2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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
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.*;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.SequenceI;
26 import jalview.ws.seqfetcher.DbSourceProxy;
28 import java.util.List;
30 import org.junit.Before;
31 import org.junit.Test;
33 public class PDBSequenceFetcherTest
39 public void setUp() throws Exception
41 sf = new SequenceFetcher(false);
45 public void testPdbPerChainRetrieve() throws Exception
47 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
48 AlignmentI response = sps.get(0).getSequenceRecords("1QIPA");
49 assertTrue(response != null);
50 assertTrue(response.getHeight() == 1);
54 public void testRnaSeqRetrieve() throws Exception
56 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
57 AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
58 assertTrue(response != null);
59 assertTrue(response.getHeight() == 1);
60 for (SequenceI sq : response.getSequences())
62 assertTrue("No annotation transfered to sequence.",
63 sq.getAnnotation().length > 0);
64 assertTrue("No PDBEntry on sequence.", sq.getPDBId().size() > 0);
65 assertTrue("No RNA annotation on sequence.", sq.getRNA() != null);