Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DBRefUtilsTest	42	121	9	1.0100%	Show methods

Class DBRefUtilsTest

Class DBRefUtilsTest	Line # 42	Total Statements 121	Complexity 9	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4545	2.02	1.01	1.0 1.0100%
testSelectRefs() : void   testSelectRefs() : void	5656	30.030	1.01	1.0 1.0100%
testGetCanonicalName() : void   testGetCanonicalName() : void	102102	12.012	1.01	1.0 1.0100%
testParseToDbRef() : void   testParseToDbRef() : void	127127	12.012	1.01	1.0 1.0100%
testParseToDbRef_PDB() : void   testParseToDbRef_PDB() : void	149149	14.014	1.01	1.0 1.0100%
testSearchRefs_noMapping() : void   testSearchRefs_noMapping() : void	177177	12.012	1.01	1.0 1.0100%
testSearchRefs_withMapping() : void   testSearchRefs_withMapping() : void	206206	14.014	1.01	1.0 1.0100%
testSearchRefs_accessionid() : void   testSearchRefs_accessionid() : void	239239	12.012	1.01	1.0 1.0100%
testSearchRefs_wildcardAccessionid() : void   testSearchRefs_wildcardAccessionid() : void	266266	13.013	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.23846154	jalview.util.DBRefUtilsTest.testSelectRefsjalview.util.DBRefUtilsTest.testSelectRefs	1PASS
	0.115384616	jalview.util.DBRefUtilsTest.testSearchRefs_withMappingjalview.util.DBRefUtilsTest.testSearchRefs_withMapping	1PASS
	0.115384616	jalview.util.DBRefUtilsTest.testParseToDbRef_PDBjalview.util.DBRefUtilsTest.testParseToDbRef_PDB	1PASS
	0.10769231	jalview.util.DBRefUtilsTest.testSearchRefs_wildcardAccessionidjalview.util.DBRefUtilsTest.testSearchRefs_wildcardAccessionid	1PASS
	0.1	jalview.util.DBRefUtilsTest.testParseToDbRefjalview.util.DBRefUtilsTest.testParseToDbRef	1PASS
	0.1	jalview.util.DBRefUtilsTest.testGetCanonicalNamejalview.util.DBRefUtilsTest.testGetCanonicalName	1PASS
	0.1	jalview.util.DBRefUtilsTest.testSearchRefs_noMappingjalview.util.DBRefUtilsTest.testSearchRefs_noMapping	1PASS
	0.1	jalview.util.DBRefUtilsTest.testSearchRefs_accessionidjalview.util.DBRefUtilsTest.testSearchRefs_accessionid	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.assertNull;
25		import static org.testng.AssertJUnit.assertSame;
26		import static org.testng.AssertJUnit.assertTrue;
27
28		import jalview.datamodel.DBRefEntry;
29		import jalview.datamodel.DBRefSource;
30		import jalview.datamodel.Mapping;
31		import jalview.datamodel.PDBEntry;
32		import jalview.datamodel.Sequence;
33		import jalview.datamodel.SequenceI;
34		import jalview.gui.JvOptionPane;
35
36		import java.util.Arrays;
37		import java.util.List;
38
39		import org.testng.annotations.BeforeClass;
40		import org.testng.annotations.Test;
41
		100% Uncovered Elements: 0 (130) Complexity: 9 Complexity Density: 0.07
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	List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3 });
67	1	String[] sources = new String[] { "EMBL", "UNIPROT" };
68
69	1	List<DBRefEntry> selected = DBRefUtils.selectRefs(dbrefs, sources);
70	1	assertEquals(3, selected.size());
71	1	assertSame(ref1, selected.get(0));
72	1	assertSame(ref2, selected.get(1));
73	1	assertSame(ref3, selected.get(2));
74
75	1	sources = new String[] { "EMBL" };
76	1	selected = DBRefUtils.selectRefs(dbrefs, sources);
77	1	assertEquals(1, selected.size());
78	1	assertSame(ref1, selected.get(0));
79
80	1	sources = new String[] { "UNIPROT" };
81	1	selected = DBRefUtils.selectRefs(dbrefs, sources);
82	1	assertEquals(2, selected.size());
83	1	assertSame(ref2, selected.get(0));
84	1	assertSame(ref3, selected.get(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.size());
93	1	assertSame(ref1, selected.get(0));
94	1	assertSame(ref2, selected.get(1));
95	1	assertSame(ref3, selected.get(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		/**
125		* Test 'parsing' a DBRef - non PDB case
126		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
127	1	@Test(groups = { "Functional" })...
128		public void testParseToDbRef()
129		{
130	1	SequenceI seq = new Sequence("Seq1", "ABCD");
131	1	DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
132	1	List<DBRefEntry> refs = seq.getDBRefs();
133	1	assertEquals(1, refs.size());
134	1	assertSame(ref, refs.get(0));
135	1	assertEquals("EMBL", ref.getSource());
136	1	assertEquals("1.2", ref.getVersion());
137	1	assertEquals("a7890", ref.getAccessionId());
138	1	assertTrue(seq.getAllPDBEntries().isEmpty());
139	1	SequenceI seq2 = new Sequence("Seq2", "ABCD");
140		// Check that whitespace doesn't confuse parseToDbRef
141	1	DBRefEntry ref2 = DBRefUtils.parseToDbRef(seq2, "EMBL", "1.2",
142		" a7890");
143	1	assertEquals(ref, ref2);
144		}
145
146		/**
147		* Test 'parsing' a DBRef - Stockholm PDB format
148		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
149	1	@Test(groups = { "Functional" })...
150		public void testParseToDbRef_PDB()
151		{
152	1	SequenceI seq = new Sequence("Seq1", "ABCD");
153	1	DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
154		"1WRI A; 7-80;");
155		// TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
156		// PDB ref in Stockholm
157
158	1	List<DBRefEntry> refs = seq.getDBRefs();
159	1	assertEquals(1, refs.size());
160	1	assertSame(ref, refs.get(0));
161	1	assertEquals("PDB", ref.getSource());
162	1	assertEquals("1.2", ref.getVersion());
163		// DBRef id is pdbId + chain code
164	1	assertEquals("1WRIA", ref.getAccessionId());
165	1	assertEquals(1, seq.getAllPDBEntries().size());
166	1	PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
167	1	assertEquals("1WRI", pdbRef.getId());
168	1	assertNull(pdbRef.getFile());
169	1	assertEquals("A", pdbRef.getChainCode());
170	1	assertEquals("PDB", pdbRef.getType());
171		}
172
173		/**
174		* Test the method that searches for matches references - case when we are
175		* matching a reference with no mappings
176		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
177	1	@Test(groups = { "Functional" })...
178		public void testSearchRefs_noMapping()
179		{
180	1	DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
181
182	1	DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
183		// constructor changes embl to EMBL
184	1	DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
185		// constructor does not upper-case accession id
186	1	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
187	1	DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
188		// ref5 matches although it has a mapping - ignored
189	1	DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
190	1	ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
191		1 }, 1, 1)));
192
193	1	List<DBRefEntry> matches = DBRefUtils.searchRefs(
194		Arrays.asList(new DBRefEntry[] {
195		ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
196	1	assertEquals(3, matches.size());
197	1	assertSame(ref1, matches.get(0));
198	1	assertSame(ref2, matches.get(1));
199	1	assertSame(ref5, matches.get(2));
200		}
201
202		/**
203		* Test the method that searches for matches references - case when we are
204		* matching a reference with a mapping
205		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
206	1	@Test(groups = { "Functional" })...
207		public void testSearchRefs_withMapping()
208		{
209	1	DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
210	1	final Mapping map1 = new Mapping(new MapList(new int[] { 1, 1 },
211		new int[] { 1, 1 }, 1, 1));
212	1	target.setMap(map1);
213
214		// these all match target iff mappings match
215	1	DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
216	1	DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
217	1	final Mapping map2 = new Mapping(new MapList(new int[] { 1, 1 },
218		new int[] { 1, 1 }, 1, 1));
219	1	ref2.setMap(map2);
220
221		// different map: no match
222	1	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
223	1	final Mapping map3 = new Mapping(new MapList(new int[] { 1, 1 },
224		new int[] { 1, 1 }, 2, 2));
225	1	ref3.setMap(map3);
226
227	1	List<DBRefEntry> matches = DBRefUtils.searchRefs(
228		Arrays.asList(new DBRefEntry[] {
229		ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
230	1	assertEquals(2, matches.size());
231	1	assertSame(ref1, matches.get(0));
232	1	assertSame(ref2, matches.get(1));
233		}
234
235		/**
236		* Test the method that searches for matching references based on accession id
237		* only
238		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
239	1	@Test(groups = { "Functional" })...
240		public void testSearchRefs_accessionid()
241		{
242
243	1	DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
244	1	DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
245		// constructor does not upper-case accession id
246	1	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
247	1	DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
248		// ref5 matches although it has a mapping - ignored
249	1	DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
250	1	ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
251		1 }, 1, 1)));
252
253	1	List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] {
254		ref1, ref2, ref3, ref4, ref5 });
255	1	List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
256	1	assertEquals(3, matches.size());
257	1	assertSame(ref1, matches.get(0));
258	1	assertSame(ref2, matches.get(1));
259	1	assertSame(ref5, matches.get(2));
260		}
261
262		/**
263		* Test the method that searches for matches references - case when we are
264		* matching a reference with null (any) accession id
265		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
266	1	@Test(groups = { "Functional" })...
267		public void testSearchRefs_wildcardAccessionid()
268		{
269	1	DBRefEntry target = new DBRefEntry("EMBL", "2", null);
270
271	1	DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
272		// constructor changes embl to EMBL
273	1	DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
274		// constructor does not upper-case accession id
275	1	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
276	1	DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
277		// ref5 matches although it has a mapping - ignored
278	1	DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
279	1	ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
280		1 }, 1, 1)));
281
282	1	List<DBRefEntry> matches = DBRefUtils.searchRefs(
283		Arrays.asList(new DBRefEntry[] {
284		ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
285	1	assertEquals(4, matches.size());
286	1	assertSame(ref1, matches.get(0));
287	1	assertSame(ref2, matches.get(1));
288	1	assertSame(ref3, matches.get(2));
289	1	assertSame(ref5, matches.get(3));
290		}
291		}