/*
* Copyright (c) 2007-2013 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* 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.
*/
package org.broad.igv.plugin.mongocollab;
import com.mongodb.DBCollection;
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.track.FeatureTrack;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackClickEvent;
import org.broad.igv.track.TrackMenuUtils;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.action.SearchCommand;
import org.broad.igv.ui.panel.IGVPopupMenu;
import org.broad.igv.ui.panel.ReferenceFrame;
import htsjdk.tribble.Feature;
import javax.swing.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Arrays;
/**
* @author jacob
* @date 2013-Sep-27
*/
public class MongoFeatureTrack extends FeatureTrack{
public MongoFeatureTrack(String id, String name, MongoFeatureSource source) {
super(id, name, source);
}
@Override
public void dispose() {
super.dispose();
SearchCommand.unregisterNamedFeatureSearcher((MongoFeatureSource) source);
}
/**
* Return a menu entry for adding a new feature, or editing a feature the user clicked on.
* @param te
* @param selFeat Selected feature. {@code null} indicates adding a new feature
* @return
*/
private JMenuItem createEditAnnotMenuEntry(TrackClickEvent te, final DBFeature.IGVFeat selFeat){
ReferenceFrame frame = te.getFrame();
boolean hasFrame = frame != null;
if(!hasFrame) return null;
final boolean editing = selFeat != null;
final String chr = editing ? selFeat.getChr() : frame.getChrName();
final int start = editing ? selFeat.getStart() : (int) te.getChromosomePosition();
final int end = editing ? selFeat.getEnd() : (int) Math.ceil(frame.getChromosomePosition(te.getMouseEvent().getX() + 1));
String featDispName = editing && selFeat.getName() != null ? selFeat.getName() : "Feature";
String name = editing ? "Edit " + featDispName : "Add annotation to " + MongoFeatureTrack.this.getName();
JMenuItem item = new JMenuItem(name);
item.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
Feature feat = editing ? selFeat.getDBFeature() : new BasicFeature(chr, start, end);
FeatureAnnotDialog dialog = new FeatureAnnotDialog(IGV.getMainFrame(), getCollection(), feat);
dialog.setVisible(true);
}
});
return item;
}
private DBCollection getCollection(){
return ((MongoFeatureSource) source).getCollection();
}
@Override
public IGVPopupMenu getPopupMenu(TrackClickEvent te) {
String title = getName();
IGVPopupMenu menu = TrackMenuUtils.getPopupMenu(Arrays.<Track>asList(this), title, te);
//Add annotation or edit existing one
Feature feat = getFeatureAtMousePosition(te);
JMenuItem item = createEditAnnotMenuEntry(te, (DBFeature.IGVFeat) feat);
if(item != null) menu.add(item);
return menu;
}
}