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.Assert.assertEquals;
24 import static org.testng.AssertJUnit.assertTrue;
26 import jalview.bin.Cache;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.JvOptionPane;
30 import jalview.structure.StructureImportSettings;
31 import jalview.structure.StructureImportSettings.StructureParser;
32 import jalview.ws.seqfetcher.DbSourceProxy;
34 import java.util.Arrays;
35 import java.util.List;
37 import org.testng.annotations.BeforeClass;
38 import org.testng.annotations.BeforeMethod;
39 import org.testng.annotations.Test;
41 public class PDBSequenceFetcherTest
44 @BeforeClass(alwaysRun = true)
45 public void setUpJvOptionPane()
47 JvOptionPane.setInteractiveMode(false);
48 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53 @BeforeMethod(alwaysRun = true)
54 public void setUp() throws Exception
56 Cache.loadProperties("test/jalview/io/testProps.jvprops");
57 // ensure 'add annotation from structure' is selected
58 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
59 Boolean.TRUE.toString());
60 Cache.applicationProperties.setProperty("ADD_SS_ANN",
61 Boolean.TRUE.toString());
63 sf = new SequenceFetcher(false);
67 * Test that RNA structure can be added by a call to the RNAML service.
69 * Note this test depends on http://arn-ibmc.in2p3.fr/api/compute/2d which is
70 * not always reliable.
74 @Test(groups = { "Network" }, enabled = true)
75 public void testRnaSeqRetrieve() throws Exception
77 Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
78 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
79 AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
80 assertTrue(response != null);
81 assertTrue(response.getHeight() == 1);
82 for (SequenceI sq : response.getSequences())
84 assertTrue("No annotation transfered to sequence.",
85 sq.getAnnotation().length > 0);
86 assertTrue("No PDBEntry on sequence.",
87 sq.getAllPDBEntries().size() > 0);
89 "No RNA annotation on sequence, possibly http://arn-ibmc.in2p3.fr/api/compute/2d not available?",
94 @Test(groups = { "Network" }, enabled = true)
95 public void testPdbSeqRetrieve() throws Exception
97 StructureImportSettings.setDefaultStructureFileFormat("PDB");
98 StructureImportSettings
99 .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
101 testRetrieveProteinSeqFromPDB();
104 @Test(groups = { "Network" }, enabled = true)
105 public void testmmCifSeqRetrieve() throws Exception
107 StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
108 testRetrieveProteinSeqFromPDB();
111 private class TestRetrieveObject
117 public TestRetrieveObject(String id, int expectedHeight)
121 this.expectedHeight = expectedHeight;
126 private List<TestRetrieveObject> toRetrieve = Arrays.asList(
127 new TestRetrieveObject("1QIP", 4),
128 new TestRetrieveObject("4IM2", 1));
130 private void testRetrieveProteinSeqFromPDB() throws Exception
132 List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
133 for (TestRetrieveObject str : toRetrieve)
135 AlignmentI response = sps.get(0).getSequenceRecords(str.id);
136 assertTrue("No aligment for " + str.id, response != null);
137 assertEquals(response.getHeight(), str.expectedHeight,
138 "Number of chains for " + str.id);
139 for (SequenceI sq : response.getSequences())
141 assertTrue("No annotation transfered to sequence " + sq.getName(),
142 sq.getAnnotation().length > 0);
143 assertTrue("No PDBEntry on sequence " + sq.getName(),
144 sq.getAllPDBEntries().size() > 0);
145 org.testng.Assert.assertEquals(sq.getEnd() - sq.getStart() + 1,
147 "Sequence start/end doesn't match number of residues in sequence for "