public static ProcessedIrtAverages ProcessRetentionTimes(IProgressMonitor monitor,
IEnumerable <IRetentionTimeProvider> providers, int countProviders,
DbIrtPeptide[] standardPeptideList, DbIrtPeptide[] items)
{
IProgressStatus status = new ProgressStatus(Resources.LibraryGridViewDriver_ProcessRetentionTimes_Adding_retention_times);
var dictProviderData = new List <KeyValuePair <string, RetentionTimeProviderData> >();
var dictPeptideAverages = new Dictionary <Target, IrtPeptideAverages>();
var runCount = 0;
foreach (var retentionTimeProvider in providers)
{
if (monitor.IsCanceled)
{
return(null);
}
var message = string.Format(Resources.LibraryGridViewDriver_ProcessRetentionTimes_Converting_retention_times_from__0__, retentionTimeProvider.Name);
monitor.UpdateProgress(status = status.ChangeMessage(message));
runCount++;
var data = new RetentionTimeProviderData(retentionTimeProvider, standardPeptideList.OrderBy(peptide => peptide.Irt));
if (data.RegressionSuccess || data.CalcRegressionWith(retentionTimeProvider, standardPeptideList, items))
{
// Trace.WriteLine(string.Format("slope = {0}, intercept = {1}", data.RegressionRefined.Slope, data.RegressionRefined.Intercept));
AddRetentionTimesToDict(retentionTimeProvider, data.RegressionRefined, dictPeptideAverages, standardPeptideList);
}
dictProviderData.Add(new KeyValuePair <string, RetentionTimeProviderData>(retentionTimeProvider.Name, data));
monitor.UpdateProgress(status = status.ChangePercentComplete(runCount * 100 / countProviders));
}
monitor.UpdateProgress(status.Complete());
return(new ProcessedIrtAverages(dictPeptideAverages, dictProviderData));
}
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));
}
public static ProcessedIrtAverages ProcessRetentionTimes(IProgressMonitor monitor,
IRetentionTimeProvider[] providers, DbIrtPeptide[] standardPeptideList, DbIrtPeptide[] items, IrtRegressionType regressionType)
{
var heavyStandards = new DbIrtPeptide[standardPeptideList.Length];
var matchedStandard = IrtStandard.WhichStandard(standardPeptideList.Select(pep => pep.ModifiedTarget));
if (matchedStandard != null && matchedStandard.HasDocument)
{
// Check embedded standard document for known standard to determine if the standard peptides should be heavy
// Import iRT standard document into an empty document (rather than just getting the document), because importing also imports the modifications
var standardDoc = matchedStandard.ImportTo(new SrmDocument(SrmSettingsList.GetDefault()));
standardPeptideList = standardPeptideList.Select(pep => new DbIrtPeptide(pep)).ToArray();
foreach (var dummyPep in standardDoc.Molecules.Where(pep => pep.HasExplicitMods))
{
var standardPepIdx = standardPeptideList.IndexOf(pep => dummyPep.ModifiedTarget.Equals(pep.ModifiedTarget));
if (standardPepIdx < 0)
{
continue;
}
var heavyTarget = standardDoc.Settings.GetModifiedSequence(dummyPep.ModifiedTarget, IsotopeLabelType.heavy, dummyPep.ExplicitMods);
if (!standardPeptideList[standardPepIdx].ModifiedTarget.Equals(heavyTarget))
{
heavyStandards[standardPepIdx] = new DbIrtPeptide(standardPeptideList[standardPepIdx])
{
ModifiedTarget = heavyTarget
}
}
;
}
}
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(regressionType, retentionTimeProvider, standardPeptideList, heavyStandards);
if (data.RegressionSuccess ||
(ReferenceEquals(regressionType, IrtRegressionType.LINEAR) && 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));
}
