X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FSimilarityParams.java;fp=src%2Fjalview%2Fanalysis%2Fscoremodels%2FSimilarityParams.java;h=69ca4035ec09e0f0c5078257f72627eb72b144bd;hb=f820a6e0b7ec599b0e040109c3361cdb3e6d9aa0;hp=5c477035c3a403e9989e3950d50b62bea8719d85;hpb=51327103b12f9f1045d880ab1a4fac9317d88a05;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
index 5c47703..69ca4035 100644
--- a/src/jalview/analysis/scoremodels/SimilarityParams.java
+++ b/src/jalview/analysis/scoremodels/SimilarityParams.java
@@ -104,6 +104,7 @@ public class SimilarityParams implements SimilarityParamsI
 
   private boolean denominateByShortestLength;
 
+
   /**
    * Constructor
    * 
@@ -124,6 +125,19 @@ public class SimilarityParams implements SimilarityParamsI
     denominateByShortestLength = shortestLength;
   }
 
+  /**
+   * BH added a non-Groovy "standard" set for JalviewJS
+   * 
+   * @param isPCA
+   */
+  public SimilarityParams(boolean isPCA)
+  {
+    includeGappedColumns = true;
+    matchGaps = !isPCA;
+    includeGaps = true;
+    denominateByShortestLength = false;
+  }
+
   @Override
   public boolean includeGaps()
   {