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

   1 package jalview.ext.rbvi.chimera;
   2
   3 import static org.junit.Assert.assertTrue;
   4
   5 import org.junit.AfterClass;
   6 import org.junit.BeforeClass;
   7 import org.junit.Test;
   8
   9 import jalview.datamodel.PDBEntry;
  10 import jalview.datamodel.SequenceI;
  11 import jalview.gui.AlignFrame;
  12 import jalview.gui.StructureViewer;
  13 import jalview.gui.StructureViewer.ViewerType;
  14 import jalview.io.FormatAdapter;
  15
  16 public class JalviewChimeraView
  17 {
  18
  19   /**
  20    * @throws java.lang.Exception
  21    */
  22   @BeforeClass
  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
  46   @Test
  47   public void testSingleSeqView()
  48   {
  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       SequenceI dsq=sq.getDatasetSequence();
  56       while (dsq.getDatasetSequence()!=null)
  57       {
  58         dsq=dsq.getDatasetSequence();
  59       }
  60       if (dsq.getPDBId()!=null && dsq.getPDBId().size()>0) {
  61         for (int q=0;q<dsq.getPDBId().size();q++)
  62         {
  63           new StructureViewer(af.getViewport()
  64                   .getStructureSelectionManager()).viewStructures(
  65                   ViewerType.JMOL,
  66                   af.getCurrentView().getAlignPanel(),
  67                   new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
  68                   new SequenceI[][] { new SequenceI[] { sq } });
  69
  70           new StructureViewer(af.getViewport()
  71                   .getStructureSelectionManager()).viewStructures(
  72                   ViewerType.CHIMERA,
  73                   af.getCurrentView().getAlignPanel(),
  74                   new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
  75                   new SequenceI[][] { new SequenceI[] { sq } });
  76           // todo: break here means only once through this loop?
  77           break;
  78         }
  79         break;
  80       }
  81    }
  82     // try {
  83       // why?
  84 //      Thread.sleep(200000);
  85 //    } catch (InterruptedException q)
  86 //    {
  87     // }
  88   }
  89 }