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.testng.AssertJUnit.assertTrue;
25 import jalview.bin.Cache;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.SequenceI;
28 import jalview.ws.seqfetcher.DbSourceProxy;
30 import java.util.List;
32 import org.testng.annotations.BeforeMethod;
33 import org.testng.annotations.Test;
35 public class PDBSequenceFetcherTest
40 @BeforeMethod(alwaysRun = true)
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 * Test that RNA structure can be added by a call to the RNAML service.
55 * Note this test depends on http://arn-ibmc.in2p3.fr/api/compute/2d which is
56 * not always reliable.
60 @Test(groups = { "Network" }, enabled = true)
61 public void testRnaSeqRetrieve() throws Exception
63 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
64 AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
65 assertTrue(response != null);
66 assertTrue(response.getHeight() == 1);
67 for (SequenceI sq : response.getSequences())
69 assertTrue("No annotation transfered to sequence.",
70 sq.getAnnotation().length > 0);
71 assertTrue("No PDBEntry on sequence.",
72 sq.getAllPDBEntries().size() > 0);
74 "No RNA annotation on sequence, possibly http://arn-ibmc.in2p3.fr/api/compute/2d not available?",