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 // 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("STRUCT_FROM_PDB",
66 Boolean.TRUE.toString());
67 Cache.applicationProperties.setProperty("DEFAULT_STRUCTURE_FORMAT",
69 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
70 AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
71 assertTrue(response != null);
72 assertTrue(response.getHeight() == 1);
73 for (SequenceI sq : response.getSequences())
75 assertTrue("No annotation transfered to sequence.",
76 sq.getAnnotation().length > 0);
77 assertTrue("No PDBEntry on sequence.",
78 sq.getAllPDBEntries().size() > 0);
80 "No RNA annotation on sequence, possibly http://arn-ibmc.in2p3.fr/api/compute/2d not available?",
85 @Test(groups = { "Network" }, enabled = true)
86 public void testPdbSeqRetrieve() throws Exception
88 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
89 Boolean.TRUE.toString());
90 StructureImportSettings.setDefaultStructureFileFormat("PDB");
91 StructureImportSettings
92 .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
94 testRetrieveProteinSeqFromPDB();
97 @Test(groups = { "Network" }, enabled = true)
98 public void testmmCifSeqRetrieve() throws Exception
100 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
101 Boolean.TRUE.toString());
102 StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
103 testRetrieveProteinSeqFromPDB();
106 private void testRetrieveProteinSeqFromPDB() throws Exception
108 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
109 AlignmentI response = sps.get(0).getSequenceRecords("1QIP");
110 assertTrue(response != null);
111 assertTrue(response.getHeight() == 4);
112 for (SequenceI sq : response.getSequences())
114 assertTrue("No annotation transfered to sequence.",
115 sq.getAnnotation().length > 0);
116 assertTrue("No PDBEntry on sequence.",
117 sq.getAllPDBEntries().size() > 0);
119 .assertEquals(sq.getEnd() - sq.getStart() + 1,
121 "Sequence start/end doesn't match number of residues in sequence");