package jalview.analysis.scoremodels;

import static org.testng.Assert.assertEquals;

import jalview.util.Comparison;

import org.testng.annotations.Test;

public class PIDModelTest
{
  private static final double DELTA = 0.00001D;

  @Test(groups = "Functional")
  public void testGetPairwiseScore()
  {
    PIDModel sm = new PIDModel();
    assertEquals(sm.getPairwiseScore('A', 'A'), 1f);
    assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
    assertEquals(sm.getPairwiseScore('a', 'A'), 1f);
    assertEquals(sm.getPairwiseScore('A', 'B'), 0f);
    assertEquals(sm.getPairwiseScore('A', ' '), 0f);
    assertEquals(sm.getPairwiseScore(' ', ' '), 0f);
    assertEquals(sm.getPairwiseScore('.', '.'), 0f);
    assertEquals(sm.getPairwiseScore('-', '-'), 0f);
  }

  /**
   * Regression test to verify that a (suitably configured) PIDModel computes
   * the same percentage identities as the Comparison.PID method
   */
  @Test(groups = "Functional")
  public void testComputePID_matchesComparisonPID()
  {
    /*
     * same length, no gaps
     */
    String s1 = "ARFNQDWSGI";
    String s2 = "ARKNQDQSGI";
    double newScore = new PIDModel().computePID(s1, s2,
            SimilarityParams.Jalview);
    double oldScore = Comparison.PID(s1, s2);
    assertEquals(newScore, oldScore, DELTA);

    /*
     * same length, with gaps
     */
    s1 = "-RFNQDWSGI";
    s2 = "ARKNQ-QSGI";
    newScore = new PIDModel().computePID(s1, s2,
            SimilarityParams.Jalview);
    oldScore = Comparison.PID(s1, s2);
    assertEquals(newScore, oldScore, DELTA);

    /*
     * s2 longer than s1, with gaps
     */
    s1 = "ARK-";
    s2 = "-RFNQ";
    newScore = new PIDModel().computePID(s1, s2,
            SimilarityParams.Jalview);
    oldScore = Comparison.PID(s1, s2);
    assertEquals(newScore, oldScore, DELTA);

    /*
     * s1 longer than s2, with gaps
     */
    s1 = "-RFNQ";
    s2 = "ARK-";
    newScore = new PIDModel().computePID(s1, s2,
            SimilarityParams.Jalview);
    oldScore = Comparison.PID(s1, s2);
    assertEquals(newScore, oldScore, DELTA);

    /*
     * same but now also with gapped columns
     */
    s1 = "-R-F-NQ";
    s2 = "AR-K--";
    newScore = new PIDModel().computePID(s1, s2, SimilarityParams.Jalview);
    oldScore = Comparison.PID(s1, s2);
    assertEquals(newScore, oldScore, DELTA);
  }
}