--- /dev/null
+package jalview.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.Test;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+public class DBRefUtilsTest
+{
+
+ /**
+ * Test the method that selects DBRefEntry items whose source is in a supplied
+ * list
+ */
+ @Test
+ public void testSelectRefs()
+ {
+ assertNull(DBRefUtils.selectRefs(null, null));
+ assertNull(DBRefUtils.selectRefs(null, DBRefSource.CODINGDBS));
+
+ DBRefEntry ref1 = new DBRefEntry("EMBL", "1.2", "A12345");
+ DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
+ // Source is converted to upper-case by this constructor!
+ DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
+ DBRefEntry[] dbrefs = new DBRefEntry[]
+ { ref1, ref2, ref3 };
+ String[] sources = new String[]
+ { "EMBL", "UNIPROT" };
+
+ DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources);
+ assertEquals(3, selected.length);
+ assertSame(ref1, selected[0]);
+ assertSame(ref2, selected[1]);
+ assertSame(ref3, selected[2]);
+
+ sources = new String[]
+ { "EMBL" };
+ selected = DBRefUtils.selectRefs(dbrefs, sources);
+ assertEquals(1, selected.length);
+ assertSame(ref1, selected[0]);
+
+ sources = new String[]
+ { "UNIPROT" };
+ selected = DBRefUtils.selectRefs(dbrefs, sources);
+ assertEquals(2, selected.length);
+ assertSame(ref2, selected[0]);
+ assertSame(ref3, selected[1]);
+
+ sources = new String[]
+ { "Uniprot", "EMBLCDS" };
+ selected = DBRefUtils.selectRefs(dbrefs, sources);
+ assertNull(selected);
+ }
+
+ /**
+ * Test the method that converts (currently three) database names to a
+ * canonical name (not case-sensitive)
+ */
+ @Test
+ public void testGetCanonicalName()
+ {
+ assertNull(DBRefUtils.getCanonicalName(null));
+ assertEquals("", DBRefUtils.getCanonicalName(""));
+ assertEquals("PDB", DBRefUtils.getCanonicalName("pdb"));
+ assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
+ assertEquals("UNIPROT",
+ DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
+ assertEquals("UNIPROT", DBRefUtils.getCanonicalName("uniprotkb/trembl"));
+ assertEquals("UNIPROT",
+ DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
+ assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
+ assertEquals("UNIPROTKB/SWISS-CHEESE",
+ DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
+ }
+
+ @Test
+ public void testIsDasCoordinateSystem()
+ {
+ assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
+ assertFalse(DBRefUtils.isDasCoordinateSystem("pdbresnum", null));
+ assertFalse(DBRefUtils.isDasCoordinateSystem(null, new DBRefEntry(
+ "PDB", "v1", "a1")));
+
+ assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
+ new DBRefEntry("PDB", "v1", "a1")));
+ assertTrue(DBRefUtils.isDasCoordinateSystem("PDBRESNUM",
+ new DBRefEntry("PDB", "v1", "a1")));
+ // "pdb" is converted to upper-case in DBRefEntry constructor
+ assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
+ new DBRefEntry("pdb", "v1", "a1")));
+ assertFalse(DBRefUtils.isDasCoordinateSystem("pdb", new DBRefEntry(
+ "pdb", "v1", "a1")));
+
+ assertTrue(DBRefUtils.isDasCoordinateSystem("UNIPROT", new DBRefEntry(
+ "Uniprot", "v1", "a1")));
+ assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
+ "UNIPROT", "v1", "a1")));
+ assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
+ new DBRefEntry(
+ "pdb", "v1", "a1")));
+
+ assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
+ "EMBL", "v1", "a1")));
+ assertTrue(DBRefUtils.isDasCoordinateSystem("embl", new DBRefEntry(
+ "embl", "v1", "a1")));
+ }
+
+ /**
+ * Test 'parsing' a DBRef - non PDB case
+ */
+ @Test
+ public void testParseToDbRef()
+ {
+ SequenceI seq = new Sequence("Seq1", "ABCD");
+ DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
+ DBRefEntry[] refs = seq.getDBRef();
+ assertEquals(1, refs.length);
+ assertSame(ref, refs[0]);
+ assertEquals("EMBL", ref.getSource());
+ assertEquals("1.2", ref.getVersion());
+ assertEquals("a7890", ref.getAccessionId());
+ assertNull(seq.getPDBId());
+ }
+
+ /**
+ * Test 'parsing' a DBRef - Stockholm PDB format
+ */
+ @Test
+ public void testParseToDbRef_PDB()
+ {
+ SequenceI seq = new Sequence("Seq1", "ABCD");
+ DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
+ "1WRI A; 7-80;");
+ DBRefEntry[] refs = seq.getDBRef();
+ assertEquals(1, refs.length);
+ assertSame(ref, refs[0]);
+ assertEquals("PDB", ref.getSource());
+ assertEquals("1.2", ref.getVersion());
+ // DBRef id is pdbId + chain code
+ assertEquals("1WRIA", ref.getAccessionId());
+ assertEquals(1, seq.getPDBId().size());
+ PDBEntry pdbRef = seq.getPDBId().get(0);
+ assertEquals("1WRI", pdbRef.getId());
+ assertNull(pdbRef.getFile());
+ assertEquals("A", pdbRef.getProperty().get("CHAIN"));
+ assertNull(pdbRef.getType());
+ }
+
+ /**
+ * Test the method that searches for matches references - case when we are
+ * matching a reference with no mappings
+ */
+ @Test
+ public void testSearchRefs_noMapping()
+ {
+ DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
+
+ DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
+ // constructor changes embl to EMBL
+ DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
+ // constructor does not upper-case accession id
+ DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
+ DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
+ // ref5 matches although it has a mapping - ignored
+ DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
+ ref5.setMap(new Mapping(new MapList(new int[]
+ { 1, 1 }, new int[]
+ { 1, 1 }, 1, 1)));
+
+ DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[]
+ { ref1, ref2, ref3, ref4, ref5 }, target);
+ assertEquals(3, matches.length);
+ assertSame(ref1, matches[0]);
+ assertSame(ref2, matches[1]);
+ assertSame(ref5, matches[2]);
+ }
+
+ /**
+ * Test the method that searches for matches references - case when we are
+ * matching a reference with a mapping
+ */
+ @Test
+ public void testSearchRefs_withMapping()
+ {
+ DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
+ final Mapping map1 = new Mapping(new MapList(new int[]
+ { 1, 1 }, new int[]
+ { 1, 1 }, 1, 1));
+ target.setMap(map1);
+
+ // these all match target iff mappings match
+ DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
+ DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
+ final Mapping map2 = new Mapping(new MapList(new int[]
+ { 1, 1 }, new int[]
+ { 1, 1 }, 1, 1));
+ ref2.setMap(map2);
+
+ // different map: no match
+ DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
+ final Mapping map3 = new Mapping(new MapList(new int[]
+ { 1, 1 }, new int[]
+ { 1, 1 }, 2, 2));
+ ref3.setMap(map3);
+
+ DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[]
+ { ref1, ref2, ref3 }, target);
+ assertEquals(2, matches.length);
+ assertSame(ref1, matches[0]);
+ assertSame(ref2, matches[1]);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff