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.assertNull;
25 import static org.testng.AssertJUnit.assertSame;
26 import static org.testng.AssertJUnit.assertTrue;
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;
36 import java.util.Arrays;
37 import java.util.List;
39 import org.testng.annotations.BeforeClass;
40 import org.testng.annotations.Test;
42 public class DBRefUtilsTest
45 @BeforeClass(alwaysRun = true)
46 public void setUpJvOptionPane()
48 JvOptionPane.setInteractiveMode(false);
49 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53 * Test the method that selects DBRefEntry items whose source is in a supplied
56 @Test(groups = { "Functional" })
57 public void testSelectRefs()
59 assertNull(DBRefUtils.selectRefs(null, null));
60 assertNull(DBRefUtils.selectRefs(null, DBRefSource.CODINGDBS));
62 DBRefEntry ref1 = new DBRefEntry("EMBL", "1.2", "A12345");
63 DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
64 // Source is converted to upper-case by this constructor!
65 DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
66 List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3 });
67 String[] sources = new String[] { "EMBL", "UNIPROT" };
69 List<DBRefEntry> selected = DBRefUtils.selectRefs(dbrefs, sources);
70 assertEquals(3, selected.size());
71 assertSame(ref1, selected.get(0));
72 assertSame(ref2, selected.get(1));
73 assertSame(ref3, selected.get(2));
75 sources = new String[] { "EMBL" };
76 selected = DBRefUtils.selectRefs(dbrefs, sources);
77 assertEquals(1, selected.size());
78 assertSame(ref1, selected.get(0));
80 sources = new String[] { "UNIPROT" };
81 selected = DBRefUtils.selectRefs(dbrefs, sources);
82 assertEquals(2, selected.size());
83 assertSame(ref2, selected.get(0));
84 assertSame(ref3, selected.get(1));
86 sources = new String[] { "EMBLCDS" };
87 selected = DBRefUtils.selectRefs(dbrefs, sources);
90 sources = new String[] { "embl", "uniprot" };
91 selected = DBRefUtils.selectRefs(dbrefs, sources);
92 assertEquals(3, selected.size());
93 assertSame(ref1, selected.get(0));
94 assertSame(ref2, selected.get(1));
95 assertSame(ref3, selected.get(2));
99 * Test the method that converts (currently three) database names to a
100 * canonical name (not case-sensitive)
102 @Test(groups = { "Functional" })
103 public void testGetCanonicalName()
105 assertNull(DBRefUtils.getCanonicalName(null));
106 assertEquals("", DBRefUtils.getCanonicalName(""));
107 assertEquals("PDB", DBRefUtils.getCanonicalName("pdb"));
108 assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
109 assertEquals("UNIPROT",
110 DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
111 assertEquals("UNIPROT", DBRefUtils.getCanonicalName("uniprotkb/trembl"));
112 assertEquals("UNIPROT",
113 DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
114 assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
115 assertEquals("UNIPROTKB/SWISS-CHEESE",
116 DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
117 assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
119 // these are not 'known' to Jalview
120 assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
121 assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
125 * Test 'parsing' a DBRef - non PDB case
127 @Test(groups = { "Functional" })
128 public void testParseToDbRef()
130 SequenceI seq = new Sequence("Seq1", "ABCD");
131 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
132 List<DBRefEntry> refs = seq.getDBRefs();
133 assertEquals(1, refs.size());
134 assertSame(ref, refs.get(0));
135 assertEquals("EMBL", ref.getSource());
136 assertEquals("1.2", ref.getVersion());
137 assertEquals("a7890", ref.getAccessionId());
138 assertTrue(seq.getAllPDBEntries().isEmpty());
139 SequenceI seq2 = new Sequence("Seq2", "ABCD");
140 // Check that whitespace doesn't confuse parseToDbRef
141 DBRefEntry ref2 = DBRefUtils.parseToDbRef(seq2, "EMBL", "1.2",
143 assertEquals(ref, ref2);
147 * Test 'parsing' a DBRef - Stockholm PDB format
149 @Test(groups = { "Functional" })
150 public void testParseToDbRef_PDB()
152 SequenceI seq = new Sequence("Seq1", "ABCD");
153 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
155 // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
156 // PDB ref in Stockholm
158 List<DBRefEntry> refs = seq.getDBRefs();
159 assertEquals(1, refs.size());
160 assertSame(ref, refs.get(0));
161 assertEquals("PDB", ref.getSource());
162 assertEquals("1.2", ref.getVersion());
163 // DBRef id is pdbId + chain code
164 assertEquals("1WRIA", ref.getAccessionId());
165 assertEquals(1, seq.getAllPDBEntries().size());
166 PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
167 assertEquals("1WRI", pdbRef.getId());
168 assertNull(pdbRef.getFile());
169 assertEquals("A", pdbRef.getChainCode());
170 assertEquals("PDB", pdbRef.getType());
174 * Test the method that searches for matches references - case when we are
175 * matching a reference with no mappings
177 @Test(groups = { "Functional" })
178 public void testSearchRefs_noMapping()
180 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
182 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
183 // constructor changes embl to EMBL
184 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
185 // constructor does not upper-case accession id
186 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
187 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
188 // ref5 matches although it has a mapping - ignored
189 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
190 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
193 List<DBRefEntry> matches = DBRefUtils.searchRefs(
194 Arrays.asList(new DBRefEntry[] {
195 ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
196 assertEquals(3, matches.size());
197 assertSame(ref1, matches.get(0));
198 assertSame(ref2, matches.get(1));
199 assertSame(ref5, matches.get(2));
203 * Test the method that searches for matches references - case when we are
204 * matching a reference with a mapping
206 @Test(groups = { "Functional" })
207 public void testSearchRefs_withMapping()
209 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
210 final Mapping map1 = new Mapping(new MapList(new int[] { 1, 1 },
211 new int[] { 1, 1 }, 1, 1));
214 // these all match target iff mappings match
215 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
216 DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
217 final Mapping map2 = new Mapping(new MapList(new int[] { 1, 1 },
218 new int[] { 1, 1 }, 1, 1));
221 // different map: no match
222 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
223 final Mapping map3 = new Mapping(new MapList(new int[] { 1, 1 },
224 new int[] { 1, 1 }, 2, 2));
227 List<DBRefEntry> matches = DBRefUtils.searchRefs(
228 Arrays.asList(new DBRefEntry[] {
229 ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
230 assertEquals(2, matches.size());
231 assertSame(ref1, matches.get(0));
232 assertSame(ref2, matches.get(1));
236 * Test the method that searches for matching references based on accession id
239 @Test(groups = { "Functional" })
240 public void testSearchRefs_accessionid()
243 DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
244 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
245 // constructor does not upper-case accession id
246 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
247 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
248 // ref5 matches although it has a mapping - ignored
249 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
250 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
253 List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] {
254 ref1, ref2, ref3, ref4, ref5 });
255 List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
256 assertEquals(3, matches.size());
257 assertSame(ref1, matches.get(0));
258 assertSame(ref2, matches.get(1));
259 assertSame(ref5, matches.get(2));
263 * Test the method that searches for matches references - case when we are
264 * matching a reference with null (any) accession id
266 @Test(groups = { "Functional" })
267 public void testSearchRefs_wildcardAccessionid()
269 DBRefEntry target = new DBRefEntry("EMBL", "2", null);
271 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
272 // constructor changes embl to EMBL
273 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
274 // constructor does not upper-case accession id
275 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
276 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
277 // ref5 matches although it has a mapping - ignored
278 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
279 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
282 List<DBRefEntry> matches = DBRefUtils.searchRefs(
283 Arrays.asList(new DBRefEntry[] {
284 ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
285 assertEquals(4, matches.size());
286 assertSame(ref1, matches.get(0));
287 assertSame(ref2, matches.get(1));
288 assertSame(ref3, matches.get(2));
289 assertSame(ref5, matches.get(3));