1 package jalview.api.analysis;
3 import jalview.datamodel.AlignmentView;
4 import jalview.math.MatrixI;
7 * A sequence distance score models, that provides a method to compute distances
8 * between pairs of sequences. The options parameter provides configuration
9 * choices for how the similarity score is calculated.
14 public interface DistanceScoreModelI extends ScoreModelI
17 * Returns a distance score for the given sequence regions, that is, a matrix
18 * whose value [i][j] is the distance of sequence i from sequence j by some
25 MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);