private static SrmDocument CopyPaste(SrmDocument sourceDoc, IEnumerable <DocNode> nodes, SrmDocument targetDoc, IdentityPath to)
{
SetDefaultModifications(targetDoc);
if (nodes != null)
{
sourceDoc = sourceDoc.RemoveAllBut(nodes);
}
var stringWriter = new XmlStringWriter();
using (var writer = new XmlTextWriter(stringWriter)
{
Formatting = Formatting.Indented
})
{
XmlSerializer ser = new XmlSerializer(typeof(SrmDocument));
ser.Serialize(writer, sourceDoc);
}
IdentityPath newPath, nextAdd;
targetDoc = targetDoc.ImportDocumentXml(new StringReader(stringWriter.ToString()),
null,
MeasuredResults.MergeAction.remove,
false,
null,
Settings.Default.StaticModList,
Settings.Default.HeavyModList,
to,
out newPath,
out nextAdd,
false);
return(targetDoc);
}
public SrmDocument ImportTo(SrmDocument document, PeptideLibraries.FindLibrary findLibrary, out IdentityPath firstAdded)
{
firstAdded = null;
using (var reader = GetReader())
{
return(reader != null
? document.ImportDocumentXml(reader,
string.Empty,
MeasuredResults.MergeAction.remove,
false,
findLibrary,
Settings.Default.StaticModList,
Settings.Default.HeavyModList,
document.Children.Any()?new IdentityPath(document.Children.First().Id) : null,
out firstAdded,
out _,
false)
: null);
}
}
public static ProcessedIrtAverages ProcessRetentionTimes(IProgressMonitor monitor,
IRetentionTimeProvider[] providers, DbIrtPeptide[] standardPeptideList, DbIrtPeptide[] items)
{
var matchedStandard = IrtStandard.WhichStandard(standardPeptideList.Select(pep => pep.ModifiedTarget));
if (matchedStandard != null)
{
var dummyDoc = new SrmDocument(SrmSettingsList.GetDefault());
using (var reader = matchedStandard.GetDocumentReader())
{
if (reader != null)
{
dummyDoc = dummyDoc.ImportDocumentXml(reader,
string.Empty,
MeasuredResults.MergeAction.remove,
false,
null,
Settings.Default.StaticModList,
Settings.Default.HeavyModList,
null,
out _,
out _,
false);
standardPeptideList = standardPeptideList.Select(pep => new DbIrtPeptide(pep)).ToArray();
foreach (var dummyPep in dummyDoc.Molecules.Where(pep => pep.HasExplicitMods))
{
var standardPepIdx = standardPeptideList.IndexOf(pep => dummyPep.ModifiedTarget.Equals(pep.ModifiedTarget));
standardPeptideList[standardPepIdx] = new DbIrtPeptide(standardPeptideList[standardPepIdx])
{
ModifiedTarget = dummyDoc.Settings.GetModifiedSequence(dummyPep.ModifiedTarget, IsotopeLabelType.heavy, dummyPep.ExplicitMods)
};
}
}
}
}
IProgressStatus status = new ProgressStatus(Resources.LibraryGridViewDriver_ProcessRetentionTimes_Adding_retention_times);
var dictPeptideAverages = new Dictionary <Target, IrtPeptideAverages>();
var providerData = new List <RetentionTimeProviderData>();
var runCount = 0;
foreach (var retentionTimeProvider in providers)
{
if (monitor.IsCanceled)
{
return(null);
}
monitor.UpdateProgress(status = status.ChangeMessage(string.Format(
Resources.LibraryGridViewDriver_ProcessRetentionTimes_Converting_retention_times_from__0__,
retentionTimeProvider.Name)));
runCount++;
var data = new RetentionTimeProviderData(retentionTimeProvider, standardPeptideList);
if (data.RegressionSuccess || data.CalcRegressionWith(retentionTimeProvider, standardPeptideList, items))
{
AddRetentionTimesToDict(retentionTimeProvider, data.RegressionRefined, dictPeptideAverages, standardPeptideList);
}
providerData.Add(data);
monitor.UpdateProgress(status = status.ChangePercentComplete(runCount * 100 / providers.Length));
}
monitor.UpdateProgress(status.Complete());
return(new ProcessedIrtAverages(dictPeptideAverages, providerData));
}
private static SrmDocument CopyPaste(SrmDocument sourceDoc, IEnumerable<DocNode> nodes, SrmDocument targetDoc, IdentityPath to)
{
SetDefaultModifications(targetDoc);
if(nodes != null)
sourceDoc = sourceDoc.RemoveAllBut(nodes);
var stringWriter = new XmlStringWriter();
using (var writer = new XmlTextWriter(stringWriter) { Formatting = Formatting.Indented })
{
XmlSerializer ser = new XmlSerializer(typeof(SrmDocument));
ser.Serialize(writer, sourceDoc);
}
IdentityPath newPath, nextAdd;
targetDoc = targetDoc.ImportDocumentXml(new StringReader(stringWriter.ToString()),
null,
MeasuredResults.MergeAction.remove,
false,
null,
Settings.Default.StaticModList,
Settings.Default.HeavyModList,
to,
out newPath,
out nextAdd,
false);
return targetDoc;
}
