/*
* 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.
*/
package org.broad.igv.ui.action;
import org.apache.log4j.Logger;
import org.broad.igv.track.RegionScoreType;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackType;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.UIConstants;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.util.MessageUtils;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.List;
/**
* @author jrobinso
* @date Nov 7, 2010
*/
public class ExportTrackNamesMenuAction extends MenuAction {
static Logger log = Logger.getLogger(ClearRegionsMenuAction.class);
IGV igv;
public ExportTrackNamesMenuAction(String label, IGV mainFrame) {
super(label, null);
this.igv = mainFrame;
setToolTipText(UIConstants.EXPORT_REGION_TOOLTIP);
}
@Override
public void actionPerformed(ActionEvent e) {
FileDialog fd = new FileDialog(igv.getMainFrame());
fd.setModal(true);
fd.setMode(FileDialog.SAVE);
fd.setVisible(true);
String fname = fd.getFile();
if (fname == null) {
return;
}
File outputFile = new File(fd.getDirectory(), fname);
PrintWriter pw = null;
try {
pw = new PrintWriter(new FileWriter(outputFile));
final List<ReferenceFrame> referenceFrames = FrameManager.getFrames();
if (referenceFrames.size() > 1) {
pw.print("Sample");
for (ReferenceFrame frame : referenceFrames) {
pw.print("\t" + frame.getName());
}
pw.println();
}
for (Track t : igv.getAllTracks()) {
if (t.getTrackType() == TrackType.COPY_NUMBER || t.getTrackType() == TrackType.CNV) {
pw.print(t.getName());
for (ReferenceFrame frame : referenceFrames) {
//track.getRegionScore(chr, start, end, zoom, type, frame));
String chr = frame.getChrName();
int start = (int) frame.getOrigin();
int end = (int) frame.getEnd();
float score = t.getRegionScore(chr, start, end, frame.getZoom(), RegionScoreType.SCORE, frame.getName());
pw.print("\t" + score);
}
pw.println();
}
}
} catch (IOException ex) {
MessageUtils.showMessage("IO Error: " + ex.getMessage());
} finally {
if (pw != null) {
pw.close();
}
}
}
}