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 public class JalviewChimeraView
  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     { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" });
  30   }
  31
  32   /**
  33    * @throws java.lang.Exception
  34    */
  35   @AfterClass
  36   public static void tearDownAfterClass() throws Exception
  37   {
  38     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
  39   }
  40
  41   @Test(groups ={ "Functional" })
  42   public void testSingleSeqViewJMol()
  43   {
  44     Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
  45     String inFile = "examples/1gaq.txt";
  46     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  47             inFile, FormatAdapter.FILE);
  48     assertTrue("Didn't read input file " + inFile, af != null);
  49     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
  50     {
  51       SequenceI dsq = sq.getDatasetSequence();
  52       while (dsq.getDatasetSequence() != null)
  53       {
  54         dsq = dsq.getDatasetSequence();
  55       }
  56       if (dsq.getAllPDBEntries() != null && dsq.getAllPDBEntries().size() > 0)
  57       {
  58         for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
  59         {
  60           final StructureViewer structureViewer = new StructureViewer(af
  61                   .getViewport().getStructureSelectionManager());
  62           structureViewer.setViewerType(ViewerType.JMOL);
  63           JalviewStructureDisplayI jmolViewer = structureViewer
  64                   .viewStructures(dsq.getAllPDBEntries().elementAt(q),
  65                           new SequenceI[]
  66                   { sq }, af.getCurrentView().getAlignPanel());
  67           /*
  68            * Wait for viewer load thread to complete
  69            */
  70           try
  71           {
  72             while (!jmolViewer.getBinding().isFinishedInit())
  73             {
  74               Thread.sleep(500);
  75             }
  76           } catch (InterruptedException e)
  77           {
  78           }
  79
  80           jmolViewer.closeViewer(true);
  81           // todo: break here means only once through this loop?
  82           break;
  83         }
  84         break;
  85       }
  86     }
  87   }
  88
  89   @Test(groups ={ "Functional" })
  90   public void testSingleSeqViewChimera()
  91   {
  92     Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
  93             ViewerType.CHIMERA.name());
  94     String inFile = "examples/1gaq.txt";
  95     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  96             inFile, FormatAdapter.FILE);
  97     assertTrue("Didn't read input file " + inFile, af != null);
  98     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
  99     {
 100       System.out.println("** sq=" + sq.getName());
 101       SequenceI dsq = sq.getDatasetSequence();
 102       while (dsq.getDatasetSequence() != null)
 103       {
 104         dsq = dsq.getDatasetSequence();
 105       }
 106       if (dsq.getAllPDBEntries() != null && dsq.getAllPDBEntries().size() > 0)
 107       {
 108         for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
 109         {
 110           final StructureViewer structureViewer = new StructureViewer(af
 111                   .getViewport().getStructureSelectionManager());
 112           structureViewer.setViewerType(ViewerType.CHIMERA);
 113           JalviewStructureDisplayI chimeraViewer = structureViewer
 114                   .viewStructures(dsq.getAllPDBEntries().elementAt(q),
 115                           new SequenceI[]
 116                           { sq }, af.getCurrentView().getAlignPanel());
 117           /*
 118            * Wait for viewer load thread to complete
 119            */
 120           while (!chimeraViewer.getBinding().isFinishedInit())
 121           {
 122             try
 123             {
 124               Thread.sleep(500);
 125             } catch (InterruptedException e)
 126             {
 127             }
 128           }
 129           assertEquals(1, chimeraViewer.getBinding().getPdbCount());
 130           chimeraViewer.closeViewer(true);
 131           // todo: break here means only once through this loop?
 132           break;
 133         }
 134         break;
 135       }
 136     }
 137   }
 138 }