public static double GetPrecursorPercentage(this PeakList <Peak> isolationPeaks, double ppmTolerance)
{
var defaultValue = 0.0;
if (isolationPeaks.Count == 0)
{
return(defaultValue);
}
//parentPkl.ForEach(m => Console.WriteLine("new Peak({0:0.0000},{1:0.0},{2}),",m.Mz, m.Intensity,m.Charge));
var totalIntensity = isolationPeaks.Sum(m => m.Intensity);
if (0.0 == totalIntensity)
{
throw new ArgumentException("There is no intensity information in argument isolationPeaks");
}
var precursorPeak = isolationPeaks.Precursor;
var mzTolerance = PrecursorUtils.ppm2mz(precursorPeak.MonoIsotopicMass, ppmTolerance);
if (precursorPeak.Charge == 0)
{
var pPeak = isolationPeaks.FindAll(m => Math.Abs(m.Mz - precursorPeak.MonoIsotopicMass) < mzTolerance);
if (0 == pPeak.Count)
{
return(defaultValue);
}
var maxIntensity = pPeak.Max(m => m.Intensity);
pPeak.Find(m => m.Intensity == maxIntensity).Tag = 1;
return(maxIntensity / totalIntensity);
}
else
{
var pPeak = isolationPeaks.FindEnvelope(precursorPeak.MonoIsotopicMass, precursorPeak.Charge, mzTolerance, true);
if (0 == pPeak.Count)
{
return(defaultValue);
}
for (int i = 0; i < pPeak.Count; i++)
{
pPeak[i].Tag = i + 1;
}
return(pPeak.GetTotalIntensity() / totalIntensity);
}
}
private SilacPeakListPair GetLightHeavyPeakList(IRawFile rawFile, SilacCompoundInfo sci, int maxIndex, double mzTolerance, int scan, bool force = false)
{
PeakList <Peak> pkl = rawFile.GetPeakList(scan);
if (pkl.Count == 0)
{
return(null);
}
var scantime = new ScanTime(scan, rawFile.ScanToRetentionTime(scan));
PeakList <Peak> light = pkl.FindEnvelopeDirectly(sci.Light.Profile, option.ProfileLength, mzTolerance, () => new Peak());
//如果电荷不对，则认为该scan无效。
if (!CheckPeakListCharge(light, maxIndex, sci.Light.Charge) && !force)
{
return(null);
}
PeakList <Peak> heavy = pkl.FindEnvelopeDirectly(sci.Heavy.Profile, option.ProfileLength, mzTolerance, () => new Peak());
//如果电荷不对，则认为该scan无效。
if (!CheckPeakListCharge(heavy, maxIndex, sci.Heavy.Charge) && !force)
{
return(null);
}
//如果轻或者重的总强度为0，则认为该scan无效。
if ((0 == light.Sum(m => m.Intensity) || 0 == heavy.Sum(m => m.Intensity)) && !force)
{
return(null);
}
light.ScanTimes.Add(scantime);
heavy.ScanTimes.Add(scantime);
return(new SilacPeakListPair(light, heavy));
}
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 */
}
