private static void addAdditionalInfo(TargetedResultDTO tr, DeuteratedTargetedResultObject result)
{
var r = (DeuteratedTargetedResultDTO)tr;
r.HydrogenI0 = result.HydrogenI0;
r.HydrogenI1 = result.HydrogenI1;
r.HydrogenI2 = result.HydrogenI2;
r.HydrogenI3 = result.HydrogenI3;
r.HydrogenI4 = result.HydrogenI4;
r.DeuteriumI0 = result.DeuteriumI0;
r.DeuteriumI1 = result.DeuteriumI1;
r.DeuteriumI2 = result.DeuteriumI2;
r.DeuteriumI3 = result.DeuteriumI3;
r.DeuteriumI4 = result.DeuteriumI4;
r.TheoryI0 = result.TheoryI0;
r.TheoryI1 = result.TheoryI1;
r.TheoryI2 = result.TheoryI2;
r.TheoryI3 = result.TheoryI3;
r.TheoryI4 = result.TheoryI4;
r.RawI0 = result.RawI0;
r.RawI1 = result.RawI1;
r.RawI2 = result.RawI2;
r.RawI3 = result.RawI3;
r.RawI4 = result.RawI4;
r.LabelingEfficiency = result.LabelingEfficiency;
r.RatioDH = result.RatioDH;
r.IntensityI0HydrogenMono = result.IntensityI0HydrogenMono;
r.IndegratedLcAbundance = result.IndegratedLcAbundance;
}
private static void addAdditionalInfo(TargetedResultDTO tr, N14N15_TResult result)
{
var r = tr as N14N15TargetedResultDTO;
r.FitScoreN15 = (float)result.ScoreN15;
r.IScoreN15 = (float)result.InterferenceScoreN15;
r.IntensityN15 = result.IsotopicProfileLabeled == null ? 0f : (float)result.IntensityAggregate;
r.MonoMZN15 = result.IsotopicProfileLabeled == null ? 0 : result.IsotopicProfileLabeled.MonoPeakMZ;
r.MonoMassCalibratedN15 = result.IsotopicProfileLabeled == null ? 0d : -1 * ((result.Target.IsotopicProfileLabelled.MonoIsotopicMass * tr.MassErrorBeforeCalibration / 1e6) -
result.Target.IsotopicProfileLabelled.MonoIsotopicMass); // massError= (theorMZ-alignedObsMZ)/theorMZ * 1e6
r.MonoMassN15 = result.IsotopicProfileLabeled == null ? 0 : result.IsotopicProfileLabeled.MonoIsotopicMass;
r.NETN15 = (float)result.GetNETN15();
r.NumChromPeaksWithinTolN15 = (short)result.NumChromPeaksWithinToleranceForN15Profile;
r.NumQualityChromPeaksWithinTolN15 = (short)result.NumChromPeaksWithinToleranceForN15Profile;
r.Ratio = (float)result.RatioN14N15;
r.RatioContributionN14 = (float)result.RatioContributionN14;
r.RatioContributionN15 = (float)result.RatioContributionN15;
r.ScanN15 = result.GetScanNumN15();
if (result.ChromPeakSelectedN15 != null)
{
var sigma = result.ChromPeakSelectedN15.Width / 2.35;
r.ScanN15Start = (int)Math.Round(result.ChromPeakSelectedN15.XValue - sigma);
r.ScanN15End = (int)Math.Round(result.ChromPeakSelectedN15.XValue + sigma);
}
}
public static void writeStandardInfoToResult(TargetedResultDTO tr, TargetedResultBase result)
{
if (result.Target == null)
{
throw new ArgumentNullException("Cannot create result object. MassTag is null.");
}
if (result.Run == null)
{
throw new ArgumentNullException("Cannot create result object. Run is null.");
}
tr.DatasetName = result.Run.DatasetName;
tr.TargetID = result.Target.ID;
tr.ChargeState = result.Target.ChargeState;
tr.NumMSScansSummed = result.NumMSScansSummed;
tr.EmpiricalFormula = result.Target.EmpiricalFormula;
tr.Code = result.Target.Code;
tr.IndexOfMostAbundantPeak = result.IsotopicProfile == null ? (short)0 : (short)result.IsotopicProfile.GetIndexOfMostIntensePeak();
tr.Intensity = result.IsotopicProfile == null ? 0f : (float)result.IntensityAggregate;
tr.IntensityI0 = result.IsotopicProfile == null ? 0f : (float)result.IsotopicProfile.GetMonoAbundance();
tr.IntensityMostAbundantPeak = result.IsotopicProfile == null ? 0f : (float)result.IsotopicProfile.getMostIntensePeak().Height;
tr.IScore = (float)result.InterferenceScore;
tr.MonoMass = result.IsotopicProfile == null ? result.Target.MonoIsotopicMass : result.IsotopicProfile.MonoIsotopicMass;
tr.MonoMZ = result.IsotopicProfile == null ? result.Target.MZ : result.IsotopicProfile.MonoPeakMZ;
tr.MonoMassCalibrated = result.MonoIsotopicMassCalibrated;
tr.MassErrorBeforeCalibration = result.MassErrorBeforeAlignment;
tr.MassErrorAfterCalibration = result.MassErrorAfterAlignment;
tr.ScanLC = result.GetScanNum();
tr.NET = (float)result.GetNET();
tr.NETError = result.Target.NormalizedElutionTime - tr.NET;
tr.NumChromPeaksWithinTol = result.NumChromPeaksWithinTolerance;
tr.NumQualityChromPeaksWithinTol = result.NumQualityChromPeaks;
tr.FitScore = (float)result.Score;
if (result.ChromPeakSelected != null)
{
var sigma = result.ChromPeakSelected.Width / 2.35;
tr.ScanLCStart = (int)Math.Round(result.ChromPeakSelected.XValue - sigma);
tr.ScanLCEnd = (int)Math.Round(result.ChromPeakSelected.XValue + sigma);
}
if (result.FailedResult)
{
tr.FailureType = result.FailureType.ToString();
}
tr.ErrorDescription = result.ErrorDescription ?? "";
}
private static void addAdditionalInfo(TargetedResultDTO tr, TopDownTargetedResult result)
{
var r = (TopDownTargetedResultDTO)tr;
r.PrsmList = null;
r.ChargeStateList = null;
r.Quantitation = result.ChromPeakSelected != null ? result.ChromPeakSelected.Height : 0;
r.MatchedMassTagID = ((LcmsFeatureTarget)result.Target).FeatureToMassTagID;
//r.ProteinName = "";
//r.ProteinMass = 0.0;
r.PeptideSequence = result.Target.Code;
r.MostAbundantChargeState = r.ChargeState;
r.ChromPeakSelectedHeight = result.ChromPeakSelected != null ? result.ChromPeakSelected.Height : 0;
}
private static void addAdditionalInfo(TargetedResultDTO tr, O16O18TargetedResultObject result)
{
var r = (O16O18TargetedResultDTO)tr;
r.IntensityI0 = getIntensityFromIso(result.IsotopicProfile, 0);
r.IntensityI2 = getIntensityFromIso(result.IsotopicProfile, 2);
r.IntensityI4 = getIntensityFromIso(result.IsotopicProfile, 4);
r.IntensityTheorI0 = getIntensityFromIso(result.Target.IsotopicProfile, 0);
r.IntensityTheorI2 = getIntensityFromIso(result.Target.IsotopicProfile, 2);
r.IntensityTheorI4 = getIntensityFromIso(result.Target.IsotopicProfile, 4);
r.IntensityI4Adjusted = result.IntensityI4Adjusted;
r.ChromCorrO16O18DoubleLabel = (float)(result.ChromCorrO16O18DoubleLabel ?? 0f);
r.ChromCorrO16O18SingleLabel = (float)(result.ChromCorrO16O18SingleLabel ?? 0f);
r.Ratio = result.RatioO16O18;
r.RatioFromChromCorr = result.RatioO16O18FromChromCorr;
}
private static void addAdditionalInfo(TargetedResultDTO tr, SipperLcmsTargetedResult result)
{
var r = (SipperLcmsFeatureTargetedResultDTO)tr;
r.MatchedMassTagID = ((LcmsFeatureTarget)result.Target).FeatureToMassTagID;
r.AreaUnderDifferenceCurve = result.AreaUnderDifferenceCurve;
r.AreaUnderRatioCurve = result.AreaUnderRatioCurve;
r.AreaUnderRatioCurveRevised = result.AreaUnderRatioCurveRevised;
r.ChromCorrelationMin = result.ChromCorrelationMin;
r.ChromCorrelationMax = result.ChromCorrelationMax;
r.ChromCorrelationAverage = result.ChromCorrelationAverage;
r.ChromCorrelationMedian = result.ChromCorrelationMedian;
r.ChromCorrelationStdev = result.ChromCorrelationStdev;
r.NumCarbonsLabelled = result.NumCarbonsLabelled;
r.PercentPeptideLabelled = result.PercentPeptideLabelled;
r.PercentCarbonsLabelled = result.PercentCarbonsLabelled;
r.NumHighQualityProfilePeaks = result.NumHighQualityProfilePeaks;
r.LabelDistributionVals = result.LabelDistributionVals == null ? null : result.LabelDistributionVals.ToArray();
r.FitScoreLabeledProfile = result.FitScoreLabeledProfile;
r.ContiguousnessScore = result.ContiguousnessScore;
r.RSquaredValForRatioCurve = result.RSquaredValForRatioCurve;
}
private static void addAdditionalInfo(TargetedResultDTO tr, MassTagResult massTagResult)
{
// no other info needed now
}
public static void CreateTargetedResult(TargetedResultBase result, TargetedResultDTO resultLight)
{
writeStandardInfoToResult(resultLight, result);
}