public void AddModification(StaticMod mod, ModType type)
{
if (mod == null)
{
return;
}
ImportPeptideSearch.UserDefinedTypedMods.Add(mod);
PeptideModifications peptideModifications = DocumentContainer.Document.Settings.PeptideSettings.Modifications;
if (type == ModType.structural)
{
peptideModifications = peptideModifications.ChangeStaticModifications(
peptideModifications.StaticModifications.Concat(new[] { mod }).ToArray());
}
else
{
peptideModifications = peptideModifications.AddHeavyModifications(new[] { mod });
}
DocumentContainer.ModifyDocumentNoUndo(doc => doc.ChangeSettings(DocumentContainer.Document.Settings.ChangePeptideSettings(
DocumentContainer.Document.Settings.PeptideSettings.ChangeModifications(peptideModifications))));
DocumentContainer.Document.Settings.UpdateDefaultModifications(false);
FillLists(DocumentContainer.Document);
}
private bool AddExistingLibrary(CancelEventArgs e)
{
string libraryPath = ValidateLibraryPath();
if (libraryPath == null)
{
e.Cancel = true;
return(false);
}
var peptideLibraries = DocumentContainer.Document.Settings.PeptideSettings.Libraries;
var docLibSpec = peptideLibraries.LibrarySpecs.FirstOrDefault(spec => spec.FilePath == libraryPath);
if (docLibSpec == null)
{
docLibSpec =
Settings.Default.SpectralLibraryList.FirstOrDefault(spec => spec.FilePath == libraryPath);
if (docLibSpec == null)
{
var existingNames = new HashSet <string>();
existingNames.UnionWith(Settings.Default.SpectralLibraryList.Select(spec => spec.Name));
existingNames.UnionWith(peptideLibraries.LibrarySpecs.Select(spec => spec.Name));
string libraryName =
Helpers.GetUniqueName(Path.GetFileNameWithoutExtension(libraryPath), existingNames);
docLibSpec = LibrarySpec.CreateFromPath(libraryName, libraryPath);
Settings.Default.SpectralLibraryList.SetValue(docLibSpec);
}
}
if (!LoadPeptideSearchLibrary(docLibSpec))
{
return(false);
}
DocumentContainer.ModifyDocumentNoUndo(doc => ImportPeptideSearch.AddDocumentSpectralLibrary(doc, docLibSpec));
return(true);
}
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);
}
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);
}