public TransitionDocNode(Transition id,
TransitionLosses losses,
TypedMass massH,
TransitionQuantInfo quantInfo,
ExplicitTransitionValues explicitTransitionValues)
: this(id, Annotations.EMPTY, losses, massH, quantInfo, explicitTransitionValues, null)
{
}
protected bool Equals(ExplicitTransitionValues other)
{
return(Equals(CollisionEnergy, other.CollisionEnergy) &&
Equals(IonMobilityHighEnergyOffset, other.IonMobilityHighEnergyOffset) &&
Equals(SLens, other.SLens) &&
Equals(ConeVoltage, other.ConeVoltage) &&
DeclusteringPotential.Equals(other.DeclusteringPotential));
}
public ExplicitTransitionValues(ExplicitTransitionValues other)
: this(
(other == null) ? null : other.CollisionEnergy,
(other == null) ? null : other.IonMobilityHighEnergyOffset,
(other == null) ? null : other.SLens,
(other == null) ? null : other.ConeVoltage,
(other == null) ? null : other.DeclusteringPotential)
{
}
/// <summary>
/// return a new object with values set only where they differ betwwen this and other, using the values of other
/// </summary>
public ExplicitTransitionValues Diff(ExplicitTransitionValues other)
{
if (other == null || other.Equals(EMPTY))
{
return(this);
}
return(Create(Equals(other.CollisionEnergy, CollisionEnergy) ? null : other.CollisionEnergy,
Equals(other.IonMobilityHighEnergyOffset, IonMobilityHighEnergyOffset) ? null : other.IonMobilityHighEnergyOffset,
Equals(other.SLens, SLens) ? null : other.SLens,
Equals(other.ConeVoltage, ConeVoltage) ? null : other.ConeVoltage,
Equals(other.DeclusteringPotential, DeclusteringPotential) ? null : other.DeclusteringPotential));
}
/// <summary>
/// return a new object with values taken from other, only where this lacks values
/// </summary>
public ExplicitTransitionValues Merge(ExplicitTransitionValues other)
{
if (other == null || other.Equals(EMPTY))
{
return(this);
}
return(Create(CollisionEnergy.HasValue ? CollisionEnergy : other.CollisionEnergy,
IonMobilityHighEnergyOffset.HasValue ? IonMobilityHighEnergyOffset : other.IonMobilityHighEnergyOffset,
SLens.HasValue ? SLens : other.SLens,
ConeVoltage.HasValue ? ConeVoltage : other.ConeVoltage,
DeclusteringPotential.HasValue ? DeclusteringPotential : other.DeclusteringPotential));
}
public TransitionDocNode(Transition id,
Annotations annotations,
TransitionLosses losses,
TypedMass mass,
TransitionQuantInfo transitionQuantInfo,
ExplicitTransitionValues explicitTransitionValues,
Results <TransitionChromInfo> results)
: base(id, annotations)
{
Losses = losses;
if (losses != null)
{
mass -= losses.Mass;
}
Mz = id.IsCustom() ?
new SignedMz(id.Adduct.MzFromNeutralMass(mass), id.IsNegative()) :
new SignedMz(SequenceMassCalc.GetMZ(mass, id.Adduct) + SequenceMassCalc.GetPeptideInterval(id.DecoyMassShift), id.IsNegative());
MzMassType = mass.MassType;
IsotopeDistInfo = transitionQuantInfo.IsotopeDistInfo;
LibInfo = transitionQuantInfo.LibInfo;
Results = results;
ExplicitQuantitative = transitionQuantInfo.Quantititative;
ExplicitValues = explicitTransitionValues ?? ExplicitTransitionValues.EMPTY;
}
public TransitionDocNode ChangeExplicitValues(ExplicitTransitionValues prop)
{
return(ChangeProp(ImClone(this), im => im.ExplicitValues = 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));
}
