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.structure.StructureImportSettings.StructureParser;
30 import jalview.ws.seqfetcher.DbSourceProxy;
32 import java.util.List;
34 import org.testng.annotations.BeforeMethod;
35 import org.testng.annotations.Test;
37 public class PDBSequenceFetcherTest
42 @BeforeMethod(alwaysRun = true)
43 public void setUp() throws Exception
45 Cache.loadProperties("test/jalview/io/testProps.jvprops");
46 // ensure 'add annotation from structure' is selected
47 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
48 Boolean.TRUE.toString());
49 Cache.applicationProperties.setProperty("ADD_SS_ANN",
50 Boolean.TRUE.toString());
52 sf = new SequenceFetcher(false);
56 * Test that RNA structure can be added by a call to the RNAML service.
58 * Note this test depends on http://arn-ibmc.in2p3.fr/api/compute/2d which is
59 * not always reliable.
63 @Test(groups = { "Network" }, enabled = true)
64 public void testRnaSeqRetrieve() throws Exception
66 Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT",
68 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
69 AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
70 assertTrue(response != null);
71 assertTrue(response.getHeight() == 1);
72 for (SequenceI sq : response.getSequences())
74 assertTrue("No annotation transfered to sequence.",
75 sq.getAnnotation().length > 0);
76 assertTrue("No PDBEntry on sequence.",
77 sq.getAllPDBEntries().size() > 0);
79 "No RNA annotation on sequence, possibly http://arn-ibmc.in2p3.fr/api/compute/2d not available?",
84 @Test(groups = { "Network" }, enabled = true)
85 public void testPdbSeqRetrieve() throws Exception
87 StructureImportSettings.setDefaultStructureFileFormat("PDB");
88 StructureImportSettings
89 .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
91 testRetrieveProteinSeqFromPDB();
94 @Test(groups = { "Network" }, enabled = true)
95 public void testmmCifSeqRetrieve() throws Exception
97 StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
98 testRetrieveProteinSeqFromPDB();
101 private void testRetrieveProteinSeqFromPDB() throws Exception
103 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
104 AlignmentI response = sps.get(0).getSequenceRecords("1QIP");
105 assertTrue(response != null);
106 assertTrue(response.getHeight() == 4);
107 for (SequenceI sq : response.getSequences())
109 assertTrue("No annotation transfered to sequence.",
110 sq.getAnnotation().length > 0);
111 assertTrue("No PDBEntry on sequence.",
112 sq.getAllPDBEntries().size() > 0);
114 .assertEquals(sq.getEnd() - sq.getStart() + 1,
116 "Sequence start/end doesn't match number of residues in sequence");