source: src/main/java/weka/gui/explorer/AttributeSelectionPanel.java @ 18

/*
 *    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.
 */

/*
 *    AttributeSelectionPanel.java
 *    Copyright (C) 1999 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.gui.explorer;

import weka.attributeSelection.ASEvaluation;
import weka.attributeSelection.ASSearch;
import weka.attributeSelection.AttributeEvaluator;
import weka.attributeSelection.AttributeSelection;
import weka.attributeSelection.AttributeTransformer;
import weka.attributeSelection.Ranker;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.CapabilitiesHandler;
import weka.core.FastVector;
import weka.core.Instances;
import weka.core.OptionHandler;
import weka.core.Utils;
import weka.gui.ExtensionFileFilter;
import weka.gui.GenericObjectEditor;
import weka.gui.Logger;
import weka.gui.PropertyPanel;
import weka.gui.ResultHistoryPanel;
import weka.gui.SaveBuffer;
import weka.gui.SysErrLog;
import weka.gui.TaskLogger;
import weka.gui.explorer.Explorer.CapabilitiesFilterChangeEvent;
import weka.gui.explorer.Explorer.CapabilitiesFilterChangeListener;
import weka.gui.explorer.Explorer.ExplorerPanel;
import weka.gui.explorer.Explorer.LogHandler;
import weka.gui.visualize.MatrixPanel;

import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
import java.awt.Insets;
import java.awt.Point;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.InputEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.Random;
import java.util.Vector;

import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.DefaultComboBoxModel;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.JViewport;
import javax.swing.SwingConstants;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;

/** 
 * This panel allows the user to select and configure an attribute
 * evaluator and a search method, set the
 * attribute of the current dataset to be used as the class, and perform
 * attribute selection using one of two  selection modes (select using all the
 * training data or perform a n-fold cross validation---on each trial
 * selecting features using n-1 folds of the data).
 * The results of attribute selection runs are stored in a results history
 * so that previous results are accessible.
 *
 * @author Mark Hall (mhall@cs.waikato.ac.nz)
 * @version $Revision: 5385 $
 */
public class AttributeSelectionPanel 
  extends JPanel
  implements CapabilitiesFilterChangeListener, ExplorerPanel, LogHandler {
  
  /** for serialization */
  static final long serialVersionUID = 5627185966993476142L;

  /** the parent frame */
  protected Explorer m_Explorer = null;

  /** Lets the user configure the attribute evaluator */
  protected GenericObjectEditor m_AttributeEvaluatorEditor =
    new GenericObjectEditor();

  /** Lets the user configure the search method */
  protected GenericObjectEditor m_AttributeSearchEditor = 
    new GenericObjectEditor();

  /** The panel showing the current attribute evaluation method */
  protected PropertyPanel m_AEEPanel = 
    new PropertyPanel(m_AttributeEvaluatorEditor);

  /** The panel showing the current search method */
  protected PropertyPanel m_ASEPanel = 
    new PropertyPanel(m_AttributeSearchEditor);
  
  /** The output area for attribute selection results */
  protected JTextArea m_OutText = new JTextArea(20, 40);

  /** The destination for log/status messages */
  protected Logger m_Log = new SysErrLog();

  /** The buffer saving object for saving output */
  SaveBuffer m_SaveOut = new SaveBuffer(m_Log, this);

  /** A panel controlling results viewing */
  protected ResultHistoryPanel m_History = new ResultHistoryPanel(m_OutText);

  /** Lets the user select the class column */
  protected JComboBox m_ClassCombo = new JComboBox();

  /** Click to set evaluation mode to cross-validation */
  protected JRadioButton m_CVBut = new JRadioButton("Cross-validation");

  /** Click to set test mode to test on training data */
  protected JRadioButton m_TrainBut = 
    new JRadioButton("Use full training set");

  /** Label by where the cv folds are entered */
  protected JLabel m_CVLab = new JLabel("Folds", SwingConstants.RIGHT);

  /** The field where the cv folds are entered */
  protected JTextField m_CVText = new JTextField("10");

  /** Label by where cv random seed is entered */
  protected JLabel m_SeedLab = new JLabel("Seed",SwingConstants.RIGHT);

  /** The field where the seed value is entered */
  protected JTextField m_SeedText = new JTextField("1");

  /**
   * Alters the enabled/disabled status of elements associated with each
   * radio button
   */
  ActionListener m_RadioListener = new ActionListener() {
    public void actionPerformed(ActionEvent e) {
      updateRadioLinks();
    }
  };

  /** Click to start running the attribute selector */
  protected JButton m_StartBut = new JButton("Start");

  /** Click to stop a running classifier */
  protected JButton m_StopBut = new JButton("Stop");

 /** Stop the class combo from taking up to much space */
  private Dimension COMBO_SIZE = new Dimension(150, m_StartBut
                                               .getPreferredSize().height);
  
  /** The main set of instances we're playing with */
  protected Instances m_Instances;

  /** A thread that attribute selection runs in */
  protected Thread m_RunThread;

  /* Register the property editors we need */
  static {
     GenericObjectEditor.registerEditors();
  }
  
  /**
   * Creates the classifier panel
   */
  public AttributeSelectionPanel() {

    // Connect / configure the components
    m_OutText.setEditable(false);
    m_OutText.setFont(new Font("Monospaced", Font.PLAIN, 12));
    m_OutText.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    m_OutText.addMouseListener(new MouseAdapter() {
      public void mouseClicked(MouseEvent e) {
        if ((e.getModifiers() & InputEvent.BUTTON1_MASK)
            != InputEvent.BUTTON1_MASK) {
          m_OutText.selectAll();
        }
      }
    });
    m_History.setBorder(BorderFactory.createTitledBorder("Result list (right-click for options)"));
    m_AttributeEvaluatorEditor.setClassType(ASEvaluation.class);
    m_AttributeEvaluatorEditor.setValue(ExplorerDefaults.getASEvaluator());
    m_AttributeEvaluatorEditor.
      addPropertyChangeListener(new PropertyChangeListener() {
      public void propertyChange(PropertyChangeEvent e) {
        if (m_AttributeEvaluatorEditor.getValue() instanceof AttributeEvaluator) {
          if (!(m_AttributeSearchEditor.getValue() instanceof Ranker)) {
            Object backup = m_AttributeEvaluatorEditor.getBackup();
            int result = 
              JOptionPane.showConfirmDialog(null, "You must use use the Ranker search method "
                                            +"in order to use\n"
                                            +m_AttributeEvaluatorEditor.getValue().getClass().getName()
                                            +".\nShould I select the Ranker search method for you?",
                                            "Alert!", JOptionPane.YES_NO_OPTION);
            if (result == JOptionPane.YES_OPTION) {
              m_AttributeSearchEditor.setValue(new Ranker());
            } else {
              // restore to what was there previously (if possible)
              if (backup != null) {
                m_AttributeEvaluatorEditor.setValue(backup);
              }             
            }
          }
        } else {
          if (m_AttributeSearchEditor.getValue() instanceof Ranker) {
            Object backup = m_AttributeEvaluatorEditor.getBackup();
            int result = 
              JOptionPane.showConfirmDialog(null, "You must use use a search method that explores \n"
                                            +"the space of attribute subsets (such as GreedyStepwise) in "
                                            +"order to use\n"
                                            +m_AttributeEvaluatorEditor.getValue().getClass().getName()
                                            +".\nShould I select the GreedyStepwise search method for "
                                            +"you?\n(you can always switch to a different method afterwards)",
                                            "Alert!", JOptionPane.YES_NO_OPTION);
            if (result == JOptionPane.YES_OPTION) {
              m_AttributeSearchEditor.setValue(new weka.attributeSelection.GreedyStepwise());
            } else {
              // restore to what was there previously (if possible)
              if (backup != null) {
                m_AttributeEvaluatorEditor.setValue(backup);
              } 
            }
          }
        }
        updateRadioLinks();
        
        m_StartBut.setEnabled(true);
        // check capabilities...
        Capabilities currentFilter = m_AttributeEvaluatorEditor.getCapabilitiesFilter();
        ASEvaluation evaluator = (ASEvaluation) m_AttributeEvaluatorEditor.getValue();
        Capabilities currentSchemeCapabilities =  null;
        if (evaluator != null && currentFilter != null && 
            (evaluator instanceof CapabilitiesHandler)) {
          currentSchemeCapabilities = ((CapabilitiesHandler)evaluator).getCapabilities();
          
          if (!currentSchemeCapabilities.supportsMaybe(currentFilter) &&
              !currentSchemeCapabilities.supports(currentFilter)) {
            m_StartBut.setEnabled(false);
          }
        }
        repaint();
      }
    });

    m_AttributeSearchEditor.setClassType(ASSearch.class);
    m_AttributeSearchEditor.setValue(ExplorerDefaults.getASSearch());
    m_AttributeSearchEditor.
      addPropertyChangeListener(new PropertyChangeListener() {
        public void propertyChange(PropertyChangeEvent e) {
          if (m_AttributeSearchEditor.getValue() instanceof Ranker) {
            if (!(m_AttributeEvaluatorEditor.getValue() instanceof AttributeEvaluator)) {
              Object backup = m_AttributeSearchEditor.getBackup();
              int result = 
                JOptionPane.showConfirmDialog(null, "You must use use an evaluator that evaluates\n"
                                              +"single attributes (such as InfoGain) in order to use\n"
                                              +"the Ranker. Should I select the InfoGain evaluator "
                                              +"for you?\n"
                                              +"(You can always switch to a different method afterwards)" ,
                                              "Alert!", JOptionPane.YES_NO_OPTION);
              if (result == JOptionPane.YES_OPTION) {
                m_AttributeEvaluatorEditor.setValue(new weka.attributeSelection.InfoGainAttributeEval());
              } else {
                // restore to what was there previously (if possible)
                if (backup != null) {
                  m_AttributeSearchEditor.setValue(backup);
                }             
              }
            }
          } else {
            if (m_AttributeEvaluatorEditor.getValue() instanceof AttributeEvaluator) {
              Object backup = m_AttributeSearchEditor.getBackup();
              int result = 
                JOptionPane.showConfirmDialog(null, "You must use use an evaluator that evaluates\n"
                                              +"subsets of attributes (such as CFS) in order to use\n"
                                              +m_AttributeEvaluatorEditor.getValue().getClass().getName()
                                              +".\nShould I select the CFS subset evaluator for you?"
                                              +"\n(you can always switch to a different method afterwards)",
                                              "Alert!", JOptionPane.YES_NO_OPTION);

              if (result == JOptionPane.YES_OPTION) {
                m_AttributeEvaluatorEditor.setValue(new weka.attributeSelection.CfsSubsetEval());
              } else {
                // restore to what was there previously (if possible)
                if (backup != null) {
                  m_AttributeSearchEditor.setValue(backup);
                }              
              }
            }
          }
          repaint();
        }
      });
    
    m_ClassCombo.addActionListener(new ActionListener() {
      public void actionPerformed(ActionEvent e) {
        updateCapabilitiesFilter(m_AttributeEvaluatorEditor.getCapabilitiesFilter());
      }
    });

    m_ClassCombo.setToolTipText("Select the attribute to use as the class");
    m_TrainBut.setToolTipText("select attributes using the full training "
                              + "dataset");
    m_CVBut.setToolTipText("Perform a n-fold cross-validation");

    m_StartBut.setToolTipText("Starts attribute selection");
    m_StopBut.setToolTipText("Stops a attribute selection task");
    
    m_ClassCombo.setPreferredSize(COMBO_SIZE);
    m_ClassCombo.setMaximumSize(COMBO_SIZE);
    m_ClassCombo.setMinimumSize(COMBO_SIZE);
    m_History.setPreferredSize(COMBO_SIZE);
    m_History.setMaximumSize(COMBO_SIZE);
    m_History.setMinimumSize(COMBO_SIZE);
    
    m_ClassCombo.setEnabled(false);
    m_TrainBut.setSelected(ExplorerDefaults.getASTestMode() == 0);
    m_CVBut.setSelected(ExplorerDefaults.getASTestMode() == 1);
    updateRadioLinks();
    ButtonGroup bg = new ButtonGroup();
    bg.add(m_TrainBut);
    bg.add(m_CVBut);

    m_TrainBut.addActionListener(m_RadioListener);
    m_CVBut.addActionListener(m_RadioListener);

    m_CVText.setText("" + ExplorerDefaults.getASCrossvalidationFolds());
    m_SeedText.setText("" + ExplorerDefaults.getASRandomSeed());
    
    m_StartBut.setEnabled(false);
    m_StopBut.setEnabled(false);

    m_StartBut.addActionListener(new ActionListener() {
      public void actionPerformed(ActionEvent e) {
        startAttributeSelection();
      }
    });
    m_StopBut.addActionListener(new ActionListener() {
      public void actionPerformed(ActionEvent e) {
        stopAttributeSelection();
      }
    });
    
    m_History.setHandleRightClicks(false);
    // see if we can popup a menu for the selected result
    m_History.getList().addMouseListener(new MouseAdapter() {
        public void mouseClicked(MouseEvent e) {
          if (((e.getModifiers() & InputEvent.BUTTON1_MASK)
               != InputEvent.BUTTON1_MASK) || e.isAltDown()) {
            int index = m_History.getList().locationToIndex(e.getPoint());
            if (index != -1) {
              String name = m_History.getNameAtIndex(index);
              visualize(name, e.getX(), e.getY());
            } else {
              visualize(null, e.getX(), e.getY());
            }
          }
        }
      });

    // Layout the GUI
    JPanel p1 = new JPanel();
    p1.setBorder(BorderFactory.createCompoundBorder(
                 BorderFactory.createTitledBorder("Attribute Evaluator"),
                 BorderFactory.createEmptyBorder(0, 5, 5, 5)
                 ));
    p1.setLayout(new BorderLayout());
    p1.add(m_AEEPanel, BorderLayout.NORTH);

    JPanel p1_1 = new JPanel();
    p1_1.setBorder(BorderFactory.createCompoundBorder(
                 BorderFactory.createTitledBorder("Search Method"),
                 BorderFactory.createEmptyBorder(0, 5, 5, 5)
                 ));
    p1_1.setLayout(new BorderLayout());
    p1_1.add(m_ASEPanel, BorderLayout.NORTH);

    JPanel p_new = new JPanel();
    p_new.setLayout(new BorderLayout());
    p_new.add(p1, BorderLayout.NORTH);
    p_new.add(p1_1, BorderLayout.CENTER);

    JPanel p2 = new JPanel();
    GridBagLayout gbL = new GridBagLayout();
    p2.setLayout(gbL);
    p2.setBorder(BorderFactory.createCompoundBorder(
                 BorderFactory.createTitledBorder("Attribute Selection Mode"),
                 BorderFactory.createEmptyBorder(0, 5, 5, 5)
                 ));
    GridBagConstraints gbC = new GridBagConstraints();
    gbC.anchor = GridBagConstraints.WEST;
    gbC.gridy = 2;     gbC.gridx = 0;
    gbL.setConstraints(m_TrainBut, gbC);
    p2.add(m_TrainBut);

    gbC = new GridBagConstraints();
    gbC.anchor = GridBagConstraints.WEST;
    gbC.gridy = 4;     gbC.gridx = 0;
    gbL.setConstraints(m_CVBut, gbC);
    p2.add(m_CVBut);

    gbC = new GridBagConstraints();
    gbC.anchor = GridBagConstraints.EAST;
    gbC.fill = GridBagConstraints.HORIZONTAL;
    gbC.gridy = 4;     gbC.gridx = 1;
    gbC.insets = new Insets(2, 10, 2, 10);
    gbL.setConstraints(m_CVLab, gbC);
    p2.add(m_CVLab);

    gbC = new GridBagConstraints();
    gbC.anchor = GridBagConstraints.EAST;
    gbC.fill = GridBagConstraints.HORIZONTAL;
    gbC.gridy = 4;     gbC.gridx = 2;  gbC.weightx = 100;
    gbC.ipadx = 20;
    gbL.setConstraints(m_CVText, gbC);
    p2.add(m_CVText);

    gbC = new GridBagConstraints();
    gbC.anchor = GridBagConstraints.EAST;
    gbC.fill = GridBagConstraints.HORIZONTAL;
    gbC.gridy = 6;     gbC.gridx = 1;
    gbC.insets = new Insets(2, 10, 2, 10);
    gbL.setConstraints(m_SeedLab, gbC);
    p2.add(m_SeedLab);

    gbC = new GridBagConstraints();
    gbC.anchor = GridBagConstraints.EAST;
    gbC.fill = GridBagConstraints.HORIZONTAL;
    gbC.gridy = 6;     gbC.gridx = 2;  gbC.weightx = 100;
    gbC.ipadx = 20;
    gbL.setConstraints(m_SeedText, gbC);
    p2.add(m_SeedText);


    JPanel buttons = new JPanel();
    buttons.setLayout(new GridLayout(2, 2));
    buttons.add(m_ClassCombo);
    m_ClassCombo.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    JPanel ssButs = new JPanel();
    ssButs.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    ssButs.setLayout(new GridLayout(1, 2, 5, 5));
    ssButs.add(m_StartBut);
    ssButs.add(m_StopBut);
    buttons.add(ssButs);
    
    JPanel p3 = new JPanel();
    p3.setBorder(BorderFactory.
                 createTitledBorder("Attribute selection output"));
    p3.setLayout(new BorderLayout());
    final JScrollPane js = new JScrollPane(m_OutText);
    p3.add(js, BorderLayout.CENTER);
    js.getViewport().addChangeListener(new ChangeListener() {
      private int lastHeight;
      public void stateChanged(ChangeEvent e) {
        JViewport vp = (JViewport)e.getSource();
        int h = vp.getViewSize().height; 
        if (h != lastHeight) { // i.e. an addition not just a user scrolling
          lastHeight = h;
          int x = h - vp.getExtentSize().height;
          vp.setViewPosition(new Point(0, x));
        }
      }
    });

    JPanel mondo = new JPanel();
    gbL = new GridBagLayout();
    mondo.setLayout(gbL);
    gbC = new GridBagConstraints();
    gbC.fill = GridBagConstraints.HORIZONTAL;
    gbC.gridy = 0;     gbC.gridx = 0; gbC.weightx = 0;
    gbL.setConstraints(p2, gbC);
    mondo.add(p2);
    gbC = new GridBagConstraints();
    gbC.anchor = GridBagConstraints.NORTH;
    gbC.fill = GridBagConstraints.HORIZONTAL;
    gbC.gridy = 1;     gbC.gridx = 0; gbC.weightx = 0;
    gbL.setConstraints(buttons, gbC);
    mondo.add(buttons);
    gbC = new GridBagConstraints();
    gbC.fill = GridBagConstraints.BOTH;
    gbC.gridy = 2;     gbC.gridx = 0; gbC.weightx = 0; gbC.weighty = 100;
    gbL.setConstraints(m_History, gbC);
    mondo.add(m_History);
    gbC = new GridBagConstraints();
    gbC.fill = GridBagConstraints.BOTH;
    gbC.gridy = 0;     gbC.gridx = 1;
    gbC.gridheight = 3;
    gbC.weightx = 100; gbC.weighty = 100;
    gbL.setConstraints(p3, gbC);
    mondo.add(p3);

    setLayout(new BorderLayout());
    add(p_new, BorderLayout.NORTH);
    add(mondo, BorderLayout.CENTER);
  }

  
  /**
   * Updates the enabled status of the input fields and labels.
   */
  protected void updateRadioLinks() {
    m_CVBut.setEnabled(true);
    m_CVText.setEnabled(m_CVBut.isSelected());
    m_CVLab.setEnabled(m_CVBut.isSelected());
    m_SeedText.setEnabled(m_CVBut.isSelected());
    m_SeedLab.setEnabled(m_CVBut.isSelected());
    
    if (m_AttributeEvaluatorEditor.getValue() 
        instanceof AttributeTransformer) {
      m_CVBut.setSelected(false);
      m_CVBut.setEnabled(false);
      m_CVText.setEnabled(false);
      m_CVLab.setEnabled(false);
      m_SeedText.setEnabled(false);
      m_SeedLab.setEnabled(false);
      m_TrainBut.setSelected(true);
    }
  }
  
  /**
   * Sets the Logger to receive informational messages
   *
   * @param newLog the Logger that will now get info messages
   */
  public void setLog(Logger newLog) {

    m_Log = newLog;
  }
  
  /**
   * Tells the panel to use a new set of instances.
   *
   * @param inst a set of Instances
   */
  public void setInstances(Instances inst) {
    
    m_Instances = inst;
    String [] attribNames = new String [m_Instances.numAttributes()];
    for (int i = 0; i < attribNames.length; i++) {
      String type = "";
      switch (m_Instances.attribute(i).type()) {
      case Attribute.NOMINAL:
        type = "(Nom) ";
        break;
      case Attribute.NUMERIC:
        type = "(Num) ";
        break;
      case Attribute.STRING:
        type = "(Str) ";
        break;
      case Attribute.DATE:
        type = "(Dat) ";
        break;
      case Attribute.RELATIONAL:
        type = "(Rel) ";
        break;
      default:
        type = "(???) ";
      }
      String attnm = m_Instances.attribute(i).name();
     
      attribNames[i] = type + attnm;
    }
    m_StartBut.setEnabled(m_RunThread == null);
    m_StopBut.setEnabled(m_RunThread != null);
    m_ClassCombo.setModel(new DefaultComboBoxModel(attribNames));
    if (inst.classIndex() == -1)
      m_ClassCombo.setSelectedIndex(attribNames.length - 1);
    else
      m_ClassCombo.setSelectedIndex(inst.classIndex());
    m_ClassCombo.setEnabled(true);
  }
  
  /**
   * Starts running the currently configured attribute evaluator and
   * search method. This is run in a separate thread, and will only start if
   * there is no attribute selection  already running. The attribute selection
   * output is sent to the results history panel.
   */
  protected void startAttributeSelection() {

    if (m_RunThread == null) {
      m_StartBut.setEnabled(false);
      m_StopBut.setEnabled(true);
      m_RunThread = new Thread() {
        public void run() {
          // Copy the current state of things
          m_Log.statusMessage("Setting up...");
          Instances inst = new Instances(m_Instances);

          int testMode = 0;
          int numFolds = 10;
          int seed = 1;
          int classIndex = m_ClassCombo.getSelectedIndex();
          ASEvaluation evaluator = 
             (ASEvaluation) m_AttributeEvaluatorEditor.getValue();

          ASSearch search = (ASSearch) m_AttributeSearchEditor.getValue();

          StringBuffer outBuff = new StringBuffer();
          String name = (new SimpleDateFormat("HH:mm:ss - "))
          .format(new Date());
          String sname = search.getClass().getName();
          if (sname.startsWith("weka.attributeSelection.")) {
            name += sname.substring("weka.attributeSelection.".length());
          } else {
            name += sname;
          }
          String ename = evaluator.getClass().getName();
          if (ename.startsWith("weka.attributeSelection.")) {
            name += (" + "
                     +ename.substring("weka.attributeSelection.".length()));
          } else {
            name += (" + "+ename);
          }
          
          // assemble commands
          String cmd;
          String cmdFilter;
          String cmdClassifier;
          
          // 1. attribute selection command
          Vector<String> list = new Vector<String>();
          list.add("-s");
          if (search instanceof OptionHandler)
            list.add(sname + " " + Utils.joinOptions(((OptionHandler) search).getOptions()));
          else
            list.add(sname);
          if (evaluator instanceof OptionHandler) {
            String[] opt = ((OptionHandler) evaluator).getOptions();
            for (int i = 0; i < opt.length; i++)
              list.add(opt[i]);
          }
          cmd =   ename + " " 
                + Utils.joinOptions(list.toArray(new String[list.size()]));

          // 2. filter command
          weka.filters.supervised.attribute.AttributeSelection filter = 
            new weka.filters.supervised.attribute.AttributeSelection();
          filter.setEvaluator((ASEvaluation) m_AttributeEvaluatorEditor.getValue());
          filter.setSearch((ASSearch) m_AttributeSearchEditor.getValue());
          cmdFilter =   filter.getClass().getName() + " " 
                      + Utils.joinOptions(((OptionHandler) filter).getOptions());

          // 3. meta-classifier command
          weka.classifiers.meta.AttributeSelectedClassifier cls = 
            new weka.classifiers.meta.AttributeSelectedClassifier();
          cls.setEvaluator((ASEvaluation) m_AttributeEvaluatorEditor.getValue());
          cls.setSearch((ASSearch) m_AttributeSearchEditor.getValue());
          cmdClassifier =   cls.getClass().getName() + " " 
                          + Utils.joinOptions(cls.getOptions());
          
          AttributeSelection eval = null;

          try {
            if (m_CVBut.isSelected()) {
              testMode = 1;
              numFolds = Integer.parseInt(m_CVText.getText());
              seed = Integer.parseInt(m_SeedText.getText());
              if (numFolds <= 1) {
                throw new Exception("Number of folds must be greater than 1");
              }
            } 
            inst.setClassIndex(classIndex);

            // Output some header information
            m_Log.logMessage("Started " + ename);
            m_Log.logMessage("Command: " + cmd);
            m_Log.logMessage("Filter command: " + cmdFilter);
            m_Log.logMessage("Meta-classifier command: " + cmdClassifier);
            if (m_Log instanceof TaskLogger) {
              ((TaskLogger)m_Log).taskStarted();
            }
            outBuff.append("=== Run information ===\n\n");
            outBuff.append("Evaluator:    " + ename);
            if (evaluator instanceof OptionHandler) {
              String [] o = ((OptionHandler) evaluator).getOptions();
              outBuff.append(" " + Utils.joinOptions(o));
            }
            outBuff.append("\nSearch:       " + sname);
            if (search instanceof OptionHandler) {
              String [] o = ((OptionHandler) search).getOptions();
              outBuff.append(" " + Utils.joinOptions(o));
            }
            outBuff.append("\n");
            outBuff.append("Relation:     " + inst.relationName() + '\n');
            outBuff.append("Instances:    " + inst.numInstances() + '\n');
            outBuff.append("Attributes:   " + inst.numAttributes() + '\n');
            if (inst.numAttributes() < 100) {
              for (int i = 0; i < inst.numAttributes(); i++) {
                outBuff.append("              " + inst.attribute(i).name()
                               + '\n');
              }
            } else {
              outBuff.append("              [list of attributes omitted]\n");
            }
            outBuff.append("Evaluation mode:    ");
            switch (testMode) {
              case 0: // select using all training
              outBuff.append("evaluate on all training data\n");
              break;
              case 1: // CV mode
              outBuff.append("" + numFolds + "-fold cross-validation\n");
              break;
            }
            outBuff.append("\n");
            m_History.addResult(name, outBuff);
            m_History.setSingle(name);
            
            // Do the feature selection and output the results.
            m_Log.statusMessage("Doing feature selection...");
            m_History.updateResult(name);
            
            eval = new AttributeSelection();
            eval.setEvaluator(evaluator);
            eval.setSearch(search);
            eval.setFolds(numFolds);
            eval.setSeed(seed);
            if (testMode == 1) {
              eval.setXval(true);
            }
                    
            switch (testMode) {
              case 0: // select using training
              m_Log.statusMessage("Evaluating on training data...");
              eval.SelectAttributes(inst);
              break;

              case 1: // CV mode
              m_Log.statusMessage("Randomizing instances...");
              Random random = new Random(seed);
              inst.randomize(random);
              if (inst.attribute(classIndex).isNominal()) {
                m_Log.statusMessage("Stratifying instances...");
                inst.stratify(numFolds);
              }
              for (int fold = 0; fold < numFolds;fold++) {
                m_Log.statusMessage("Creating splits for fold "
                                    + (fold + 1) + "...");
                Instances train = inst.trainCV(numFolds, fold, random);
                m_Log.statusMessage("Selecting attributes using all but fold "
                                    + (fold + 1) + "...");
                
                eval.selectAttributesCVSplit(train);
              }
              break;
              default:
              throw new Exception("Test mode not implemented");
            }

            if (testMode == 0) {
              outBuff.append(eval.toResultsString());
            } else {
              outBuff.append(eval.CVResultsString());
            }
          
            outBuff.append("\n");
            m_History.updateResult(name);
            m_Log.logMessage("Finished " + ename+" "+sname);
            m_Log.statusMessage("OK");
          } catch (Exception ex) {
            m_Log.logMessage(ex.getMessage());
            m_Log.statusMessage("See error log");
          } finally {
            if (evaluator instanceof AttributeTransformer) {
              try {
                Instances transformed = 
                  ((AttributeTransformer)evaluator).transformedData(inst);
                transformed.
                  setRelationName("AT: "+transformed.relationName());

                FastVector vv = new FastVector();
                vv.addElement(transformed);
                m_History.addObject(name, vv);
              } catch (Exception ex) {
                System.err.println(ex);
                ex.printStackTrace();
              }
            } else if (testMode == 0) {
              try {
                Instances reducedInst = eval.reduceDimensionality(inst);
                FastVector vv = new FastVector();
                vv.addElement(reducedInst);
                m_History.addObject(name, vv);
              } catch (Exception ex) {
                ex.printStackTrace();
              }
            }
            if (isInterrupted()) {
              m_Log.logMessage("Interrupted " + ename+" "+sname);
              m_Log.statusMessage("See error log");
            }
            m_RunThread = null;
            m_StartBut.setEnabled(true);
            m_StopBut.setEnabled(false);
            if (m_Log instanceof TaskLogger) {
              ((TaskLogger)m_Log).taskFinished();
            }
          }
        }
      };
      m_RunThread.setPriority(Thread.MIN_PRIORITY);
      m_RunThread.start();
    }
  }
  
  /**
   * Stops the currently running attribute selection (if any).
   */
  protected void stopAttributeSelection() {

    if (m_RunThread != null) {
      m_RunThread.interrupt();
      
      // This is deprecated (and theoretically the interrupt should do).
      m_RunThread.stop();
      
    }
  }
  
  /**
   * Save the named buffer to a file.
   * @param name the name of the buffer to be saved.
   */
  protected void saveBuffer(String name) {
    StringBuffer sb = m_History.getNamedBuffer(name);
    if (sb != null) {
      if (m_SaveOut.save(sb)) {
        m_Log.logMessage("Save succesful.");
      }
    }
  }

  /**
   * Popup a visualize panel for viewing transformed data
   * 
   * @param ti          the Instances to display
   */
  protected void visualizeTransformedData(Instances ti) {
    if (ti != null) {
      MatrixPanel mp = new MatrixPanel();
      mp.setInstances(ti);
      String plotName = ti.relationName();
      final javax.swing.JFrame jf = 
        new javax.swing.JFrame("Weka Attribute Selection Visualize: "
                               +plotName);
      jf.setSize(800,600);
      jf.getContentPane().setLayout(new BorderLayout());
      jf.getContentPane().add(mp, BorderLayout.CENTER);
      jf.addWindowListener(new java.awt.event.WindowAdapter() {
          public void windowClosing(java.awt.event.WindowEvent e) {
            jf.dispose();
          }
        });

      jf.setVisible(true);
    }
  }

  /**
   * Popup a SaveDialog for saving the transformed data
   * 
   * @param ti          the Instances to display
   */
  protected void saveTransformedData(Instances ti) {
    JFileChooser        fc;
    int                 retVal;
    BufferedWriter      writer;
    ExtensionFileFilter filter;

    fc     = new JFileChooser();
    filter = new ExtensionFileFilter(".arff", "ARFF data files");
    fc.setFileFilter(filter);
    retVal = fc.showSaveDialog(this);

    if (retVal == JFileChooser.APPROVE_OPTION) {
      try {
        writer = new BufferedWriter(new FileWriter(fc.getSelectedFile()));
        writer.write(ti.toString());
        writer.flush();
        writer.close();
      }
      catch (Exception e) {
        e.printStackTrace();
        m_Log.logMessage("Problem saving data: " + e.getMessage());
        JOptionPane.showMessageDialog(
            this, 
            "Problem saving data:\n" + e.getMessage(), 
            "Error", 
            JOptionPane.ERROR_MESSAGE);
      }
    }
  }

  /**
   * Handles constructing a popup menu with visualization options
   * @param name the name of the result history list entry clicked on by
   * the user.
   * @param x the x coordinate for popping up the menu
   * @param y the y coordinate for popping up the menu
   */
  protected void visualize(String name, int x, int y) {
    final String selectedName = name;
    JPopupMenu resultListMenu = new JPopupMenu();

    JMenuItem visMainBuffer = new JMenuItem("View in main window");
    if (selectedName != null) {
      visMainBuffer.addActionListener(new ActionListener() {
          public void actionPerformed(ActionEvent e) {
            m_History.setSingle(selectedName);
          }
        });
    } else {
      visMainBuffer.setEnabled(false);
    }
    resultListMenu.add(visMainBuffer);

    JMenuItem visSepBuffer = new JMenuItem("View in separate window");
    if (selectedName != null) {
    visSepBuffer.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
          m_History.openFrame(selectedName);
        }
      });
    } else {
      visSepBuffer.setEnabled(false);
    }
    resultListMenu.add(visSepBuffer);

    JMenuItem saveOutput = new JMenuItem("Save result buffer");
    if (selectedName != null) {
    saveOutput.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
          saveBuffer(selectedName);
        }
      });
    } else {
      saveOutput.setEnabled(false);
    }
    resultListMenu.add(saveOutput);
    
    JMenuItem deleteOutput = new JMenuItem("Delete result buffer");
    if (selectedName != null) {
      deleteOutput.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
          m_History.removeResult(selectedName);
        }
      });
    } else {
      deleteOutput.setEnabled(false);
    }
    resultListMenu.add(deleteOutput);


    FastVector o = null;
    if (selectedName != null) {
      o = (FastVector)m_History.getNamedObject(selectedName);
    }    

    //    VisualizePanel temp_vp = null;
    Instances tempTransformed = null;

    if (o != null) {
      for (int i = 0; i < o.size(); i++) {
        Object temp = o.elementAt(i);
        //      if (temp instanceof VisualizePanel) {
        if (temp instanceof Instances) {
          //      temp_vp = (VisualizePanel)temp;
          tempTransformed = (Instances) temp;
        } 
      }
    }
    
    //    final VisualizePanel vp = temp_vp;
    final Instances ti = tempTransformed;
    JMenuItem visTrans = null;
    
    if (ti != null) {
      if (ti.relationName().startsWith("AT:")) {
        visTrans = new JMenuItem("Visualize transformed data");
      } else {
        visTrans = new JMenuItem("Visualize reduced data");
      }
      resultListMenu.addSeparator();
    }

    //    JMenuItem visTrans = new JMenuItem("Visualize transformed data");
    if (ti != null && visTrans != null) {
      visTrans.addActionListener(new ActionListener() {
          public void actionPerformed(ActionEvent e) {
            visualizeTransformedData(ti);
          }
        });
    }
     
    if (visTrans != null) {
      resultListMenu.add(visTrans);
    }
    
    JMenuItem saveTrans = null;
    if (ti != null) {
      if (ti.relationName().startsWith("AT:"))
        saveTrans = new JMenuItem("Save transformed data...");
      else
        saveTrans = new JMenuItem("Save reduced data...");
    }
    if (saveTrans != null) {
      saveTrans.addActionListener(new ActionListener() {
          public void actionPerformed(ActionEvent e) {
            saveTransformedData(ti);
          }
      });
      resultListMenu.add(saveTrans);
    }
    
    resultListMenu.show(m_History.getList(), x, y);
  }
  
  /**
   * updates the capabilities filter of the GOE
   * 
   * @param filter      the new filter to use
   */
  protected void updateCapabilitiesFilter(Capabilities filter) {
    Instances           tempInst;
    Capabilities        filterClass;

    if (filter == null) {
      m_AttributeEvaluatorEditor.setCapabilitiesFilter(new Capabilities(null));
      m_AttributeSearchEditor.setCapabilitiesFilter(new Capabilities(null));
      return;
    }
    
    if (!ExplorerDefaults.getInitGenericObjectEditorFilter())
      tempInst = new Instances(m_Instances, 0);
    else
      tempInst = new Instances(m_Instances);
    tempInst.setClassIndex(m_ClassCombo.getSelectedIndex());

    try {
      filterClass = Capabilities.forInstances(tempInst);
    }
    catch (Exception e) {
      filterClass = new Capabilities(null);
    }
    
    // set new filter
    m_AttributeEvaluatorEditor.setCapabilitiesFilter(filterClass);
    m_AttributeSearchEditor.setCapabilitiesFilter(filterClass);
    
    m_StartBut.setEnabled(true);
    // check capabilities...
    Capabilities currentFilter = m_AttributeEvaluatorEditor.getCapabilitiesFilter();
    ASEvaluation evaluator = (ASEvaluation) m_AttributeEvaluatorEditor.getValue();
    Capabilities currentSchemeCapabilities =  null;
    if (evaluator != null && currentFilter != null && 
        (evaluator instanceof CapabilitiesHandler)) {
      currentSchemeCapabilities = ((CapabilitiesHandler)evaluator).getCapabilities();
      
      if (!currentSchemeCapabilities.supportsMaybe(currentFilter) &&
          !currentSchemeCapabilities.supports(currentFilter)) {
        m_StartBut.setEnabled(false);
      }
    }
  }
  
  /**
   * method gets called in case of a change event
   * 
   * @param e           the associated change event
   */
  public void capabilitiesFilterChanged(CapabilitiesFilterChangeEvent e) {
    if (e.getFilter() == null)
      updateCapabilitiesFilter(null);
    else
      updateCapabilitiesFilter((Capabilities) e.getFilter().clone());
  }

  /**
   * Sets the Explorer to use as parent frame (used for sending notifications
   * about changes in the data)
   * 
   * @param parent      the parent frame
   */
  public void setExplorer(Explorer parent) {
    m_Explorer = parent;
  }
  
  /**
   * returns the parent Explorer frame
   * 
   * @return            the parent
   */
  public Explorer getExplorer() {
    return m_Explorer;
  }
  
  /**
   * Returns the title for the tab in the Explorer
   * 
   * @return            the title of this tab
   */
  public String getTabTitle() {
    return "Select attributes";
  }
  
  /**
   * Returns the tooltip for the tab in the Explorer
   * 
   * @return            the tooltip of this tab
   */
  public String getTabTitleToolTip() {
    return "Determine relevance of attributes";
  }

  /**
   * Tests out the attribute selection panel from the command line.
   *
   * @param args may optionally contain the name of a dataset to load.
   */
  public static void main(String [] args) {

    try {
      final javax.swing.JFrame jf =
        new javax.swing.JFrame("Weka Explorer: Select attributes");
      jf.getContentPane().setLayout(new BorderLayout());
      final AttributeSelectionPanel sp = new AttributeSelectionPanel();
      jf.getContentPane().add(sp, BorderLayout.CENTER);
      weka.gui.LogPanel lp = new weka.gui.LogPanel();
      sp.setLog(lp);
      jf.getContentPane().add(lp, BorderLayout.SOUTH);
      jf.addWindowListener(new java.awt.event.WindowAdapter() {
        public void windowClosing(java.awt.event.WindowEvent e) {
          jf.dispose();
          System.exit(0);
        }
      });
      jf.pack();
      jf.setVisible(true);
      if (args.length == 1) {
        System.err.println("Loading instances from " + args[0]);
        java.io.Reader r = new java.io.BufferedReader(
                           new java.io.FileReader(args[0]));
        Instances i = new Instances(r);
        sp.setInstances(i);
      }
    } catch (Exception ex) {
      ex.printStackTrace();
      System.err.println(ex.getMessage());
    }
  }
}