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;
28 import java.util.List;
30 import org.junit.Assert;
31 import org.testng.annotations.AfterClass;
32 import org.testng.annotations.BeforeClass;
33 import org.testng.annotations.BeforeMethod;
34 import org.testng.annotations.Test;
36 import jalview.bin.Cache;
37 import jalview.datamodel.AlignmentAnnotation;
38 import jalview.datamodel.AlignmentI;
39 import jalview.datamodel.PDBEntry;
40 import jalview.datamodel.SequenceFeature;
41 import jalview.datamodel.SequenceI;
42 import jalview.datamodel.features.SequenceFeatures;
43 import jalview.gui.AlignFrame;
44 import jalview.gui.Desktop;
45 import jalview.gui.JvOptionPane;
46 import jalview.structure.StructureImportSettings;
47 import jalview.structure.StructureImportSettings.StructureParser;
49 public class AnnotatedPDBFileInputTest
52 @BeforeClass(alwaysRun = true)
53 public void setUpJvOptionPane()
55 JvOptionPane.setInteractiveMode(false);
56 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
64 * Ensure 'process secondary structure from PDB and add annotations' are set
65 * in preferences, and load PDB example file 1gaq
69 @BeforeMethod(alwaysRun = true)
70 public void setup() throws Exception
72 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
73 Boolean.TRUE.toString());
74 Cache.applicationProperties.setProperty("ADD_SS_ANN",
75 Boolean.TRUE.toString());
76 FileLoader loader = new FileLoader(false);
77 AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
79 al = af.getViewport().getAlignment();
80 pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
82 StructureImportSettings.setDefaultStructureFileFormat("PDB");
83 // StructureImportSettings
84 // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
87 @Test(groups = { "Functional" })
88 public void checkNoDuplicates()
90 // not strictly a requirement, but strange things may happen if multiple
91 // instances of the same annotation are placed in the alignment annotation
93 assertNotNull(al.getAlignmentAnnotation());
94 // verify that all sequence annotation is doubly referenced
95 AlignmentAnnotation[] avec = al.getAlignmentAnnotation();
96 for (int p = 0; p < avec.length; p++)
98 for (int q = p + 1; q < avec.length; q++)
100 assertTrue("Found a duplicate annotation row " + avec[p].label,
106 @Test(groups = { "Functional" }, enabled = false)
107 public void checkPDBannotationSource()
110 "This test is incorrect - does not verify that JmolParser's annotation rows can be recognised as generated by the Jmol parser.");
111 for (SequenceI asq : al.getSequences())
113 for (AlignmentAnnotation aa : asq.getAnnotation())
116 System.out.println("CalcId: " + aa.getCalcId());
117 if (StructureImportSettings.getDefaultPDBFileParser()
118 .equals(StructureParser.JALVIEW_PARSER))
120 assertTrue(mc_view.PDBfile.isCalcIdForFile(aa, pdbId));
127 * Check sequence features have been added
129 @Test(groups = { "Functional" })
130 public void checkPDBSequenceFeatures()
135 List<SequenceFeature> sf = al.getSequenceAt(0).getSequenceFeatures();
136 SequenceFeatures.sortFeatures(sf, true);
137 assertEquals(296, sf.size());
138 assertEquals("RESNUM", sf.get(0).getType());
139 assertEquals("GLU: 19 1gaqA", sf.get(0).getDescription());
140 assertEquals("RESNUM", sf.get(295).getType());
141 assertEquals("TYR: 314 1gaqA", sf.get(295).getDescription());
146 sf = al.getSequenceAt(1).getSequenceFeatures();
147 SequenceFeatures.sortFeatures(sf, true);
148 assertEquals(98, sf.size());
149 assertEquals("RESNUM", sf.get(0).getType());
150 assertEquals("ALA: 1 1gaqB", sf.get(0).getDescription());
151 assertEquals("RESNUM", sf.get(97).getType());
152 assertEquals("ALA: 98 1gaqB", sf.get(97).getDescription());
157 sf = al.getSequenceAt(2).getSequenceFeatures();
158 SequenceFeatures.sortFeatures(sf, true);
159 assertEquals(296, sf.size());
160 assertEquals("RESNUM", sf.get(0).getType());
161 assertEquals("GLU: 19 1gaqC", sf.get(0).getDescription());
162 assertEquals("RESNUM", sf.get(295).getType());
163 assertEquals("TYR: 314 1gaqC", sf.get(295).getDescription());
166 @Test(groups = { "Functional" })
167 public void checkAnnotationWiring()
169 assertTrue(al.getAlignmentAnnotation() != null);
170 // verify that all sequence annotation is doubly referenced
171 for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
173 if (aa.sequenceRef != null)
175 assertTrue(al.getSequences().contains(aa.sequenceRef));
176 assertNotNull(aa.sequenceRef.getAnnotation());
177 boolean found = false;
178 for (AlignmentAnnotation sqan : aa.sequenceRef.getAnnotation())
186 assertTrue("Couldn't find sequence associated annotation "
188 + " on the sequence it is associated with.\nSequence associated editing will fail.",
195 * @throws java.lang.Exception
197 @BeforeClass(alwaysRun = true)
198 public static void setUpBeforeClass() throws Exception
202 { "--props", "test/jalview/io/testProps.jvprops" });
206 * @throws java.lang.Exception
208 @AfterClass(alwaysRun = true)
209 public static void tearDownAfterClass() throws Exception
211 if (Desktop.instance != null)
212 Desktop.instance.closeAll_actionPerformed(null);
215 @Test(groups = { "Functional" })
216 public void testJalviewProjectRelocationAnnotation() throws Exception
219 String inFile = "examples/1gaq.txt";
220 String tfile = File.createTempFile("JalviewTest", ".jvp")
222 AlignFrame af = new jalview.io.FileLoader()
223 .LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
224 assertTrue("Didn't read input file " + inFile, af != null);
225 af.saveAlignment(tfile, FileFormat.Jalview);
226 assertTrue("Failed to store as a project.",
227 af.isSaveAlignmentSuccessful());
228 af.closeMenuItem_actionPerformed(true);
230 af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
231 DataSourceType.FILE);
232 assertTrue("Failed to import new project", af != null);
233 for (SequenceI asq : af.getViewport().getAlignment().getSequences())
236 while (sq.getDatasetSequence() != null)
238 sq = sq.getDatasetSequence();
240 assertNotNull(sq.getAllPDBEntries());
241 assertEquals("Expected only one PDB ID", 1,
242 sq.getAllPDBEntries().size());
243 for (PDBEntry pdbentry : sq.getAllPDBEntries())
246 "PDB Entry " + pdbentry.getId() + " " + pdbentry.getFile());
247 boolean exists = false, found = false;
248 for (AlignmentAnnotation ana : sq.getAnnotation())
250 System.err.println("CalcId " + ana.getCalcId());
251 if (ana.getCalcId() != null
252 && mc_view.PDBfile.isCalcIdHandled(ana.getCalcId()))
255 if (mc_view.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
264 "Couldn't find any annotation for " + pdbentry.getId()
265 + " (file handle " + pdbentry.getFile() + ")",