/*
* 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.
*/
/*
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* 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.feature.RegionOfInterest;
import org.broad.igv.prefs.PreferencesManager;
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 = PreferencesManager.getPreferences().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);
}
}
}