private void HandleSpectrum(
ref SpectrumTrackingInfo trackingInfo,
Dictionary <int, List <int> > isolationMzBinToScanNums,
Spectrum spec)
{
trackingInfo.SpecRead += 1;
//Console.WriteLine("Reading Scan {0}; {1} peaks", spec.ScanNum, spec.Peaks.Length);
ScanNumToMsLevel[spec.ScanNum] = spec.MsLevel;
ScanNumElutionTimeMap[spec.ScanNum] = spec.ElutionTime;
if (spec.MsLevel == 1)
{
if (trackingInfo.PrecursorSignalToNoiseRatioThreshold > 0.0)
{
spec.FilterNoise(trackingInfo.PrecursorSignalToNoiseRatioThreshold);
}
//foreach (var peak in spec.Peaks)
//{
// _ms1PeakList.Add(new LcMsPeak(peak.Mz, peak.Intensity, spec.ScanNum));
//}
_ms1PeakList.AddRange(spec.Peaks.Select(peak => new LcMsPeak(peak.Mz, peak.Intensity, spec.ScanNum)));
_scanNumSpecMap.Add(spec.ScanNum, spec);
}
else if (spec.MsLevel == 2)
{
var productSpec = spec as ProductSpectrum;
if (productSpec != null)
{
if (trackingInfo.ProductSignalToNoiseRatioThreshold > 0.0)
{
productSpec.FilterNoise(trackingInfo.ProductSignalToNoiseRatioThreshold);
}
var isolationWindow = productSpec.IsolationWindow;
var minBinNum = (int)Math.Round(isolationWindow.MinMz * IsolationWindowBinningFactor);
var maxBinNum = (int)Math.Round(isolationWindow.MaxMz * IsolationWindowBinningFactor);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
List <int> scanNumList;
if (!isolationMzBinToScanNums.TryGetValue(binNum, out scanNumList))
{
scanNumList = new List <int>();
isolationMzBinToScanNums[binNum] = scanNumList;
}
scanNumList.Add(productSpec.ScanNum);
}
_scanNumSpecMap.Add(spec.ScanNum, productSpec);
}
}
if (spec.ScanNum < trackingInfo.MinScanNum)
{
trackingInfo.MinScanNum = spec.ScanNum;
}
if (spec.ScanNum > trackingInfo.MaxScanNum)
{
trackingInfo.MaxScanNum = spec.ScanNum;
}
if (spec.MsLevel < trackingInfo.MinMsLevel)
{
trackingInfo.MinMsLevel = spec.MsLevel;
}
if (spec.MsLevel > trackingInfo.MaxMsLevel)
{
trackingInfo.MaxMsLevel = spec.MsLevel;
}
}
private void HandleSpectrum(
ref SpectrumTrackingInfo trackingInfo,
Dictionary<int, List<int>> isolationMzBinToScanNums,
Spectrum spec)
{
trackingInfo.SpecRead += 1;
//Console.WriteLine("Reading Scan {0}; {1} peaks", spec.ScanNum, spec.Peaks.Length);
ScanNumToMsLevel[spec.ScanNum] = spec.MsLevel;
ScanNumElutionTimeMap[spec.ScanNum] = spec.ElutionTime;
if (spec.MsLevel == 1)
{
if (trackingInfo.PrecursorSignalToNoiseRatioThreshold > 0.0)
spec.FilterNoise(trackingInfo.PrecursorSignalToNoiseRatioThreshold);
//foreach (var peak in spec.Peaks)
//{
// _ms1PeakList.Add(new LcMsPeak(peak.Mz, peak.Intensity, spec.ScanNum));
//}
_ms1PeakList.AddRange(spec.Peaks.Select(peak => new LcMsPeak(peak.Mz, peak.Intensity, spec.ScanNum)));
_scanNumSpecMap.Add(spec.ScanNum, spec);
}
else if (spec.MsLevel == 2)
{
var productSpec = spec as ProductSpectrum;
if (productSpec != null)
{
if (trackingInfo.ProductSignalToNoiseRatioThreshold > 0.0)
productSpec.FilterNoise(trackingInfo.ProductSignalToNoiseRatioThreshold);
var isolationWindow = productSpec.IsolationWindow;
var minBinNum = (int)Math.Round(isolationWindow.MinMz * IsolationWindowBinningFactor);
var maxBinNum = (int)Math.Round(isolationWindow.MaxMz * IsolationWindowBinningFactor);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
List<int> scanNumList;
if (!isolationMzBinToScanNums.TryGetValue(binNum, out scanNumList))
{
scanNumList = new List<int>();
isolationMzBinToScanNums[binNum] = scanNumList;
}
scanNumList.Add(productSpec.ScanNum);
}
_scanNumSpecMap.Add(spec.ScanNum, productSpec);
}
}
if (spec.ScanNum < trackingInfo.MinScanNum) trackingInfo.MinScanNum = spec.ScanNum;
if (spec.ScanNum > trackingInfo.MaxScanNum) trackingInfo.MaxScanNum = spec.ScanNum;
if (spec.MsLevel < trackingInfo.MinMsLevel) trackingInfo.MinMsLevel = spec.MsLevel;
if (spec.MsLevel > trackingInfo.MaxMsLevel) trackingInfo.MaxMsLevel = spec.MsLevel;
}
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();
}
