FigtreeNewickGraph.java

/*
 *    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., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

/*
 * FigtreeNewickGraph.java
 * Copyright (C) 2009 University of Waikato, Hamilton, New Zealand
 */

package wekaexamples.gui.visualize.plugins;

import weka.gui.visualize.plugins.TreeVisualizePlugin;

import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.Serializable;

import javax.swing.JMenuItem;
import javax.swing.JOptionPane;

import figtree.application.FigTreeFrame;

/**
 * Example for displaying a graph in
 * <a href="http://en.wikipedia.org/wiki/Newick_format" target="_blank">Newick format</a>
 * generated by Weka's HierarchicalClusterer with
 * <a href="http://tree.bio.ed.ac.uk/software/figtree/" target="_blank">FigTree</a>.
 * <p/>
 * <b>Note:</b> the leaves must have unique labels (normally the last attribute
 * in the dataset), otherwise an error message about duplicate taxons will
 * pop up.
 *
 * @author  FracPete (fracpete at waikato dot ac dot nz)
 * @version $Revision$
 */
public class FigtreeNewickGraph
  implements Serializable, TreeVisualizePlugin {

  /** for serialization. */
  private static final long serialVersionUID = -2495407885027981487L;

  /**
   * Get a JMenu or JMenuItem which contain action listeners
   * that perform the visualization of the graph in newick format.
   * Exceptions thrown because of changes in Weka since compilation need to
   * be caught by the implementer.
   *
   * @see NoClassDefFoundError
   * @see IncompatibleClassChangeError
   *
   * @param newick 	the graph in newick format
   * @param name	the name of the item (in the Explorer's history list)
   * @return menuitem 	for opening visualization(s), or null
   *         		to indicate no visualization is applicable for the input
   */
  public JMenuItem getVisualizeMenuItem(String newick, String name) {
    JMenuItem	result;

    final String newickF = newick;
    final String nameF = name;
    result = new JMenuItem("FigTree graph");
    result.addActionListener(new ActionListener() {
      public void actionPerformed(ActionEvent e) {
	display(newickF, nameF);
      }
    });

    return result;
  }

  /**
   * Displays the graph.
   *
   * @param newick	the graph in newick format
   * @param name	the name of the graph
   */
  protected void display(String newick, String name) {
    FigTreeFrame	frame;

    // create frame
    frame = new FigTreeFrame("FigTree graph [" + name + "]");
    frame.initializeComponents();
    frame.setLocationRelativeTo(null);
    frame.setVisible(true);

    // parse and display graph
    try {
      frame.readFromString(newick);
    }
    catch (Exception e) {
      e.printStackTrace();
      JOptionPane.showMessageDialog(
	  frame,
	  "Error displaying graph in Newick format: " + e,
	  "Error",
	  JOptionPane.ERROR_MESSAGE);
    }
  }

  /**
   * Get the minimum version of Weka, inclusive, the class
   * is designed to work with.  eg: <code>3.5.0</code>
   *
   * @return		the minimum version
   */
  public String getMinVersion() {
    return "3.7.1";
  }

  /**
   * Get the maximum version of Weka, exclusive, the class
   * is designed to work with.  eg: <code>3.6.0</code>
   *
   * @return		the maximum version
   */
  public String getMaxVersion() {
    return "3.8.0";
  }

  /**
   * Get the specific version of Weka the class is designed for.
   * eg: <code>3.5.1</code>
   *
   * @return		the version the plugin was designed for
   */
  public String getDesignVersion() {
    return "3.7.1";
  }
}