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;
26 import jalview.analysis.CrossRef;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.DBRefEntry;
29 import jalview.datamodel.DBRefSource;
30 import jalview.util.DBRefUtils;
31 import jalview.ws.SequenceFetcher;
33 import java.util.ArrayList;
34 import java.util.List;
36 import org.junit.AfterClass;
37 import org.junit.BeforeClass;
38 import org.junit.Test;
44 public class DbRefFetcherTest
48 * @throws java.lang.Exception
51 public static void setUpBeforeClass() throws Exception
53 jalview.bin.Cache.initLogger();
57 * @throws java.lang.Exception
60 public static void tearDownAfterClass() throws Exception
65 public void testStandardProtDbs()
67 String[] defdb = DBRefSource.PROTEINDBS;
68 List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
69 for (String ddb : defdb)
71 SequenceFetcher sfetcher = new SequenceFetcher();
72 List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
74 if (srcesfordb != null)
76 srces.addAll(srcesfordb);
79 DbSourceProxy uniprot = null;
81 // append the selected sequence sources to the default dbs
82 for (DbSourceProxy s : srces)
84 if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
89 if (s instanceof jalview.ws.dbsources.Uniprot)
96 assertTrue("Failed to find Uniprot source as first source amongst "
97 + srces.size() + " sources (source was at position " + i + ")",
98 uniprot != null && i < 2);
102 public void testEmblUniprotProductRecovery() throws Exception
104 String retrievalId = "CAA23748"; // "V00488";
105 DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
106 assertNotNull("Couldn't find the EMBL retrieval client", embl);
107 verifyProteinNucleotideXref(retrievalId, embl);
111 public void testEmblCDSUniprotProductRecovery() throws Exception
113 String retrievalId = "AAH29712";
114 DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
115 DBRefSource.EMBLCDS).get(0);
116 assertNotNull("Couldn't find the EMBL retrieval client", embl);
117 verifyProteinNucleotideXref(retrievalId, embl);
120 private void verifyProteinNucleotideXref(String retrievalId,
121 DbSourceProxy embl) throws Exception
123 AlignmentI alsq = embl.getSequenceRecords(retrievalId);
124 assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
125 assertEquals("Didn't retrieve right number of records", 1, alsq.getHeight());
126 DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
128 assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
129 assertEquals("Expected cross refernce map to be one amino acid", dr[0]
130 .getMap().getMappedWidth(), 1);
131 assertEquals("Expected local refernce map to be 3 nucleotides", dr[0]
132 .getMap().getWidth(), 3);
133 AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
135 "Couldn't recover cross reference sequence from dataset. Was it ever added ?",