test/jalview/ext/jmol/JmolViewerTest.java

   1 package jalview.ext.jmol;
   2
   3 import static org.testng.AssertJUnit.assertTrue;
   4
   5 import jalview.api.structures.JalviewStructureDisplayI;
   6 import jalview.bin.Cache;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.gui.AlignFrame;
   9 import jalview.gui.Preferences;
  10 import jalview.gui.StructureViewer;
  11 import jalview.gui.StructureViewer.ViewerType;
  12 import jalview.io.FormatAdapter;
  13
  14 import org.testng.annotations.AfterClass;
  15 import org.testng.annotations.BeforeClass;
  16 import org.testng.annotations.Test;
  17
  18 @Test(singleThreaded = true)
  19 public class JmolViewerTest
  20 {
  21
  22   /**
  23    * @throws java.lang.Exception
  24    */
  25   @BeforeClass(alwaysRun = true)
  26   public static void setUpBeforeClass() throws Exception
  27   {
  28     jalview.bin.Jalview.main(new String[]
  29  {
  30         "-noquestionnaire -nonews -props",
  31         "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
  32   }
  33
  34   /**
  35    * @throws java.lang.Exception
  36    */
  37   @AfterClass
  38   public static void tearDownAfterClass() throws Exception
  39   {
  40     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
  41   }
  42
  43   @Test(groups ={ "Functional" })
  44   public void testSingleSeqViewJMol()
  45   {
  46     Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
  47     String inFile = "examples/1gaq.txt";
  48     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  49             inFile, FormatAdapter.FILE);
  50     assertTrue("Didn't read input file " + inFile, af != null);
  51     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
  52     {
  53       SequenceI dsq = sq.getDatasetSequence();
  54       while (dsq.getDatasetSequence() != null)
  55       {
  56         dsq = dsq.getDatasetSequence();
  57       }
  58       if (dsq.getAllPDBEntries() != null && dsq.getAllPDBEntries().size() > 0)
  59       {
  60         for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
  61         {
  62           final StructureViewer structureViewer = new StructureViewer(af
  63                   .getViewport().getStructureSelectionManager());
  64           structureViewer.setViewerType(ViewerType.JMOL);
  65           JalviewStructureDisplayI jmolViewer = structureViewer
  66                   .viewStructures(dsq.getAllPDBEntries().elementAt(q),
  67                           new SequenceI[]
  68                   { sq }, af.getCurrentView().getAlignPanel());
  69           /*
  70            * Wait for viewer load thread to complete
  71            */
  72           try
  73           {
  74             while (!jmolViewer.getBinding().isFinishedInit())
  75             {
  76               Thread.sleep(500);
  77             }
  78           } catch (InterruptedException e)
  79           {
  80           }
  81
  82           jmolViewer.closeViewer(true);
  83           // todo: break here means only once through this loop?
  84           break;
  85         }
  86         break;
  87       }
  88     }
  89   }
  90 }