protected override float Calculate(PeakScoringContext context, IPeptidePeakData <ISummaryPeakData> summaryPeakData)
{
float max = float.MinValue;
foreach (var peakData in GetIncludedGroups(summaryPeakData))
{
max = Math.Max(max, (float)CalcCountScore(peakData));
}
return(max != float.MinValue ? max : float.NaN);
}
public PeptidePeakDataConverter(IPeptidePeakData <TData> peptidePeakData)
{
_peptidePeakData = peptidePeakData;
var groupPeakData = _peptidePeakData.TransitionGroupPeakData;
TransitionGroupPeakData = groupPeakData == null ? new List <ITransitionGroupPeakData <ISummaryPeakData> >()
: groupPeakData.Select(gp =>
new TransitionGroupPeakDataConverter <TData>(gp) as ITransitionGroupPeakData <ISummaryPeakData>).ToList();
AnalyteGroupPeakData = TransitionGroupPeakData.Where(t => !t.IsStandard).ToArray();
StandardGroupPeakData = TransitionGroupPeakData.Where(t => t.IsStandard).ToArray();
}
protected override float Calculate(PeakScoringContext context,
IPeptidePeakData <ISummaryPeakData> summaryPeakData)
{
var massErrors = new List <double>();
var weights = new List <double>();
bool noTransitions = true;
bool allZeroWeights = true;
foreach (var tranGroup in GetTransitionGroups(summaryPeakData))
{
foreach (var pdTran in tranGroup.TransitionPeakData)
{
if (!IsIonType(pdTran.NodeTran))
{
continue;
}
noTransitions = false;
var peakData = pdTran.PeakData;
double?massError = peakData.MassError;
if (massError.HasValue)
{
massErrors.Add(MassErrorFunction(massError.Value));
double weight = GetWeight(peakData);
weights.Add(weight);
if (weight != 0)
{
allZeroWeights = false;
}
}
}
}
// If there are no qualifying transitions, return NaN
if (noTransitions)
{
return(float.NaN);
}
// If there are qualifying tranistions but they all have null mass error,
// then return maximum possible mass error
if (massErrors.Count == 0)
{
return((float)MaximumValue(context));
}
if (allZeroWeights)
{
weights = weights.ConvertAll(weight => 1.0);
}
var massStats = new Statistics(massErrors);
var weightsStats = new Statistics(weights);
return((float)massStats.Mean(weightsStats));
}
protected override float Calculate(PeakScoringContext context, IPeptidePeakData <ISummaryPeakData> summaryPeakData)
{
foreach (var groupPeakData in summaryPeakData.TransitionGroupPeakData)
{
foreach (var peakData in groupPeakData.TransitionPeakData)
{
if (peakData.PeakData.Identified != PeakIdentification.FALSE)
{
return(1);
}
}
}
return(0);
}
protected override float Calculate(PeakScoringContext context,
IPeptidePeakData <ISummaryPeakData> summaryPeakData)
{
bool noTransitions = true;
bool allZeroWeights = true;
// Use running mean calculation to avoid allocations which show up in a profiler
double weightedMeanMassError = 0;
double totalWeight = 0;
double unweightedMeanMassError = 0;
int totalSeen = 0;
foreach (var pdTran in GetIonTypes(GetTransitionGroups(summaryPeakData)))
{
noTransitions = false;
var peakData = pdTran.PeakData;
double?massError = peakData.MassError;
if (massError.HasValue)
{
double error = MassErrorFunction(massError.Value);
double weight = GetWeight(peakData);
if (weight != 0)
{
allZeroWeights = false;
totalWeight += weight;
weightedMeanMassError += (error - weightedMeanMassError) * weight / totalWeight;
}
totalSeen++;
unweightedMeanMassError += (error - unweightedMeanMassError) / totalSeen;
}
}
// If there are no qualifying transitions, return NaN
if (noTransitions)
{
return(float.NaN);
}
// If there are qualifying tranistions but they all have null mass error,
// then return maximum possible mass error
if (totalSeen == 0)
{
return((float)MaximumValue(context));
}
if (allZeroWeights)
{
return((float)unweightedMeanMassError);
}
return((float)weightedMeanMassError);
}
protected override float Calculate(PeakScoringContext context,
IPeptidePeakData <IDetailedPeakData> summaryPeakData)
{
var tranGroupPeakDatas = GetTransitionGroups(summaryPeakData);
if (tranGroupPeakDatas.Count == 0)
{
return(float.NaN);
}
var snValues = new List <double>();
var weights = new List <double>();
foreach (var pdTran in GetIonTypes(tranGroupPeakDatas))
{
var peakData = pdTran.PeakData;
if (peakData == null || peakData.Intensities == null || peakData.Intensities.Length == 0)
{
continue;
}
double?snValue = GetSnValue(peakData);
if (snValue.HasValue)
{
snValues.Add(Math.Abs(snValue.Value));
weights.Add(GetWeight(peakData));
}
}
if (snValues.Count == 0)
{
return(float.NaN);
}
var snStats = new Statistics(snValues);
var weightsStats = new Statistics(weights);
if (weights.All(weight => weight == 0))
{
return(0);
}
return((float)snStats.Mean(weightsStats));
}
private double SummedArea(IPeptidePeakData <ISummaryPeakData> summaryPeakData, bool isStandard)
{
// Slightly verbose implementation, because simpler implementation using
// Linq showed up in a profiler.
double sumArea = 0;
foreach (var groupPd in summaryPeakData.TransitionGroupPeakData)
{
if (groupPd.IsStandard != isStandard)
{
continue;
}
foreach (var pd in groupPd.TransitionPeakData)
{
if (!pd.PeakData.IsForcedIntegration)
{
sumArea += pd.PeakData.Area;
}
}
}
return(sumArea);
}
protected override float Calculate(PeakScoringContext context, IPeptidePeakData <ISummaryPeakData> summaryPeakData)
{
return(MQuestHelpers.CalculateIdotp(context, summaryPeakData));
}
protected override IEnumerable <ITransitionGroupPeakData <TData> > GetTransitionGroups <TData>(
IPeptidePeakData <TData> summaryPeakData)
{
return(MQuestHelpers.GetAnalyteGroups(summaryPeakData));
}
protected abstract float Calculate(PeakScoringContext context, IPeptidePeakData <IDetailedPeakData> summaryPeakData);
protected override IList <ITransitionGroupPeakData <ISummaryPeakData> > GetIncludedGroups(IPeptidePeakData <ISummaryPeakData> summaryPeakData)
{
return(MQuestHelpers.GetBestAvailableGroups(summaryPeakData));
}
public void MQuestScoreEquals(IPeakFeatureCalculator calc, double score, IPeptidePeakData peptidePeakData)
{
AreCloseEnough(calc.Calculate(new PeakScoringContext(null), peptidePeakData), score);
}
protected abstract IList <ITransitionGroupPeakData <ISummaryPeakData> > GetIncludedGroups(IPeptidePeakData <ISummaryPeakData> summaryPeakData);
protected override float Calculate(PeakScoringContext context, IPeptidePeakData <ISummaryPeakData> summaryPeakData)
{
return(Score(SummedArea(summaryPeakData, false), SummedArea(summaryPeakData, true)));
}
protected abstract IList <ITransitionGroupPeakData <TData> > GetTransitionGroups <TData>(
IPeptidePeakData <TData> summaryPeakData);
protected override IList <ITransitionGroupPeakData <TData> > GetTransitionGroups <TData>(
IPeptidePeakData <TData> summaryPeakData)
{
return(MQuestHelpers.GetStandardGroups(summaryPeakData));
}
public float Calculate(PeakScoringContext context, IPeptidePeakData peakGroupData)
{
return(Calculate(context, (IPeptidePeakData <IDetailedPeakData>)peakGroupData));
}