JAL-838 added 'SeqSpace' PID mode, added parameters to findDistances and

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

diff --git a/src/jalview/api/analysis/SimilarityScoreModelI.java b/src/jalview/api/analysis/SimilarityScoreModelI.java
index 96208a3..0c2624f 100644 (file)
--- a/src/jalview/api/analysis/SimilarityScoreModelI.java
+++ b/src/jalview/api/analysis/SimilarityScoreModelI.java
@@ -15,10 +15,12 @@ public interface SimilarityScoreModelI extends ScoreModelI
   /**
    * Returns a similarity score for the given sequence regions, that is, a
    * matrix whose value [i][j] is the similarity of sequence i to sequence j by
-   * some measure
+   * some measure. The options parameter provides configuration choices for how
+   * the similarity score is calculated.
    * 
    * @param seqData
+   * @param options
    * @return
    */
-  MatrixI findSimilarities(AlignmentView seqData);
+  MatrixI findSimilarities(AlignmentView seqData, SimilarityParamsI options);
 }