/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
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.prefs.Constants;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.track.Track;
import org.broad.igv.ui.IGV;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.util.List;
/**
* @author jrobinso
*/
public class SetTrackHeightMenuAction extends MenuAction {
IGV 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, IGV mainFrame) {
super(label, null, mnemonic);
this.mainFrame = mainFrame;
}
/**
* 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.getMainFrame(), 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());
IGV.getInstance().setAllTrackHeights(newTrackHeight);
lastTrackHeight = newTrackHeight;
doRefresh = true;
}
catch (NumberFormatException numberFormatException) {
JOptionPane.showMessageDialog(mainFrame.getMainFrame(), "Track height must be an integer number.");
}
}
finally {
// Refresh view
if (doRefresh) {
// Update the state of the current tracks for drawing purposes
mainFrame.doRefresh();
}
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 = IGV.getInstance().getAllTracks();
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 PreferencesManager.getPreferences().getAsInt(Constants.INITIAL_TRACK_HEIGHT);
}
}