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.
21 package jalview.ext.jmol;
23 import static org.testng.AssertJUnit.assertTrue;
25 import jalview.api.structures.JalviewStructureDisplayI;
26 import jalview.bin.Cache;
27 import jalview.datamodel.SequenceI;
28 import jalview.gui.AlignFrame;
29 import jalview.gui.Preferences;
30 import jalview.gui.StructureViewer;
31 import jalview.gui.StructureViewer.ViewerType;
32 import jalview.io.FormatAdapter;
34 import org.testng.annotations.AfterClass;
35 import org.testng.annotations.BeforeClass;
36 import org.testng.annotations.Test;
38 @Test(singleThreaded = true)
39 public class JmolViewerTest
43 * @throws java.lang.Exception
45 @BeforeClass(alwaysRun = true)
46 public static void setUpBeforeClass() throws Exception
48 jalview.bin.Jalview.main(new String[] {
49 "-noquestionnaire -nonews -props",
50 "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
54 * @throws java.lang.Exception
57 public static void tearDownAfterClass() throws Exception
59 jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
62 @Test(groups = { "Functional" })
63 public void testSingleSeqViewJMol()
65 Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
66 String inFile = "examples/1gaq.txt";
67 AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
68 inFile, FormatAdapter.FILE);
69 assertTrue("Didn't read input file " + inFile, af != null);
70 for (SequenceI sq : af.getViewport().getAlignment().getSequences())
72 SequenceI dsq = sq.getDatasetSequence();
73 while (dsq.getDatasetSequence() != null)
75 dsq = dsq.getDatasetSequence();
77 if (dsq.getAllPDBEntries() != null
78 && dsq.getAllPDBEntries().size() > 0)
80 for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
82 final StructureViewer structureViewer = new StructureViewer(af
83 .getViewport().getStructureSelectionManager());
84 structureViewer.setViewerType(ViewerType.JMOL);
85 JalviewStructureDisplayI jmolViewer = structureViewer
86 .viewStructures(dsq.getAllPDBEntries().elementAt(q),
87 new SequenceI[] { sq }, af.getCurrentView()
90 * Wait for viewer load thread to complete
94 while (!jmolViewer.getBinding().isFinishedInit())
98 } catch (InterruptedException e)
102 jmolViewer.closeViewer(true);
103 // todo: break here means only once through this loop?