package org.broad.igv.cursor;
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.feature.tribble.CodecFactory;
import org.broad.igv.track.TrackProperties;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.AsciiFeatureCodec;
import java.awt.*;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.util.*;
import java.util.List;
/**
* @author jrobinso
* Date: 1/14/14
* Time: 4:35 PM
*/
public class CursorUtils {
public static List<CursorRegion> createRegions(CursorTrack track) {
List<CursorRegion> frames = new ArrayList();
Map<String, List<BasicFeature>> featureMap = track.getFeatureMap();
for (List<BasicFeature> flist : featureMap.values()) {
for (BasicFeature feature : flist) {
int locaction = (feature.getStart() + feature.getEnd()) / 2;
frames.add(new CursorRegion(feature.getChr(), locaction));
}
}
return frames;
}
public static CursorTrack loadTrack(String peakFile) throws IOException {
AsciiFeatureCodec codec = (AsciiFeatureCodec) CodecFactory.getCodec(new ResourceLocator(peakFile), null);
// if(codec == null) {
// // TODO -- inform user
// System.out.println("Skipping " + peakFile);
// return null;
// }
// EncodePeakCodec codec = new EncodePeakCodec();
Map<String, List<BasicFeature>> featureMap = new HashMap<String, List<BasicFeature>>();
BufferedReader br = null;
TrackProperties props = null;
try {
br = ParsingUtils.openBufferedReader(peakFile);
String nextLine;
while ((nextLine = br.readLine()) != null) {
if (nextLine.startsWith("track")) {
props = new TrackProperties();
ParsingUtils.parseTrackLine(nextLine, props);
} else {
BasicFeature f = (BasicFeature) codec.decode(nextLine);
if (f != null) {
String chr = f.getChr();
List<BasicFeature> featureList = featureMap.get(chr);
if (featureList == null) {
featureList = new ArrayList<BasicFeature>();
featureMap.put(chr, featureList);
}
featureList.add(f);
}
}
}
} finally {
if (br != null) br.close();
}
for (List<BasicFeature> featureList : featureMap.values()) {
Collections.sort(featureList, new Comparator<BasicFeature>() {
@Override
public int compare(BasicFeature o1, BasicFeature o2) {
return o1.getStart() - o2.getStart();
}
});
}
CursorTrack track = new CursorTrack(featureMap, codec.getFeatureType());
String trackName = (new File(peakFile)).getName();
Color trackColor = null;
if (props != null) {
trackColor = props.getColor();
trackName = props.getName();
}
if (trackColor == null && trackName != null) {
if (trackName.toLowerCase().contains("k4me3")) {
trackColor = new Color(0, 150, 0);
} else if (trackName.toLowerCase().contains("k27me3")) {
trackColor = new Color(150, 0, 0);
}
}
if(trackName != null) track.setName(trackName);
if(trackColor != null) track.setColor(trackColor);
return track;
}
}