/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.ext.jmol;

import static org.testng.AssertJUnit.assertTrue;

import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Preferences;
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;

@Test(singleThreaded = true)
public class JmolViewerTest
{

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

  /**
   * @throws java.lang.Exception
   */
  @AfterClass(alwaysRun = true)
  public static void tearDownAfterClass() throws Exception
  {
    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
  }

  @Test(groups = { "Functional" })
  public void testSingleSeqViewJMol()
  {
    Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
    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.getAllPDBEntries() != null
              && dsq.getAllPDBEntries().size() > 0)
      {
        for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
        {
          final StructureViewer structureViewer = new StructureViewer(af
                  .getViewport().getStructureSelectionManager());
          structureViewer.setViewerType(ViewerType.JMOL);
          JalviewStructureDisplayI jmolViewer = structureViewer
                  .viewStructures(dsq.getAllPDBEntries().elementAt(q),
                          new SequenceI[] { sq }, af.getCurrentView()
                                  .getAlignPanel());
          /*
           * Wait for viewer load thread to complete
           */
          try
          {
            while (!jmolViewer.getBinding().isFinishedInit())
            {
              Thread.sleep(500);
            }
          } catch (InterruptedException e)
          {
          }

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