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.
23 import static org.junit.Assert.assertTrue;
25 import java.util.List;
27 import org.junit.Before;
28 import org.junit.Test;
30 import jalview.bin.Cache;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.SequenceI;
33 import jalview.ws.seqfetcher.DbSourceProxy;
35 public class PDBSequenceFetcherTest
41 public void setUp() throws Exception
43 // ensure 'add annotation from structure' is selected
44 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
45 Boolean.TRUE.toString());
46 Cache.applicationProperties.setProperty("ADD_SS_ANN",
47 Boolean.TRUE.toString());
49 sf = new SequenceFetcher(false);
53 public void testRnaSeqRetrieve() throws Exception
55 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
56 AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
57 assertTrue(response != null);
58 assertTrue(response.getHeight() == 1);
59 for (SequenceI sq : response.getSequences())
61 assertTrue("No annotation transfered to sequence.",
62 sq.getAnnotation().length > 0);
63 assertTrue("No PDBEntry on sequence.", sq.getPDBId().size() > 0);
64 assertTrue("No RNA annotation on sequence.", sq.getRNA() != null);