/*
* 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.action;
import org.apache.log4j.Logger;
import org.broad.igv.feature.RegionOfInterest;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.UIConstants;
import org.broad.igv.ui.util.FileDialogUtils;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.ui.util.UIUtilities;
import java.awt.event.ActionEvent;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
/**
* @author jrobinso
*/
public class ImportRegionsMenuAction extends MenuAction {
static Logger log = Logger.getLogger(ImportRegionsMenuAction.class);
IGV mainFrame;
public ImportRegionsMenuAction(String label, int mnemonic, IGV mainFrame) {
super(label, null, mnemonic);
this.mainFrame = mainFrame;
setToolTipText(UIConstants.IMPORT_REGION_TOOLTIP);
}
@Override
public void actionPerformed(ActionEvent e) {
UIUtilities.invokeOnEventThread(new Runnable() {
public void run() {
File file = FileDialogUtils.chooseFile("Import regions of interest");
if (file != null) {
readRegionsOfInterestFile(file);
}
}
});
}
private void readRegionsOfInterestFile(File roiFile) {
if (roiFile == null) {
log.info("No regions found in file");
return;
}
if (!roiFile.exists()) {
MessageUtils.showMessage(roiFile.getAbsolutePath() + " not found");
return;
}
try {
BufferedReader reader = null;
int coordConvention = 0;
try {
reader = new BufferedReader(new FileReader(roiFile));
while (true) {
String dataRecord = reader.readLine();
if (dataRecord == null) {
return;
} else if (dataRecord.startsWith("track")) {
// Skip track line
continue;
} else if (dataRecord.startsWith("#coords")) {
String[] tmp = dataRecord.split("=");
if (tmp.length > 1) {
try {
coordConvention = Integer.parseInt(tmp[1]);
} catch (NumberFormatException e) {
log.error("Error parsing coordinate convention direction for file: " + roiFile);
}
}
}
String[] data = dataRecord.split("\t");
if (data.length >= 2) {
try {
String name = data.length > 3 ? data[3] : null;
int start = Integer.parseInt(data[1]) - coordConvention;
int end = data.length > 2 ? Integer.parseInt(data[2]) : start + 1;
RegionOfInterest regionOfInterest = new RegionOfInterest(data[0], start, end, name);
mainFrame.addRegionOfInterest(regionOfInterest);
} catch (NumberFormatException numberFormatException) {
log.error("Error importing regions of interest", numberFormatException);
}
}
}
} finally {
if (reader != null) {
reader.close();
}
mainFrame.doRefresh();
}
} catch (Exception e) {
log.error("Failed to write Region of Interest export file!", e);
}
}
}