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.bin.Jalview;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.AlignFrame;
30 import jalview.gui.JvOptionPane;
31 import jalview.gui.Preferences;
32 import jalview.gui.StructureViewer;
33 import jalview.gui.StructureViewer.ViewerType;
34 import jalview.io.DataSourceType;
36 import org.testng.annotations.AfterClass;
37 import org.testng.annotations.BeforeClass;
38 import org.testng.annotations.Test;
40 @Test(singleThreaded = true)
41 public class JmolViewerTest
44 @BeforeClass(alwaysRun = true)
45 public void setUpJvOptionPane()
47 JvOptionPane.setInteractiveMode(false);
48 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52 * @throws java.lang.Exception
54 @BeforeClass(alwaysRun = true)
55 public static void setUpBeforeClass() throws Exception
57 Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props",
58 "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
62 * @throws java.lang.Exception
64 @AfterClass(alwaysRun = true)
65 public static void tearDownAfterClass() throws Exception
67 jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
70 @Test(groups = { "Functional" })
71 public void testSingleSeqViewJMol()
73 Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
74 String inFile = "examples/1gaq.txt";
75 AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
76 inFile, DataSourceType.FILE);
77 assertTrue("Didn't read input file " + inFile, af != null);
78 for (SequenceI sq : af.getViewport().getAlignment().getSequences())
80 SequenceI dsq = sq.getDatasetSequence();
81 while (dsq.getDatasetSequence() != null)
83 dsq = dsq.getDatasetSequence();
85 if (dsq.getAllPDBEntries() != null
86 && dsq.getAllPDBEntries().size() > 0)
88 for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
90 final StructureViewer structureViewer = new StructureViewer(af
91 .getViewport().getStructureSelectionManager());
92 structureViewer.setViewerType(ViewerType.JMOL);
93 JalviewStructureDisplayI jmolViewer = structureViewer
94 .viewStructures(dsq.getAllPDBEntries().elementAt(q),
95 new SequenceI[] { sq }, af.getCurrentView()
98 * Wait for viewer load thread to complete
102 while (!jmolViewer.getBinding().isFinishedInit())
106 } catch (InterruptedException e)
110 jmolViewer.closeViewer(true);
111 // todo: break here means only once through this loop?