/*
* 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.
*/
package org.broad.igv.session;
import org.apache.log4j.Logger;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackProperties;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.TrackPanel;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Class to parse a UCSC session file
*
* @author Jim Robinson
* @date 1/12/12
*/
public class UCSCSessionReader implements SessionReader {
private static Logger log = Logger.getLogger(UCSCSessionReader.class);
IGV igv;
public UCSCSessionReader(IGV igv) {
this.igv = igv;
}
/**
* Load a UCSC session from the given stream.
*
* @param inputStream
* @param session
* @param sessionName
* @throws IOException
*/
public void loadSession(InputStream inputStream, Session session, String sessionName) throws IOException {
BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream));
String trackLine = null;
String nextLine;
final List<String> errors = new ArrayList<String>();
final HashMap<String, List<Track>> loadedTracks = new HashMap();
List<ResourceLocator> aSync = new ArrayList();
// UCSC sessions do not have means to set genome, or if they do we don't use it
Genome genome = GenomeManager.getInstance().getCurrentGenome();
if (genome != null) {
IGV.getInstance().setGenomeTracks(genome.getGeneTrack());
}
while ((nextLine = reader.readLine()) != null) {
ResourceLocator locator = null;
try {
if (nextLine.startsWith("#")) {
continue;
} else if (nextLine.startsWith("browser")) {
parseBrowserLine(nextLine, session);
} else if (nextLine.startsWith("track")) {
trackLine = nextLine;
String dataURL = getDataURL(trackLine);
if (dataURL != null) {
locator = new ResourceLocator(dataURL);
loadedTracks.put(dataURL, igv.load(locator));
}
} else {
locator = new ResourceLocator(nextLine);
}
if (locator != null) {
locator.setTrackLine(trackLine);
// Alignment tracks must be loaded synchronously
if (isAlignmentFile(locator.getPath())) {
TrackPanel panel = igv.getPanelFor(locator);
panel.addTracks(igv.load(locator));
} else {
aSync.add(locator);
}
trackLine = null; // Reset for next time
locator = null;
}
} catch (Exception e) {
log.error("Error loading resource " + locator.getPath(), e);
String ms = "<b>" + locator.getPath() + "</b><br>&nbs;p " + e.toString() + "<br>";
errors.add(ms);
}
}
loadAsynchronous(aSync, loadedTracks, errors);
if (errors.size() > 0) {
displayErrors(errors);
}
}
private void loadAsynchronous(List<ResourceLocator> aSync, final HashMap<String, List<Track>> loadedTracks,
final List<String> errors) {
List<Thread> threads = new ArrayList(aSync.size());
for (final ResourceLocator locator : aSync) {
Runnable runnable = new Runnable() {
public void run() {
// TODO handle errors
try {
loadedTracks.put(locator.getPath(), igv.load(locator));
} catch (Exception e) {
log.error("Error loading resource " + locator.getPath(), e);
String ms = "<b>" + locator.getPath() + "</b><br>&nbs;p " + e.toString() + "<br>";
errors.add(ms);
}
}
};
Thread t = new Thread(runnable);
threads.add(t);
t.start();
}
// Wait for all threads to complete
for (Thread t : threads) {
try {
t.join();
} catch (InterruptedException ignore) {
}
}
placeTracksInPanels(aSync, loadedTracks);
}
private String getDataURL(String nextLine) {
TrackProperties props = new TrackProperties();
ParsingUtils.parseTrackLine(nextLine, props);
return props.getDataURL();
}
private void placeTracksInPanels(List<ResourceLocator> locatorPaths, Map<String, List<Track>> loadedTracks) {
for (ResourceLocator loc : locatorPaths) {
//TrackPanel panel = IGV.getInstance().getPanelFor(new ResourceLocator(path));
// If loading from UCSC use a single panel
TrackPanel panel = igv.getTrackPanel(IGV.DATA_PANEL_NAME);
String path = loc.getPath();
if (loadedTracks.containsKey(path)) {
panel.addTracks(loadedTracks.get(path));
}
}
}
private boolean isAlignmentFile(String path) {
return path.endsWith(".bam") || path.endsWith(".entries") || path.endsWith(".sam");
}
/**
* Browser lines have 2 or 3 tokens, e.g.
* browser position chr19:11500000-12000000
*
* @param line
*/
private void parseBrowserLine(String line, Session session) {
String[] tokens = line.split("\\s+");
if (tokens.length >= 3 && tokens[1].equals("position")) {
session.setLocus(tokens[2]);
}
}
private void displayErrors(List<String> errors) {
StringBuffer buffer = new StringBuffer();
buffer.append("<html>Errors were encountered while loading session:<br>");
for (String e : errors) {
buffer.append(e);
}
MessageUtils.showMessage(buffer.toString());
}
}