/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.util; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.Mapping; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import org.testng.annotations.Test; public class DBRefUtilsTest { /** * Test the method that selects DBRefEntry items whose source is in a supplied * list */ @Test(groups = { "Functional" }) 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(groups = { "Functional" }) 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(groups = { "Functional" }) 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(groups = { "Functional" }) 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.getAllPDBEntries()); } /** * Test 'parsing' a DBRef - Stockholm PDB format */ @Test(groups = { "Functional" }) 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.getAllPDBEntries().size()); PDBEntry pdbRef = seq.getAllPDBEntries().get(0); assertEquals("1WRI", pdbRef.getId()); assertNull(pdbRef.getFile()); assertEquals("A", pdbRef.getChainCode()); assertEquals("PDB", pdbRef.getType()); } /** * Test the method that searches for matches references - case when we are * matching a reference with no mappings */ @Test(groups = { "Functional" }) 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(groups = { "Functional" }) 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]); } }