private void WriteSICStatsFlatFileEntry(
TextWriter sicStatsWriter,
char delimiter,
clsSICOptions sicOptions,
clsScanList scanList,
clsParentIonInfo parentIon,
int parentIonIndex,
int surveyScanNumber,
float surveyScanTime,
int fragScanIndex,
bool includeScanTimesInSICStatsFile)
{
var dataValues = new List <string>(40);
float fragScanTime = 0;
float optimalPeakApexScanTime = 0;
dataValues.Add(sicOptions.DatasetID.ToString()); // Dataset ID
dataValues.Add(parentIonIndex.ToString()); // Parent Ion Index
dataValues.Add(StringUtilities.DblToString(parentIon.MZ, 4)); // MZ
dataValues.Add(surveyScanNumber.ToString()); // Survey scan number
double interferenceScore;
if (fragScanIndex < scanList.FragScans.Count)
{
var fragScanNumber = scanList.FragScans[parentIon.FragScanIndices[fragScanIndex]].ScanNumber;
dataValues.Add(fragScanNumber.ToString()); // Fragmentation scan number
interferenceScore = scanList.FragScans[parentIon.FragScanIndices[fragScanIndex]].FragScanInfo.InterferenceScore;
}
else
{
dataValues.Add("0"); // Fragmentation scan does not exist
interferenceScore = 0;
}
dataValues.Add(parentIon.OptimalPeakApexScanNumber.ToString()); // Optimal peak apex scan number
if (includeScanTimesInSICStatsFile)
{
if (fragScanIndex < scanList.FragScans.Count)
{
fragScanTime = scanList.FragScans[parentIon.FragScanIndices[fragScanIndex]].ScanTime;
}
else
{
fragScanTime = 0; // Fragmentation scan does not exist
}
optimalPeakApexScanTime = ScanNumberToScanTime(scanList, parentIon.OptimalPeakApexScanNumber);
}
dataValues.Add(parentIon.PeakApexOverrideParentIonIndex.ToString()); // Parent Ion Index that supplied the optimal peak apex scan number
if (parentIon.CustomSICPeak)
{
dataValues.Add("1"); // Custom SIC peak, record 1
}
else
{
dataValues.Add("0"); // Not a Custom SIC peak, record 0
}
var currentSIC = parentIon.SICStats;
if (currentSIC.ScanTypeForPeakIndices == clsScanList.eScanTypeConstants.FragScan)
{
dataValues.Add(scanList.FragScans[currentSIC.PeakScanIndexStart].ScanNumber.ToString()); // Peak Scan Start
dataValues.Add(scanList.FragScans[currentSIC.PeakScanIndexEnd].ScanNumber.ToString()); // Peak Scan End
dataValues.Add(scanList.FragScans[currentSIC.PeakScanIndexMax].ScanNumber.ToString()); // Peak Scan Max Intensity
}
else
{
dataValues.Add(scanList.SurveyScans[currentSIC.PeakScanIndexStart].ScanNumber.ToString()); // Peak Scan Start
dataValues.Add(scanList.SurveyScans[currentSIC.PeakScanIndexEnd].ScanNumber.ToString()); // Peak Scan End
dataValues.Add(scanList.SurveyScans[currentSIC.PeakScanIndexMax].ScanNumber.ToString()); // Peak Scan Max Intensity
}
var currentPeak = currentSIC.Peak;
dataValues.Add(StringUtilities.ValueToString(currentPeak.MaxIntensityValue, 5)); // Peak Intensity
dataValues.Add(StringUtilities.ValueToString(currentPeak.SignalToNoiseRatio, 4)); // Peak signal to noise ratio
dataValues.Add(currentPeak.FWHMScanWidth.ToString()); // Full width at half max (in scans)
dataValues.Add(StringUtilities.ValueToString(currentPeak.Area, 5)); // Peak area
dataValues.Add(StringUtilities.ValueToString(currentPeak.ParentIonIntensity, 5)); // Intensity of the parent ion (just before the fragmentation scan)
dataValues.Add(StringUtilities.ValueToString(currentPeak.BaselineNoiseStats.NoiseLevel, 5));
dataValues.Add(StringUtilities.ValueToString(currentPeak.BaselineNoiseStats.NoiseStDev, 3));
dataValues.Add(currentPeak.BaselineNoiseStats.PointsUsed.ToString());
var statMoments = currentPeak.StatisticalMoments;
dataValues.Add(StringUtilities.ValueToString(statMoments.Area, 5));
dataValues.Add(statMoments.CenterOfMassScan.ToString());
dataValues.Add(StringUtilities.ValueToString(statMoments.StDev, 3));
dataValues.Add(StringUtilities.ValueToString(statMoments.Skew, 4));
dataValues.Add(StringUtilities.ValueToString(statMoments.KSStat, 4));
dataValues.Add(statMoments.DataCountUsed.ToString());
dataValues.Add(StringUtilities.ValueToString(interferenceScore, 4)); // Interference Score
if (includeScanTimesInSICStatsFile)
{
dataValues.Add(StringUtilities.DblToString(surveyScanTime, 5)); // SurveyScanTime
dataValues.Add(StringUtilities.DblToString(fragScanTime, 5)); // FragScanTime
dataValues.Add(StringUtilities.DblToString(optimalPeakApexScanTime, 5)); // OptimalPeakApexScanTime
}
sicStatsWriter.WriteLine(string.Join(delimiter.ToString(), dataValues));
}
private clsParentIonInfo GetFakeParentIonForFragScan(clsScanList scanList, int fragScanIndex)
{
var currentFragScan = scanList.FragScans[fragScanIndex];
var newParentIon = new clsParentIonInfo(currentFragScan.BasePeakIonMZ)
{
SurveyScanIndex = 0
};
// Find the previous MS1 scan that occurs before the frag scan
var surveyScanNumberAbsolute = currentFragScan.ScanNumber - 1;
newParentIon.FragScanIndices.Add(fragScanIndex);
if (scanList.MasterScanOrderCount > 0)
{
var surveyScanIndexMatch = clsBinarySearch.BinarySearchFindNearest(
scanList.MasterScanNumList,
surveyScanNumberAbsolute,
clsBinarySearch.eMissingDataModeConstants.ReturnClosestPoint);
while (surveyScanIndexMatch >= 0 && scanList.MasterScanOrder[surveyScanIndexMatch].ScanType == clsScanList.eScanTypeConstants.FragScan)
{
surveyScanIndexMatch -= 1;
}
if (surveyScanIndexMatch < 0)
{
// Did not find the previous survey scan; find the next survey scan
surveyScanIndexMatch += 1;
while (surveyScanIndexMatch < scanList.MasterScanOrderCount && scanList.MasterScanOrder[surveyScanIndexMatch].ScanType == clsScanList.eScanTypeConstants.FragScan)
{
surveyScanIndexMatch += 1;
}
if (surveyScanIndexMatch >= scanList.MasterScanOrderCount)
{
surveyScanIndexMatch = 0;
}
}
newParentIon.SurveyScanIndex = scanList.MasterScanOrder[surveyScanIndexMatch].ScanIndexPointer;
}
if (newParentIon.SurveyScanIndex < scanList.SurveyScans.Count)
{
newParentIon.OptimalPeakApexScanNumber = scanList.SurveyScans[newParentIon.SurveyScanIndex].ScanNumber;
}
else
{
newParentIon.OptimalPeakApexScanNumber = surveyScanNumberAbsolute;
}
newParentIon.PeakApexOverrideParentIonIndex = -1;
newParentIon.SICStats.ScanTypeForPeakIndices = clsScanList.eScanTypeConstants.FragScan;
newParentIon.SICStats.PeakScanIndexStart = fragScanIndex;
newParentIon.SICStats.PeakScanIndexEnd = fragScanIndex;
newParentIon.SICStats.PeakScanIndexMax = fragScanIndex;
var peak = newParentIon.SICStats.Peak;
peak.MaxIntensityValue = currentFragScan.BasePeakIonIntensity;
peak.SignalToNoiseRatio = 1;
peak.FWHMScanWidth = 1;
peak.Area = currentFragScan.BasePeakIonIntensity;
peak.ParentIonIntensity = currentFragScan.BasePeakIonIntensity;
return(newParentIon);
}
