3 import static org.testng.AssertJUnit.assertSame;
4 import static org.testng.AssertJUnit.assertEquals;
5 import static org.testng.AssertJUnit.assertFalse;
6 import static org.testng.AssertJUnit.assertTrue;
7 import static org.testng.AssertJUnit.assertNull;
8 import org.testng.annotations.Test;
9 import jalview.datamodel.DBRefEntry;
10 import jalview.datamodel.DBRefSource;
11 import jalview.datamodel.Mapping;
12 import jalview.datamodel.PDBEntry;
13 import jalview.datamodel.Sequence;
14 import jalview.datamodel.SequenceI;
16 public class DBRefUtilsTest
20 * Test the method that selects DBRefEntry items whose source is in a supplied
24 public void testSelectRefs()
26 assertNull(DBRefUtils.selectRefs(null, null));
27 assertNull(DBRefUtils.selectRefs(null, DBRefSource.CODINGDBS));
29 DBRefEntry ref1 = new DBRefEntry("EMBL", "1.2", "A12345");
30 DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
31 // Source is converted to upper-case by this constructor!
32 DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
33 DBRefEntry[] dbrefs = new DBRefEntry[]
35 String[] sources = new String[]
36 { "EMBL", "UNIPROT" };
38 DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources);
39 assertEquals(3, selected.length);
40 assertSame(ref1, selected[0]);
41 assertSame(ref2, selected[1]);
42 assertSame(ref3, selected[2]);
44 sources = new String[]
46 selected = DBRefUtils.selectRefs(dbrefs, sources);
47 assertEquals(1, selected.length);
48 assertSame(ref1, selected[0]);
50 sources = new String[]
52 selected = DBRefUtils.selectRefs(dbrefs, sources);
53 assertEquals(2, selected.length);
54 assertSame(ref2, selected[0]);
55 assertSame(ref3, selected[1]);
57 sources = new String[]
58 { "Uniprot", "EMBLCDS" };
59 selected = DBRefUtils.selectRefs(dbrefs, sources);
64 * Test the method that converts (currently three) database names to a
65 * canonical name (not case-sensitive)
68 public void testGetCanonicalName()
70 assertNull(DBRefUtils.getCanonicalName(null));
71 assertEquals("", DBRefUtils.getCanonicalName(""));
72 assertEquals("PDB", DBRefUtils.getCanonicalName("pdb"));
73 assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
74 assertEquals("UNIPROT",
75 DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
76 assertEquals("UNIPROT", DBRefUtils.getCanonicalName("uniprotkb/trembl"));
77 assertEquals("UNIPROT",
78 DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
79 assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
80 assertEquals("UNIPROTKB/SWISS-CHEESE",
81 DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
85 public void testIsDasCoordinateSystem()
87 assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
88 assertFalse(DBRefUtils.isDasCoordinateSystem("pdbresnum", null));
89 assertFalse(DBRefUtils.isDasCoordinateSystem(null, new DBRefEntry(
92 assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
93 new DBRefEntry("PDB", "v1", "a1")));
94 assertTrue(DBRefUtils.isDasCoordinateSystem("PDBRESNUM",
95 new DBRefEntry("PDB", "v1", "a1")));
96 // "pdb" is converted to upper-case in DBRefEntry constructor
97 assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
98 new DBRefEntry("pdb", "v1", "a1")));
99 assertFalse(DBRefUtils.isDasCoordinateSystem("pdb", new DBRefEntry(
100 "pdb", "v1", "a1")));
102 assertTrue(DBRefUtils.isDasCoordinateSystem("UNIPROT", new DBRefEntry(
103 "Uniprot", "v1", "a1")));
104 assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
105 "UNIPROT", "v1", "a1")));
106 assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
108 "pdb", "v1", "a1")));
110 assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
111 "EMBL", "v1", "a1")));
112 assertTrue(DBRefUtils.isDasCoordinateSystem("embl", new DBRefEntry(
113 "embl", "v1", "a1")));
117 * Test 'parsing' a DBRef - non PDB case
120 public void testParseToDbRef()
122 SequenceI seq = new Sequence("Seq1", "ABCD");
123 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
124 DBRefEntry[] refs = seq.getDBRef();
125 assertEquals(1, refs.length);
126 assertSame(ref, refs[0]);
127 assertEquals("EMBL", ref.getSource());
128 assertEquals("1.2", ref.getVersion());
129 assertEquals("a7890", ref.getAccessionId());
130 assertNull(seq.getPDBId());
134 * Test 'parsing' a DBRef - Stockholm PDB format
137 public void testParseToDbRef_PDB()
139 SequenceI seq = new Sequence("Seq1", "ABCD");
140 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
142 DBRefEntry[] refs = seq.getDBRef();
143 assertEquals(1, refs.length);
144 assertSame(ref, refs[0]);
145 assertEquals("PDB", ref.getSource());
146 assertEquals("1.2", ref.getVersion());
147 // DBRef id is pdbId + chain code
148 assertEquals("1WRIA", ref.getAccessionId());
149 assertEquals(1, seq.getPDBId().size());
150 PDBEntry pdbRef = seq.getPDBId().get(0);
151 assertEquals("1WRI", pdbRef.getId());
152 assertNull(pdbRef.getFile());
153 assertEquals("A", pdbRef.getChainCode());
154 assertEquals("PDB", pdbRef.getType());
158 * Test the method that searches for matches references - case when we are
159 * matching a reference with no mappings
162 public void testSearchRefs_noMapping()
164 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
166 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
167 // constructor changes embl to EMBL
168 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
169 // constructor does not upper-case accession id
170 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
171 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
172 // ref5 matches although it has a mapping - ignored
173 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
174 ref5.setMap(new Mapping(new MapList(new int[]
178 DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[]
179 { ref1, ref2, ref3, ref4, ref5 }, target);
180 assertEquals(3, matches.length);
181 assertSame(ref1, matches[0]);
182 assertSame(ref2, matches[1]);
183 assertSame(ref5, matches[2]);
187 * Test the method that searches for matches references - case when we are
188 * matching a reference with a mapping
191 public void testSearchRefs_withMapping()
193 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
194 final Mapping map1 = new Mapping(new MapList(new int[]
199 // these all match target iff mappings match
200 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
201 DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
202 final Mapping map2 = new Mapping(new MapList(new int[]
207 // different map: no match
208 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
209 final Mapping map3 = new Mapping(new MapList(new int[]
214 DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[]
215 { ref1, ref2, ref3 }, target);
216 assertEquals(2, matches.length);
217 assertSame(ref1, matches[0]);
218 assertSame(ref2, matches[1]);