package jalview.datamodel;

import static org.testng.Assert.assertEquals;

import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.HMMFile;

import java.io.IOException;
import java.net.MalformedURLException;

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

public class HMMNodeTest
{
  private HiddenMarkovModel hmm;

  @BeforeClass(alwaysRun = true)
  public void setUp() throws MalformedURLException, IOException
  {
    /*
     * load hmm model of a Kinase domain to a HiddenMarkovModel
     */
    HMMFile file = new HMMFile(new FileParse(
            "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
    hmm = file.getHMM();
  }

  @Test(groups="Functional")
  public void testGetMaxMatchEmissionIdex()
  {
    assertEquals(hmm.getAlphabetType(), "amino");
    String symbols = hmm.getSymbols();

    assertEquals(hmm.getNode(1).getMaxMatchEmissionIndex(),
            symbols.indexOf('Y'));

    assertEquals(hmm.getNode(17).getMaxMatchEmissionIndex(),
            symbols.indexOf('K'));
  }
}