/**
* Note: This is an exact copy of the method in ExpressionFileParser. Refactor to merge these two
* parsers, or share a common base class.
*
* @param comment
* @param dataset
*/
private void parseDirective(String comment, IGVDataset dataset) {
String tmp = comment.substring(1, comment.length());
if (tmp.startsWith("track")) {
ParsingUtils.parseTrackLine(tmp, dataset.getTrackProperties());
} else if (tmp.startsWith("columns")) {
parseColumnLine(tmp);
} else {
String[] tokens = tmp.split("=");
if (tokens.length != 2) {
return;
}
String key = tokens[0].trim().toLowerCase();
if (key.equals("name")) {
dataset.setName(tokens[1].trim());
} else if (key.equals("type")) {
try {
dataset.setTrackType(TrackType.valueOf(tokens[1].trim().toUpperCase()));
} catch (Exception exception) {
// Ignore
}
} else if (key.equals("coords")) {
startBase = Integer.parseInt(tokens[1].trim());
}
}
}
/**
* 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;
}
