public void CalculateLabelingDistributionTest2()
{
//mass_tag_id monoisotopic_mass NET obs mod_count mod_description pmt peptide peptideex
//355176429 1538.8166126 0.42422 1 0 2.00000 LFLASACLYGAALAGV R.LFLASACLYGAALAGV.C
//------------------------load theor data ------------------------------------
var peptideUtils = new PeptideUtils();
var peptide = new PeptideTarget();
peptide.Code = "LFLASACLYGAALAGV";
peptide.EmpiricalFormula = new PeptideUtils().GetEmpiricalFormulaForPeptideSequence(peptide.Code);
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
theorFeatureGenerator.GenerateTheorFeature(peptide);
var theorProfile = peptide.IsotopicProfile;
var theorIntensities = theorProfile.Peaklist.Select(p => (double)p.Height).ToList();
Console.WriteLine("Total carbons = " + peptideUtils.GetNumAtomsForElement("C", peptide.EmpiricalFormula));
var obsIntensities = new List <double>(new[]
{
1, 0.8335001, 0.4029815, 0.1846439, 0.1116047, 0.09458135, 0.07157851, 0.04972008,
0.03036686, 0.01545749, 0.008299164, 0.004003931, 0.001711554, 0.000766305,
0.000484514
});
var relexCorrectedIntensities = new List <double>(new[]
{
1, 0.84416, 0.4174013, 0.1843375, 0.1073706, 0.09557419, 0.07190877, 0.04823519,
0.02991197, 0.01456759, 0.008299164, 0.004003931, 0.001711554, 0.000766305,
0.000484514
});
/*
*
* Data for observed profile:
* LCMSFeature 8517 from Yellow_C13_070_23Mar10_Griffin_10-01-28
* *
* peak mz relIntens width sn
* 0 770.418569278349 1 0.008119391 285.256
* 1 770.919748892834 0.8335001 0.008161238 884.9909
* 2 771.421020812818 0.4029815 0.008248929 566.6187
* 3 771.922575912402 0.1846439 0.008058954 703.6938
* 4 772.424544684666 0.1116047 0.007997629 358.0133
* 5 772.926348484216 0.09458135 0.008128829 677.3434
* 6 773.428080290323 0.07157851 0.008151106 100
* 7 773.929769365137 0.04972008 0.008104968 100
* 8 774.431542463583 0.03036686 0.007982519 100
* 9 774.933237566856 0.01545749 0.008024476 100
* 10 775.434950373045 0.008299164 0.008166174 740.9502
* 11 775.936532837365 0.004003931 0.007899459 100
* 12 776.438361528879 0.001711554 0.00877683 44.79652
* 13 776.940072709136 0.0007663054 0.007601836 17.12788
* 14 777.441663634739 0.0004845143 0.007320933 100
*
*/
var labelDistCalc = new LabelingDistributionCalculator();
double[] solvedXVals;
double[] solvedYvals;
var d = 0.1;
labelDistCalc.CalculateLabelingDistribution(theorIntensities, obsIntensities, d, d, out solvedXVals, out solvedYvals);
var xydata = new XYData();
xydata.Xvalues = solvedXVals;
xydata.Yvalues = solvedYvals;
Console.WriteLine();
Console.WriteLine("threshold= " + d);
xydata.Display();
labelDistCalc.CalculateLabelingDistribution(theorIntensities, relexCorrectedIntensities, d, d, out solvedXVals, out solvedYvals);
xydata.Xvalues = solvedXVals;
xydata.Yvalues = solvedYvals;
Console.WriteLine();
Console.WriteLine("Relex-corrected isotopic profile= " + d);
xydata.Display();
double fractionUnlabelled, fractionLabelled, averageLabelsIncorporated;
labelDistCalc.OutputLabelingInfo(solvedYvals.ToList(), out fractionUnlabelled, out fractionLabelled,
out averageLabelsIncorporated);
Console.WriteLine();
Console.WriteLine("fractionUnlabelled= " + fractionUnlabelled);
Console.WriteLine("fractionLabelled= " + fractionLabelled);
Console.WriteLine("averageAmountLabelIncorp= " + averageLabelsIncorporated);
//for (double d = 0; d < 2.1; d+=0.1)
//{
// labelDistCalc.CalculateLabelingDistribution(theorIntensities, obsIntensities, d, d, out solvedXVals, out solvedYvals);
// XYData xydata = new XYData();
// xydata.Xvalues = solvedXVals;
// xydata.Yvalues = solvedYvals;
// Console.WriteLine();
// Console.WriteLine("threshold= " + d);
// xydata.Display();
//}
}
public override void Execute(ResultCollection resultList)
{
Check.Require(resultList.CurrentTargetedResult is SipperLcmsTargetedResult, "Sipper Quantifier only works on Sipper-type result objects");
Check.Require(resultList.Run.CurrentMassTag != null, this.Name + " failed; CurrentMassTag is empty");
Check.Require(resultList.Run.CurrentMassTag.IsotopicProfile != null, this.Name + " failed; Theor isotopic profile is empty. Run a TheorFeatureGenerator");
var result = (SipperLcmsTargetedResult)resultList.CurrentTargetedResult;
result.AreaUnderDifferenceCurve = -9999;
result.AreaUnderRatioCurve = -9999;
RatioVals.Xvalues = new double[] { 1, 2, 3, 4, 5, 6, 7 };
RatioVals.Yvalues = new double[] { 0, 0, 0, 0, 0, 0, 0 };
RatioLogVals.Xvalues = new double[] { 1, 2, 3, 4, 5, 6, 7 };
RatioLogVals.Yvalues = new double[] { 0, 0, 0, 0, 0, 0, 0 };
ChromatogramRSquaredVals.Clear();
Check.Require(result != null, "No MassTagResult has been generated for CurrentMassTag");
if (result.IsotopicProfile == null || result.IsotopicProfile.Peaklist == null || result.IsotopicProfile.Peaklist.Count < 2)
{
return;
}
var theorUnlabelledIso = resultList.Run.CurrentMassTag.IsotopicProfile.CloneIsotopicProfile();
IsotopicProfileUtilities.NormalizeIsotopicProfile(theorUnlabelledIso);
//PeakUtilities.TrimIsotopicProfile(unlabeledIso, 0.001);
var sb = new StringBuilder();
sb.Append(result.Target.ID + "\t" + result.Target.MZ.ToString("0.0000") + "\t" + result.Target.ChargeState +
"-----------------------------\n");
var indexMostAbundantTheorPeak = theorUnlabelledIso.GetIndexOfMostIntensePeak();
NormalizedIso = result.IsotopicProfile.CloneIsotopicProfile();
IsotopicProfileUtilities.NormalizeIsotopicProfileToSpecificPeak(NormalizedIso, indexMostAbundantTheorPeak);
// return;
if (result.Flags.Count > 0)
{
var flagstring = "";
foreach (var resultFlag in result.Flags)
{
flagstring += resultFlag.Description + ";";
}
result.ErrorDescription = flagstring.TrimEnd(';');
result.FailedResult = true;
if (flagstring.Contains("PeakToTheLeft"))
{
result.FailureType = Globals.TargetedResultFailureType.DeisotopingProblemDetected;
}
else
{
result.FailureType = Globals.TargetedResultFailureType.QuantifierFailure;
}
}
var resultPassesMinimalCriteria = (result.Score < MaximumFitScoreForFurtherProcessing && result.Flags.Count == 0);
if (resultPassesMinimalCriteria)
{
//------------------------------------- Get chromatogramCorrelation data -------------------------------
if (IsChromatogramCorrelationPerformed)
{
GetChromatogramCorrelationData(result);
}
NormalizedAdjustedIso = NormalizedIso.CloneIsotopicProfile();
//this is experimental!! it attempts to correct the problems caused by Orbitraps on isotopic profile intensities
//UpdateIsoIntensitiesUsingChromCorrData(result.ChromCorrelationData, NormalizedAdjustedIso);
//----------------- create ratio data -------------------------------------------------------
var ratioData = NormalizedAdjustedIso.CloneIsotopicProfile();
for (var i = 0; i < NormalizedIso.Peaklist.Count; i++)
{
if (i < theorUnlabelledIso.Peaklist.Count && theorUnlabelledIso.Peaklist[i].Height > MinimumRelativeIntensityForRatioCalc)
{
ratioData.Peaklist[i].Height = (NormalizedIso.Peaklist[i].Height / theorUnlabelledIso.Peaklist[i].Height - 1);
}
else
{
ratioData.Peaklist[i].Height = 0;
}
}
//trim off zeros from ratio data
for (var i = ratioData.Peaklist.Count - 1; i >= 0; i--)
{
if (ratioData.Peaklist[i].Height == 0)
{
ratioData.Peaklist.RemoveAt(i);
}
else
{
break;
}
}
var xvals = ratioData.Peaklist.Select((p, i) => new { peak = p, index = i }).Select(n => (double)n.index).ToList();
var yvals = ratioData.Peaklist.Select(p => (double)p.Height).ToList();
result.AreaUnderRatioCurve = yvals.Sum();
RatioVals.Xvalues = xvals.ToArray();
RatioVals.Yvalues = yvals.ToArray();
GetLinearRegressionData(result, xvals, yvals);
//------------- subtract unlabelled profile from normalized profile ----------------------
var subtractedIsoData = NormalizedAdjustedIso.CloneIsotopicProfile();
for (var i = 0; i < subtractedIsoData.Peaklist.Count; i++)
{
float intensityTheorPeak = 0;
if (i < theorUnlabelledIso.Peaklist.Count)
{
intensityTheorPeak = theorUnlabelledIso.Peaklist[i].Height;
}
var subtractedIntensity = subtractedIsoData.Peaklist[i].Height - intensityTheorPeak;
if (subtractedIntensity < 0)
{
subtractedIntensity = 0;
}
subtractedIsoData.Peaklist[i].Height = subtractedIntensity;
}
result.AreaUnderDifferenceCurve = subtractedIsoData.Peaklist.Select(p => p.Height).Sum();
result.NumCarbonsLabelled = calculateNumCarbonsFromSubtractedProfile(subtractedIsoData);
//-------------- calculate Label Distribution ------------------------------------------------
double[] numLabelVals;
double[] labelDistributionVals;
var theorIntensityVals = theorUnlabelledIso.Peaklist.Select(p => (double)p.Height).ToList();
var normalizedCorrectedIntensityVals = NormalizedAdjustedIso.Peaklist.Select(p => (double)p.Height).ToList();
var numRightPads = 3;
_labelingDistributionCalculator.CalculateLabelingDistribution(theorIntensityVals, normalizedCorrectedIntensityVals,
LabeldistCalcIntensityThreshold,
LabeldistCalcIntensityThreshold,
out numLabelVals,
out labelDistributionVals, true, true, 0, numRightPads, 0, 0);
//negative distribution values are zeroed out. And, then the remaining values are adjusted such that they add up to 1.
result.LabelDistributionVals = AdjustLabelDistributionVals(labelDistributionVals);
double distFractionUnlabelled, distFractionLabelled, distAverageLabelsIncorporated;
_labelingDistributionCalculator.OutputLabelingInfo(result.LabelDistributionVals, out distFractionUnlabelled,
out distFractionLabelled,
out distAverageLabelsIncorporated);
//-------------- make calculations using inputs from chrom correlation data -------------------
HighQualitySubtractedProfile = GetIsoDataPassingChromCorrelation(result.ChromCorrelationData, subtractedIsoData);
var highQualityRatioProfileData = GetIsoDataPassingChromCorrelation(result.ChromCorrelationData, ratioData);
if (highQualityRatioProfileData.Peaklist != null && highQualityRatioProfileData.Peaklist.Count > 0)
{
result.AreaUnderDifferenceCurve = HighQualitySubtractedProfile.Peaklist.Select(p => p.Height).Sum();
}
else
{
result.AreaUnderDifferenceCurve = 0;
}
if (HighQualitySubtractedProfile.Peaklist != null && HighQualitySubtractedProfile.Peaklist.Count > 0)
{
result.AreaUnderRatioCurveRevised = highQualityRatioProfileData.Peaklist.Select(p => p.Height).Sum();
}
else
{
result.AreaUnderRatioCurveRevised = 0;
}
var numCarbonsLabelled = GetNumCarbonsLabelledUsingAverageMassDifferences(theorUnlabelledIso,
HighQualitySubtractedProfile);
//result.NumCarbonsLabelled = numCarbonsLabelled;
result.NumCarbonsLabelled = distAverageLabelsIncorporated;
var numCarbons = result.Target.GetAtomCountForElement("C");
result.PercentCarbonsLabelled = (result.NumCarbonsLabelled / numCarbons) * 100;
result.PercentPeptideLabelled = distFractionLabelled * 100;
//if (HighQualitySubtractedProfile.Peaklist != null && HighQualitySubtractedProfile.Peaklist.Count > 0)
//{
// result.PercentPeptideLabelled = HighQualitySubtractedProfile.Peaklist.Max(p => p.Height) * 100;
//}
//else
//{
// result.PercentPeptideLabelled = 0;
//}
result.NumHighQualityProfilePeaks = highQualityRatioProfileData.Peaklist != null
? highQualityRatioProfileData.Peaklist.Count
: 0;
//Console.WriteLine();
//Console.WriteLine(result);
//foreach (var val in ChromatogramRSquaredVals)
//{
// Console.WriteLine(val);
//}
}
else
{
result.FailedResult = true;
if (result.FailureType == Globals.TargetedResultFailureType.None)
{
result.FailureType = Globals.TargetedResultFailureType.MinimalCriteriaNotMet;
}
}
}
public void CalculateLabelingDistributionTest1()
{
// LabelDistribution calculation is based on John Chik's work
// He provided a standard set of data here: http://people.ucalgary.ca/~dschriem/CalcDeut/CalcDeut/
// We will use his test values and pass it through our implementation
/*
*#<<<Isotope Calculation Result >>>
#Formula: ISO:|VDWCPTGF| H2O + (H)1
#Resolution: 10000 resolving power
#Threshold (%): 1.0000
#Isotope List - 5 Mass(es)
#
#Isotope Mass Relative Intensity
# 924.39202 100.0000
# 925.39495 53.0190
# 926.39553 20.6161
# 927.39655 5.9286
# 928.39781 1.3694
*/
//observed: (from J. Chik's data) 118.8932 73.8074 34.413 14.4563 6.3169
/*
* Output Data from 'CalcDeut' testing from Dave Schriemer's data (see link above)
* File: MS924.3_Z1_10.0-10.2_A344-351_dist.xml
*
* <DeutDist startdeut='-0.0' chisq='5.80293903626e-05' content_type='numlist' distsum='1.00331024913' entries='5'>
* 0.832945525577
* 0.0747772118716
* 0.0305125766799
* 0.0704222225599
* -0.00534728755986
* </DeutDist>
*
*
*/
var theorIntensities = new List <double>(new[] { 1, 0.530190, 0.206161, 0.059286, 0.013694 });
var obsIntensities = new List <double>(new[] { 118.8932, 73.8074, 34.413, 14.4563, 6.3169 });
var labelDistCalc = new LabelingDistributionCalculator();
double[] solvedXVals;
double[] solvedYvals;
var intensityThreshold = 0.01;
labelDistCalc.CalculateLabelingDistribution(theorIntensities, obsIntensities, intensityThreshold, intensityThreshold, out solvedXVals, out solvedYvals,
truncateTheorBasedOnRelIntensity: false,
truncateObservedBasedOnRelIntensity: false,
leftPadding: 0,
rightPadding: 2,
numPeaksForAbsoluteTheorList: 3,
numPeaksForAbsoluteObsList: 5);
Assert.AreEqual(0.8329455, Math.Round(solvedYvals[0]), 7);
Assert.AreEqual(0.0747772, Math.Round(solvedYvals[1]), 7);
Assert.AreEqual(0.0305126, Math.Round(solvedYvals[2]), 7);
Assert.AreEqual(0.0704222, Math.Round(solvedYvals[3]), 7);
Assert.AreEqual(-0.0053473, Math.Round(solvedYvals[4]), 7);
var xydata = new XYData();
xydata.Xvalues = solvedXVals;
xydata.Yvalues = solvedYvals;
Console.WriteLine();
xydata.Display();
double fractionUnlabelled, fractionLabelled, averageLabelsIncorporated;
labelDistCalc.OutputLabelingInfo(solvedYvals.ToList(), out fractionUnlabelled, out fractionLabelled,
out averageLabelsIncorporated);
Console.WriteLine();
Console.WriteLine("fractionUnlabelled= " + fractionUnlabelled);
Console.WriteLine("fractionLabelled= " + fractionLabelled);
Console.WriteLine("averageAmountLabelIncorp= " + averageLabelsIncorporated);
}
public override void Execute(ResultCollection resultList)
{
Check.Require(resultList.CurrentTargetedResult is SipperLcmsTargetedResult, "Sipper Quantifier only works on Sipper-type result objects");
Check.Require(resultList.Run.CurrentMassTag != null, this.Name + " failed; CurrentMassTag is empty");
Check.Require(resultList.Run.CurrentMassTag.IsotopicProfile != null, this.Name + " failed; Theor isotopic profile is empty. Run a TheorFeatureGenerator");
ResetQuantifierData();
var result = (SipperLcmsTargetedResult)resultList.CurrentTargetedResult;
result.AreaUnderDifferenceCurve = -9999;
result.AreaUnderRatioCurve = -9999;
RatioVals.Xvalues = new double[] { 1, 2, 3, 4, 5, 6, 7 };
RatioVals.Yvalues = new double[] { 0, 0, 0, 0, 0, 0, 0 };
ChromatogramRSquaredVals.Clear();
FitScoreData.Clear();
Check.Require(result != null, "No MassTagResult has been generated for CurrentMassTag");
if (result.IsotopicProfile == null || result.IsotopicProfile.Peaklist == null || result.IsotopicProfile.Peaklist.Count < 2)
{
return;
}
var theorUnlabelledIso = resultList.Run.CurrentMassTag.IsotopicProfile.CloneIsotopicProfile();
IsotopicProfileUtilities.NormalizeIsotopicProfile(theorUnlabelledIso);
//PeakUtilities.TrimIsotopicProfile(unlabeledIso, 0.001);
var indexOfCorrespondingObservedPeak = PeakUtilities.getIndexOfClosestValue(result.IsotopicProfile.Peaklist,
theorUnlabelledIso.getMostIntensePeak().XValue, 0, result.IsotopicProfile.Peaklist.Count - 1, 0.1);
NormalizedIso = result.IsotopicProfile.CloneIsotopicProfile();
if (indexOfCorrespondingObservedPeak >= 0)
{
IsotopicProfileUtilities.NormalizeIsotopicProfileToSpecificPeak(NormalizedIso, indexOfCorrespondingObservedPeak);
}
else
{
IsotopicProfileUtilities.NormalizeIsotopicProfile(NormalizedIso);
}
//insert zero intensity peaks into observed
// return;
if (result.Flags.Count > 0)
{
var flagstring = "";
foreach (var resultFlag in result.Flags)
{
flagstring += resultFlag.Description + ";";
}
result.ErrorDescription = flagstring.TrimEnd(';');
result.FailedResult = true;
if (flagstring.Contains("PeakToTheLeft"))
{
result.FailureType = Globals.TargetedResultFailureType.DeisotopingProblemDetected;
}
else
{
result.FailureType = Globals.TargetedResultFailureType.QuantifierFailure;
}
}
var resultPassesMinimalCriteria = (result.Score < MaximumFitScoreForFurtherProcessing && result.Flags.Count == 0);
if (resultPassesMinimalCriteria)
{
//------------------------------------- Get chromatogramCorrelation data -------------------------------
if (IsChromatogramCorrelationPerformed)
{
GetChromatogramCorrelationData(result);
}
NormalizedAdjustedIso = NormalizedIso.CloneIsotopicProfile();
//this is experimental!! it attempts to correct the problems caused by Orbitraps on isotopic profile intensities
//UpdateIsoIntensitiesUsingChromCorrData(result.ChromCorrelationData, NormalizedAdjustedIso);
//----------------- create ratio data -------------------------------------------------------
var ratioData = NormalizedAdjustedIso.CloneIsotopicProfile();
for (var i = 0; i < NormalizedIso.Peaklist.Count; i++)
{
if (i < theorUnlabelledIso.Peaklist.Count && theorUnlabelledIso.Peaklist[i].Height > MinimumRelativeIntensityForRatioCalc)
{
ratioData.Peaklist[i].Height = (NormalizedIso.Peaklist[i].Height / theorUnlabelledIso.Peaklist[i].Height - 1);
}
else
{
ratioData.Peaklist[i].Height = 0;
}
}
//trim off zeros from ratio data
for (var i = ratioData.Peaklist.Count - 1; i >= 0; i--)
{
if (ratioData.Peaklist[i].Height == 0)
{
ratioData.Peaklist.RemoveAt(i);
}
else
{
break;
}
}
var xvals = ratioData.Peaklist.Select((p, i) => new { peak = p, index = i }).Select(n => (double)n.index).ToList();
var yvals = ratioData.Peaklist.Select(p => (double)p.Height).ToList();
result.AreaUnderRatioCurve = yvals.Sum();
RatioVals.Xvalues = xvals.ToArray();
RatioVals.Yvalues = yvals.ToArray();
//NOTE: Sept 23, 2013 - the 'R is no longer used.
result.RSquaredValForRatioCurve = GetLinearRegressionData(result, xvals, yvals);
//------------- subtract unlabelled profile from normalized profile ----------------------
var subtractedIsoData = NormalizedAdjustedIso.CloneIsotopicProfile();
for (var i = 0; i < subtractedIsoData.Peaklist.Count; i++)
{
float intensityTheorPeak = 0;
if (i < theorUnlabelledIso.Peaklist.Count)
{
intensityTheorPeak = theorUnlabelledIso.Peaklist[i].Height;
}
var subtractedIntensity = subtractedIsoData.Peaklist[i].Height - intensityTheorPeak;
if (subtractedIntensity < 0)
{
subtractedIntensity = 0;
}
subtractedIsoData.Peaklist[i].Height = subtractedIntensity;
}
result.AreaUnderDifferenceCurve = subtractedIsoData.Peaklist.Select(p => p.Height).Sum();
//----------- get data for the subtracted, labeled isotopic profile------------------------
var peaksForLabeledIsoQuant = new List <Peak>(subtractedIsoData.Peaklist.Where(p => p.Height > 0));
// var isoFromPartialLabelingQuantifier = _partialLabelingQuantifier.FindBestLabeledProfile(result.Target, peaksForLabeledIsoQuant);
//FitScoreData = _partialLabelingQuantifier.FitScoreData;
//result.FitScoreLabeledProfile = isoFromPartialLabelingQuantifier.IsotopicProfile == null ? 1.00d : isoFromPartialLabelingQuantifier.IsotopicProfile.Score;
//result.PercentCarbonsLabelled = isoFromPartialLabelingQuantifier.PercentLabeling;
//int numCarbons = result.Target.GetAtomCountForElement("C");
//result.NumCarbonsLabelled = result.PercentCarbonsLabelled * numCarbons / 100;
//StringBuilder sb = new StringBuilder();
//sb.Append(result.Target.ID + "\t" + result.Target.MZ.ToString("0.0000") + "\t" + result.Target.ChargeState +
// "-----------------------------\n");
//int counter = 0;
//foreach (var fsData in _partialLabelingQuantifier.FitScoreData)
//{
// sb.Append(fsData.Key + "\t" + fsData.Value.ToString("0.000") + "\n");
// counter++;
//}
//Console.WriteLine(sb.ToString());
//-------------- make calculations using inputs from chrom correlation data -------------------
HighQualitySubtractedProfile = GetIsoDataPassingChromCorrelation(result.ChromCorrelationData, subtractedIsoData);
var contiguousnessScore = GetContiguousnessScore(HighQualitySubtractedProfile);
result.ContiguousnessScore = contiguousnessScore;
//GORD ------------- note this section is a duplicate of the above.... choose one or the other ------------------------
//Feb 26, 2013... I processed the results and these look really good. ROC curve nice
peaksForLabeledIsoQuant = new List <Peak>(HighQualitySubtractedProfile.Peaklist.Where(p => p.Height > 0));
//calculate labeled fit score
var isoFromPartialLabelingQuantifier = _partialLabelingQuantifier.FindBestLabeledProfile(result.Target, peaksForLabeledIsoQuant);
FitScoreData = _partialLabelingQuantifier.FitScoreData;
result.FitScoreLabeledProfile = isoFromPartialLabelingQuantifier.IsotopicProfile == null ? 1.00d : isoFromPartialLabelingQuantifier.IsotopicProfile.Score;
result.PercentCarbonsLabelled = isoFromPartialLabelingQuantifier.PercentLabeling;
var numCarbons = result.Target.GetAtomCountForElement("C");
result.NumCarbonsLabelled = result.PercentCarbonsLabelled * numCarbons / 100;
//end of section --------------------------------------------------------------------------
//-------------- calculate Label Distribution ------------------------------------------------
// see Chik et al: http://pubs.acs.org/doi/abs/10.1021/ac050988l ; Also see Sipper paper.
double[] numLabelVals;
double[] labelDistributionVals;
var theorIntensityVals = theorUnlabelledIso.Peaklist.Select(p => (double)p.Height).ToList();
if (isoFromPartialLabelingQuantifier.IsotopicProfile != null)
{
var normalizedCorrectedIntensityVals = NormalizedAdjustedIso.Peaklist.Select(p => (double)p.Height).ToList();
var numRightPads = 3;
_labelingDistributionCalculator.CalculateLabelingDistribution(theorIntensityVals, normalizedCorrectedIntensityVals,
LabeldistCalcIntensityThreshold,
LabeldistCalcIntensityThreshold,
out numLabelVals,
out labelDistributionVals, true, true, 0, numRightPads, 0, 0);
//negative distribution values are zeroed out. And, then the remaining values are adjusted such that they add up to 1.
result.LabelDistributionVals = AdjustLabelDistributionVals(labelDistributionVals);
double distFractionUnlabelled, distFractionLabelled, distAverageLabelsIncorporated;
_labelingDistributionCalculator.OutputLabelingInfo(result.LabelDistributionVals, out distFractionUnlabelled,
out distFractionLabelled,
out distAverageLabelsIncorporated);
result.PercentPeptideLabelled = distFractionLabelled * 100;
}
else
{
result.PercentCarbonsLabelled = 0;
}
var highQualityRatioProfileData = GetIsoDataPassingChromCorrelation(result.ChromCorrelationData, ratioData);
if (highQualityRatioProfileData.Peaklist != null && highQualityRatioProfileData.Peaklist.Count > 0)
{
result.AreaUnderDifferenceCurve = HighQualitySubtractedProfile.Peaklist.Select(p => p.Height).Sum();
}
else
{
result.AreaUnderDifferenceCurve = 0;
}
if (HighQualitySubtractedProfile.Peaklist != null && HighQualitySubtractedProfile.Peaklist.Count > 0)
{
result.AreaUnderRatioCurveRevised = highQualityRatioProfileData.Peaklist.Select(p => p.Height).Sum();
}
else
{
result.AreaUnderRatioCurveRevised = 0;
}
result.NumHighQualityProfilePeaks = highQualityRatioProfileData.Peaklist != null
? highQualityRatioProfileData.Peaklist.Count
: 0;
}
else
{
result.FailedResult = true;
if (result.FailureType == Globals.TargetedResultFailureType.None)
{
result.FailureType = Globals.TargetedResultFailureType.MinimalCriteriaNotMet;
}
}
}