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

   1 package jalview.ext.rbvi.chimera;
   2
   3 import static org.testng.AssertJUnit.assertTrue;
   4 import org.testng.annotations.AfterClass;
   5 import org.testng.annotations.Test;
   6 import org.testng.annotations.BeforeClass;
   7 import jalview.api.structures.JalviewStructureDisplayI;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.gui.AlignFrame;
  10 import jalview.gui.StructureViewer;
  11 import jalview.gui.StructureViewer.ViewerType;
  12 import jalview.io.FormatAdapter;
  13
  14 public class JalviewChimeraView
  15 {
  16
  17   /**
  18    * @throws java.lang.Exception
  19    */
  20   @BeforeClass
  21   public static void setUpBeforeClass() throws Exception
  22   {
  23     jalview.bin.Jalview.main(new String[]
  24     { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" });
  25   }
  26
  27   /**
  28    * @throws java.lang.Exception
  29    */
  30   @AfterClass
  31   public static void tearDownAfterClass() throws Exception
  32   {
  33     try
  34     {
  35     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
  36     } catch (Exception e)
  37     {
  38       // ignore NullPointerException thrown by JMol
  39     }
  40
  41   }
  42
  43   @Test
  44   public void testSingleSeqViewJMol()
  45   {
  46     String inFile = "examples/1gaq.txt";
  47     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  48             inFile, FormatAdapter.FILE);
  49     assertTrue("Didn't read input file " + inFile, af != null);
  50     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
  51     {
  52       SequenceI dsq = sq.getDatasetSequence();
  53       while (dsq.getDatasetSequence() != null)
  54       {
  55         dsq = dsq.getDatasetSequence();
  56       }
  57       if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
  58       {
  59         for (int q = 0; q < dsq.getPDBId().size(); q++)
  60         {
  61           final StructureViewer structureViewer = new StructureViewer(af
  62                   .getViewport().getStructureSelectionManager());
  63           structureViewer.setViewerType(ViewerType.JMOL);
  64           JalviewStructureDisplayI jmolViewer = structureViewer
  65                   .viewStructures(dsq.getPDBId().elementAt(q),
  66                           new SequenceI[]
  67                   { sq }, af.getCurrentView().getAlignPanel());
  68           /*
  69            * Wait for viewer thread to start
  70            */
  71           try
  72           {
  73             Thread.sleep(1000);
  74           } catch (InterruptedException e)
  75           {
  76           }
  77
  78           jmolViewer.closeViewer(true);
  79           // todo: break here means only once through this loop?
  80           break;
  81         }
  82         break;
  83       }
  84     }
  85   }
  86
  87   @Test
  88   public void testSingleSeqViewChimera()
  89   {
  90     String inFile = "examples/1gaq.txt";
  91     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  92             inFile, FormatAdapter.FILE);
  93     assertTrue("Didn't read input file " + inFile, af != null);
  94     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
  95     {
  96       SequenceI dsq = sq.getDatasetSequence();
  97       while (dsq.getDatasetSequence() != null)
  98       {
  99         dsq = dsq.getDatasetSequence();
 100       }
 101       if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
 102       {
 103         for (int q = 0; q < dsq.getPDBId().size(); q++)
 104         {
 105           final StructureViewer structureViewer = new StructureViewer(af
 106                   .getViewport().getStructureSelectionManager());
 107           structureViewer.setViewerType(ViewerType.CHIMERA);
 108           JalviewStructureDisplayI chimeraViewer = structureViewer
 109                   .viewStructures(dsq.getPDBId().elementAt(q),
 110                           new SequenceI[]
 111                           { sq }, af.getCurrentView().getAlignPanel());
 112           /*
 113            * Wait for viewer thread to start
 114            */
 115           try
 116           {
 117             Thread.sleep(1000);
 118           } catch (InterruptedException e)
 119           {
 120           }
 121           chimeraViewer.closeViewer(true);
 122           // todo: break here means only once through this loop?
 123           break;
 124         }
 125         break;
 126       }
 127     }
 128   }
 129 }