/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.gui;

import jalview.analysis.NJTree;
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.DistanceScoreModelI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.util.MessageManager;

import java.awt.Color;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.beans.PropertyVetoException;

import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;

/**
 * A dialog to allow a user to select and action Tree calculation options
 */
public class TreeChooser extends JPanel
{
  private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);

  AlignFrame af;

  JRadioButton pca;

  JRadioButton tree;

  JRadioButton neighbourJoining;

  JRadioButton averageDistance;

  JComboBox<String> modelNames;

  private JInternalFrame frame;

  private ButtonGroup treeTypes;

  private JCheckBox includeGaps;

  private JCheckBox matchGaps;

  private JCheckBox includeGappedColumns;

  private JCheckBox shorterSequence;

  /**
   * Constructor
   * 
   * @param af
   */
  public TreeChooser(AlignFrame alignFrame)
  {
    this.af = alignFrame;
    init();
  }

  /**
   * Lays out the panel and adds it to the desktop
   */
  void init()
  {
    frame = new JInternalFrame();
    frame.setContentPane(this);
    this.setBackground(Color.white);

    /*
     * Layout consists of 5 panels:
     * - first with choice of Tree or PCA
     * - second with choice of tree method NJ or AV
     * - third with choice of score model
     * - fourth with score model parameter options
     * - fifth with OK and Cancel
     */
    tree = new JRadioButton(MessageManager.getString("label.tree"));
    tree.setOpaque(false);
    pca = new JRadioButton(
            MessageManager.getString("label.principal_component_analysis"));
    pca.setOpaque(false);
    neighbourJoining = new JRadioButton(
            MessageManager.getString("label.tree_calc_nj"));
    averageDistance = new JRadioButton(
            MessageManager.getString("label.tree_calc_av"));
    ItemListener listener = new ItemListener()
    {
      @Override
      public void itemStateChanged(ItemEvent e)
      {
        neighbourJoining.setEnabled(tree.isSelected());
        averageDistance.setEnabled(tree.isSelected());
      }
    };
    pca.addItemListener(listener);
    tree.addItemListener(listener);
    ButtonGroup calcTypes = new ButtonGroup();
    calcTypes.add(pca);
    calcTypes.add(tree);
    JPanel calcChoicePanel = new JPanel();
    calcChoicePanel.setOpaque(false);
    tree.setSelected(true);
    calcChoicePanel.add(tree);
    calcChoicePanel.add(pca);

    neighbourJoining.setOpaque(false);
    treeTypes = new ButtonGroup();
    treeTypes.add(neighbourJoining);
    treeTypes.add(averageDistance);
    neighbourJoining.setSelected(true);
    JPanel treeChoicePanel = new JPanel();
    treeChoicePanel.setOpaque(false);
    treeChoicePanel.add(neighbourJoining);
    treeChoicePanel.add(averageDistance);

    /*
     * score model drop-down
     */
    modelNames = new JComboBox<String>();
    ScoreModels scoreModels = ScoreModels.getInstance();
    for (ScoreModelI sm : scoreModels.getModels())
    {
      boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
      if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
      {
        modelNames.addItem(sm.getName());
      }
    }
    modelNames.addItemListener(new ItemListener()
    {

      @Override
      public void itemStateChanged(ItemEvent e)
      {
        if (e.getStateChange() == ItemEvent.SELECTED)
        {
          scoreModelChanged((String) e.getItem());
        }
      }
    });
    JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
    scoreModelPanel.setOpaque(false);
    scoreModelPanel.add(modelNames, FlowLayout.LEFT);

    /*
     * score model parameters
     */
    JPanel paramsPanel = new JPanel(new GridLayout(5, 1));
    paramsPanel.setOpaque(false);
    includeGaps = new JCheckBox("Include gaps");
    matchGaps = new JCheckBox("Match gaps");
    includeGappedColumns = new JCheckBox("Include gapped columns");
    shorterSequence = new JCheckBox("Match on shorter sequence");
    paramsPanel.add(new JLabel("Pairwise sequence scoring options"));
    paramsPanel.add(includeGaps);
    paramsPanel.add(matchGaps);
    paramsPanel.add(includeGappedColumns);
    paramsPanel.add(shorterSequence);
    // configure initial state of options
    scoreModelChanged(modelNames.getItemAt(0));

    /*
     * OK / Cancel buttons
     */
    JButton ok = new JButton(MessageManager.getString("action.ok"));
    ok.setFont(VERDANA_11PT);
    ok.addActionListener(new java.awt.event.ActionListener()
    {
      @Override
      public void actionPerformed(ActionEvent e)
      {
        ok_actionPerformed(e);
      }
    });
    JButton cancel = new JButton(MessageManager.getString("action.cancel"));
    cancel.setFont(VERDANA_11PT);
    cancel.addActionListener(new java.awt.event.ActionListener()
    {
      @Override
      public void actionPerformed(ActionEvent e)
      {
        cancel_actionPerformed(e);
      }
    });
    JPanel actionPanel = new JPanel();
    actionPanel.setOpaque(false);
    actionPanel.add(ok);
    actionPanel.add(cancel);

    this.add(calcChoicePanel);
    this.add(treeChoicePanel);
    this.add(scoreModelPanel);
    this.add(paramsPanel);
    this.add(actionPanel);

    Desktop.addInternalFrame(frame,
            MessageManager.getString("label.choose_tree"), 400, 400, false);

    frame.setLayer(JLayeredPane.PALETTE_LAYER);
  }

  /**
   * Action on selection of score model
   * 
   * @param item
   */
  protected void scoreModelChanged(String modelName)
  {
    /*
     * enable/disable options appropriate to score model
     * NB this is temporary - will get score models to provide
     * their own parameters
     */
    includeGaps.setEnabled(true);
    matchGaps.setEnabled(true);
    includeGappedColumns.setEnabled(true);
    shorterSequence.setEnabled(true);

    ScoreModelI sm = ScoreModels.getInstance().forName(modelName);
    if (sm instanceof DistanceScoreModelI)
    {
      matchGaps.setEnabled(false);
      includeGappedColumns.setEnabled(false);
      shorterSequence.setEnabled(false);
    }
    if (sm instanceof ScoreMatrix)
    {
      matchGaps.setEnabled(false);
    }
    if (tree.isSelected())
    {
      // ?? tree requires specific parameter settings??
      includeGaps.setSelected(true);
      includeGaps.setEnabled(false);
      matchGaps.setSelected(true);
      includeGappedColumns.setSelected(true);
      includeGappedColumns.setEnabled(false);
      shorterSequence.setSelected(false);
      shorterSequence.setEnabled(false);
    }
  }

  /**
   * Open and calculate the selected tree on 'OK'
   * 
   * @param e
   */
  protected void ok_actionPerformed(ActionEvent e)
  {
    ScoreModelI sm = ScoreModels.getInstance().forName(
            modelNames.getSelectedItem().toString());
    SimilarityParamsI params = getSimilarityParameters();

    if (pca.isSelected())
    {
      AlignViewport viewport = af.getViewport();
      if (((viewport.getSelectionGroup() != null)
              && (viewport.getSelectionGroup().getSize() < 4) && (viewport
              .getSelectionGroup().getSize() > 0))
              || (viewport.getAlignment().getHeight() < 4))
      {
        JvOptionPane
                .showInternalMessageDialog(
                        this,
                        MessageManager
                                .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
                        MessageManager
                                .getString("label.sequence_selection_insufficient"),
                        JvOptionPane.WARNING_MESSAGE);
        return;
      }
      new PCAPanel(af.alignPanel, sm, params);
    }
    else
    {
      String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
              : NJTree.AVERAGE_DISTANCE;
      af.newTreePanel(treeType, sm, params);
    }

    // closeFrame();
  }

  /**
   * 
   */
  protected void closeFrame()
  {
    try
    {
      frame.setClosed(true);
    } catch (PropertyVetoException ex)
    {
    }
  }

  private SimilarityParamsI getSimilarityParameters()
  {
    SimilarityParamsI params = new SimilarityParams(
            includeGappedColumns.isSelected(), matchGaps.isSelected(),
            includeGaps.isSelected(), shorterSequence.isSelected());
    return params;
  }

  /**
   * Closes dialog on cancel
   * 
   * @param e
   */
  protected void cancel_actionPerformed(ActionEvent e)
  {
    try
    {
      frame.setClosed(true);
    } catch (Exception ex)
    {
    }
  }
}