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.datamodel;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNull;
26 import static org.testng.AssertJUnit.assertSame;
27 import static org.testng.AssertJUnit.assertTrue;
29 import java.util.ArrayList;
30 import java.util.List;
32 import org.testng.annotations.BeforeClass;
33 import org.testng.annotations.Test;
35 import jalview.gui.JvOptionPane;
36 import jalview.util.MapList;
38 public class SequenceFeatureTest
41 @BeforeClass(alwaysRun = true)
42 public void setUpJvOptionPane()
44 JvOptionPane.setInteractiveMode(false);
45 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
48 @Test(groups = { "Functional" })
49 public void testCopyConstructors()
51 SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
53 sf1.setValue("STRAND", "+");
54 sf1.setValue("Note", "Testing");
55 Integer count = Integer.valueOf(7);
56 sf1.setValue("Count", count);
58 SequenceFeature sf2 = new SequenceFeature(sf1);
59 assertEquals("type", sf2.getType());
60 assertEquals("desc", sf2.getDescription());
61 assertEquals(22, sf2.getBegin());
62 assertEquals(33, sf2.getEnd());
63 assertEquals(12.5f, sf2.getScore());
64 assertEquals("+", sf2.getValue("STRAND"));
65 assertEquals("Testing", sf2.getValue("Note"));
66 // shallow clone of otherDetails map - contains the same object values!
67 assertSame(count, sf2.getValue("Count"));
70 * copy constructor modifying begin/end/group/score
72 SequenceFeature sf3 = new SequenceFeature(sf1, 11, 14, "group2", 17.4f);
73 assertEquals("type", sf3.getType());
74 assertEquals("desc", sf3.getDescription());
75 assertEquals(11, sf3.getBegin());
76 assertEquals(14, sf3.getEnd());
77 assertEquals(17.4f, sf3.getScore());
78 assertEquals("+", sf3.getValue("STRAND"));
79 assertEquals("Testing", sf3.getValue("Note"));
80 // shallow clone of otherDetails map - contains the same object values!
81 assertSame(count, sf3.getValue("Count"));
84 * copy constructor modifying type/begin/end/group/score
86 SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12, 15,
88 assertEquals("Disulfide bond", sf4.getType());
89 assertTrue(sf4.isContactFeature());
90 assertEquals("desc", sf4.getDescription());
91 assertEquals(12, sf4.getBegin());
92 assertEquals(15, sf4.getEnd());
93 assertEquals(-9.1f, sf4.getScore());
94 assertEquals("+", sf4.getValue("STRAND"));
95 assertEquals("Testing", sf4.getValue("Note"));
96 // shallow clone of otherDetails map - contains the same object values!
97 assertSame(count, sf4.getValue("Count"));
101 * Tests for retrieving a 'miscellaneous details' property value, with or
102 * without a supplied default
104 @Test(groups = { "Functional" })
105 public void testGetValue()
107 SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
109 sf1.setValue("STRAND", "+");
110 assertEquals("+", sf1.getValue("STRAND"));
111 assertNull(sf1.getValue("strand")); // case-sensitive
112 assertEquals(".", sf1.getValue("unknown", "."));
113 Integer i = Integer.valueOf(27);
114 assertSame(i, sf1.getValue("Unknown", i));
118 * Tests the method that returns 1 / -1 / 0 for strand "+" / "-" / other
120 @Test(groups = { "Functional" })
121 public void testGetStrand()
123 SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
125 assertEquals(0, sf.getStrand());
126 sf.setValue("STRAND", "+");
127 assertEquals(1, sf.getStrand());
128 sf.setValue("STRAND", "-");
129 assertEquals(-1, sf.getStrand());
130 sf.setValue("STRAND", ".");
131 assertEquals(0, sf.getStrand());
135 * Tests for equality, and that equal objects have the same hashCode
137 @Test(groups = { "Functional" })
138 public void testEqualsAndHashCode()
140 SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
142 sf1.setValue("ID", "id");
143 sf1.setValue("Name", "name");
144 sf1.setValue("Parent", "parent");
147 SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
149 sf2.setValue("ID", "id");
150 sf2.setValue("Name", "name");
151 sf2.setValue("Parent", "parent");
155 assertFalse(sf1.equals(null));
156 assertTrue(sf1.equals(sf2));
157 assertTrue(sf2.equals(sf1));
158 assertEquals(sf1.hashCode(), sf2.hashCode());
160 // changing type breaks equals:
161 SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
163 SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33, 12.5f,
165 assertFalse(sf3.equals(sf4));
167 // changing description breaks equals:
168 String restores = sf2.getDescription();
169 sf2.setDescription("Desc");
170 assertFalse(sf1.equals(sf2));
171 sf2.setDescription(restores);
173 // changing score breaks equals:
174 float restoref = sf2.getScore();
175 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
176 sf2.getFeatureGroup(), 10f);
177 assertFalse(sf1.equals(sf2));
178 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
179 sf2.getFeatureGroup(), restoref);
181 // NaN doesn't match a number
182 restoref = sf2.getScore();
183 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
184 sf2.getFeatureGroup(), Float.NaN);
185 assertFalse(sf1.equals(sf2));
188 sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
189 sf1.getFeatureGroup(), Float.NaN);
190 assertTrue(sf1.equals(sf2));
191 sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
192 sf1.getFeatureGroup(), restoref);
193 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
194 sf2.getFeatureGroup(), restoref);
196 // changing start position breaks equals:
197 int restorei = sf2.getBegin();
198 sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(),
200 assertFalse(sf1.equals(sf2));
201 sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
202 sf2.getFeatureGroup(), sf2.getScore());
204 // changing end position breaks equals:
205 restorei = sf2.getEnd();
206 sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32,
207 sf2.getFeatureGroup(), sf2.getScore());
208 assertFalse(sf1.equals(sf2));
209 sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei,
210 sf2.getFeatureGroup(), sf2.getScore());
212 // changing feature group breaks equals:
213 restores = sf2.getFeatureGroup();
214 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group",
216 assertFalse(sf1.equals(sf2));
217 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores,
220 // changing ID breaks equals:
221 restores = (String) sf2.getValue("ID");
222 sf2.setValue("ID", "id2");
223 assertFalse(sf1.equals(sf2));
224 sf2.setValue("ID", restores);
226 // changing Name breaks equals:
227 restores = (String) sf2.getValue("Name");
228 sf2.setValue("Name", "Name");
229 assertFalse(sf1.equals(sf2));
230 sf2.setValue("Name", restores);
232 // changing Parent breaks equals:
233 restores = (String) sf1.getValue("Parent");
234 sf1.setValue("Parent", "Parent");
235 assertFalse(sf1.equals(sf2));
236 sf1.setValue("Parent", restores);
238 // changing strand breaks equals:
239 restorei = sf2.getStrand();
241 assertFalse(sf1.equals(sf2));
242 sf2.setStrand(restorei == 1 ? "+" : "-");
244 // changing phase breaks equals:
245 restores = sf1.getPhase();
247 assertFalse(sf1.equals(sf2));
248 sf1.setPhase(restores);
250 // restore equality as sanity check:
251 assertTrue(sf1.equals(sf2));
252 assertTrue(sf2.equals(sf1));
253 assertEquals(sf1.hashCode(), sf2.hashCode());
255 // changing status doesn't change equals:
256 sf1.setStatus("new");
257 assertTrue(sf1.equals(sf2));
260 @Test(groups = { "Functional" })
261 public void testIsContactFeature()
263 SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
265 assertFalse(sf.isContactFeature());
266 sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group");
267 assertFalse(sf.isContactFeature());
268 sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group");
269 assertFalse(sf.isContactFeature());
270 sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f,
272 assertTrue(sf.isContactFeature());
273 sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f,
275 assertTrue(sf.isContactFeature());
276 sf = new SequenceFeature("Disulphide Bond", "desc", 22, 33, 12.5f,
278 assertTrue(sf.isContactFeature());
279 sf = new SequenceFeature("disulphide bond", "desc", 22, 33, 12.5f,
281 assertTrue(sf.isContactFeature());
284 @Test(groups = { "Functional" })
285 public void testGetDetailsReport()
287 SequenceI seq = new Sequence("TestSeq", "PLRFQMD");
288 String seqName = seq.getName();
290 // single locus, no group, no score
291 SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22,
293 String expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22</td></tr>"
294 + "<tr><td>Type</td><td>variant</td><td></td></tr>"
295 + "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
296 assertEquals(expected, sf.getDetailsReport(seqName, null));
299 sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
301 expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>28:31</td></tr>"
302 + "<tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
303 + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
304 assertEquals(expected, sf.getDetailsReport(seqName, null));
306 sf = new SequenceFeature("variant", "G,C", 22, 33, 12.5f, "group");
307 sf.setValue("Parent", "ENSG001");
308 sf.setValue("Child", "ENSP002");
309 expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22-33</td></tr>"
310 + "<tr><td>Type</td><td>variant</td><td></td></tr>"
311 + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
312 + "<tr><td>Score</td><td>12.5</td><td></td></tr>"
313 + "<tr><td>Group</td><td>group</td><td></td></tr>"
314 + "<tr><td>Child</td><td></td><td>ENSP002</td></tr>"
315 + "<tr><td>Parent</td><td></td><td>ENSG001</td></tr></table>";
316 assertEquals(expected, sf.getDetailsReport(seqName, null));
319 * feature with embedded html link in description
321 String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>";
322 sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
323 expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>8-83</td></tr>"
324 + "<tr><td>Type</td><td>Pfam</td><td></td></tr>"
325 + "<tr><td>Description</td><td>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></td><td></td></tr>"
326 + "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>";
327 assertEquals(expected, sf.getDetailsReport(seqName, null));
331 * Feature details report for a virtual feature should include original and
332 * mapped locations, and also derived peptide consequence if it can be
335 @Test(groups = { "Functional" })
336 public void testGetDetailsReport_virtualFeature()
338 SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
339 SequenceI seq = new Sequence("TestSeq/8-14", "PLRFQMD");
340 MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
342 Mapping mapping = new Mapping(seq, map);
343 List<SequenceFeature> features = new ArrayList<>();
344 // vary ttg (Leu) to ttc (Phe)
345 SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
347 sf.setValue("alleles", "G,C"); // needed to compute peptide consequence!
350 MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
352 String expected = "<br><table><tr><td>Location</td><td>Cds</td><td>106</td></tr>"
353 + "<tr><td>Peptide Location</td><td>TestSeq</td><td>9</td></tr>"
354 + "<tr><td>Type</td><td>variant</td><td></td></tr>"
355 + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
356 + "<tr><td>Consequence</td><td><i>Translated by Jalview</i></td><td>p.Leu9Phe</td></tr>"
357 + "<tr><td>alleles</td><td></td><td>G,C</td></tr>" + "</table>";
359 assertEquals(expected, sf.getDetailsReport(seq.getName(), mf));
362 * exon feature extending beyond mapped range; mapped location should be
363 * restricted to peptide mapped range limit i.e. 10-13
365 SequenceFeature sf2 = new SequenceFeature("exon", "exon 1", 109, 230,
368 expected = "<br><table><tr><td>Location</td><td>Cds</td><td>109-230</td></tr>"
369 + "<tr><td>Peptide Location</td><td>TestSeq</td><td>10-13</td></tr>"
370 + "<tr><td>Type</td><td>exon</td><td></td></tr>"
371 + "<tr><td>Description</td><td>exon 1</td><td></td></tr>"
373 assertEquals(expected, sf2.getDetailsReport(seq.getName(), mf));