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.api.structures.JalviewStructureDisplayI;
  10 import jalview.datamodel.PDBEntry;
  11 import jalview.datamodel.SequenceI;
  12 import jalview.gui.AlignFrame;
  13 import jalview.gui.StructureViewer;
  14 import jalview.gui.StructureViewer.ViewerType;
  15 import jalview.io.FormatAdapter;
  16
  17 public class JalviewChimeraView
  18 {
  19
  20   /**
  21    * @throws java.lang.Exception
  22    */
  23   @BeforeClass
  24   public static void setUpBeforeClass() throws Exception
  25   {
  26     jalview.bin.Jalview.main(new String[]
  27     { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" });
  28   }
  29
  30   /**
  31    * @throws java.lang.Exception
  32    */
  33   @AfterClass
  34   public static void tearDownAfterClass() throws Exception
  35   {
  36     try
  37     {
  38     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
  39     } catch (Exception e)
  40     {
  41       // ignore NullPointerException thrown by JMol
  42     }
  43
  44   }
  45
  46   @Test
  47   public void testSingleSeqViewJMol()
  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       {
  62         for (int q = 0; q < dsq.getPDBId().size(); q++)
  63         {
  64           final StructureViewer structureViewer = new StructureViewer(af
  65                   .getViewport().getStructureSelectionManager());
  66
  67           JalviewStructureDisplayI jmolViewer = structureViewer
  68                   .viewStructures(ViewerType.JMOL, af.getCurrentView()
  69                           .getAlignPanel(), new PDBEntry[]
  70                   { (PDBEntry) dsq.getPDBId().elementAt(q) },
  71                           new SequenceI[][]
  72                           { new SequenceI[]
  73                           { sq } });
  74           /*
  75            * Wait for viewer thread to start
  76            */
  77           try
  78           {
  79             Thread.sleep(1000);
  80           } catch (InterruptedException e)
  81           {
  82           }
  83
  84           jmolViewer.closeViewer(true);
  85           // todo: break here means only once through this loop?
  86           break;
  87         }
  88         break;
  89       }
  90     }
  91   }
  92
  93   @Test
  94   public void testSingleSeqViewChimera()
  95   {
  96     String inFile = "examples/1gaq.txt";
  97     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  98             inFile, FormatAdapter.FILE);
  99     assertTrue("Didn't read input file " + inFile, af != null);
 100     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
 101     {
 102       SequenceI dsq = sq.getDatasetSequence();
 103       while (dsq.getDatasetSequence() != null)
 104       {
 105         dsq = dsq.getDatasetSequence();
 106       }
 107       if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
 108       {
 109         for (int q = 0; q < dsq.getPDBId().size(); q++)
 110         {
 111           final StructureViewer structureViewer = new StructureViewer(af
 112                   .getViewport().getStructureSelectionManager());
 113
 114           JalviewStructureDisplayI chimeraViewer = structureViewer
 115                   .viewStructures(ViewerType.CHIMERA, af.getCurrentView()
 116                           .getAlignPanel(), new PDBEntry[]
 117                   { (PDBEntry) dsq.getPDBId().elementAt(q) },
 118                           new SequenceI[][]
 119                           { new SequenceI[]
 120                           { sq } });
 121           /*
 122            * Wait for viewer thread to start
 123            */
 124           try
 125           {
 126             Thread.sleep(1000);
 127           } catch (InterruptedException e)
 128           {
 129           }
 130           chimeraViewer.closeViewer(true);
 131           // todo: break here means only once through this loop?
 132           break;
 133         }
 134         break;
 135       }
 136     }
 137   }
 138 }