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());
138 SequenceI seq2 = new Sequence("Seq2", "ABCD");
139 // Check that whitespace doesn't confuse parseToDbRef
140 DBRefEntry ref2 = DBRefUtils.parseToDbRef(seq2, "EMBL", "1.2",
142 assertEquals(ref, ref2);
146 * Test 'parsing' a DBRef - Stockholm PDB format
148 @Test(groups = { "Functional" })
149 public void testParseToDbRef_PDB()
151 SequenceI seq = new Sequence("Seq1", "ABCD");
152 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
154 // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
155 // PDB ref in Stockholm
157 DBRefEntry[] refs = seq.getDBRefs();
158 assertEquals(1, refs.length);
159 assertSame(ref, refs[0]);
160 assertEquals("PDB", ref.getSource());
161 assertEquals("1.2", ref.getVersion());
162 // DBRef id is pdbId + chain code
163 assertEquals("1WRIA", ref.getAccessionId());
164 assertEquals(1, seq.getAllPDBEntries().size());
165 PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
166 assertEquals("1WRI", pdbRef.getId());
167 assertNull(pdbRef.getFile());
168 assertEquals("A", pdbRef.getChainCode());
169 assertEquals("PDB", pdbRef.getType());
173 * Test the method that searches for matches references - case when we are
174 * matching a reference with no mappings
176 @Test(groups = { "Functional" })
177 public void testSearchRefs_noMapping()
179 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
181 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
182 // constructor changes embl to EMBL
183 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
184 // constructor does not upper-case accession id
185 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
186 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
187 // ref5 matches although it has a mapping - ignored
188 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
189 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
192 List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
193 ref1, ref2, ref3, ref4, ref5 }, target);
194 assertEquals(3, matches.size());
195 assertSame(ref1, matches.get(0));
196 assertSame(ref2, matches.get(1));
197 assertSame(ref5, matches.get(2));
201 * Test the method that searches for matches references - case when we are
202 * matching a reference with a mapping
204 @Test(groups = { "Functional" })
205 public void testSearchRefs_withMapping()
207 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
208 final Mapping map1 = new Mapping(new MapList(new int[] { 1, 1 },
209 new int[] { 1, 1 }, 1, 1));
212 // these all match target iff mappings match
213 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
214 DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
215 final Mapping map2 = new Mapping(new MapList(new int[] { 1, 1 },
216 new int[] { 1, 1 }, 1, 1));
219 // different map: no match
220 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
221 final Mapping map3 = new Mapping(new MapList(new int[] { 1, 1 },
222 new int[] { 1, 1 }, 2, 2));
225 List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
226 ref1, ref2, ref3 }, target);
227 assertEquals(2, matches.size());
228 assertSame(ref1, matches.get(0));
229 assertSame(ref2, matches.get(1));
233 * Test the method that searches for matching references based on accession id
236 @Test(groups = { "Functional" })
237 public void testSearchRefs_accessionid()
240 DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
241 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
242 // constructor does not upper-case accession id
243 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
244 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
245 // ref5 matches although it has a mapping - ignored
246 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
247 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
250 DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5 };
251 List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
252 assertEquals(3, matches.size());
253 assertSame(ref1, matches.get(0));
254 assertSame(ref2, matches.get(1));
255 assertSame(ref5, matches.get(2));
259 * Test the method that searches for matches references - case when we are
260 * matching a reference with null (any) accession id
262 @Test(groups = { "Functional" })
263 public void testSearchRefs_wildcardAccessionid()
265 DBRefEntry target = new DBRefEntry("EMBL", "2", null);
267 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
268 // constructor changes embl to EMBL
269 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
270 // constructor does not upper-case accession id
271 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
272 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
273 // ref5 matches although it has a mapping - ignored
274 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
275 ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
278 List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
279 ref1, ref2, ref3, ref4, ref5 }, target);
280 assertEquals(4, matches.size());
281 assertSame(ref1, matches.get(0));
282 assertSame(ref2, matches.get(1));
283 assertSame(ref3, matches.get(2));
284 assertSame(ref5, matches.get(3));