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

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