/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
 * is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
 * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
 * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
 * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
 * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
 * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
 * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
 * FOREGOING.
 */


/*
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package org.broad.igv.ui.action;

//~--- non-JDK imports --------------------------------------------------------

import org.apache.commons.math.stat.StatUtils;
import org.apache.log4j.Logger;
import org.broad.igv.PreferenceManager;
import org.broad.igv.track.Track;
import org.broad.igv.ui.IGVMainFrame;
import org.broad.igv.ui.UIConstants;

import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.util.List;

/**
 * @author jrobinso
 */
public class SetTrackHeightMenuAction extends MenuAction {

    IGVMainFrame mainFrame;
    static Logger log = Logger.getLogger(SetTrackHeightMenuAction.class);

    static int lastTrackHeight = -1;

    /**
     * Constructs ...
     *
     * @param label
     * @param mnemonic
     * @param mainFrame
     */
    public SetTrackHeightMenuAction(String label, int mnemonic, IGVMainFrame mainFrame) {
        super(label, null, mnemonic);
        this.mainFrame = mainFrame;
        setToolTipText(UIConstants.SET_DEFAULT_TRACK_HEIGHT_TOOLTIP);
    }

    /**
     * Method description
     *
     * @param e
     */
    @Override
    public void actionPerformed(ActionEvent e) {
        doSetTrackHeight();

    }

    /**
     * Method description
     */
    final public void doSetTrackHeight() {

        boolean doRefresh = false;
        try {
            JPanel container = new JPanel();
            JLabel trackHeightLabel = new JLabel("Track Height (pixels)");
            JTextField trackHeightField = new JTextField();
            Dimension preferredSize = trackHeightField.getPreferredSize();
            trackHeightField.setPreferredSize(new Dimension(50, (int) preferredSize.getHeight()));
            container.add(trackHeightLabel);
            container.add(trackHeightField);

            int repTrackHeight = getRepresentativeTrackHeight();
            trackHeightField.setText(String.valueOf(repTrackHeight));

            int status = JOptionPane.showConfirmDialog(mainFrame, container, "Set Track Height",
                    JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null);

            if ((status == JOptionPane.CANCEL_OPTION) || (status == JOptionPane.CLOSED_OPTION)) {
                return;
            }

            try {
                int newTrackHeight = Integer.parseInt(trackHeightField.getText().trim());
                IGVMainFrame.getInstance().getTrackManager().setAllTrackHeights(newTrackHeight);
                lastTrackHeight = newTrackHeight;
                doRefresh = true;
            }
            catch (NumberFormatException numberFormatException) {
                JOptionPane.showMessageDialog(mainFrame, "Track height must be an integer number.");
            }

        }
        finally {

            // Refresh view
            if (doRefresh) {

                // Update the state of the current tracks for drawing purposes
                // NOTE this method itself is wrapped in an invokeLater call.
                // What is the consequence of nested invokeLaters?
                mainFrame.updateTrackState();
            }
            mainFrame.resetStatusMessage();
        }

    }

    /**
     * Return a representative track height to use as the default.  For now
     * using the median track height.
     *
     * @return
     */
    private int getRepresentativeTrackHeight() {

        if (lastTrackHeight > 0) {
            return lastTrackHeight;
        }

        // Get all tracks except the gene track
        List<Track> tracks = IGVMainFrame.getInstance().getTrackManager().getAllTracks(false);


        double[] heights = new double[tracks.size()];
        for (int i = 0; i < tracks.size(); i++) {
            heights[i] = tracks.get(i).getHeight();
        }
        int medianTrackHeight = (int) Math.round(StatUtils.percentile(heights, 50));
        if (medianTrackHeight > 0) {
            return medianTrackHeight;
        }

        return PreferenceManager.getInstance().getDefaultTrackHeight();

    }
}
