/*
* 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.panel;
import org.broad.igv.Globals;
import org.broad.igv.feature.Strand;
import org.broad.igv.util.blat.BlatClient;
import org.broad.igv.feature.RegionOfInterest;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.util.LongRunningTask;
import org.broad.igv.util.NamedRunnable;
import javax.swing.*;
import javax.swing.event.MouseInputAdapter;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.util.Collection;
/**
* @author eflakes
*/
public class RegionOfInterestPanel extends JPanel {
PopupMenu popup;
ReferenceFrame frame;
// There can only be 1 selected region, irrespective of the number of panels
private static RegionOfInterest selectedRegion = null;
public RegionOfInterestPanel(ReferenceFrame frame) {
setToolTipText("Regions of Interest");
this.frame = frame;
MouseInputAdapter ma = new ROIMouseAdapater();
addMouseListener(ma);
addMouseMotionListener(ma);
}
@Override
public void paintComponent(final Graphics g) {
super.paintComponent(g);
// Draw regions of interest?
drawRegionsOfInterest((Graphics2D) g, getHeight());
g.setColor(Color.BLACK);
g.drawRect(0, 0, getWidth(), getHeight());
}
public void drawRegionsOfInterest(final Graphics2D g, int height) {
Collection<RegionOfInterest> regions = getRegions();
if (regions == null || regions.isEmpty()) {
return;
}
for (RegionOfInterest regionOfInterest : regions) {
int regionStart = regionOfInterest.getStart();
int regionEnd = regionOfInterest.getEnd();
// This is ugly, but neccessary the way the "whole genome" is treated as another chromosome
if (frame.getChrName().equals(Globals.CHR_ALL)) {
Genome genome = GenomeManager.getInstance().getCurrentGenome();
regionStart = genome.getGenomeCoordinate(regionOfInterest.getChr(), regionStart);
regionEnd = genome.getGenomeCoordinate(regionOfInterest.getChr(), regionEnd);
}
int start = frame.getScreenPosition(regionStart);
int end = frame.getScreenPosition(regionEnd);
int regionWidth = Math.max(1, end - start);
g.setColor(regionOfInterest.getBackgroundColor());
g.fillRect(start, 0, regionWidth, height);
}
}
/**
* Return the region of interest at the screen pixel location.
*
* @param px
* @return
*/
RegionOfInterest getRegionOfInterest(int px) {
double pos = frame.getChromosomePosition(px);
Collection<RegionOfInterest> roiList = getRegions();
if (roiList != null) {
for (RegionOfInterest roi : roiList) {
if (pos > roi.getStart() && pos < roi.getEnd()) {
return roi;
}
}
}
return null;
}
protected static JPopupMenu getPopupMenu(final Component parent, final RegionOfInterest roi, final ReferenceFrame frame) {
//Set<TrackType> loadedTypes = IGV.getInstance().getLoadedTypes();
JPopupMenu popupMenu = new RegionMenu(roi, frame);
popupMenu.addSeparator();
JMenuItem item = new JMenuItem("Zoom");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
frame.jumpTo(roi.getChr(), roi.getStart(), roi.getEnd());
String locusString = roi.getLocusString();
IGV.getInstance().getSession().getHistory().push(locusString, frame.getZoom());
}
});
popupMenu.add(item);
item = new JMenuItem("Edit description...");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
String desc = JOptionPane.showInputDialog(parent, "Add or edit region description:", roi.getDescription());
roi.setDescription(desc);
IGV.getInstance().getSession().getRegionsOfInterestObservable().setChangedAndNotify();
}
});
popupMenu.add(item);
item = new JMenuItem("Copy sequence");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
LongRunningTask.submit(new NamedRunnable() {
public String getName() {
return "Copy sequence";
}
public void run() {
Genome genome = GenomeManager.getInstance().getCurrentGenome();
IGV.copySequenceToClipboard(genome, roi.getChr(), roi.getStart(), roi.getEnd(), Strand.NONE);
}
});
}
});
popupMenu.add(item);
// Disable copySequence if region exceeds 1 MB
if (roi.getEnd() - roi.getStart() > 1000000) {
item.setEnabled(false);
}
popupMenu.add(item);
item = new JMenuItem("Blat sequence");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
BlatClient.doBlatQuery(roi.getChr(), roi.getStart(), roi.getEnd(), Strand.NONE);
}
});
popupMenu.add(item);
popupMenu.add(new JSeparator());
item = new JMenuItem("Delete");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
IGV.getInstance().getSession().getRegionsOfInterest(frame.getChrName()).remove(roi);
IGV.getInstance().revalidateTrackPanels();
}
});
popupMenu.add(item);
return popupMenu;
}
public static RegionOfInterest getSelectedRegion() {
return selectedRegion;
}
public static void setSelectedRegion(RegionOfInterest region) {
selectedRegion = region;
}
class ROIMouseAdapater extends MouseInputAdapter {
@Override
public void mousePressed(MouseEvent e) {
showPopup(e);
}
@Override
public void mouseReleased(MouseEvent e) {
//showPopup(e);
}
@Override
public void mouseMoved(MouseEvent e) {
RegionOfInterest roi = getRegionOfInterest(e.getX());
if (roi != null) {
setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
setToolTipText(roi.getTooltip());
if (selectedRegion != roi) {
selectedRegion = roi;
IGV.getInstance().revalidateTrackPanels();
}
} else {
if (selectedRegion != null) {
selectedRegion = null;
IGV.getInstance().revalidateTrackPanels();
}
setToolTipText("");
setCursor(Cursor.getDefaultCursor());
}
}
@Override
public void mouseExited(MouseEvent mouseEvent) {
if (selectedRegion != null) {
selectedRegion = null;
IGV.getInstance().revalidateTrackPanels();
}
}
private void showPopup(MouseEvent e) {
RegionOfInterest roi = getRegionOfInterest(e.getX());
if (roi != null) {
getPopupMenu(RegionOfInterestPanel.this, roi, frame).show(e.getComponent(), e.getX(), e.getY());
}
}
}
/**
* A convenience method for returning the regions of interest for the current frame.
*/
private Collection<RegionOfInterest> getRegions() {
return IGV.getInstance().getSession().getRegionsOfInterest(frame.getChrName());
}
}