public List <XYPair> GetIMSScanProfileFromMSFeatures()
{
GetMinAndMaxScanIMS(out var scanIMSMinimum, out var scanIMSMaximum);
var xyPairs = new List <XYPair>();
for (var imsScan = scanIMSMinimum; imsScan <= scanIMSMaximum; imsScan++)
{
float summedIntensityForIMSScan = 0;
foreach (var imsMsFeature in imsMsFeatureList)
{
summedIntensityForIMSScan +=
imsMsFeature.MSFeatureList.Where(p => p.ScanIMS == imsScan).Select(p => (float)p.IntensityUnSummed).Sum //note: need float due overflow exception from value exceeding int32
();
}
var pair = new XYPair(imsScan, summedIntensityForIMSScan);
xyPairs.Add(pair);
}
ConformationDetection.PadXYPairsWithZeros(ref xyPairs, 5);
return(xyPairs);
}
public List <XYPair> GetIMSScanProfileFromRawData(DataReader uimfReader, UIMFData.FrameType frameType, double binWidth, double calibrationSlope, double calibrationIntercept)
{
GetMinAndMaxScanLCAndScanIMSAndMSFeatureRep(
out var scanLCMinimum, out var scanLCMaximum,
out var scanIMSMinimum, out var scanIMSMaximum, out var msFeatureRep);
// double currentFWHM = msFeatureRep.Fwhm;
// var currentMonoMZ = msFeatureRep.MassMonoisotopic/msFeatureRep.Charge + 1.0072649;
var mzMostAbundantIsotope = msFeatureRep.MassMostAbundantIsotope / msFeatureRep.Charge + 1.00727649;
////[gord] the following commented-out code sets the m/z range too wide. Can be removed later
//List<double> startMZ = new List<double>();
//List<double> endMZ = new List<double>();
//// Set ranges over which to look for the original data in the UIMF.
//double charge = Convert.ToDouble(this.Charge);
//for (int i = 0; i < 3; i++)
//{
// startMZ.Add(currentMonoMZ + (1.003 * i / charge) - (0.5 * currentFWHM));
// endMZ.Add(currentMonoMZ + (1.003 * i / charge) + (0.5 * currentFWHM));
//}
//double minMZ = startMZ[0];
//double maxMZ = endMZ[endMZ.Count - 1];
//double midPointMZ = (maxMZ + minMZ) / 2;
//double wideToleranceInMZ = midPointMZ - minMZ;
var frameMinimum = ScanLCMap.Mapping[scanLCMinimum];
var frameMaximum = ScanLCMap.Mapping[scanLCMaximum];
int[] scanValues = null;
int[] intensityValues = null;
var sigma = msFeatureRep.Fwhm / 2.35;
var toleranceInMZ = 2 * sigma; // this is a +/- value; so 4* sigma = 95% of a normal distribution
//Before: a wide m/z was used when generating the drift time profile.
//uimfReader.GetDriftTimeProfile(frameIndexMinimum, frameIndexMaximum, frameType, scanIMSMinimum, scanIMSMaximum, midPointMZ, wideToleranceInMZ, ref scanValues, ref intensityValues);
//now: a narrow m/z range is used when generating the drift time profile
uimfReader.GetDriftTimeProfile(frameMinimum, frameMaximum, frameType, scanIMSMinimum, scanIMSMaximum, mzMostAbundantIsotope, toleranceInMZ, ref scanValues, ref intensityValues);
var imsScanProfile = intensityValues.Select((t, i) => new XYPair(scanIMSMinimum + i, t)).ToList();
ConformationDetection.PadXYPairsWithZeros(ref imsScanProfile, 5);
return(imsScanProfile);
}
public void Execute()
{
{
Logger.Log("Total number of MS Features in _isos.csv file = " + m_isosReader.NumOfUnfilteredMSFeatures);
Logger.Log("Total number of MS Features we'll consider = " + m_isosReader.MSFeatureList.Count);
Logger.Log("Creating IMS-MS Features...");
var filteredMSFeatureList = m_isosReader.MSFeatureList;
var imsmsfeatureBag = new ConcurrentBag <IMSMSFeature>();
if (Settings.UseCharge)
{
var groupByScanLCAndChargeQuery = from msFeature in filteredMSFeatureList
group msFeature by new { msFeature.ScanLC, msFeature.Charge } into newGroup
select newGroup;
Parallel.ForEach(groupByScanLCAndChargeQuery, msFeatureGroup =>
{
var imsmsFeatureList = ClusterMSFeatures.ClusterByMass(msFeatureGroup);
foreach (var imsmsFeature in imsmsFeatureList)
{
imsmsfeatureBag.Add(imsmsFeature);
}
});
}
else
{
var groupByScanLCQuery = from msFeature in filteredMSFeatureList
group msFeature by msFeature.ScanLC into newGroup
select newGroup;
Parallel.ForEach(groupByScanLCQuery, msFeatureGroup =>
{
var imsmsFeatureList = ClusterMSFeatures.ClusterByMass(msFeatureGroup);
foreach (var imsmsFeature in imsmsFeatureList)
{
imsmsfeatureBag.Add(imsmsFeature);
}
});
}
Logger.Log("Total Number of Unfiltered IMS-MS Features = " + imsmsfeatureBag.Count);
//Logger.Log("Filtering out short IMS-MS Features...");
//IEnumerable<IMSMSFeature> imsmsFeatureEnumerable = FeatureUtil.FilterByMemberCount(imsmsfeatureBag);
//imsmsfeatureBag = null;
//Logger.Log("Total Number of Filtered IMS-MS Features = " + imsmsFeatureEnumerable.Count());
Logger.Log("Creating LC-IMS-MS Features...");
var lcimsmsFeatureBag = new ConcurrentBag <LCIMSMSFeature>();
if (Settings.UseCharge)
{
var groupByChargeQuery = from imsmsFeature in imsmsfeatureBag
group imsmsFeature by imsmsFeature.Charge into newGroup
select newGroup;
Parallel.ForEach(groupByChargeQuery, imsmsFeatureGroup =>
{
var lcimsmsFeatureList = ClusterIMSMSFeatures.ClusterByMassAndScanLC(imsmsFeatureGroup);
foreach (var lcimsmsFeature in lcimsmsFeatureList)
{
lcimsmsFeatureBag.Add(lcimsmsFeature);
}
});
}
else
{
var lcimsmsFeatureList = ClusterIMSMSFeatures.ClusterByMassAndScanLC(imsmsfeatureBag);
foreach (var lcimsmsFeature in lcimsmsFeatureList)
{
lcimsmsFeatureBag.Add(lcimsmsFeature);
}
}
Logger.Log("Total Number of LC-IMS-MS Features = " + lcimsmsFeatureBag.Count);
IEnumerable <LCIMSMSFeature> lcimsmsFeatureEnumerable;
if (Settings.IMSDaCorrectionMax > 0 && !Settings.FilterFlaggedData)
{
Logger.Log("Executing Dalton Correction Algorithm on LC-IMS-MS Features...");
var daCorrectedLCIMSMSFeatureBag = new ConcurrentBag <LCIMSMSFeature>();
var lcimsmsFeatureListBag = new ConcurrentBag <IEnumerable <LCIMSMSFeature> >();
if (Settings.UseCharge)
{
var groupByChargeQuery2 = from lcimsmsFeature in lcimsmsFeatureBag
group lcimsmsFeature by lcimsmsFeature.Charge into newGroup
select newGroup;
Parallel.ForEach(groupByChargeQuery2, lcimsmsFeatureGroup =>
{
IEnumerable <IEnumerable <LCIMSMSFeature> > returnList = FeatureUtil.PartitionFeaturesByMass(lcimsmsFeatureGroup);
foreach (var lcimsmsFeatureList in returnList)
{
lcimsmsFeatureListBag.Add(lcimsmsFeatureList);
}
});
}
else
{
IEnumerable <IEnumerable <LCIMSMSFeature> > returnList = FeatureUtil.PartitionFeaturesByMass(lcimsmsFeatureBag);
foreach (var lcimsmsFeatureList in returnList)
{
lcimsmsFeatureListBag.Add(lcimsmsFeatureList);
}
}
Parallel.ForEach(lcimsmsFeatureListBag, lcimsmsFeatureGroup =>
{
var lcimsmsFeatureList = DaltonCorrection.CorrectLCIMSMSFeatures(lcimsmsFeatureGroup);
foreach (var lcimsmsFeature in lcimsmsFeatureList)
{
daCorrectedLCIMSMSFeatureBag.Add(lcimsmsFeature);
}
});
lcimsmsFeatureEnumerable = daCorrectedLCIMSMSFeatureBag;
Logger.Log("Total Number of Dalton Corrected LC-IMS-MS Features = " + lcimsmsFeatureEnumerable.Count());
}
else
{
lcimsmsFeatureEnumerable = lcimsmsFeatureBag;
}
Logger.Log("Filtering LC-IMS-MS features based on Member Count...");
lcimsmsFeatureEnumerable = FeatureUtil.FilterByMemberCount(lcimsmsFeatureEnumerable);
Logger.Log("Total Number of Filtered LC-IMS-MS Features = " + lcimsmsFeatureEnumerable.Count());
Logger.Log("Splitting LC-IMS-MS Features by LC Scan...");
lcimsmsFeatureEnumerable = FeatureUtil.SplitLCIMSMSFeaturesByScanLC(lcimsmsFeatureEnumerable);
if (!Settings.UseConformationDetection)
{
lcimsmsFeatureEnumerable = FeatureUtil.FilterSingleLCScan(lcimsmsFeatureEnumerable);
}
Logger.Log("New Total Number of Filtered LC-IMS-MS Features = " + lcimsmsFeatureEnumerable.Count());
if (Settings.UseConformationDetection)
{
Logger.Log("Conformation Detection...");
lcimsmsFeatureEnumerable = ConformationDetection.DetectConformationsUsingRawData(lcimsmsFeatureEnumerable.ToList());
//lcimsmsFeatureEnumerable = FeatureUtil.FilterSingleLCScan(lcimsmsFeatureEnumerable);
lcimsmsFeatureEnumerable = FeatureUtil.FilterByMemberCount(lcimsmsFeatureEnumerable);
Logger.Log("New Total Number of LC-IMS-MS Features = " + lcimsmsFeatureEnumerable.Count());
}
lcimsmsFeatureEnumerable = FeatureUtil.SortByMass(lcimsmsFeatureEnumerable);
Logger.Log("Creating filtered Isos file...");
var msFeatureListOutput = new List <MSFeature>();
foreach (var lcimsmsFeature in lcimsmsFeatureEnumerable)
{
if (Settings.FilterIsosToSinglePoint)
{
var msFeatureRep = lcimsmsFeature.GetMSFeatureRep();
msFeatureListOutput.Add(msFeatureRep);
}
else
{
foreach (var imsmsFeature in lcimsmsFeature.IMSMSFeatureList)
{
msFeatureListOutput.AddRange(imsmsFeature.MSFeatureList);
}
}
}
var isosWriter = new IsosWriter(msFeatureListOutput, m_isosReader.ColumnMap);
Logger.Log("Writing output files...");
FeatureUtil.WriteLCIMSMSFeatureToFile(lcimsmsFeatureEnumerable);
LCimsmsFeatures = lcimsmsFeatureEnumerable;
}
}
