/*
* 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.
*/
package org.broad.igv.plugin.mongovariant;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.dev.api.IGVPlugin;
import org.broad.igv.dev.api.LoadHandler;
import org.broad.igv.track.*;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.PanelName;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.Utilities;
import org.broad.igv.variant.Variant;
import org.broad.igv.variant.VariantTrack;
import org.broad.igv.variant.vcf.VCFVariant;
import org.broadinstitute.gatk.tools.walkers.na12878kb.core.NA12878DBArgumentCollection;
import htsjdk.variant.variantcontext.VariantContext;
import javax.swing.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
/**
* User: jacob
* Date: 2012-Dec-21
*/
public class VariantReviewPlugin implements IGVPlugin{
private static Logger log = Logger.getLogger(VariantTrack.class);
//TODO Experimental. Let user choose opinion and send info to DB
private static final String SHOW_REVIEW_KEY = "SHOW_VARIANT_REVIEW";
private static boolean hasReviewTrack = false;
private static boolean showReviewOption = Boolean.parseBoolean(IGV.getInstance().getSession().getPersistent(SHOW_REVIEW_KEY, "false"));
private static final String VARIANT_DB_EXT = "variant.db.json";
private static ResourceLocator defaultLocator;
@Override
public void init(){
if (showReviewOption) {
//Test loading a class, won't work if running old Java
if(!Globals.checkJavaVersion("1.7")){
log.error("VariantReviewPlugin requires Java 7 or higher. This plugin will be disabled");
return;
}
//Test that we can load this class, plugin loader will catch the exception and
//not load plugin if it can't be loaded
NA12878DBArgumentCollection col = new NA12878DBArgumentCollection();
initMenuItems();
TrackLoader.registerHandler(VARIANT_DB_EXT, new TrackLoadHandler());
}
}
/**
*
* @param tracks
* @return true iff {@code tracks} is a single track of type {@code VariantTrack}
*/
private boolean isSingleVariantTrack(Collection<Track> tracks){
if (tracks.size() != 1) return false;
Track track = tracks.iterator().next();
return (track instanceof VariantTrack);
}
private static ResourceLocator loadVariantReviewTrack(String dbSpecPath,java.util.List<Track> newTracks, String trackName){
ResourceLocator locator = new ResourceLocator(dbSpecPath);
locator.setName(trackName);
VariantReviewSource.loadVariantReview(locator, newTracks);
return locator;
}
private void initMenuItems() {
//Menu item for loading review track
final JMenuItem loadReviewTrackItem = new JMenuItem("Load Review Track");
loadReviewTrackItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
java.util.List<Track> newTracks = new ArrayList<Track>(1);
ResourceLocator locator = loadVariantReviewTrack(VariantReviewPlugin.getDbSpecPath(), newTracks, "NA12878 KB");
if(defaultLocator == null) defaultLocator = locator;
IGV.getInstance().addTracks(newTracks, PanelName.DATA_PANEL);
hasReviewTrack = true;
loadReviewTrackItem.setEnabled(!hasReviewTrack);
}
});
IGV.getInstance().addOtherToolMenu(loadReviewTrackItem);
//Menu item for submitting new review
TrackMenuUtils.addTrackMenuItemBuilder(new TrackMenuItemBuilder() {
@Override
public JMenuItem build(Collection<Track> selectedTracks, TrackClickEvent te) {
if(!isSingleVariantTrack(selectedTracks)){
return null;
}
Track track = selectedTracks.iterator().next();
final VariantTrack vTrack = (VariantTrack) track;
final Variant variant = vTrack.getSelectedVariant(te);
ResourceLocator trackLocator = vTrack.getResourceLocator();
//If the track isn't connected to a database, use the default
if(!trackLocator.getPath().toLowerCase().endsWith(VARIANT_DB_EXT) && defaultLocator != null){
trackLocator = defaultLocator;
}
String dbName = trackLocator.getName();
final String dbSpecPath = trackLocator.getPath();
JMenuItem addReviewMenuItem = new JMenuItem("Submit Review to " + dbName);
addReviewMenuItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
VariantContext vc = VCFVariant.getVariantContext(variant);
(new VariantReviewDialog(IGV.getMainFrame(), vc, dbSpecPath)).setVisible(true);
}
});
addReviewMenuItem.setEnabled(variant != null);
return addReviewMenuItem;
}
});
}
//All of this is is for loading from a db specified in the preferences / command line
private static final String DB_PATH_KEY = "VARIANT_DB_PATH";
public static final String DB_PATH_DEFAULT = NA12878DBArgumentCollection.DEFAULT_SPEC_PATH;
private static final String PREFERENTIAL_SAMPLE_KEY = "PREFERENTIAL_SAMPLE";
public static final String DEFAULT_PREFERENTIAL_SAMPLE = "NA12878";
private static String preferentialSampleName;
private static String dbSpecPath;
public static String getPreferentialSampleName() {
if(preferentialSampleName == null){
preferentialSampleName = IGV.getPersistent(PREFERENTIAL_SAMPLE_KEY, DEFAULT_PREFERENTIAL_SAMPLE);
}
return preferentialSampleName;
}
public static String getDbSpecPath(){
if(dbSpecPath == null){
dbSpecPath = IGV.getPersistent(DB_PATH_KEY, DB_PATH_DEFAULT);
}
return dbSpecPath;
}
//------------//
//For loading from a spec file
private static class TrackLoadHandler implements LoadHandler{
@Override
public void load(String path, List<Track> newTracks) throws IOException {
//TODO Put the track name in the dbSpec
String name = Utilities.getFileNameFromURL(path);
ResourceLocator locator = loadVariantReviewTrack(path, newTracks, name);
if(defaultLocator == null) defaultLocator = locator;
}
}
}