Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DBRefUtilsTest	42	121	9	0.00%	Show methods

Class DBRefUtilsTest

Class DBRefUtilsTest	Line # 42	Total Statements 121	Complexity 9	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4545	2.02	1.01	0.0 0.00%
testSelectRefs() : void   testSelectRefs() : void	5656	30.030	1.01	0.0 0.00%
testGetCanonicalName() : void   testGetCanonicalName() : void	104104	12.012	1.01	0.0 0.00%
testParseToDbRef() : void   testParseToDbRef() : void	132132	12.012	1.01	0.0 0.00%
testParseToDbRef_PDB() : void   testParseToDbRef_PDB() : void	154154	14.014	1.01	0.0 0.00%
testSearchRefs_noMapping() : void   testSearchRefs_noMapping() : void	182182	12.012	1.01	0.0 0.00%
testSearchRefs_withMapping() : void   testSearchRefs_withMapping() : void	213213	14.014	1.01	0.0 0.00%
testSearchRefs_accessionid() : void   testSearchRefs_accessionid() : void	249249	12.012	1.01	0.0 0.00%
testSearchRefs_wildcardAccessionid() : void   testSearchRefs_wildcardAccessionid() : void	278278	13.013	1.01	0.0 0.00%

 

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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
		0% Uncovered Elements: 130 (130) Complexity: 9 Complexity Density: 0.07
42		public class DBRefUtilsTest
43		{
44
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
45	0	@BeforeClass(alwaysRun = true)...
46		public void setUpJvOptionPane()
47		{
48	0	JvOptionPane.setInteractiveMode(false);
49	0	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		*/
		0% Uncovered Elements: 30 (30) Complexity: 1 Complexity Density: 0.03 4-
56	0	@Test(groups = { "Functional" })...
57		public void testSelectRefs()
58		{
59	0	assertNull(DBRefUtils.selectRefs(null, null));
60	0	assertNull(DBRefUtils.selectRefs(null, DBRefSource.CODINGDBS));
61
62	0	DBRefEntry ref1 = new DBRefEntry("EMBL", "1.2", "A12345");
63	0	DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
64		// Source is converted to upper-case by this constructor!
65	0	DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
66	0	List<DBRefEntry> dbrefs = Arrays
67		.asList(new DBRefEntry[]
68		{ ref1, ref2, ref3 });
69	0	String[] sources = new String[] { "EMBL", "UNIPROT" };
70
71	0	List<DBRefEntry> selected = DBRefUtils.selectRefs(dbrefs, sources);
72	0	assertEquals(3, selected.size());
73	0	assertSame(ref1, selected.get(0));
74	0	assertSame(ref2, selected.get(1));
75	0	assertSame(ref3, selected.get(2));
76
77	0	sources = new String[] { "EMBL" };
78	0	selected = DBRefUtils.selectRefs(dbrefs, sources);
79	0	assertEquals(1, selected.size());
80	0	assertSame(ref1, selected.get(0));
81
82	0	sources = new String[] { "UNIPROT" };
83	0	selected = DBRefUtils.selectRefs(dbrefs, sources);
84	0	assertEquals(2, selected.size());
85	0	assertSame(ref2, selected.get(0));
86	0	assertSame(ref3, selected.get(1));
87
88	0	sources = new String[] { "EMBLCDS" };
89	0	selected = DBRefUtils.selectRefs(dbrefs, sources);
90	0	assertNull(selected);
91
92	0	sources = new String[] { "embl", "uniprot" };
93	0	selected = DBRefUtils.selectRefs(dbrefs, sources);
94	0	assertEquals(3, selected.size());
95	0	assertSame(ref1, selected.get(0));
96	0	assertSame(ref2, selected.get(1));
97	0	assertSame(ref3, selected.get(2));
98		}
99
100		/**
101		* Test the method that converts (currently three) database names to a
102		* canonical name (not case-sensitive)
103		*/
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08 4-
104	0	@Test(groups = { "Functional" })...
105		public void testGetCanonicalName()
106		{
107	0	assertNull(DBRefUtils.getCanonicalName(null));
108	0	assertEquals("", DBRefUtils.getCanonicalName(""));
109	0	assertEquals("PDB", DBRefUtils.getCanonicalName("pdb"));
110	0	assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
111	0	assertEquals("UNIPROT",
112		DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
113	0	assertEquals("UNIPROT",
114		DBRefUtils.getCanonicalName("uniprotkb/trembl"));
115	0	assertEquals("UNIPROT",
116		DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
117	0	assertEquals("UNIPROT",
118		DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
119	0	assertEquals("UNIPROTKB/SWISS-CHEESE",
120		DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
121	0	assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
122
123		// these are not 'known' to Jalview
124	0	assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
125	0	assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
126
127		}
128
129		/**
130		* Test 'parsing' a DBRef - non PDB case
131		*/
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08 4-
132	0	@Test(groups = { "Functional" })...
133		public void testParseToDbRef()
134		{
135	0	SequenceI seq = new Sequence("Seq1", "ABCD");
136	0	DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
137	0	List<DBRefEntry> refs = seq.getDBRefs();
138	0	assertEquals(1, refs.size());
139	0	assertSame(ref, refs.get(0));
140	0	assertEquals("EMBL", ref.getSource());
141	0	assertEquals("1.2", ref.getVersion());
142	0	assertEquals("a7890", ref.getAccessionId());
143	0	assertTrue(seq.getAllPDBEntries().isEmpty());
144	0	SequenceI seq2 = new Sequence("Seq2", "ABCD");
145		// Check that whitespace doesn't confuse parseToDbRef
146	0	DBRefEntry ref2 = DBRefUtils.parseToDbRef(seq2, "EMBL", "1.2",
147		" a7890");
148	0	assertEquals(ref, ref2);
149		}
150
151		/**
152		* Test 'parsing' a DBRef - Stockholm PDB format
153		*/
		0% Uncovered Elements: 14 (14) Complexity: 1 Complexity Density: 0.07 4-
154	0	@Test(groups = { "Functional" })...
155		public void testParseToDbRef_PDB()
156		{
157	0	SequenceI seq = new Sequence("Seq1", "ABCD");
158	0	DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
159		"1WRI A; 7-80;");
160		// TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
161		// PDB ref in Stockholm
162
163	0	List<DBRefEntry> refs = seq.getDBRefs();
164	0	assertEquals(1, refs.size());
165	0	assertSame(ref, refs.get(0));
166	0	assertEquals("PDB", ref.getSource());
167	0	assertEquals("1.2", ref.getVersion());
168		// DBRef id is pdbId + chain code
169	0	assertEquals("1WRIA", ref.getAccessionId());
170	0	assertEquals(1, seq.getAllPDBEntries().size());
171	0	PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
172	0	assertEquals("1WRI", pdbRef.getId());
173	0	assertNull(pdbRef.getFile());
174	0	assertEquals("A", pdbRef.getChainCode());
175	0	assertEquals("PDB", pdbRef.getType());
176		}
177
178		/**
179		* Test the method that searches for matches references - case when we are
180		* matching a reference with no mappings
181		*/
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08 4-
182	0	@Test(groups = { "Functional" })...
183		public void testSearchRefs_noMapping()
184		{
185	0	DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
186
187	0	DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
188		// constructor changes embl to EMBL
189	0	DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
190		// constructor does not upper-case accession id
191	0	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
192	0	DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
193		// ref5 matches although it has a mapping - ignored
194	0	DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
195	0	ref5.setMap(
196		new Mapping(new MapList(new int[]
197		{ 1, 1 }, new int[] { 1, 1 }, 1, 1)));
198
199	0	List<DBRefEntry> matches = DBRefUtils
200		.searchRefs(Arrays.asList(new DBRefEntry[]
201		{ ref1, ref2, ref3, ref4, ref5 }), target,
202		DBRefUtils.SEARCH_MODE_FULL);
203	0	assertEquals(3, matches.size());
204	0	assertSame(ref1, matches.get(0));
205	0	assertSame(ref2, matches.get(1));
206	0	assertSame(ref5, matches.get(2));
207		}
208
209		/**
210		* Test the method that searches for matches references - case when we are
211		* matching a reference with a mapping
212		*/
		0% Uncovered Elements: 14 (14) Complexity: 1 Complexity Density: 0.07 4-
213	0	@Test(groups = { "Functional" })...
214		public void testSearchRefs_withMapping()
215		{
216	0	DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
217	0	final Mapping map1 = new Mapping(
218		new MapList(new int[]
219		{ 1, 1 }, new int[] { 1, 1 }, 1, 1));
220	0	target.setMap(map1);
221
222		// these all match target iff mappings match
223	0	DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
224	0	DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
225	0	final Mapping map2 = new Mapping(
226		new MapList(new int[]
227		{ 1, 1 }, new int[] { 1, 1 }, 1, 1));
228	0	ref2.setMap(map2);
229
230		// different map: no match
231	0	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
232	0	final Mapping map3 = new Mapping(
233		new MapList(new int[]
234		{ 1, 1 }, new int[] { 1, 1 }, 2, 2));
235	0	ref3.setMap(map3);
236
237	0	List<DBRefEntry> matches = DBRefUtils
238		.searchRefs(Arrays.asList(new DBRefEntry[]
239		{ ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
240	0	assertEquals(2, matches.size());
241	0	assertSame(ref1, matches.get(0));
242	0	assertSame(ref2, matches.get(1));
243		}
244
245		/**
246		* Test the method that searches for matching references based on accession id
247		* only
248		*/
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08 4-
249	0	@Test(groups = { "Functional" })...
250		public void testSearchRefs_accessionid()
251		{
252
253	0	DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
254	0	DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
255		// constructor does not upper-case accession id
256	0	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
257	0	DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
258		// ref5 matches although it has a mapping - ignored
259	0	DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
260	0	ref5.setMap(
261		new Mapping(new MapList(new int[]
262		{ 1, 1 }, new int[] { 1, 1 }, 1, 1)));
263
264	0	List<DBRefEntry> dbrefs = Arrays
265		.asList(new DBRefEntry[]
266		{ ref1, ref2, ref3, ref4, ref5 });
267	0	List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
268	0	assertEquals(3, matches.size());
269	0	assertSame(ref1, matches.get(0));
270	0	assertSame(ref2, matches.get(1));
271	0	assertSame(ref5, matches.get(2));
272		}
273
274		/**
275		* Test the method that searches for matches references - case when we are
276		* matching a reference with null (any) accession id
277		*/
		0% Uncovered Elements: 13 (13) Complexity: 1 Complexity Density: 0.08 4-
278	0	@Test(groups = { "Functional" })...
279		public void testSearchRefs_wildcardAccessionid()
280		{
281	0	DBRefEntry target = new DBRefEntry("EMBL", "2", null);
282
283	0	DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
284		// constructor changes embl to EMBL
285	0	DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
286		// constructor does not upper-case accession id
287	0	DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
288	0	DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
289		// ref5 matches although it has a mapping - ignored
290	0	DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
291	0	ref5.setMap(
292		new Mapping(new MapList(new int[]
293		{ 1, 1 }, new int[] { 1, 1 }, 1, 1)));
294
295	0	List<DBRefEntry> matches = DBRefUtils
296		.searchRefs(Arrays.asList(new DBRefEntry[]
297		{ ref1, ref2, ref3, ref4, ref5 }), target,
298		DBRefUtils.SEARCH_MODE_FULL);
299	0	assertEquals(4, matches.size());
300	0	assertSame(ref1, matches.get(0));
301	0	assertSame(ref2, matches.get(1));
302	0	assertSame(ref3, matches.get(2));
303	0	assertSame(ref5, matches.get(3));
304		}
305		}