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;
37 import org.junit.Assert;
38 import org.testng.annotations.AfterClass;
39 import org.testng.annotations.BeforeClass;
40 import org.testng.annotations.BeforeMethod;
41 import org.testng.annotations.Test;
43 public class AnnotatedPDBFileInputTest
51 * Ensure 'process secondary structure from PDB and add annotations' are set
52 * in preferences, and load PDB example file 1gaq
56 @BeforeMethod(alwaysRun = true)
57 public void setup() throws Exception
59 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
60 Boolean.TRUE.toString());
61 Cache.applicationProperties.setProperty("ADD_SS_ANN",
62 Boolean.TRUE.toString());
63 FileLoader loader = new FileLoader(false);
64 AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
66 al = af.getViewport().getAlignment();
67 pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
71 @Test(groups = { "Functional" })
72 public void checkNoDuplicates()
74 // not strictly a requirement, but strange things may happen if multiple
75 // instances of the same annotation are placed in the alignment annotation
77 assertNotNull(al.getAlignmentAnnotation());
78 // verify that all sequence annotation is doubly referenced
79 AlignmentAnnotation[] avec = al.getAlignmentAnnotation();
80 for (int p = 0; p < avec.length; p++)
82 for (int q = p + 1; q < avec.length; q++)
84 Assert.assertNotEquals("Found a duplicate annotation row "
85 + avec[p].label, avec[p], avec[q]);
90 @Test(groups = { "Functional" })
91 public void checkPDBannotationSource()
94 for (SequenceI asq : al.getSequences())
96 for (AlignmentAnnotation aa : asq.getAnnotation())
99 System.out.println("CalcId: " + aa.getCalcId());
100 assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
106 * Check sequence features have been added
108 @Test(groups = { "Functional" })
109 public void checkPDBSequenceFeatures()
114 SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
115 assertEquals(296, sf.length);
116 assertEquals("RESNUM", sf[0].getType());
117 assertEquals("GLU: 19 1gaqA", sf[0].getDescription());
118 assertEquals("RESNUM", sf[295].getType());
119 assertEquals("TYR: 314 1gaqA", sf[295].getDescription());
124 sf = al.getSequenceAt(1).getSequenceFeatures();
125 assertEquals(98, sf.length);
126 assertEquals("RESNUM", sf[0].getType());
127 assertEquals("ALA: 1 1gaqB", sf[0].getDescription());
128 assertEquals("RESNUM", sf[97].getType());
129 assertEquals("ALA: 98 1gaqB", sf[97].getDescription());
134 sf = al.getSequenceAt(2).getSequenceFeatures();
135 assertEquals(296, sf.length);
136 assertEquals("RESNUM", sf[0].getType());
137 assertEquals("GLU: 19 1gaqC", sf[0].getDescription());
138 assertEquals("RESNUM", sf[295].getType());
139 assertEquals("TYR: 314 1gaqC", sf[295].getDescription());
142 @Test(groups = { "Functional" })
143 public void checkAnnotationWiring()
145 assertTrue(al.getAlignmentAnnotation() != null);
146 // verify that all sequence annotation is doubly referenced
147 for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
149 if (aa.sequenceRef != null)
151 assertTrue(al.getSequences().contains(aa.sequenceRef));
152 assertNotNull(aa.sequenceRef.getAnnotation());
153 boolean found = false;
154 for (AlignmentAnnotation sqan : aa.sequenceRef.getAnnotation())
163 "Couldn't find sequence associated annotation "
165 + " on the sequence it is associated with.\nSequence associated editing will fail.",
172 * @throws java.lang.Exception
174 @BeforeClass(alwaysRun = true)
175 public static void setUpBeforeClass() throws Exception
177 jalview.bin.Jalview.main(new String[] { "-props",
178 "test/jalview/io/testProps.jvprops" });
182 * @throws java.lang.Exception
185 public static void tearDownAfterClass() throws Exception
187 jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
191 @Test(groups = { "Functional" })
192 public void testJalviewProjectRelocationAnnotation() throws Exception
195 String inFile = "examples/1gaq.txt";
196 String tfile = File.createTempFile("JalviewTest", ".jvp")
198 AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
199 inFile, FormatAdapter.FILE);
200 assertTrue("Didn't read input file " + inFile, af != null);
201 assertTrue("Failed to store as a project.",
202 af.saveAlignment(tfile, "Jalview"));
203 af.closeMenuItem_actionPerformed(true);
205 af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
207 assertTrue("Failed to import new project", af != null);
208 for (SequenceI asq : af.getViewport().getAlignment().getSequences())
211 while (sq.getDatasetSequence() != null)
213 sq = sq.getDatasetSequence();
215 assertNotNull(sq.getAllPDBEntries());
216 assertEquals("Expected only one PDB ID",
217 sq.getAllPDBEntries().size(), 1);
218 for (PDBEntry pdbentry : sq.getAllPDBEntries())
220 System.err.println("PDB Entry " + pdbentry.getId() + " "
221 + pdbentry.getFile());
222 boolean exists = false, found = false;
223 for (AlignmentAnnotation ana : sq.getAnnotation())
225 System.err.println("CalcId " + ana.getCalcId());
226 if (ana.getCalcId() != null
227 && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
230 if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
238 assertTrue("Couldn't find any annotation for " + pdbentry.getId()
239 + " (file handle " + pdbentry.getFile() + ")", found);