package jalview.ext.rbvi.chimera;
-import static org.junit.Assert.*;
-import jalview.datamodel.PDBEntry;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.StructureViewer;
-import jalview.gui.StructureViewer.Viewer;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.FormatAdapter;
-import java.awt.Desktop;
-import java.io.File;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
public class JalviewChimeraView
{
/**
* @throws java.lang.Exception
*/
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
jalview.bin.Jalview.main(new String[]
@AfterClass
public static void tearDownAfterClass() throws Exception
{
+ try
+ {
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ } catch (Exception e)
+ {
+ // ignore NullPointerException thrown by JMol
+ }
}
-
- @Test
- public void testSingleSeqView()
+ @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())
+ for (SequenceI sq : af.getViewport().getAlignment().getSequences())
{
- SequenceI dsq=sq.getDatasetSequence();
- while (dsq.getDatasetSequence()!=null)
+ SequenceI dsq = sq.getDatasetSequence();
+ while (dsq.getDatasetSequence() != null)
{
- dsq=dsq.getDatasetSequence();
+ dsq = dsq.getDatasetSequence();
}
- if (dsq.getPDBId()!=null && dsq.getPDBId().size()>0) {
- for (int q=0;q<dsq.getPDBId().size();q++)
+ if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
+ {
+ for (int q = 0; q < dsq.getPDBId().size(); q++)
{
- new StructureViewer(af.getViewport().getStructureSelectionManager()).viewStructures(Viewer.JMOL,
- af.getCurrentView().getAlignPanel(),
- new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
- new SequenceI[][] { new SequenceI[] { sq } });
+ 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)
+ {
+ }
- new StructureViewer(af.getViewport().getStructureSelectionManager()).viewStructures(Viewer.CHIMERA,
- af.getCurrentView().getAlignPanel(),
- new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
- new SequenceI[][] { new SequenceI[] { sq } });
+ jmolViewer.closeViewer(true);
+ // todo: break here means only once through this loop?
break;
}
break;
}
- }
- try {
- Thread.sleep(200000);
- } catch (InterruptedException q)
+ }
+ }
+
+ @Test(groups ={ "Functional" })
+ public void testSingleSeqViewChimera()
+ {
+ 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.CHIMERA);
+ JalviewStructureDisplayI chimeraViewer = 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)
+ {
+ }
+ chimeraViewer.closeViewer(true);
+ // todo: break here means only once through this loop?
+ break;
+ }
+ break;
+ }
}
}
}