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.List;
38 import org.testng.annotations.BeforeClass;
39 import org.testng.annotations.Test;
41 public class DBRefUtilsTest
44 @BeforeClass(alwaysRun = true)
45 public void setUpJvOptionPane()
47 JvOptionPane.setInteractiveMode(false);
48 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52 * Test the method that selects DBRefEntry items whose source is in a supplied
55 @Test(groups = { "Functional" })
56 public void testSelectRefs()
58 assertNull(DBRefUtils.selectRefs(null, null));
59 assertNull(DBRefUtils.selectRefs(null, DBRefSource.CODINGDBS));
61 DBRefEntry ref1 = new DBRefEntry("EMBL", "1.2", "A12345");
62 DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
63 // Source is converted to upper-case by this constructor!
64 DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
65 DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3 };
66 String[] sources = new String[] { "EMBL", "UNIPROT" };
68 DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources);
69 assertEquals(3, selected.length);
70 assertSame(ref1, selected[0]);
71 assertSame(ref2, selected[1]);
72 assertSame(ref3, selected[2]);
74 sources = new String[] { "EMBL" };
75 selected = DBRefUtils.selectRefs(dbrefs, sources);
76 assertEquals(1, selected.length);
77 assertSame(ref1, selected[0]);
79 sources = new String[] { "UNIPROT" };
80 selected = DBRefUtils.selectRefs(dbrefs, sources);
81 assertEquals(2, selected.length);
82 assertSame(ref2, selected[0]);
83 assertSame(ref3, selected[1]);
85 sources = new String[] { "EMBLCDS" };
86 selected = DBRefUtils.selectRefs(dbrefs, sources);
89 sources = new String[] { "embl", "uniprot" };
90 selected = DBRefUtils.selectRefs(dbrefs, sources);
91 assertEquals(3, selected.length);
92 assertSame(ref1, selected[0]);
93 assertSame(ref2, selected[1]);
94 assertSame(ref3, selected[2]);
98 * Test the method that converts (currently three) database names to a
99 * canonical name (not case-sensitive)
101 @Test(groups = { "Functional" })
102 public void testGetCanonicalName()
104 assertNull(DBRefUtils.getCanonicalName(null));
105 assertEquals("", DBRefUtils.getCanonicalName(""));
106 assertEquals("PDB", DBRefUtils.getCanonicalName("pdb"));
107 assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
108 assertEquals("UNIPROT",
109 DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
110 assertEquals("UNIPROT", DBRefUtils.getCanonicalName("uniprotkb/trembl"));
111 assertEquals("UNIPROT",
112 DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
113 assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
114 assertEquals("UNIPROTKB/SWISS-CHEESE",
115 DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
116 assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
118 // these are not 'known' to Jalview
119 assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
120 assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
124 * Test 'parsing' a DBRef - non PDB case
126 @Test(groups = { "Functional" })
127 public void testParseToDbRef()
129 SequenceI seq = new Sequence("Seq1", "ABCD");
130 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
131 DBRefEntry[] refs = seq.getDBRefs();
132 assertEquals(1, refs.length);
133 assertSame(ref, refs[0]);
134 assertEquals("EMBL", ref.getSource());
135 assertEquals("1.2", ref.getVersion());
136 assertEquals("a7890", ref.getAccessionId());
137 assertTrue(seq.getAllPDBEntries().isEmpty());
141 * Test 'parsing' a DBRef - Stockholm PDB format
143 @Test(groups = { "Functional" })
144 public void testParseToDbRef_PDB()
146 SequenceI seq = new Sequence("Seq1", "ABCD");
147 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
149 // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
150 // PDB ref in Stockholm
152 DBRefEntry[] refs = seq.getDBRefs();
153 assertEquals(1, refs.length);
154 assertSame(ref, refs[0]);
155 assertEquals("PDB", ref.getSource());
156 assertEquals("1.2", ref.getVersion());
157 // DBRef id is pdbId + chain code
158 assertEquals("1WRIA", ref.getAccessionId());
159 assertEquals(1, seq.getAllPDBEntries().size());
160 PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
161 assertEquals("1WRI", pdbRef.getId());
162 assertNull(pdbRef.getFile());
163 assertEquals("A", pdbRef.getChainCode());
164 assertEquals("PDB", pdbRef.getType());
168 * Test the method that searches for matches references - case when we are
169 * matching a reference with no mappings
171 @Test(groups = { "Functional" })
172 public void testSearchRefs_noMapping()
174 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
176 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
177 // constructor changes embl to EMBL
178 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
179 // constructor does not upper-case accession id
180 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
181 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
182 // ref5 matches although it has a mapping - ignored
183 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
184 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
187 List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
188 ref1, ref2, ref3, ref4, ref5 }, target);
189 assertEquals(3, matches.size());
190 assertSame(ref1, matches.get(0));
191 assertSame(ref2, matches.get(1));
192 assertSame(ref5, matches.get(2));
196 * Test the method that searches for matches references - case when we are
197 * matching a reference with a mapping
199 @Test(groups = { "Functional" })
200 public void testSearchRefs_withMapping()
202 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
203 final Mapping map1 = new Mapping(new MapList(new int[] { 1, 1 },
204 new int[] { 1, 1 }, 1, 1));
207 // these all match target iff mappings match
208 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
209 DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
210 final Mapping map2 = new Mapping(new MapList(new int[] { 1, 1 },
211 new int[] { 1, 1 }, 1, 1));
214 // different map: no match
215 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
216 final Mapping map3 = new Mapping(new MapList(new int[] { 1, 1 },
217 new int[] { 1, 1 }, 2, 2));
220 List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
221 ref1, ref2, ref3 }, target);
222 assertEquals(2, matches.size());
223 assertSame(ref1, matches.get(0));
224 assertSame(ref2, matches.get(1));
228 * Test the method that searches for matching references based on accession id
231 @Test(groups = { "Functional" })
232 public void testSearchRefs_accessionid()
235 DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
236 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
237 // constructor does not upper-case accession id
238 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
239 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
240 // ref5 matches although it has a mapping - ignored
241 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
242 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
245 DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5 };
246 List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
247 assertEquals(3, matches.size());
248 assertSame(ref1, matches.get(0));
249 assertSame(ref2, matches.get(1));
250 assertSame(ref5, matches.get(2));
254 * Test the method that searches for matches references - case when we are
255 * matching a reference with null (any) accession id
257 @Test(groups = { "Functional" })
258 public void testSearchRefs_wildcardAccessionid()
260 DBRefEntry target = new DBRefEntry("EMBL", "2", null);
262 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
263 // constructor changes embl to EMBL
264 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
265 // constructor does not upper-case accession id
266 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
267 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
268 // ref5 matches although it has a mapping - ignored
269 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
270 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
273 List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
274 ref1, ref2, ref3, ref4, ref5 }, target);
275 assertEquals(4, matches.size());
276 assertSame(ref1, matches.get(0));
277 assertSame(ref2, matches.get(1));
278 assertSame(ref3, matches.get(2));
279 assertSame(ref5, matches.get(3));