/*
 * 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.TreeBuilder;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.util.MessageManager;

import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.GridLayout;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.beans.PropertyVetoException;
import java.util.ArrayList;
import java.util.List;

import javax.swing.BorderFactory;
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;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;

/**
 * A dialog where a user can choose and action Tree or PCA calculation options
 */
public class CalculationChooser extends JPanel
{
  /*
   * flag for whether gap matches residue in the PID calculation for a Tree
   * - true gives Jalview 2.10.1 behaviour
   * - set to false (using Groovy) for a more correct tree
   * (JAL-374)
   */
  private static boolean treeMatchGaps = true;

  private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);

  AlignFrame af;

  JRadioButton pca;

  JRadioButton neighbourJoining;

  JRadioButton averageDistance;

  JComboBox<String> modelNames;

  JButton ok;

  private JInternalFrame frame;

  private JCheckBox includeGaps;

  private JCheckBox matchGaps;

  private JCheckBox includeGappedColumns;

  private JCheckBox shorterSequence;

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

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

    /*
     * Layout consists of 3 or 4 panels:
     * - first with choice of PCA or tree method NJ or AV
     * - second with choice of score model
     * - third with score model parameter options [suppressed]
     * - fourth with OK and Cancel
     */
    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"));
    neighbourJoining.setOpaque(false);

    JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
    calcChoicePanel.setOpaque(false);

    // first create the Tree calculation's border panel
    JPanel treePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
    treePanel.setOpaque(false);

    treePanel.setBorder(BorderFactory.createTitledBorder(MessageManager
            .getString("label.tree")));

    // then copy the inset dimensions for the border-less PCA panel
    JPanel pcaBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT));
    Insets b = treePanel.getBorder().getBorderInsets(treePanel);
    pcaBorderless.setBorder(BorderFactory.createEmptyBorder(2, b.left, 2,
            b.right));
    pcaBorderless.setOpaque(false);

    pcaBorderless.add(pca, FlowLayout.LEFT);
    calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT);


    treePanel.add(neighbourJoining);
    treePanel.add(averageDistance);

    calcChoicePanel.add(treePanel);

    ButtonGroup calcTypes = new ButtonGroup();
    calcTypes.add(pca);
    calcTypes.add(neighbourJoining);
    calcTypes.add(averageDistance);
    {
      @Override
      public void itemStateChanged(ItemEvent e)
      {
        neighbourJoining.setEnabled(tree.isSelected());
        averageDistance.setEnabled(tree.isSelected());
      }
    };

    /*
     * score models drop-down - with added tooltips!
     */
    modelNames = buildModelOptionsList();

    JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
    scoreModelPanel.setOpaque(false);
    scoreModelPanel.add(modelNames);

    /*
     * 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);

    /*
     * 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();
      }
    });
    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);

    boolean includeParams = false;
    this.add(calcChoicePanel, BorderLayout.CENTER);
    calcChoicePanel.add(scoreModelPanel);
    if (includeParams)
    {
      scoreModelPanel.add(paramsPanel);
    }
    this.add(actionPanel, BorderLayout.SOUTH);

    int width = 350;
    int height = includeParams ? 420 : 240;

    setMinimumSize(new Dimension(325, height - 10));
    String title = MessageManager.getString("label.choose_calculation");
    if (af.getViewport().viewName != null)
    {
      title = title + " (" + af.getViewport().viewName + ")";
    }

    Desktop.addInternalFrame(frame,
            title, width,
            height, false);
    calcChoicePanel.doLayout();
    revalidate();
    /*
     * null the AlignmentPanel's reference to the dialog when it is closed
     */
    frame.addInternalFrameListener(new InternalFrameAdapter()
    {
      @Override
      public void internalFrameClosed(InternalFrameEvent evt)
      {
        af.alignPanel.setCalculationDialog(null);
      };
    });

    frame.setLayer(JLayeredPane.PALETTE_LAYER);
  }

  /**
   * A rather elaborate helper method (blame Swing, not me) that builds a
   * drop-down list of score models (by name) with descriptions as tooltips.
   * There is also a tooltip shown for the currently selected item when hovering
   * over it (without opening the list).
   */
  protected JComboBox<String> buildModelOptionsList()
  {
    final JComboBox<String> comboBox = new JComboBox<String>();
    ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
    comboBox.setRenderer(renderer);
    final List<String> tips = new ArrayList<String>();

    /*
     * show tooltip on mouse over the combobox
     * note the listener has to be on the components that make up
     * the combobox, doesn't work if just on the combobox
     */
    MouseAdapter mouseListener = new MouseAdapter()
    {
      @Override
      public void mouseEntered(MouseEvent e)
      {
        comboBox.setToolTipText(tips.get(comboBox.getSelectedIndex()));
      }

      @Override
      public void mouseExited(MouseEvent e)
      {
        comboBox.setToolTipText(null);
      }
    };
    for (Component c : comboBox.getComponents())
    {
      c.addMouseListener(mouseListener);
    }

    /*
     * now we can actually add entries to the combobox,
     * remembering their descriptions for tooltips
     */
    ScoreModels scoreModels = ScoreModels.getInstance();
    for (ScoreModelI sm : scoreModels.getModels())
    {
      boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
      if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
      {
        comboBox.addItem(sm.getName());

        /*
         * tooltip is description if provided, else text lookup with
         * fallback on the model name
         */
        String tooltip = sm.getDescription();
        if (tooltip == null)
        {
          tooltip = MessageManager.getStringOrReturn("label.score_model_",
                  sm.getName());
        }
        tips.add(tooltip);
      }

      /*
       * set the list of tooltips on the combobox's renderer
       */
      renderer.setTooltips(tips);
    }

    return comboBox;
  }

  /**
   * Open and calculate the selected tree or PCA on 'OK'
   */
  protected void ok_actionPerformed()
  {
    boolean doPCA = pca.isSelected();
    String modelName = modelNames.getSelectedItem().toString();
    SimilarityParamsI params = getSimilarityParameters(doPCA);

    if (doPCA)
    {
      openPcaPanel(modelName, params);
    }
    else
    {
      openTreePanel(modelName, params);
    }

    // closeFrame();
  }

  /**
   * Open a new Tree panel on the desktop
   * 
   * @param modelName
   * @param params
   */
  protected void openTreePanel(String modelName, SimilarityParamsI params)
  {
    String treeType = neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING
            : TreeBuilder.AVERAGE_DISTANCE;
    af.newTreePanel(treeType, modelName, params);
  }

  /**
   * Open a new PCA panel on the desktop
   * 
   * @param modelName
   * @param params
   */
  protected void openPcaPanel(String modelName, SimilarityParamsI params)
  {
    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, modelName, params);
  }

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

  /**
   * Returns a data bean holding parameters for similarity (or distance) model
   * calculation
   * 
   * @param doPCA
   * @return
   */
  protected SimilarityParamsI getSimilarityParameters(boolean doPCA)
  {
    // commented out: parameter choices read from gui widgets
    // SimilarityParamsI params = new SimilarityParams(
    // includeGappedColumns.isSelected(), matchGaps.isSelected(),
    // includeGaps.isSelected(), shorterSequence.isSelected());

    boolean includeGapGap = true;
    boolean includeGapResidue = true;
    boolean matchOnShortestLength = false;

    /*
     * 'matchGaps' flag is only used in the PID calculation
     * - set to false for PCA so that PCA using PID reproduces SeqSpace PCA
     * - set to true for Tree to reproduce Jalview 2.10.1 calculation
     * - set to false for Tree for a more correct calculation (JAL-374)
     */
    boolean matchGap = doPCA ? false : treeMatchGaps;

    return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength);
  }

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