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); } }