X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=a4521cc1bb5cc478816e856c0d8a23aa4af4eb21;hb=90ae01c1c1504e0ae42817f78116f1d35b317c47;hp=5e14fce7d3fa1410e1ed54ae8b041c08e26941e0;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 5e14fce..a4521cc 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -41,6 +41,7 @@ import jalview.datamodel.NodeTransformI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
+import jalview.ext.archaeopteryx.ArchaeopteryxInit;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.NewickFile;
@@ -170,6 +171,7 @@ public class TreePanel extends GTreePanel
       }
     });
 
+
     TreeLoader tl = new TreeLoader(newTree, inputData);
     tl.start();
 
@@ -256,9 +258,11 @@ public class TreePanel extends GTreePanel
       {
         // Must be outside run(), as Jalview2XML tries to
         // update distance/bootstrap visibility at the same time
-        showBootstrap(newickFile.HasBootstrap());
-        showDistances(newickFile.HasDistances());
+        showBootstrap(newickFile.hasBootstrap());
+        showDistances(newickFile.hasDistances());
+
       }
+
     }
 
     @Override
@@ -273,6 +277,10 @@ public class TreePanel extends GTreePanel
         {
           originalSeqData.setVisible(false);
         }
+
+        ArchaeopteryxInit archae = new ArchaeopteryxInit(newtree);
+        archae.startArchaeopteryx();
+
       }
       else
       {
@@ -283,12 +291,17 @@ 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());
       tree.findHeight(tree.getTopNode());
       treeCanvas.setTree(tree);
       treeCanvas.repaint();
+
       av.setCurrentTree(tree);
       if (av.getSortByTree())
       {
@@ -493,7 +506,7 @@ public class TreePanel extends GTreePanel
 
     if (treeCanvas.applyToAllViews)
     {
-      final ArrayList<CommandI> commands = new ArrayList<CommandI>();
+      final ArrayList<CommandI> commands = new ArrayList<>();
       for (AlignmentPanel ap : PaintRefresher
               .getAssociatedPanels(av.getSequenceSetId()))
       {