package jalview.hmmer;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotEquals;
import static org.testng.Assert.fail;

import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.io.DataSourceType;
import jalview.io.FastaFile;
import jalview.io.FileParse;
import jalview.ws.params.ArgumentI;

import java.io.IOException;
import java.net.MalformedURLException;
import java.util.ArrayList;
import java.util.List;

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


public class HMMERTest {

  AlignFrame frame;

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

  @AfterClass(alwaysRun = true)
  public static void tearDownAfterClass() throws Exception
  {
    Desktop.instance.closeAll_actionPerformed(null);
  }

  @Test(priority = 0)
  public void testHMMBuild() throws MalformedURLException, IOException
  {
    FastaFile file = null;
    try
    {
      file = new FastaFile(
              new FileParse("examples/uniref50.fa", DataSourceType.FILE));
    } catch (IOException e)
    {
      e.printStackTrace();
      fail();
    }
    SequenceI[] seqs = file.getSeqsAsArray();
    AlignmentI al = new Alignment(seqs);
    frame = new AlignFrame(al, 150, 20);

    HMMBuildThread thread = new HMMBuildThread(frame,
            new ArrayList<ArgumentI>());
    thread.hmmbuildWaitTillComplete();

    SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
    HiddenMarkovModel hmm = seq.getHMM();
    if (hmm == null)
    {
      fail();
    }

    assertEquals(hmm.getLength().intValue(), 148);
    assertEquals(hmm.getAlphabetType(), "amino");
    assertEquals(hmm.getName(), "Alignment");
    assertEquals(hmm.getEffectiveNumberOfSequences(), 0.648193, 0.0001);
    assertEquals(hmm.getConsensusAtAlignColumn(15), 's');
  }

  @Test(priority = 1)
  public void testHMMAlign() throws MalformedURLException, IOException
  {
    HMMAlignThread thread = new HMMAlignThread(frame, true,
            new ArrayList<ArgumentI>());
    try
    {
      thread.hmmalignWaitTillComplete();
    } catch (Exception e)
    {
      e.printStackTrace();
      fail();
    }

    if (Desktop.getAlignFrames() == null)
    {
      fail();
    }

    AlignFrame frame = Desktop.getAlignFrames()[0];
    AlignmentI al = frame.getViewport().getAlignment();
    assertNotEquals(al, null);
    List<SequenceI> hmmSeqs = al.getHMMConsensusSequences(false);
    assertNotEquals(hmmSeqs, null);

  }
}