package org.broad.igv.ui.action;
import org.apache.log4j.Logger;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.session.SessionXmlAdapters;
import org.broad.igv.track.AttributeManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.collections.CI;
import org.broad.igv.util.encode.EncodeFileBrowser;
import org.broad.igv.util.encode.EncodeFileRecord;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* @author jrobinso
* Date: 11/2/13
* Time: 6:39 PM
*/
public class BrowseEncodeAction extends MenuAction {
private static Logger log = Logger.getLogger(BrowseEncodeAction.class);
private static Map<String, Color> colors;
static {
colors = new HashMap<String, Color>();
colors.put("H3K27AC", new Color(200, 0, 0));
colors.put("H3K27ME3", new Color(200, 0, 0));
colors.put("H3K36ME3", new Color(0, 0, 150));
colors.put("H3K4ME1", new Color(0, 150, 0));
colors.put("H3K4ME2", new Color(0, 150, 0));
colors.put("H3K4ME3", new Color(0, 150, 0));
colors.put("H3K9AC", new Color(100, 0, 0));
colors.put("H3K9ME1", new Color(100, 0, 0));
}
IGV igv;
public BrowseEncodeAction(String label, int mnemonic, IGV igv) {
super(label, null, mnemonic);
this.igv = igv;
}
@Override
public void actionPerformed(ActionEvent event) {
String [] visibleAttributes = { "dataType", "cell","antibody", "lab"};
try {
Genome genome = igv.getGenomeManager().getCurrentGenome();
EncodeFileBrowser browser = EncodeFileBrowser.getInstance(genome.getId());
if (browser == null) {
MessageUtils.showMessage("Encode data is not available for " + genome.getDisplayName() + " through IGV.");
return;
}
browser.setVisible(true);
if (browser.isCanceled()) return;
java.util.List<EncodeFileRecord> records = browser.getSelectedRecords();
if (records.size() > 0) {
List<ResourceLocator> locators = new ArrayList<ResourceLocator>(records.size());
for (EncodeFileRecord record : records) {
ResourceLocator rl = new ResourceLocator(record.getPath());
rl.setName(record.getTrackName());
final String antibody = record.getAttributeValue("antibody");
if (antibody != null) {
rl.setColor(colors.get(antibody.toUpperCase()));
}
for(String name : visibleAttributes) {
String value = record.getAttributeValue(name);
if(value != null) {
AttributeManager.getInstance().addAttribute(rl.getName(), name, value);
}
}
locators.add(rl);
}
igv.loadTracks(locators);
}
} catch (IOException e) {
log.error("Error opening Encode browser", e);
}
}
}