2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.ws.seqfetcher;
21 import static org.junit.Assert.*;
23 import java.util.ArrayList;
24 import java.util.List;
26 import jalview.datamodel.DBRefSource;
27 import jalview.ws.DBRefFetcher;
28 import jalview.ws.SequenceFetcher;
29 import jalview.ws.dbsources.das.api.jalviewSourceI;
31 import org.junit.AfterClass;
32 import org.junit.BeforeClass;
33 import org.junit.Test;
39 public class DbRefFetcherTest
43 * @throws java.lang.Exception
46 public static void setUpBeforeClass() throws Exception
51 * @throws java.lang.Exception
54 public static void tearDownAfterClass() throws Exception
59 public void testStandardProtDbs()
61 String[] defdb = DBRefSource.PROTEINDBS;
62 List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
63 for (String ddb : defdb)
65 SequenceFetcher sfetcher= new SequenceFetcher();
66 List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
68 if (srcesfordb != null)
70 srces.addAll(srcesfordb);
73 DbSourceProxy uniprot=null;
75 // append the selected sequence sources to the default dbs
76 for (DbSourceProxy s:srces)
78 if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
83 if (s instanceof jalview.ws.dbsources.Uniprot)
90 assertTrue("Failed to find Uniprot source as first source amongst "+srces.size()+" sources (source was at position "+i+")", uniprot!=null && i<2);