Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
UniprotTest	46	127	6	1.0100%	Show methods

Class UniprotTest

Class UniprotTest	Line # 46	Total Statements 127	Complexity 6	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4949	2.02	1.01	1.0 1.0100%
testGetUniprotEntries() : void   testGetUniprotEntries() : void	8585	85.085	1.01	1.0 1.0100%
testGetUniprotSequence() : void   testGetUniprotSequence() : void	210210	6.06	1.01	1.0 1.0100%
testGetUniprotEntryId() : void   testGetUniprotEntryId() : void	228228	4.04	1.01	1.0 1.0100%
testGetUniprotEntryDescription() : void   testGetUniprotEntryDescription() : void	247247	3.03	1.01	1.0 1.0100%
testGetDescription() : void   testGetDescription() : void	258258	27.027	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.6466165	jalview.ws.dbsources.UniprotTest.testGetUniprotEntriesjalview.ws.dbsources.UniprotTest.testGetUniprotEntries	1PASS
	0.21052632	jalview.ws.dbsources.UniprotTest.testGetDescriptionjalview.ws.dbsources.UniprotTest.testGetDescription	1PASS
	0.05263158	jalview.ws.dbsources.UniprotTest.testGetUniprotSequencejalview.ws.dbsources.UniprotTest.testGetUniprotSequence	1PASS
	0.037593983	jalview.ws.dbsources.UniprotTest.testGetUniprotEntryIdjalview.ws.dbsources.UniprotTest.testGetUniprotEntryId	1PASS
	0.030075189	jalview.ws.dbsources.UniprotTest.testGetUniprotEntryDescriptionjalview.ws.dbsources.UniprotTest.testGetUniprotEntryDescription	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.ws.dbsources;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNotNull;
25		import static org.testng.AssertJUnit.assertNull;
26		import static org.testng.AssertJUnit.assertTrue;
27
28		import jalview.datamodel.SequenceI;
29		import jalview.gui.JvOptionPane;
30		import jalview.xml.binding.uniprot.DbReferenceType;
31		import jalview.xml.binding.uniprot.Entry;
32		import jalview.xml.binding.uniprot.FeatureType;
33		import jalview.xml.binding.uniprot.LocationType;
34		import jalview.xml.binding.uniprot.PositionType;
35
36		import java.io.ByteArrayInputStream;
37		import java.io.InputStream;
38		import java.io.UnsupportedEncodingException;
39		import java.math.BigInteger;
40		import java.util.List;
41
42		import org.testng.Assert;
43		import org.testng.annotations.BeforeClass;
44		import org.testng.annotations.Test;
45
		100% Uncovered Elements: 0 (133) Complexity: 6 Complexity Density: 0.05
46		public class UniprotTest
47		{
48
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
49	1	@BeforeClass(alwaysRun = true)...
50		public void setUpJvOptionPane()
51		{
52	1	JvOptionPane.setInteractiveMode(false);
53	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54		}
55
56		// adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
57		private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
58		+ "<uniprot xmlns=\"http://uniprot.org/uniprot\">"
59		+ "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
60		+ "<accession>A9CKP4</accession>"
61		+ "<accession>A9CKP5</accession>"
62		+ "<name>A9CKP4_AGRT5</name>"
63		+ "<name>A9CKP4_AGRT6</name>"
64		+ "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName></recommendedName></protein>"
65		+ "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
66		+ "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
67		+ "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
68		+ "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
69		+ "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
70		+ "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
71		+ "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
72		+ "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
73		+ "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
74		+ "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
75		+ "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
76		+ "<feature type=\"sequence variant\" description=\"Foo Too\"><variation>LL</variation><variation>LMVK</variation><original>MLML</original><location><begin position=\"42\"/><end position=\"45\"/></location></feature>"
77		+ "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
78		+ "</uniprot>";
79
80		/**
81		* Test the method that unmarshals XML to a Uniprot model
82		*
83		* @throws UnsupportedEncodingException
84		*/
		100% Uncovered Elements: 0 (85) Complexity: 1 Complexity Density: 0.01 1PASS
85	1	@Test(groups = { "Functional" })...
86		public void testGetUniprotEntries() throws UnsupportedEncodingException
87		{
88	1	Uniprot u = new Uniprot();
89	1	InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
90	1	List<Entry> entries = u.getUniprotEntries(is);
91	1	assertEquals(1, entries.size());
92	1	Entry entry = entries.get(0);
93	1	assertEquals(2, entry.getName().size());
94	1	assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
95	1	assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
96	1	assertEquals(2, entry.getAccession().size());
97	1	assertEquals("A9CKP4", entry.getAccession().get(0));
98	1	assertEquals("A9CKP5", entry.getAccession().get(1));
99
100	1	assertEquals("MHAPL VSKDL", entry.getSequence().getValue());
101
102	1	assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
103		.getRecommendedName().getFullName().getValue());
104
105		/*
106		* Check sequence features
107		*/
108	1	List<FeatureType> features = entry.getFeature();
109	1	assertEquals(9, features.size());
110	1	FeatureType sf = features.get(0);
111	1	assertEquals("signal peptide", sf.getType());
112	1	assertNull(sf.getDescription());
113	1	assertNull(sf.getStatus());
114	1	assertNull(sf.getLocation().getPosition());
115	1	assertEquals(1, sf.getLocation().getBegin().getPosition().intValue());
116	1	assertEquals(18, sf.getLocation().getEnd().getPosition().intValue());
117	1	sf = features.get(1);
118	1	assertEquals("propeptide", sf.getType());
119	1	assertEquals("Activation peptide", sf.getDescription());
120	1	assertNull(sf.getLocation().getPosition());
121	1	assertEquals(19, sf.getLocation().getBegin().getPosition().intValue());
122	1	assertEquals(20, sf.getLocation().getEnd().getPosition().intValue());
123	1	sf = features.get(2);
124	1	assertEquals("chain", sf.getType());
125	1	assertEquals("Granzyme B", sf.getDescription());
126	1	assertNull(sf.getLocation().getPosition());
127	1	assertEquals(21, sf.getLocation().getBegin().getPosition().intValue());
128	1	assertEquals(247, sf.getLocation().getEnd().getPosition().intValue());
129
130	1	sf = features.get(3);
131	1	assertEquals("sequence variant", sf.getType());
132	1	assertNull(sf.getDescription());
133	1	assertEquals(41,
134		sf.getLocation().getPosition().getPosition().intValue());
135	1	assertNull(sf.getLocation().getBegin());
136	1	assertNull(sf.getLocation().getEnd());
137
138	1	sf = features.get(4);
139	1	assertEquals("sequence variant", sf.getType());
140	1	assertEquals("Pathogenic", sf.getDescription());
141	1	assertEquals(41,
142		sf.getLocation().getPosition().getPosition().intValue());
143	1	assertNull(sf.getLocation().getBegin());
144	1	assertNull(sf.getLocation().getEnd());
145
146	1	sf = features.get(5);
147	1	assertEquals("sequence variant", sf.getType());
148	1	assertEquals("Pathogenic", sf.getDescription());
149	1	assertEquals(41,
150		sf.getLocation().getPosition().getPosition().intValue());
151	1	assertNull(sf.getLocation().getBegin());
152	1	assertNull(sf.getLocation().getEnd());
153
154	1	sf = features.get(6);
155	1	assertEquals("sequence variant", sf.getType());
156	1	assertEquals("Foo",
157		sf.getDescription());
158	1	assertEquals(42,
159		sf.getLocation().getPosition().getPosition().intValue());
160	1	assertNull(sf.getLocation().getBegin());
161	1	assertNull(sf.getLocation().getEnd());
162	1	Assert.assertEquals(Uniprot.getDescription(sf),
163		"<html>p.Met42Leu" + "<br/>&nbsp;&nbsp;"
164		+ "p.Met42LeuMetVal Foo</html>");
165
166	1	sf = features.get(7);
167	1	assertNull(sf.getLocation().getPosition());
168	1	assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
169	1	assertEquals(43, sf.getLocation().getEnd().getPosition().intValue());
170	1	Assert.assertEquals(Uniprot.getDescription(sf),
171		"<html>p.MetLeu42LeuLeu" + "<br/>&nbsp;&nbsp;"
172		+ "p.MetLeu42LeuMetVal Foo</html>");
173
174	1	sf = features.get(8);
175	1	assertNull(sf.getLocation().getPosition());
176	1	assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
177	1	assertEquals(45, sf.getLocation().getEnd().getPosition().intValue());
178	1	Assert.assertEquals(Uniprot.getDescription(sf),
179		"<html>p.MLML42LeuLeu" + "<br/>&nbsp;&nbsp;"
180		+ "p.MLML42LMVK Foo Too</html>");
181
182		/*
183		* Check cross-references
184		*/
185	1	List<DbReferenceType> xrefs = entry.getDbReference();
186	1	assertEquals(3, xrefs.size());
187
188	1	DbReferenceType xref = xrefs.get(0);
189	1	assertEquals("2FSQ", xref.getId());
190	1	assertEquals("PDB", xref.getType());
191	1	assertEquals("X-ray",
192		Uniprot.getProperty(xref.getProperty(), "method"));
193	1	assertEquals("1.40",
194		Uniprot.getProperty(xref.getProperty(), "resolution"));
195
196	1	xref = xrefs.get(1);
197	1	assertEquals("2FSR", xref.getId());
198	1	assertEquals("PDBsum", xref.getType());
199	1	assertTrue(xref.getProperty().isEmpty());
200
201	1	xref = xrefs.get(2);
202	1	assertEquals("AE007869", xref.getId());
203	1	assertEquals("EMBL", xref.getType());
204	1	assertEquals("AAK85932.1",
205		Uniprot.getProperty(xref.getProperty(), "protein sequence ID"));
206	1	assertEquals("Genomic_DNA",
207		Uniprot.getProperty(xref.getProperty(), "molecule type"));
208		}
209
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
210	1	@Test(groups = { "Functional" })...
211		public void testGetUniprotSequence() throws UnsupportedEncodingException
212		{
213	1	InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
214	1	Entry entry = new Uniprot().getUniprotEntries(
215		is).get(0);
216	1	SequenceI seq = new Uniprot().uniprotEntryToSequence(entry);
217	1	assertNotNull(seq);
218	1	assertEquals(6, seq.getDBRefs().size()); // 2*Uniprot, PDB, PDBsum, 2*EMBL
219	1	assertEquals(seq.getSequenceAsString(),
220		seq.createDatasetSequence().getSequenceAsString());
221		}
222
223		/**
224		* Test the method that formats the sequence id
225		*
226		* @throws UnsupportedEncodingException
227		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
228	1	@Test(groups = { "Functional" })...
229		public void testGetUniprotEntryId() throws UnsupportedEncodingException
230		{
231	1	InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
232	1	Entry entry = new Uniprot().getUniprotEntries(is).get(0);
233
234		/*
235		* name formatted with Uniprot Entry name
236		*/
237	1	String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
238	1	assertEquals(expectedName,
239		Uniprot.getUniprotEntryId(entry));
240		}
241
242		/**
243		* Test the method that formats the sequence description
244		*
245		* @throws UnsupportedEncodingException
246		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
247	1	@Test(groups = { "Functional" })...
248		public void testGetUniprotEntryDescription()
249		throws UnsupportedEncodingException
250		{
251	1	InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
252	1	Entry entry = new Uniprot().getUniprotEntries(is).get(0);
253
254	1	assertEquals("Mitogen-activated protein kinase 13",
255		Uniprot.getUniprotEntryDescription(entry));
256		}
257
		100% Uncovered Elements: 0 (27) Complexity: 1 Complexity Density: 0.04 1PASS
258	1	@Test(groups = { "Functional" })...
259		public void testGetDescription()
260		{
261	1	FeatureType ft = new FeatureType();
262	1	assertEquals("", Uniprot.getDescription(ft));
263
264	1	ft.setDescription("Hello");
265	1	assertEquals("Hello", Uniprot.getDescription(ft));
266
267	1	ft.setLocation(new LocationType());
268	1	ft.getLocation().setPosition(new PositionType());
269	1	ft.getLocation().getPosition().setPosition(BigInteger.valueOf(23));
270	1	ft.setOriginal("K");
271	1	ft.getVariation().add("y");
272	1	assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(ft));
273
274		// multiple variants generate an html description over more than one line
275	1	ft.getVariation().add("W");
276	1	assertEquals("<html>p.Lys23Tyr<br/>&nbsp;&nbsp;p.Lys23Trp Hello</html>",
277		Uniprot.getDescription(ft));
278
279		/*
280		* indel cases
281		* up to 3 bases (original or variant) are shown using 3 letter code
282		*/
283	1	ft.getVariation().clear();
284	1	ft.getVariation().add("KWE");
285	1	ft.setOriginal("KLS");
286	1	assertEquals("p.LysLeuSer23LysTrpGlu Hello",
287		Uniprot.getDescription(ft));
288
289		// adding a fourth original base switches to single letter code
290	1	ft.setOriginal("KLST");
291	1	assertEquals("p.KLST23LysTrpGlu Hello", Uniprot.getDescription(ft));
292
293		// adding a fourth variant switches to single letter code
294	1	ft.getVariation().clear();
295	1	ft.getVariation().add("KWES");
296	1	assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(ft));
297
298	1	ft.getVariation().clear();
299	1	ft.getVariation().add("z"); // unknown variant - fails gracefully
300	1	ft.setOriginal("K");
301	1	assertEquals("p.Lys23z Hello", Uniprot.getDescription(ft));
302
303	1	ft.getVariation().clear(); // variant missing - is ignored
304	1	assertEquals("Hello", Uniprot.getDescription(ft));
305		}
306		}