Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceFeatureTest	38	167	9	0.9943502599.4%	Show methods

Class SequenceFeatureTest

Class SequenceFeatureTest	Line # 38	Total Statements 167	Complexity 9	TOTAL Coverage 0.9943502599.4%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4141	2.02	1.01	1.0 1.0100%
testCopyConstructors() : void   testCopyConstructors() : void	4848	33.033	1.01	1.0 1.0100%
testGetValue() : void   testGetValue() : void	104104	7.07	1.01	1.0 1.0100%
testGetStrand() : void   testGetStrand() : void	120120	8.08	1.01	1.0 1.0100%
testEqualsAndHashCode() : void   testEqualsAndHashCode() : void	137137	71.071	2.02	0.98630136 0.9863013698.6%
testIsContactFeature() : void   testIsContactFeature() : void	260260	14.014	1.01	1.0 1.0100%
testGetDetailsReport() : void   testGetDetailsReport() : void	284284	17.017	1.01	1.0 1.0100%
testGetDetailsReport_virtualFeature() : void   testGetDetailsReport_virtualFeature() : void	335335	15.015	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.4124294	jalview.datamodel.SequenceFeatureTest.testEqualsAndHashCodejalview.datamodel.SequenceFeatureTest.testEqualsAndHashCode	1PASS
	0.19209039	jalview.datamodel.SequenceFeatureTest.testCopyConstructorsjalview.datamodel.SequenceFeatureTest.testCopyConstructors	1PASS
	0.10169491	jalview.datamodel.SequenceFeatureTest.testGetDetailsReportjalview.datamodel.SequenceFeatureTest.testGetDetailsReport	1PASS
	0.09039548	jalview.datamodel.SequenceFeatureTest.testGetDetailsReport_virtualFeaturejalview.datamodel.SequenceFeatureTest.testGetDetailsReport_virtualFeature	1PASS
	0.084745765	jalview.datamodel.SequenceFeatureTest.testIsContactFeaturejalview.datamodel.SequenceFeatureTest.testIsContactFeature	1PASS
	0.050847456	jalview.datamodel.SequenceFeatureTest.testGetStrandjalview.datamodel.SequenceFeatureTest.testGetStrand	1PASS
	0.04519774	jalview.datamodel.SequenceFeatureTest.testGetValuejalview.datamodel.SequenceFeatureTest.testGetValue	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
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.
11		*
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.
16		*
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.
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 java.util.ArrayList;
30		import java.util.List;
31
32		import org.testng.annotations.BeforeClass;
33		import org.testng.annotations.Test;
34
35		import jalview.gui.JvOptionPane;
36		import jalview.util.MapList;
37
		99.4% Uncovered Elements: 1 (177) Complexity: 9 Complexity Density: 0.05
38		public class SequenceFeatureTest
39		{
40
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
41	1	@BeforeClass(alwaysRun = true)...
42		public void setUpJvOptionPane()
43		{
44	1	JvOptionPane.setInteractiveMode(false);
45	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
46		}
47
		100% Uncovered Elements: 0 (33) Complexity: 1 Complexity Density: 0.03 1PASS
48	1	@Test(groups = { "Functional" })...
49		public void testCopyConstructors()
50		{
51	1	SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
52		"group");
53	1	sf1.setValue("STRAND", "+");
54	1	sf1.setValue("Note", "Testing");
55	1	Integer count = Integer.valueOf(7);
56	1	sf1.setValue("Count", count);
57
58	1	SequenceFeature sf2 = new SequenceFeature(sf1);
59	1	assertEquals("type", sf2.getType());
60	1	assertEquals("desc", sf2.getDescription());
61	1	assertEquals(22, sf2.getBegin());
62	1	assertEquals(33, sf2.getEnd());
63	1	assertEquals(12.5f, sf2.getScore());
64	1	assertEquals("+", sf2.getValue("STRAND"));
65	1	assertEquals("Testing", sf2.getValue("Note"));
66		// shallow clone of otherDetails map - contains the same object values!
67	1	assertSame(count, sf2.getValue("Count"));
68
69		/*
70		* copy constructor modifying begin/end/group/score
71		*/
72	1	SequenceFeature sf3 = new SequenceFeature(sf1, 11, 14, "group2", 17.4f);
73	1	assertEquals("type", sf3.getType());
74	1	assertEquals("desc", sf3.getDescription());
75	1	assertEquals(11, sf3.getBegin());
76	1	assertEquals(14, sf3.getEnd());
77	1	assertEquals(17.4f, sf3.getScore());
78	1	assertEquals("+", sf3.getValue("STRAND"));
79	1	assertEquals("Testing", sf3.getValue("Note"));
80		// shallow clone of otherDetails map - contains the same object values!
81	1	assertSame(count, sf3.getValue("Count"));
82
83		/*
84		* copy constructor modifying type/begin/end/group/score
85		*/
86	1	SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12, 15,
87		"group3", -9.1f);
88	1	assertEquals("Disulfide bond", sf4.getType());
89	1	assertTrue(sf4.isContactFeature());
90	1	assertEquals("desc", sf4.getDescription());
91	1	assertEquals(12, sf4.getBegin());
92	1	assertEquals(15, sf4.getEnd());
93	1	assertEquals(-9.1f, sf4.getScore());
94	1	assertEquals("+", sf4.getValue("STRAND"));
95	1	assertEquals("Testing", sf4.getValue("Note"));
96		// shallow clone of otherDetails map - contains the same object values!
97	1	assertSame(count, sf4.getValue("Count"));
98		}
99
100		/**
101		* Tests for retrieving a 'miscellaneous details' property value, with or
102		* without a supplied default
103		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
104	1	@Test(groups = { "Functional" })...
105		public void testGetValue()
106		{
107	1	SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
108		"group");
109	1	sf1.setValue("STRAND", "+");
110	1	assertEquals("+", sf1.getValue("STRAND"));
111	1	assertNull(sf1.getValue("strand")); // case-sensitive
112	1	assertEquals(".", sf1.getValue("unknown", "."));
113	1	Integer i = Integer.valueOf(27);
114	1	assertSame(i, sf1.getValue("Unknown", i));
115		}
116
117		/**
118		* Tests the method that returns 1 / -1 / 0 for strand "+" / "-" / other
119		*/
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
120	1	@Test(groups = { "Functional" })...
121		public void testGetStrand()
122		{
123	1	SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
124		"group");
125	1	assertEquals(0, sf.getStrand());
126	1	sf.setValue("STRAND", "+");
127	1	assertEquals(1, sf.getStrand());
128	1	sf.setValue("STRAND", "-");
129	1	assertEquals(-1, sf.getStrand());
130	1	sf.setValue("STRAND", ".");
131	1	assertEquals(0, sf.getStrand());
132		}
133
134		/**
135		* Tests for equality, and that equal objects have the same hashCode
136		*/
		98.6% Uncovered Elements: 1 (73) Complexity: 2 Complexity Density: 0.03 1PASS
137	1	@Test(groups = { "Functional" })...
138		public void testEqualsAndHashCode()
139		{
140	1	SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
141		"group");
142	1	sf1.setValue("ID", "id");
143	1	sf1.setValue("Name", "name");
144	1	sf1.setValue("Parent", "parent");
145	1	sf1.setStrand("+");
146	1	sf1.setPhase("1");
147	1	SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
148		"group");
149	1	sf2.setValue("ID", "id");
150	1	sf2.setValue("Name", "name");
151	1	sf2.setValue("Parent", "parent");
152	1	sf2.setStrand("+");
153	1	sf2.setPhase("1");
154
155	1	assertFalse(sf1.equals(null));
156	1	assertTrue(sf1.equals(sf2));
157	1	assertTrue(sf2.equals(sf1));
158	1	assertEquals(sf1.hashCode(), sf2.hashCode());
159
160		// changing type breaks equals:
161	1	SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
162		"group");
163	1	SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33, 12.5f,
164		"group");
165	1	assertFalse(sf3.equals(sf4));
166
167		// changing description breaks equals:
168	1	String restores = sf2.getDescription();
169	1	sf2.setDescription("Desc");
170	1	assertFalse(sf1.equals(sf2));
171	1	sf2.setDescription(restores);
172
173		// changing score breaks equals:
174	1	float restoref = sf2.getScore();
175	1	sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
176		sf2.getFeatureGroup(), 10f);
177	1	assertFalse(sf1.equals(sf2));
178	1	sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
179		sf2.getFeatureGroup(), restoref);
180
181		// NaN doesn't match a number
182	1	restoref = sf2.getScore();
183	1	sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
184		sf2.getFeatureGroup(), Float.NaN);
185	1	assertFalse(sf1.equals(sf2));
186
187		// NaN matches NaN
188	1	sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
189		sf1.getFeatureGroup(), Float.NaN);
190	1	assertTrue(sf1.equals(sf2));
191	1	sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
192		sf1.getFeatureGroup(), restoref);
193	1	sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
194		sf2.getFeatureGroup(), restoref);
195
196		// changing start position breaks equals:
197	1	int restorei = sf2.getBegin();
198	1	sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(),
199		sf2.getScore());
200	1	assertFalse(sf1.equals(sf2));
201	1	sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
202		sf2.getFeatureGroup(), sf2.getScore());
203
204		// changing end position breaks equals:
205	1	restorei = sf2.getEnd();
206	1	sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32,
207		sf2.getFeatureGroup(), sf2.getScore());
208	1	assertFalse(sf1.equals(sf2));
209	1	sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei,
210		sf2.getFeatureGroup(), sf2.getScore());
211
212		// changing feature group breaks equals:
213	1	restores = sf2.getFeatureGroup();
214	1	sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group",
215		sf2.getScore());
216	1	assertFalse(sf1.equals(sf2));
217	1	sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores,
218		sf2.getScore());
219
220		// changing ID breaks equals:
221	1	restores = (String) sf2.getValue("ID");
222	1	sf2.setValue("ID", "id2");
223	1	assertFalse(sf1.equals(sf2));
224	1	sf2.setValue("ID", restores);
225
226		// changing Name breaks equals:
227	1	restores = (String) sf2.getValue("Name");
228	1	sf2.setValue("Name", "Name");
229	1	assertFalse(sf1.equals(sf2));
230	1	sf2.setValue("Name", restores);
231
232		// changing Parent breaks equals:
233	1	restores = (String) sf1.getValue("Parent");
234	1	sf1.setValue("Parent", "Parent");
235	1	assertFalse(sf1.equals(sf2));
236	1	sf1.setValue("Parent", restores);
237
238		// changing strand breaks equals:
239	1	restorei = sf2.getStrand();
240	1	sf2.setStrand("-");
241	1	assertFalse(sf1.equals(sf2));
242	1	sf2.setStrand(restorei == 1 ? "+" : "-");
243
244		// changing phase breaks equals:
245	1	restores = sf1.getPhase();
246	1	sf1.setPhase("2");
247	1	assertFalse(sf1.equals(sf2));
248	1	sf1.setPhase(restores);
249
250		// restore equality as sanity check:
251	1	assertTrue(sf1.equals(sf2));
252	1	assertTrue(sf2.equals(sf1));
253	1	assertEquals(sf1.hashCode(), sf2.hashCode());
254
255		// changing status doesn't change equals:
256	1	sf1.setStatus("new");
257	1	assertTrue(sf1.equals(sf2));
258		}
259
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
260	1	@Test(groups = { "Functional" })...
261		public void testIsContactFeature()
262		{
263	1	SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
264		"group");
265	1	assertFalse(sf.isContactFeature());
266	1	sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group");
267	1	assertFalse(sf.isContactFeature());
268	1	sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group");
269	1	assertFalse(sf.isContactFeature());
270	1	sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f,
271		"group");
272	1	assertTrue(sf.isContactFeature());
273	1	sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f,
274		"group");
275	1	assertTrue(sf.isContactFeature());
276	1	sf = new SequenceFeature("Disulphide Bond", "desc", 22, 33, 12.5f,
277		"group");
278	1	assertTrue(sf.isContactFeature());
279	1	sf = new SequenceFeature("disulphide bond", "desc", 22, 33, 12.5f,
280		"group");
281	1	assertTrue(sf.isContactFeature());
282		}
283
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
284	1	@Test(groups = { "Functional" })...
285		public void testGetDetailsReport()
286		{
287	1	SequenceI seq = new Sequence("TestSeq", "PLRFQMD");
288	1	String seqName = seq.getName();
289
290		// single locus, no group, no score
291	1	SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22,
292		null);
293	1	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	1	assertEquals(expected, sf.getDetailsReport(seqName, null));
297
298		// contact feature
299	1	sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
300		null);
301	1	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	1	assertEquals(expected, sf.getDetailsReport(seqName, null));
305
306	1	sf = new SequenceFeature("variant", "G,C", 22, 33, 12.5f, "group");
307	1	sf.setValue("Parent", "ENSG001");
308	1	sf.setValue("Child", "ENSP002");
309	1	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	1	assertEquals(expected, sf.getDetailsReport(seqName, null));
317
318		/*
319		* feature with embedded html link in description
320		*/
321	1	String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>";
322	1	sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
323	1	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	1	assertEquals(expected, sf.getDetailsReport(seqName, null));
328		}
329
330		/**
331		* Feature details report for a virtual feature should include original and
332		* mapped locations, and also derived peptide consequence if it can be
333		* determined
334		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
335	1	@Test(groups = { "Functional" })...
336		public void testGetDetailsReport_virtualFeature()
337		{
338	1	SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
339	1	SequenceI seq = new Sequence("TestSeq/8-14", "PLRFQMD");
340	1	MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
341		3, 1);
342	1	Mapping mapping = new Mapping(seq, map);
343	1	List<SequenceFeature> features = new ArrayList<>();
344		// vary ttg (Leu) to ttc (Phe)
345	1	SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
346		null);
347	1	sf.setValue("alleles", "G,C"); // needed to compute peptide consequence!
348	1	features.add(sf);
349
350	1	MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
351
352	1	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>";
358
359	1	assertEquals(expected, sf.getDetailsReport(seq.getName(), mf));
360
361		/*
362		* exon feature extending beyond mapped range; mapped location should be
363		* restricted to peptide mapped range limit i.e. 10-13
364		*/
365	1	SequenceFeature sf2 = new SequenceFeature("exon", "exon 1", 109, 230,
366		null);
367	1	features.add(sf2);
368	1	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>"
372		+ "</table>";
373	1	assertEquals(expected, sf2.getDetailsReport(seq.getName(), mf));
374		}
375		}