/*
* Copyright (c) 2007-2012 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.ui.action;
import org.apache.log4j.Logger;
import org.broad.igv.DirectoryManager;
import org.broad.igv.PreferenceManager;
import org.broad.igv.feature.RegionOfInterest;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.RegionNavigatorDialog;
import org.broad.igv.ui.util.FileDialogUtils;
import org.broad.igv.ui.util.UIUtilities;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.io.File;
import java.io.PrintWriter;
import java.util.Collection;
/**
* @author jrobinso
*/
public class ExportRegionsMenuAction extends MenuAction {
static Logger log = Logger.getLogger(ExportRegionsMenuAction.class);
IGV mainFrame;
public ExportRegionsMenuAction(String label, int mnemonic, IGV mainFrame) {
super(label, null, mnemonic);
this.mainFrame = mainFrame;
}
@Override
public void actionPerformed(ActionEvent e) {
UIUtilities.invokeOnEventThread(new Runnable() {
public void run() {
exportRegionsOfInterest();
}
});
}
public final void exportRegionsOfInterest() {
//dhmay adding 20110505: There was an intermittent bug in which the regions list was not getting
//synched when the user made changes to the regions table in the region navigator dialog. I'm addressing
//this with a change to RegionNavigatorDialog, but, due to the intermittent nature of the bug, I'm adding
//a catchall here, too. This synchs everything from the nav dialog.
RegionNavigatorDialog navDialog = RegionNavigatorDialog.getInstance();
if (navDialog != null) navDialog.updateROIsFromRegionTable();
File exportRegionDirectory = PreferenceManager.getInstance().getLastExportedRegionDirectory();
if (exportRegionDirectory == null) {
exportRegionDirectory = DirectoryManager.getUserDirectory();
}
String title = "Export Regions of Interest ...";
File file = FileDialogUtils.chooseFile(title, exportRegionDirectory, new File("regions.bed"), FileDialog.SAVE);
if (file == null) {
return;
}
writeRegionsOfInterestFile(file);
}
private void writeRegionsOfInterestFile(File roiFile) {
if (roiFile == null) {
log.info("A blank Region of Interest export file was supplied!");
return;
}
try {
Collection<RegionOfInterest> regions = IGV.getInstance().getSession().getAllRegionsOfInterest();
if (regions == null || regions.isEmpty()) {
return;
}
// Create export file
roiFile.createNewFile();
PrintWriter writer = null;
try {
writer = new PrintWriter(roiFile);
for (RegionOfInterest regionOfInterest : regions) {
Integer regionStart = regionOfInterest.getStart();
if (regionStart == null) {
// skip - null starts are bad regions of interest
continue;
}
Integer regionEnd = regionOfInterest.getEnd();
if (regionEnd == null) {
regionEnd = regionStart;
}
// Write info in BED format
writer.print(regionOfInterest.getChr());
writer.print("\t");
writer.print(regionStart);
writer.print("\t");
writer.print(regionEnd);
if (regionOfInterest.getDescription() != null) {
writer.print("\t");
writer.println(regionOfInterest.getDescription());
} else {
writer.println();
}
}
} finally {
if (writer != null) {
writer.close();
}
}
} catch (Exception e) {
log.error("Failed to write Region of Interest export file!", e);
}
}
}