public BasicTFF(double toleranceInPPM, bool requiresMonoPeak, Globals.IsotopicProfileType isotopicProfileTarget)
{
ToleranceInPPM = toleranceInPPM;
NeedMonoIsotopicPeak = requiresMonoPeak;
IsotopicProfileType = isotopicProfileTarget;
NumPeaksUsedInAbundance = 1;
}
private IsotopicProfile getTheorProfile(TargetBase massTag, Globals.IsotopicProfileType isotopicProfileType)
{
switch (isotopicProfileType)
{
case Globals.IsotopicProfileType.UNLABELED:
return(massTag.IsotopicProfile);
case Globals.IsotopicProfileType.LABELED:
return(massTag.IsotopicProfileLabeled);
default:
return(massTag.IsotopicProfile);
}
}
public PeakChromatogramGenerator(double tolerance, Globals.ChromatogramGeneratorMode chromMode,
Globals.IsotopicProfileType isotopicProfileTarget, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
Tolerance = tolerance;
ChromatogramGeneratorMode = chromMode;
IsotopicProfileTarget = isotopicProfileTarget;
TopNPeaksLowerCutOff = 0.3;
ChromWindowWidthForNonAlignedData = 0.4f;
ChromWindowWidthForAlignedData = 0.1f;
ToleranceUnit = toleranceUnit;
_chromGen = new ChromatogramGenerator();
}
public virtual void AddSelectedChromPeakAndScanSet(ChromPeak bestPeak, ScanSet scanset, Globals.IsotopicProfileType isotopicProfileType = Globals.IsotopicProfileType.UNLABELLED)
{
if (isotopicProfileType == Globals.IsotopicProfileType.UNLABELLED)
{
ChromPeakSelected = bestPeak;
ScanSet = scanset;
if (ScanSet != null)
{
NumMSScansSummed = ScanSet.IndexValues.Count;
}
var failedChromPeakSelection = (ChromPeakSelected == null || ChromPeakSelected.XValue == 0);
if (failedChromPeakSelection)
{
FailedResult = true;
FailureType = Globals.TargetedResultFailureType.ChrompeakNotFoundWithinTolerances;
}
else
{
FailedResult = false;
FailureType = Globals.TargetedResultFailureType.None;
}
}
else
{
throw new NotSupportedException("Cannot add data for a labeled result in this base class");
}
}
public IsotopicPeakFitScoreCalculator(Globals.IsotopicProfileType labelType, int numberOfPeaksToLeftForPenalty)
{
IsotopicProfileType = labelType;
NumberOfPeaksToLeftForPenalty = numberOfPeaksToLeftForPenalty;
}
public IsotopicProfileFitScoreCalculator(Globals.IsotopicProfileType labelType)
{
IsotopicProfileType = labelType;
}
public IsotopicProfileFitScoreCalculator()
{
IsotopicProfileType = Globals.IsotopicProfileType.UNLABELED;
}
public override void AddSelectedChromPeakAndScanSet(ChromPeak bestPeak, ScanSet scanset, Globals.IsotopicProfileType isotopicProfileType)
{
//if result was not previously processed, will do a standard add of selected chrom peak and scanset
//if result was previously processed, add new data to the Labelled results
if (isotopicProfileType == Globals.IsotopicProfileType.UNLABELLED)
{
base.AddSelectedChromPeakAndScanSet(bestPeak, scanset, isotopicProfileType);
}
else
{
ChromPeakSelectedN15 = bestPeak;
ScanSetForN15Profile = scanset;
}
}
