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.assertEquals;
24 import static org.testng.AssertJUnit.assertNotNull;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.bin.Cache;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.PDBEntry;
31 import jalview.datamodel.SequenceFeature;
32 import jalview.datamodel.SequenceI;
33 import jalview.datamodel.features.SequenceFeatures;
34 import jalview.gui.AlignFrame;
35 import jalview.gui.JvOptionPane;
36 import jalview.structure.StructureImportSettings;
37 import jalview.structure.StructureImportSettings.StructureParser;
40 import java.util.List;
42 import org.testng.annotations.AfterClass;
43 import org.testng.annotations.BeforeClass;
44 import org.testng.annotations.BeforeMethod;
45 import org.testng.annotations.Test;
47 public class AnnotatedPDBFileInputTest
50 @BeforeClass(alwaysRun = true)
51 public void setUpJvOptionPane()
53 JvOptionPane.setInteractiveMode(false);
54 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
62 * Ensure 'process secondary structure from PDB and add annotations' are set
63 * in preferences, and load PDB example file 1gaq
67 @BeforeMethod(alwaysRun = true)
68 public void setup() throws Exception
70 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
71 Boolean.TRUE.toString());
72 Cache.applicationProperties.setProperty("ADD_SS_ANN",
73 Boolean.TRUE.toString());
74 FileLoader loader = new FileLoader(false);
75 AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
77 al = af.getViewport().getAlignment();
78 pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
80 StructureImportSettings.setDefaultStructureFileFormat("PDB");
81 // StructureImportSettings
82 // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
85 @Test(groups = { "Functional" })
86 public void checkNoDuplicates()
88 // not strictly a requirement, but strange things may happen if multiple
89 // instances of the same annotation are placed in the alignment annotation
91 assertNotNull(al.getAlignmentAnnotation());
92 // verify that all sequence annotation is doubly referenced
93 AlignmentAnnotation[] avec = al.getAlignmentAnnotation();
94 for (int p = 0; p < avec.length; p++)
96 for (int q = p + 1; q < avec.length; q++)
98 assertTrue("Found a duplicate annotation row " + avec[p].label,
104 @Test(groups = { "Functional" })
105 public void checkPDBannotationSource()
108 for (SequenceI asq : al.getSequences())
110 for (AlignmentAnnotation aa : asq.getAnnotation())
113 System.out.println("CalcId: " + aa.getCalcId());
114 if (StructureImportSettings.getDefaultPDBFileParser().equals(
115 StructureParser.JALVIEW_PARSER))
117 assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
124 * Check sequence features have been added
126 @Test(groups = { "Functional" })
127 public void checkPDBSequenceFeatures()
132 List<SequenceFeature> sf = al.getSequenceAt(0).getSequenceFeatures();
133 SequenceFeatures.sortFeatures(sf, true);
134 assertEquals(296, sf.size());
135 assertEquals("RESNUM", sf.get(0).getType());
136 assertEquals("GLU: 19 1gaqA", sf.get(0).getDescription());
137 assertEquals("RESNUM", sf.get(295).getType());
138 assertEquals("TYR: 314 1gaqA", sf.get(295).getDescription());
143 sf = al.getSequenceAt(1).getSequenceFeatures();
144 SequenceFeatures.sortFeatures(sf, true);
145 assertEquals(98, sf.size());
146 assertEquals("RESNUM", sf.get(0).getType());
147 assertEquals("ALA: 1 1gaqB", sf.get(0).getDescription());
148 assertEquals("RESNUM", sf.get(97).getType());
149 assertEquals("ALA: 98 1gaqB", sf.get(97).getDescription());
154 sf = al.getSequenceAt(2).getSequenceFeatures();
155 SequenceFeatures.sortFeatures(sf, true);
156 assertEquals(296, sf.size());
157 assertEquals("RESNUM", sf.get(0).getType());
158 assertEquals("GLU: 19 1gaqC", sf.get(0).getDescription());
159 assertEquals("RESNUM", sf.get(295).getType());
160 assertEquals("TYR: 314 1gaqC", sf.get(295).getDescription());
163 @Test(groups = { "Functional" })
164 public void checkAnnotationWiring()
166 assertTrue(al.getAlignmentAnnotation() != null);
167 // verify that all sequence annotation is doubly referenced
168 for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
170 if (aa.sequenceRef != null)
172 assertTrue(al.getSequences().contains(aa.sequenceRef));
173 assertNotNull(aa.sequenceRef.getAnnotation());
174 boolean found = false;
175 for (AlignmentAnnotation sqan : aa.sequenceRef.getAnnotation())
184 "Couldn't find sequence associated annotation "
186 + " on the sequence it is associated with.\nSequence associated editing will fail.",
193 * @throws java.lang.Exception
195 @BeforeClass(alwaysRun = true)
196 public static void setUpBeforeClass() throws Exception
198 jalview.bin.Jalview.main(new String[] { "-props",
199 "test/jalview/io/testProps.jvprops" });
203 * @throws java.lang.Exception
205 @AfterClass(alwaysRun = true)
206 public static void tearDownAfterClass() throws Exception
208 jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
212 @Test(groups = { "Functional" })
213 public void testJalviewProjectRelocationAnnotation() throws Exception
216 String inFile = "examples/1gaq.txt";
217 String tfile = File.createTempFile("JalviewTest", ".jvp")
219 AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
220 inFile, DataSourceType.FILE);
221 assertTrue("Didn't read input file " + inFile, af != null);
222 assertTrue("Failed to store as a project.",
223 af.saveAlignment(tfile, FileFormat.Jalview));
224 af.closeMenuItem_actionPerformed(true);
226 af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
227 DataSourceType.FILE);
228 assertTrue("Failed to import new project", af != null);
229 for (SequenceI asq : af.getViewport().getAlignment().getSequences())
232 while (sq.getDatasetSequence() != null)
234 sq = sq.getDatasetSequence();
236 assertNotNull(sq.getAllPDBEntries());
237 assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
239 for (PDBEntry pdbentry : sq.getAllPDBEntries())
241 System.err.println("PDB Entry " + pdbentry.getId() + " "
242 + pdbentry.getFile());
243 boolean exists = false, found = false;
244 for (AlignmentAnnotation ana : sq.getAnnotation())
246 System.err.println("CalcId " + ana.getCalcId());
247 if (ana.getCalcId() != null
248 && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
251 if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
259 assertTrue("Couldn't find any annotation for " + pdbentry.getId()
260 + " (file handle " + pdbentry.getFile() + ")", found);