X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=366b97f202712e0084b30b1f4b1524e446f12a88;hb=53b99b41ed7f26f2724f3ed87d524eb83c5208f4;hp=80f0c73c4ea80fd1b78880a858086ef7ae50f10e;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 80f0c73..366b97f 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();
 
@@ -243,36 +245,41 @@ public class TreePanel extends GTreePanel
 
   class TreeLoader extends Thread
   {
-    private NewickFile newtree;
+    private NewickFile newTree;
 
     private AlignmentView odata = null;
 
     public TreeLoader(NewickFile newickFile, AlignmentView inputData)
     {
-      this.newtree = newickFile;
+      this.newTree = newickFile;
       this.odata = inputData;
 
-      if (newickFile != null)
+      if (newTree != null)
       {
         // Must be outside run(), as Jalview2XML tries to
         // update distance/bootstrap visibility at the same time
-        showBootstrap(newickFile.HasBootstrap());
-        showDistances(newickFile.HasDistances());
+        showBootstrap(newTree.hasBootstrap());
+        showDistances(newTree.hasDistances());
+
       }
+
     }
 
     @Override
     public void run()
     {
 
-      if (newtree != null)
+      if (newTree != null)
       {
         tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
-                newtree);
+                newTree);
         if (tree.getOriginalData() == null)
         {
           originalSeqData.setVisible(false);
         }
+
+
+
       }
       else
       {
@@ -283,12 +290,18 @@ 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()))
       {
@@ -793,19 +806,17 @@ public class TreePanel extends GTreePanel
             }
             if (newname == null)
             {
-              SequenceFeature sf[] = sq.getSequenceFeatures();
-              for (int i = 0; sf != null && i < sf.length; i++)
+              List<SequenceFeature> features = sq.getFeatures()
+                      .getPositionalFeatures(labelClass);
+              for (SequenceFeature feature : features)
               {
-                if (sf[i].getType().equals(labelClass))
+                if (newname == null)
+                {
+                  newname = feature.getDescription();
+                }
+                else
                 {
-                  if (newname == null)
-                  {
-                    newname = new String(sf[i].getDescription());
-                  }
-                  else
-                  {
-                    newname = newname + "; " + sf[i].getDescription();
-                  }
+                  newname = newname + "; " + feature.getDescription();
                 }
               }
             }