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.SequenceDummy;
28 import jalview.datamodel.SequenceFeature;
29 import jalview.datamodel.SequenceI;
30 import jalview.io.gff.SequenceOntologyFactory;
31 import jalview.io.gff.SequenceOntologyLite;
32 import jalview.util.MapList;
34 import java.util.List;
36 import org.testng.annotations.AfterClass;
37 import org.testng.annotations.BeforeClass;
38 import org.testng.annotations.Test;
40 public class EnsemblGenomeTest
42 @BeforeClass(alwaysRun = true)
45 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
48 @AfterClass(alwaysRun = true)
49 public void tearDown()
51 SequenceOntologyFactory.setInstance(null);
55 * Test that the genomic sequence part of genomic sequence is correctly
56 * identified by 'transcript' features (or subtypes) with the correct gene ID
58 @Test(groups = "Functional")
59 public void testGetGenomicRangesFromFeatures()
61 EnsemblGenome testee = new EnsemblGenome();
62 SequenceI genomic = new SequenceDummy("chr7");
63 genomic.setStart(10000);
64 genomic.setEnd(50000);
65 String transcriptId = "ABC123";
67 // transcript at (start+10000) length 501
68 SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
70 sf.setValue("ID", "transcript:" + transcriptId);
72 genomic.addSequenceFeature(sf);
74 // transcript (sub-type) at (start + 10500) length 101
75 sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
76 sf.setValue("ID", "transcript:" + transcriptId);
78 genomic.addSequenceFeature(sf);
80 // Ensembl treats NMD_transcript_variant as if transcript
81 // although strictly it is a sequence_variant in SO
82 sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
84 sf.setValue("ID", "transcript:" + transcriptId);
86 genomic.addSequenceFeature(sf);
88 // transcript with a different ID doesn't count
89 sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
90 sf.setValue("ID", "transcript:anotherOne");
91 genomic.addSequenceFeature(sf);
93 // parent of transcript feature doesn't count
94 sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
96 genomic.addSequenceFeature(sf);
98 MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
100 List<int[]> fromRanges = ranges.getFromRanges();
101 assertEquals(3, fromRanges.size());
102 // from ranges should be sorted by start order
103 assertEquals(10500, fromRanges.get(0)[0]);
104 assertEquals(10600, fromRanges.get(0)[1]);
105 assertEquals(11000, fromRanges.get(1)[0]);
106 assertEquals(12000, fromRanges.get(1)[1]);
107 assertEquals(20000, fromRanges.get(2)[0]);
108 assertEquals(20500, fromRanges.get(2)[1]);
109 // to range should start from given start numbering
110 List<int[]> toRanges = ranges.getToRanges();
111 assertEquals(1, toRanges.size());
112 assertEquals(23, toRanges.get(0)[0]);
113 assertEquals(1625, toRanges.get(0)[1]);
117 * Test the method that retains features except for 'transcript' (or
118 * sub-type), or those with parent other than the given id
120 @Test(groups = "Functional")
121 public void testRetainFeature()
123 String accId = "ABC123";
124 EnsemblGenome testee = new EnsemblGenome();
126 SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
128 assertFalse(testee.retainFeature(sf, accId));
130 sf.setType("mature_transcript");
131 assertFalse(testee.retainFeature(sf, accId));
133 sf.setType("NMD_transcript_variant");
134 assertFalse(testee.retainFeature(sf, accId));
136 // other feature with no parent is kept
137 sf.setType("anything");
138 assertTrue(testee.retainFeature(sf, accId));
140 // other feature with correct parent is kept
141 sf.setValue("Parent", "transcript:" + accId);
142 assertTrue(testee.retainFeature(sf, accId));
144 // other feature with wrong parent is not kept
145 sf.setValue("Parent", "transcript:XYZ");
146 assertFalse(testee.retainFeature(sf, accId));
150 * Test the method that picks out 'transcript' (or subtype) features with the
153 @Test(groups = "Functional")
154 public void testIdentifiesSequence()
156 String accId = "ABC123";
157 EnsemblGenome testee = new EnsemblGenome();
159 // transcript with no ID not valid
160 SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
162 assertFalse(testee.identifiesSequence(sf, accId));
164 // transcript with wrong ID not valid
165 sf.setValue("ID", "transcript");
166 assertFalse(testee.identifiesSequence(sf, accId));
168 // transcript with right ID is valid
169 sf.setValue("ID", "transcript:" + accId);
170 assertTrue(testee.identifiesSequence(sf, accId));
172 // transcript sub-type with right ID is valid
174 assertTrue(testee.identifiesSequence(sf, accId));
176 // Ensembl treats NMD_transcript_variant as if a transcript
177 sf.setType("NMD_transcript_variant");
178 assertTrue(testee.identifiesSequence(sf, accId));
182 assertFalse(testee.identifiesSequence(sf, accId));
186 assertFalse(testee.identifiesSequence(sf, accId));