package jalview.analysis.scoremodels;

import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.AlignmentView;
import jalview.math.MatrixI;

public abstract class DistanceScoreModel implements ScoreModelI
{
  /**
   * A similarity score is calculated by first computing a distance score, and
   * then reversing the min-max range of the score values
   */
  @Override
  public MatrixI findSimilarities(AlignmentView seqData,
          SimilarityParamsI options)
  {
    MatrixI distances = findDistances(seqData, options);

    MatrixI similarities = distanceToSimilarity(distances);

    return similarities;
  }

  /**
   * Converts distance scores to similarity scores, by reversing the range of
   * score values so that max becomes min and vice versa. The input matrix is
   * not modified.
   * 
   * @param distances
   */
  public static MatrixI distanceToSimilarity(MatrixI distances)
  {
    MatrixI similarities = distances.copy();

    similarities.reverseRange(false);

    return similarities;
  }
}