X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FPIDModel.java;h=aff12107789906e2453e20c1896b38136c59f190;hb=8717834368bd00d8adfa47ee099288acd34363ef;hp=58667c070c2f1a01351ffa220cb44441d785bd3a;hpb=70af62ad365829d2fc430db10336cf13c4d4ce1a;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java
index 58667c0..aff1210 100644
--- a/src/jalview/analysis/scoremodels/PIDModel.java
+++ b/src/jalview/analysis/scoremodels/PIDModel.java
@@ -62,11 +62,11 @@ public class PIDModel implements SimilarityScoreModelI,
   }
 
   @Override
-  public MatrixI findSimilarities(AlignmentView seqData)
+  public MatrixI findSimilarities(AlignmentView seqData,
+          SimilarityParamsI options)
   {
-    // TODO reuse code in ScoreMatrix instead somehow
     String[] seqs = seqData.getSequenceStrings(' ');
-    return findSimilarities(seqs, SimilarityParams.Jalview);
+    return findSimilarities(seqs, options);
   }
 
   /**
@@ -80,6 +80,7 @@ public class PIDModel implements SimilarityScoreModelI,
   protected MatrixI findSimilarities(String[] seqs,
           SimilarityParamsI options)
   {
+    // TODO reuse code in ScoreMatrix instead somehow
     double[][] values = new double[seqs.length][];
     for (int row = 0; row < seqs.length; row++)
     {