JAL-3210 Barebones gradle/buildship/eclipse. See README

[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 69ca403..5c47703 100644 (file)
--- a/src/jalview/analysis/scoremodels/SimilarityParams.java
+++ b/src/jalview/analysis/scoremodels/SimilarityParams.java
@@ -104,7 +104,6 @@ public class SimilarityParams implements SimilarityParamsI
 
   private boolean denominateByShortestLength;
 
-
   /**
    * Constructor
    * 
@@ -125,19 +124,6 @@ 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()
   {