From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 24 Mar 2017 12:21:33 +0000 (+0000)
Subject: JAL-1632 named parameters
X-Git-Tag: Release_2_10_2~3^2~105^2~2^2~59
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9a20339fe0483d2757c6c6b11b60e7332f828811;p=jalview.git

JAL-1632 named parameters
---

diff --git a/src/jalview/gui/TreeChooser.java b/src/jalview/gui/TreeChooser.java
index 4f972ae..fa1195c 100644
--- a/src/jalview/gui/TreeChooser.java
+++ b/src/jalview/gui/TreeChooser.java
@@ -301,12 +301,15 @@ public class TreeChooser extends JPanel
      * matchOnShortestSequence = false
      * matchGaps = true except false for PCA by PID (to match SeqSpace)
      */
+    boolean includeGapGap = true;
+    boolean includeGapResidue = true;
+    boolean matchOnShortestLength = false;
     boolean matchGap = true;
     if (doPCA && (sm instanceof PIDModel))
     {
       matchGap = false;
     }
-    return new SimilarityParams(true, matchGap, true, false);
+    return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength);
   }
 
   /**