test/jalview/ext/rbvi/chimera/JalviewChimeraView.java

   1 package jalview.ext.rbvi.chimera;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertTrue;
   5
   6 import jalview.api.structures.JalviewStructureDisplayI;
   7 import jalview.bin.Cache;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.gui.AlignFrame;
  10 import jalview.gui.Preferences;
  11 import jalview.gui.StructureViewer;
  12 import jalview.gui.StructureViewer.ViewerType;
  13 import jalview.io.FormatAdapter;
  14
  15 import org.testng.annotations.AfterClass;
  16 import org.testng.annotations.BeforeClass;
  17 import org.testng.annotations.Test;
  18
  19 @Test(singleThreaded = true)
  20 public class JalviewChimeraView
  21 {
  22
  23   /**
  24    * @throws java.lang.Exception
  25    */
  26   @BeforeClass(alwaysRun = true)
  27   public static void setUpBeforeClass() throws Exception
  28   {
  29     jalview.bin.Jalview.main(new String[]
  30  {
  31         "-noquestionnaire -nonews -props",
  32         "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
  33   }
  34
  35   /**
  36    * @throws java.lang.Exception
  37    */
  38   @AfterClass
  39   public static void tearDownAfterClass() throws Exception
  40   {
  41     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
  42   }
  43
  44   @Test(groups ={ "Functional" })
  45   public void testSingleSeqViewChimera()
  46   {
  47     Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
  48             ViewerType.CHIMERA.name());
  49     String inFile = "examples/1gaq.txt";
  50     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  51             inFile, FormatAdapter.FILE);
  52     assertTrue("Didn't read input file " + inFile, af != null);
  53     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
  54     {
  55       System.out.println("** sq=" + sq.getName());
  56       SequenceI dsq = sq.getDatasetSequence();
  57       while (dsq.getDatasetSequence() != null)
  58       {
  59         dsq = dsq.getDatasetSequence();
  60       }
  61       if (dsq.getAllPDBEntries() != null && dsq.getAllPDBEntries().size() > 0)
  62       {
  63         for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
  64         {
  65           final StructureViewer structureViewer = new StructureViewer(af
  66                   .getViewport().getStructureSelectionManager());
  67           structureViewer.setViewerType(ViewerType.CHIMERA);
  68           JalviewStructureDisplayI chimeraViewer = structureViewer
  69                   .viewStructures(dsq.getAllPDBEntries().elementAt(q),
  70                           new SequenceI[]
  71                           { sq }, af.getCurrentView().getAlignPanel());
  72           /*
  73            * Wait for viewer load thread to complete
  74            */
  75           while (!chimeraViewer.getBinding().isFinishedInit())
  76           {
  77             try
  78             {
  79               Thread.sleep(500);
  80             } catch (InterruptedException e)
  81             {
  82             }
  83           }
  84           assertEquals(1, chimeraViewer.getBinding().getPdbCount());
  85           chimeraViewer.closeViewer(true);
  86           // todo: break here means only once through this loop?
  87           break;
  88         }
  89         break;
  90       }
  91     }
  92   }
  93 }