1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
|
9 |
|
|
10 |
|
|
11 |
|
|
12 |
|
|
13 |
|
|
14 |
|
|
15 |
|
|
16 |
|
|
17 |
|
|
18 |
|
|
19 |
|
|
20 |
|
|
21 |
|
package jalview.datamodel; |
22 |
|
|
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; |
28 |
|
|
29 |
|
import jalview.gui.JvOptionPane; |
30 |
|
|
31 |
|
import org.testng.annotations.BeforeClass; |
32 |
|
import org.testng.annotations.Test; |
33 |
|
|
|
|
| 99.4% |
Uncovered Elements: 1 (159) |
Complexity: 8 |
Complexity Density: 0.05 |
|
34 |
|
public class SequenceFeatureTest |
35 |
|
{ |
36 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
37 |
1 |
@BeforeClass(alwaysRun = true)... |
38 |
|
public void setUpJvOptionPane() |
39 |
|
{ |
40 |
1 |
JvOptionPane.setInteractiveMode(false); |
41 |
1 |
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
42 |
|
} |
43 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (33) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
44 |
1 |
@Test(groups = { "Functional" })... |
45 |
|
public void testCopyConstructors() |
46 |
|
{ |
47 |
1 |
SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, |
48 |
|
12.5f, "group"); |
49 |
1 |
sf1.setValue("STRAND", "+"); |
50 |
1 |
sf1.setValue("Note", "Testing"); |
51 |
1 |
Integer count = new Integer(7); |
52 |
1 |
sf1.setValue("Count", count); |
53 |
|
|
54 |
1 |
SequenceFeature sf2 = new SequenceFeature(sf1); |
55 |
1 |
assertEquals("type", sf2.getType()); |
56 |
1 |
assertEquals("desc", sf2.getDescription()); |
57 |
1 |
assertEquals(22, sf2.getBegin()); |
58 |
1 |
assertEquals(33, sf2.getEnd()); |
59 |
1 |
assertEquals(12.5f, sf2.getScore()); |
60 |
1 |
assertEquals("+", sf2.getValue("STRAND")); |
61 |
1 |
assertEquals("Testing", sf2.getValue("Note")); |
62 |
|
|
63 |
1 |
assertSame(count, sf2.getValue("Count")); |
64 |
|
|
65 |
|
|
66 |
|
|
67 |
|
|
68 |
1 |
SequenceFeature sf3 = new SequenceFeature(sf1, 11, 14, "group2", 17.4f); |
69 |
1 |
assertEquals("type", sf3.getType()); |
70 |
1 |
assertEquals("desc", sf3.getDescription()); |
71 |
1 |
assertEquals(11, sf3.getBegin()); |
72 |
1 |
assertEquals(14, sf3.getEnd()); |
73 |
1 |
assertEquals(17.4f, sf3.getScore()); |
74 |
1 |
assertEquals("+", sf3.getValue("STRAND")); |
75 |
1 |
assertEquals("Testing", sf3.getValue("Note")); |
76 |
|
|
77 |
1 |
assertSame(count, sf3.getValue("Count")); |
78 |
|
|
79 |
|
|
80 |
|
|
81 |
|
|
82 |
1 |
SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12, |
83 |
|
15, "group3", -9.1f); |
84 |
1 |
assertEquals("Disulfide bond", sf4.getType()); |
85 |
1 |
assertTrue(sf4.isContactFeature()); |
86 |
1 |
assertEquals("desc", sf4.getDescription()); |
87 |
1 |
assertEquals(12, sf4.getBegin()); |
88 |
1 |
assertEquals(15, sf4.getEnd()); |
89 |
1 |
assertEquals(-9.1f, sf4.getScore()); |
90 |
1 |
assertEquals("+", sf4.getValue("STRAND")); |
91 |
1 |
assertEquals("Testing", sf4.getValue("Note")); |
92 |
|
|
93 |
1 |
assertSame(count, sf4.getValue("Count")); |
94 |
|
} |
95 |
|
|
96 |
|
|
97 |
|
|
98 |
|
|
99 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
|
|
100 |
1 |
@Test(groups = { "Functional" })... |
101 |
|
public void testGetValue() |
102 |
|
{ |
103 |
1 |
SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, |
104 |
|
12.5f, "group"); |
105 |
1 |
sf1.setValue("STRAND", "+"); |
106 |
1 |
assertEquals("+", sf1.getValue("STRAND")); |
107 |
1 |
assertNull(sf1.getValue("strand")); |
108 |
1 |
assertEquals(".", sf1.getValue("unknown", ".")); |
109 |
1 |
Integer i = new Integer(27); |
110 |
1 |
assertSame(i, sf1.getValue("Unknown", i)); |
111 |
|
} |
112 |
|
|
113 |
|
|
114 |
|
|
115 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
|
|
116 |
1 |
@Test(groups = { "Functional" })... |
117 |
|
public void testGetStrand() |
118 |
|
{ |
119 |
1 |
SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f, |
120 |
|
"group"); |
121 |
1 |
assertEquals(0, sf.getStrand()); |
122 |
1 |
sf.setValue("STRAND", "+"); |
123 |
1 |
assertEquals(1, sf.getStrand()); |
124 |
1 |
sf.setValue("STRAND", "-"); |
125 |
1 |
assertEquals(-1, sf.getStrand()); |
126 |
1 |
sf.setValue("STRAND", "."); |
127 |
1 |
assertEquals(0, sf.getStrand()); |
128 |
|
} |
129 |
|
|
130 |
|
|
131 |
|
|
132 |
|
|
|
|
| 98.6% |
Uncovered Elements: 1 (73) |
Complexity: 2 |
Complexity Density: 0.03 |
1PASS
|
|
133 |
1 |
@Test(groups = { "Functional" })... |
134 |
|
public void testEqualsAndHashCode() |
135 |
|
{ |
136 |
1 |
SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, |
137 |
|
12.5f, "group"); |
138 |
1 |
sf1.setValue("ID", "id"); |
139 |
1 |
sf1.setValue("Name", "name"); |
140 |
1 |
sf1.setValue("Parent", "parent"); |
141 |
1 |
sf1.setStrand("+"); |
142 |
1 |
sf1.setPhase("1"); |
143 |
1 |
SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33, |
144 |
|
12.5f, "group"); |
145 |
1 |
sf2.setValue("ID", "id"); |
146 |
1 |
sf2.setValue("Name", "name"); |
147 |
1 |
sf2.setValue("Parent", "parent"); |
148 |
1 |
sf2.setStrand("+"); |
149 |
1 |
sf2.setPhase("1"); |
150 |
|
|
151 |
1 |
assertFalse(sf1.equals(null)); |
152 |
1 |
assertTrue(sf1.equals(sf2)); |
153 |
1 |
assertTrue(sf2.equals(sf1)); |
154 |
1 |
assertEquals(sf1.hashCode(), sf2.hashCode()); |
155 |
|
|
156 |
|
|
157 |
1 |
SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33, |
158 |
|
12.5f, "group"); |
159 |
1 |
SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33, |
160 |
|
12.5f, "group"); |
161 |
1 |
assertFalse(sf3.equals(sf4)); |
162 |
|
|
163 |
|
|
164 |
1 |
String restores = sf2.getDescription(); |
165 |
1 |
sf2.setDescription("Desc"); |
166 |
1 |
assertFalse(sf1.equals(sf2)); |
167 |
1 |
sf2.setDescription(restores); |
168 |
|
|
169 |
|
|
170 |
1 |
float restoref = sf2.getScore(); |
171 |
1 |
sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), |
172 |
|
sf2.getFeatureGroup(), 10f); |
173 |
1 |
assertFalse(sf1.equals(sf2)); |
174 |
1 |
sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), |
175 |
|
sf2.getFeatureGroup(), restoref); |
176 |
|
|
177 |
|
|
178 |
1 |
restoref = sf2.getScore(); |
179 |
1 |
sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), |
180 |
|
sf2.getFeatureGroup(), Float.NaN); |
181 |
1 |
assertFalse(sf1.equals(sf2)); |
182 |
|
|
183 |
|
|
184 |
1 |
sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(), |
185 |
|
sf1.getFeatureGroup(), Float.NaN); |
186 |
1 |
assertTrue(sf1.equals(sf2)); |
187 |
1 |
sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(), |
188 |
|
sf1.getFeatureGroup(), restoref); |
189 |
1 |
sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), |
190 |
|
sf2.getFeatureGroup(), restoref); |
191 |
|
|
192 |
|
|
193 |
1 |
int restorei = sf2.getBegin(); |
194 |
1 |
sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(), sf2.getScore()); |
195 |
1 |
assertFalse(sf1.equals(sf2)); |
196 |
1 |
sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(), |
197 |
|
sf2.getFeatureGroup(), sf2.getScore()); |
198 |
|
|
199 |
|
|
200 |
1 |
restorei = sf2.getEnd(); |
201 |
1 |
sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32, |
202 |
|
sf2.getFeatureGroup(), sf2.getScore()); |
203 |
1 |
assertFalse(sf1.equals(sf2)); |
204 |
1 |
sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei, |
205 |
|
sf2.getFeatureGroup(), sf2.getScore()); |
206 |
|
|
207 |
|
|
208 |
1 |
restores = sf2.getFeatureGroup(); |
209 |
1 |
sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group", sf2.getScore()); |
210 |
1 |
assertFalse(sf1.equals(sf2)); |
211 |
1 |
sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores, sf2.getScore()); |
212 |
|
|
213 |
|
|
214 |
1 |
restores = (String) sf2.getValue("ID"); |
215 |
1 |
sf2.setValue("ID", "id2"); |
216 |
1 |
assertFalse(sf1.equals(sf2)); |
217 |
1 |
sf2.setValue("ID", restores); |
218 |
|
|
219 |
|
|
220 |
1 |
restores = (String) sf2.getValue("Name"); |
221 |
1 |
sf2.setValue("Name", "Name"); |
222 |
1 |
assertFalse(sf1.equals(sf2)); |
223 |
1 |
sf2.setValue("Name", restores); |
224 |
|
|
225 |
|
|
226 |
1 |
restores = (String) sf1.getValue("Parent"); |
227 |
1 |
sf1.setValue("Parent", "Parent"); |
228 |
1 |
assertFalse(sf1.equals(sf2)); |
229 |
1 |
sf1.setValue("Parent", restores); |
230 |
|
|
231 |
|
|
232 |
1 |
restorei = sf2.getStrand(); |
233 |
1 |
sf2.setStrand("-"); |
234 |
1 |
assertFalse(sf1.equals(sf2)); |
235 |
1 |
sf2.setStrand(restorei == 1 ? "+" : "-"); |
236 |
|
|
237 |
|
|
238 |
1 |
restores = sf1.getPhase(); |
239 |
1 |
sf1.setPhase("2"); |
240 |
1 |
assertFalse(sf1.equals(sf2)); |
241 |
1 |
sf1.setPhase(restores); |
242 |
|
|
243 |
|
|
244 |
1 |
assertTrue(sf1.equals(sf2)); |
245 |
1 |
assertTrue(sf2.equals(sf1)); |
246 |
1 |
assertEquals(sf1.hashCode(), sf2.hashCode()); |
247 |
|
|
248 |
|
|
249 |
1 |
sf1.setStatus("new"); |
250 |
1 |
assertTrue(sf1.equals(sf2)); |
251 |
|
} |
252 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (14) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
253 |
1 |
@Test(groups = { "Functional" })... |
254 |
|
public void testIsContactFeature() |
255 |
|
{ |
256 |
1 |
SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f, |
257 |
|
"group"); |
258 |
1 |
assertFalse(sf.isContactFeature()); |
259 |
1 |
sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group"); |
260 |
1 |
assertFalse(sf.isContactFeature()); |
261 |
1 |
sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group"); |
262 |
1 |
assertFalse(sf.isContactFeature()); |
263 |
1 |
sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f, |
264 |
|
"group"); |
265 |
1 |
assertTrue(sf.isContactFeature()); |
266 |
1 |
sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f, |
267 |
|
"group"); |
268 |
1 |
assertTrue(sf.isContactFeature()); |
269 |
1 |
sf = new SequenceFeature("Disulphide Bond", "desc", 22, 33, 12.5f, |
270 |
|
"group"); |
271 |
1 |
assertTrue(sf.isContactFeature()); |
272 |
1 |
sf = new SequenceFeature("disulphide bond", "desc", 22, 33, 12.5f, |
273 |
|
"group"); |
274 |
1 |
assertTrue(sf.isContactFeature()); |
275 |
|
} |
276 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
277 |
1 |
@Test(groups = { "Functional" })... |
278 |
|
public void testGetDetailsReport() |
279 |
|
{ |
280 |
|
|
281 |
1 |
SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null); |
282 |
1 |
String expected = "<br><table><tr><td>Type</td><td>variant</td><td></td></tr>" |
283 |
|
+ "<tr><td>Start/end</td><td>22</td><td></td></tr>" |
284 |
|
+ "<tr><td>Description</td><td>G,C</td><td></td></tr></table>"; |
285 |
1 |
assertEquals(expected, sf.getDetailsReport()); |
286 |
|
|
287 |
|
|
288 |
1 |
sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31, |
289 |
|
null); |
290 |
1 |
expected = "<br><table><tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>" |
291 |
|
+ "<tr><td>Start/end</td><td>28:31</td><td></td></tr>" |
292 |
|
+ "<tr><td>Description</td><td>a description</td><td></td></tr></table>"; |
293 |
1 |
assertEquals(expected, sf.getDetailsReport()); |
294 |
|
|
295 |
1 |
sf = new SequenceFeature("variant", "G,C", 22, 33, |
296 |
|
12.5f, "group"); |
297 |
1 |
sf.setValue("Parent", "ENSG001"); |
298 |
1 |
sf.setValue("Child", "ENSP002"); |
299 |
1 |
expected = "<br><table><tr><td>Type</td><td>variant</td><td></td></tr>" |
300 |
|
+ "<tr><td>Start/end</td><td>22-33</td><td></td></tr>" |
301 |
|
+ "<tr><td>Description</td><td>G,C</td><td></td></tr>" |
302 |
|
+ "<tr><td>Score</td><td>12.5</td><td></td></tr>" |
303 |
|
+ "<tr><td>Group</td><td>group</td><td></td></tr>" |
304 |
|
+ "<tr><td>Child</td><td></td><td>ENSP002</td></tr>" |
305 |
|
+ "<tr><td>Parent</td><td></td><td>ENSG001</td></tr></table>"; |
306 |
1 |
assertEquals(expected, sf.getDetailsReport()); |
307 |
|
|
308 |
|
|
309 |
|
|
310 |
|
|
311 |
1 |
String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>"; |
312 |
1 |
sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot"); |
313 |
1 |
expected = "<br><table><tr><td>Type</td><td>Pfam</td><td></td></tr>" |
314 |
|
+ "<tr><td>Start/end</td><td>8-83</td><td></td></tr>" |
315 |
|
+ "<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>" |
316 |
|
+ "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>"; |
317 |
1 |
assertEquals(expected, sf.getDetailsReport()); |
318 |
|
} |
319 |
|
} |