Exemplo n.º 1
0
        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;
                        }

                    }
                }

            }
        }
Exemplo n.º 3
0
        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;
 }
Exemplo n.º 6
0
 public static void ApplyAveragineBasedLooseFilter(SipperLcmsFeatureTargetedResultDTO result)
 {
     var resultList = new List<SipperLcmsFeatureTargetedResultDTO> { result };
     ApplyAveragineBasedLooseFilter(resultList);
 }
Exemplo n.º 7
0
 public static void ApplyAutoValidationCodeF2LooseFilter(SipperLcmsFeatureTargetedResultDTO result)
 {
     var resultList = new List<SipperLcmsFeatureTargetedResultDTO> { result };
     ApplyAutoValidationCodeF2LooseFilter(resultList);
 }