JAL-2795 Reverted code changes needed to cluster from Forester

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 30b83b3..0cd340e 100644 (file)
--- 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 (file)
--- 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);