/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.analysis.scoremodels;

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

import jalview.api.analysis.PairwiseScoreModelI;
import jalview.api.analysis.ScoreModelI;

import java.util.Iterator;

import org.testng.annotations.Test;

public class ScoreModelsTest
{
  /**
   * Verify that the singleton constructor successfully loads Jalview's built-in
   * score models
   */
  @Test(groups = "Functional")
  public void testConstructor()
  {
    Iterator<ScoreModelI> models = ScoreModels.getInstance().getModels()
            .iterator();
    assertTrue(models.hasNext());

    /*
     * models are served in order of addition
     */
    ScoreModelI sm = models.next();
    assertTrue(sm instanceof SimilarityScoreModel);
    assertTrue(sm instanceof PairwiseScoreModelI);
    assertFalse(sm instanceof DistanceScoreModel);
    assertEquals(sm.getName(), "BLOSUM62");
    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'),
            -3f);

    sm = models.next();
    assertTrue(sm instanceof SimilarityScoreModel);
    assertTrue(sm instanceof PairwiseScoreModelI);
    assertFalse(sm instanceof DistanceScoreModel);
    assertEquals(sm.getName(), "PAM250");
    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'),
            -4f);

    sm = models.next();
    assertTrue(sm instanceof SimilarityScoreModel);
    assertTrue(sm instanceof PairwiseScoreModelI);
    assertFalse(sm instanceof DistanceScoreModel);
    assertEquals(sm.getName(), "DNA");
    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);

    sm = models.next();
    assertTrue(sm instanceof SimilarityScoreModel);
    assertTrue(sm instanceof PairwiseScoreModelI);
    assertFalse(sm instanceof DistanceScoreModel);
    assertEquals(sm.getName(), "PID");
    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);

    sm = models.next();
    assertFalse(sm instanceof SimilarityScoreModel);
    assertFalse(sm instanceof PairwiseScoreModelI);
    assertTrue(sm instanceof DistanceScoreModel);
    assertEquals(sm.getName(), "Sequence Feature Similarity");
  }

  /**
   * 'Test' that prints out score matrices in tab-delimited format. This test is
   * intentionally not assigned to any group so would not be run as part of a
   * suite. It makes no assertions and is just provided as a utility method for
   * printing out matrices. Relocated here from ScoreMatrixPrinter.
   */
  @Test(groups = "none")
  public void printAllMatrices_tabDelimited()
  {
    printAllMatrices(false);
  }

  /**
   * 'Test' that prints out score matrices in html format. This test is
   * intentionally not assigned to any group so would not be run as part of a
   * suite. It makes no assertions and is just provided as a utility method for
   * printing out matrices. Relocated here from ScoreMatrixPrinter.
   */
  @Test(groups = "none")
  public void printAllMatrices_asHtml()
  {
    printAllMatrices(true);
  }

  /**
   * Print all registered ScoreMatrix as plain or html tables
   * 
   * @param asHtml
   */
  protected void printAllMatrices(boolean asHtml)
  {
    for (ScoreModelI sm : ScoreModels.getInstance().getModels())
    {
      if (sm instanceof ScoreMatrix)
      {
        System.out.println(((ScoreMatrix) sm).outputMatrix(asHtml));
      }
    }
  }
}