/// <summary>
/// Serializes the contents of a single <see cref="TransitionGroupDocNode"/>
/// to XML.
/// </summary>
/// <param name="writer">The XML writer</param>
/// <param name="nodePep">The parent peptide document node</param>
/// <param name="node">The transition group document node</param>
private void WriteTransitionGroupXml(XmlWriter writer, PeptideDocNode nodePep, TransitionGroupDocNode node)
{
TransitionGroup group = node.TransitionGroup;
var isCustomIon = nodePep.Peptide.IsCustomMolecule;
writer.WriteAttribute(ATTR.charge, group.PrecursorAdduct.AdductCharge);
if (!group.LabelType.IsLight)
{
writer.WriteAttribute(ATTR.isotope_label, group.LabelType);
}
if (!isCustomIon)
{
writer.WriteAttribute(ATTR.calc_neutral_mass, node.GetPrecursorIonPersistentNeutralMass());
}
writer.WriteAttribute(ATTR.precursor_mz, SequenceMassCalc.PersistentMZ(node.PrecursorMz));
WriteExplicitTransitionGroupValuesAttributes(writer, node.ExplicitValues);
writer.WriteAttribute(ATTR.auto_manage_children, node.AutoManageChildren, true);
writer.WriteAttributeNullable(ATTR.decoy_mass_shift, group.DecoyMassShift);
writer.WriteAttributeNullable(ATTR.precursor_concentration, node.PrecursorConcentration);
TransitionPrediction predict = Settings.TransitionSettings.Prediction;
double regressionMz = Settings.GetRegressionMz(nodePep, node);
var ce = predict.CollisionEnergy.GetCollisionEnergy(node.TransitionGroup.PrecursorAdduct, regressionMz);
writer.WriteAttribute(ATTR.collision_energy, ce);
var dpRegression = predict.DeclusteringPotential;
if (dpRegression != null)
{
var dp = dpRegression.GetDeclustringPotential(regressionMz);
writer.WriteAttribute(ATTR.declustering_potential, dp);
}
if (!isCustomIon)
{
// modified sequence
var calcPre = Settings.GetPrecursorCalc(node.TransitionGroup.LabelType, nodePep.ExplicitMods);
var seq = node.TransitionGroup.Peptide.Target;
writer.WriteAttribute(ATTR.modified_sequence, calcPre.GetModifiedSequence(seq,
false)); // formatNarrow = false; We want InvariantCulture, not the local format
Assume.IsTrue(group.PrecursorAdduct.IsProteomic);
}
else
{
// Custom ion
node.CustomMolecule.WriteXml(writer, group.PrecursorAdduct);
}
// Write child elements
WriteAnnotations(writer, node.Annotations);
if (node.HasLibInfo)
{
var helpers = PeptideLibraries.SpectrumHeaderXmlHelpers;
writer.WriteElements(new[] { node.LibInfo }, helpers);
}
if (node.HasResults)
{
WriteResults(writer, Settings, node.Results,
EL.precursor_results, EL.precursor_peak, WriteTransitionGroupChromInfo);
}
if (UseCompactFormat())
{
writer.WriteStartElement(EL.transition_data);
var transitionData = new SkylineDocumentProto.Types.TransitionData();
transitionData.Transitions.AddRange(node.Transitions.Select(transition => transition.ToTransitionProto(Settings)));
byte[] bytes = transitionData.ToByteArray();
writer.WriteBase64(bytes, 0, bytes.Length);
writer.WriteEndElement();
if (WroteTransitions != null)
{
WroteTransitions(node.TransitionCount);
}
}
else
{
foreach (TransitionDocNode nodeTransition in node.Children)
{
writer.WriteStartElement(EL.transition);
WriteTransitionXml(writer, nodePep, node, nodeTransition);
writer.WriteEndElement();
}
}
}