public string GenerateDocumentXml(SrmDocument doc, string oldXml)
{
if (doc == null)
{
return(null);
}
// Minimize document to only the peptides we need
var minimalPeptides = StandardPeptides.ToHashSet();
var oldPeptides = new Dictionary <Target, PeptideDocNode>();
if (!string.IsNullOrEmpty(oldXml))
{
try
{
using (var reader = new StringReader(oldXml))
{
var oldDoc = (SrmDocument) new XmlSerializer(typeof(SrmDocument)).Deserialize(reader);
oldPeptides = oldDoc.Molecules.Where(pep => minimalPeptides.Contains(pep.Target)).ToDictionary(pep => pep.Target, pep => pep);
}
}
catch
{
// ignored
}
}
var addPeptides = new List <PeptideDocNode>();
foreach (var nodePep in doc.Molecules.Where(pep => minimalPeptides.Contains(pep.Target)))
{
if (oldPeptides.TryGetValue(nodePep.Target, out var nodePepOld))
{
addPeptides.Add(nodePep.Merge(nodePepOld));
oldPeptides.Remove(nodePep.Target);
}
else
{
addPeptides.Add(nodePep);
}
}
addPeptides.AddRange(oldPeptides.Values);
var peptides = new List <PeptideDocNode>();
foreach (var nodePep in addPeptides)
{
var precursors = new List <DocNode>();
foreach (TransitionGroupDocNode nodeTranGroup in nodePep.Children)
{
var transitions = nodeTranGroup.Transitions.Where(tran => tran.ResultsRank.HasValue).OrderBy(tran => tran.ResultsRank.Value).Cast <DocNode>().ToList();
if (transitions.Count > 0)
{
precursors.Add(nodeTranGroup.ChangeChildren(transitions));
}
}
if (precursors.Count > 0)
{
peptides.Add((PeptideDocNode)nodePep.ChangeChildren(precursors));
}
}
if (peptides.Count == 0)
{
return(null);
}
peptides.Sort((nodePep1, nodePep2) => nodePep1.ModifiedTarget.CompareTo(nodePep2.ModifiedTarget));
doc = (SrmDocument)doc.ChangeChildren(new[] { new PeptideGroupDocNode(new PeptideGroup(), Resources.IrtDb_MakeDocumentXml_iRT_standards, string.Empty, peptides.ToArray()) });
// Clear some settings to make the document smaller and so that they won't get imported into a document
// TODO: Convert all modifications to explicit?
doc = doc.ChangeMeasuredResults(null);
doc = doc.ChangeSettings(doc.Settings.ChangePeptideLibraries(libs => libs.ChangeLibraries(new List <LibrarySpec>(), new List <Library>())));
using (var writer = new StringWriter())
using (var writer2 = new XmlTextWriter(writer))
{
doc.Serialize(writer2, null, SkylineVersion.CURRENT, null);
return(writer.ToString());
}
}
