/// <summary>
/// Reads a Spectrum from the DPBF file with isotope peaks populated
/// </summary>
/// <param name="fullData">The file used to create the DPBF file (throws <see cref="System.ArgumentException"/> if it is not) - PBF file preferred.</param>
/// <param name="scanNum">The scan to read</param>
/// <returns></returns>
/// <exception cref="System.ArgumentException">If the checksum of the source file does not match the checksum stored in the DPBF file</exception>
public DeconvolutedSpectrum GetSpectrumWithIsotopePeaks(IMassSpecDataReader fullData, int scanNum)
{
if (SrcFileChecksum != fullData.SrcFileChecksum || (fullData is PbfLcMsRun && SrcFileChecksum != ((PbfLcMsRun)fullData).PbfFileChecksum))
{
throw new ArgumentException("Supplied file was not used to create this DPBF file!", nameof(fullData));
}
if (!(GetSpectrum(scanNum, true) is DeconvolutedSpectrum spec))
{
return(null);
}
var pbfSpec = fullData.ReadMassSpectrum(scanNum, true);
foreach (var peakBase in spec.Peaks)
{
var peak = peakBase as DeconvolutedPeak;
if (peak == null)
{
continue;
}
peak.SetObservedPeaksFromSpectrum(pbfSpec);
}
return(spec);
}
public InMemoryLcMsRun(
IMassSpecDataReader massSpecDataReader,
double precursorSignalToNoiseRatioThreshold,
double productSignalToNoiseRatioThreshold,
IProgress <ProgressData> progress = null,
int scanStart = 0,
int scanEnd = 0)
{
ScanNumElutionTimeMap = new Dictionary <int, double>();
ScanNumToMsLevel = new Dictionary <int, int>();
IsolationMzBinToScanNums = new Dictionary <int, int[]>();
_ms1PeakList = new List <LcMsPeak>();
_scanNumSpecMap = new Dictionary <int, Spectrum>();
var isolationMzBinToScanNums = new Dictionary <int, List <int> >();
// Read all spectra
var progressData = new ProgressData(progress)
{
Status = "Reading spectra from file"
};
var trackingInfo = new SpectrumTrackingInfo
{
NumSpectra = massSpecDataReader.NumSpectra,
PrecursorSignalToNoiseRatioThreshold = precursorSignalToNoiseRatioThreshold,
ProductSignalToNoiseRatioThreshold = productSignalToNoiseRatioThreshold,
SpecRead = 0,
MinScanNum = int.MaxValue,
MaxScanNum = int.MinValue,
MinMsLevel = int.MaxValue,
MaxMsLevel = int.MinValue
};
NumSpectra = massSpecDataReader.NumSpectra;
progressData.StepRange(95.0);
if (scanStart > 0 && scanEnd >= scanStart)
{
for (var scanNum = scanStart; scanNum <= scanEnd; scanNum++)
{
var spec = massSpecDataReader.ReadMassSpectrum(scanNum);
progressData.Report(trackingInfo.SpecRead, trackingInfo.NumSpectra);
HandleSpectrum(ref trackingInfo, isolationMzBinToScanNums, spec);
}
}
else
{
foreach (var spec in massSpecDataReader.ReadAllSpectra())
{
progressData.Report(trackingInfo.SpecRead, trackingInfo.NumSpectra);
HandleSpectrum(ref trackingInfo, isolationMzBinToScanNums, spec);
}
}
progressData.Status = "Processing Isolation Bins";
progressData.IsPartialRange = false;
progressData.Report(95.1);
foreach (var entry in isolationMzBinToScanNums)
{
var binNum = entry.Key;
entry.Value.Sort();
var scanNumList = entry.Value.ToArray();
IsolationMzBinToScanNums[binNum] = scanNumList;
}
_ms1PeakList.Sort();
//_ms2PeakList.Sort();
progressData.Report(99.5);
// Read MS levels and precursor information
MinLcScan = trackingInfo.MinScanNum;
MaxLcScan = trackingInfo.MaxScanNum;
MinMsLevel = trackingInfo.MinMsLevel;
MaxMsLevel = trackingInfo.MaxMsLevel;
//var precursorMap = new Dictionary<int, int>();
//var nextScanMap = new Dictionary<int, int>();
//
//for (var msLevel = MinMsLevel; msLevel <= maxMsLevel; msLevel++)
//{
// precursorMap[msLevel] = 0;
// nextScanMap[msLevel] = MaxLcScan + 1;
//}
//progressData.Report(99.8);
progressData.Report(100.0);
CreatePrecursorNextScanMap();
}
public InMemoryLcMsRun(
IMassSpecDataReader massSpecDataReader,
double precursorSignalToNoiseRatioThreshold,
double productSignalToNoiseRatioThreshold,
IProgress<ProgressData> progress = null,
int scanStart = 0,
int scanEnd = 0)
{
ScanNumElutionTimeMap = new Dictionary<int, double>();
ScanNumToMsLevel = new Dictionary<int, int>();
IsolationMzBinToScanNums = new Dictionary<int, int[]>();
_ms1PeakList = new List<LcMsPeak>();
_scanNumSpecMap = new Dictionary<int, Spectrum>();
var isolationMzBinToScanNums = new Dictionary<int, List<int>>();
// Read all spectra
var progressData = new ProgressData(progress)
{
Status = "Reading spectra from file"
};
var trackingInfo = new SpectrumTrackingInfo
{
NumSpectra = massSpecDataReader.NumSpectra,
PrecursorSignalToNoiseRatioThreshold = precursorSignalToNoiseRatioThreshold,
ProductSignalToNoiseRatioThreshold = productSignalToNoiseRatioThreshold,
SpecRead = 0,
MinScanNum = int.MaxValue,
MaxScanNum = int.MinValue,
MinMsLevel = int.MaxValue,
MaxMsLevel = int.MinValue
};
NumSpectra = massSpecDataReader.NumSpectra;
progressData.StepRange(95.0);
if (scanStart > 0 && scanEnd >= scanStart)
{
for (var scanNum = scanStart; scanNum <= scanEnd; scanNum++)
{
var spec = massSpecDataReader.ReadMassSpectrum(scanNum);
progressData.Report(trackingInfo.SpecRead, trackingInfo.NumSpectra);
HandleSpectrum(ref trackingInfo, isolationMzBinToScanNums, spec);
}
}
else
{
foreach (var spec in massSpecDataReader.ReadAllSpectra())
{
progressData.Report(trackingInfo.SpecRead, trackingInfo.NumSpectra);
HandleSpectrum(ref trackingInfo, isolationMzBinToScanNums, spec);
}
}
progressData.Status = "Processing Isolation Bins";
progressData.IsPartialRange = false;
progressData.Report(95.1);
foreach (var entry in isolationMzBinToScanNums)
{
var binNum = entry.Key;
entry.Value.Sort();
var scanNumList = entry.Value.ToArray();
IsolationMzBinToScanNums[binNum] = scanNumList;
}
_ms1PeakList.Sort();
//_ms2PeakList.Sort();
progressData.Report(99.5);
// Read MS levels and precursor information
MinLcScan = trackingInfo.MinScanNum;
MaxLcScan = trackingInfo.MaxScanNum;
MinMsLevel = trackingInfo.MinMsLevel;
MaxMsLevel = trackingInfo.MaxMsLevel;
//var precursorMap = new Dictionary<int, int>();
//var nextScanMap = new Dictionary<int, int>();
//
//for (var msLevel = MinMsLevel; msLevel <= maxMsLevel; msLevel++)
//{
// precursorMap[msLevel] = 0;
// nextScanMap[msLevel] = MaxLcScan + 1;
//}
//progressData.Report(99.8);
progressData.Report(100.0);
CreatePrecursorNextScanMap();
}