/*
* 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
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
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package org.broad.igv.gitools;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.math.stat.StatUtils;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.dev.api.IGVPlugin;
import org.broad.igv.feature.FeatureDB;
import org.broad.igv.feature.Locus;
import org.broad.igv.feature.NamedFeature;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.lists.GeneList;
import org.broad.igv.lists.GeneListManagerUI;
import org.broad.igv.track.DataTrack;
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.util.FileDialogUtils;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.ui.util.UIUtilities;
import org.broad.igv.util.collections.DoubleArrayList;
import javax.swing.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.*;
import java.net.Socket;
import java.util.*;
/**
* Class for integrating with Gitools. Writes out data in TDM format.
* We implement GeneListUIActionListener so the gene list can be selected using
* our current UI
* @author jrobinso
* Date: 11/13/12
* Time: 9:26 PM
*/
public class Gitools implements IGVPlugin{
private static Logger log = Logger.getLogger(Gitools.class);
public static final String ENABLE_PROPERTY = "enableGitools";
private static int port = 50151;
private static String host = "localhost";
@Override
public void init() {
UIUtilities.invokeAndWaitOnEventThread(() ->addMenuItems());
}
private static void addMenuItems(){
boolean showTDMButton = Boolean.parseBoolean(System.getProperty(Gitools.ENABLE_PROPERTY, "true"));
if(showTDMButton){
JMenu gitoolsMenu = new JMenu("Gitools Heatmaps");
JMenuItem directLoadItem = new JMenuItem("Load Gene Matrix in Gitools");
directLoadItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
if (Gitools.canConnect() ) {
GeneListManagerUI dialog = GeneListManagerUI.getInstance(IGV.getMainFrame(),
"Gitools Load", new Gitools.DirectLoadListener());
dialog.setVisible(true);
} else {
JOptionPane.showMessageDialog(IGV.getMainFrame(), "To be able to browse the gene matrix you need to install and open Gitools.\n Download it from http://www.gitools.org.");
}
}
});
gitoolsMenu.add(directLoadItem);
JMenuItem gitoolsItem = new JMenuItem("Export Gene Matrix (TDM)...");
gitoolsItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
GeneListManagerUI dialog = GeneListManagerUI.getInstance(IGV.getMainFrame(),
"Export TDM", new Gitools.ExportFileListener());
dialog.setVisible(true);
}
});
gitoolsMenu.add(gitoolsItem);
IGV.getInstance().addOtherToolMenu(gitoolsMenu);
}
}
public static void main(String[] args){
try {
sendCommand("version");
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Send a command to gitools, and read the response.
* @param command
* @return First line of response only TODO This is stupid but readLine is hanging so hack it for now
* @throws IOException
*/
private static List<String> sendCommand(String command) throws IOException{
Socket socket = null;
try{
socket = new Socket(host, port);
socket.setSoTimeout(1000);
PrintWriter out = new PrintWriter(socket.getOutputStream(),
true);
BufferedReader in = new BufferedReader(new InputStreamReader(
socket.getInputStream()));
out.println(command);
List<String> response = new ArrayList<String>();
String line;
while( (line = in.readLine()) != null){
response.add(line);
break;
}
return response;
}catch(IOException e){
System.out.println(e);
throw new IOException("Error communicating with gitools", e);
}finally{
if(socket != null) socket.close();
}
}
public static boolean canConnect(){
boolean canConnect = false;
try{
List<String> version = sendCommand("version");
canConnect = version.get(0).toLowerCase().contains("gitools");
} catch (IOException e) {
//
}
return canConnect;
}
/**
* Export data at specified loci to temp file, and tell gitools to load it.
* gitools must already be running
* @param lociStrings
* @return
* @throws IOException
*/
public static List<String> gitoolsLoad(String name, List<String> lociStrings) throws IOException{
String prefix = name + "-igv";
prefix = prefix.replace(" ", "_");
File tmpFile = File.createTempFile(prefix, ".tdm");
exportTDM(lociStrings, tmpFile);
return sendCommand(String.format("load %s", tmpFile.getAbsolutePath()));
}
public static void exportTDM(List<String> lociStrings, File file) throws IOException {
// Convert the loci strings to a list of loci, if the loci represents multiple features (e.g. isoforms) use the largest
int averageFeatureSize = 0;
List<NamedFeature> loci = new ArrayList<NamedFeature>(lociStrings.size());
for (String l : lociStrings) {
NamedFeature feature = FeatureDB.getFeature(l);
if (feature == null) {
feature = Locus.fromString(l);
}
if (feature != null) {
loci.add(feature);
averageFeatureSize += (feature.getEnd() - feature.getStart());
}
}
if (loci.size() > 0) averageFeatureSize /= loci.size();
// Determine data types -- all data tracks + mutation, and samples
LinkedHashSet<TrackType> loadedTypes = new LinkedHashSet<TrackType>();
List<Track> tracks = IGV.getInstance().getAllTracks();
for (Track t : tracks) {
if ((t instanceof DataTrack || t.getTrackType() == TrackType.MUTATION) && t.isVisible()) {
loadedTypes.add(t.getTrackType());
//samples.add(t.getSample());
}
}
// set an appropriate zoom level for this feature set. Very approximate
int zoom = 0;
Genome genome = GenomeManager.getInstance().getCurrentGenome();
if (genome != null) {
double averageChrLength = genome.getTotalLength() / genome.getChromosomes().size();
zoom = (int) (Math.log(averageChrLength / averageFeatureSize) / Globals.log2) + 1;
}
// Loop though tracks and loci and gather data by sample & gene
Map<String, SampleData> sampleDataMap = new LinkedHashMap<String, SampleData>();
for (Track t : tracks) {
if (!t.isVisible()) continue;
String sampleName = t.getSample();
List<Track> overlays = IGV.getInstance().getOverlayTracks(t);
for (NamedFeature locus : loci) {
double regionScore;
if (t instanceof DataTrack) {
DataTrack dataTrack = (DataTrack) t;
regionScore = dataTrack.getAverageScore(locus.getChr(), locus.getStart(), locus.getEnd(), zoom);
addToSampleData(sampleDataMap, sampleName, locus.getName(), t.getTrackType(), regionScore);
}
if(overlays != null) {
for (Track overlay : overlays) {
if (overlay.getTrackType() == TrackType.MUTATION) {
regionScore = overlay.getRegionScore(locus.getChr(), locus.getStart(), locus.getEnd(), zoom,
RegionScoreType.MUTATION_COUNT, locus.getName());
//Only add if we found a mutation. Should we put it in anyway?
if (regionScore > 0) {
addToSampleData(sampleDataMap, sampleName, locus.getName(), overlay.getTrackType(), regionScore);
}
}
}
}
}
}
writeTDM(loadedTypes, sampleDataMap, file);
}
/**
* Export calculated data to file
* @param loadedTypes Ordered set of track types
* @param sampleDataMap Map from sample name to SampleData
* @param file Output file
* @throws IOException
*/
private static void writeTDM(LinkedHashSet<TrackType> loadedTypes, Map<String, SampleData> sampleDataMap, File file) throws IOException {
PrintWriter pw = null;
try {
pw = new PrintWriter(new BufferedWriter(new FileWriter(file)));
pw.print("Sample\tLocus");
for (TrackType tt : loadedTypes) {
pw.print("\t" + tt.name());
}
pw.println();
for (SampleData sd : sampleDataMap.values()) {
pw.print(sd.sample + "\t" + sd.locus);
for (TrackType tt : loadedTypes) {
pw.print('\t');
double[] values = sd.getValues(tt);
if (values == null) {
pw.print("-");
} else {
double avg = StatUtils.max(values);
pw.print(avg);
}
}
pw.println();
}
} catch(IOException e){
throw new IOException("Error exporting TDM", e);
} finally{
if (pw != null) pw.close();
}
}
private static void addToSampleData(Map<String, SampleData> sampleDataMap, String sampleName, String locusString, TrackType tt, double regionScore){
if (!Double.isNaN(regionScore)) {
//String locusString = locus.getName();
String key = sampleName + "_" + locusString;
SampleData sd = sampleDataMap.get(key);
if (sd == null) {
sd = new SampleData(sampleName, locusString);
sampleDataMap.put(key, sd);
}
sd.addValue(tt, regionScore);
}
}
static class SampleData {
String sample;
String locus;
Map<TrackType, DoubleArrayList> valueMap;
SampleData(String sample, String locus) {
this.sample = sample;
this.locus = locus;
this.valueMap = new HashMap<TrackType, DoubleArrayList>();
}
void addValue(TrackType tt, double value) {
DoubleArrayList vlist = valueMap.get(tt);
if (vlist == null) {
vlist = new DoubleArrayList();
valueMap.put(tt, vlist);
}
vlist.add(value);
}
public double[] getValues(TrackType tt) {
DoubleArrayList dal = valueMap.get(tt);
return dal == null ? null : dal.toArray();
}
}
public static class ExportFileListener implements GeneListManagerUI.GeneListListener{
@Override
public void actionPerformed(JDialog dialog, GeneList geneList) {
File file = FileDialogUtils.chooseFile("Export TDM file", null, FileDialogUtils.SAVE);
// Check file TDM extension
String currentExtension = FilenameUtils.getExtension(file.getName());
if (!currentExtension.equalsIgnoreCase("TDM")) {
file = new File(file.getAbsolutePath() + ".tdm");
}
if (file != null) {
try {
Gitools.exportTDM(geneList.getLoci(), file);
} catch (IOException exc) {
MessageUtils.showErrorMessage("Error exporting TDM", exc);
}
}
}
}
public static class DirectLoadListener implements GeneListManagerUI.GeneListListener{
@Override
public void actionPerformed(JDialog dialog, GeneList geneList) {
//Test communication
boolean canConnect = canConnect();
if(!canConnect){
MessageUtils.showMessage("Cannot communicate with gitools, check that it is running on port " + port);
return;
}
try {
gitoolsLoad(geneList.getName(), geneList.getLoci());
} catch (IOException exc) {
MessageUtils.showErrorMessage(exc.getMessage(), exc);
}
}
}
}