private void AddRetentionTimePredictor(LibraryManager.BuildState buildState)
{
var predictorName = Helpers.GetUniqueName(buildState.LibrarySpec.Name, Settings.Default.RetentionTimeList.Select(rt => rt.Name).ToArray());
using (var addPredictorDlg = new AddRetentionTimePredictorDlg(predictorName, buildState.LibrarySpec.FilePath, false))
{
if (addPredictorDlg.ShowDialog(TopMostApplicationForm) == DialogResult.OK)
{
Settings.Default.RTScoreCalculatorList.Add(addPredictorDlg.Calculator);
Settings.Default.RetentionTimeList.Add(addPredictorDlg.Regression);
NotificationContainer.ModifyDocument(Resources.LibraryBuildNotificationHandler_AddRetentionTimePredictor_Add_retention_time_predictor,
doc => doc.ChangeSettings(doc.Settings.ChangePeptidePrediction(predict =>
predict.ChangeRetentionTime(addPredictorDlg.Regression))));
}
}
}
public void LibraryBuildCompleteCallback(LibraryManager.BuildState buildState, bool success)
{
// Completion needs to happen on a separate thread because of the access to UI elements
// In order to make sure the thread handle is released, it needs to call Application.ThreadExit()
var threadComplete = BackgroundEventThreads.CreateThreadForAction(() =>
{
if (success && NotificationContainerForm.IsHandleCreated)
{
// Only one form showing at a time
lock (this)
{
RemoveLibraryBuildNotification();
var frm = new BuildLibraryNotification(buildState.LibrarySpec.Name);
frm.Activated += notification_Activated;
frm.Shown += notification_Shown;
frm.ExploreLibrary += notification_ExploreLibrary;
frm.NotificationComplete += notification_NotificationComplete;
Point anchor = NotificationAnchor;
frm.Left = anchor.X;
frm.Top = anchor.Y - frm.Height;
NotificationContainerForm.BeginInvoke(new Action(() =>
{
if (!string.IsNullOrEmpty(buildState.ExtraMessage))
{
MessageDlg.Show(TopMostApplicationForm, buildState.ExtraMessage);
}
if (buildState.IrtStandard != null && !buildState.IrtStandard.Name.Equals(IrtStandard.EMPTY.Name) && AddIrts(buildState))
{
AddRetentionTimePredictor(buildState);
}
}));
frm.Start();
Assume.IsNull(Interlocked.Exchange(ref _notification, frm));
}
}
});
threadComplete.Name = @"Library Build Completion";
threadComplete.Start();
}
private bool AddIrts(LibraryManager.BuildState buildState)
{
try
{
Library lib;
ProcessedIrtAverages processed = null;
var initialMessage = Resources.LibraryBuildNotificationHandler_LibraryBuildCompleteCallback_Adding_iRTs_to_library;
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_LibraryBuildCompleteCallback_Adding_iRTs_to_library
})
{
var status = longWait.PerformWork(TopMostApplicationForm, 800, monitor =>
{
var initStatus = new ProgressStatus(initialMessage).ChangeSegments(0, 2);
monitor.UpdateProgress(initStatus);
lib = NotificationContainer.LibraryManager.TryGetLibrary(buildState.LibrarySpec) ??
NotificationContainer.LibraryManager.LoadLibrary(buildState.LibrarySpec, () => new DefaultFileLoadMonitor(monitor));
foreach (var stream in lib.ReadStreams)
{
stream.CloseStream();
}
if (longWait.IsCanceled)
{
return;
}
var irtProviders = lib.RetentionTimeProvidersIrt.ToArray();
if (!irtProviders.Any())
{
irtProviders = lib.RetentionTimeProviders.ToArray();
}
processed = RCalcIrt.ProcessRetentionTimes(monitor, irtProviders, irtProviders.Length,
buildState.IrtStandard.Peptides.ToArray(), new DbIrtPeptide[0]);
});
if (status.IsCanceled)
{
return(false);
}
if (status.IsError)
{
throw status.ErrorException;
}
}
using (var resultsDlg = new AddIrtPeptidesDlg(AddIrtPeptidesLocation.spectral_library, processed))
{
if (resultsDlg.ShowDialog(TopMostApplicationForm) != DialogResult.OK)
{
return(false);
}
}
var recalibrate = false;
if (processed.CanRecalibrateStandards(buildState.IrtStandard.Peptides))
{
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))
{
if (dlg.ShowDialog(TopMostApplicationForm) == DialogResult.Yes)
{
recalibrate = true;
}
}
}
var processedDbIrtPeptides = processed.DbIrtPeptides.ToArray();
if (!processedDbIrtPeptides.Any())
{
return(false);
}
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_LibraryBuildCompleteCallback_Adding_iRTs_to_library
})
{
ImmutableList <DbIrtPeptide> newStandards = null;
var status = longWait.PerformWork(TopMostApplicationForm, 800, monitor =>
{
if (recalibrate)
{
monitor.UpdateProgress(new ProgressStatus().ChangeSegments(0, 2));
newStandards = ImmutableList.ValueOf(processed.RecalibrateStandards(buildState.IrtStandard.Peptides));
processed = RCalcIrt.ProcessRetentionTimes(
monitor, processed.ProviderData.Select(data => data.Value.RetentionTimeProvider),
processed.ProviderData.Count, newStandards.ToArray(), new DbIrtPeptide[0]);
}
var irtDb = IrtDb.CreateIrtDb(buildState.LibrarySpec.FilePath);
irtDb.AddPeptides(monitor, (newStandards ?? buildState.IrtStandard.Peptides).Concat(processedDbIrtPeptides).ToList());
});
if (status.IsError)
{
throw status.ErrorException;
}
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(TopMostApplicationForm,
TextUtil.LineSeparate(Resources.LibraryBuildNotificationHandler_LibraryBuildCompleteCallback_An_error_occurred_trying_to_add_iRTs_to_the_library_, x.Message), x);
return(false);
}
return(true);
}
public void LibraryBuildCompleteCallback(LibraryManager.BuildState buildState, bool success)
{
// Completion needs to happen on a separate thread because of the access to UI elements
// In order to make sure the thread handle is released, it needs to call Application.ThreadExit()
var threadComplete = BackgroundEventThreads.CreateThreadForAction(() =>
{
if (success && NotificationContainerForm.IsHandleCreated)
{
// Only one form showing at a time
lock (this)
{
RemoveLibraryBuildNotification();
var frm = new BuildLibraryNotification(buildState.LibrarySpec.Name);
frm.Activated += notification_Activated;
frm.Shown += notification_Shown;
frm.ExploreLibrary += notification_ExploreLibrary;
frm.NotificationComplete += notification_NotificationComplete;
Point anchor = NotificationAnchor;
frm.Left = anchor.X;
frm.Top = anchor.Y - frm.Height;
NotificationContainerForm.BeginInvoke(new Action(() =>
{
if (!string.IsNullOrEmpty(buildState.ExtraMessage))
{
MessageDlg.Show(TopMostApplicationForm, buildState.ExtraMessage);
}
if (buildState.IrtStandard != null && !buildState.IrtStandard.Name.Equals(IrtStandard.EMPTY.Name))
{
// Load library
Library lib = null;
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_AddIrts_Loading_library
})
{
var status = longWait.PerformWork(TopMostApplicationForm, 800, monitor =>
{
lib = NotificationContainer.LibraryManager.TryGetLibrary(buildState.LibrarySpec) ??
NotificationContainer.LibraryManager.LoadLibrary(buildState.LibrarySpec, () => new DefaultFileLoadMonitor(monitor));
foreach (var stream in lib.ReadStreams)
{
stream.CloseStream();
}
});
if (status.IsCanceled)
{
lib = null;
}
if (status.IsError)
{
throw status.ErrorException;
}
}
// Add iRTs to library
if (AddIrts(lib, buildState.LibrarySpec, buildState.IrtStandard, NotificationContainerForm, true))
{
AddRetentionTimePredictor(buildState);
}
}
}));
frm.Start();
Assume.IsNull(Interlocked.Exchange(ref _notification, frm));
}
}
});
threadComplete.Name = @"Library Build Completion";
threadComplete.Start();
}
private bool BuildPeptideSearchLibrary(CancelEventArgs e)
{
// Nothing to build, if now search files were specified
if (!SearchFilenames.Any())
{
var libraries = DocumentContainer.Document.Settings.PeptideSettings.Libraries;
if (!libraries.HasLibraries)
{
return(false);
}
var libSpec = libraries.LibrarySpecs.FirstOrDefault(s => s.IsDocumentLibrary);
return(libSpec != null && LoadPeptideSearchLibrary(libSpec));
}
double cutOffScore;
MessageBoxHelper helper = new MessageBoxHelper(WizardForm);
if (!helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
e.Cancel = true;
return(false);
}
ImportPeptideSearch.CutoffScore = cutOffScore;
BiblioSpecLiteBuilder builder;
try
{
builder = ImportPeptideSearch.GetLibBuilder(DocumentContainer.Document, DocumentContainer.DocumentFilePath, cbIncludeAmbiguousMatches.Checked);
builder.PreferEmbeddedSpectra = PreferEmbeddedSpectra;
builder.DebugMode = DebugMode;
}
catch (FileEx.DeleteException de)
{
MessageDlg.ShowException(this, de);
return(false);
}
bool retry = false;
do
{
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_Peptide_Search_Library,
Message = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_document_library_for_peptide_search_,
})
{
// Disable the wizard, because the LongWaitDlg does not
try
{
ImportPeptideSearch.ClosePeptideSearchLibraryStreams(DocumentContainer.Document);
var buildState = new LibraryManager.BuildState(null, null);
var status = longWaitDlg.PerformWork(WizardForm, 800,
monitor => LibraryManager.BuildLibraryBackground(DocumentContainer, builder, monitor, buildState));
LastBuildCommandArgs = buildState.BuildCommandArgs;
LastBuildOutput = buildState.BuildOutput;
if (status.IsError)
{
// E.g. could not find external raw data for MaxQuant msms.txt; ask user if they want to retry with "prefer embedded spectra" option
if (BiblioSpecLiteBuilder.IsLibraryMissingExternalSpectraError(status.ErrorException))
{
var response = ShowLibraryMissingExternalSpectraError(WizardForm, status.ErrorException);
if (response == UpdateProgressResponse.cancel)
{
return(false);
}
else if (response == UpdateProgressResponse.normal)
{
builder.PreferEmbeddedSpectra = true;
}
retry = true;
}
else
{
MessageDlg.ShowException(WizardForm, status.ErrorException);
return(false);
}
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(WizardForm, TextUtil.LineSeparate(string.Format(Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Failed_to_build_the_library__0__,
Path.GetFileName(BiblioSpecLiteSpec.GetLibraryFileName(DocumentContainer.DocumentFilePath))), x.Message), x);
return(false);
}
}
} while (retry);
var docLibSpec = builder.LibrarySpec.ChangeDocumentLibrary(true);
Settings.Default.SpectralLibraryList.Insert(0, docLibSpec);
// Go ahead and load the library - we'll need it for
// the modifications and chromatograms page.
if (!LoadPeptideSearchLibrary(docLibSpec))
{
return(false);
}
var selectedIrtStandard = _driverStandards.SelectedItem;
var addedIrts = false;
if (selectedIrtStandard != null && !selectedIrtStandard.Name.Equals(IrtStandard.EMPTY.Name))
{
addedIrts = AddIrtLibraryTable(docLibSpec.FilePath, selectedIrtStandard);
}
var docNew = ImportPeptideSearch.AddDocumentSpectralLibrary(DocumentContainer.Document, docLibSpec);
if (docNew == null)
{
return(false);
}
if (addedIrts)
{
docNew = ImportPeptideSearch.AddRetentionTimePredictor(docNew, docLibSpec);
}
DocumentContainer.ModifyDocumentNoUndo(doc => docNew);
if (!string.IsNullOrEmpty(builder.AmbiguousMatchesMessage))
{
MessageDlg.Show(WizardForm, builder.AmbiguousMatchesMessage);
}
return(true);
}
