/*
* 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.tools.motiffinder;
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;
/**
* Search for a motif (currently can be a regex or IUPAC code)
*/
public class MotifFinderPlugin {
/**
* Add menu entry for activating SequenceMatchDialog
*/
public static JMenuItem getMenuItem() {
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);
}
});
return 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;
}
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();
}
}
}