package jalview.io;

import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.gui.Desktop;

import java.time.Instant;
import java.util.Date;

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

public class Jalview2xmlBase
{

  /**
   * @throws java.lang.Exception
   */
  @BeforeClass(alwaysRun = true)
  public static void setUpBeforeClass() throws Exception
  {
    jalview.bin.Jalview.main(new String[] { "-props",
        "test/jalview/io/testProps_nodas.jvprops" });
    jalview.bin.Cache.setProperty(
            "JALVIEW_NEWS_RSS_LASTMODIFIED",
            Cache.date_format.format(Date.from(Instant.now().plusSeconds(
                    3600))));
  }

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

  @BeforeTest(alwaysRun = true)
  public static void clearDesktop()
  {
    if (Desktop.instance != null && Desktop.getAlignFrames() != null)
    {
      Desktop.instance.closeAll_actionPerformed(null);
    }
  }

  public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
  {
    int numdsann = 0;
    for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
    {
      if (sq.getAnnotation() != null)
      {
        for (AlignmentAnnotation dssa : sq.getAnnotation())
        {
          if (dssa.isValidStruc())
          {
            numdsann++;
          }
        }
      }
    }
    return numdsann;
  }

}