JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
index 5c47703..69ca403 100644 (file)
--- 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()
   {