private void WriteDecon2LSScanFileEntry(
StreamWriter writer,
clsScanInfo currentScan,
clsSpectraCache spectraCache)
{
int numPeaks;
if (spectraCache == null)
{
numPeaks = 0;
}
else
{
if (!spectraCache.GetSpectrum(currentScan.ScanNumber, out var spectrum, true))
{
SetLocalErrorCode(clsMASIC.eMasicErrorCodes.ErrorUncachingSpectrum);
return;
}
numPeaks = spectrum.IonCount;
}
var scanNumber = currentScan.ScanNumber;
var msLevel = currentScan.FragScanInfo.MSLevel;
if (msLevel < 1)
{
msLevel = 1;
}
var numIsotopicSignatures = 0;
WriteDecon2LSScanFileEntry(writer, currentScan, scanNumber, msLevel, numPeaks, numIsotopicSignatures);
}
private void SavePEKFileToDiskWork(
TextWriter writer,
clsScanInfo currentScan,
clsSpectraCache spectraCache,
string inputFileName,
bool fragmentationScan,
ref int spectrumExportCount)
{
var exportCount = 0;
if (!spectraCache.GetSpectrum(currentScan.ScanNumber, out var spectrum, true))
{
SetLocalErrorCode(clsMASIC.eMasicErrorCodes.ErrorUncachingSpectrum);
return;
}
spectrumExportCount += 1;
writer.WriteLine("Time domain signal level:" + "\t" + currentScan.BasePeakIonIntensity.ToString("0.000")); // Store the base peak ion intensity as the time domain signal level value
writer.WriteLine("MASIC " + mOptions.MASICVersion); // Software version
var dataLine = "MS/MS-based PEK file";
if (mOptions.RawDataExportOptions.IncludeMSMS)
{
dataLine += " (includes both survey scans and fragmentation spectra)";
}
else
{
dataLine += " (includes only survey scans)";
}
writer.WriteLine(dataLine);
int scanNumber;
if (mOptions.RawDataExportOptions.RenumberScans)
{
scanNumber = spectrumExportCount;
}
else
{
scanNumber = currentScan.ScanNumber;
}
dataLine = "Filename: " + inputFileName + "." + scanNumber.ToString("00000");
writer.WriteLine(dataLine);
if (fragmentationScan)
{
writer.WriteLine("ScanType: Fragmentation Scan");
}
else
{
writer.WriteLine("ScanType: Survey Scan");
}
writer.WriteLine("Charge state mass transform results:");
writer.WriteLine("First CS, Number of CS, Abundance, Mass, Standard deviation");
if (spectrum.IonCount > 0)
{
// Populate intensities and pointerArray()
var intensities = new double[spectrum.IonCount];
var pointerArray = new int[spectrum.IonCount];
for (var ionIndex = 0; ionIndex < spectrum.IonCount; ionIndex++)
{
intensities[ionIndex] = spectrum.IonsIntensity[ionIndex];
pointerArray[ionIndex] = ionIndex;
}
// Sort pointerArray() based on the intensities in intensities
Array.Sort(intensities, pointerArray);
int startIndex;
if (mOptions.RawDataExportOptions.MaxIonCountPerScan > 0)
{
// Possibly limit the number of ions to maxIonCount
startIndex = spectrum.IonCount - mOptions.RawDataExportOptions.MaxIonCountPerScan;
if (startIndex < 0)
{
startIndex = 0;
}
}
else
{
startIndex = 0;
}
// Define the minimum data point intensity value
var minimumIntensityCurrentScan = spectrum.IonsIntensity[pointerArray[startIndex]];
// Update the minimum intensity if a higher minimum intensity is defined in .IntensityMinimum
minimumIntensityCurrentScan = Math.Max(minimumIntensityCurrentScan, mOptions.RawDataExportOptions.IntensityMinimum);
// If mOptions.RawDataExportOptions.MinimumSignalToNoiseRatio is > 0, then possibly update minimumIntensityCurrentScan
if (mOptions.RawDataExportOptions.MinimumSignalToNoiseRatio > 0)
{
minimumIntensityCurrentScan = Math.Max(minimumIntensityCurrentScan, currentScan.BaselineNoiseStats.NoiseLevel * mOptions.RawDataExportOptions.MinimumSignalToNoiseRatio);
}
exportCount = 0;
for (var ionIndex = 0; ionIndex < spectrum.IonCount; ionIndex++)
{
if (spectrum.IonsIntensity[ionIndex] >= minimumIntensityCurrentScan)
{
var dataLine1 =
"1" + "\t" +
"1" + "\t" +
spectrum.IonsIntensity[ionIndex] + "\t" +
spectrum.IonsMZ[ionIndex] + "\t" +
"0";
writer.WriteLine(dataLine1);
exportCount += 1;
}
}
}
writer.WriteLine("Number of peaks in spectrum = " + spectrum.IonCount.ToString());
writer.WriteLine("Number of isotopic distributions detected = " + exportCount.ToString());
writer.WriteLine();
}
private void SaveCSVFilesToDiskWork(
StreamWriter dataWriter,
StreamWriter scanInfoWriter,
clsScanInfo currentScan,
clsSpectraCache spectraCache,
bool fragmentationScan,
ref int spectrumExportCount)
{
int scanNumber;
if (!spectraCache.GetSpectrum(currentScan.ScanNumber, out var spectrum, true))
{
SetLocalErrorCode(clsMASIC.eMasicErrorCodes.ErrorUncachingSpectrum);
return;
}
spectrumExportCount += 1;
// First, write an entry to the "_scans.csv" file
if (mOptions.RawDataExportOptions.RenumberScans)
{
scanNumber = spectrumExportCount;
}
else
{
scanNumber = currentScan.ScanNumber;
}
int msLevel;
if (fragmentationScan)
{
msLevel = currentScan.FragScanInfo.MSLevel;
}
else
{
msLevel = 1;
}
var numIsotopicSignatures = 0;
var numPeaks = spectrum.IonCount;
var baselineNoiseLevel = currentScan.BaselineNoiseStats.NoiseLevel;
if (baselineNoiseLevel < 1)
{
baselineNoiseLevel = 1;
}
mBPIWriter.WriteDecon2LSScanFileEntry(scanInfoWriter, currentScan, scanNumber, msLevel, numPeaks, numIsotopicSignatures);
// Now write an entry to the "_isos.csv" file
if (spectrum.IonCount > 0)
{
// Populate intensities and pointerArray()
var intensities = new double[spectrum.IonCount];
var pointerArray = new int[spectrum.IonCount];
for (var ionIndex = 0; ionIndex < spectrum.IonCount; ionIndex++)
{
intensities[ionIndex] = spectrum.IonsIntensity[ionIndex];
pointerArray[ionIndex] = ionIndex;
}
// Sort pointerArray() based on the intensities in intensities
Array.Sort(intensities, pointerArray);
int startIndex;
if (mOptions.RawDataExportOptions.MaxIonCountPerScan > 0)
{
// Possibly limit the number of ions to maxIonCount
startIndex = spectrum.IonCount - mOptions.RawDataExportOptions.MaxIonCountPerScan;
if (startIndex < 0)
{
startIndex = 0;
}
}
else
{
startIndex = 0;
}
// Define the minimum data point intensity value
var minimumIntensityCurrentScan = spectrum.IonsIntensity[pointerArray[startIndex]];
// Update the minimum intensity if a higher minimum intensity is defined in .IntensityMinimum
minimumIntensityCurrentScan = Math.Max(minimumIntensityCurrentScan, mOptions.RawDataExportOptions.IntensityMinimum);
// If mOptions.RawDataExportOptions.MinimumSignalToNoiseRatio is > 0, then possibly update minimumIntensityCurrentScan
if (mOptions.RawDataExportOptions.MinimumSignalToNoiseRatio > 0)
{
minimumIntensityCurrentScan = Math.Max(minimumIntensityCurrentScan, currentScan.BaselineNoiseStats.NoiseLevel * mOptions.RawDataExportOptions.MinimumSignalToNoiseRatio);
}
for (var ionIndex = 0; ionIndex < spectrum.IonCount; ionIndex++)
{
if (spectrum.IonsIntensity[ionIndex] >= minimumIntensityCurrentScan)
{
var charge = 1;
var isoFit = 0;
var mass = clsUtilities.ConvoluteMass(spectrum.IonsMZ[ionIndex], 1, 0);
var peakFWHM = 0;
var signalToNoise = spectrum.IonsIntensity[ionIndex] / baselineNoiseLevel;
var monoisotopicAbu = -10;
var monoPlus2Abu = -10;
mBPIWriter.WriteDecon2LSIsosFileEntry(
dataWriter, scanNumber, charge,
spectrum.IonsIntensity[ionIndex], spectrum.IonsMZ[ionIndex],
isoFit, mass, mass, mass,
peakFWHM, signalToNoise, monoisotopicAbu, monoPlus2Abu);
}
}
}
}
