public static List<FeatureTrack> loadTracks(
Iterable<Feature> features,
ResourceLocator locator,
Genome genome,
TrackProperties trackProperties) {
FeatureCollectionSource source = new FeatureCollectionSource(features, genome);
// Load into FeatureDB for searching
if (IGV.hasInstance() || Globals.isTesting()) {
Set<String> chrs = source.getChrs();
for (String chr : chrs) {
List<Feature> feats = source.getFeatures(chr);
for (Feature f : feats) {
if (f instanceof NamedFeature) {
FeatureDB.addFeature((NamedFeature) f);
}
}
}
}
FeatureTrack track = new FeatureTrack(locator, source);
track.setName(locator.getTrackName());
track.setRendererClass(IGVFeatureRenderer.class);
track.setHeight(45);
if (trackProperties != null) {
track.setProperties(trackProperties);
}
List<FeatureTrack> tracks = new ArrayList();
tracks.add(track);
return tracks;
}
/**
* Load all features in this file.
*
* @param reader
* @param maxLines
* @return
*/
public List<org.broad.tribble.Feature> loadFeatures(BufferedReader reader, int maxLines) {
List<org.broad.tribble.Feature> features = new ArrayList<org.broad.tribble.Feature>();
String nextLine = null;
int nLines = 0;
try {
while ((nextLine = reader.readLine()) != null) {
nextLine = nextLine.trim();
if (nextLine.length() == 0) continue;
nLines++;
if ((maxLines > 0) && (nLines > maxLines)) {
break;
}
try {
if (nextLine.startsWith("#")) {
if (nextLine.startsWith("#type")) {
String[] tokens = Globals.equalPattern.split(nextLine);
if (tokens.length > 1) {
try {
// TODO: type is not currently used, is there any reason to keep this?
TrackType type = TrackType.valueOf(tokens[1]);
} catch (Exception e) {
log.error("Error converting track type: " + tokens[1]);
}
}
} else if (nextLine.startsWith("#track")) {
TrackProperties tp = new TrackProperties();
ParsingUtils.parseTrackLine(nextLine, tp);
setTrackProperties(tp);
if (tp.isGffTags()) {
gffTags = true;
}
} else if (nextLine.startsWith("#coords")) {
try {
String[] tokens = Globals.equalPattern.split(nextLine);
startBase = Integer.parseInt(tokens[1]);
} catch (Exception e) {
log.error("Error parsing coords line: " + nextLine, e);
}
} else if (nextLine.startsWith("#gffTags")) {
gffTags = true;
}
} else {
Feature feature = parseLine(nextLine);
if (feature != null) {
features.add(feature);
}
}
} catch (NumberFormatException e) {
// Expected condition -- for example comments. don't log as it slows down
// the parsing and is not useful information.
}
}
} catch (java.io.EOFException e) {
// This exception is due to a known bug with java zip library. Not
// in general a real error, and nothing we can do about it in any
// event.
return features;
} catch (Exception e) {
if (nextLine != null && nLines != 0) {
throw new ParserException(e.getMessage(), e, nLines, nextLine);
} else {
throw new RuntimeException(e);
}
}
// TODO -- why is this test here? This will break igvtools processing of expression files
// if (IGV.hasInstance() || Globals.isTesting()) {
FeatureDB.addFeatures(features);
// }
return features;
}
