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;
}
}
