public ChooseIrtStandardPeptidesDlg(SrmDocument document, string documentFilePath, IEnumerable <PeptideGroupDocNode> peptideGroups)
{
InitializeComponent();
Document = document;
_documentFilePath = documentFilePath;
_librarySpectra = new List <SpectrumMzInfo>();
_irtPeptides = new List <MeasuredRetentionTime>();
_irtPeptideSequences = null;
PeptideGroupDocNode[] proteinsContainingCommonIrts, proteinsNotContainingCommonIrts;
CreateIrtCalculatorDlg.SeparateProteinGroups(peptideGroups, out proteinsContainingCommonIrts, out proteinsNotContainingCommonIrts);
foreach (var protein in proteinsContainingCommonIrts.Concat(proteinsNotContainingCommonIrts))
{
comboProteins.Items.Add(new PeptideGroupItem(protein));
}
if (proteinsContainingCommonIrts.Any())
{
comboProteins.SelectedIndex = 0;
}
UpdateSelection(this, null);
}
public ChooseIrtStandardPeptidesDlg(SrmDocument document, string documentFilePath, ICollection <DbIrtPeptide> dbIrtPeptides, IEnumerable <PeptideGroupDocNode> peptideGroups)
{
InitializeComponent();
Document = document;
Regression = null;
_documentFilePath = documentFilePath;
_dbIrtPeptides = dbIrtPeptides;
_librarySpectra = new List <SpectrumMzInfo>();
_irtAdd = new List <MeasuredRetentionTime>();
_irtTargets = null;
comboExisting.Items.AddRange(IrtStandard.ALL.Where(standard => !standard.Name.Equals(IrtStandard.EMPTY.Name) && !standard.Name.Equals(IrtStandard.AUTO.Name))
.Cast <object>().ToArray());
comboExisting.SelectedIndex = 0;
PeptideGroupDocNode[] proteinsContainingCommonIrts, proteinsNotContainingCommonIrts;
CreateIrtCalculatorDlg.SeparateProteinGroups(peptideGroups, out proteinsContainingCommonIrts, out proteinsNotContainingCommonIrts);
foreach (var protein in proteinsContainingCommonIrts.Concat(proteinsNotContainingCommonIrts))
{
comboProteins.Items.Add(new PeptideGroupItem(protein));
}
if (proteinsContainingCommonIrts.Any())
{
comboProteins.SelectedIndex = 0;
}
UpdateSelection(this, null);
}
private void ImportMassList(MassListInputs inputs, string description)
{
SrmTreeNode nodePaste = SequenceTree.SelectedNode as SrmTreeNode;
IdentityPath insertPath = nodePaste != null ? nodePaste.Path : null;
IdentityPath selectPath = null;
List<MeasuredRetentionTime> irtPeptides = null;
List<SpectrumMzInfo> librarySpectra = null;
List<TransitionImportErrorInfo> errorList = null;
List<PeptideGroupDocNode> peptideGroups = null;
RetentionTimeRegression retentionTimeRegressionStore = null;
var docCurrent = DocumentUI;
SrmDocument docNew = null;
var retentionTimeRegression = docCurrent.Settings.PeptideSettings.Prediction.RetentionTime;
RCalcIrt calcIrt = retentionTimeRegression != null ? (retentionTimeRegression.Calculator as RCalcIrt) : null;
using (var longWaitDlg = new LongWaitDlg(this) {Text = description})
{
longWaitDlg.PerformWork(this, 1000, longWaitBroker =>
{
docNew = docCurrent.ImportMassList(inputs, longWaitBroker,
insertPath, out selectPath, out irtPeptides, out librarySpectra, out errorList, out peptideGroups);
});
}
bool isDocumentSame = ReferenceEquals(docNew, docCurrent);
// If nothing was imported (e.g. operation was canceled or zero error-free transitions) and also no errors, just return
if (isDocumentSame && !errorList.Any())
return;
// Show the errors, giving the option to accept the transitions without errors,
// if there are any
if (errorList.Any())
{
using (var errorDlg = new ImportTransitionListErrorDlg(errorList, isDocumentSame))
{
if (errorDlg.ShowDialog(this) == DialogResult.Cancel || isDocumentSame)
{
return;
}
}
}
var dbIrtPeptides = irtPeptides.Select(rt => new DbIrtPeptide(rt.PeptideSequence, rt.RetentionTime, false, TimeSource.scan)).ToList();
var dbIrtPeptidesFilter = ImportAssayLibraryHelper.GetUnscoredIrtPeptides(dbIrtPeptides, calcIrt);
bool overwriteExisting = false;
MassListInputs irtInputs = null;
// If there are no iRT peptides or none with different values than the database, don't import any iRT's
if (dbIrtPeptidesFilter.Any())
{
// Ask whether or not to include iRT peptides in the paste
string useIrtMessage = calcIrt == null
? Resources.SkylineWindow_ImportMassList_The_transition_list_appears_to_contain_iRT_values__but_the_document_does_not_have_an_iRT_calculator___Create_a_new_calculator_and_add_these_iRT_values_
: Resources.SkylineWindow_ImportMassList_The_transition_list_appears_to_contain_iRT_library_values___Add_these_iRT_values_to_the_iRT_calculator_;
string yesButton = calcIrt == null
? Resources.SkylineWindow_ImportMassList__Create___
: Resources.SkylineWindow_ImportMassList_Add;
var useIrtResult = MultiButtonMsgDlg.Show(this, useIrtMessage,
yesButton, Resources.SkylineWindow_ImportMassList__Skip, true);
if (useIrtResult == DialogResult.Cancel)
{
return;
}
if (useIrtResult == DialogResult.Yes)
{
if (calcIrt == null)
{
// If there is no iRT calculator, ask the user to create one
using (var dlg = new CreateIrtCalculatorDlg(docNew, DocumentFilePath, Settings.Default.RTScoreCalculatorList, peptideGroups))
{
if (dlg.ShowDialog(this) != DialogResult.OK)
{
return;
}
docNew = dlg.Document;
calcIrt = (RCalcIrt)docNew.Settings.PeptideSettings.Prediction.RetentionTime.Calculator;
dlg.UpdateLists(librarySpectra, dbIrtPeptidesFilter);
if (!string.IsNullOrEmpty(dlg.IrtFile))
irtInputs = new MassListInputs(dlg.IrtFile);
}
}
string dbPath = calcIrt.DatabasePath;
IrtDb db = File.Exists(dbPath) ? IrtDb.GetIrtDb(dbPath, null) : IrtDb.CreateIrtDb(dbPath);
var oldPeptides = db.GetPeptides().ToList();
IList<DbIrtPeptide.Conflict> conflicts;
dbIrtPeptidesFilter = DbIrtPeptide.MakeUnique(dbIrtPeptidesFilter);
DbIrtPeptide.FindNonConflicts(oldPeptides, dbIrtPeptidesFilter, null, out conflicts);
// Ask whether to keep or overwrite peptides that are present in the import and already in the database
if (conflicts.Any())
{
string messageOverwrite = string.Format(Resources.SkylineWindow_ImportMassList_The_iRT_calculator_already_contains__0__of_the_imported_peptides_,
conflicts.Count);
var overwriteResult = MultiButtonMsgDlg.Show(this,
TextUtil.LineSeparate(messageOverwrite, conflicts.Count == 1
? Resources.SkylineWindow_ImportMassList_Keep_the_existing_iRT_value_or_overwrite_with_the_imported_value_
: Resources.SkylineWindow_ImportMassList_Keep_the_existing_iRT_values_or_overwrite_with_imported_values_),
Resources.SkylineWindow_ImportMassList__Keep, Resources.SkylineWindow_ImportMassList__Overwrite, true);
if (overwriteResult == DialogResult.Cancel)
{
return;
}
overwriteExisting = overwriteResult == DialogResult.No;
}
using (var longWaitDlg = new LongWaitDlg(this) { Text = Resources.SkylineWindow_ImportMassList_Adding_iRT_values_})
{
longWaitDlg.PerformWork(this, 100, progressMonitor =>
docNew = docNew.AddIrtPeptides(dbIrtPeptidesFilter, overwriteExisting, progressMonitor));
}
if (docNew == null)
return;
retentionTimeRegressionStore = docNew.Settings.PeptideSettings.Prediction.RetentionTime;
}
}
BiblioSpecLiteSpec docLibrarySpec = null;
BiblioSpecLiteLibrary docLibrary = null;
int indexOldLibrary = -1;
if (librarySpectra.Any())
{
string addLibraryMessage = Resources.SkylineWindow_ImportMassList_The_transition_list_appears_to_contain_spectral_library_intensities___Create_a_document_library_from_these_intensities_;
var addLibraryResult = MultiButtonMsgDlg.Show(this, addLibraryMessage,
Resources.SkylineWindow_ImportMassList__Create___, Resources.SkylineWindow_ImportMassList__Skip,
true);
if (addLibraryResult == DialogResult.Cancel)
{
return;
}
if (addLibraryResult == DialogResult.Yes)
{
// Can't name a library after the document if the document is unsaved
// In this case, prompt to save
if (DocumentFilePath == null)
{
string saveDocumentMessage = Resources.SkylineWindow_ImportMassList_You_must_save_the_Skyline_document_in_order_to_create_a_spectral_library_from_a_transition_list_;
var saveDocumentResult = MultiButtonMsgDlg.Show(this, saveDocumentMessage, MultiButtonMsgDlg.BUTTON_OK);
if (saveDocumentResult == DialogResult.Cancel)
{
return;
}
else if (!SaveDocumentAs())
{
return;
}
}
librarySpectra = SpectrumMzInfo.RemoveDuplicateSpectra(librarySpectra);
string documentLibrary = BiblioSpecLiteSpec.GetLibraryFileName(DocumentFilePath);
// ReSharper disable once AssignNullToNotNullAttribute
string outputPath = Path.Combine(Path.GetDirectoryName(documentLibrary),
Path.GetFileNameWithoutExtension(documentLibrary) + BiblioSpecLiteSpec.ASSAY_NAME + BiblioSpecLiteSpec.EXT);
bool libraryExists = File.Exists(outputPath);
string name = Path.GetFileNameWithoutExtension(DocumentFilePath) + BiblioSpecLiteSpec.ASSAY_NAME;
indexOldLibrary = docNew.Settings.PeptideSettings.Libraries.LibrarySpecs.IndexOf(spec => spec != null && spec.FilePath == outputPath);
bool libraryLinkedToDoc = indexOldLibrary != -1;
if (libraryLinkedToDoc)
{
string oldName = docNew.Settings.PeptideSettings.Libraries.LibrarySpecs[indexOldLibrary].Name;
var libraryOld = docNew.Settings.PeptideSettings.Libraries.GetLibrary(oldName);
var additionalSpectra = SpectrumMzInfo.GetInfoFromLibrary(libraryOld);
additionalSpectra = SpectrumMzInfo.RemoveDuplicateSpectra(additionalSpectra);
librarySpectra = SpectrumMzInfo.MergeWithOverwrite(librarySpectra, additionalSpectra);
foreach (var stream in libraryOld.ReadStreams)
stream.CloseStream();
}
if (libraryExists && !libraryLinkedToDoc)
{
string replaceLibraryMessage = string.Format(Resources.SkylineWindow_ImportMassList_There_is_an_existing_library_with_the_same_name__0__as_the_document_library_to_be_created___Overwrite_this_library_or_skip_import_of_library_intensities_,
name);
// If the document does not have an assay library linked to it, then ask if user wants to delete the one that we have found
var replaceLibraryResult = MultiButtonMsgDlg.Show(this, replaceLibraryMessage,
Resources.SkylineWindow_ImportMassList__Overwrite, Resources.SkylineWindow_ImportMassList__Skip, true);
if (replaceLibraryResult == DialogResult.Cancel)
return;
if (replaceLibraryResult == DialogResult.No)
librarySpectra.Clear();
}
if (librarySpectra.Any())
{
// Delete the existing library; either it's not tied to the document or we've already extracted the spectra
if (libraryExists)
{
FileEx.SafeDelete(outputPath);
FileEx.SafeDelete(Path.ChangeExtension(outputPath, BiblioSpecLiteSpec.EXT_REDUNDANT));
}
using (var blibDb = BlibDb.CreateBlibDb(outputPath))
{
docLibrarySpec = new BiblioSpecLiteSpec(name, outputPath);
using (var longWaitDlg = new LongWaitDlg(this) { Text = Resources.SkylineWindow_ImportMassList_Creating_Spectral_Library })
{
longWaitDlg.PerformWork(this, 1000, progressMonitor =>
{
docLibrary = blibDb.CreateLibraryFromSpectra(docLibrarySpec, librarySpectra, name, progressMonitor);
if (docLibrary == null)
return;
var newSettings = docNew.Settings.ChangePeptideLibraries(libs => libs.ChangeLibrary(docLibrary, docLibrarySpec, indexOldLibrary));
var status = new ProgressStatus(Resources.SkylineWindow_ImportMassList_Finishing_up_import);
progressMonitor.UpdateProgress(status);
progressMonitor.UpdateProgress(status.ChangePercentComplete(100));
docNew = docNew.ChangeSettings(newSettings);
});
if (docLibrary == null)
return;
}
}
}
}
}
ModifyDocument(description, doc =>
{
if (ReferenceEquals(doc, docCurrent))
return docNew;
try
{
// If the document was changed during the operation, try all the changes again
// using the information given by the user.
docCurrent = DocumentUI;
doc = doc.ImportMassList(inputs, insertPath, out selectPath);
if (irtInputs != null)
{
doc = doc.ImportMassList(irtInputs, null, out selectPath);
}
var newSettings = doc.Settings;
if (retentionTimeRegressionStore != null)
{
newSettings = newSettings.ChangePeptidePrediction(prediction =>
prediction.ChangeRetentionTime(retentionTimeRegressionStore));
}
if (docLibrarySpec != null)
{
newSettings = newSettings.ChangePeptideLibraries(libs =>
libs.ChangeLibrary(docLibrary, docLibrarySpec, indexOldLibrary));
}
if (!ReferenceEquals(doc.Settings, newSettings))
doc = doc.ChangeSettings(newSettings);
}
catch (Exception x)
{
throw new InvalidDataException(string.Format(Resources.SkylineWindow_ImportMassList_Unexpected_document_change_during_operation___0_, x.Message, x));
}
return doc;
});
if (selectPath != null)
SequenceTree.SelectedPath = selectPath;
if (retentionTimeRegressionStore != null)
{
Settings.Default.RetentionTimeList.Add(retentionTimeRegressionStore);
Settings.Default.RTScoreCalculatorList.Add(retentionTimeRegressionStore.Calculator);
}
if (docLibrarySpec != null)
{
Settings.Default.SpectralLibraryList.Insert(0, docLibrarySpec);
}
}