private clsUMC convertDeconToolsTargetedFeatureToUMC(TargetedResultDTO result)
{
var umc = new clsUMC();
umc.AbundanceMax = result.Intensity;
umc.AbundanceSum = (long)result.Intensity;
umc.AverageDeconFitScore = result.FitScore;
umc.AverageInterferenceScore = result.IScore;
umc.ChargeMax = result.ChargeState;
umc.ChargeRepresentative = (short)result.ChargeState;
umc.ClusterId = 0;
umc.CombinedScore = 0;
umc.ConformationFitScore = 0;
umc.ConformationId = 0;
umc.DatasetId = 0;
umc.DriftTime = 0;
umc.DriftTimeUncorrected = 0;
umc.Id = (int)result.TargetID;
umc.Mass = result.MonoMass;
umc.MZForCharge = result.MonoMZ;
umc.Net = result.NET;
umc.Scan = result.ScanLC;
umc.ScanStart = result.ScanLCStart;
umc.ScanEnd = result.ScanLCEnd;
umc.SpectralCount = 0;
return(umc);
}
protected override string addAdditionalInfo(TargetedResultDTO result)
{
var o16o18result = (O16O18TargetedResultDTO)result;
var sb = new StringBuilder();
sb.Append(Delimiter);
sb.Append(o16o18result.IntensityTheorI0);
sb.Append(Delimiter);
sb.Append(o16o18result.IntensityTheorI2);
sb.Append(Delimiter);
sb.Append(o16o18result.IntensityTheorI4);
sb.Append(Delimiter);
sb.Append(o16o18result.IntensityI0);
sb.Append(Delimiter);
sb.Append(o16o18result.IntensityI2);
sb.Append(Delimiter);
sb.Append(o16o18result.IntensityI4);
sb.Append(Delimiter);
sb.Append(o16o18result.IntensityI4Adjusted);
sb.Append(Delimiter);
sb.Append(o16o18result.ChromCorrO16O18SingleLabel.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(o16o18result.ChromCorrO16O18DoubleLabel.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(o16o18result.Ratio.ToString("0.0000"));
sb.Append(Delimiter);
sb.Append(o16o18result.RatioFromChromCorr.ToString("0.0000"));
return(sb.ToString());
}
protected override string addAdditionalInfo(TargetedResultDTO result)
{
var deuteratedResult = (DeuteratedTargetedResultDTO)result;
var sb = new StringBuilder();
sb.Append(Delimiter);
sb.Append(deuteratedResult.HydrogenI0);
sb.Append(Delimiter);
sb.Append(deuteratedResult.HydrogenI1);
sb.Append(Delimiter);
sb.Append(deuteratedResult.HydrogenI2);
sb.Append(Delimiter);
sb.Append(deuteratedResult.HydrogenI3);
sb.Append(Delimiter);
sb.Append(deuteratedResult.HydrogenI4);
sb.Append(Delimiter);
sb.Append(0);
sb.Append(Delimiter);
sb.Append(deuteratedResult.DeuteriumI0);
sb.Append(Delimiter);
sb.Append(deuteratedResult.DeuteriumI1);
sb.Append(Delimiter);
sb.Append(deuteratedResult.DeuteriumI2);
sb.Append(Delimiter);
sb.Append(deuteratedResult.DeuteriumI3);
sb.Append(Delimiter);
sb.Append(deuteratedResult.DeuteriumI4);
sb.Append(Delimiter);
sb.Append(deuteratedResult.TheoryI0);
sb.Append(Delimiter);
sb.Append(deuteratedResult.TheoryI1);
sb.Append(Delimiter);
sb.Append(deuteratedResult.TheoryI2);
sb.Append(Delimiter);
sb.Append(deuteratedResult.TheoryI3);
sb.Append(Delimiter);
sb.Append(deuteratedResult.TheoryI4);
sb.Append(Delimiter);
sb.Append(deuteratedResult.RawI0);
sb.Append(Delimiter);
sb.Append(deuteratedResult.RawI1);
sb.Append(Delimiter);
sb.Append(deuteratedResult.RawI2);
sb.Append(Delimiter);
sb.Append(deuteratedResult.RawI3);
sb.Append(Delimiter);
sb.Append(deuteratedResult.RawI4);
sb.Append(Delimiter);
sb.Append(deuteratedResult.LabelingEfficiency);
sb.Append(Delimiter);
sb.Append(deuteratedResult.RatioDH.ToString("0.0000"));
return(sb.ToString());
}
protected override string addBasicTargetedResult(TargetedResultDTO result)
{
var topDownResult = (TopDownTargetedResultDTO)result;
if (topDownResult.PrsmList == null)
{
throw new NullReferenceException(
"Top down exporter failed when trying to process a result. The 'PrsmList' object is null.");
}
var sb = new StringBuilder();
var prsmList = new StringBuilder();
foreach (var prsm in topDownResult.PrsmList)
{
if (prsmList.Length > 0)
{
prsmList.Append(", ");
}
prsmList.Append(prsm);
}
var chargeList = new StringBuilder();
foreach (var charge in topDownResult.ChargeStateList)
{
if (chargeList.Length > 0)
{
chargeList.Append(", ");
}
chargeList.Append(charge);
}
sb.Append(topDownResult.MatchedMassTagID);
sb.Append(Delimiter);
sb.Append(prsmList.ToString());
sb.Append(Delimiter);
sb.Append(chargeList.ToString());
sb.Append(Delimiter);
sb.Append(topDownResult.ProteinName);
sb.Append(Delimiter);
sb.Append(topDownResult.ProteinMass);
sb.Append(Delimiter);
sb.Append(topDownResult.PeptideSequence);
sb.Append(Delimiter);
sb.Append(topDownResult.EmpiricalFormula);
sb.Append(Delimiter);
sb.Append(topDownResult.Quantitation);
sb.Append(Delimiter);
sb.Append(topDownResult.MostAbundantChargeState);
sb.Append(Delimiter);
sb.Append(topDownResult.ScanLC);
return(sb.ToString());
}
protected virtual void GetBasicResultDTOData(List <string> rowData, TargetedResultDTO result)
{
result.DatasetName = LookupData(rowData, datasetHeaders);
result.ChargeState = ParseIntField(LookupData(rowData, chargeStateHeaders));
result.FitScore = ParseFloatField(LookupData(rowData, fitScoreHeaders));
result.Intensity = ParseFloatField(LookupData(rowData, intensityRepHeaders));
result.IntensityI0 = ParseFloatField(LookupData(rowData, intensityI0Headers));
result.IScore = ParseFloatField(LookupData(rowData, iscoreHeaders));
result.TargetID = ParseLongField(LookupData(rowData, targetIDHeaders));
result.MonoMass = ParseDoubleField(LookupData(rowData, monomassHeaders));
result.MonoMassCalibrated = ParseDoubleField(LookupData(rowData, monomassCalibratedHeaders));
result.MassErrorBeforeCalibration = ParseDoubleField(LookupData(rowData, massErrorBeforeCalibrationHeaders));
result.MassErrorAfterCalibration = ParseDoubleField(LookupData(rowData, massErrorAfterCalibrationHeaders));
result.MonoMZ = ParseDoubleField(LookupData(rowData, mzHeaders));
result.NET = ParseFloatField(LookupData(rowData, netHeaders));
result.NETError = ParseFloatField(LookupData(rowData, netErrorHeaders));
result.NumChromPeaksWithinTol = ParseIntField(LookupData(rowData, numchromPeaksWithinTolHeaders));
result.NumQualityChromPeaksWithinTol = ParseIntField(LookupData(rowData, numQualitychromPeaksWithinTolHeaders));
result.ScanLC = ParseIntField(LookupData(rowData, scanHeaders));
result.ScanLCEnd = ParseIntField(LookupData(rowData, scanEndHeaders));
result.ScanLCStart = ParseIntField(LookupData(rowData, scanStartHeaders));
result.ErrorDescription = LookupData(rowData, failureTypeHeaders);
result.EmpiricalFormula = LookupData(rowData, empiricalFormulaHeaders);
result.Code = LookupData(rowData, codeHeaders);
var validationCode = LookupData(rowData, validationCodeHeaders);
if (String.IsNullOrEmpty(validationCode))
{
result.ValidationCode = ValidationCode.None;
}
else
{
if (Enum.IsDefined(typeof(ValidationCode), validationCode))
{
result.ValidationCode = (ValidationCode)Enum.Parse(typeof(ValidationCode), validationCode, true);
}
else
{
result.ValidationCode = ValidationCode.None;
}
}
}
protected override string addAdditionalInfo(TargetedResultDTO result)
{
var sipperResult = (SipperLcmsFeatureTargetedResultDTO)result;
var sb = new StringBuilder();
sb.Append(Delimiter);
sb.Append(sipperResult.MatchedMassTagID);
sb.Append(Delimiter);
sb.Append(sipperResult.NumHighQualityProfilePeaks.ToString("0"));
sb.Append(Delimiter);
sb.Append(sipperResult.FitScoreLabeledProfile.ToString("0.0000"));
sb.Append(Delimiter);
sb.Append(sipperResult.AreaUnderDifferenceCurve.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(sipperResult.AreaUnderRatioCurve.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(sipperResult.AreaUnderRatioCurveRevised.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(sipperResult.ChromCorrelationMin.ToString("0.00000"));
sb.Append(Delimiter);
sb.Append(sipperResult.ChromCorrelationMax.ToString("0.00000"));
sb.Append(Delimiter);
sb.Append(sipperResult.ChromCorrelationAverage.ToString("0.00000"));
sb.Append(Delimiter);
sb.Append(sipperResult.ChromCorrelationMedian.ToString("0.00000"));
sb.Append(Delimiter);
sb.Append(sipperResult.ChromCorrelationStdev.ToString("0.00000"));
sb.Append(Delimiter);
sb.Append(sipperResult.NumCarbonsLabelled.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(sipperResult.PercentCarbonsLabelled.ToString("0.00"));
sb.Append(Delimiter);
sb.Append(sipperResult.PercentPeptideLabelled.ToString("0.00"));
sb.Append(Delimiter);
sb.Append(sipperResult.ContiguousnessScore.ToString("0"));
sb.Append(Delimiter);
sb.Append(sipperResult.RSquaredValForRatioCurve.ToString("0.0000"));
sb.Append(Delimiter);
//sb.Append(GetLabelDistributionDataAsString(sipperResult));
//sb.Append(Delimiter);
sb.Append(sipperResult.ValidationCode == ValidationCode.None ? string.Empty : sipperResult.ValidationCode.ToString());
return(sb.ToString());
}
private void SetCurrentWorkflowTarget(TargetedResultDTO result)
{
TargetBase target = new LcmsFeatureTarget();
target.ChargeState = (short)result.ChargeState;
target.ChargeStateTargets.Add(target.ChargeState);
target.ElutionTimeUnit = DeconTools.Backend.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;
}
protected override string addAdditionalInfo(TargetedResultDTO result)
{
var n14result = (N14N15TargetedResultDTO)result;
var sb = new StringBuilder();
sb.Append(Delimiter);
sb.Append(n14result.ScanN15);
sb.Append(Delimiter);
sb.Append(n14result.ScanN15Start);
sb.Append(Delimiter);
sb.Append(n14result.ScanN15End);
sb.Append(Delimiter);
sb.Append(n14result.NETN15);
sb.Append(Delimiter);
sb.Append(n14result.NumChromPeaksWithinTolN15);
sb.Append(Delimiter);
sb.Append(n14result.NumQualityChromPeaksWithinTolN15);
sb.Append(Delimiter);
sb.Append(n14result.MonoMassN15);
sb.Append(Delimiter);
sb.Append(n14result.MonoMassCalibratedN15);
sb.Append(Delimiter);
sb.Append(n14result.MonoMZN15);
sb.Append(Delimiter);
sb.Append(n14result.IntensityN15);
sb.Append(Delimiter);
sb.Append(n14result.FitScoreN15);
sb.Append(Delimiter);
sb.Append(n14result.IScoreN15);
sb.Append(Delimiter);
sb.Append(n14result.RatioContributionN14);
sb.Append(Delimiter);
sb.Append(n14result.RatioContributionN15);
sb.Append(Delimiter);
sb.Append(n14result.Ratio);
return(sb.ToString());
}
private void ReadResultsFromDB(List <TargetedResultDTO> results, DbDataReader reader)
{
while (reader.Read())
{
var result = new TargetedResultDTO();
result.DatasetName = readString(reader, "Dataset");
result.TargetID = readInt(reader, "UMC_Ind");
result.MatchedMassTagID = readInt(reader, "Mass_Tag_ID");
result.FailureType = "";
//result.FitScore = readFloat(reader,"
result.IndexOfMostAbundantPeak = -1;
result.ChargeState = readInt(reader, "Class_Stats_Charge_Basis");
result.Intensity = readFloat(reader, "Class_Abundance");
result.IntensityI0 = result.Intensity;
result.IntensityMostAbundantPeak = result.Intensity;
result.IScore = 0;
result.MassErrorBeforeCalibration = readFloat(reader, "MassErrorPPM");
result.MonoMass = readDouble(reader, "Class_Mass");
result.MonoMassCalibrated = result.MonoMass;
result.MonoMZ = result.MonoMass / result.ChargeState + 1.00727649;
result.NET = readFloat(reader, "ElutionTime");
result.NETError = readFloat(reader, "NET_Error");
result.NumChromPeaksWithinTol = 1;
result.NumQualityChromPeaksWithinTol = 1;
result.ScanLC = readInt(reader, "Scan_Max_Abundance");
result.ScanLCStart = readInt(reader, "Scan_First");
result.ScanLCEnd = readInt(reader, "Scan_Last");
results.Add(result);
}
}
public override void Execute()
{
if (string.IsNullOrEmpty(ExecutorParameters.TargetsFilePath))
{
throw new ApplicationException("Processing failed. TargetsFilePath is empty. Check your parameter file.");
}
if (!File.Exists(ExecutorParameters.TargetsFilePath))
{
throw new FileNotFoundException("File not found error for the TargetsFilePath. Check your parameter file for " + ExecutorParameters.TargetsFilePath);
}
TargetedResultFromTextImporter resultImporter = new UnlabelledTargetedResultFromTextImporter(ExecutorParameters.TargetsFilePath);
var allresults = resultImporter.Import();
var resultsSortedByDataset = allresults.Results.OrderBy(p => p.DatasetName);
var totalResults = resultsSortedByDataset.Count();
ResultRepository.Clear();
//iterate over results
var resultCounter = 0;
foreach (var result in resultsSortedByDataset)
{
resultCounter++;
_currentResult = result;
if (result.DatasetName != _currentDatasetName)
{
if (Run != null)
{
Run.Close();
}
InitializeRun(result.DatasetName);
if (Run == null)
{
throw new ApplicationException("Error initializing dataset. (Run is null)");
}
_currentDatasetName = Run.DatasetName;
}
SetCurrentWorkflowTarget(result);
try
{
this.TargetedWorkflow.Execute();
ResultRepository.AddResult(this.TargetedWorkflow.Result);
}
catch (Exception ex)
{
var errorString = "Error on MT\t" + result.TargetID + "\tchargeState\t" + result.ChargeState + "\t" + ex.Message + "\t" + ex.StackTrace;
ReportProcessingProgress(errorString, resultCounter);
throw;
}
var progressString = "Processed " + resultCounter + " of " + totalResults;
if (_backgroundWorker != null)
{
if (_backgroundWorker.CancellationPending)
{
return;
}
}
ReportProcessingProgress(progressString, resultCounter);
}
}
