package jalview.ext.rbvi.chimera;

import static org.junit.Assert.*;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.Viewer;
import jalview.io.FormatAdapter;

import java.awt.Desktop;
import java.io.File;

import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.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
  {
    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);

  }


  @Test
  public void testSingleSeqView()
  {
    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++) 
        {
          new StructureViewer(af.getViewport().getStructureSelectionManager()).viewStructures(Viewer.JMOL,
                  af.getCurrentView().getAlignPanel(),
                  new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
                  new SequenceI[][] { new SequenceI[] { sq } });

          new StructureViewer(af.getViewport().getStructureSelectionManager()).viewStructures(Viewer.CHIMERA,
                  af.getCurrentView().getAlignPanel(),
                  new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
                  new SequenceI[][] { new SequenceI[] { sq } });
          break;
        }
        break;
      }
   }
    try {
      Thread.sleep(200000);
    } catch (InterruptedException q)
    {
      
    }
  }
}