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.
21 package jalview.ws.seqfetcher;
23 import static org.junit.Assert.assertEquals;
24 import static org.junit.Assert.assertNotNull;
25 import static org.junit.Assert.assertTrue;
27 import java.util.ArrayList;
28 import java.util.List;
30 import org.junit.AfterClass;
31 import org.junit.BeforeClass;
32 import org.junit.Test;
34 import jalview.analysis.CrossRef;
35 import jalview.datamodel.AlignmentI;
36 import jalview.datamodel.DBRefEntry;
37 import jalview.datamodel.DBRefSource;
38 import jalview.util.DBRefUtils;
39 import jalview.ws.SequenceFetcher;
45 public class DbRefFetcherTest
49 * @throws java.lang.Exception
52 public static void setUpBeforeClass() throws Exception
54 jalview.bin.Cache.initLogger();
58 * @throws java.lang.Exception
61 public static void tearDownAfterClass() throws Exception
66 public void testStandardProtDbs()
68 String[] defdb = DBRefSource.PROTEINDBS;
69 List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
70 for (String ddb : defdb)
72 SequenceFetcher sfetcher = new SequenceFetcher();
73 List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
75 if (srcesfordb != null)
77 srces.addAll(srcesfordb);
80 DbSourceProxy uniprot = null;
82 // append the selected sequence sources to the default dbs
83 for (DbSourceProxy s : srces)
85 if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
90 if (s instanceof jalview.ws.dbsources.Uniprot)
97 assertTrue("Failed to find Uniprot source as first source amongst "
98 + srces.size() + " sources (source was at position " + i + ")",
99 uniprot != null && i < 2);
103 public void testEmblUniprotProductRecovery() throws Exception
105 String retrievalId = "CAA23748"; // "V00488";
106 DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
107 assertNotNull("Couldn't find the EMBL retrieval client", embl);
108 verifyProteinNucleotideXref(retrievalId, embl);
112 public void testEmblCDSUniprotProductRecovery() throws Exception
114 String retrievalId = "AAH29712";
115 DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
116 DBRefSource.EMBLCDS).get(0);
117 assertNotNull("Couldn't find the EMBL retrieval client", embl);
118 verifyProteinNucleotideXref(retrievalId, embl);
121 private void verifyProteinNucleotideXref(String retrievalId,
122 DbSourceProxy embl) throws Exception
124 AlignmentI alsq = embl.getSequenceRecords(retrievalId);
125 assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
126 assertEquals("Didn't retrieve right number of records", 1, alsq.getHeight());
127 DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
129 assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
130 assertEquals("Expected cross refernce map to be one amino acid", dr[0]
131 .getMap().getMappedWidth(), 1);
132 assertEquals("Expected local refernce map to be 3 nucleotides", dr[0]
133 .getMap().getWidth(), 3);
134 AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
136 "Couldn't recover cross reference sequence from dataset. Was it ever added ?",