package jalview.ext.rbvi.chimera;

import static org.testng.AssertJUnit.assertTrue;

import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.FormatAdapter;

import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;

public class JalviewChimeraView
{

  /**
   * @throws java.lang.Exception
   */
  @BeforeClass
  public static void setUpBeforeClass() throws Exception
  {
    jalview.bin.Jalview.main(new String[]
    { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" });
  }

  /**
   * @throws java.lang.Exception
   */
  @AfterClass
  public static void tearDownAfterClass() throws Exception
  {
    try
    {
    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
    } catch (Exception e)
    {
      // ignore NullPointerException thrown by JMol
    }

  }

  @Test(groups ={ "Functional" })
  public void testSingleSeqViewJMol()
  {
    String inFile = "examples/1gaq.txt";
    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
            inFile, FormatAdapter.FILE);
    assertTrue("Didn't read input file " + inFile, af != null);
    for (SequenceI sq : af.getViewport().getAlignment().getSequences())
    {
      SequenceI dsq = sq.getDatasetSequence();
      while (dsq.getDatasetSequence() != null)
      {
        dsq = dsq.getDatasetSequence();
      }
      if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
      {
        for (int q = 0; q < dsq.getPDBId().size(); q++)
        {
          final StructureViewer structureViewer = new StructureViewer(af
                  .getViewport().getStructureSelectionManager());
          structureViewer.setViewerType(ViewerType.JMOL);
          JalviewStructureDisplayI jmolViewer = structureViewer
                  .viewStructures(dsq.getPDBId().elementAt(q),
                          new SequenceI[]
                  { sq }, af.getCurrentView().getAlignPanel());
          /*
           * Wait for viewer thread to start
           */
          try
          {
            Thread.sleep(1000);
          } catch (InterruptedException e)
          {
          }

          jmolViewer.closeViewer(true);
          // todo: break here means only once through this loop?
          break;
        }
        break;
      }
    }
  }

  @Test(groups ={ "Functional" })
  public void testSingleSeqViewChimera()
  {
    String inFile = "examples/1gaq.txt";
    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
            inFile, FormatAdapter.FILE);
    assertTrue("Didn't read input file " + inFile, af != null);
    for (SequenceI sq : af.getViewport().getAlignment().getSequences())
    {
      SequenceI dsq = sq.getDatasetSequence();
      while (dsq.getDatasetSequence() != null)
      {
        dsq = dsq.getDatasetSequence();
      }
      if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
      {
        for (int q = 0; q < dsq.getPDBId().size(); q++)
        {
          final StructureViewer structureViewer = new StructureViewer(af
                  .getViewport().getStructureSelectionManager());
          structureViewer.setViewerType(ViewerType.CHIMERA);
          JalviewStructureDisplayI chimeraViewer = structureViewer
                  .viewStructures(dsq.getPDBId().elementAt(q),
                          new SequenceI[]
                          { sq }, af.getCurrentView().getAlignPanel());
          /*
           * Wait for viewer thread to start
           */
          try
          {
            Thread.sleep(1000);
          } catch (InterruptedException e)
          {
          }
          chimeraViewer.closeViewer(true);
          // todo: break here means only once through this loop?
          break;
        }
        break;
      }
    }
  }
}