public bool Initialize(SrmDocument document)
{
if (!ImportPeptideSearch.HasDocLib)
{
return(false);
}
ImportPeptideSearch.InitializeModifications(document);
FillLists(document);
return(modificationsListBox.Items.Count > 1 || unmatchedListBox.Items.Count > 1);
}
public SrmSettings AddCheckedModifications(SrmDocument document)
{
var firstHeavyModificationType = document.Settings.PeptideSettings.Modifications
.GetHeavyModificationTypes().FirstOrDefault();
// in the non-DDA case, AddCheckedModifications is only additive, so no checked items is a no-op
if (modificationsListBox.CheckedItems.Count == 0)
{
if (!ImportPeptideSearch.IsDDASearch)
{
return(document.Settings);
}
else
{
// in DDA-case, return empty mod lists
var emptyPeptideMods = document.Settings.PeptideSettings.Modifications
.ChangeStaticModifications(new List <StaticMod>());
emptyPeptideMods = emptyPeptideMods.ChangeModifications(firstHeavyModificationType, new List <StaticMod>());
return(ImportPeptideSearch.AddModifications(document, emptyPeptideMods));
}
}
// Find checked mods
List <StaticMod> structuralMods;
List <StaticMod> heavyMods;
if (ImportPeptideSearch.IsDDASearch)
{
var selectedMods = modificationsListBox.CheckedItems.Cast <ListBoxModification>().Select(o => o.Mod).ToList();
structuralMods = selectedMods.Where(o => o.LabelAtoms == LabelAtoms.None).ToList();
heavyMods = selectedMods.Where(o => o.LabelAtoms != LabelAtoms.None).ToList();
}
else
{
structuralMods = (from mod in ImportPeptideSearch.MatcherPepMods.StaticModifications
from ListBoxModification checkedMod in modificationsListBox.CheckedItems
where mod.Equivalent(checkedMod.Mod)
select mod).ToList();
// Find checked heavy mods
heavyMods = (from mod in ImportPeptideSearch.MatcherHeavyMods
from ListBoxModification checkedMod in modificationsListBox.CheckedItems
where mod.Equivalent(checkedMod.Mod)
select mod).ToList();
}
// Update document modifications
var newPeptideMods = document.Settings.PeptideSettings.Modifications.ChangeStaticModifications(structuralMods);
newPeptideMods = newPeptideMods.ChangeModifications(firstHeavyModificationType, heavyMods);
return(ImportPeptideSearch.AddModifications(document, newPeptideMods));
}
public BuildPeptideSearchLibraryControl(SkylineWindow skylineWindow, ImportPeptideSearch importPeptideSearch, LibraryManager libraryManager)
{
SkylineWindow = skylineWindow;
ImportPeptideSearch = importPeptideSearch;
LibraryManager = libraryManager;
InitializeComponent();
textCutoff.Text = ImportPeptideSearch.CutoffScore.ToString(LocalizationHelper.CurrentCulture);
if (SkylineWindow.Document.PeptideCount == 0)
{
cbFilterForDocumentPeptides.Hide();
}
}
private void FillLists(SrmDocument document)
{
IList <StaticMod> modsToAdd, modsToCheck;
if (ImportPeptideSearch.IsDDASearch)
{
modsToAdd = Settings.Default.StaticModList.ToList();
modsToAdd.AddRange(Settings.Default.HeavyModList.Distinct());
modsToCheck = document.Settings.PeptideSettings.Modifications.StaticModifications.ToList();
modsToCheck.AddRange(document.Settings.PeptideSettings.Modifications.AllHeavyModifications.Distinct());
//modsToAdd = ImportPeptideSearch.UserDefinedTypedMods;
}
else
{
ImportPeptideSearch.UpdateModificationMatches(document);
modsToAdd = ImportPeptideSearch.GetMatchedMods().ToList();
modsToCheck = new List <StaticMod>(); // don't check any mods
}
modificationsListBox.Items.Clear();
unmatchedListBox.Items.Clear();
foreach (var match in modsToAdd)
{
modificationsListBox.Items.Add(new ListBoxModification(match, ImportPeptideSearch.IsDDASearch), modsToCheck.Contains(match));
}
var unmatched = ImportPeptideSearch.GetUnmatchedSequences();
if (unmatched != null && unmatched.Any())
{
splitContainer.Panel2Collapsed = false;
foreach (var uninterpretedMod in unmatched)
{
unmatchedListBox.Items.Add(uninterpretedMod);
}
}
else
{
splitContainer.Panel2Collapsed = true;
}
if (modificationsListBox.Items.Count <= 3)
{
cbSelectAll.Visible = false;
modificationsListBox.Height += cbSelectAll.Bottom - modificationsListBox.Bottom;
}
}
public BuildPeptideSearchLibraryControl(IModifyDocumentContainer documentContainer, ImportPeptideSearch importPeptideSearch, LibraryManager libraryManager)
{
DocumentContainer = documentContainer;
ImportPeptideSearch = importPeptideSearch;
LibraryManager = libraryManager;
InitializeComponent();
textCutoff.Text = ImportPeptideSearch.CutoffScore.ToString(LocalizationHelper.CurrentCulture);
if (DocumentContainer.Document.PeptideCount == 0)
{
cbFilterForDocumentPeptides.Hide();
}
_driverStandards = new SettingsListComboDriver <IrtStandard>(comboStandards, Settings.Default.IrtStandardList);
_driverStandards.LoadList(IrtStandard.EMPTY.GetKey());
}
public bool Initialize(SrmDocument document)
{
Document = document;
if (!ImportPeptideSearch.HasDocLib && !ImportPeptideSearch.IsDDASearch)
{
return(false);
}
if (ImportPeptideSearch.IsDDASearch)
{
labelModifications.Text = Resources.MatchModificationsControl_ModificationLabelText_DDA_Search;
btnAddModification.Text = Resources.MatchModificationsControl_Initialize__Edit_modifications;
menuItemAddStructuralModification.Text = Resources.MatchModificationsControl_Initialize_Edit__structural_modifications___;
menuItemAddHeavyModification.Text = Resources.MatchModificationsControl_Initialize_Edit__heavy_modifications___;
}
ImportPeptideSearch.InitializeModifications(document);
FillLists(document);
return(modificationsListBox.Items.Count > 1 || unmatchedListBox.Items.Count > 1);
}
public BuildPeptideSearchLibraryControl(IModifyDocumentContainer documentContainer, ImportPeptideSearch importPeptideSearch, LibraryManager libraryManager)
{
DocumentContainer = documentContainer;
ImportPeptideSearch = importPeptideSearch;
LibraryManager = libraryManager;
InitializeComponent();
textCutoff.Text = ImportPeptideSearch.CutoffScore.ToString(LocalizationHelper.CurrentCulture);
if (DocumentContainer.Document.PeptideCount == 0)
{
cbFilterForDocumentPeptides.Hide();
}
foreach (var standard in IrtStandard.ALL)
{
comboStandards.Items.Add(standard);
}
}
public SrmSettings AddCheckedModifications(SrmDocument document)
{
if (modificationsListBox.CheckedItems.Count == 0)
{
return(document.Settings);
}
// Find checked static mods
var newStructuralMods = (from mod in ImportPeptideSearch.MatcherPepMods.StaticModifications
from ListBoxModification checkedMod in modificationsListBox.CheckedItems
where mod.Equivalent(checkedMod.Mod)
select mod).ToList();
// Find checked heavy mods
var newHeavyMods = (from mod in ImportPeptideSearch.MatcherHeavyMods
from ListBoxModification checkedMod in modificationsListBox.CheckedItems
where mod.Equivalent(checkedMod.Mod)
select mod).ToList();
// Update document modifications
return(ImportPeptideSearch.AddModifications(document,
new PeptideModifications(newStructuralMods, new[] { new TypedModifications(IsotopeLabelType.heavy, newHeavyMods) })));
}
public bool UpdateResultsFiles(IEnumerable <string> dirPaths, bool overwrite)
{
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.ImportResultsControl_FindResultsFiles_Searching_for_Results_Files
})
{
try
{
longWaitDlg.PerformWork(WizardForm, 1000, longWaitBroker =>
ImportPeptideSearch.UpdateSpectrumSourceFilesFromDirs(dirPaths, overwrite, longWaitBroker));
}
catch (Exception x)
{
MessageDlg.ShowWithException(WizardForm, TextUtil.LineSeparate(
Resources.ImportResultsControl_FindResultsFiles_An_error_occurred_attempting_to_find_results_files_,
x.Message), x);
}
}
UpdateResultsFilesUI();
return(!MissingResultsFiles.Any());
}
public bool BuildPeptideSearchLibrary(CancelEventArgs e)
{
// Nothing to build, if now search files were specified
if (!SearchFilenames.Any())
{
var libraries = SkylineWindow.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(SkylineWindow.Document, SkylineWindow.DocumentFilePath, cbIncludeAmbiguousMatches.Checked);
}
catch (FileEx.DeleteException de)
{
MessageDlg.ShowException(this, de);
return(false);
}
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(SkylineWindow.DocumentUI);
var status = longWaitDlg.PerformWork(WizardForm, 800,
monitor => LibraryManager.BuildLibraryBackground(SkylineWindow, builder, monitor, new LibraryManager.BuildState(null, null)));
if (status.IsError)
{
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(SkylineWindow.DocumentFilePath))), x.Message), x);
return(false);
}
}
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 = comboStandards.SelectedItem as IrtStandard;
var addedIrts = false;
if (selectedIrtStandard != null && selectedIrtStandard != IrtStandard.NULL)
{
addedIrts = AddIrtLibraryTable(docLibSpec.FilePath, selectedIrtStandard);
}
var docNew = ImportPeptideSearch.AddDocumentSpectralLibrary(SkylineWindow.Document, docLibSpec);
if (docNew == null)
{
return(false);
}
if (addedIrts)
{
docNew = ImportPeptideSearch.AddRetentionTimePredictor(docNew, docLibSpec);
}
SkylineWindow.ModifyDocument(Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Add_document_spectral_library, doc => docNew);
if (!string.IsNullOrEmpty(builder.AmbiguousMatchesMessage))
{
MessageDlg.Show(WizardForm, builder.AmbiguousMatchesMessage);
}
return(true);
}
public bool ImportFasta()
{
var settings = SkylineWindow.Document.Settings;
var peptideSettings = settings.PeptideSettings;
int missedCleavages = MaxMissedCleavages;
var enzyme = Enzyme;
if (!Equals(missedCleavages, peptideSettings.DigestSettings.MaxMissedCleavages) || !Equals(enzyme, peptideSettings.Enzyme))
{
var digest = new DigestSettings(missedCleavages, peptideSettings.DigestSettings.ExcludeRaggedEnds);
peptideSettings = peptideSettings.ChangeDigestSettings(digest).ChangeEnzyme(enzyme);
SkylineWindow.ModifyDocument(string.Format(Resources.ImportFastaControl_ImportFasta_Change_digestion_settings), doc =>
doc.ChangeSettings(settings.ChangePeptideSettings(peptideSettings)));
}
if (!ContainsFastaContent) // The user didn't specify any FASTA content
{
var docCurrent = SkylineWindow.DocumentUI;
// If the document has precursor transitions already, then just trust the user
// knows what they are doing, and this document is already set up for MS1 filtering
if (HasPrecursorTransitions(docCurrent))
{
return(true);
}
if (docCurrent.PeptideCount == 0)
{
MessageDlg.Show(WizardForm, TextUtil.LineSeparate(Resources.ImportFastaControl_ImportFasta_The_document_does_not_contain_any_peptides_,
Resources.ImportFastaControl_ImportFasta_Please_import_FASTA_to_add_peptides_to_the_document_));
return(false);
}
if (MessageBox.Show(WizardForm, TextUtil.LineSeparate(Resources.ImportFastaControl_ImportFasta_The_document_does_not_contain_any_precursor_transitions_,
Resources.ImportFastaControl_ImportFasta_Would_you_like_to_change_the_document_settings_to_automatically_pick_the_precursor_transitions_specified_in_the_full_scan_settings_),
Program.Name, MessageBoxButtons.OKCancel) != DialogResult.OK)
{
return(false);
}
SkylineWindow.ModifyDocument(Resources.ImportFastaControl_ImportFasta_Change_settings_to_add_precursors, doc => ImportPeptideSearch.ChangeAutoManageChildren(doc, PickLevel.transitions, true));
}
else // The user specified some FASTA content
{
// If the user is about to add any new transitions by importing
// FASTA, set FragmentType='p' and AutoSelect=true
var docCurrent = SkylineWindow.Document;
var docNew = ImportPeptideSearch.PrepareImportFasta(docCurrent);
var nodeInsert = SkylineWindow.SequenceTree.SelectedNode as SrmTreeNode;
IdentityPath selectedPath = nodeInsert != null ? nodeInsert.Path : null;
int emptyPeptideGroups = 0;
if (!_fastaFile)
{
// Import FASTA as content
docNew = ImportFastaHelper.AddFasta(docNew, ref selectedPath, out emptyPeptideGroups);
// Document will be null if there was an error
if (docNew == null)
{
return(false);
}
}
else
{
// Import FASTA as file
var fastaPath = tbxFasta.Text;
try
{
using (var longWaitDlg = new LongWaitDlg(SkylineWindow)
{
Text = Resources.ImportFastaControl_ImportFasta_Insert_FASTA
})
{
IdentityPath to = selectedPath;
var docImportFasta = docNew;
longWaitDlg.PerformWork(WizardForm, 1000, longWaitBroker =>
{
IdentityPath nextAdd;
docImportFasta = ImportPeptideSearch.ImportFasta(docImportFasta, fastaPath,
longWaitBroker, to, out selectedPath, out nextAdd, out emptyPeptideGroups);
});
docNew = docImportFasta;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.SkylineWindow_ImportFastaFile_Failed_reading_the_file__0__1__,
fastaPath, x.Message), x);
return(false);
}
}
// Check for empty proteins
docNew = ImportFastaHelper.HandleEmptyPeptideGroups(WizardForm, emptyPeptideGroups, docNew);
// Document will be null if user was given option to keep or remove empty proteins and pressed cancel
if (docNew == null)
{
return(false);
}
SkylineWindow.ModifyDocument(Resources.ImportFastaControl_ImportFasta_Insert_FASTA, doc =>
{
if (!ReferenceEquals(doc, docCurrent))
{
throw new InvalidDataException(Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
}
return(docNew);
});
if (!VerifyAtLeastOnePrecursorTransition(SkylineWindow.Document))
{
return(false);
}
}
return(true);
}
public void CloseWizard(DialogResult result)
{
// Close file handles to the peptide search library
ImportPeptideSearch.ClosePeptideSearchLibraryStreams(Document);
DialogResult = result;
}
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)
{
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(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);
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>();
}
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();
}
public void InitializeChromatogramsPage(SrmDocument document)
{
ImportPeptideSearch.InitializeSpectrumSourceFiles(document);
UpdateResultsFiles(ImportPeptideSearch.GetDirsToSearch(DocumentDirectory), false);
}
public bool ImportFasta()
{
var settings = SkylineWindow.Document.Settings;
var peptideSettings = settings.PeptideSettings;
int missedCleavages = MaxMissedCleavages;
var enzyme = Enzyme;
if (!Equals(missedCleavages, peptideSettings.DigestSettings.MaxMissedCleavages) || !Equals(enzyme, peptideSettings.Enzyme))
{
var digest = new DigestSettings(missedCleavages, peptideSettings.DigestSettings.ExcludeRaggedEnds);
peptideSettings = peptideSettings.ChangeDigestSettings(digest).ChangeEnzyme(enzyme);
SkylineWindow.ModifyDocument(string.Format(Resources.ImportFastaControl_ImportFasta_Change_digestion_settings), doc =>
doc.ChangeSettings(settings.ChangePeptideSettings(peptideSettings)));
}
if (!string.IsNullOrEmpty(DecoyGenerationMethod))
{
if (!NumDecoys.HasValue || NumDecoys < 0)
{
MessageDlg.Show(WizardForm, Resources.ImportFastaControl_ImportFasta_Please_enter_a_valid_non_negative_number_of_decoys_per_target_);
txtNumDecoys.Focus();
return(false);
}
else if (Equals(DecoyGenerationMethod, DecoyGeneration.REVERSE_SEQUENCE) && NumDecoys > 1)
{
MessageDlg.Show(WizardForm, Resources.ImportFastaControl_ImportFasta_A_maximum_of_one_decoy_per_target_may_be_generated_when_using_reversed_decoys_);
txtNumDecoys.Focus();
return(false);
}
}
if (!ContainsFastaContent) // The user didn't specify any FASTA content
{
var docCurrent = SkylineWindow.DocumentUI;
// If the document has precursor transitions already, then just trust the user
// knows what they are doing, and this document is already set up for MS1 filtering
if (HasPrecursorTransitions(docCurrent))
{
return(true);
}
if (docCurrent.PeptideCount == 0)
{
MessageDlg.Show(WizardForm, TextUtil.LineSeparate(Resources.ImportFastaControl_ImportFasta_The_document_does_not_contain_any_peptides_,
Resources.ImportFastaControl_ImportFasta_Please_import_FASTA_to_add_peptides_to_the_document_));
return(false);
}
if (MessageBox.Show(WizardForm, TextUtil.LineSeparate(Resources.ImportFastaControl_ImportFasta_The_document_does_not_contain_any_precursor_transitions_,
Resources.ImportFastaControl_ImportFasta_Would_you_like_to_change_the_document_settings_to_automatically_pick_the_precursor_transitions_specified_in_the_full_scan_settings_),
Program.Name, MessageBoxButtons.OKCancel) != DialogResult.OK)
{
return(false);
}
SkylineWindow.ModifyDocument(Resources.ImportFastaControl_ImportFasta_Change_settings_to_add_precursors, doc => ImportPeptideSearch.ChangeAutoManageChildren(doc, PickLevel.transitions, true));
}
else // The user specified some FASTA content
{
// If the user is about to add any new transitions by importing
// FASTA, set FragmentType='p' and AutoSelect=true
var docCurrent = SkylineWindow.Document;
var docNew = ImportPeptideSearch.PrepareImportFasta(docCurrent);
var nodeInsert = SkylineWindow.SequenceTree.SelectedNode as SrmTreeNode;
IdentityPath selectedPath = nodeInsert != null ? nodeInsert.Path : null;
var newPeptideGroups = new List <PeptideGroupDocNode>();
if (!_fastaFile)
{
// Import FASTA as content
using (var longWaitDlg = new LongWaitDlg(SkylineWindow)
{
Text = Resources.ImportFastaControl_ImportFasta_Insert_FASTA
})
{
var docImportFasta = docNew;
longWaitDlg.PerformWork(WizardForm, 1000, longWaitBroker =>
{
docImportFasta = ImportFastaHelper.AddFasta(docImportFasta, longWaitBroker, ref selectedPath, out newPeptideGroups);
});
docNew = docImportFasta;
}
// Document will be null if there was an error
if (docNew == null)
{
return(false);
}
}
else
{
// Import FASTA as file
var fastaPath = tbxFasta.Text;
try
{
using (var longWaitDlg = new LongWaitDlg(SkylineWindow)
{
Text = Resources.ImportFastaControl_ImportFasta_Insert_FASTA
})
{
IdentityPath to = selectedPath;
var docImportFasta = docNew;
longWaitDlg.PerformWork(WizardForm, 1000, longWaitBroker =>
{
IdentityPath nextAdd;
docImportFasta = ImportPeptideSearch.ImportFasta(docImportFasta, fastaPath, longWaitBroker, to, out selectedPath, out nextAdd, out newPeptideGroups);
});
docNew = docImportFasta;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.SkylineWindow_ImportFastaFile_Failed_reading_the_file__0__1__,
fastaPath, x.Message), x);
return(false);
}
}
if (!newPeptideGroups.Any())
{
MessageDlg.Show(this, Resources.ImportFastaControl_ImportFasta_Importing_the_FASTA_did_not_create_any_target_proteins_);
return(false);
}
// Filter proteins based on number of peptides and add decoys
using (var dlg = new PeptidesPerProteinDlg(docNew, newPeptideGroups, DecoyGenerationMethod, NumDecoys ?? 0))
{
docNew = dlg.ShowDialog(WizardForm) == DialogResult.OK ? dlg.DocumentFinal : null;
}
// Document will be null if user was given option to keep or remove empty proteins and pressed cancel
if (docNew == null)
{
return(false);
}
if (AutoTrain)
{
docNew = docNew.ChangeSettings(docNew.Settings.ChangePeptideIntegration(integration => integration.ChangeAutoTrain(true)));
}
SkylineWindow.ModifyDocument(Resources.ImportFastaControl_ImportFasta_Insert_FASTA, doc =>
{
if (!ReferenceEquals(doc, docCurrent))
{
throw new InvalidDataException(Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
}
return(docNew);
});
if (RequirePrecursorTransition && !VerifyAtLeastOnePrecursorTransition(SkylineWindow.Document))
{
return(false);
}
}
return(true);
}
public bool ImportFasta(IrtStandard irtStandard)
{
var settings = DocumentContainer.Document.Settings;
var peptideSettings = settings.PeptideSettings;
int missedCleavages = MaxMissedCleavages;
var enzyme = Enzyme;
if (!Equals(missedCleavages, peptideSettings.DigestSettings.MaxMissedCleavages) || !Equals(enzyme, peptideSettings.Enzyme))
{
var digest = new DigestSettings(missedCleavages, peptideSettings.DigestSettings.ExcludeRaggedEnds);
peptideSettings = peptideSettings.ChangeDigestSettings(digest).ChangeEnzyme(enzyme);
DocumentContainer.ModifyDocumentNoUndo(doc =>
doc.ChangeSettings(settings.ChangePeptideSettings(peptideSettings)));
}
if (!string.IsNullOrEmpty(DecoyGenerationMethod))
{
if (!NumDecoys.HasValue || NumDecoys <= 0)
{
MessageDlg.Show(WizardForm, Resources.ImportFastaControl_ImportFasta_Please_enter_a_valid_number_of_decoys_per_target_greater_than_0_);
txtNumDecoys.Focus();
return(false);
}
else if (Equals(DecoyGenerationMethod, DecoyGeneration.REVERSE_SEQUENCE) && NumDecoys > 1)
{
MessageDlg.Show(WizardForm, Resources.ImportFastaControl_ImportFasta_A_maximum_of_one_decoy_per_target_may_be_generated_when_using_reversed_decoys_);
txtNumDecoys.Focus();
return(false);
}
}
if (!ContainsFastaContent) // The user didn't specify any FASTA content
{
var docCurrent = DocumentContainer.Document;
// If the document has precursor transitions already, then just trust the user
// knows what they are doing, and this document is already set up for MS1 filtering
if (HasPrecursorTransitions(docCurrent))
{
return(true);
}
if (docCurrent.PeptideCount == 0)
{
MessageDlg.Show(WizardForm, TextUtil.LineSeparate(Resources.ImportFastaControl_ImportFasta_The_document_does_not_contain_any_peptides_,
Resources.ImportFastaControl_ImportFasta_Please_import_FASTA_to_add_peptides_to_the_document_));
return(false);
}
if (MessageBox.Show(WizardForm, TextUtil.LineSeparate(Resources.ImportFastaControl_ImportFasta_The_document_does_not_contain_any_precursor_transitions_,
Resources.ImportFastaControl_ImportFasta_Would_you_like_to_change_the_document_settings_to_automatically_pick_the_precursor_transitions_specified_in_the_full_scan_settings_),
Program.Name, MessageBoxButtons.OKCancel) != DialogResult.OK)
{
return(false);
}
DocumentContainer.ModifyDocumentNoUndo(doc => ImportPeptideSearch.ChangeAutoManageChildren(doc, PickLevel.transitions, true));
}
else // The user specified some FASTA content
{
// If the user is about to add any new transitions by importing
// FASTA, set FragmentType='p' and AutoSelect=true
var docCurrent = DocumentContainer.Document;
var docNew = ImportPeptideSearch.PrepareImportFasta(docCurrent);
var nodeInsert = _sequenceTree.SelectedNode as SrmTreeNode;
IdentityPath selectedPath = nodeInsert != null ? nodeInsert.Path : null;
var newPeptideGroups = new List <PeptideGroupDocNode>();
if (!_fastaFile)
{
FastaText = tbxFasta.Text;
PasteError error = null;
// Import FASTA as content
using (var longWaitDlg = new LongWaitDlg(DocumentContainer)
{
Text = Resources.ImportFastaControl_ImportFasta_Insert_FASTA
})
{
var docImportFasta = docNew;
longWaitDlg.PerformWork(WizardForm, 1000, longWaitBroker =>
{
docImportFasta = ImportFastaHelper.AddFasta(docImportFasta, longWaitBroker, ref selectedPath, out newPeptideGroups, out error);
});
docNew = docImportFasta;
}
// Document will be null if there was an error
if (docNew == null)
{
ImportFastaHelper.ShowFastaError(error);
return(false);
}
}
else
{
// Import FASTA as file
var fastaPath = tbxFasta.Text;
try
{
using (var longWaitDlg = new LongWaitDlg(DocumentContainer)
{
Text = Resources.ImportFastaControl_ImportFasta_Insert_FASTA
})
{
IdentityPath to = selectedPath;
var docImportFasta = docNew;
longWaitDlg.PerformWork(WizardForm, 1000, longWaitBroker =>
{
IdentityPath nextAdd;
docImportFasta = ImportPeptideSearch.ImportFasta(docImportFasta, fastaPath, longWaitBroker, to, out selectedPath, out nextAdd, out newPeptideGroups);
});
docNew = docImportFasta;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.SkylineWindow_ImportFastaFile_Failed_reading_the_file__0__1__,
fastaPath, x.Message), x);
return(false);
}
}
if (!newPeptideGroups.Any())
{
MessageDlg.Show(this, Resources.ImportFastaControl_ImportFasta_Importing_the_FASTA_did_not_create_any_target_proteins_);
return(false);
}
// Filter proteins based on number of peptides and add decoys
using (var dlg = new PeptidesPerProteinDlg(docNew, newPeptideGroups, DecoyGenerationMethod, NumDecoys ?? 0))
{
docNew = dlg.ShowDialog(WizardForm) == DialogResult.OK ? dlg.DocumentFinal : null;
}
// Document will be null if user was given option to keep or remove empty proteins and pressed cancel
if (docNew == null)
{
return(false);
}
// Add iRT standards if not present
if (irtStandard != null && !irtStandard.Name.Equals(IrtStandard.EMPTY.Name))
{
using (var reader = irtStandard.GetDocumentReader())
{
if (reader != null)
{
var standardMap = new TargetMap <bool>(irtStandard.Peptides.Select(pep => new KeyValuePair <Target, bool>(pep.ModifiedTarget, true)));
var docStandards = new TargetMap <bool>(docNew.Peptides
.Where(nodePep => standardMap.ContainsKey(nodePep.ModifiedTarget)).Select(nodePep =>
new KeyValuePair <Target, bool>(nodePep.ModifiedTarget, true)));
if (irtStandard.Peptides.Any(pep => !docStandards.ContainsKey(pep.ModifiedTarget)))
{
docNew = docNew.ImportDocumentXml(reader,
string.Empty,
Model.Results.MeasuredResults.MergeAction.remove,
false,
null,
Settings.Default.StaticModList,
Settings.Default.HeavyModList,
new IdentityPath(docNew.Children.First().Id),
out _,
out _,
false);
}
}
}
}
if (AutoTrain)
{
if (!docNew.Peptides.Any(pep => pep.IsDecoy))
{
MessageDlg.Show(this, Resources.ImportFastaControl_ImportFasta_Cannot_automatically_train_mProphet_model_without_decoys__but_decoy_options_resulted_in_no_decoys_being_generated__Please_increase_number_of_decoys_per_target__or_disable_automatic_training_of_mProphet_model_);
return(false);
}
docNew = docNew.ChangeSettings(docNew.Settings.ChangePeptideIntegration(integration => integration.ChangeAutoTrain(true)));
}
DocumentContainer.ModifyDocumentNoUndo(doc =>
{
if (!ReferenceEquals(doc, docCurrent))
{
throw new InvalidDataException(Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
}
return(docNew);
});
if (RequirePrecursorTransition && !VerifyAtLeastOnePrecursorTransition(DocumentContainer.Document))
{
return(false);
}
}
return(true);
}
public DDASearchControl(ImportPeptideSearch importPeptideSearch)
{
InitializeComponent();
ImportPeptideSearch = importPeptideSearch;
UpdateUI = UpdateSearchEngineProgress;
}
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;
}
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 status = longWaitDlg.PerformWork(WizardForm, 800,
monitor => LibraryManager.BuildLibraryBackground(DocumentContainer, builder, monitor, new LibraryManager.BuildState(null, null)));
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 = comboStandards.SelectedItem as IrtStandard;
var addedIrts = false;
if (selectedIrtStandard != null && selectedIrtStandard != IrtStandard.EMPTY)
{
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);
}
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;
}
}
private SrmDocument GetDocumentFinal(CancellationToken cancellationToken, SrmDocument doc, int minPeptides, bool removeRepeated, bool removeDuplicate, out int?emptyProteins)
{
emptyProteins = null;
// Remove repeated/duplicate peptides
var newDoc = removeRepeated || removeDuplicate
? new RefinementSettings {
RemoveRepeatedPeptides = removeRepeated, RemoveDuplicatePeptides = removeDuplicate
}.Refine(doc)
: doc;
if (cancellationToken.IsCancellationRequested)
{
return(null);
}
// Remove proteins without enough peptides
newDoc = ImportPeptideSearch.RemoveProteinsByPeptideCount(newDoc, minPeptides);
if (cancellationToken.IsCancellationRequested)
{
return(null);
}
// Move iRT proteins to top
var irtPeptides = new HashSet <Target>(RCalcIrt.IrtPeptides(newDoc));
var proteins = new List <PeptideGroupDocNode>(newDoc.PeptideGroups);
var proteinsIrt = new List <PeptideGroupDocNode>();
for (var i = 0; i < proteins.Count; i++)
{
var nodePepGroup = proteins[i];
if (nodePepGroup.Peptides.All(nodePep => irtPeptides.Contains(new Target(nodePep.ModifiedSequence))))
{
proteinsIrt.Add(nodePepGroup);
proteins.RemoveAt(i--);
}
}
if (proteinsIrt.Any())
{
newDoc = (SrmDocument)newDoc.ChangeChildrenChecked(proteinsIrt.Concat(proteins).Cast <DocNode>().ToArray());
}
if (cancellationToken.IsCancellationRequested)
{
return(null);
}
// Add decoys
newDoc = AddDecoys(newDoc);
if (cancellationToken.IsCancellationRequested)
{
return(null);
}
// Count empty proteins
emptyProteins = newDoc.PeptideGroups.Count(pepGroup => pepGroup.PeptideCount == 0);
if (cancellationToken.IsCancellationRequested)
{
return(null);
}
return(newDoc);
}
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);
}
