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

[jalview.git] / src / jalview / analysis / scoremodels / ScoreMatrix.java

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 7f71d0f..84835a4 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -21,6 +21,7 @@
 package jalview.analysis.scoremodels;
 
 import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.api.analysis.SimilarityScoreModelI;
 import jalview.datamodel.AlignmentView;
 import jalview.math.Matrix;
@@ -345,19 +346,22 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    * </ul>
    */
   @Override
-  public MatrixI findSimilarities(AlignmentView seqstrings)
+  public MatrixI findSimilarities(AlignmentView seqstrings,
+          SimilarityParamsI options)
   {
     char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X') : ' ';
     String[] seqs = seqstrings.getSequenceStrings(gapChar);
-    return findSimilarities(seqs);
+    return findSimilarities(seqs, options);
   }
 
   /**
    * @param seqs
    * @return
    */
-  protected MatrixI findSimilarities(String[] seqs)
+  protected MatrixI findSimilarities(String[] seqs,
+          SimilarityParamsI options)
   {
+    // todo use options in calculation
     double[][] values = new double[seqs.length][];
     for (int row = 0; row < seqs.length; row++)
     {