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.gui.AlignFrame;
34 import jalview.structure.StructureImportSettings;
35 import jalview.structure.StructureImportSettings.StructureParser;
39 import org.testng.annotations.AfterClass;
40 import org.testng.annotations.BeforeClass;
41 import org.testng.annotations.BeforeMethod;
42 import org.testng.annotations.Test;
44 public class AnnotatedPDBFileInputTest
52 * Ensure 'process secondary structure from PDB and add annotations' are set
53 * in preferences, and load PDB example file 1gaq
57 @BeforeMethod(alwaysRun = true)
58 public void setup() throws Exception
60 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
61 Boolean.TRUE.toString());
62 Cache.applicationProperties.setProperty("ADD_SS_ANN",
63 Boolean.TRUE.toString());
64 FileLoader loader = new FileLoader(false);
65 AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
67 al = af.getViewport().getAlignment();
68 pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
70 StructureImportSettings.setDefaultStructureFileFormat("PDB");
71 // StructureImportSettings
72 // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
75 @Test(groups = { "Functional" })
76 public void checkNoDuplicates()
78 // not strictly a requirement, but strange things may happen if multiple
79 // instances of the same annotation are placed in the alignment annotation
81 assertNotNull(al.getAlignmentAnnotation());
82 // verify that all sequence annotation is doubly referenced
83 AlignmentAnnotation[] avec = al.getAlignmentAnnotation();
84 for (int p = 0; p < avec.length; p++)
86 for (int q = p + 1; q < avec.length; q++)
88 assertTrue("Found a duplicate annotation row "
89 + avec[p].label, avec[p] != avec[q]);
94 @Test(groups = { "Functional" })
95 public void checkPDBannotationSource()
98 for (SequenceI asq : al.getSequences())
100 for (AlignmentAnnotation aa : asq.getAnnotation())
103 System.out.println("CalcId: " + aa.getCalcId());
104 if (StructureImportSettings.getDefaultPDBFileParser().equals(
105 StructureParser.JALVIEW_PARSER))
107 assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
114 * Check sequence features have been added
116 @Test(groups = { "Functional" })
117 public void checkPDBSequenceFeatures()
122 SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
123 assertEquals(296, sf.length);
124 assertEquals("RESNUM", sf[0].getType());
125 assertEquals("GLU:19 1gaqA", sf[0].getDescription());
126 assertEquals("RESNUM", sf[295].getType());
127 assertEquals("TYR:314 1gaqA", sf[295].getDescription());
132 sf = al.getSequenceAt(1).getSequenceFeatures();
133 assertEquals(98, sf.length);
134 assertEquals("RESNUM", sf[0].getType());
135 assertEquals("ALA:1 1gaqB", sf[0].getDescription());
136 assertEquals("RESNUM", sf[97].getType());
137 assertEquals("ALA:98 1gaqB", sf[97].getDescription());
142 sf = al.getSequenceAt(2).getSequenceFeatures();
143 assertEquals(296, sf.length);
144 assertEquals("RESNUM", sf[0].getType());
145 assertEquals("GLU:19 1gaqC", sf[0].getDescription());
146 assertEquals("RESNUM", sf[295].getType());
147 assertEquals("TYR:314 1gaqC", sf[295].getDescription());
150 @Test(groups = { "Functional" })
151 public void checkAnnotationWiring()
153 assertTrue(al.getAlignmentAnnotation() != null);
154 // verify that all sequence annotation is doubly referenced
155 for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
157 if (aa.sequenceRef != null)
159 assertTrue(al.getSequences().contains(aa.sequenceRef));
160 assertNotNull(aa.sequenceRef.getAnnotation());
161 boolean found = false;
162 for (AlignmentAnnotation sqan : aa.sequenceRef.getAnnotation())
171 "Couldn't find sequence associated annotation "
173 + " on the sequence it is associated with.\nSequence associated editing will fail.",
180 * @throws java.lang.Exception
182 @BeforeClass(alwaysRun = true)
183 public static void setUpBeforeClass() throws Exception
185 jalview.bin.Jalview.main(new String[] { "-props",
186 "test/jalview/io/testProps.jvprops" });
190 * @throws java.lang.Exception
192 @AfterClass(alwaysRun = true)
193 public static void tearDownAfterClass() throws Exception
195 jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
199 @Test(groups = { "Functional" })
200 public void testJalviewProjectRelocationAnnotation() throws Exception
203 String inFile = "examples/1gaq.txt";
204 String tfile = File.createTempFile("JalviewTest", ".jvp")
206 AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
207 inFile, FormatAdapter.FILE);
208 assertTrue("Didn't read input file " + inFile, af != null);
209 assertTrue("Failed to store as a project.",
210 af.saveAlignment(tfile, "Jalview"));
211 af.closeMenuItem_actionPerformed(true);
213 af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
215 assertTrue("Failed to import new project", af != null);
216 for (SequenceI asq : af.getViewport().getAlignment().getSequences())
219 while (sq.getDatasetSequence() != null)
221 sq = sq.getDatasetSequence();
223 assertNotNull(sq.getAllPDBEntries());
224 assertEquals("Expected only one PDB ID",
225 sq.getAllPDBEntries().size(), 1);
226 for (PDBEntry pdbentry : sq.getAllPDBEntries())
228 System.err.println("PDB Entry " + pdbentry.getId() + " "
229 + pdbentry.getFile());
230 boolean exists = false, found = false;
231 for (AlignmentAnnotation ana : sq.getAnnotation())
233 System.err.println("CalcId " + ana.getCalcId());
234 if (ana.getCalcId() != null
235 && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
238 if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
246 assertTrue("Couldn't find any annotation for " + pdbentry.getId()
247 + " (file handle " + pdbentry.getFile() + ")", found);