X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=f4543ed83ef71d56e17e0e82bbc4c3d7a7f8b8e1;hb=77c35fa912621cbadcf5ec74da4c6d45de6322e1;hp=ff02d49ec487eef6189d2acba088ca4b4267e9bf;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index ff02d49..f4543ed 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,456 +1,631 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import org.jibble.epsgraphics.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-
-import java.io.*;
-
-import java.util.*;
-
-import javax.imageio.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class TreePanel extends GTreePanel
-{
-    SequenceI[] seq;
-    String type;
-    String pwtype;
-    int start;
-    int end;
-    TreeCanvas treeCanvas;
-    NJTree tree;
-
-    /**
-     * Creates a new TreePanel object.
-     *
-     * @param av DOCUMENT ME!
-     * @param seqVector DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     * @param pwtype DOCUMENT ME!
-     * @param s DOCUMENT ME!
-     * @param e DOCUMENT ME!
-     */
-    public TreePanel(AlignViewport av, Vector seqVector, String type,
-        String pwtype, int s, int e)
-    {
-        super();
-
-        this.type = type;
-        this.pwtype = pwtype;
-
-        start = s;
-        end = e;
-
-        String longestName = "";
-        seq = new Sequence[seqVector.size()];
-
-        for (int i = 0; i < seqVector.size(); i++)
-        {
-            seq[i] = (Sequence) seqVector.elementAt(i);
-
-            if (seq[i].getName().length() > longestName.length())
-            {
-                longestName = seq[i].getName();
-            }
-        }
-
-        tree = new NJTree(seq, type, pwtype, start, end);
-
-        treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-        treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
-        setViewStateFromTreeCanvas(treeCanvas);
-        tree.reCount(tree.getTopNode());
-        tree.findHeight(tree.getTopNode());
-        scrollPane.setViewportView(treeCanvas);
-    }
-
-    /**
-     * Creates a new TreePanel object.
-     *
-     * @param av DOCUMENT ME!
-     * @param seqVector DOCUMENT ME!
-     * @param newtree DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     * @param pwtype DOCUMENT ME!
-     */
-    public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-        String type, String pwtype)
-    {
-        super();
-
-        // These are probably only  arbitrary strings reflecting source of tree
-        this.type = type;
-        this.pwtype = pwtype;
-
-        start = 0;
-        end = seqVector.size();
-
-        String longestName = "";
-        seq = new Sequence[seqVector.size()];
-
-        for (int i = 0; i < seqVector.size(); i++)
-        {
-            seq[i] = (Sequence) seqVector.elementAt(i);
-        }
-
-        // This constructor matches sequence names to treenodes and sets up the tree layouts.
-        tree = new NJTree(seq, newtree);
-
-        // Now have to calculate longest name based on the leaves
-        Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
-        boolean has_placeholders = false;
-
-        for (int i = 0; i < leaves.size(); i++)
-        {
-            SequenceNode lf = (SequenceNode) leaves.elementAt(i);
-
-            if (lf.isPlaceholder())
-            {
-                has_placeholders = true;
-            }
-
-            if (longestName.length() < ((Sequence) lf.element()).getName()
-                                            .length())
-            {
-                longestName = TreeCanvas.PLACEHOLDER +
-                    ((Sequence) lf.element()).getName();
-            }
-        }
-
-        tree.reCount(tree.getTopNode());
-        tree.findHeight(tree.getTopNode());
-
-        treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-        treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-        treeCanvas.setShowDistances(newtree.HasDistances());
-        scrollPane.setViewportView(treeCanvas);
-        treeCanvas.setMarkPlaceholders(has_placeholders);
-        setViewStateFromTreeCanvas(treeCanvas);
-
-        // JBPNote TODO: preference for always marking placeholders in new associated tree
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public NJTree getTree()
-    {
-        return tree;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tree DOCUMENT ME!
-     */
-    private void setViewStateFromTreeCanvas(TreeCanvas tree)
-    {
-        // update view menu state from treeCanvas render state
-        distanceMenu.setSelected(tree.showDistances);
-        bootstrapMenu.setSelected(tree.showBootstrap);
-        placeholdersMenu.setSelected(tree.markPlaceholders);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tree DOCUMENT ME!
-     */
-    private void setTreeCanvasFromViewState(TreeCanvas tree)
-    {
-        // update view menu state from treeCanvas render state
-        tree.showDistances = distanceMenu.isSelected();
-        tree.showBootstrap = bootstrapMenu.isSelected();
-        tree.markPlaceholders = placeholdersMenu.isSelected();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void textbox_actionPerformed(ActionEvent e)
-    {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-
-        StringBuffer buffer = new StringBuffer();
-
-        if (type.equals("AV"))
-        {
-            buffer.append("Average distance tree using ");
-        }
-        else
-        {
-            buffer.append("Neighbour joining tree using ");
-        }
-
-        if (pwtype.equals("BL"))
-        {
-            buffer.append("BLOSUM62");
-        }
-        else
-        {
-            buffer.append("PID");
-        }
-
-        Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
-
-        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-        cap.setText(fout.print(false, true));
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void saveAsNewick_actionPerformed(ActionEvent e)
-    {
-        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
-                    "LAST_DIRECTORY"));
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Save tree as newick file");
-        chooser.setToolTipText("Save");
-
-        int value = chooser.showSaveDialog(null);
-
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            String choice = chooser.getSelectedFile().getPath();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
-
-            try
-            {
-                jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-                String output = fout.print(false, true); // distances only
-                java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
-                            choice));
-                out.println(output);
-                out.close();
-            }
-            catch (Exception ex)
-            {
-                ex.printStackTrace();
-            }
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void printMenu_actionPerformed(ActionEvent e)
-    {
-        //Putting in a thread avoids Swing painting problems
-        treeCanvas.startPrinting();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void fitToWindow_actionPerformed(ActionEvent e)
-    {
-        treeCanvas.fitToWindow = fitToWindow.isSelected();
-        repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void fontSize_actionPerformed(ActionEvent e)
-    {
-        if (treeCanvas == null)
-        {
-            return;
-        }
-
-        String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +
-                1);
-
-        Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
-                "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,
-                null,
-                new String[]
-                {
-                    "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"
-                }, "Font Size - " + size);
-
-        if (selection != null)
-        {
-            fontSize.setText("Font Size - " + selection);
-
-            int i = Integer.parseInt(selection.toString());
-            treeCanvas.setFontSize(i);
-        }
-
-        scrollPane.setViewportView(treeCanvas);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void distanceMenu_actionPerformed(ActionEvent e)
-    {
-        treeCanvas.setShowDistances(distanceMenu.isSelected());
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void bootstrapMenu_actionPerformed(ActionEvent e)
-    {
-        treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void placeholdersMenu_actionPerformed(ActionEvent e)
-    {
-        treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void epsTree_actionPerformed(ActionEvent e)
-    {
-        int width = treeCanvas.getWidth();
-        int height = treeCanvas.getHeight();
-
-        try
-        {
-            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-                        "LAST_DIRECTORY"), new String[] { "eps" },
-                    new String[] { "Encapsulated Postscript" },
-                    "Encapsulated Postscript");
-            chooser.setFileView(new jalview.io.JalviewFileView());
-            chooser.setDialogTitle("Create EPS file from tree");
-            chooser.setToolTipText("Save");
-
-            int value = chooser.showSaveDialog(this);
-
-            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-            {
-                return;
-            }
-
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
-
-            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-            EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
-                    height);
-
-            treeCanvas.draw(pg, width, height);
-
-            pg.flush();
-            pg.close();
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void pngTree_actionPerformed(ActionEvent e)
-    {
-        int width = treeCanvas.getWidth();
-        int height = treeCanvas.getHeight();
-
-        try
-        {
-            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-                        "LAST_DIRECTORY"), new String[] { "png" },
-                    new String[] { "Portable network graphics" },
-                    "Portable network graphics");
-
-            chooser.setFileView(new jalview.io.JalviewFileView());
-            chooser.setDialogTitle("Create PNG image from tree");
-            chooser.setToolTipText("Save");
-
-            int value = chooser.showSaveDialog(this);
-
-            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-            {
-                return;
-            }
-
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
-
-            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-
-            BufferedImage bi = new BufferedImage(width, height,
-                    BufferedImage.TYPE_INT_RGB);
-            Graphics png = bi.getGraphics();
-
-            treeCanvas.draw(png, width, height);
-
-            ImageIO.write(bi, "png", out);
-            out.close();
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
+import jalview.jbgui.*;
+
+import org.jibble.epsgraphics.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+
+import java.io.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.imageio.*;
+
+import java.beans.PropertyChangeEvent;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreePanel extends GTreePanel
+{
+    String type;
+    String pwtype;
+    TreeCanvas treeCanvas;
+    NJTree tree;
+    AlignViewport av;
+
+    /**
+     * Creates a new TreePanel object.
+     *
+     * @param av DOCUMENT ME!
+     * @param seqVector DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     * @param pwtype DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     * @param e DOCUMENT ME!
+     */
+    public TreePanel(AlignmentPanel ap, String type, String pwtype)
+    {
+      super();
+      initTreePanel(ap, type, pwtype, null, null);
+
+      // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+      // showDistances(true);
+    }
+
+    /**
+     * Creates a new TreePanel object.
+     *
+     * @param av DOCUMENT ME!
+     * @param seqVector DOCUMENT ME!
+     * @param newtree DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     * @param pwtype DOCUMENT ME!
+     */
+    public TreePanel(AlignmentPanel ap,
+                     String type,
+                     String pwtype,
+                     NewickFile newtree)
+    {
+      super();
+      initTreePanel(ap, type, pwtype, newtree, null);
+    }
+
+    public TreePanel(AlignmentPanel av,
+        String type,
+        String pwtype,
+        NewickFile newtree, AlignmentView inputData) {
+     super();
+     initTreePanel(av,type,pwtype,newtree,inputData);
+    }
+
+    public AlignmentI getAlignment()
+    {
+      return treeCanvas.av.getAlignment();
+    }
+    public AlignViewport getViewPort() {
+      return treeCanvas.av;
+    }
+
+    void initTreePanel(AlignmentPanel ap, String type,  String pwtype,
+                       NewickFile newTree, AlignmentView inputData)
+    {
+
+      av = ap.av;
+      this.type = type;
+      this.pwtype = pwtype;
+
+      treeCanvas = new TreeCanvas(this, ap, scrollPane);
+      scrollPane.setViewportView(treeCanvas);
+
+      PaintRefresher.Register(this, ap.av.getSequenceSetId());
+
+      buildAssociatedViewMenu();
+
+      av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+      {
+        public void propertyChange(PropertyChangeEvent evt)
+        {
+          if (evt.getPropertyName().equals("alignment"))
+          {
+            if(tree==null)
+              System.out.println("tree is null");
+            if(evt.getNewValue()==null)
+              System.out.println("new alignment sequences vector value is null");
+
+            tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
+            treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
+            repaint();
+          }
+        }
+      });
+
+      TreeLoader tl = new TreeLoader(newTree);
+      if (inputData!=null) {
+        tl.odata=inputData;
+      }
+      tl.start();
+
+    }
+
+    public void viewMenu_menuSelected()
+    {
+      buildAssociatedViewMenu();
+    }
+
+
+    void buildAssociatedViewMenu()
+    {
+      AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
+      if(aps.length==1 && treeCanvas.ap==aps[0])
+      {
+        associateLeavesMenu.setVisible(false);
+        return;
+      }
+
+      associateLeavesMenu.setVisible(true);
+
+      if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))
+      {
+        viewMenu.insertSeparator(viewMenu.getItemCount()-1);
+      }
+
+      associateLeavesMenu.removeAll();
+
+
+      JRadioButtonMenuItem item;
+      ButtonGroup buttonGroup = new ButtonGroup();
+      int i, iSize = aps.length;
+      final TreePanel thisTreePanel = this;
+      for(i=0; i<iSize; i++)
+      {
+          final AlignmentPanel ap = aps[i];
+          item = new JRadioButtonMenuItem(ap.av.viewName, ap==treeCanvas.ap );
+          buttonGroup.add(item);
+          item.addActionListener(new ActionListener()
+              {
+                public void actionPerformed(ActionEvent evt)
+                {
+                  treeCanvas.applyToAllViews = false;
+                  treeCanvas.ap = ap;
+                  treeCanvas.av = ap.av;
+                  PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
+                }
+              });
+
+          associateLeavesMenu.add(item);
+      }
+
+      final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+      buttonGroup.add(itemf);
+      itemf.setSelected(treeCanvas.applyToAllViews);
+      itemf.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent evt)
+        {
+          treeCanvas.applyToAllViews = itemf.isSelected();
+        }
+      });
+      associateLeavesMenu.add(itemf);
+
+    }
+
+    class TreeLoader extends Thread
+    {
+      NewickFile newtree;
+      jalview.datamodel.AlignmentView odata=null;
+      public TreeLoader(NewickFile newtree)
+      {
+        this.newtree = newtree;
+        if (newtree != null)
+        {
+          // Must be outside run(), as Jalview2XML tries to
+          // update distance/bootstrap visibility at the same time
+          showBootstrap(newtree.HasBootstrap());
+          showDistances(newtree.HasDistances());
+        }
+      }
+
+      public void run()
+      {
+
+        if(newtree!=null)
+        {
+          if (odata==null) {
+            tree = new NJTree(av.alignment.getSequencesArray(),
+                              newtree);
+          } else {
+            tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+          }
+          if (!tree.hasOriginalSequenceData())
+            allowOriginalSeqData(false);
+        }
+        else
+        {
+          int start, end;
+          SequenceI [] seqs;
+          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+          if(av.getSelectionGroup()==null)
+          {
+            start = 0;
+            end = av.alignment.getWidth();
+            seqs = av.alignment.getSequencesArray();
+          }
+          else
+          {
+            start = av.getSelectionGroup().getStartRes();
+            end = av.getSelectionGroup().getEndRes()+1;
+            seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+          }
+
+          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+          showDistances(true);
+        }
+
+
+        tree.reCount(tree.getTopNode());
+        tree.findHeight(tree.getTopNode());
+        treeCanvas.setTree(tree);
+        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);
+    }
+
+    private void allowOriginalSeqData(boolean b) {
+      originalSeqData.setVisible(b);
+    }
+
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public NJTree getTree()
+    {
+        return tree;
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void textbox_actionPerformed(ActionEvent e)
+    {
+        CutAndPasteTransfer cap = new CutAndPasteTransfer();
+
+        StringBuffer buffer = new StringBuffer();
+
+        if (type.equals("AV"))
+        {
+            buffer.append("Average distance tree using ");
+        }
+        else
+        {
+            buffer.append("Neighbour joining tree using ");
+        }
+
+        if (pwtype.equals("BL"))
+        {
+            buffer.append("BLOSUM62");
+        }
+        else
+        {
+            buffer.append("PID");
+        }
+
+        Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+
+        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+        cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void saveAsNewick_actionPerformed(ActionEvent e)
+    {
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"));
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Save tree as newick file");
+        chooser.setToolTipText("Save");
+
+        int value = chooser.showSaveDialog(null);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            String choice = chooser.getSelectedFile().getPath();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
+
+            try
+            {
+                jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+                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);
+                out.close();
+            }
+            catch (Exception ex)
+            {
+                ex.printStackTrace();
+            }
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void printMenu_actionPerformed(ActionEvent e)
+    {
+        //Putting in a thread avoids Swing painting problems
+        treeCanvas.startPrinting();
+    }
+
+
+    public void originalSeqData_actionPerformed(ActionEvent e)
+    {
+      if (!tree.hasOriginalSequenceData())
+      {
+        jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+        return;
+      }
+      // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+      // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+      // or create a selection box around columns in alignment view
+      // test Alignment(SeqCigar[])
+      Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
+          getGapCharacter());
+
+
+      if (alAndColsel != null && alAndColsel[0]!=null)
+       {
+         // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+         Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+         Alignment dataset = av.getAlignment().getDataset();
+         if (dataset != null)
+         {
+           al.setDataset(dataset);
+         }
+
+         if (true)
+         {
+           // make a new frame!
+           AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
+                                           AlignFrame.DEFAULT_WIDTH,
+                                           AlignFrame.DEFAULT_HEIGHT
+);
+
+           //>>>This is a fix for the moment, until a better solution is found!!<<<
+           // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
+       //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
+       //                                     msaorder);
+
+           Desktop.addInternalFrame(af, "Original Data for " + this.title,
+                                    AlignFrame.DEFAULT_WIDTH,
+                                    AlignFrame.DEFAULT_HEIGHT);
+         }
+       }
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void fitToWindow_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.fitToWindow = fitToWindow.isSelected();
+        repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void font_actionPerformed(ActionEvent e)
+    {
+        if (treeCanvas == null)
+        {
+            return;
+        }
+
+        new FontChooser(this);
+    }
+
+    public Font getTreeFont()
+    {
+        return treeCanvas.font;
+    }
+
+    public void setTreeFont(Font font)
+    {
+      if(treeCanvas!=null)
+      treeCanvas.setFont(font);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void distanceMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setShowDistances(distanceMenu.isSelected());
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void bootstrapMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void placeholdersMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void epsTree_actionPerformed(ActionEvent e)
+    {
+      boolean accurateText = true;
+
+      String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+          "Prompt each time");
+
+    // If we need to prompt, and if the GUI is visible then
+    // Prompt for EPS rendering style
+      if (renderStyle.equalsIgnoreCase("Prompt each time")
+          && !
+          (System.getProperty("java.awt.headless") != null
+           && System.getProperty("java.awt.headless").equals("true")))
+      {
+        EPSOptions eps = new EPSOptions();
+        renderStyle = eps.getValue();
+
+        if (renderStyle==null || eps.cancelled)
+          return;
+
+
+      }
+
+      if (renderStyle.equalsIgnoreCase("text"))
+      {
+        accurateText = false;
+      }
+
+        int width = treeCanvas.getWidth();
+        int height = treeCanvas.getHeight();
+
+        try
+        {
+            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+                        "LAST_DIRECTORY"), new String[] { "eps" },
+                    new String[] { "Encapsulated Postscript" },
+                    "Encapsulated Postscript");
+            chooser.setFileView(new jalview.io.JalviewFileView());
+            chooser.setDialogTitle("Create EPS file from tree");
+            chooser.setToolTipText("Save");
+
+            int value = chooser.showSaveDialog(this);
+
+            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+            {
+                return;
+            }
+
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                          chooser.getSelectedFile().getParent());
+
+            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+            EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+                                                 height);
+
+            pg.setAccurateTextMode(accurateText);
+
+            treeCanvas.draw(pg, width, height);
+
+            pg.flush();
+            pg.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void pngTree_actionPerformed(ActionEvent e)
+    {
+        int width = treeCanvas.getWidth();
+        int height = treeCanvas.getHeight();
+
+        try
+        {
+            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+                        "LAST_DIRECTORY"), new String[] { "png" },
+                    new String[] { "Portable network graphics" },
+                    "Portable network graphics");
+
+            chooser.setFileView(new jalview.io.JalviewFileView());
+            chooser.setDialogTitle("Create PNG image from tree");
+            chooser.setToolTipText("Save");
+
+            int value = chooser.showSaveDialog(this);
+
+            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+            {
+                return;
+            }
+
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
+
+            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+
+            BufferedImage bi = new BufferedImage(width, height,
+                    BufferedImage.TYPE_INT_RGB);
+            Graphics png = bi.getGraphics();
+
+            treeCanvas.draw(png, width, height);
+
+            ImageIO.write(bi, "png", out);
+            out.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
+}