private void WriteXmlScan(StreamWriter sw, int scan, List <Pair <int, long> > scanIndeies)
{
sw.Flush();
scanIndeies.Add(new Pair <int, long>(scan, sw.BaseStream.Position));
var rcf = new RawScanFilter();
rcf.Filter = this.rawFile.GetFilterForScanNum(scan);
double retentionTime = this.rawFile.ScanToRetentionTime(scan);
PeakList <Peak> pkl = this.rawFile.GetMassListFromScanNum(scan, this.doCentroid);
/* scan header info begin */
int numPakets = 0;
double RT = 0;
double lowMass = 0;
double highMass = 0;
double TIC = 0;
double basePeakMass = 0;
double basePeakIntensity = 0;
int channel = 0;
int uniformTime = 0;
double frequency = 0;
this.rawFile.GetScanHeaderInfoForScanNum(
scan,
ref numPakets,
ref RT,
ref lowMass,
ref highMass,
ref TIC,
ref basePeakMass,
ref basePeakIntensity,
ref channel,
ref uniformTime,
ref frequency);
sw.Write(MyConvert.Format(" <scan num=\"{0}\"" + lf
+ " msLevel=\"{1}\"" + lf
+ " peaksCount=\"{2}\"" + lf
+ " polarity=\"{3}\"" + lf
+ " scanType=\"{4}\"" + lf
+ " retentionTime=\"PT{5:0.00}S\"" + lf,
scan,
rcf.MsLevel,
pkl.Count,
rcf.Polarity,
rcf.ScanType,
retentionTime * 60));
if (rcf.MsLevel > 1)
{
sw.Write(" collisionEnergy=\"{0:0}\"" + lf, rcf.CollisionEnergy);
}
sw.Write(MyConvert.Format(" lowMz=\"{0:0}\"" + lf
+ " highMz=\"{1:0}\"" + lf
+ " basePeakMz=\"{2:0.000}\"" + lf
+ " basePeakIntensity=\"{3:0}\"" + lf
+ " totIonCurrent=\"{4}\">" + lf,
lowMass,
highMass,
basePeakMass,
basePeakIntensity,
TIC));
if (rcf.MsLevel > 1)
{
this.rawFile.GetPeakListInfo(scan, pkl);
sw.Write(MyConvert.Format(" <precursorMz precursorIntensity=\"{0:0.#####}\"", pkl.PrecursorIntensity));
if (pkl.PrecursorCharge > 0)
{
sw.Write(" precursorCharge=\"" + pkl.PrecursorCharge + "\"");
}
sw.Write(">");
sw.Write(MyConvert.Format("{0:0.######}</precursorMz>" + lf, pkl.PrecursorMZ));
}
/* scan header info end */
/* peak list info begin */
sw.Write(" <peaks precision=\"32\"" + lf
+ " byteOrder=\"network\"" + lf
+ " pairOrder=\"m/z-int\">");
sw.Write(MzxmlHelper.PeakListToBase64(pkl) + "</peaks>" + lf);
/* peak list info end */
//I don't care if this scan is an child of last scan, just close it
sw.Write(" </scan>" + lf);
}
protected override void DoWritePeakList(IRawFile rawFile, PeakList <Peak> pkl, string rawFileName, List <string> result)
{
sw.Flush();
scanIndeies.Add(new Pair <int, long>(pkl.ScanTimes[0].Scan, sw.BaseStream.Position));
int scan = pkl.ScanTimes[0].Scan;
var retentionTime = pkl.ScanTimes[0].RetentionTime;
var activationMethod = string.Empty;
var intent = GetScanIntent(pkl.MsLevel);
if (rawFile is RawFileImpl)
{
var impl = rawFile as RawFileImpl;
var rcf = new RawScanFilter();
rcf.Filter = impl.GetFilterForScanNum(scan);
activationMethod = rcf.ActivationMethod.ToUpper();
/* scan header info begin */
int numPakets = 0;
double RT = 0;
double lowMass = 0;
double highMass = 0;
double TIC = 0;
double basePeakMass = 0;
double basePeakIntensity = 0;
int channel = 0;
int uniformTime = 0;
double frequency = 0;
impl.GetScanHeaderInfoForScanNum(
scan,
ref numPakets,
ref RT,
ref lowMass,
ref highMass,
ref TIC,
ref basePeakMass,
ref basePeakIntensity,
ref channel,
ref uniformTime,
ref frequency);
lowMass = pkl.First().Mz;
highMass = pkl.Last().Mz;
sw.Write(MyConvert.Format(intent + "<scan num=\"{0}\"" + lf
+ intent + " msLevel=\"{1}\"" + lf
+ intent + " peaksCount=\"{2}\"" + lf
+ intent + " polarity=\"{3}\"" + lf
+ intent + " scanType=\"{4}\"" + lf
+ intent + " filterLine=\"{5}\"" + lf
+ intent + " retentionTime=\"PT{6:G6}S\"" + lf,
scan,
rcf.MsLevel,
pkl.Count,
rcf.Polarity,
rcf.ScanType,
rcf.Filter,
retentionTime * 60));
sw.Write(MyConvert.Format(intent + " lowMz=\"{0:G6}\"" + lf
+ intent + " highMz=\"{1:G6}\"" + lf
+ intent + " basePeakMz=\"{2:G6}\"" + lf
+ intent + " basePeakIntensity=\"{3:e5}\"" + lf
+ intent + " totIonCurrent=\"{4:e5}\" >" + lf,
lowMass,
highMass,
basePeakMass,
basePeakIntensity,
TIC));
if (rcf.MsLevel > 1)
{
sw.Write(intent + " collisionEnergy=\"{0:0}\"" + lf, rcf.CollisionEnergy);
}
pkl.PrecursorIntensity = impl.GetPrecursorPeak(scan).Intensity;
}
else
{
sw.Write(MyConvert.Format(intent + "<scan num=\"{0}\"" + lf
+ intent + " msLevel=\"{1}\"" + lf
+ intent + " peaksCount=\"{2}\"" + lf
+ intent + " scanType=\"{3}\"" + lf
+ intent + " retentionTime=\"PT{4:G8}S\"" + lf,
scan,
pkl.MsLevel,
pkl.Count,
pkl.ScanMode,
retentionTime * 60));
var basePeak = pkl.FindMaxIntensityPeak();
var TIC = pkl.Sum(m => m.Intensity);
sw.Write(MyConvert.Format(intent + " lowMz=\"{0:0}\"" + lf
+ intent + " highMz=\"{1:0}\"" + lf
+ intent + " basePeakMz=\"{2:G6}\"" + lf
+ intent + " basePeakIntensity=\"{3:e5}\"" + lf
+ intent + " totIonCurrent=\"{4:e5}\" >" + lf,
pkl.First().Mz,
pkl.Last().Mz,
basePeak.Mz,
basePeak.Intensity,
TIC));
}
if (pkl.MsLevel > 1)
{
sw.Write(MyConvert.Format(intent + " <precursorMz precursorIntensity=\"{0:0.#####}\"", pkl.PrecursorIntensity));
if (!string.IsNullOrEmpty(activationMethod))
{
sw.Write(" activationMethod=\"{0}\"", activationMethod);
}
if (pkl.PrecursorCharge > 0)
{
sw.Write(" precursorCharge=\"{0}\"", pkl.PrecursorCharge);
}
sw.Write(" >");
sw.Write(MyConvert.Format("{0:0.######}</precursorMz>" + lf, pkl.PrecursorMZ));
}
/* scan header info end */
/* peak list info begin */
sw.WriteLine(intent + " <peaks precision=\"32\"");
sw.WriteLine(intent + " byteOrder=\"network\"");
sw.WriteLine(intent + " contentType=\"m/z-int\"");
sw.WriteLine(intent + " compressionType=\"none\"");
sw.WriteLine(intent + " compressedLen=\"0\" >" + MzxmlHelper.PeakListToBase64(pkl) + "</peaks>");
/* peak list info end */
}
