/*
* 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.
*/
/*
* Created by JFormDesigner on Tue May 17 18:20:38 EDT 2011
*/
package org.broad.igv.peaks;
import java.awt.event.*;
import javax.swing.border.*;
import org.broad.igv.feature.RegionOfInterest;
import org.broad.igv.track.RegionScoreType;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.util.MessageUtils;
import java.awt.*;
import javax.swing.*;
import javax.swing.event.*;
/**
* @author Stan Diamond
*/
public class PeakCommandBar extends JPanel {
public PeakCommandBar() {
initComponents();
scoreSlider.setValue((int) PeakTrack.getScoreThreshold());
foldChangeSlider.setValue((int) PeakTrack.getFoldChangeThreshold());
this.colorByScoresButton.setSelected(PeakTrack.getColorOption() == PeakTrack.ColorOption.SCORE);
this.colorByChangeButton.setSelected(PeakTrack.getColorOption() == PeakTrack.ColorOption.FOLD_CHANGE);
this.peaksButton.setSelected(PeakTrack.isShowPeaks() && !PeakTrack.isShowSignals());
this.signalsButton.setSelected(!PeakTrack.isShowPeaks() && PeakTrack.isShowSignals());
this.bothButton.setSelected(PeakTrack.isShowPeaks() && PeakTrack.isShowSignals());
//peaksCB.setSelected(PeakTrack.isShowPeaks());
//signalsCB.setSelected(PeakTrack.isShowSignals());
}
private void scoreSliderStateChanged(ChangeEvent e) {
PeakTrack.setScoreThreshold(scoreSlider.getValue());
IGV.getInstance().revalidateTrackPanels();
}
private void foldChangeSliderStateChanged(ChangeEvent e) {
PeakTrack.setFoldChangeThreshold(foldChangeSlider.getValue());
IGV.getInstance().revalidateTrackPanels();
}
private void radioButtonActionPerformed(ActionEvent e) {
if (bothButton.isSelected()) {
PeakTrack.setShowPeaks(true);
PeakTrack.setShowSignals(true);
} else if (peaksButton.isSelected()) {
PeakTrack.setShowPeaks(true);
PeakTrack.setShowSignals(false);
} else {
PeakTrack.setShowPeaks(false);
PeakTrack.setShowSignals(true);
}
IGV.getInstance().repaint();
}
/* private void peaksCBActionPerformed(ActionEvent e) {
PeakTrack.setShowPeaks(peaksCB.isSelected());
IGV.getInstance().repaint();
}
private void signalsCBActionPerformed(ActionEvent e) {
PeakTrack.setShowSignals(signalsCB.isSelected());
IGV.getInstance().repaint();
}
*/
private void colorByActionPeformed(ActionEvent e) {
if (colorByChangeButton.isSelected()) {
PeakTrack.setShadeOption(PeakTrack.ColorOption.FOLD_CHANGE);
} else {
PeakTrack.setShadeOption(PeakTrack.ColorOption.SCORE);
}
IGV.getInstance().repaint();
}
private void sortButtonActionPerformed(ActionEvent e) {
// Create a region based on current view
// TODO -- do right thing if in geneListView
if (FrameManager.isGeneListMode()) {
MessageUtils.showMessage("To sort in gene list mode right-click the header of a gene panel.");
} else {
ReferenceFrame frame = FrameManager.getDefaultFrame();
RegionOfInterest roi = new RegionOfInterest(frame.getChrName(), (int) frame.getOrigin(), (int) frame.getEnd(), "");
IGV.getInstance().sortByRegionScore(roi, RegionScoreType.SCORE, frame);
}
}
private void signalsButtonActionPerformed(ActionEvent e) {
colorByScoresButton.setEnabled(false);
colorByChangeButton.setEnabled(false);
}
private void peaksButtonActionPerformed(ActionEvent e) {
colorByScoresButton.setEnabled(true);
colorByChangeButton.setEnabled(true);
}
private void bothButtonActionPerformed(ActionEvent e) {
colorByScoresButton.setEnabled(true);
colorByChangeButton.setEnabled(true);
}
private void initComponents() {
// JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
panel3 = new JPanel();
label1 = new JLabel();
foldChangeSlider = new JSlider();
panel2 = new JPanel();
label2 = new JLabel();
scoreSlider = new JSlider();
hSpacer1 = new JPanel(null);
panel1 = new JPanel();
label3 = new JLabel();
peaksButton = new JRadioButton();
signalsButton = new JRadioButton();
bothButton = new JRadioButton();
hSpacer2 = new JPanel(null);
colorByPanel = new JPanel();
label4 = new JLabel();
colorByScoresButton = new JRadioButton();
colorByChangeButton = new JRadioButton();
sortButton = new JButton();
//======== this ========
setLayout(new FlowLayout(FlowLayout.LEFT, 5, 0));
//======== panel3 ========
{
panel3.setLayout(new FlowLayout());
//---- label1 ----
label1.setText("<html>Fold change<br>threshold");
panel3.add(label1);
//---- foldChangeSlider ----
foldChangeSlider.setPaintTicks(true);
foldChangeSlider.setToolTipText("Adjust score threshold");
foldChangeSlider.setMajorTickSpacing(2);
foldChangeSlider.setMinorTickSpacing(1);
foldChangeSlider.setMaximum(10);
foldChangeSlider.setValue(0);
foldChangeSlider.setPaintLabels(true);
foldChangeSlider.setPreferredSize(new Dimension(150, 52));
foldChangeSlider.addChangeListener(new ChangeListener() {
public void stateChanged(ChangeEvent e) {
foldChangeSliderStateChanged(e);
}
});
panel3.add(foldChangeSlider);
}
add(panel3);
//======== panel2 ========
{
panel2.setLayout(new FlowLayout());
//---- label2 ----
label2.setText("<html>Score<br>threshold");
panel2.add(label2);
//---- scoreSlider ----
scoreSlider.setPaintTicks(true);
scoreSlider.setToolTipText("Adjust score threshold");
scoreSlider.setMajorTickSpacing(20);
scoreSlider.setPaintLabels(true);
scoreSlider.setPreferredSize(new Dimension(150, 52));
scoreSlider.addChangeListener(new ChangeListener() {
public void stateChanged(ChangeEvent e) {
scoreSliderStateChanged(e);
}
});
panel2.add(scoreSlider);
panel2.add(hSpacer1);
}
add(panel2);
//======== panel1 ========
{
panel1.setBorder(new EtchedBorder(EtchedBorder.RAISED));
panel1.setMinimumSize(new Dimension(250, 37));
panel1.setLayout(new FlowLayout());
//---- label3 ----
label3.setText("Show:");
panel1.add(label3);
//---- peaksButton ----
peaksButton.setText("Peaks");
peaksButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
radioButtonActionPerformed(e);
peaksButtonActionPerformed(e);
}
});
panel1.add(peaksButton);
//---- signalsButton ----
signalsButton.setText("Signals");
signalsButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
radioButtonActionPerformed(e);
signalsButtonActionPerformed(e);
}
});
panel1.add(signalsButton);
//---- bothButton ----
bothButton.setText("Both");
bothButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
radioButtonActionPerformed(e);
bothButtonActionPerformed(e);
}
});
panel1.add(bothButton);
}
add(panel1);
add(hSpacer2);
//======== colorByPanel ========
{
colorByPanel.setBorder(new EtchedBorder(EtchedBorder.RAISED));
colorByPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
//---- label4 ----
label4.setText("Color peaks by:");
colorByPanel.add(label4);
//---- colorByScoresButton ----
colorByScoresButton.setText("Factor");
colorByScoresButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
colorByActionPeformed(e);
}
});
colorByPanel.add(colorByScoresButton);
//---- colorByChangeButton ----
colorByChangeButton.setText("Change");
colorByChangeButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
colorByActionPeformed(e);
}
});
colorByPanel.add(colorByChangeButton);
}
add(colorByPanel);
//---- sortButton ----
sortButton.setText("Sort");
sortButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
sortButtonActionPerformed(e);
}
});
add(sortButton);
//---- buttonGroup1 ----
ButtonGroup buttonGroup1 = new ButtonGroup();
buttonGroup1.add(peaksButton);
buttonGroup1.add(signalsButton);
buttonGroup1.add(bothButton);
//---- buttonGroup2 ----
ButtonGroup buttonGroup2 = new ButtonGroup();
buttonGroup2.add(colorByScoresButton);
buttonGroup2.add(colorByChangeButton);
// JFormDesigner - End of component initialization //GEN-END:initComponents
}
// JFormDesigner - Variables declaration - DO NOT MODIFY //GEN-BEGIN:variables
// Generated using JFormDesigner non-commercial license
private JPanel panel3;
private JLabel label1;
private JSlider foldChangeSlider;
private JPanel panel2;
private JLabel label2;
private JSlider scoreSlider;
private JPanel hSpacer1;
private JPanel panel1;
private JLabel label3;
private JRadioButton peaksButton;
private JRadioButton signalsButton;
private JRadioButton bothButton;
private JPanel hSpacer2;
private JPanel colorByPanel;
private JLabel label4;
private JRadioButton colorByScoresButton;
private JRadioButton colorByChangeButton;
private JButton sortButton;
// JFormDesigner - End of variables declaration //GEN-END:variables
}