/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ 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.ws.seqfetcher; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertTrue; import jalview.analysis.CrossRef; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.FeatureProperties; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.util.DBRefUtils; import jalview.ws.SequenceFetcher; import jalview.ws.dbsources.Pdb; import jalview.ws.dbsources.Uniprot; import java.util.ArrayList; import java.util.List; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; /** * @author jimp * */ public class DbRefFetcherTest { /** * @throws java.lang.Exception */ @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { jalview.bin.Cache.initLogger(); } /** * @throws java.lang.Exception */ @AfterClass(alwaysRun = true) public static void tearDownAfterClass() throws Exception { } /** * Tests that standard protein database sources include Uniprot (as the first) * and also PDB. (Additional sources are dependent on availability of DAS * services.) */ @Test(groups = { "Functional" }) public void testStandardProtDbs() { String[] defdb = DBRefSource.PROTEINDBS; List srces = new ArrayList(); SequenceFetcher sfetcher = new SequenceFetcher(); boolean pdbFound = false; for (String ddb : defdb) { List srcesfordb = sfetcher.getSourceProxy(ddb); if (srcesfordb != null) { // TODO is this right? get duplicate entries srces.addAll(srcesfordb); } } int i = 0; int uniprotPos = -1; for (DbSourceProxy s : srces) { if (s instanceof Uniprot && uniprotPos == -1) { uniprotPos = i; } if (s instanceof Pdb) { pdbFound = true; } i++; } assertTrue("Failed to find Uniprot source as first source amongst " + srces.size() + " sources (source was at position " + uniprotPos + ")", uniprotPos == 0); assertTrue("Failed to find PDB source amongst " + srces.size() + " sources", pdbFound); } /** * Tests retrieval of one entry from EMBL. Test is dependent on availability * of network and the EMBL service. * * @throws Exception */ @Test(groups = { "External" }) public void testEmblUniprotProductRecovery() throws Exception { String retrievalId = "V00488"; DbSourceProxy embl = new SequenceFetcher().getSourceProxy( DBRefSource.EMBL).get(0); assertNotNull("Couldn't find the EMBL retrieval client", embl); verifyProteinNucleotideXref(retrievalId, embl); } /** * Tests retrieval of one entry from EMBLCDS. Test is dependent on * availability of network and the EMBLCDS service. * * @throws Exception */ @Test(groups = { "External" }) public void testEmblCDSUniprotProductRecovery() throws Exception { String retrievalId = "AAH29712"; DbSourceProxy embl = new SequenceFetcher().getSourceProxy( DBRefSource.EMBLCDS).get(0); assertNotNull("Couldn't find the EMBL retrieval client", embl); verifyProteinNucleotideXref(retrievalId, embl); } /** * Helper method to perform database retrieval and verification of results. * * @param retrievalId * @param embl * @throws Exception */ private void verifyProteinNucleotideXref(String retrievalId, DbSourceProxy embl) throws Exception { AlignmentI alsq = embl.getSequenceRecords(retrievalId); assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq); assertEquals("Didn't retrieve right number of records", 1, alsq.getHeight()); SequenceI seq = alsq.getSequenceAt(0); assertEquals("Wrong sequence name", embl.getDbSource() + "|" + retrievalId, seq.getName()); SequenceFeature[] sfs = seq.getSequenceFeatures(); assertNotNull("Sequence features missing", sfs); assertTrue( "Feature not CDS", FeatureProperties.isCodingFeature(embl.getDbSource(), sfs[0].getType())); assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup()); DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(), new String[] { DBRefSource.UNIPROT, DBRefSource.UNIPROTKB, DBRefSource.EMBLCDSProduct, DBRefSource.ENSEMBL }); assertNotNull(dr); assertEquals("Expected a single Uniprot cross reference", 1, dr.length); assertEquals("Expected cross reference map to be one amino acid", dr[0] .getMap().getMappedWidth(), 1); assertEquals("Expected local reference map to be 3 nucleotides", dr[0] .getMap().getWidth(), 3); AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq) .findXrefSequences(dr[0].getSource()); assertNotNull( "Couldn't recover cross reference sequence from dataset. Was it ever added ?", sprods); assertEquals("Didn't xref right number of records", 1, sprods.getHeight()); SequenceI proteinSeq = sprods.getSequenceAt(0); assertEquals(proteinSeq.getSequenceAsString(), dr[0].getMap().getTo() .getSequenceAsString()); assertEquals(dr[0].getSource() + "|" + dr[0].getAccessionId(), proteinSeq.getName()); } }