1 package jalview.api.analysis;
4 * A description of options when computing percentage identity of two aligned
7 public interface SimilarityParamsI
10 * Answers true if gap-gap aligned positions should be included in the
15 boolean includeGappedColumns();
18 * Answers true if gap-residue alignment is considered a match
25 * Answers true if the demoninator (normalisation factor) of the score count
26 * includes gap-residue positions, false if it only includes residue-residue
27 * aligned positions. Gap-gap positions are included if this and
28 * includeGappedColumns both answer true.
32 boolean denominatorIncludesGaps();
35 * Answers true if only the shortest sequence length is used to divide the
36 * total score, false if the longest sequence length
40 boolean denominateByShortestLength();