package jalview.hmmer;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import static org.testng.Assert.fail;

import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.io.HMMFile;
import jalview.util.MessageManager;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.simple.Option;

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 void setUpBeforeClass() throws Exception
  {
    /*
     * NB: check HMMER_PATH in testProps.jvprops is valid for
     * the machine on which this runs
     */
    Jalview.main(
            new String[]
    { "-noquestionnaire", "-nonews", "-props",
                "test/jalview/hmmer/testProps.jvprops", "-open",
                "examples/uniref50.fa" });
    frame = Desktop.getAlignFrames()[0];
  }

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

  /**
   * Test with a dependency on locally installed hmmbuild binaries
   * 
   * @throws MalformedURLException
   * @throws IOException
   */
  @Test(groups = "External")
  public void testHMMBuildThenHMMAlign()
          throws MalformedURLException, IOException
  {
    /*
     * run hmmbuild
     */
    testHMMBuild();
    List<SequenceI> hmms = frame.getViewport().getAlignment()
            .getHmmSequences();
    assertFalse(hmms.isEmpty());

    /*
     * now run hmmalign - by default with respect to the added HMM profile
     */
    testHMMAlign();
  }

  public void testHMMBuild()
  {
    /*
     * set up argument to run hmmbuild for the alignment
     */
    ArrayList<ArgumentI> params = new ArrayList<>();
    String argName = MessageManager.getString("label.hmmbuild_for");
    String argValue = MessageManager.getString("label.alignment");
    params.add(
            new Option(argName, null, false, null, argValue, null, null));

    HMMBuild builder = new HMMBuild(frame, params);
    builder.run();

    SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
    HiddenMarkovModel hmm = seq.getHMM();
    assertNotNull(hmm);

    assertEquals(hmm.getLength(), 148);
    assertEquals(hmm.getAlphabetType(), "amino");
    assertEquals(hmm.getName(), "Alignment_HMM");
    assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
            "0.648193");
  }

  public void testHMMAlign()
  {
    HmmerCommand thread = new HMMAlign(frame,
            new ArrayList<ArgumentI>());
    thread.run();

    AlignFrame[] alignFrames = Desktop.getAlignFrames();
    if (alignFrames == null)
    {
      fail("No align frame loaded");
    }

    /*
     * now have the original align frame, and another for realigned sequences
     */
    assertEquals(alignFrames.length, 2);
    AlignmentI original = alignFrames[0].getViewport().getAlignment();
    assertNotNull(original);
    AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
    assertNotNull(realigned);
    assertFalse(original.getHmmSequences().isEmpty());
    assertFalse(realigned.getHmmSequences().isEmpty());

    SequenceI ferCapan = original.findName("FER_CAPAN");
    assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));

    SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
    assertTrue(ferCapanRealigned.getSequenceAsString()
            .startsWith("-------m-A----SVSAT"));
  }
}