public string ToXML(FAIMStoMzXMLProcessor processor)
{
// place scan byte depth into our tracking list
var index = new Index(processor.ByteTracking.CurrentScan, processor.ByteTracking.ByteDepth + 3);
processor.ByteTracking.ScanOffsets.Add(index);
FilterLine = FixFilterLine();
var sb = new StringBuilder();
sb.AppendFormat(" <scan num=\"{0}\"", processor.ByteTracking.CurrentScan).AppendLine();
sb.AppendFormat(" msLevel=\"{0}\"", MsLevel).AppendLine();
sb.AppendFormat(" peaksCount=\"{0}\"", PeaksCount).AppendLine();
sb.AppendFormat(" polarity=\"{0}\"", Polarity).AppendLine();
sb.AppendFormat(" scanType=\"{0}\"", ScanType).AppendLine();
sb.AppendFormat(" filterLine=\"{0}\"", FilterLine).AppendLine();
sb.AppendFormat(" retentionTime=\"{0}\"", RetentionTime).AppendLine();
sb.AppendFormat(" lowMz=\"" + Math.Round(LowMz, 3) + "\"").AppendLine();
sb.AppendFormat(" highMz=\"" + Math.Round(HighMz, 3) + "\"").AppendLine();
sb.AppendFormat(" basePeakMz=\"" + Math.Round(BasePeakMz, 3) + "\"").AppendLine();
sb.AppendFormat(" basePeakIntensity=\"" + FormatSpecialNumber(BasePeakIntensity) + "\"").AppendLine();
sb.AppendFormat(" totIonCurrent=\"" + FormatSpecialNumber(TotIonCurrent) + "\"").AppendLine();
sb.AppendFormat(" collisionEnergy=\"" + CollisionEnergy + "\">").AppendLine();
sb.AppendLine(PrecursorMz.ToXML());
sb.AppendLine(PeakData.ToXML(4));
sb.Append(" </scan>");
processor.ByteTracking.CurrentScan++;
return(sb.ToString());
}
// for outputting valid MzXML strings to file
public string ToXML(FAIMStoMzXMLProcessor processor)
{
// place scan byte depth into our tracking list
var index = new Index(processor.ByteTracking.CurrentScan, processor.ByteTracking.ByteDepth + 2);
processor.ByteTracking.ScanOffsets.Add(index);
FilterLine = FixFilterLine();
var sb = new StringBuilder();
sb.AppendFormat(" <scan num=\"{0}\"", processor.ByteTracking.CurrentScan).AppendLine();
sb.AppendFormat(" msLevel=\"{0}\"", MsLevel).AppendLine();
sb.AppendFormat(" peaksCount=\"{0}\"", PeaksCount).AppendLine();
sb.AppendFormat(" polarity=\"{0}\"", Polarity).AppendLine();
sb.AppendFormat(" scanType=\"{0}\"", ScanType).AppendLine();
sb.AppendFormat(" filterLine=\"{0}\"", FilterLine).AppendLine();
sb.AppendFormat(" retentionTime=\"{0}\"", RetentionTime).AppendLine();
sb.AppendFormat(" lowMz=\"" + Math.Round(LowMz, 3) + "\"").AppendLine();
sb.AppendFormat(" highMz=\"" + Math.Round(HighMz, 3) + "\"").AppendLine();
sb.AppendFormat(" basePeakMz=\"" + Math.Round(BasePeakMz, 3) + "\"").AppendLine();
sb.AppendFormat(" basePeakIntensity=\"" + FormatSpecialNumber(BasePeakIntensity) + "\"").AppendLine();
sb.AppendFormat(" totIonCurrent=\"" + FormatSpecialNumber(TotIonCurrent) + "\">").AppendLine();
sb.AppendLine(PeakData.ToXML(3));
// advance the byteTracker for Ms2 Indices
processor.ByteTracker(sb.ToString(), true);
processor.ByteTracking.CurrentScan++;
foreach (var ms2 in Ms2s)
{
var ms2String = ms2.ToXML(processor);
sb.AppendLine(ms2String);
// advance byteTracker for the Ms2 Entry
processor.ByteTracker(ms2String);
}
sb.Append(" </scan>");
processor.ByteTracker(" </scan>");
return(sb.ToString());
}
