public void GetChromatograms(List <Protein> targets, double tolerance)
{
MsDataSpectrum defaultSpectrum = new MsDataSpectrum();
MsDataSpectrum[] msDataSpectrums = new MsDataSpectrum[1];
msDataSpectrums[0] = defaultSpectrum;
_chromatograms = new List <Chromatogram>();
var Channels = (from spectrum in _msDataFileImpl.MsDataSpectrums
group spectrum by spectrum.PrecursorMZ into spectrumgroup
select new { ChannelMS1 = spectrumgroup.Key, ChannelSpectrums = spectrumgroup }).ToDictionary(di => di.ChannelMS1, di => di.ChannelSpectrums);
var Proteins = targets;
var Targets = from protein in Proteins
from peptide in protein.Peptides
from precursor in peptide.Precursors
select new
{
ProteinName = protein.Name,
PeptideName = peptide.Name,
PrecursorIsoform = precursor.IsotopeLabelType,
PrecursorMZ = precursor.PrecursorMZ,
Products = precursor.Products
};
foreach (var Target in Targets)
{
var SpectrumsForChannel = from channel in Channels
where ProcessRawDataTools.InMZTolerance(channel.Key, Target.PrecursorMZ, tolerance) == true
select channel.Value;
if (SpectrumsForChannel.Any())
{
var ExtraChromatograms = from mzspectrum in SpectrumsForChannel.Single()
select new
{
mzspectrum.PrecursorMZ,
mzspectrum.RetentionTime,
mzspectrum.IonIT,
mzspectrum.TIC,
SumOfIntensities = mzspectrum.Intensities.Sum(),
SumOfPositiveMatch = ProcessRawDataTools.AggIonCounts(mzspectrum.Mzs, mzspectrum.Intensities, Target.Products, tolerance)[0],
SumOfNegativeMatch = ProcessRawDataTools.AggIonCounts(mzspectrum.Mzs, mzspectrum.Intensities, Target.Products, tolerance)[1]
};
_chromatograms.Add(new Chromatogram()
{
Protein = Target.ProteinName,
Peptide = Target.ProteinName,
IsotopeLabelType = Target.PrecursorIsoform,
PrecursorMZ = Target.PrecursorMZ,
RetentionTimes = ExtraChromatograms.Select(ec => ec.RetentionTime.GetValueOrDefault(0)).ToArray(),
IonInjectionTimes = ExtraChromatograms.Select(ec => ec.IonIT.GetValueOrDefault(0)).ToArray(),
SumOfIntensities = ExtraChromatograms.Select(ec => ec.SumOfIntensities).ToArray(),
SumOfPositiveMatch = ExtraChromatograms.Select(ec => ec.SumOfPositiveMatch).ToArray(),
SumOfNegativeMatch = ExtraChromatograms.Select(ec => ec.SumOfNegativeMatch).ToArray()
});
}
}
}
public void GetChromatograms(double tolerance)
{
_chromatograms = new List <Chromatogram>();
var Channels = from spectrum in _msDataFileImpl.MsDataSpectrums
group spectrum by spectrum.PrecursorMZ into spectrumgroup
select new { ChannelMS1 = spectrumgroup.Key, ChannelSpectrums = spectrumgroup };
var Proteins = Analysis.AnalysisTargets.GetDefaultProteins();
var Targets = from protein in Proteins
from peptide in protein.Peptides
from precursor in peptide.Precursors
select new
{
ProteinName = protein.Name,
PeptideName = peptide.Name,
PrecursorIsoform = precursor.IsotopeLabelType,
PrecursorMZ = precursor.PrecursorMZ,
Products = precursor.Products
};
foreach (var Target in Targets)
{
var ExtraChromatograms = from mzspectrum in Channels
.Where(ch => ProcessRawDataTools.InMZTolerance(ch.ChannelMS1, Target.PrecursorMZ, tolerance))
.Select(s => s.ChannelSpectrums).FirstOrDefault()
select new
{
mzspectrum.PrecursorMZ,
mzspectrum.RetentionTime,
mzspectrum.IonIT,
mzspectrum.TIC,
SumOfIntensities = mzspectrum.Intensities.Sum(),
SumOfPositiveMatch = ProcessRawDataTools.AggIonCounts(mzspectrum.Mzs, mzspectrum.Intensities, Target.Products, tolerance)[0],
SumOfNegativeMatch = ProcessRawDataTools.AggIonCounts(mzspectrum.Mzs, mzspectrum.Intensities, Target.Products, tolerance)[1]
};
_chromatograms.Add(new Chromatogram()
{
Protein = Target.ProteinName,
Peptide = Target.ProteinName,
IsotopeLabelType = Target.PrecursorIsoform,
PrecursorMZ = Target.PrecursorMZ,
RetentionTimes = ExtraChromatograms.Select(ec => ec.RetentionTime.GetValueOrDefault(0)).ToArray(),
IonInjectionTimes = ExtraChromatograms.Select(ec => ec.IonIT.GetValueOrDefault(0)).ToArray(),
SumOfIntensities = ExtraChromatograms.Select(ec => ec.SumOfIntensities).ToArray(),
SumOfPositiveMatch = ExtraChromatograms.Select(ec => ec.SumOfPositiveMatch).ToArray(),
SumOfNegativeMatch = ExtraChromatograms.Select(ec => ec.SumOfNegativeMatch).ToArray()
});
}
}
