+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.rbvi.chimera;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.Preferences;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.FormatAdapter;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+@Test(singleThreaded = true)
public class JalviewChimeraView
{
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Jalview.main(new String[]
- { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" });
+ jalview.bin.Jalview.main(new String[] {
+ "-noquestionnaire -nonews -props",
+ "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
}
/**
@AfterClass
public static void tearDownAfterClass() throws Exception
{
- try
- {
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
- } catch (Exception e)
- {
- // ignore NullPointerException thrown by JMol
- }
-
}
- @Test(groups ={ "Functional" })
- public void testSingleSeqViewJMol()
- {
- String inFile = "examples/1gaq.txt";
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
- assertTrue("Didn't read input file " + inFile, af != null);
- for (SequenceI sq : af.getViewport().getAlignment().getSequences())
- {
- SequenceI dsq = sq.getDatasetSequence();
- while (dsq.getDatasetSequence() != null)
- {
- dsq = dsq.getDatasetSequence();
- }
- if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
- {
- for (int q = 0; q < dsq.getPDBId().size(); q++)
- {
- final StructureViewer structureViewer = new StructureViewer(af
- .getViewport().getStructureSelectionManager());
- structureViewer.setViewerType(ViewerType.JMOL);
- JalviewStructureDisplayI jmolViewer = structureViewer
- .viewStructures(dsq.getPDBId().elementAt(q),
- new SequenceI[]
- { sq }, af.getCurrentView().getAlignPanel());
- /*
- * Wait for viewer thread to start
- */
- try
- {
- Thread.sleep(1000);
- } catch (InterruptedException e)
- {
- }
-
- jmolViewer.closeViewer(true);
- // todo: break here means only once through this loop?
- break;
- }
- break;
- }
- }
- }
-
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSingleSeqViewChimera()
{
+ Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+ ViewerType.CHIMERA.name());
String inFile = "examples/1gaq.txt";
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
inFile, FormatAdapter.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
for (SequenceI sq : af.getViewport().getAlignment().getSequences())
{
+ System.out.println("** sq=" + sq.getName());
SequenceI dsq = sq.getDatasetSequence();
while (dsq.getDatasetSequence() != null)
{
dsq = dsq.getDatasetSequence();
}
- if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
+ if (dsq.getAllPDBEntries() != null
+ && dsq.getAllPDBEntries().size() > 0)
{
- for (int q = 0; q < dsq.getPDBId().size(); q++)
+ for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
{
final StructureViewer structureViewer = new StructureViewer(af
.getViewport().getStructureSelectionManager());
structureViewer.setViewerType(ViewerType.CHIMERA);
JalviewStructureDisplayI chimeraViewer = structureViewer
- .viewStructures(dsq.getPDBId().elementAt(q),
- new SequenceI[]
- { sq }, af.getCurrentView().getAlignPanel());
+ .viewStructures(dsq.getAllPDBEntries().elementAt(q),
+ new SequenceI[] { sq }, af.getCurrentView()
+ .getAlignPanel());
/*
- * Wait for viewer thread to start
+ * Wait for viewer load thread to complete
*/
- try
- {
- Thread.sleep(1000);
- } catch (InterruptedException e)
+ while (!chimeraViewer.getBinding().isFinishedInit())
{
+ try
+ {
+ Thread.sleep(500);
+ } catch (InterruptedException e)
+ {
+ }
}
+ assertEquals(1, chimeraViewer.getBinding().getPdbCount());
chimeraViewer.closeViewer(true);
// todo: break here means only once through this loop?
break;
git://source.jalview.org / jalview.git / blobdiff