public ImportPeptideSearchDlg(SkylineWindow skylineWindow, LibraryManager libraryManager)
{
SkylineWindow = skylineWindow;
ImportPeptideSearch = new ImportPeptideSearch();
InitializeComponent();
Icon = Resources.Skyline;
CurrentPage = Pages.spectra_page;
btnNext.Text = Resources.ImportPeptideSearchDlg_ImportPeptideSearchDlg_Next;
AcceptButton = btnNext;
btnNext.Enabled = HasUnmatchedLibraryRuns(SkylineWindow.DocumentUI);
// Create and add wizard pages
BuildPepSearchLibControl = new BuildPeptideSearchLibraryControl(SkylineWindow, ImportPeptideSearch, libraryManager)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(2, 50)
};
BuildPepSearchLibControl.InputFilesChanged += BuildPepSearchLibForm_OnInputFilesChanged;
buildSearchSpecLibPage.Controls.Add(BuildPepSearchLibControl);
ImportFastaControl = new ImportFastaControl(SkylineWindow)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(2, 60)
};
importFastaPage.Controls.Add(ImportFastaControl);
MatchModificationsControl = new MatchModificationsControl(SkylineWindow, ImportPeptideSearch)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(2, 60)
};
matchModificationsPage.Controls.Add(MatchModificationsControl);
TransitionSettingsControl = new TransitionSettingsControl(SkylineWindow)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(18, 60)
};
transitionSettingsUiPage.Controls.Add(TransitionSettingsControl);
FullScanSettingsControl = new FullScanSettingsControl(SkylineWindow)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(18, 50)
};
ms1FullScanSettingsPage.Controls.Add(FullScanSettingsControl);
ImportResultsControl = new ImportResultsControl(ImportPeptideSearch, SkylineWindow.DocumentFilePath)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right),
Location = new Point(2, 60)
};
getChromatogramsPage.Controls.Add((Control)ImportResultsControl);
_pagesToSkip = new HashSet <Pages>();
}
private bool UpdateFullScanSettings()
{
var helper = new MessageBoxHelper(this);
// Validate and store MS1 full-scan settings
// If high resolution MS1 filtering is enabled, make sure precursor m/z type
// is monoisotopic and isotope enrichments are set
var precursorIsotopes = FullScanSettingsControl.PrecursorIsotopesCurrent;
var precursorAnalyzerType = FullScanSettingsControl.PrecursorMassAnalyzer;
var precursorMassType = TransitionSettings.Prediction.PrecursorMassType;
if (precursorIsotopes == FullScanPrecursorIsotopes.None)
{
if (WorkflowType != Workflow.dia)
{
MessageDlg.Show(this, Resources.ImportPeptideSearchDlg_UpdateFullScanSettings_Full_scan_MS1_filtering_must_be_enabled_in_order_to_import_a_peptide_search_);
return(false);
}
else if (FullScanSettingsControl.AcquisitionMethod == FullScanAcquisitionMethod.None)
{
MessageDlg.Show(this, Resources.ImportPeptideSearchDlg_UpdateFullScanSettings_Full_scan_MS1_or_MS_MS_filtering_must_be_enabled_in_order_to_import_a_peptide_search_);
return(false);
}
}
else if (precursorAnalyzerType != FullScanMassAnalyzerType.qit)
{
precursorMassType = MassType.Monoisotopic;
if (FullScanSettingsControl.Enrichments == null)
{
MessageDlg.Show(GetParentForm(this), Resources.TransitionSettingsUI_OkDialog_Isotope_enrichment_settings_are_required_for_MS1_filtering_on_high_resolution_mass_spectrometers);
return(false);
}
}
if (FullScanSettingsControl.IsolationScheme == null && FullScanSettingsControl.AcquisitionMethod == FullScanAcquisitionMethod.DIA)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_An_isolation_scheme_is_required_to_match_multiple_precursors);
return(false);
}
TransitionFilter filter = TransitionSettings.Filter;
if (FullScanSettingsControl.PrecursorChargesTextBox.Visible)
{
Adduct[] precursorCharges;
if (!TransitionSettingsControl.ValidateAdductListTextBox(helper, FullScanSettingsControl.PrecursorChargesTextBox, true, TransitionGroup.MIN_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE, out precursorCharges))
{
return(false);
}
precursorCharges = precursorCharges.Distinct().ToArray();
FullScanSettingsControl.PrecursorChargesString = TransitionFilter.AdductListToString(precursorCharges);
filter = TransitionSettings.Filter.ChangePeptidePrecursorCharges(precursorCharges);
}
if (WorkflowType == Workflow.dda && !filter.PeptideIonTypes.Contains(IonType.precursor))
{
filter = filter.ChangePeptideIonTypes(new[] { IonType.precursor });
}
if (!filter.AutoSelect)
{
filter = filter.ChangeAutoSelect(true);
}
Helpers.AssignIfEquals(ref filter, TransitionSettings.Filter);
if (FullScanSettingsControl.IsDIA() && filter.ExclusionUseDIAWindow)
{
if (FullScanSettingsControl.IsolationScheme.IsAllIons)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Cannot_use_DIA_window_for_precusor_exclusion_when__All_Ions__is_selected_as_the_isolation_scheme___To_use_the_DIA_window_for_precusor_exclusion__change_the_isolation_scheme_in_the_Full_Scan_settings_);
return(false);
}
if (FullScanSettingsControl.IsolationScheme.FromResults)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Cannot_use_DIA_window_for_precursor_exclusion_when_isolation_scheme_does_not_contain_prespecified_windows___Please_select_an_isolation_scheme_with_prespecified_windows_);
return(false);
}
}
TransitionFullScan fullScan;
if (!FullScanSettingsControl.ValidateFullScanSettings(helper, out fullScan))
{
return(false);
}
Helpers.AssignIfEquals(ref fullScan, TransitionSettings.FullScan);
var prediction = TransitionSettings.Prediction.ChangePrecursorMassType(precursorMassType);
Helpers.AssignIfEquals(ref prediction, TransitionSettings.Prediction);
TransitionSettings settings;
try
{
settings = new TransitionSettings(prediction, filter,
TransitionSettings.Libraries, TransitionSettings.Integration, TransitionSettings.Instrument, fullScan);
}
catch (Exception x)
{
MessageDlg.Show(this, x.Message);
return(false);
}
// Did user change the "use spectral libary ion mobility" values?
PeptidePrediction updatedPeptidePrediction;
bool peptidePredictionChanged = false;
try
{
updatedPeptidePrediction =
FullScanSettingsControl.UseSpectralLibraryIonMobilityValuesControl.ValidateNewSettings(true);
if (updatedPeptidePrediction == null)
{
return(false);
}
peptidePredictionChanged = !Equals(Document.Settings.PeptideSettings.Prediction, updatedPeptidePrediction);
}
catch (Exception)
{
return(false);
}
// Only update, if anything changed
if (Equals(settings, TransitionSettings) && !peptidePredictionChanged)
{
return(true);
}
ModifyDocumentNoUndo(doc => doc.ChangeSettings(doc.Settings.ChangeTransitionSettings(settings).ChangePeptideSettings(doc.Settings.PeptideSettings.ChangePrediction(updatedPeptidePrediction))));
_fullScanSettingsChanged = true;
return(true);
}
private void NextPage()
{
switch (CurrentPage)
{
case Pages.spectra_page:
{
HasPeakBoundaries = BuildPepSearchLibControl.SearchFilenames.All(f => f.EndsWith(BiblioSpecLiteBuilder.EXT_TSV));
if (BuildPepSearchLibControl.SearchFilenames.Any(f => f.EndsWith(BiblioSpecLiteBuilder.EXT_TSV)) && !HasPeakBoundaries)
{
MessageDlg.Show(this, Resources.ImportPeptideSearchDlg_NextPage_Cannot_build_library_from_OpenSWATH_results_mixed_with_results_from_other_tools_);
return;
}
var eCancel = new CancelEventArgs();
if (!BuildPeptideSearchLibrary(eCancel))
{
// Page shows error
if (eCancel.Cancel)
{
return;
}
CloseWizard(DialogResult.Cancel);
}
// The user had the option to finish right after
// building the peptide search library, but they
// did not, so hide the "early finish" button for
// the rest of the wizard pages.
ShowEarlyFinish(false);
if (FastaOptional)
{
lblFasta.Text = Resources.ImportPeptideSearchDlg_NextPage_Import_FASTA__optional_;
}
// The next page is going to be the chromatograms page.
var oldImportResultsControl = (ImportResultsControl)ImportResultsControl;
if (WorkflowType != Workflow.dia || HasPeakBoundaries)
{
oldImportResultsControl.InitializeChromatogramsPage(Document);
if (WorkflowType == Workflow.dda)
{
_pagesToSkip.Add(Pages.transition_settings_page);
}
}
else
{
// DIA workflow, replace old ImportResultsControl
ImportResultsControl = new ImportResultsDIAControl(this)
{
Anchor = oldImportResultsControl.Anchor,
Location = oldImportResultsControl.Location
};
getChromatogramsPage.Controls.Remove(oldImportResultsControl);
getChromatogramsPage.Controls.Add((Control)ImportResultsControl);
}
ImportResultsControl.ResultsFilesChanged += ImportResultsControl_OnResultsFilesChanged;
// Set up full scan settings page
TransitionSettingsControl.Initialize(WorkflowType);
FullScanSettingsControl.ModifyOptionsForImportPeptideSearchWizard(WorkflowType);
if (!MatchModificationsControl.Initialize(Document))
{
_pagesToSkip.Add(Pages.match_modifications_page);
}
if (BuildPepSearchLibControl.FilterForDocumentPeptides)
{
_pagesToSkip.Add(Pages.import_fasta_page);
}
// Decoy options enabled only for DIA
ImportFastaControl.RequirePrecursorTransition = WorkflowType != Workflow.dia;
ImportFastaControl.DecoyGenerationEnabled = WorkflowType == Workflow.dia && !HasPeakBoundaries;
}
break;
case Pages.chromatograms_page:
{
if (!ImportPeptideSearch.VerifyRetentionTimes(ImportResultsControl.FoundResultsFiles.Select(f => f.Path)))
{
MessageDlg.Show(this, TextUtil.LineSeparate(Resources.ImportPeptideSearchDlg_NextPage_The_document_specific_spectral_library_does_not_have_valid_retention_times_,
Resources.ImportPeptideSearchDlg_NextPage_Please_check_your_peptide_search_pipeline_or_contact_Skyline_support_to_ensure_retention_times_appear_in_your_spectral_libraries_));
CloseWizard(DialogResult.Cancel);
}
if (ImportResultsControl.ResultsFilesMissing)
{
if (MessageBox.Show(this, Resources.ImportPeptideSearchDlg_NextPage_Some_results_files_are_still_missing__Are_you_sure_you_want_to_continue_,
Program.Name, MessageBoxButtons.OKCancel) == DialogResult.Cancel)
{
return;
}
}
var foundResults = ImportResultsControl.FoundResultsFiles;
if (foundResults.Count > 1)
{
// Older Resharper code inspection implementations insist on warning here
// Resharper disable PossibleMultipleEnumeration
string[] resultNames = foundResults.Select(f => f.Name).ToArray();
string prefix = ImportResultsDlg.GetCommonPrefix(resultNames);
string suffix = ImportResultsDlg.GetCommonSuffix(resultNames);
// Resharper restore PossibleMultipleEnumeration
if (!string.IsNullOrEmpty(prefix) || !string.IsNullOrEmpty(suffix))
{
using (var dlgName = new ImportResultsNameDlg(prefix, suffix, resultNames))
{
var result = dlgName.ShowDialog(this);
if (result == DialogResult.Cancel)
{
return;
}
else if (dlgName.IsRemove)
{
ImportResultsControl.FoundResultsFiles = ImportResultsControl.FoundResultsFiles.Select(f =>
new ImportPeptideSearch.FoundResultsFile(dlgName.ApplyNameChange(f.Name), f.Path)).ToList();
ImportResultsControl.Prefix =
string.IsNullOrEmpty(prefix) ? null : prefix;
ImportResultsControl.Suffix =
string.IsNullOrEmpty(suffix) ? null : suffix;
}
}
}
}
}
break;
case Pages.match_modifications_page:
if (!UpdateModificationSettings())
{
return;
}
break;
case Pages.transition_settings_page:
// Try to accept changes to transition settings
if (!UpdateTransitionSettings())
{
return;
}
break;
case Pages.full_scan_settings_page:
// Try to accept changes to MS1 full-scan settings
if (!UpdateFullScanSettings())
{
// We can't allow the user to progress any further until
// we can verify that the MS1 full scan settings are valid.
return;
}
break;
case Pages.import_fasta_page: // This is the last page
if (FastaOptional && !ImportFastaControl.ContainsFastaContent || ImportFastaControl.ImportFasta())
{
WizardFinish();
}
return;
}
var newPage = CurrentPage + 1;
while (_pagesToSkip.Contains(newPage))
{
++newPage;
}
// Skip import FASTA if user filters for document peptides
if (newPage > Pages.import_fasta_page)
{
WizardFinish();
return;
}
CurrentPage = newPage;
UpdateButtons();
}
private void NextPage()
{
switch (CurrentPage)
{
case Pages.spectra_page:
{
var eCancel = new CancelEventArgs();
if (!BuildPepSearchLibControl.BuildPeptideSearchLibrary(eCancel))
{
// Page shows error
if (eCancel.Cancel)
{
return;
}
CloseWizard(DialogResult.Cancel);
}
// The user had the option to finish right after
// building the peptide search library, but they
// did not, so hide the "early finish" button for
// the rest of the wizard pages.
ShowEarlyFinish(false);
if (FastaOptional)
{
lblFasta.Text = Resources.ImportPeptideSearchDlg_NextPage_Import_FASTA__optional_;
}
// The next page is going to be the chromatograms page.
var oldImportResultsControl = (ImportResultsControl)ImportResultsControl;
if (WorkflowType != Workflow.dia)
{
oldImportResultsControl.InitializeChromatogramsPage(SkylineWindow.DocumentUI);
if (WorkflowType == Workflow.dda)
{
_pagesToSkip.Add(Pages.transition_settings_page);
}
}
else
{
// DIA workflow, replace old ImportResultsControl
ImportResultsControl = new ImportResultsDIAControl(SkylineWindow)
{
Anchor = oldImportResultsControl.Anchor,
Location = oldImportResultsControl.Location
};
getChromatogramsPage.Controls.Remove(oldImportResultsControl);
getChromatogramsPage.Controls.Add((Control)ImportResultsControl);
}
ImportResultsControl.ResultsFilesChanged += ImportResultsControl_OnResultsFilesChanged;
// Set up full scan settings page
TransitionSettingsControl.Initialize(WorkflowType);
FullScanSettingsControl.ModifyOptionsForImportPeptideSearchWizard(WorkflowType);
if (!MatchModificationsControl.Initialize(SkylineWindow.Document))
{
_pagesToSkip.Add(Pages.match_modifications_page);
}
if (BuildPepSearchLibControl.FilterForDocumentPeptides)
{
_pagesToSkip.Add(Pages.import_fasta_page);
}
}
break;
case Pages.chromatograms_page:
{
if (!ImportPeptideSearch.VerifyRetentionTimes(ImportResultsControl.FoundResultsFiles.Select(f => f.Path)))
{
MessageDlg.Show(this, TextUtil.LineSeparate(Resources.ImportPeptideSearchDlg_NextPage_The_document_specific_spectral_library_does_not_have_valid_retention_times_,
Resources.ImportPeptideSearchDlg_NextPage_Please_check_your_peptide_search_pipeline_or_contact_Skyline_support_to_ensure_retention_times_appear_in_your_spectral_libraries_));
CloseWizard(DialogResult.Cancel);
}
if (ImportResultsControl.ResultsFilesMissing)
{
if (MessageBox.Show(this, Resources.ImportPeptideSearchDlg_NextPage_Some_results_files_are_still_missing__Are_you_sure_you_want_to_continue_,
Program.Name, MessageBoxButtons.OKCancel) == DialogResult.Cancel)
{
return;
}
}
if (ImportResultsControl.FoundResultsFiles.Count > 1)
{
string prefix = ImportResultsDlg.GetCommonPrefix(ImportResultsControl.FoundResultsFiles.Select(f => f.Name));
if (prefix.Length >= ImportResultsDlg.MIN_COMMON_PREFIX_LENGTH)
{
using (var dlgName = new ImportResultsNameDlg(prefix))
{
var result = dlgName.ShowDialog(this);
if (result == DialogResult.Cancel)
{
return;
}
else if (result == DialogResult.Yes)
{
// Rename all the replicates to remove the specified prefix.
ImportResultsControl.FoundResultsFiles = ImportResultsControl.FoundResultsFiles.Select(f =>
new ImportPeptideSearch.FoundResultsFile(f.Name.Substring(dlgName.Prefix.Length), f.Path)).ToList();
}
}
}
}
}
break;
case Pages.match_modifications_page:
{
var newSettings = MatchModificationsControl.AddCheckedModifications(SkylineWindow.Document);
if (!ReferenceEquals(SkylineWindow.Document.Settings, newSettings))
{
SkylineWindow.ChangeSettings(newSettings, true, Resources.MatchModificationsControl_AddCheckedModifications_Add_checked_modifications);
SkylineWindow.Document.Settings.UpdateDefaultModifications(false);
}
// The next page is going to be the MS1 Full-Scan Settings
// page, so initialize it.
// FullScanSettingsControl.InitializeMs1FullScanSettingsPage();
}
break;
case Pages.transition_settings_page:
// Try to accept changes to transition settings
if (!UpdateTransitionSettings())
{
return;
}
break;
case Pages.full_scan_settings_page:
// Try to accept changes to MS1 full-scan settings
if (!UpdateFullScanSettings())
{
// We can't allow the user to progress any further until
// we can verify that the MS1 full scan settings are valid.
return;
}
break;
case Pages.import_fasta_page: // This is the last page
if ((FastaOptional && !ImportFastaControl.ContainsFastaContent) ||
ImportFastaControl.ImportFasta())
{
WizardFinish();
}
return;
}
Pages newPage = CurrentPage + 1;
while (_pagesToSkip.Contains(newPage))
{
++newPage;
}
// Skip import FASTA if user filters for document peptides
if (newPage > Pages.import_fasta_page)
{
WizardFinish();
return;
}
CurrentPage = newPage;
if (CurrentPage == LastPage)
{
btnNext.Text = Resources.ImportPeptideSearchDlg_NextPage_Finish;
}
}
public ImportPeptideSearchDlg(SkylineWindow skylineWindow, LibraryManager libraryManager)
{
SkylineWindow = skylineWindow;
_documents = new Stack <SrmDocument>();
SetDocument(skylineWindow.Document, null);
ImportPeptideSearch = new ImportPeptideSearch();
InitializeComponent();
Icon = Resources.Skyline;
btnEarlyFinish.Location = btnBack.Location;
CurrentPage = Pages.spectra_page;
btnNext.Text = Resources.ImportPeptideSearchDlg_ImportPeptideSearchDlg_Next;
AcceptButton = btnNext;
btnNext.Enabled = HasUnmatchedLibraryRuns(Document);
// Create and add wizard pages
BuildPepSearchLibControl = new BuildPeptideSearchLibraryControl(this, ImportPeptideSearch, libraryManager)
{
Dock = DockStyle.Fill,
};
BuildPepSearchLibControl.InputFilesChanged += BuildPepSearchLibForm_OnInputFilesChanged;
buildLibraryPanel.Controls.Add(BuildPepSearchLibControl);
ImportFastaControl = new ImportFastaControl(this, SkylineWindow.SequenceTree)
{
Anchor = AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right,
Location = new Point(2, 60)
};
importFastaPage.Controls.Add(ImportFastaControl);
MatchModificationsControl = new MatchModificationsControl(this, ImportPeptideSearch)
{
Anchor = AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right,
Location = new Point(2, 60)
};
matchModificationsPage.Controls.Add(MatchModificationsControl);
TransitionSettingsControl = new TransitionSettingsControl(this)
{
Anchor = AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right,
Location = new Point(18, 60)
};
transitionSettingsUiPage.Controls.Add(TransitionSettingsControl);
FullScanSettingsControl = new FullScanSettingsControl(this)
{
Anchor = AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right,
Location = new Point(18, 50)
};
ms1FullScanSettingsPage.Controls.Add(FullScanSettingsControl);
FullScanSettingsControl.FullScanEnabledChanged += OnFullScanEnabledChanged; // Adjusts ion settings when full scan settings change
ImportResultsControl = new ImportResultsControl(ImportPeptideSearch, DocumentFilePath)
{
Anchor = AnchorStyles.Top | AnchorStyles.Bottom | AnchorStyles.Left | AnchorStyles.Right,
Location = new Point(2, 60)
};
getChromatogramsPage.Controls.Add((Control)ImportResultsControl);
_pagesToSkip = new HashSet <Pages>();
}
