1 package jalview.analysis.scoremodels;
3 import jalview.api.analysis.ScoreModelI;
4 import jalview.api.analysis.SimilarityParamsI;
5 import jalview.datamodel.AlignmentView;
6 import jalview.math.MatrixI;
8 public abstract class SimilarityScoreModel implements ScoreModelI
12 * Computed similarity scores are converted to distance scores by subtracting
13 * every value from the maximum value. That is, maximum similarity corresponds
14 * to zero distance, and smaller similarities to larger distances.
17 public MatrixI findDistances(AlignmentView seqData,
18 SimilarityParamsI options)
20 MatrixI similarities = findSimilarities(seqData, options);
22 MatrixI distances = similarityToDistance(similarities);
28 * Converts a matrix of similarity scores to distance scores, by reversing the
29 * range of the scores, mapping the maximum to zero. The input matrix is not
34 public static MatrixI similarityToDistance(MatrixI similarities)
36 MatrixI distances = similarities.copy();
38 distances.reverseRange(true);