X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FSimilarityParams.java;h=4d8c3fc276ae8e3767b9f516fe584e567a4692d8;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=e5751ca6e61d6aac1a3eb1b7a3ccef14820d8689;hpb=15e5ce4fe2019ff41fcab75395e9280d952145a8;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
index e5751ca..4d8c3fc 100644
--- a/src/jalview/analysis/scoremodels/SimilarityParams.java
+++ b/src/jalview/analysis/scoremodels/SimilarityParams.java
@@ -20,8 +20,8 @@ public class SimilarityParams implements SimilarityParamsI
    * Based on Jalview's Comparison.PID method, which includes gaps and counts
    * them as matching; it counts over the length of the shorter sequence
    */
-  public static final SimilarityParamsI Jalview = new SimilarityParams(
-          true, true, true, true);
+  public static final SimilarityParamsI Jalview = new SimilarityParams(true,
+          true, true, true);
 
   /**
    * 'SeqSpace' mode PCA calculation includes gaps but does not count them as