1 package jalview.api.analysis;
3 import jalview.datamodel.AlignmentView;
4 import jalview.math.MatrixI;
7 * A class that provides a method to compute similarity scores of pairs of
13 public interface SimilarityScoreModelI extends ScoreModelI
16 * Returns a similarity score for the given sequence regions, that is, a
17 * matrix whose value [i][j] is the similarity of sequence i to sequence j by
18 * some measure. The options parameter provides configuration choices for how
19 * the similarity score is calculated.
25 MatrixI findSimilarities(AlignmentView seqData, SimilarityParamsI options);