Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
SequenceFeatureTest	34	150	8	1	0.993710799.4%	Show methods

Class SequenceFeatureTest

Class SequenceFeatureTest	Line # 34	Total Statements 150	Complexity 8	Uncovered Elements 1	TOTAL Coverage 0.993710799.4%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3737	2.02	1.01	0.00	1.0 1.0100%
testCopyConstructors() : void   testCopyConstructors() : void	4444	33.033	1.01	0.00	1.0 1.0100%
testGetValue() : void   testGetValue() : void	100100	7.07	1.01	0.00	1.0 1.0100%
testGetStrand() : void   testGetStrand() : void	116116	8.08	1.01	0.00	1.0 1.0100%
testEqualsAndHashCode() : void   testEqualsAndHashCode() : void	133133	71.071	2.02	1.01	0.98630136 0.9863013698.6%
testIsContactFeature() : void   testIsContactFeature() : void	253253	14.014	1.01	0.00	1.0 1.0100%
testGetDetailsReport() : void   testGetDetailsReport() : void	277277	15.015	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.4591195	jalview.datamodel.SequenceFeatureTest.testEqualsAndHashCodejalview.datamodel.SequenceFeatureTest.testEqualsAndHashCode	1PASS
	0.21383648	jalview.datamodel.SequenceFeatureTest.testCopyConstructorsjalview.datamodel.SequenceFeatureTest.testCopyConstructors	1PASS
	0.10062893	jalview.datamodel.SequenceFeatureTest.testGetDetailsReportjalview.datamodel.SequenceFeatureTest.testGetDetailsReport	1PASS
	0.094339624	jalview.datamodel.SequenceFeatureTest.testIsContactFeaturejalview.datamodel.SequenceFeatureTest.testIsContactFeature	1PASS
	0.056603774	jalview.datamodel.SequenceFeatureTest.testGetStrandjalview.datamodel.SequenceFeatureTest.testGetStrand	1PASS
	0.050314464	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 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		// shallow clone of otherDetails map - contains the same object values!
63	1	assertSame(count, sf2.getValue("Count"));
64
65		/*
66		* copy constructor modifying begin/end/group/score
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		// shallow clone of otherDetails map - contains the same object values!
77	1	assertSame(count, sf3.getValue("Count"));
78
79		/*
80		* copy constructor modifying type/begin/end/group/score
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		// shallow clone of otherDetails map - contains the same object values!
93	1	assertSame(count, sf4.getValue("Count"));
94		}
95
96		/**
97		* Tests for retrieving a 'miscellaneous details' property value, with or
98		* without a supplied default
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")); // case-sensitive
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		* Tests the method that returns 1 / -1 / 0 for strand "+" / "-" / other
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		* Tests for equality, and that equal objects have the same hashCode
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		// changing type breaks equals:
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		// changing description breaks equals:
164	1	String restores = sf2.getDescription();
165	1	sf2.setDescription("Desc");
166	1	assertFalse(sf1.equals(sf2));
167	1	sf2.setDescription(restores);
168
169		// changing score breaks equals:
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		// NaN doesn't match a number
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		// NaN matches NaN
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		// changing start position breaks equals:
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		// changing end position breaks equals:
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		// changing feature group breaks equals:
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		// changing ID breaks equals:
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		// changing Name breaks equals:
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		// changing Parent breaks equals:
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		// changing strand breaks equals:
232	1	restorei = sf2.getStrand();
233	1	sf2.setStrand("-");
234	1	assertFalse(sf1.equals(sf2));
235	1	sf2.setStrand(restorei == 1 ? "+" : "-");
236
237		// changing phase breaks equals:
238	1	restores = sf1.getPhase();
239	1	sf1.setPhase("2");
240	1	assertFalse(sf1.equals(sf2));
241	1	sf1.setPhase(restores);
242
243		// restore equality as sanity check:
244	1	assertTrue(sf1.equals(sf2));
245	1	assertTrue(sf2.equals(sf1));
246	1	assertEquals(sf1.hashCode(), sf2.hashCode());
247
248		// changing status doesn't change equals:
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		// single locus, no group, no score
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		// contact feature
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		* feature with embedded html link in description
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		}