protected virtual void ReadAttributes(XmlReader reader, out Adduct embeddedAdduct)
{
var formula = reader.GetAttribute(ATTR.formula);
if (!string.IsNullOrEmpty(formula))
{
formula = BioMassCalc.AddH(formula); // Update this old style formula to current by adding the hydrogen we formerly left out due to assuming protonation
}
else
{
var text = reader.GetAttribute(ATTR.ion_formula) ?? reader.GetAttribute(ATTR.neutral_formula);
if (text != null)
{
text = text.Trim(); // We've seen some trailing spaces in the wild
}
formula = text;
}
string neutralFormula;
Molecule mol;
// We commonly see the adduct inline with the neutral formula ("C12H5[M+Na]"), so be ready to preserve that
if (IonInfo.IsFormulaWithAdduct(formula, out mol, out embeddedAdduct, out neutralFormula))
{
formula = neutralFormula;
}
else
{
embeddedAdduct = Adduct.EMPTY;
}
if (string.IsNullOrEmpty(formula))
{
AverageMass = ReadAverageMass(reader);
MonoisotopicMass = ReadMonoisotopicMass(reader);
}
Formula = formula;
Name = reader.GetAttribute(ATTR.custom_ion_name);
if (string.IsNullOrEmpty(Name))
{
Name = reader.GetAttribute(ATTR.name) ?? string.Empty;
}
AccessionNumbers = MoleculeAccessionNumbers.FromSerializableString(reader.GetAttribute(ATTR.id));
Validate();
}
public static CustomMolecule FromSerializableString(string val)
{
var tsv = MoleculeAccessionNumbers.UnescapeTabsForXML(val);
return(FromTSV(tsv));
}
public CustomMolecule(string formula, TypedMass monoisotopicMass, TypedMass averageMass, string name, MoleculeAccessionNumbers moleculeAccessionNumbers)
{
Formula = formula;
MonoisotopicMass = monoisotopicMass;
AverageMass = averageMass;
Name = name ?? string.Empty;
AccessionNumbers = moleculeAccessionNumbers ?? MoleculeAccessionNumbers.EMPTY;
Validate();
}
public CustomMolecule(TypedMass monoisotopicMass, TypedMass averageMass, string name = null, MoleculeAccessionNumbers moleculeAccessionNumbers = null)
: this(null, monoisotopicMass, averageMass, name, moleculeAccessionNumbers)
{
}
public CustomMolecule(string formula, string name = null, MoleculeAccessionNumbers moleculeAccessionNumbers = null)
: this(formula, null, null, name, moleculeAccessionNumbers)
{
}
/// <summary>
/// A simple object used to represent any molecule
/// </summary>
/// <param name="formula">The molecular formula of the molecule, possibly including an adduct description if subclassed as a CustomIon</param>
/// <param name="monoisotopicMass">The monoisotopic mass of the molecule(can be calculated from formula)</param>
/// <param name="averageMass">The average mass of the molecule (can be calculated by the formula)</param>
/// <param name="name">The arbitrary name given to this molecule</param>
/// <param name="moleculeAccessionNumbers">Provides InChiKey, CAS number etc</param>
protected CustomMolecule(string formula, double?monoisotopicMass, double?averageMass, string name, MoleculeAccessionNumbers moleculeAccessionNumbers = null)
: this(formula, new TypedMass(monoisotopicMass ?? averageMass ?? 0, MassType.Monoisotopic),
new TypedMass(averageMass ?? monoisotopicMass ?? 0, MassType.Average), name, moleculeAccessionNumbers)
{
}
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));
}
