X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fapi%2Fanalysis%2FDistanceScoreModelI.java;h=0a39c0b4153ff611e1bb290c9887c50f07107276;hb=567c2595554096f10feab130153f97286f3f7d80;hp=27003e8b1c5cd6d63757606726d0fbc64c42718e;hpb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;p=jalview.git

diff --git a/src/jalview/api/analysis/DistanceScoreModelI.java b/src/jalview/api/analysis/DistanceScoreModelI.java
index 27003e8..0a39c0b 100644
--- 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);
 }