public TransitionDocNode(Transition id, Annotations annotations, TransitionLosses losses, double massH, TransitionIsotopeDistInfo isotopeDistInfo, TransitionLibInfo libInfo, Results <TransitionChromInfo> results) : base(id, annotations) { Losses = losses; if (losses != null) { massH -= losses.Mass; } if (id.IsCustom()) { Mz = new SignedMz(BioMassCalc.CalculateIonMz(massH, id.Charge), id.IsNegative()); } else { Mz = new SignedMz(SequenceMassCalc.GetMZ(massH, id.Charge) + SequenceMassCalc.GetPeptideInterval(id.DecoyMassShift), id.IsNegative()); } IsotopeDistInfo = isotopeDistInfo; LibInfo = libInfo; Results = results; }
public TransitionQuantInfo ChangeLibInfo(TransitionLibInfo libInfo) { var quantInfo = this; quantInfo.LibInfo = libInfo; return(quantInfo); }
public TransitionQuantInfo(TransitionIsotopeDistInfo isotopeDistInfo, TransitionLibInfo libInfo, bool quantitative) : this() { IsotopeDistInfo = isotopeDistInfo; LibInfo = libInfo; Quantititative = quantitative; }
public TransitionDocNode(Transition id, TransitionLosses losses, double massH, TransitionIsotopeDistInfo isotopeDistInfo, TransitionLibInfo libInfo) : this(id, Annotations.EMPTY, losses, massH, isotopeDistInfo, libInfo, null) { }
public static TransitionQuantInfo GetLibTransitionQuantInfo(Transition transition, TransitionLosses losses, TypedMass massH, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> ranks) { LibraryRankedSpectrumInfo.RankedMI rmi = null; if (ranks != null) { ranks.TryGetValue(SequenceMassCalc.GetMZ(massH, transition.Adduct), out rmi); } TransitionLibInfo transitionLibInfo = null; if (rmi != null) { transitionLibInfo = new TransitionLibInfo(rmi.Rank, rmi.Intensity); } return(new TransitionQuantInfo(null, transitionLibInfo, rmi == null || rmi.Quantitative)); }
public TransitionDocNode ChangeLibInfo(TransitionLibInfo prop) { return(ChangeProp(ImClone(this), im => im.LibInfo = prop)); }
public static TransitionDocNode FromTransitionProto(AnnotationScrubber scrubber, SrmSettings settings, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues, SkylineDocumentProto.Types.Transition transitionProto) { var stringPool = scrubber.StringPool; IonType ionType = DataValues.FromIonType(transitionProto.FragmentType); MeasuredIon measuredIon = null; if (transitionProto.MeasuredIonName != null) { measuredIon = settings.TransitionSettings.Filter.MeasuredIons.SingleOrDefault( i => i.Name.Equals(transitionProto.MeasuredIonName.Value)); if (measuredIon == null) { throw new InvalidDataException(string.Format(Resources.TransitionInfo_ReadXmlAttributes_The_reporter_ion__0__was_not_found_in_the_transition_filter_settings_, transitionProto.MeasuredIonName)); } ionType = IonType.custom; } bool isCustom = Transition.IsCustom(ionType, group); bool isPrecursor = Transition.IsPrecursor(ionType); CustomMolecule customIon = null; if (isCustom) { if (measuredIon != null) { customIon = measuredIon.SettingsCustomIon; } else if (isPrecursor) { customIon = group.CustomMolecule; } else { var formula = DataValues.FromOptional(transitionProto.Formula); var moleculeID = MoleculeAccessionNumbers.FromString(DataValues.FromOptional(transitionProto.MoleculeId)); // Tab separated list of InChiKey, CAS etc var monoMassH = DataValues.FromOptional(transitionProto.MonoMassH); var averageMassH = DataValues.FromOptional(transitionProto.AverageMassH); var monoMass = DataValues.FromOptional(transitionProto.MonoMass) ?? monoMassH; var averageMass = DataValues.FromOptional(transitionProto.AverageMass) ?? averageMassH; customIon = new CustomMolecule(formula, new TypedMass(monoMass.Value, monoMassH.HasValue ? MassType.MonoisotopicMassH : MassType.Monoisotopic), new TypedMass(averageMass.Value, averageMassH.HasValue ? MassType.AverageMassH : MassType.Average), DataValues.FromOptional(transitionProto.CustomIonName), moleculeID); } } Transition transition; var adductString = DataValues.FromOptional(transitionProto.Adduct); var adduct = string.IsNullOrEmpty(adductString) ? Adduct.FromChargeProtonated(transitionProto.Charge) : Adduct.FromStringAssumeChargeOnly(adductString); if (isCustom) { transition = new Transition(group, isPrecursor ? group.PrecursorAdduct :adduct, transitionProto.MassIndex, customIon, ionType); } else if (isPrecursor) { transition = new Transition(group, ionType, group.Peptide.Length - 1, transitionProto.MassIndex, group.PrecursorAdduct, DataValues.FromOptional(transitionProto.DecoyMassShift)); } else { int offset = Transition.OrdinalToOffset(ionType, transitionProto.FragmentOrdinal, group.Peptide.Length); transition = new Transition(group, ionType, offset, transitionProto.MassIndex, adduct, DataValues.FromOptional(transitionProto.DecoyMassShift)); } var losses = TransitionLosses.FromLossProtos(settings, transitionProto.Losses); var mass = settings.GetFragmentMass(group, mods, transition, isotopeDist); var isotopeDistInfo = GetIsotopeDistInfo(transition, losses, isotopeDist); if (group.DecoyMassShift.HasValue && transitionProto.DecoyMassShift == null) { throw new InvalidDataException(Resources.SrmDocument_ReadTransitionXml_All_transitions_of_decoy_precursors_must_have_a_decoy_mass_shift); } TransitionLibInfo libInfo = null; if (transitionProto.LibInfo != null) { libInfo = new TransitionLibInfo(transitionProto.LibInfo.Rank, transitionProto.LibInfo.Intensity); } var annotations = scrubber.ScrubAnnotations(Annotations.FromProtoAnnotations(transitionProto.Annotations), AnnotationDef.AnnotationTarget.transition); var results = TransitionChromInfo.FromProtoTransitionResults(scrubber, settings, transitionProto.Results); var explicitTransitionValues = pre422ExplicitTransitionValues ?? ExplicitTransitionValues.Create( DataValues.FromOptional(transitionProto.ExplicitCollisionEnergy), DataValues.FromOptional(transitionProto.ExplicitIonMobilityHighEnergyOffset), DataValues.FromOptional(transitionProto.ExplicitSLens), DataValues.FromOptional(transitionProto.ExplicitConeVoltage), DataValues.FromOptional(transitionProto.ExplicitDeclusteringPotential)); return(new TransitionDocNode(transition, annotations, losses, mass, new TransitionQuantInfo(isotopeDistInfo, libInfo, !transitionProto.NotQuantitative), explicitTransitionValues, results)); }