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

   1 package jalview.ext.rbvi.chimera;
   2
   3 import static org.testng.AssertJUnit.assertTrue;
   4
   5 import jalview.api.structures.JalviewStructureDisplayI;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.gui.AlignFrame;
   8 import jalview.gui.StructureViewer;
   9 import jalview.gui.StructureViewer.ViewerType;
  10 import jalview.io.FormatAdapter;
  11
  12 import org.testng.annotations.AfterClass;
  13 import org.testng.annotations.BeforeClass;
  14 import org.testng.annotations.Test;
  15
  16 public class JalviewChimeraView
  17 {
  18
  19   /**
  20    * @throws java.lang.Exception
  21    */
  22   @BeforeClass(alwaysRun = true)
  23   public static void setUpBeforeClass() throws Exception
  24   {
  25     jalview.bin.Jalview.main(new String[]
  26     { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" });
  27   }
  28
  29   /**
  30    * @throws java.lang.Exception
  31    */
  32   @AfterClass
  33   public static void tearDownAfterClass() throws Exception
  34   {
  35     try
  36     {
  37     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
  38     } catch (Exception e)
  39     {
  40       // ignore NullPointerException thrown by JMol
  41     }
  42
  43   }
  44
  45   @Test(groups ={ "Functional" })
  46   public void testSingleSeqViewJMol()
  47   {
  48     String inFile = "examples/1gaq.txt";
  49     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  50             inFile, FormatAdapter.FILE);
  51     assertTrue("Didn't read input file " + inFile, af != null);
  52     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
  53     {
  54       SequenceI dsq = sq.getDatasetSequence();
  55       while (dsq.getDatasetSequence() != null)
  56       {
  57         dsq = dsq.getDatasetSequence();
  58       }
  59       if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
  60       {
  61         for (int q = 0; q < dsq.getPDBId().size(); q++)
  62         {
  63           final StructureViewer structureViewer = new StructureViewer(af
  64                   .getViewport().getStructureSelectionManager());
  65           structureViewer.setViewerType(ViewerType.JMOL);
  66           JalviewStructureDisplayI jmolViewer = structureViewer
  67                   .viewStructures(dsq.getPDBId().elementAt(q),
  68                           new SequenceI[]
  69                   { sq }, af.getCurrentView().getAlignPanel());
  70           /*
  71            * Wait for viewer thread to start
  72            */
  73           try
  74           {
  75             Thread.sleep(1000);
  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     String inFile = "examples/1gaq.txt";
  93     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  94             inFile, FormatAdapter.FILE);
  95     assertTrue("Didn't read input file " + inFile, af != null);
  96     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
  97     {
  98       SequenceI dsq = sq.getDatasetSequence();
  99       while (dsq.getDatasetSequence() != null)
 100       {
 101         dsq = dsq.getDatasetSequence();
 102       }
 103       if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
 104       {
 105         for (int q = 0; q < dsq.getPDBId().size(); q++)
 106         {
 107           final StructureViewer structureViewer = new StructureViewer(af
 108                   .getViewport().getStructureSelectionManager());
 109           structureViewer.setViewerType(ViewerType.CHIMERA);
 110           JalviewStructureDisplayI chimeraViewer = structureViewer
 111                   .viewStructures(dsq.getPDBId().elementAt(q),
 112                           new SequenceI[]
 113                           { sq }, af.getCurrentView().getAlignPanel());
 114           /*
 115            * Wait for viewer thread to start
 116            */
 117           try
 118           {
 119             Thread.sleep(1000);
 120           } catch (InterruptedException e)
 121           {
 122           }
 123           chimeraViewer.closeViewer(true);
 124           // todo: break here means only once through this loop?
 125           break;
 126         }
 127         break;
 128       }
 129     }
 130   }
 131 }