From 24003ce252e653972ece110e077acd16ed47fe15 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Thu, 2 Nov 2017 17:06:48 +0000
Subject: [PATCH] JAL-2795 Reverted code changes needed to cluster from
 Forester

---
 src/jalview/analysis/TreeBuilder.java                       |    4 +---
 .../ext/archaeopteryx/ArchaeopteryxTreeConverter.java       |   11 +++++------
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 30b83b3..0cd340e 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -53,8 +53,6 @@ public abstract class TreeBuilder
 
   protected MatrixI distances;
 
-  public MatrixI testDistances;
-
   protected int mini;
 
   protected int minj;
@@ -305,8 +303,8 @@ public abstract class TreeBuilder
     this.scoreModel = sm;
     this.scoreParams = scoreOptions;
 
-    testDistances = scoreModel.findDistances(seqData, scoreParams);
     distances = scoreModel.findDistances(seqData, scoreParams);
+
     makeLeaves();
 
     noClus = clusters.size();
diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
index ce603f5..53cc2c2 100644
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
@@ -5,7 +5,6 @@ import jalview.datamodel.SequenceI;
 import jalview.ext.forester.ForesterMatrix;
 import jalview.util.MessageManager;
 
-import org.forester.evoinference.distance.NeighborJoiningF;
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
@@ -31,7 +30,7 @@ public class ArchaeopteryxTreeConverter
     jalviewTree = calculatedTree;
     sequences = jalviewTree.getSequences();
     distances = ForesterMatrix.convertJalviewToForester(
-            jalviewTree.testDistances, sequences);
+            jalviewTree.getDistances(), sequences);
     aptxTree = new Phylogeny();
     rootNode = new PhylogenyNode();
 
@@ -44,17 +43,17 @@ public class ArchaeopteryxTreeConverter
 
     buildAptxTree();
 
-
     return aptxTree;
 
   }
 
   public Phylogeny buildAptxTree()
   {
+    // NeighborJoiningF foresterClustering = NeighborJoiningF
+    // .createInstance();
+    // aptxTree = foresterClustering.execute(distances);
+
 
-    NeighborJoiningF foresterClustering = NeighborJoiningF
-            .createInstance();
-    aptxTree = foresterClustering.execute(distances);
     treeTitle = generateTreeName();
     aptxTree.setName(treeTitle);
 
-- 
1.7.10.2