protected override Results.TargetedResultDTO ConvertTextToDataObject(List <string> processedData)
{
var result = new SipperLcmsFeatureTargetedResultDTO();
result.DatasetName = LookupData(processedData, datasetHeaders);
if (result.DatasetName == "-1")
{
result.DatasetName = TryGetDatasetNameFromFileName();
}
GetBasicResultDTOData(processedData, result);
result.AreaUnderDifferenceCurve = ParseDoubleField(LookupData(processedData, _areaUnderDiffCurveHeaders));
result.AreaUnderRatioCurve = ParseDoubleField(LookupData(processedData, _areaUnderRatioCurveHeaders));
result.AreaUnderRatioCurveRevised = ParseDoubleField(LookupData(processedData, _areaUnderRatioRevisedHeaders));
result.MatchedMassTagID = ParseIntField(LookupData(processedData, matchedMassTagIDHeaders));
result.ChromCorrelationMin = ParseDoubleField(LookupData(processedData, _chromCorrMinHeaders));
result.ChromCorrelationMax = ParseDoubleField(LookupData(processedData, _chromCorrMaxHeaders));
result.ChromCorrelationAverage = ParseDoubleField(LookupData(processedData, _chromCorrAverageHeaders));
result.ChromCorrelationMedian = ParseDoubleField(LookupData(processedData, _chromCorrMedianHeaders));
result.ChromCorrelationStdev = ParseDoubleField(LookupData(processedData, _chromCorrStdevHeaders));
result.PercentPeptideLabelled = ParseDoubleField(LookupData(processedData, _percentPeptidesLabelledHeaders));
result.NumCarbonsLabelled = ParseDoubleField(LookupData(processedData, _numCarbonsLabelledHeaders));
result.PercentCarbonsLabelled = ParseDoubleField(LookupData(processedData, _percentCarbonsLabelledHeaders));
result.NumHighQualityProfilePeaks = ParseIntField(LookupData(processedData, _numHQProfilePeaksHeaders));
result.LabelDistributionVals = ConvertLabelDistStringToArray(LookupData(processedData, _labelDistribHeaders));
result.FitScoreLabeledProfile = ParseDoubleField(LookupData(processedData, _fitScoreLabeledHeaders));
result.ContiguousnessScore = ParseIntField(LookupData(processedData, _contigScoreHeaders));
result.RSquaredValForRatioCurve = ParseDoubleField(LookupData(processedData, _RSquaredForRatio));
return(result);
}
public static void ApplyFilteringScheme2(SipperLcmsFeatureTargetedResultDTO result)
{
if (result.AreaUnderRatioCurveRevised > 0)
{
if (result.ChromCorrelationAverage > 0.85 && result.ChromCorrelationMedian > 0.9)
{
if (result.RSquaredValForRatioCurve > 0.85)
{
//high quality results
if (result.RSquaredValForRatioCurve > 0.95 && result.AreaUnderRatioCurve > 75)
{
if (result.IScore <= 0.4)
{
result.PassesFilter = true;
}
}
//high quality results
else if (result.RSquaredValForRatioCurve > 0.5 && result.AreaUnderRatioCurveRevised > 15)
{
if (result.IScore <= 0.4)
{
result.PassesFilter = true;
}
}
else if (result.ChromCorrelationMedian > 0.99 && result.ChromCorrelationAverage > 0.99)
{
if (result.IScore <= 0.4)
{
result.PassesFilter = true;
}
}
//high intensity results
else if (result.RSquaredValForRatioCurve > 0.95 && result.Intensity > 1e5)
{
if (result.IScore <= 0.4)
{
result.PassesFilter = true;
}
}
//all other results -
else if (result.RSquaredValForRatioCurve > 0.95 && result.IScore <= 0.25)
{
result.PassesFilter = true;
}
}
}
}
}
private string GetLabelDistributionDataAsString(SipperLcmsFeatureTargetedResultDTO sipperResult)
{
if (sipperResult.LabelDistributionVals == null || sipperResult.LabelDistributionVals.Length == 0)
{
return(string.Empty);
}
var sb = new StringBuilder();
var delim = ',';
foreach (var labelDistributionVal in sipperResult.LabelDistributionVals)
{
sb.Append(labelDistributionVal.ToString("0.#####"));
sb.Append(delim);
}
return(sb.ToString().TrimEnd(delim));
}
private void SetCurrentWorkflowTarget(SipperLcmsFeatureTargetedResultDTO result)
{
TargetBase target = new LcmsFeatureTarget();
target.ChargeState = (short)result.ChargeState;
target.ChargeStateTargets.Add(target.ChargeState);
target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum;
target.EmpiricalFormula = result.EmpiricalFormula;
target.ID = (int)result.TargetID;
target.IsotopicProfile = null; //workflow will determine this
target.MZ = result.MonoMZ;
target.MonoIsotopicMass = result.MonoMass;
target.ScanLCTarget = result.ScanLC;
Run.CurrentMassTag = target;
}
public ResultWithImageInfo(SipperLcmsFeatureTargetedResultDTO result)
{
Result = result;
}
public static void ApplyAveragineBasedLooseFilter(SipperLcmsFeatureTargetedResultDTO result)
{
var resultList = new List<SipperLcmsFeatureTargetedResultDTO> { result };
ApplyAveragineBasedLooseFilter(resultList);
}
public static void ApplyAutoValidationCodeF2LooseFilter(SipperLcmsFeatureTargetedResultDTO result)
{
var resultList = new List<SipperLcmsFeatureTargetedResultDTO> { result };
ApplyAutoValidationCodeF2LooseFilter(resultList);
}