Begin separation of GUI and tree calculation logic

[jalview.git] / src / jalview / gui / TreePanel.java

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 3af174a..a4521cc 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -41,7 +41,7 @@ import jalview.datamodel.NodeTransformI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
-import jalview.ext.archaeopteryx.Testo;
+import jalview.ext.archaeopteryx.ArchaeopteryxInit;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.NewickFile;
@@ -56,9 +56,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.image.BufferedImage;
 import java.beans.PropertyChangeEvent;
-import java.io.File;
 import java.io.FileOutputStream;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -279,6 +277,10 @@ public class TreePanel extends GTreePanel
         {
           originalSeqData.setVisible(false);
         }
+
+        ArchaeopteryxInit archae = new ArchaeopteryxInit(newtree);
+        archae.startArchaeopteryx();
+
       }
       else
       {
@@ -289,6 +291,10 @@ public class TreePanel extends GTreePanel
                 : new AverageDistanceTree(av, sm, similarityParams);
         tree = new TreeModel(njtree);
         showDistances(true);
+
+        ArchaeopteryxInit archae = new ArchaeopteryxInit(tree);
+        archae.startArchaeopteryx();
+
       }
 
       tree.reCount(tree.getTopNode());
@@ -296,18 +302,6 @@ public class TreePanel extends GTreePanel
       treeCanvas.setTree(tree);
       treeCanvas.repaint();
 
-      Testo test = new Testo();
-      NewickFile newickTree = test.treeToNewick(tree);
-      File newickAsFile = test.newickToArchaeopteryx(newickTree);
-      try
-      {
-        String[] archaeCommandlineArgs = {
-            "-open", newickAsFile.getCanonicalPath() };
-        test.startArchaeopteryx(archaeCommandlineArgs);
-      } catch (IOException e)
-      {
-        e.printStackTrace();
-      }
       av.setCurrentTree(tree);
       if (av.getSortByTree())
       {