/*
* Copyright (c) 2007-2013 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.tools.motiffinder;
import org.broad.igv.dev.api.IGVPlugin;
import org.broad.igv.dev.api.batch.Command;
import org.broad.igv.feature.CachingFeatureSource;
import org.broad.igv.feature.Strand;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.track.FeatureTrack;
import org.broad.igv.track.Track;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.PanelName;
import org.broad.igv.util.StringUtils;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
import java.util.List;
/**
* Plugin for searching for a motif (currently can be a regex or IUPAC code)
* This plugin provides for a dialog so that the user can enter motifs manually,
* also a batch {@link org.broad.igv.dev.api.batch.Command}.
* @author jacob
* @date 2013-Oct-09
*/
public class MotifFinderPlugin implements IGVPlugin, Command {
/**
* Add menu entry for activating SequenceMatchDialog
*/
@Override
public void init() {
JMenuItem menuItem = new JMenuItem("Find Motif...");
menuItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
MotifFinderDialog dialog = new MotifFinderDialog(IGV.getMainFrame());
dialog.setVisible(true);
handleDialogResult(dialog);
}
});
IGV.getInstance().addOtherToolMenu(menuItem);
}
static void handleDialogResult(MotifFinderDialog dialog){
String[] pattern = dialog.getInputPattern();
if (pattern != null) {
String[] posTrackName = dialog.getPosTrackName();
String[] negTrackName = dialog.getNegTrackName();
addTracksForPatterns(pattern, posTrackName, negTrackName);
}
}
/**
* Generate motif-finding track and add it to IGV
* @param pattern
* @param posTrackNames
* @param negTrackNames
* @return
*/
static List<Track> addTracksForPatterns(String[] pattern, String[] posTrackNames, String[] negTrackNames){
List<Track> trackList = generateTracksForPatterns(pattern, posTrackNames, negTrackNames);
IGV.getInstance().addTracks(trackList, PanelName.FEATURE_PANEL);
return trackList;
}
/**
* Generate motif-finding tracks for the given pattern, do not add them to anything
* @param patterns
* @param posTrackNames
* @param negTrackNames
* @return
*/
static List<Track> generateTracksForPatterns(String[] patterns, String[] posTrackNames, String[] negTrackNames){
Color[] colors = {null, Color.RED};
Strand[] strands = {Strand.POSITIVE, Strand.NEGATIVE};
List<Track> trackList = new ArrayList<Track>(2*posTrackNames.length);
if (patterns != null) {
for(int pi=0; pi < patterns.length; pi++){
String pattern = patterns[pi];
String[] curTrackNames = new String[]{posTrackNames[pi], negTrackNames[pi]};
for(int ci=0; ci < curTrackNames.length; ci++){
String tName = curTrackNames[ci];
if(tName == null) continue;
MotifFinderSource src = new MotifFinderSource(pattern, strands[ci], GenomeManager.getInstance().getCurrentGenome());
CachingFeatureSource cachingSrc= new CachingFeatureSource(src);
FeatureTrack track = new FeatureTrack(tName, tName, cachingSrc);
if(colors[ci] != null) track.setColor(colors[ci]);
track.setDisplayMode(Track.DisplayMode.SQUISHED);
trackList.add(track);
}
}
}
return trackList;
}
@Override
public String run(List<String> args) {
String cmd = args.get(0);
if(cmd.equalsIgnoreCase("find")){
String pattern = args.get(1);
String[] patterns = new String[]{pattern};
String shrtPattern = StringUtils.checkLength(pattern, MotifFinderDialog.MaxTrackNameLength);
String[] posName = new String[]{shrtPattern + " Positive"};
String[] negName = new String[]{shrtPattern + " Negative"};
addTracksForPatterns(patterns, posName, negName);
return "OK";
}else{
return "ERROR: Unknown command " + cmd + " for plugin " + getClass().getName();
}
}
}