @Test(groups = "Functional")
202 public void testIsValidReference() throws Exception
204 EnsemblSequenceFetcher esq = new EnsemblCds();
205 Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
206 Assert.assertTrue(esq.isValidReference("ENST00000288602"));
207 Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
208 Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
209 Assert.assertFalse(esq.isValidReference("ENST0000288602"));
210 // non-human species have a 3 character identifier included:
211 Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));