package jalview.api.analysis;

/**
 * A description of options when computing percentage identity of two aligned
 * sequences
 */
public interface SimilarityParamsI
{
  /**
   * Answers true if gap-gap aligned positions should be included in the
   * calculation
   * 
   * @return
   */
  boolean includeGappedColumns();

  /**
   * Answers true if gap-residue alignment is considered a match
   * 
   * @return
   */
  // TODO is this specific to a PID score only?
  // score matrix will compute whatever is configured for gap-residue
  boolean matchGaps();

  /**
   * Answers true if gaps are included in the calculation. This may affect the
   * calculated score, the denominator (normalisation factor) of the score, or
   * both. Gap-gap positions are included if this and includeGappedColumns both
   * answer true.
   * 
   * @return
   */
  boolean includeGaps();

  /**
   * Answers true if only the shortest sequence length is used to divide the
   * total score, false if the longest sequence length
   * 
   * @return
   */
  boolean denominateByShortestLength();
}