Start of creating tree nodes for Aptx

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
index 18ac083..07b5bb4 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -1,8 +1,15 @@
 package jalview.ext.archaeopteryx;
 
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
 import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
 
 public class ArchaeopteryxTreeBuilder extends Phylogeny
 {
+  List<PhylogenyNode> nodes = Collections
+          .synchronizedList(new ArrayList<PhylogenyNode>());
   
 }

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 811957b..de4fd37 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -28,6 +28,7 @@ import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.SequenceGroup;
+import jalview.ext.archaeopteryx.ArchaeopteryxTreeBuilder;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -480,6 +481,8 @@ public class CalculationChooser extends JPanel
       TreeModel tree = new TreeModel(calculatedTree);
       openTreePanel(tree, treeAlgo, params);
 
+      ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder();
+
 
     }