public static ProcessedIrtAverages ProcessRetentionTimes(int?numCirt, IRetentionTimeProvider[] irtProviders,
DbIrtPeptide[] standardPeptides, DbIrtPeptide[] cirtPeptides, IrtRegressionType regressionType, IProgressMonitor monitor, out DbIrtPeptide[] newStandardPeptides)
{
newStandardPeptides = null;
var processed = !numCirt.HasValue
? RCalcIrt.ProcessRetentionTimes(monitor, irtProviders, standardPeptides, new DbIrtPeptide[0], regressionType)
: RCalcIrt.ProcessRetentionTimesCirt(monitor, irtProviders, cirtPeptides, numCirt.Value, regressionType, out newStandardPeptides);
return(processed);
}
public static void CreateIrtDb(string path, ProcessedIrtAverages processed, DbIrtPeptide[] standardPeptides, bool recalibrate, IrtRegressionType regressionType, IProgressMonitor monitor)
{
DbIrtPeptide[] newStandards = null;
if (recalibrate)
{
monitor.UpdateProgress(new ProgressStatus().ChangeSegments(0, 2));
newStandards = processed.RecalibrateStandards(standardPeptides).ToArray();
processed = RCalcIrt.ProcessRetentionTimes(monitor,
processed.ProviderData.Select(data => data.RetentionTimeProvider).ToArray(),
newStandards.ToArray(), new DbIrtPeptide[0], regressionType);
}
var irtDb = IrtDb.CreateIrtDb(path);
irtDb.AddPeptides(monitor, (newStandards ?? standardPeptides).Concat(processed.DbIrtPeptides).ToList());
}
public static bool AddIrts(IrtRegressionType regressionType, Library lib, LibrarySpec libSpec, IrtStandard standard, Control parent, bool useTopMostForm)
{
if (lib == null || !lib.IsLoaded || standard == null || standard.Name.Equals(IrtStandard.EMPTY.Name))
{
return(false);
}
Control GetParent()
{
return(useTopMostForm ? FormUtil.FindTopLevelOpenForm(f => f is BuildLibraryNotification) ?? parent : parent);
}
IRetentionTimeProvider[] irtProviders = null;
var isAuto = ReferenceEquals(standard, IrtStandard.AUTO);
List <IrtStandard> autoStandards = null;
var cirtPeptides = new DbIrtPeptide[0];
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_AddIrts_Loading_retention_time_providers
})
{
var standard1 = standard;
var status = longWait.PerformWork(GetParent(), 800, monitor =>
{
ImportPeptideSearch.GetLibIrtProviders(lib, standard1, monitor, out irtProviders, out autoStandards, out cirtPeptides);
});
if (status.IsCanceled)
{
return(false);
}
if (status.IsError)
{
throw status.ErrorException;
}
}
int?numCirt = null;
if (cirtPeptides.Length >= RCalcIrt.MIN_PEPTIDES_COUNT)
{
using (var dlg = new AddIrtStandardsDlg(cirtPeptides.Length,
string.Format(
Resources.LibraryBuildNotificationHandler_AddIrts__0__distinct_CiRT_peptides_were_found__How_many_would_you_like_to_use_as_iRT_standards_,
cirtPeptides.Length)))
{
if (dlg.ShowDialog(GetParent()) != DialogResult.OK)
{
return(false);
}
numCirt = dlg.StandardCount;
}
}
else if (isAuto)
{
switch (autoStandards.Count)
{
case 0:
standard = new IrtStandard(XmlNamedElement.NAME_INTERNAL, null, null, IrtPeptidePicker.Pick(irtProviders, 10));
break;
case 1:
standard = autoStandards[0];
break;
default:
using (var selectIrtStandardDlg = new SelectIrtStandardDlg(autoStandards))
{
if (selectIrtStandardDlg.ShowDialog(GetParent()) != DialogResult.OK)
{
return(false);
}
standard = selectIrtStandardDlg.Selected;
}
break;
}
}
var standardPeptides = standard.Peptides.ToArray();
ProcessedIrtAverages processed = null;
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_AddIrts_Processing_retention_times
})
{
try
{
var status = longWait.PerformWork(GetParent(), 800, monitor =>
{
processed = ImportPeptideSearch.ProcessRetentionTimes(numCirt, irtProviders, standardPeptides, cirtPeptides, regressionType, monitor, out var newStandardPeptides);
if (newStandardPeptides != null)
{
standardPeptides = newStandardPeptides;
}
});
if (status.IsCanceled)
{
return(false);
}
if (status.IsError)
{
throw status.ErrorException;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(GetParent(),
TextUtil.LineSeparate(
Resources.BuildPeptideSearchLibraryControl_AddIrtLibraryTable_An_error_occurred_while_processing_retention_times_,
x.Message), x);
return(false);
}
}
using (var resultsDlg = new AddIrtPeptidesDlg(AddIrtPeptidesLocation.spectral_library, processed))
{
if (resultsDlg.ShowDialog(GetParent()) != DialogResult.OK)
{
return(false);
}
}
var recalibrate = false;
if (processed.CanRecalibrateStandards(standardPeptides))
{
using (var dlg = new MultiButtonMsgDlg(
TextUtil.LineSeparate(Resources.LibraryGridViewDriver_AddToLibrary_Do_you_want_to_recalibrate_the_iRT_standard_values_relative_to_the_peptides_being_added_,
Resources.LibraryGridViewDriver_AddToLibrary_This_can_improve_retention_time_alignment_under_stable_chromatographic_conditions_),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false))
{
recalibrate = dlg.ShowDialog(GetParent()) == DialogResult.Yes;
}
}
if (!processed.DbIrtPeptides.Any())
{
return(false);
}
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_AddIrts_Adding_iRTs_to_library
})
{
try
{
var status = longWait.PerformWork(GetParent(), 800, monitor =>
{
ImportPeptideSearch.CreateIrtDb(libSpec.FilePath, processed, standardPeptides, recalibrate, regressionType, monitor);
});
if (status.IsError)
{
throw status.ErrorException;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(GetParent(),
TextUtil.LineSeparate(
Resources.LibraryBuildNotificationHandler_AddIrts_An_error_occurred_trying_to_add_iRTs_to_the_library_,
x.Message), x);
return(false);
}
}
return(true);
}
