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

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

diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java
index 58667c0..aff1210 100644 (file)
--- 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++)
     {