2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
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;
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;
36 import java.util.List;
38 import org.testng.annotations.Test;
40 public class DBRefUtilsTest
44 * Test the method that selects DBRefEntry items whose source is in a supplied
47 @Test(groups = { "Functional" })
48 public void testSelectRefs()
50 assertNull(DBRefUtils.selectRefs(null, null));
51 assertNull(DBRefUtils.selectRefs(null, DBRefSource.CODINGDBS));
53 DBRefEntry ref1 = new DBRefEntry("EMBL", "1.2", "A12345");
54 DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
55 // Source is converted to upper-case by this constructor!
56 DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
57 DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3 };
58 String[] sources = new String[] { "EMBL", "UNIPROT" };
60 DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources);
61 assertEquals(3, selected.length);
62 assertSame(ref1, selected[0]);
63 assertSame(ref2, selected[1]);
64 assertSame(ref3, selected[2]);
66 sources = new String[] { "EMBL" };
67 selected = DBRefUtils.selectRefs(dbrefs, sources);
68 assertEquals(1, selected.length);
69 assertSame(ref1, selected[0]);
71 sources = new String[] { "UNIPROT" };
72 selected = DBRefUtils.selectRefs(dbrefs, sources);
73 assertEquals(2, selected.length);
74 assertSame(ref2, selected[0]);
75 assertSame(ref3, selected[1]);
78 sources = new String[] { "Uniprot" };
79 selected = DBRefUtils.selectRefs(dbrefs, sources);
80 assertEquals(2, selected.length);
81 assertSame(ref2, selected[0]);
82 assertSame(ref3, selected[1]);
84 sources = new String[] { "EMBLCDS" };
85 selected = DBRefUtils.selectRefs(dbrefs, sources);
88 sources = new String[] { "embl", "uniprot" };
89 selected = DBRefUtils.selectRefs(dbrefs, sources);
90 assertEquals(3, selected.length);
91 assertSame(ref1, selected[0]);
92 assertSame(ref2, selected[1]);
93 assertSame(ref3, selected[2]);
97 * Test the method that converts (currently three) database names to a
98 * canonical name (not case-sensitive)
100 @Test(groups = { "Functional" })
101 public void testGetCanonicalName()
103 assertNull(DBRefUtils.getCanonicalName(null));
104 assertEquals("", DBRefUtils.getCanonicalName(""));
105 assertEquals("PDB", DBRefUtils.getCanonicalName("pdb"));
106 assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
107 assertEquals("UNIPROT",
108 DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
109 assertEquals("UNIPROT", DBRefUtils.getCanonicalName("uniprotkb/trembl"));
110 assertEquals("UNIPROT",
111 DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
112 assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
113 assertEquals("UNIPROTKB/SWISS-CHEESE",
114 DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
115 assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
117 // these are not 'known' to Jalview
118 assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
119 assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
123 @Test(groups = { "Functional" })
124 public void testIsDasCoordinateSystem()
126 assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
127 assertFalse(DBRefUtils.isDasCoordinateSystem("pdbresnum", null));
128 assertFalse(DBRefUtils.isDasCoordinateSystem(null, new DBRefEntry(
129 "PDB", "v1", "a1")));
131 assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
132 new DBRefEntry("PDB", "v1", "a1")));
133 assertTrue(DBRefUtils.isDasCoordinateSystem("PDBRESNUM",
134 new DBRefEntry("PDB", "v1", "a1")));
135 // "pdb" is converted to upper-case in DBRefEntry constructor
136 assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
137 new DBRefEntry("pdb", "v1", "a1")));
138 assertFalse(DBRefUtils.isDasCoordinateSystem("pdb", new DBRefEntry(
139 "pdb", "v1", "a1")));
141 assertTrue(DBRefUtils.isDasCoordinateSystem("UNIPROT", new DBRefEntry(
142 "Uniprot", "v1", "a1")));
143 assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
144 "UNIPROT", "v1", "a1")));
145 assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
146 new DBRefEntry("pdb", "v1", "a1")));
148 assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
149 "EMBL", "v1", "a1")));
150 assertTrue(DBRefUtils.isDasCoordinateSystem("embl", new DBRefEntry(
151 "embl", "v1", "a1")));
155 * Test 'parsing' a DBRef - non PDB case
157 @Test(groups = { "Functional" })
158 public void testParseToDbRef()
160 SequenceI seq = new Sequence("Seq1", "ABCD");
161 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
162 DBRefEntry[] refs = seq.getDBRefs();
163 assertEquals(1, refs.length);
164 assertSame(ref, refs[0]);
165 assertEquals("EMBL", ref.getSource());
166 assertEquals("1.2", ref.getVersion());
167 assertEquals("a7890", ref.getAccessionId());
168 assertTrue(seq.getAllPDBEntries().isEmpty());
172 * Test 'parsing' a DBRef - Stockholm PDB format
174 @Test(groups = { "Functional" })
175 public void testParseToDbRef_PDB()
177 SequenceI seq = new Sequence("Seq1", "ABCD");
178 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
180 // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
181 // PDB ref in Stockholm
183 DBRefEntry[] refs = seq.getDBRefs();
184 assertEquals(1, refs.length);
185 assertSame(ref, refs[0]);
186 assertEquals("PDB", ref.getSource());
187 assertEquals("1.2", ref.getVersion());
188 // DBRef id is pdbId + chain code
189 assertEquals("1WRIA", ref.getAccessionId());
190 assertEquals(1, seq.getAllPDBEntries().size());
191 PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
192 assertEquals("1WRI", pdbRef.getId());
193 assertNull(pdbRef.getFile());
194 assertEquals("A", pdbRef.getChainCode());
195 assertEquals("PDB", pdbRef.getType());
199 * Test the method that searches for matches references - case when we are
200 * matching a reference with no mappings
202 @Test(groups = { "Functional" })
203 public void testSearchRefs_noMapping()
205 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
207 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
208 // constructor changes embl to EMBL
209 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
210 // constructor does not upper-case accession id
211 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
212 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
213 // ref5 matches although it has a mapping - ignored
214 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
215 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
218 List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
219 ref1, ref2, ref3, ref4, ref5 }, target);
220 assertEquals(3, matches.size());
221 assertSame(ref1, matches.get(0));
222 assertSame(ref2, matches.get(1));
223 assertSame(ref5, matches.get(2));
227 * Test the method that searches for matches references - case when we are
228 * matching a reference with a mapping
230 @Test(groups = { "Functional" })
231 public void testSearchRefs_withMapping()
233 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
234 final Mapping map1 = new Mapping(new MapList(new int[] { 1, 1 },
235 new int[] { 1, 1 }, 1, 1));
238 // these all match target iff mappings match
239 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
240 DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
241 final Mapping map2 = new Mapping(new MapList(new int[] { 1, 1 },
242 new int[] { 1, 1 }, 1, 1));
245 // different map: no match
246 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
247 final Mapping map3 = new Mapping(new MapList(new int[] { 1, 1 },
248 new int[] { 1, 1 }, 2, 2));
251 List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
252 ref1, ref2, ref3 }, target);
253 assertEquals(2, matches.size());
254 assertSame(ref1, matches.get(0));
255 assertSame(ref2, matches.get(1));
259 * Test the method that searches for matching references based on accession id
262 @Test(groups = { "Functional" })
263 public void testSearchRefs_accessionid()
266 DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
267 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
268 // constructor does not upper-case accession id
269 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
270 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
271 // ref5 matches although it has a mapping - ignored
272 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
273 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
276 DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5 };
277 List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
278 assertEquals(3, matches.size());
279 assertSame(ref1, matches.get(0));
280 assertSame(ref2, matches.get(1));
281 assertSame(ref5, matches.get(2));
285 * Test the method that searches for matches references - case when we are
286 * matching a reference with null (any) accession id
288 @Test(groups = { "Functional" })
289 public void testSearchRefs_wildcardAccessionid()
291 DBRefEntry target = new DBRefEntry("EMBL", "2", null);
293 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
294 // constructor changes embl to EMBL
295 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
296 // constructor does not upper-case accession id
297 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
298 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
299 // ref5 matches although it has a mapping - ignored
300 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
301 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
304 List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
305 ref1, ref2, ref3, ref4, ref5 }, target);
306 assertEquals(4, matches.size());
307 assertSame(ref1, matches.get(0));
308 assertSame(ref2, matches.get(1));
309 assertSame(ref3, matches.get(2));
310 assertSame(ref5, matches.get(3));