package username.genetics;

/**
 * A sample non-trivial metric for costing changes in DNA
 * sequences.
 *
 * @author Gene Geneticist
 * @author Gena Geneticist
 * @author Samuel A. Rebelsky
 * @version 1.0 of April 2006
 */
public class SampleMetric
  implements CostMetric
{
  /**
   * The cost for deleting character sc from source.
   */
  public int deleteCost(char sc)
  {
    // It is slightly cheaper to delete A
    if ((sc == 'A') || (sc == 'a')) {
        return 2;
    }
    // It is significantly more expensive to delete G
    else if ((sc == 'G') || (sc == 'g')) {
        return 8;
    }
    // Default: Relatively cheap
    else {
        return 3;
    }
  } // deleteCost(char)

  /**
   * The cost for inserting character tc into source.
   */
  public int insertCost(char tc)
  {
      // Inserting C is cheap
      if ((tc == 'C') || (tc == 'c')) {
        return 3;
      }
      // Inserting is generally expensive.
      else {
        return 9;
      }
  } // insertCost(char)

  /**
   * The cost for changing char sc of source to char tc of target.
   */
  public int replaceCost(char sc, char tc)
  {
      // Replacing characters with their complement is cheap.
      if ( (((sc == 'a') || (sc == 'A')) && ((tc == 't') || (tc == 'T')))
           || (((sc == 't') || (sc == 'T')) && ((tc == 'a') || (tc == 'A')))
           || (((sc == 'c') || (sc == 'C')) && ((tc == 'g') || (tc == 'G')))
           || (((sc == 'g') || (sc == 'G')) && ((tc == 'c') || (tc == 'C'))) ) {
    return 1;
      }
      // Actually, replacmeent is still pretty cheap
      else {
         return 2;
      }
  } // replaceCost(char, char)
} // interface SampleMetric