X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=1b01606251cab1d3a8dffdd4fa9652cb8f360e63;hb=a8dc6956c5f305c782cd98a73acab6d26a50fa7b;hp=c6c9b5342c5e7e6a1a05f20e855261657b8094ae;hpb=e3cad17c5dba620dafc8459295ecc959cbe52938;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index c6c9b53..1b01606 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -38,7 +38,6 @@ import java.util.*;
 
 import javax.imageio.*;
 
-import javax.swing.*;
 import java.beans.PropertyChangeEvent;
 
 
@@ -57,6 +56,7 @@ public class TreePanel extends GTreePanel
     int end;
     TreeCanvas treeCanvas;
     NJTree tree;
+    AlignViewport av;
 
     /**
      * Creates a new TreePanel object.
@@ -75,8 +75,7 @@ public class TreePanel extends GTreePanel
       initTreePanel(av, seqVector, type, pwtype, s, e, null);
 
       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
-      treeCanvas.setShowDistances(true);
-      distanceMenu.setSelected(true);
+      showDistances(true);
     }
 
     /**
@@ -95,6 +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)
@@ -131,6 +135,8 @@ public class TreePanel extends GTreePanel
         }
       });
 
+      this.av = av;
+
 
       TreeLoader tl = new TreeLoader(newTree);
       tl.start();
@@ -148,11 +154,8 @@ public class TreePanel extends GTreePanel
         {
           // Must be outside run(), as Jalview2XML tries to
           // update distance/bootstrap visibility at the same time
-          treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-          bootstrapMenu.setSelected(newtree.HasBootstrap());
-
-          treeCanvas.setShowDistances(newtree.HasDistances());
-          distanceMenu.setSelected(newtree.HasDistances());
+          showBootstrap(newtree.HasBootstrap());
+          showDistances(newtree.HasDistances());
         }
       }
 
@@ -169,9 +172,31 @@ public class TreePanel extends GTreePanel
 
         treeCanvas.repaint();
 
+        av.setCurrentTree(tree);
+
       }
     }
 
+    public void showDistances(boolean b)
+    {
+      treeCanvas.setShowDistances(b);
+      distanceMenu.setSelected(b);
+    }
+
+    public void showBootstrap(boolean b)
+    {
+      treeCanvas.setShowBootstrap(b);
+      bootstrapMenu.setSelected(b);
+    }
+
+    public void showPlaceholders(boolean b)
+    {
+      placeholdersMenu.setState(b);
+      treeCanvas.setMarkPlaceholders(b);
+    }
+
+
+
 
     /**
      * DOCUMENT ME!
@@ -216,7 +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()));
     }
 
     /**
@@ -243,7 +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);