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.structure.StructureImportSettings;
29 import jalview.ws.seqfetcher.DbSourceProxy;
31 import java.util.List;
33 import org.testng.annotations.BeforeMethod;
34 import org.testng.annotations.Test;
36 public class PDBSequenceFetcherTest
41 @BeforeMethod(alwaysRun = true)
42 public void setUp() throws Exception
44 Cache.loadProperties("test/jalview/io/testProps.jvprops");
45 // ensure 'add annotation from structure' is selected
46 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
47 Boolean.TRUE.toString());
48 Cache.applicationProperties.setProperty("ADD_SS_ANN",
49 Boolean.TRUE.toString());
51 sf = new SequenceFetcher(false);
55 * Test that RNA structure can be added by a call to the RNAML service.
57 * Note this test depends on http://arn-ibmc.in2p3.fr/api/compute/2d which is
58 * not always reliable.
62 @Test(groups = { "Network" }, enabled = true)
63 public void testRnaSeqRetrieve() throws Exception
65 Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT",
67 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
68 AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
69 assertTrue(response != null);
70 assertTrue(response.getHeight() == 1);
71 for (SequenceI sq : response.getSequences())
73 assertTrue("No annotation transfered to sequence.",
74 sq.getAnnotation().length > 0);
75 assertTrue("No PDBEntry on sequence.",
76 sq.getAllPDBEntries().size() > 0);
78 "No RNA annotation on sequence, possibly http://arn-ibmc.in2p3.fr/api/compute/2d not available?",
83 @Test(groups = { "Network" }, enabled = true)
84 public void testPdbSeqRetrieve() throws Exception
86 StructureImportSettings.setDefaultStructureFileFormat("PDB");
88 testRetrieveProteinSeqFromPDB();
91 @Test(groups = { "Network" }, enabled = true)
92 public void testmmCifSeqRetrieve() throws Exception
94 StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
95 testRetrieveProteinSeqFromPDB();
98 private void testRetrieveProteinSeqFromPDB() throws Exception
100 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
101 AlignmentI response = sps.get(0).getSequenceRecords("1QIP");
102 assertTrue(response != null);
103 assertTrue(response.getHeight() == 4);
104 for (SequenceI sq : response.getSequences())
106 assertTrue("No annotation transfered to sequence.",
107 sq.getAnnotation().length > 0);
108 assertTrue("No PDBEntry on sequence.",
109 sq.getAllPDBEntries().size() > 0);
111 .assertEquals(sq.getEnd() - sq.getStart() + 1,
113 "Sequence start/end doesn't match number of residues in sequence");