titleScan = titleScan.replace("%2e", ",");
String[] tokens = titleScan.split(",");
String rawFileName = tokens[0];
int rawScanNumber = Integer.parseInt(tokens[1]);
PeptideScan scan = new PeptideScan(pepDataFile, rawFileName,
queryNumber, rawScanNumber);
Vector<SimpleDataPoint> dataPoints = new Vector<SimpleDataPoint>();
double mass, intensity;
String ions = (String) sectionMap.get("Ions1");
StringTokenizer tokenizer = new StringTokenizer(ions, ",");
while (tokenizer.hasMoreTokens()) {
tokens = tokenizer.nextToken().split(":");
mass = Double.parseDouble(tokens[0]);
intensity = Double.parseDouble(tokens[1]);
dataPoints.add(new SimpleDataPoint(mass, intensity));
}
scan.setDataPoints(dataPoints.toArray(new SimpleDataPoint[0]));
return scan;
}