X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=1b01606251cab1d3a8dffdd4fa9652cb8f360e63;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=1d197c301555e0333232057835901acac25d4a74;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 1d197c3..1b01606 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -56,6 +56,7 @@ public class TreePanel extends GTreePanel
     int end;
     TreeCanvas treeCanvas;
     NJTree tree;
+    AlignViewport av;
 
     /**
      * Creates a new TreePanel object.
@@ -93,6 +94,11 @@ public class TreePanel extends GTreePanel
       initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
     }
 
+    public AlignmentI getAlignment()
+    {
+      return treeCanvas.av.getAlignment();
+    }
+
 
     void initTreePanel(AlignViewport av, Vector seqVector, String type,
                        String pwtype, int s, int e, NewickFile newTree)
@@ -129,6 +135,8 @@ public class TreePanel extends GTreePanel
         }
       });
 
+      this.av = av;
+
 
       TreeLoader tl = new TreeLoader(newTree);
       tl.start();
@@ -164,6 +172,8 @@ public class TreePanel extends GTreePanel
 
         treeCanvas.repaint();
 
+        av.setCurrentTree(tree);
+
       }
     }
 
@@ -231,7 +241,7 @@ public class TreePanel extends GTreePanel
         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 
         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-        cap.setText(fout.print(false, true));
+        cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
     }
 
     /**
@@ -258,7 +268,7 @@ public class TreePanel extends GTreePanel
             try
             {
                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-                String output = fout.print(false, true); // distances only
+                String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
                             choice));
                 out.println(output);