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

   1 package jalview.ext.rbvi.chimera;
   2
   3 import static org.junit.Assert.assertTrue;
   4 import jalview.datamodel.PDBEntry;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.gui.AlignFrame;
   7 import jalview.gui.StructureViewer;
   8 import jalview.gui.StructureViewer.ViewerType;
   9 import jalview.io.FormatAdapter;
  10
  11 import org.junit.AfterClass;
  12 import org.junit.BeforeClass;
  13 import org.junit.Test;
  14
  15 public class JalviewChimeraView
  16 {
  17
  18   /**
  19    * @throws java.lang.Exception
  20    */
  21   @BeforeClass
  22   public static void setUpBeforeClass() throws Exception
  23   {
  24     jalview.bin.Jalview.main(new String[]
  25     { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" });
  26   }
  27
  28   /**
  29    * @throws java.lang.Exception
  30    */
  31   @AfterClass
  32   public static void tearDownAfterClass() throws Exception
  33   {
  34     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
  35
  36   }
  37
  38
  39   @Test
  40   public void testSingleSeqView()
  41   {
  42     String inFile = "examples/1gaq.txt";
  43     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
  44             inFile, FormatAdapter.FILE);
  45     assertTrue("Didn't read input file " + inFile, af != null);
  46     for (SequenceI sq:af.getViewport().getAlignment().getSequences())
  47     {
  48       SequenceI dsq=sq.getDatasetSequence();
  49       while (dsq.getDatasetSequence()!=null)
  50       {
  51         dsq=dsq.getDatasetSequence();
  52       }
  53       if (dsq.getPDBId()!=null && dsq.getPDBId().size()>0) {
  54         for (int q=0;q<dsq.getPDBId().size();q++)
  55         {
  56           new StructureViewer(af.getViewport()
  57                   .getStructureSelectionManager()).viewStructures(
  58                   ViewerType.JMOL,
  59                   af.getCurrentView().getAlignPanel(),
  60                   new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
  61                   new SequenceI[][] { new SequenceI[] { sq } });
  62
  63           new StructureViewer(af.getViewport()
  64                   .getStructureSelectionManager()).viewStructures(
  65                   ViewerType.CHIMERA,
  66                   af.getCurrentView().getAlignPanel(),
  67                   new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
  68                   new SequenceI[][] { new SequenceI[] { sq } });
  69           // todo: break here means only once through this loop?
  70           break;
  71         }
  72         break;
  73       }
  74    }
  75     // try {
  76       // why?
  77 //      Thread.sleep(200000);
  78 //    } catch (InterruptedException q)
  79 //    {
  80     // }
  81   }
  82 }