/// <summary>
/// Read in the current transition groups's precursors and try to modernize the XML so that it's in terms of a common neutral
/// molecule with adducts, while preserving the precursor mz values
/// </summary>
/// <param name="peptide">Neutral molecule associated with current reader position, may be replaced during this call</param>
/// <returns>Reader positioned at end of current precursor opening, but using cached and possibly altered XML</returns>
public XmlReader Read(ref Peptide peptide)
{
if (_precursorRawDetails.Count == 0)
{
return(ReadAhead.CreateXmlReader()); // No precursors to process
}
// Find a formula for the parent molecule, if possible
ProposeMoleculeWithCommonFormula(peptide);
// Deal with mass-only declarations if no formulas were found
if (string.IsNullOrEmpty(ProposedMolecule.Formula))
{
return(HandleMassOnlyDeclarations(ref peptide));
}
// Check to see if description already makes sense
if (_precursorRawDetails.TrueForAll(d =>
!Adduct.IsNullOrEmpty(d._nominalAdduct) &&
Math.Abs(d._declaredMz - d._nominalAdduct.MzFromNeutralMass(ProposedMolecule.MonoisotopicMass)) <= MzToler))
{
return(UpdatePeptideAndInsertAdductsInXML(ref peptide, _precursorRawDetails.Select(d => d._nominalAdduct)));
}
// See if there are simple adducts that work with common formula
if (DeriveAdductsForCommonFormula(peptide))
{
// Found a molecule that works for all precursors that declared a formula (though that may not be all precursors, users create highly variable documents)
return(UpdatePeptideAndInsertAdductsInXML(ref peptide, _precursorRawDetails.Select(d => d._proposedAdduct)));
}
// Done adjusting parent molecule, must come up with rest of adducts to make mz and base molecule agree
return(ConsiderMassShiftAdducts(ref peptide));
}
private XmlReader UpdatePeptideAndInsertAdductsInXML(ref Peptide peptide, IEnumerable <Adduct> adducts)
{
var updatedPeptide = ReferenceEquals(ProposedMolecule, peptide.CustomMolecule) ? peptide : new Peptide(ProposedMolecule);
var ionFormulas = adducts.Select(a => updatedPeptide.CustomMolecule.Formula + a.ToString()).ToList();
ReadAhead.ModifyAttributesInElement(DocumentSerializer.EL.precursor, DocumentSerializer.ATTR.ion_formula,
ionFormulas); // N.B. "ion_formula" consists of just the adduct for mass only molecules
peptide = updatedPeptide;
return(ReadAhead.CreateXmlReader()); // Return a reader that uses the updated XML
}
