Merge branch 'develop' into features/JAL-2393customMatrices

[jalview.git] / src / jalview / api / analysis / DistanceScoreModelI.java

diff --git a/src/jalview/api/analysis/DistanceScoreModelI.java b/src/jalview/api/analysis/DistanceScoreModelI.java
index 27003e8..0a39c0b 100644 (file)
--- a/src/jalview/api/analysis/DistanceScoreModelI.java
+++ b/src/jalview/api/analysis/DistanceScoreModelI.java
@@ -5,7 +5,8 @@ import jalview.math.MatrixI;
 
 /**
  * A sequence distance score models, that provides a method to compute distances
- * between pairs of sequences
+ * between pairs of sequences. The options parameter provides configuration
+ * choices for how the similarity score is calculated.
  * 
  * @author gmcarstairs
  *
@@ -18,7 +19,8 @@ public interface DistanceScoreModelI extends ScoreModelI
    * measure
    * 
    * @param seqData
+   * @param options
    * @return
    */
-  MatrixI findDistances(AlignmentView seqData);
+  MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);
 }