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,
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,
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,
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,
142 sf1.setValue("ID", "id");
143 sf1.setValue("Name", "name");
144 sf1.setValue("Parent", "parent");
147 SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33,
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,
163 SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33,
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(), sf2.getScore());
199 assertFalse(sf1.equals(sf2));
200 sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
201 sf2.getFeatureGroup(), sf2.getScore());
203 // changing end position breaks equals:
204 restorei = sf2.getEnd();
205 sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32,
206 sf2.getFeatureGroup(), sf2.getScore());
207 assertFalse(sf1.equals(sf2));
208 sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei,
209 sf2.getFeatureGroup(), sf2.getScore());
211 // changing feature group breaks equals:
212 restores = sf2.getFeatureGroup();
213 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group", sf2.getScore());
214 assertFalse(sf1.equals(sf2));
215 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores, sf2.getScore());
217 // changing ID breaks equals:
218 restores = (String) sf2.getValue("ID");
219 sf2.setValue("ID", "id2");
220 assertFalse(sf1.equals(sf2));
221 sf2.setValue("ID", restores);
223 // changing Name breaks equals:
224 restores = (String) sf2.getValue("Name");
225 sf2.setValue("Name", "Name");
226 assertFalse(sf1.equals(sf2));
227 sf2.setValue("Name", restores);
229 // changing Parent breaks equals:
230 restores = (String) sf1.getValue("Parent");
231 sf1.setValue("Parent", "Parent");
232 assertFalse(sf1.equals(sf2));
233 sf1.setValue("Parent", restores);
235 // changing strand breaks equals:
236 restorei = sf2.getStrand();
238 assertFalse(sf1.equals(sf2));
239 sf2.setStrand(restorei == 1 ? "+" : "-");
241 // changing phase breaks equals:
242 restores = sf1.getPhase();
244 assertFalse(sf1.equals(sf2));
245 sf1.setPhase(restores);
247 // restore equality as sanity check:
248 assertTrue(sf1.equals(sf2));
249 assertTrue(sf2.equals(sf1));
250 assertEquals(sf1.hashCode(), sf2.hashCode());
252 // changing status doesn't change equals:
253 sf1.setStatus("new");
254 assertTrue(sf1.equals(sf2));
257 @Test(groups = { "Functional" })
258 public void testIsContactFeature()
260 SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
262 assertFalse(sf.isContactFeature());
263 sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group");
264 assertFalse(sf.isContactFeature());
265 sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group");
266 assertFalse(sf.isContactFeature());
267 sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f,
269 assertTrue(sf.isContactFeature());
270 sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f,
272 assertTrue(sf.isContactFeature());
273 sf = new SequenceFeature("Disulphide 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());
281 @Test(groups = { "Functional" })
282 public void testGetDetailsReport()
284 SequenceI seq = new Sequence("TestSeq", "PLRFQMD");
285 String seqName = seq.getName();
287 // single locus, no group, no score
288 SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null);
289 String expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22</td></tr>"
290 + "<tr><td>Type</td><td>variant</td><td></td></tr>"
291 + "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
292 assertEquals(expected, sf.getDetailsReport(seqName, null));
295 sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
297 expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>28:31</td></tr>"
298 + "<tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
299 + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
300 assertEquals(expected, sf.getDetailsReport(seqName, null));
302 sf = new SequenceFeature("variant", "G,C", 22, 33,
304 sf.setValue("Parent", "ENSG001");
305 sf.setValue("Child", "ENSP002");
306 expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22-33</td></tr>"
307 + "<tr><td>Type</td><td>variant</td><td></td></tr>"
308 + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
309 + "<tr><td>Score</td><td>12.5</td><td></td></tr>"
310 + "<tr><td>Group</td><td>group</td><td></td></tr>"
311 + "<tr><td>Child</td><td></td><td>ENSP002</td></tr>"
312 + "<tr><td>Parent</td><td></td><td>ENSG001</td></tr></table>";
313 assertEquals(expected, sf.getDetailsReport(seqName, null));
316 * feature with embedded html link in description
318 String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>";
319 sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
320 expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>8-83</td></tr>"
321 + "<tr><td>Type</td><td>Pfam</td><td></td></tr>"
322 + "<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>"
323 + "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>";
324 assertEquals(expected, sf.getDetailsReport(seqName, null));
328 * Feature details report for a virtual feature should include original and
329 * mapped locations, and also derived peptide consequence if it can be
332 @Test(groups = { "Functional" })
333 public void testGetDetailsReport_virtualFeature()
335 SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
336 SequenceI seq = new Sequence("TestSeq/8-14", "PLRFQMD");
337 MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
339 Mapping mapping = new Mapping(seq, map);
340 List<SequenceFeature> features = new ArrayList<>();
341 // vary ttg (Leu) to ttc (Phe)
342 SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
344 sf.setValue("alleles", "G,C"); // needed to compute peptide consequence!
347 MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
349 String expected = "<br><table><tr><td>Location</td><td>Cds</td><td>106</td></tr>"
350 + "<tr><td>Peptide Location</td><td>TestSeq</td><td>9</td></tr>"
351 + "<tr><td>Type</td><td>variant</td><td></td></tr>"
352 + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
353 + "<tr><td>Consequence</td><td><i>Translated by Jalview</i></td><td>p.Leu9Phe</td></tr>"
354 + "<tr><td>alleles</td><td></td><td>G,C</td></tr>"
357 assertEquals(expected, sf.getDetailsReport(seq.getName(), mf));