From 9a20339fe0483d2757c6c6b11b60e7332f828811 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 24 Mar 2017 12:21:33 +0000
Subject: [PATCH] JAL-1632 named parameters

---
 src/jalview/gui/TreeChooser.java |    5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

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);
   }
 
   /**
-- 
1.7.10.2