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 jalview.gui.JvOptionPane;
31 import org.testng.annotations.BeforeClass;
32 import org.testng.annotations.Test;
34 public class SequenceFeatureTest
37 @BeforeClass(alwaysRun = true)
38 public void setUpJvOptionPane()
40 JvOptionPane.setInteractiveMode(false);
41 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
44 @Test(groups = { "Functional" })
45 public void testCopyConstructor()
47 SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
49 sf1.setValue("STRAND", "+");
50 sf1.setValue("Note", "Testing");
51 Integer count = new Integer(7);
52 sf1.setValue("Count", count);
54 SequenceFeature sf2 = new SequenceFeature(sf1);
55 assertEquals("type", sf2.getType());
56 assertEquals("desc", sf2.getDescription());
57 assertEquals(22, sf2.getBegin());
58 assertEquals(33, sf2.getEnd());
59 assertEquals("+", sf2.getValue("STRAND"));
60 assertEquals("Testing", sf2.getValue("Note"));
61 // shallow clone of otherDetails map - contains the same object values!
62 assertSame(count, sf2.getValue("Count"));
66 * Tests for retrieving a 'miscellaneous details' property value, with or
67 * without a supplied default
69 @Test(groups = { "Functional" })
70 public void testGetValue()
72 SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
74 sf1.setValue("STRAND", "+");
75 assertEquals("+", sf1.getValue("STRAND"));
76 assertNull(sf1.getValue("strand")); // case-sensitive
77 assertEquals(".", sf1.getValue("unknown", "."));
78 Integer i = new Integer(27);
79 assertSame(i, sf1.getValue("Unknown", i));
83 * Tests the method that returns 1 / -1 / 0 for strand "+" / "-" / other
85 @Test(groups = { "Functional" })
86 public void testGetStrand()
88 SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
90 assertEquals(0, sf.getStrand());
91 sf.setValue("STRAND", "+");
92 assertEquals(1, sf.getStrand());
93 sf.setValue("STRAND", "-");
94 assertEquals(-1, sf.getStrand());
95 sf.setValue("STRAND", ".");
96 assertEquals(0, sf.getStrand());
100 * Tests for equality, and that equal objects have the same hashCode
102 @Test(groups = { "Functional" })
103 public void testEqualsAndHashCode()
105 SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
107 sf1.setValue("ID", "id");
108 sf1.setValue("Name", "name");
109 sf1.setValue("Parent", "parent");
112 SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33,
114 sf2.setValue("ID", "id");
115 sf2.setValue("Name", "name");
116 sf2.setValue("Parent", "parent");
120 assertFalse(sf1.equals(null));
121 assertTrue(sf1.equals(sf2));
122 assertTrue(sf2.equals(sf1));
123 assertEquals(sf1.hashCode(), sf2.hashCode());
125 // changing type breaks equals:
126 SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33,
128 SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33,
130 assertFalse(sf3.equals(sf4));
132 // changing description breaks equals:
133 String restores = sf2.getDescription();
134 sf2.setDescription("Desc");
135 assertFalse(sf1.equals(sf2));
136 sf2.setDescription(restores);
138 // changing score breaks equals:
139 float restoref = sf2.getScore();
140 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
141 sf2.getFeatureGroup(), 10f);
142 assertFalse(sf1.equals(sf2));
143 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
144 sf2.getFeatureGroup(), restoref);
146 // NaN doesn't match a number
147 restoref = sf2.getScore();
148 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
149 sf2.getFeatureGroup(), Float.NaN);
150 assertFalse(sf1.equals(sf2));
153 sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
154 sf1.getFeatureGroup(), Float.NaN);
155 assertTrue(sf1.equals(sf2));
156 sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
157 sf1.getFeatureGroup(), restoref);
158 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
159 sf2.getFeatureGroup(), restoref);
161 // changing start position breaks equals:
162 int restorei = sf2.getBegin();
163 sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(), sf2.getScore());
164 assertFalse(sf1.equals(sf2));
165 sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
166 sf2.getFeatureGroup(), sf2.getScore());
168 // changing end position breaks equals:
169 restorei = sf2.getEnd();
170 sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32,
171 sf2.getFeatureGroup(), sf2.getScore());
172 assertFalse(sf1.equals(sf2));
173 sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei,
174 sf2.getFeatureGroup(), sf2.getScore());
176 // changing feature group breaks equals:
177 restores = sf2.getFeatureGroup();
178 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group", sf2.getScore());
179 assertFalse(sf1.equals(sf2));
180 sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores, sf2.getScore());
182 // changing ID breaks equals:
183 restores = (String) sf2.getValue("ID");
184 sf2.setValue("ID", "id2");
185 assertFalse(sf1.equals(sf2));
186 sf2.setValue("ID", restores);
188 // changing Name breaks equals:
189 restores = (String) sf2.getValue("Name");
190 sf2.setValue("Name", "Name");
191 assertFalse(sf1.equals(sf2));
192 sf2.setValue("Name", restores);
194 // changing Parent breaks equals:
195 restores = (String) sf1.getValue("Parent");
196 sf1.setValue("Parent", "Parent");
197 assertFalse(sf1.equals(sf2));
198 sf1.setValue("Parent", restores);
200 // changing strand breaks equals:
201 restorei = sf2.getStrand();
203 assertFalse(sf1.equals(sf2));
204 sf2.setStrand(restorei == 1 ? "+" : "-");
206 // changing phase breaks equals:
207 restores = sf1.getPhase();
209 assertFalse(sf1.equals(sf2));
210 sf1.setPhase(restores);
212 // restore equality as sanity check:
213 assertTrue(sf1.equals(sf2));
214 assertTrue(sf2.equals(sf1));
215 assertEquals(sf1.hashCode(), sf2.hashCode());
217 // changing status doesn't change equals:
218 sf1.setStatus("new");
219 assertTrue(sf1.equals(sf2));
222 @Test(groups = { "Functional" })
223 public void testIsContactFeature()
225 SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
227 assertFalse(sf.isContactFeature());
228 sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group");
229 assertFalse(sf.isContactFeature());
230 sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group");
231 assertFalse(sf.isContactFeature());
232 sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f,
234 assertTrue(sf.isContactFeature());
235 sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f,
237 assertTrue(sf.isContactFeature());
238 sf = new SequenceFeature("Disulphide Bond", "desc", 22, 33, 12.5f,
240 assertTrue(sf.isContactFeature());
241 sf = new SequenceFeature("disulphide bond", "desc", 22, 33, 12.5f,
243 assertTrue(sf.isContactFeature());