public ScoreModelUnit(SpecificFragment specificFragment, double intensityMax, double probability, double probabilityNoise)
{
FragmentationMode = specificFragment.FragmentationMode;
FragmentationType = specificFragment.FragmentationType;
FragmentDescription = specificFragment.FragmentDescription;
LipidClass = specificFragment.LipidClass;
LipidType = specificFragment.LipidType;
IntensityMax = intensityMax;
Probability = probability;
ProbabilityNoise = probabilityNoise;
}
public ScoreModel CreateScoreModel(double hcdError, double cidError)
{
const int numTopHitsToConsider = 1;
var observationDictionary = new Dictionary <SpecificFragment, List <double> >();
foreach (var datasetLocation in DatasetLocations)
{
// Setup workflow
var globalWorkflow = new GlobalWorkflow(datasetLocation);
// Run workflow
var lipidGroupSearchResults = globalWorkflow.RunGlobalWorkflow(LipidList, 30, 500);
// Group results of same scan together
var resultsGroupedByScan = lipidGroupSearchResults.GroupBy(x => x.SpectrumSearchResult.HcdSpectrum.ScanNum);
// Grab the result(s) with the best score
foreach (var group in resultsGroupedByScan)
{
var groupOrdered = group.OrderByDescending(x => x.SpectrumSearchResult.Score).ToList();
for (var i = 0; i < numTopHitsToConsider && i < groupOrdered.Count; i++)
{
var resultToAdd = groupOrdered[i];
var lipidTarget = resultToAdd.LipidTarget;
var lipidClass = lipidTarget.LipidClass;
var lipidType = lipidTarget.LipidType;
var fragmentationMode = lipidTarget.FragmentationMode;
var spectrumSearchResult = resultToAdd.SpectrumSearchResult;
var cidResultList = spectrumSearchResult.CidSearchResultList;
var hcdResultList = spectrumSearchResult.HcdSearchResultList;
var cidMaxValue = spectrumSearchResult.CidSpectrum.Peaks.Any() ? spectrumSearchResult.CidSpectrum.Peaks.Max(x => x.Intensity) : 1;
var hcdMaxValue = spectrumSearchResult.HcdSpectrum.Peaks.Any() ? spectrumSearchResult.HcdSpectrum.Peaks.Max(x => x.Intensity) : 1;
// CID Results
foreach (var cidResult in cidResultList)
{
var fragment = cidResult.TheoreticalPeak.Description;
double intensity = 0;
if (cidResult.ObservedPeak != null)
{
intensity = Math.Log10(cidResult.ObservedPeak.Intensity) / Math.Log10(cidMaxValue);
}
var specificFragment = new SpecificFragment(lipidClass, lipidType, fragment, fragmentationMode, FragmentationType.CID);
// Either update the observation list or create a new one
List <double> observationList;
if (observationDictionary.TryGetValue(specificFragment, out observationList))
{
observationList.Add(intensity);
}
else
{
observationList = new List <double> {
intensity
};
observationDictionary.Add(specificFragment, observationList);
}
}
// HCD Results
foreach (var hcdResult in hcdResultList)
{
var fragment = hcdResult.TheoreticalPeak.Description;
double intensity = 0;
if (hcdResult.ObservedPeak != null)
{
intensity = Math.Log10(hcdResult.ObservedPeak.Intensity) / Math.Log10(hcdMaxValue);
}
var specificFragment = new SpecificFragment(lipidClass, lipidType, fragment, fragmentationMode, FragmentationType.HCD);
// Either update the observation list or create a new one
List <double> observationList;
if (observationDictionary.TryGetValue(specificFragment, out observationList))
{
observationList.Add(intensity);
}
else
{
observationList = new List <double> {
intensity
};
observationDictionary.Add(specificFragment, observationList);
}
}
}
}
// Assure that the source data file is closed
globalWorkflow.LcMsRun.Close();
}
var liquidScoreModelUnitList = PartitionIntoModelUnits(observationDictionary);
var liquidScoreModel = new ScoreModel(liquidScoreModelUnitList);
return(liquidScoreModel);
}
