package jalview.analysis.scoremodels;

import jalview.api.analysis.ScoreModelI;

import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.Map;
import java.util.TreeMap;

/**
 * A class that can register and serve instances of ScoreModelI
 */
public class ScoreModels
{
  private static ScoreModels instance = new ScoreModels();

  private Map<String, ScoreModelI> models;

  public static ScoreModels getInstance()
  {
    return instance;
  }

  /**
   * Private constructor to enforce use of singleton. Registers Jalview's
   * "built-in" score models:
   * <ul>
   * <li>BLOSUM62</li>
   * <li>PAM250</li>
   * <li>DNA</li>
   * <li>Sequence Feature Similarity</li>
   * <li>Percentage Identity</li>
   * </ul>
   */
  private ScoreModels()
  {
    /*
     * using TreeMap keeps models ordered alphabetically by name
     */
    models = new TreeMap<String, ScoreModelI>(String.CASE_INSENSITIVE_ORDER);
    loadScoreMatrix("/scoreModel/blosum62.scm");
    loadScoreMatrix("/scoreModel/pam250.scm");
    loadScoreMatrix("/scoreModel/dna.scm");
    registerScoreModel(new FeatureScoreModel());
    registerScoreModel(new PIDScoreModel());
  }

  /**
   * Try to load a score matrix from the given resource file, and if successful,
   * register it. Answers true if successful, else false. Any errors are
   * reported on syserr but not thrown.
   * 
   * @param string
   */
  boolean loadScoreMatrix(String resourcePath)
  {
    URL url = this.getClass().getResource(resourcePath);
    if (url == null)
    {
      System.err.println("Failed to locate " + resourcePath);
      return false;
    }
    boolean success = false;
    InputStream is = null;
    try
    {
      is = url.openStream();
      ScoreMatrix sm = ScoreMatrix.parse(is);
      if (sm != null)
      {
        registerScoreModel(sm);
        success = true;
      }
    } catch (IOException e)
    {
    } finally
    {
      if (is != null)
      {
        try
        {
          is.close();
        } catch (IOException e)
        {
        }
      }
    }
    return success;
  }

  /**
   * Answers an iterable set of the registered score models. Currently these are
   * ordered by name (not case sensitive).
   * 
   * @return
   */
  public Iterable<ScoreModelI> getModels()
  {
    return models.values();
  }

  public ScoreModelI forName(String s)
  {
    return models.get(s);
  }

  public void registerScoreModel(ScoreModelI sm)
  {
    ScoreModelI sm2 = models.get(sm.getName());
    if (sm2 != null)
    {
      System.err.println("Warning: replacing score model " + sm2.getName());
    }
    models.put(sm.getName(), sm);
  }
}