Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
DBRefUtilsTest	42	130	10	0	1.0100%	Show methods

Class DBRefUtilsTest

Class DBRefUtilsTest	Line # 42	Total Statements 130	Complexity 10	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4545	2.02	1.01	0.00	1.0 1.0100%
testSelectRefs() : void   testSelectRefs() : void	5656	30.030	1.01	0.00	1.0 1.0100%
testGetCanonicalName() : void   testGetCanonicalName() : void	102102	12.012	1.01	0.00	1.0 1.0100%
testIsDasCoordinateSystem() : void   testIsDasCoordinateSystem() : void	125125	12.012	1.01	0.00	1.0 1.0100%
testParseToDbRef() : void   testParseToDbRef() : void	159159	9.09	1.01	0.00	1.0 1.0100%
testParseToDbRef_PDB() : void   testParseToDbRef_PDB() : void	176176	14.014	1.01	0.00	1.0 1.0100%
testSearchRefs_noMapping() : void   testSearchRefs_noMapping() : void	204204	12.012	1.01	0.00	1.0 1.0100%
testSearchRefs_withMapping() : void   testSearchRefs_withMapping() : void	232232	14.014	1.01	0.00	1.0 1.0100%
testSearchRefs_accessionid() : void   testSearchRefs_accessionid() : void	264264	12.012	1.01	0.00	1.0 1.0100%
testSearchRefs_wildcardAccessionid() : void   testSearchRefs_wildcardAccessionid() : void	290290	13.013	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.22142857	jalview.util.DBRefUtilsTest.testSelectRefsjalview.util.DBRefUtilsTest.testSelectRefs	1PASS
	0.10714286	jalview.util.DBRefUtilsTest.testParseToDbRef_PDBjalview.util.DBRefUtilsTest.testParseToDbRef_PDB	1PASS
	0.10714286	jalview.util.DBRefUtilsTest.testSearchRefs_withMappingjalview.util.DBRefUtilsTest.testSearchRefs_withMapping	1PASS
	0.1	jalview.util.DBRefUtilsTest.testSearchRefs_wildcardAccessionidjalview.util.DBRefUtilsTest.testSearchRefs_wildcardAccessionid	1PASS
	0.092857145	jalview.util.DBRefUtilsTest.testIsDasCoordinateSystemjalview.util.DBRefUtilsTest.testIsDasCoordinateSystem	1PASS
	0.092857145	jalview.util.DBRefUtilsTest.testSearchRefs_noMappingjalview.util.DBRefUtilsTest.testSearchRefs_noMapping	1PASS
	0.092857145	jalview.util.DBRefUtilsTest.testSearchRefs_accessionidjalview.util.DBRefUtilsTest.testSearchRefs_accessionid	1PASS
	0.092857145	jalview.util.DBRefUtilsTest.testGetCanonicalNamejalview.util.DBRefUtilsTest.testGetCanonicalName	1PASS
	0.071428575	jalview.util.DBRefUtilsTest.testParseToDbRefjalview.util.DBRefUtilsTest.testParseToDbRef	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.util;
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.datamodel.DBRefEntry;
30		import jalview.datamodel.DBRefSource;
31		import jalview.datamodel.Mapping;
32		import jalview.datamodel.PDBEntry;
33		import jalview.datamodel.Sequence;
34		import jalview.datamodel.SequenceI;
35		import jalview.gui.JvOptionPane;
36
37		import java.util.List;
38
39		import org.testng.annotations.BeforeClass;
40		import org.testng.annotations.Test;
41
		100% Uncovered Elements: 0 (140) Complexity: 10 Complexity Density: 0.08
42		public class DBRefUtilsTest
43		{
44
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
45	1	@BeforeClass(alwaysRun = true)...
46		public void setUpJvOptionPane()
47		{
48	1	JvOptionPane.setInteractiveMode(false);
49	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50		}
51
52		/**
53		* Test the method that selects DBRefEntry items whose source is in a supplied
54		* list
55		*/
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
56	1	@Test(groups = { "Functional" })...
57		public void testSelectRefs()
58		{
59	1	assertNull(DBRefUtils.selectRefs(null, null));
60	1	assertNull(DBRefUtils.selectRefs(null, DBRefSource.CODINGDBS));
61
62	1	DBRefEntry ref1 = new DBRefEntry("EMBL", "1.2", "A12345");
63	1	DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
64		// Source is converted to upper-case by this constructor!
65	1	DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
66	1	DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3 };
67	1	String[] sources = new String[] { "EMBL", "UNIPROT" };
68
69	1	DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources);
70	1	assertEquals(3, selected.length);
71	1	assertSame(ref1, selected[0]);
72	1	assertSame(ref2, selected[1]);
73	1	assertSame(ref3, selected[2]);
74
75	1	sources = new String[] { "EMBL" };
76	1	selected = DBRefUtils.selectRefs(dbrefs, sources);
77	1	assertEquals(1, selected.length);
78	1	assertSame(ref1, selected[0]);
79
80	1	sources = new String[] { "UNIPROT" };
81	1	selected = DBRefUtils.selectRefs(dbrefs, sources);
82	1	assertEquals(2, selected.length);
83	1	assertSame(ref2, selected[0]);
84	1	assertSame(ref3, selected[1]);
85
86	1	sources = new String[] { "EMBLCDS" };
87	1	selected = DBRefUtils.selectRefs(dbrefs, sources);
88	1	assertNull(selected);
89
90	1	sources = new String[] { "embl", "uniprot" };
91	1	selected = DBRefUtils.selectRefs(dbrefs, sources);
92	1	assertEquals(3, selected.length);
93	1	assertSame(ref1, selected[0]);
94	1	assertSame(ref2, selected[1]);
95	1	assertSame(ref3, selected[2]);
96		}
97
98		/**
99		* Test the method that converts (currently three) database names to a
100		* canonical name (not case-sensitive)
101		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
102	1	@Test(groups = { "Functional" })...
103		public void testGetCanonicalName()
104		{
105	1	assertNull(DBRefUtils.getCanonicalName(null));
106	1	assertEquals("", DBRefUtils.getCanonicalName(""));
107	1	assertEquals("PDB", DBRefUtils.getCanonicalName("pdb"));
108	1	assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
109	1	assertEquals("UNIPROT",
110		DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
111	1	assertEquals("UNIPROT", DBRefUtils.getCanonicalName("uniprotkb/trembl"));
112	1	assertEquals("UNIPROT",
113		DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
114	1	assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
115	1	assertEquals("UNIPROTKB/SWISS-CHEESE",
116		DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
117	1	assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
118
119		// these are not 'known' to Jalview
120	1	assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
121	1	assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
122
123		}
124
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
125	1	@Test(groups = { "Functional" })...
126		public void testIsDasCoordinateSystem()
127		{
128	1	assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
129	1	assertFalse(DBRefUtils.isDasCoordinateSystem("pdbresnum", null));
130	1	assertFalse(DBRefUtils.isDasCoordinateSystem(null, new DBRefEntry(
131		"PDB", "v1", "a1")));
132
133	1	assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
134		new DBRefEntry("PDB", "v1", "a1")));
135	1	assertTrue(DBRefUtils.isDasCoordinateSystem("PDBRESNUM",
136		new DBRefEntry("PDB", "v1", "a1")));
137		// "pdb" is converted to upper-case in DBRefEntry constructor
138	1	assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
139		new DBRefEntry("pdb", "v1", "a1")));
140	1	assertFalse(DBRefUtils.isDasCoordinateSystem("pdb", new DBRefEntry(
141		"pdb", "v1", "a1")));
142
143	1	assertTrue(DBRefUtils.isDasCoordinateSystem("UNIPROT", new DBRefEntry(
144		"Uniprot", "v1", "a1")));
145	1	assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
146		"UNIPROT", "v1", "a1")));
147	1	assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
148		new DBRefEntry("pdb", "v1", "a1")));
149
150	1	assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
151		"EMBL", "v1", "a1")));
152	1	assertTrue(DBRefUtils.isDasCoordinateSystem("embl", new DBRefEntry(
153		"embl", "v1", "a1")));
154		}
155
156		/**
157		* Test 'parsing' a DBRef - non PDB case
158		*/
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
159	1	@Test(groups = { "Functional" })...
160		public void testParseToDbRef()
161		{
162	1	SequenceI seq = new Sequence("Seq1", "ABCD");
163	1	DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
164	1	DBRefEntry[] refs = seq.getDBRefs();
165	1	assertEquals(1, refs.length);
166	1	assertSame(ref, refs[0]);
167	1	assertEquals("EMBL", ref.getSource());
168	1	assertEquals("1.2", ref.getVersion());
169	1	assertEquals("a7890", ref.getAccessionId());
170	1	assertTrue(seq.getAllPDBEntries().isEmpty());
171		}
172
173		/**
174		* Test 'parsing' a DBRef - Stockholm PDB format
175		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
176	1	@Test(groups = { "Functional" })...
177		public void testParseToDbRef_PDB()
178		{
179	1	SequenceI seq = new Sequence("Seq1", "ABCD");
180	1	DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
181		"1WRI A; 7-80;");
182		// TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
183		// PDB ref in Stockholm
184
185	1	DBRefEntry[] refs = seq.getDBRefs();
186	1	assertEquals(1, refs.length);
187	1	assertSame(ref, refs[0]);
188	1	assertEquals("PDB", ref.getSource());
189	1	assertEquals("1.2", ref.getVersion());
190		// DBRef id is pdbId + chain code
191	1	assertEquals("1WRIA", ref.getAccessionId());
192	1	assertEquals(1, seq.getAllPDBEntries().size());
193	1	PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
194	1	assertEquals("1WRI", pdbRef.getId());
195	1	assertNull(pdbRef.getFile());
196	1	assertEquals("A", pdbRef.getChainCode());
197	1	assertEquals("PDB", pdbRef.getType());
198		}
199
200		/**
201		* Test the method that searches for matches references - case when we are
202		* matching a reference with no mappings
203		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
204	1	@Test(groups = { "Functional" })...
205		public void testSearchRefs_noMapping()
206		{
207	1	DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
208
209	1	DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
210		// constructor changes embl to EMBL
211	1	DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
212		// constructor does not upper-case accession id
213	1	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
214	1	DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
215		// ref5 matches although it has a mapping - ignored
216	1	DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
217	1	ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
218		1 }, 1, 1)));
219
220	1	List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
221		ref1, ref2, ref3, ref4, ref5 }, target);
222	1	assertEquals(3, matches.size());
223	1	assertSame(ref1, matches.get(0));
224	1	assertSame(ref2, matches.get(1));
225	1	assertSame(ref5, matches.get(2));
226		}
227
228		/**
229		* Test the method that searches for matches references - case when we are
230		* matching a reference with a mapping
231		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
232	1	@Test(groups = { "Functional" })...
233		public void testSearchRefs_withMapping()
234		{
235	1	DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
236	1	final Mapping map1 = new Mapping(new MapList(new int[] { 1, 1 },
237		new int[] { 1, 1 }, 1, 1));
238	1	target.setMap(map1);
239
240		// these all match target iff mappings match
241	1	DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
242	1	DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
243	1	final Mapping map2 = new Mapping(new MapList(new int[] { 1, 1 },
244		new int[] { 1, 1 }, 1, 1));
245	1	ref2.setMap(map2);
246
247		// different map: no match
248	1	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
249	1	final Mapping map3 = new Mapping(new MapList(new int[] { 1, 1 },
250		new int[] { 1, 1 }, 2, 2));
251	1	ref3.setMap(map3);
252
253	1	List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
254		ref1, ref2, ref3 }, target);
255	1	assertEquals(2, matches.size());
256	1	assertSame(ref1, matches.get(0));
257	1	assertSame(ref2, matches.get(1));
258		}
259
260		/**
261		* Test the method that searches for matching references based on accession id
262		* only
263		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
264	1	@Test(groups = { "Functional" })...
265		public void testSearchRefs_accessionid()
266		{
267
268	1	DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
269	1	DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
270		// constructor does not upper-case accession id
271	1	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
272	1	DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
273		// ref5 matches although it has a mapping - ignored
274	1	DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
275	1	ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
276		1 }, 1, 1)));
277
278	1	DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5 };
279	1	List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
280	1	assertEquals(3, matches.size());
281	1	assertSame(ref1, matches.get(0));
282	1	assertSame(ref2, matches.get(1));
283	1	assertSame(ref5, matches.get(2));
284		}
285
286		/**
287		* Test the method that searches for matches references - case when we are
288		* matching a reference with null (any) accession id
289		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
290	1	@Test(groups = { "Functional" })...
291		public void testSearchRefs_wildcardAccessionid()
292		{
293	1	DBRefEntry target = new DBRefEntry("EMBL", "2", null);
294
295	1	DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
296		// constructor changes embl to EMBL
297	1	DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
298		// constructor does not upper-case accession id
299	1	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
300	1	DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
301		// ref5 matches although it has a mapping - ignored
302	1	DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
303	1	ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
304		1 }, 1, 1)));
305
306	1	List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
307		ref1, ref2, ref3, ref4, ref5 }, target);
308	1	assertEquals(4, matches.size());
309	1	assertSame(ref1, matches.get(0));
310	1	assertSame(ref2, matches.get(1));
311	1	assertSame(ref3, matches.get(2));
312	1	assertSame(ref5, matches.get(3));
313		}
314		}