protected override void DoTest()
{
// Test non-cancellable dialog.
using (var longWaitDlg = new LongWaitDlg(null, false))
{
longWaitDlg.PerformWork(Program.MainWindow, 20, () =>
{
for (int i = 0; i < 100; i += 10)
{
Thread.Sleep(5);
longWaitDlg.ProgressValue = i;
}
});
}
// Show cancellable dialog if we're running this Form from SkylineTester.
if (Program.PauseForms != null && Program.PauseForms.Contains(typeof(LongWaitDlg).Name))
{
using (var longWaitDlg = new LongWaitDlg())
{
longWaitDlg.PerformWork(Program.MainWindow, 0, () =>
{
WaitForOpenForm<LongWaitDlg>();
longWaitDlg.CancelButton.PerformClick();
});
Assert.IsTrue(longWaitDlg.IsCanceled);
}
}
}
public void AddDirectory(string dirPath)
{
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.BuildLibraryDlg_AddDirectory_Find_Input_Files,
})
{
try
{
var inputFiles = new List<string>();
longWaitDlg.PerformWork(this, 800, broker => FindInputFiles(dirPath, inputFiles, broker));
AddInputFiles(inputFiles);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.BuildLibraryDlg_AddDirectory_An_error_occurred_reading_files_in_the_directory__0__,
dirPath),
x.Message);
MessageDlg.ShowWithException(this, message, x);
}
}
}
public void ApplyPeak(bool subsequent)
{
var nodePepTree = SequenceTree.GetNodeOfType<PeptideTreeNode>();
var nodeTranGroupTree = SequenceTree.GetNodeOfType<TransitionGroupTreeNode>();
var nodeTranGroup = nodeTranGroupTree != null ? nodeTranGroupTree.DocNode : null;
using (var longWait = new LongWaitDlg(this) { Text = Resources.SkylineWindow_ApplyPeak_Applying_Peak })
{
SrmDocument doc = null;
try
{
var resultsIndex = SelectedResultsIndex;
var resultsFile = _listGraphChrom[resultsIndex].SelectedFileIndex;
longWait.PerformWork(this, 800, monitor => doc = PeakMatcher.ApplyPeak(Document, nodePepTree, nodeTranGroup, resultsIndex, resultsFile, subsequent, monitor));
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, TextUtil.LineSeparate(Resources.SkylineWindow_ApplyPeak_Failed_to_apply_peak_, x.Message), x);
}
if (!longWait.IsCanceled && doc != null && !ReferenceEquals(doc, Document))
{
ModifyDocument(Resources.SkylineWindow_PickPeakInChromatograms_Apply_picked_peak, document => doc);
}
}
}
public override void PerformLongExport(Action<IProgressMonitor> performExport)
{
if (!ShowMessages)
{
performExport(new SilentProgressMonitor());
return;
}
using (var longWait = new LongWaitDlg
{
Text = Resources.ExportDlgProperties_PerformLongExport_Exporting_Methods
})
{
try
{
var status = longWait.PerformWork(_dialog, 800, performExport);
if (status.IsError)
MessageDlg.ShowException(_dialog, status.ErrorException);
}
catch (Exception x)
{
MessageDlg.ShowWithException(_dialog, TextUtil.LineSeparate(Resources.ExportDlgProperties_PerformLongExport_An_error_occurred_attempting_to_export,
x.Message), x);
}
}
}
private bool GetR()
{
try
{
using (var dlg = new LongWaitDlg {Message = Resources.RInstaller_InstallR_Downloading_R, ProgressValue = 0})
{
// Short wait, because this can't possible happen fast enough to avoid
// showing progress, except in testing
dlg.PerformWork(this, 50, DownloadR);
}
using (var dlg = new LongWaitDlg(null, false) {Message = Resources.RInstaller_GetR_Installing_R})
{
dlg.PerformWork(this, 50, InstallR);
}
MessageDlg.Show(this, Resources.RInstaller_GetR_R_installation_complete_);
}
catch (TargetInvocationException ex)
{
if (ex.InnerException.GetType() == typeof (ToolExecutionException))
{
MessageDlg.ShowException(this, ex);
return false;
}
throw;
}
return true;
}
public bool WriteChromatograms(string filePath)
{
var fileNames = (from object fileName in checkedListVars.CheckedItems select fileName.ToString()).ToList();
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.ExportChromatogramDlg_OkDialog_Exporting_Chromatograms,
})
{
try
{
longWaitDlg.PerformWork(this, 1000,
broker => WriteChromatograms(filePath,
broker,
fileNames,
LocalizationHelper.CurrentCulture,
_chromExtractors,
_chromSources));
if (longWaitDlg.IsCanceled)
return false;
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.ExportChromatogramDlg_OkDialog_Failed_attempting_to_save_chromatograms_to__0__, filePath),
x.Message);
MessageDlg.ShowWithException(this, message, x);
}
}
return true;
}
public void AddFastaFile(string fastaFilePath)
{
String databasePath = textPath.Text;
Settings.Default.FastaDirectory = Path.GetDirectoryName(fastaFilePath);
using (var longWaitDlg = new LongWaitDlg { ProgressValue = 0 })
{
var progressMonitor = new ProgressMonitor(longWaitDlg);
try
{
longWaitDlg.PerformWork(this, 0, () =>
{
ProteomeDb proteomeDb = File.Exists(databasePath)
? ProteomeDb.OpenProteomeDb(databasePath)
: ProteomeDb.CreateProteomeDb(databasePath);
using (proteomeDb)
{
using (var reader = File.OpenText(fastaFilePath))
{
proteomeDb.AddFastaFile(reader, progressMonitor.UpdateProgress);
}
}
});
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.BuildBackgroundProteomeDlg_AddFastaFile_An_error_occurred_attempting_to_add_the_FASTA_file__0__,
fastaFilePath), x.Message);
MessageDlg.ShowWithException(this, message, x);
return;
}
}
string path = Path.GetFileName(fastaFilePath);
if (path != null)
listboxFasta.Items.Add(path);
RefreshStatus();
}
/// <summary>
/// Uses an <see cref="IToolStoreClient"/> to download (zip files) for each of the tools selected in the form's checklistbox.
/// Returns a collection of tools to be updated.
/// </summary>
private ICollection<ToolUpdateInfo> GetToolsToUpdate()
{
labelOperation.Text = Resources.ToolUpdatesDlg_GetTools_Downloading_Updates;
var toolsToDownload = new Collection<ToolUpdateInfo>();
var toolList = _tools.Keys.ToList();
// get tools to update based on which ones are checked
foreach (int index in checkedListBoxTools.CheckedIndices)
{
toolsToDownload.Add(toolList[index]);
}
ICollection<ToolUpdateInfo> successfulDownloads = null;
ICollection<string> failedDownloads = null;
using (var dlg = new LongWaitDlg {Message = Resources.ToolUpdatesDlg_GetToolsToUpdate_Downloading_Updates})
{
dlg.PerformWork(this, 1000,
longWaitBroker =>
DownloadTools(longWaitBroker, toolsToDownload, out successfulDownloads,
out failedDownloads));
}
DisplayDownloadSummary(failedDownloads);
return successfulDownloads;
}
public bool SaveDocument(String fileName, bool includingCacheFile = true)
{
if (string.IsNullOrEmpty(DocumentUI.Settings.DataSettings.DocumentGuid) ||
!Equals(DocumentFilePath, fileName))
{
SrmDocument docOriginal;
SrmDocument docNew;
do
{
docOriginal = Document;
docNew =
docOriginal.ChangeSettings(
docOriginal.Settings.ChangeDataSettings(
docOriginal.Settings.DataSettings.ChangeDocumentGuid()));
} while (!SetDocument(docNew, docOriginal));
}
SrmDocument document = Document;
try
{
using (var saver = new FileSaver(fileName))
{
saver.CheckException();
using (var longWaitDlg = new LongWaitDlg(this)
{
Text = Resources.SkylineWindow_SaveDocument_Saving___,
Message = Path.GetFileName(fileName)
})
{
longWaitDlg.PerformWork(this, 800, progressMonitor =>
{
using (var writer = new XmlWriterWithProgress(saver.SafeName, fileName, Encoding.UTF8,
document.MoleculeTransitionCount, progressMonitor)
{
Formatting = Formatting.Indented
})
{
XmlSerializer ser = new XmlSerializer(typeof(SrmDocument));
ser.Serialize(writer, document);
writer.Flush();
writer.Close();
// If the user has chosen "Save As", and the document has a
// document specific spectral library, copy this library to
// the new name.
if (!Equals(DocumentFilePath, fileName))
SaveDocumentLibraryAs(fileName);
saver.Commit();
}
});
// Sometimes this catches a cancellation that doesn't throw an OperationCanceledException.
if (longWaitDlg.IsCanceled)
return false;
}
}
}
catch (OperationCanceledException)
{
return false;
}
catch (Exception ex)
{
var message = TextUtil.LineSeparate(string.Format(Resources.SkylineWindow_SaveDocument_Failed_writing_to__0__, fileName), ex.Message);
MessageBox.Show(message);
return false;
}
DocumentFilePath = fileName;
_savedVersion = document.UserRevisionIndex;
SetActiveFile(fileName);
// Make sure settings lists contain correct values for this document.
document.Settings.UpdateLists(DocumentFilePath);
try
{
SaveLayout(fileName);
// CONSIDER: Is this really optional?
if (includingCacheFile)
{
using (var longWaitDlg = new LongWaitDlg(this)
{
Text = Resources.SkylineWindow_SaveDocument_Optimizing_data_file___,
Message = Path.GetFileName(fileName)
})
{
longWaitDlg.PerformWork(this, 800, () =>
OptimizeCache(fileName, longWaitDlg));
}
}
}
// We allow silent failures because it is OK for the cache to remain unoptimized
// or the layout to not be saved. These aren't critical as long as the document
// was saved correctly.
catch (UnauthorizedAccessException) {}
catch (IOException) {}
catch (OperationCanceledException) {}
catch (TargetInvocationException) {}
return true;
}
public bool OpenSharedFile(string zipPath)
{
try
{
var sharing = new SrmDocumentSharing(zipPath);
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.SkylineWindow_OpenSharedFile_Extracting_Files,
})
{
longWaitDlg.PerformWork(this, 1000, sharing.Extract);
if (longWaitDlg.IsCanceled)
return false;
}
// Remember the directory containing the newly extracted file
// as the active directory for the next open command.
Settings.Default.ActiveDirectory = Path.GetDirectoryName(sharing.DocumentPath);
return OpenFile(sharing.DocumentPath);
}
catch (ZipException zipException)
{
MessageDlg.ShowWithException(this, string.Format(Resources.SkylineWindow_OpenSharedFile_The_zip_file__0__cannot_be_read,
zipPath), zipException);
return false;
}
catch (Exception e)
{
var message = TextUtil.LineSeparate(string.Format(
Resources.SkylineWindow_OpenSharedFile_Failure_extracting_Skyline_document_from_zip_file__0__,
zipPath), e.Message);
MessageDlg.ShowWithException(this, message, e);
return false;
}
}
public bool OpenFile(string path, FormEx parentWindow = null)
{
// Remove any extraneous temporary chromatogram spill files.
var spillDirectory = Path.Combine(Path.GetDirectoryName(path) ?? "", "xic"); // Not L10N
if (Directory.Exists(spillDirectory))
DirectoryEx.SafeDelete(spillDirectory);
Exception exception = null;
SrmDocument document = null;
try
{
using (var longWaitDlg = new LongWaitDlg(this)
{
Text = Resources.SkylineWindow_OpenFile_Loading___,
Message = Path.GetFileName(path),
ProgressValue = 0
})
{
longWaitDlg.PerformWork(parentWindow ?? this, 500, progressMonitor =>
{
using (var reader = new StreamReaderWithProgress(path, progressMonitor))
{
XmlSerializer ser = new XmlSerializer(typeof (SrmDocument));
document = (SrmDocument) ser.Deserialize(reader);
}
});
if (longWaitDlg.IsCanceled)
document = null;
}
}
catch (Exception x)
{
exception = x;
}
if (exception == null)
{
if (document == null)
return false;
try
{
document = ConnectDocument(parentWindow ?? this, document, path);
if (document == null || !CheckResults(document, path))
return false;
// Make sure settings lists contain correct values for
// this document.
document.Settings.UpdateLists(path);
}
catch (Exception x)
{
exception = x;
}
}
if (exception == null)
{
try
{
using (new SequenceTreeForm.LockDoc(_sequenceTreeForm))
{
// Switch over to the opened document
SwitchDocument(document, path);
}
// Locking the sequenceTree can throw off the node count status
UpdateNodeCountStatus();
}
catch (Exception x)
{
exception = x;
}
}
if (exception != null)
{
new MessageBoxHelper(parentWindow ?? this).ShowXmlParsingError(
string.Format(Resources.SkylineWindow_OpenFile_Failure_opening__0__, path), path, exception);
return false;
}
if (SequenceTree != null && SequenceTree.Nodes.Count > 0 && !SequenceTree.RestoredFromPersistentString)
SequenceTree.SelectedNode = SequenceTree.Nodes[0];
return true;
}
public void ImportFiles(params string[] filePaths)
{
var resultsAction = MeasuredResults.MergeAction.remove;
var mergePeptides = false;
if (HasResults(filePaths))
{
using (var dlgResults = new ImportDocResultsDlg(!string.IsNullOrEmpty(DocumentFilePath)))
{
if (dlgResults.ShowDialog(this) != DialogResult.OK)
return;
resultsAction = dlgResults.Action;
mergePeptides = dlgResults.IsMergePeptides;
}
}
SrmTreeNode nodeSel = SequenceTree.SelectedNode as SrmTreeNode;
IdentityPath selectPath = null;
var docCurrent = DocumentUI;
SrmDocument docNew = null;
using (var longWaitDlg = new LongWaitDlg(this)
{
Text = Resources.SkylineWindow_ImportFiles_Import_Skyline_document_data,
})
{
longWaitDlg.PerformWork(this, 1000, longWaitBroker =>
docNew = ImportFiles(docCurrent,
longWaitBroker,
filePaths,
resultsAction,
mergePeptides,
nodeSel != null ? nodeSel.Path : null,
out selectPath));
if (docNew == null || ReferenceEquals(docNew, docCurrent))
return;
if (longWaitDlg.IsDocumentChanged(docCurrent))
{
MessageDlg.Show(this, Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
return;
}
}
ModifyDocument(Resources.SkylineWindow_ImportFiles_Import_Skyline_document_data, doc =>
{
docNew.ValidateResults();
if (!ReferenceEquals(doc, docCurrent))
throw new InvalidDataException(Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
return docNew;
});
if (selectPath != null)
SequenceTree.SelectedPath = selectPath;
}
private void ImportPeakBoundaries(string fileName, long lineCount, string description)
{
var docCurrent = DocumentUI;
SrmDocument docNew = null;
using (var longWaitDlg = new LongWaitDlg(this) { Text = description })
{
var peakBoundaryImporter = new PeakBoundaryImporter(docCurrent);
longWaitDlg.PerformWork(this, 1000, longWaitBroker =>
docNew = peakBoundaryImporter.Import(fileName, longWaitBroker, lineCount));
if (docNew == null)
return;
if (!peakBoundaryImporter.UnrecognizedPeptidesCancel(this))
return;
if (longWaitDlg.IsDocumentChanged(docCurrent))
{
MessageDlg.Show(this, Resources.SkylineWindow_ImportPeakBoundaries_Unexpected_document_change_during_operation);
return;
}
}
ModifyDocument(description, doc =>
{
if (!ReferenceEquals(doc, docCurrent))
throw new InvalidDataException(Resources.SkylineWindow_ImportPeakBoundaries_Unexpected_document_change_during_operation);
return docNew;
});
}
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);
}
}
public void ImportFasta(TextReader reader, long lineCount, bool peptideList, string description)
{
SrmTreeNode nodePaste = SequenceTree.SelectedNode as SrmTreeNode;
IdentityPath selectPath = null;
var to = nodePaste != null ? nodePaste.Path : null;
var docCurrent = DocumentUI;
ModificationMatcher matcher = null;
if(peptideList)
{
matcher = new ModificationMatcher();
List<string> sequences = new List<string>();
string line;
var header = reader.ReadLine(); // Read past header
while ((line = reader.ReadLine()) != null)
{
string sequence = FastaSequence.NormalizeNTerminalMod(line.Trim());
sequences.Add(sequence);
}
try
{
matcher.CreateMatches(docCurrent.Settings, sequences, Settings.Default.StaticModList, Settings.Default.HeavyModList);
var strNameMatches = matcher.FoundMatches;
if (!string.IsNullOrEmpty(strNameMatches))
{
var message = TextUtil.LineSeparate(Resources.SkylineWindow_ImportFasta_Would_you_like_to_use_the_Unimod_definitions_for_the_following_modifications,
string.Empty, strNameMatches);
if (DialogResult.Cancel == MultiButtonMsgDlg.Show(
this,
string.Format(message), Resources.SkylineWindow_ImportFasta_OK))
{
return;
}
}
}
catch(FormatException x)
{
MessageDlg.ShowException(this, x);
return;
}
reader = new StringReader(TextUtil.LineSeparate(header, TextUtil.LineSeparate(sequences.ToArray())));
}
SrmDocument docNew = null;
int emptyPeptideGroups = 0;
using (var longWaitDlg = new LongWaitDlg(this) { Text = description })
{
IdentityPath nextAdded;
longWaitDlg.PerformWork(this, 1000, longWaitBroker =>
docNew = docCurrent.ImportFasta(reader, longWaitBroker, lineCount, matcher, to, out selectPath, out nextAdded, out emptyPeptideGroups));
if (docNew == null)
return;
if (longWaitDlg.IsDocumentChanged(docCurrent))
{
MessageDlg.Show(this, Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
return;
}
}
// If importing the FASTA produced any childless proteins
docNew = ImportFastaHelper.HandleEmptyPeptideGroups(this, emptyPeptideGroups, docNew);
if (docNew == null || Equals(docCurrent, docNew))
return;
selectPath = null;
var enumGroupsCurrent = docCurrent.MoleculeGroups.GetEnumerator();
foreach (PeptideGroupDocNode nodePepGroup in docNew.MoleculeGroups)
{
if (enumGroupsCurrent.MoveNext() &&
!ReferenceEquals(nodePepGroup, enumGroupsCurrent.Current))
{
selectPath = new IdentityPath(nodePepGroup.Id);
break;
}
}
ModifyDocument(description, doc =>
{
if (!ReferenceEquals(doc, docCurrent))
throw new InvalidDataException(Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
if (matcher != null)
{
var pepModsNew = matcher.GetDocModifications(docNew);
docNew = docNew.ChangeSettings(docNew.Settings.ChangePeptideModifications(mods => pepModsNew));
docNew.Settings.UpdateDefaultModifications(false);
}
return docNew;
});
if (selectPath != null)
SequenceTree.SelectedPath = selectPath;
}
/* TODO bspratt drift time libs for small molecules
[TestMethod]
public void WatersImsMsePredictedDriftTimesChromatogramTestAsSmallMolecules()
{
WatersImsMseChromatogramTest(DriftFilterType.predictor, true);
}
[TestMethod]
public void WatersImsMseLibraryDriftTimesChromatogramTestAsSmallMolecules()
{
WatersImsMseChromatogramTest(DriftFilterType.library, true);
}
*/
private void WatersImsMseChromatogramTest(DriftFilterType mode,
RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules = RefinementSettings.ConvertToSmallMoleculesMode.none)
{
string subdir = (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.none) ? null : asSmallMolecules.ToString();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE, subdir);
TestSmallMolecules = false; // Don't need that extra magic node
bool withDriftTimePredictor = (mode == DriftFilterType.predictor); // Load the doc that has a drift time predictor?
bool withDriftTimeFilter = (mode != DriftFilterType.none); // Perform drift time filtering? (either with predictor, or with bare times in blib file)
string docPath;
SrmDocument document = InitWatersImsMseDocument(testFilesDir, withDriftTimePredictor ? "single_with_driftinfo.sky" : "single_no_driftinfo.sky", asSmallMolecules, out docPath);
AssertEx.IsDocumentState(document, (withDriftTimePredictor || (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)) ? 1 : 0, 1, 1, 1, 8); // Drift time lib load bumps the doc version
var docContainer = new ResultsTestDocumentContainer(document, docPath);
var doc = docContainer.Document;
var docOriginal = doc;
string testModeStr = withDriftTimePredictor ? "with drift time predictor" : "without drift time info";
if (withDriftTimeFilter && !withDriftTimePredictor)
{
// Use the bare drift times in the spectral library
var librarySpec = new BiblioSpecLiteSpec("drift test",
testFilesDir.GetTestPath("mse-mobility.filtered-scaled.blib"));
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec })).
ChangePeptidePrediction(p => p.ChangeLibraryDriftTimesResolvingPower(100)).
ChangePeptidePrediction(p => p.ChangeUseLibraryDriftTimes(true))
);
testModeStr = "with drift times from spectral library";
}
var listChromatograms = new List<ChromatogramSet>();
// A small subset of the QC_HDMSE_02_UCA168_3495_082213 data set (RT 21.5-22.5) from Will Thompson
const string path = @"waters-mobility.mz5";
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, new MsDataFilePath(path)) ??
new ChromatogramSet(Path.GetFileName(path).Replace('.', '_'), new[] { path }));
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = document.Settings.MeasuredResults;
Assert.AreEqual(1, document.MoleculePrecursorPairs.Count());
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assert.AreEqual(1, chromGroupInfo.Length, testModeStr);
var chromGroup = chromGroupInfo[0];
var expectedPeaks = ((asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? 6 : 5);
Assert.AreEqual(withDriftTimeFilter ? 3 : expectedPeaks, chromGroup.NumPeaks, testModeStr); // This will be higher if we don't filter on DT
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
Assert.AreEqual(withDriftTimeFilter? 5226 : 20075 , maxHeight, 1, testModeStr); // Without DT filtering, this will be much greater
// now drill down for specific values
int nPeptides = 0;
foreach (var nodePep in document.Molecules.Where(nodePep => nodePep.Results[0] != null))
{
// expecting just one peptide result in this small data set
if (nodePep.Results[0].Sum(chromInfo => chromInfo.PeakCountRatio > 0 ? 1 : 0) > 0)
{
Assert.AreEqual(21.94865, (double)nodePep.GetMeasuredRetentionTime(0), .0001, testModeStr);
Assert.AreEqual(1.0, (double)nodePep.GetPeakCountRatio(0), 0.0001, testModeStr);
nPeptides++;
}
}
Assert.AreEqual(1, nPeptides);
if (withDriftTimePredictor || withDriftTimeFilter)
{
// Verify that the .imdb pr .blib file goes out in the share zipfile
for (int complete = 0; complete <= 1; complete++)
{
var sharePath = testFilesDir.GetTestPath(complete==1?"share_complete.zip":"share_minimized.zip");
var share = new SrmDocumentSharing(document, docPath, sharePath, complete==1);
using (var longWaitDlg = new LongWaitDlg
{
// ReSharper disable once LocalizableElement
Text = "unit test WatersImsTest -- sharing document",
})
{
longWaitDlg.PerformWork(null, 1000, share.Share);
Assert.IsFalse(longWaitDlg.IsCanceled);
}
var files = share.ListEntries().ToArray();
Assert.IsTrue(files.Contains(withDriftTimePredictor ? "scaled.imdb" : "mse-mobility.filtered-scaled.blib"));
// And round trip it to make sure we haven't left out any new features in minimized imdb or blib files
using (var longWaitDlg = new LongWaitDlg
{
// ReSharper disable once LocalizableElement
Text = "unit test WatersImsTest",
})
{
longWaitDlg.PerformWork(null, 1000, share.Extract);
Assert.IsFalse(longWaitDlg.IsCanceled);
}
using (TextReader reader = new StreamReader(share.DocumentPath))
{
XmlSerializer documentSerializer = new XmlSerializer(typeof(SrmDocument));
var document2 = (SrmDocument) documentSerializer.Deserialize(reader);
Assert.IsNotNull(document2);
var im = document.Settings.GetIonMobilities(new MsDataFilePath(path));
var pep = document2.Molecules.First();
foreach (TransitionGroupDocNode nodeGroup in pep.Children)
{
double windowDT;
var centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
pep, nodeGroup, im, out windowDT);
Assert.AreEqual(3.86124, centerDriftTime.DriftTimeMsec(false) ?? 0, .0001, testModeStr);
Assert.AreEqual(0.077224865797235934, windowDT, .0001, testModeStr);
}
}
}
}
// Release file handles
docContainer.Release();
testFilesDir.Dispose();
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
}
public static void Main(string[] args = null)
{
if (String.IsNullOrEmpty(Settings.Default.InstallationId)) // Each instance to have GUID
Settings.Default.InstallationId = Guid.NewGuid().ToString();
// don't allow 64-bit Skyline to run in a 32-bit process
if (Install.Is64Bit && !Environment.Is64BitProcess)
{
string installUrl = Install.Url;
string installLabel = (installUrl == string.Empty) ? string.Empty : string.Format(Resources.Program_Main_Install_32_bit__0__, Name);
AlertLinkDlg.Show(null,
string.Format(Resources.Program_Main_You_are_attempting_to_run_a_64_bit_version_of__0__on_a_32_bit_OS_Please_install_the_32_bit_version, Name),
installLabel,
installUrl);
return;
}
CommonFormEx.TestMode = FunctionalTest;
CommonFormEx.Offscreen = SkylineOffscreen;
CommonFormEx.ShowFormNames = FormEx.ShowFormNames = ShowFormNames;
// For testing and debugging Skyline command-line interface
if (args != null && args.Length > 0)
{
if (!CommandLineRunner.HasCommandPrefix(args[0]))
{
var writer = new CommandStatusWriter(new DebugWriter());
if (args[0].Equals("--ui", StringComparison.InvariantCultureIgnoreCase)) // Not L10N
{
// ReSharper disable once ObjectCreationAsStatement
new CommandLineUI(args, writer);
}
else
{
CommandLineRunner.RunCommand(args, writer);
}
}
else
{
// For testing SkylineRunner without installation
CommandLineRunner clr = new CommandLineRunner();
clr.Start(args[0]);
}
return;
}
// The way Skyline command-line interface is run for an installation
else if (AppDomain.CurrentDomain.SetupInformation.ActivationArguments != null &&
AppDomain.CurrentDomain.SetupInformation.ActivationArguments.ActivationData != null &&
AppDomain.CurrentDomain.SetupInformation.ActivationArguments.ActivationData.Length > 0 &&
CommandLineRunner.HasCommandPrefix(AppDomain.CurrentDomain.SetupInformation.ActivationArguments.ActivationData[0])) // Not L10N
{
CommandLineRunner clr = new CommandLineRunner();
clr.Start(AppDomain.CurrentDomain.SetupInformation.ActivationArguments.ActivationData[0]);
// HACK: until the "invalid string binding" error is resolved, this will prevent an error dialog at exit
Process.GetCurrentProcess().Kill();
return;
}
try
{
Init();
if (!string.IsNullOrEmpty(Settings.Default.DisplayLanguage))
{
try
{
LocalizationHelper.CurrentUICulture =
CultureInfo.GetCultureInfo(Settings.Default.DisplayLanguage);
}
catch (CultureNotFoundException)
{
}
}
LocalizationHelper.InitThread(Thread.CurrentThread);
// Make sure the user has agreed to the current license version
// or one more recent.
int licenseVersion = Settings.Default.LicenseVersionAccepted;
if (licenseVersion < LICENSE_VERSION_CURRENT && !NoSaveSettings)
{
// If the user has never used the application before, then
// they must have agreed to the current license agreement during
// installation. Otherwise, make sure they agree to the new
// license agreement.
if (Install.Type == Install.InstallType.release &&
(licenseVersion != 0 || !Settings.Default.MainWindowSize.IsEmpty))
{
using (var dlg = new UpgradeDlg(licenseVersion))
{
if (dlg.ShowDialog() == DialogResult.Cancel)
return;
}
}
try
{
// Make sure the user never sees this again for this license version
Settings.Default.LicenseVersionAccepted = LICENSE_VERSION_CURRENT;
Settings.Default.Save();
}
// ReSharper disable EmptyGeneralCatchClause
catch (Exception)
// ReSharper restore EmptyGeneralCatchClause
{
// Just try to update the license version next time.
}
}
try
{
// If this is a new installation copy over installed external tools from previous installation location.
var toolsDirectory = ToolDescriptionHelpers.GetToolsDirectory();
if (!Directory.Exists(toolsDirectory))
{
using (var longWaitDlg = new LongWaitDlg
{
Text = Name,
Message = Resources.Program_Main_Copying_external_tools_from_a_previous_installation,
ProgressValue = 0
})
{
longWaitDlg.PerformWork(null, 1000*3, broker => CopyOldTools(toolsDirectory, broker));
}
}
}
// ReSharper disable once EmptyGeneralCatchClause
catch
{
}
// Force live reports (though tests may reset this)
//Settings.Default.EnableLiveReports = true;
if (ReportShutdownDlg.HadUnexpectedShutdown())
{
using (var reportShutdownDlg = new ReportShutdownDlg())
{
reportShutdownDlg.ShowDialog();
}
}
SystemEvents.DisplaySettingsChanged += SystemEventsOnDisplaySettingsChanged;
// Careful, a throw out of the SkylineWindow constructor without this
// catch causes Skyline just to appear to silently never start. Makes for
// some difficult debugging.
try
{
var activationArgs = AppDomain.CurrentDomain.SetupInformation.ActivationArguments;
if ((activationArgs != null &&
activationArgs.ActivationData != null &&
activationArgs.ActivationData.Length != 0) ||
!Settings.Default.ShowStartupForm)
{
MainWindow = new SkylineWindow(args);
}
else
{
StartWindow = new StartPage();
try
{
if (StartWindow.ShowDialog() != DialogResult.OK)
{
Application.Exit();
return;
}
MainWindow = StartWindow.MainWindow;
}
finally
{
StartWindow.Dispose();
StartWindow = null;
}
}
}
catch (Exception x)
{
ReportExceptionUI(x, new StackTrace(1, true));
}
ConcurrencyVisualizer.StartEvents(MainWindow);
// Position window offscreen for stress testing.
if (SkylineOffscreen)
FormEx.SetOffscreen(MainWindow);
ActionUtil.RunAsync(() =>
{
try {
SendAnalyticsHit();
} catch (Exception ex) {
Trace.TraceWarning("Exception sending analytics hit {0}", ex); // Not L10N
}
});
MainToolServiceName = Guid.NewGuid().ToString();
Application.Run(MainWindow);
StopToolService();
}
catch (Exception x)
{
// Send unhandled exceptions to the console.
Console.WriteLine(x.Message);
Console.Write(x.StackTrace);
}
MainWindow = null;
}
public bool ShareDocument(string fileDest, bool completeSharing)
{
try
{
bool success = false;
Helpers.TryTwice(() =>
{
using (var longWaitDlg = new LongWaitDlg { Text = Resources.SkylineWindow_ShareDocument_Compressing_Files, })
{
var sharing = new SrmDocumentSharing(DocumentUI, DocumentFilePath, fileDest, completeSharing);
longWaitDlg.PerformWork(this, 1000, sharing.Share);
success = !longWaitDlg.IsCanceled;
}
});
return success;
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.SkylineWindow_ShareDocument_Failed_attempting_to_create_sharing_file__0__, fileDest),
x.Message);
MessageDlg.ShowWithException(this, message, x);
}
return false;
}
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();
}
private void LaunchPeptideProteinsQuery()
{
HashSet<Protein> proteinSet = new HashSet<Protein>();
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Querying_Background_Proteome_Database,
Message = Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Looking_for_proteins_with_matching_peptide_sequences
})
{
try
{
longWaitDlg.PerformWork(this, 1000, QueryPeptideProteins);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Failed_querying_background_proteome__0__,
BackgroundProteome.Name), x.Message);
MessageDlg.ShowWithException(this, message, x);
}
}
if (_peptideProteins == null)
{
Close();
return;
}
foreach (var proteins in _peptideProteins)
{
proteinSet.UnionWith(proteins);
}
List<Protein> proteinList = new List<Protein>();
proteinList.AddRange(proteinSet);
proteinList.Sort();
foreach (var protein in proteinList)
{
ProteinColumn proteinColumn = new ProteinColumn(_proteinColumns.Count, protein);
_proteinColumns.Add(proteinColumn);
DataGridViewCheckBoxColumn column = new DataGridViewCheckBoxColumn
{
Name = proteinColumn.Name,
HeaderText = ((protein.Gene != null) ? String.Format(Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_, protein.Name, protein.Gene) : protein.Name), // Not L10N
ReadOnly = true,
ToolTipText = protein.ProteinMetadata.DisplayTextWithoutName(),
SortMode = DataGridViewColumnSortMode.Automatic,
Tag = proteinColumn,
};
dataGridView1.Columns.Add(column);
}
for (int i = 0; i < _peptideDocNodes.Count; i++)
{
var peptide = _peptideDocNodes[i];
var proteins = _peptideProteins[i];
var row = dataGridView1.Rows[dataGridView1.Rows.Add()];
row.Tag = peptide;
row.Cells[PeptideIncludedColumn.Name].Value = true;
row.Cells[PeptideColumn.Name].Value = peptide.Peptide.Sequence;
foreach (var proteinColumn in _proteinColumns)
{
row.Cells[proteinColumn.Name].Value = proteins.Contains(proteinColumn.Protein);
}
}
dataGridView1.EndEdit();
if (dataGridView1.RowCount > 0)
{
// Select the first peptide to populate the other controls in the dialog.
dataGridView1.CurrentCell = dataGridView1.Rows[0].Cells[1];
}
DrawCheckBoxOnPeptideIncludedColumnHeader();
}
private void RefreshStatus()
{
if (File.Exists(textPath.Text))
{
btnAddFastaFile.Enabled = true;
ProteomeDb proteomeDb = null;
try
{
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.BuildBackgroundProteomeDlg_RefreshStatus_Loading_Proteome_File,
Message =
string.Format(
Resources.BuildBackgroundProteomeDlg_RefreshStatus_Loading_protein_information_from__0__,
textPath.Text)
})
{
longWaitDlg.PerformWork(this, 1000, () => proteomeDb = ProteomeDb.OpenProteomeDb(textPath.Text));
}
if (proteomeDb == null)
throw new Exception();
int proteinCount = proteomeDb.GetProteinCount();
var digestions = proteomeDb.ListDigestions();
tbxStatus.Text =
string.Format(
Resources.BuildBackgroundProteomeDlg_RefreshStatus_The_proteome_file_contains__0__proteins,
proteinCount);
if (proteinCount != 0 && digestions.Count > 0)
{
tbxStatus.Text = TextUtil.LineSeparate(tbxStatus.Text,
Resources.BuildBackgroundProteomeDlg_RefreshStatus_The_proteome_has_already_been_digested);
}
}
catch (Exception)
{
tbxStatus.Text = Resources.BuildBackgroundProteomeDlg_OkDialog_The_proteome_file_is_not_valid;
btnAddFastaFile.Enabled = false;
}
finally
{
if (null != proteomeDb)
{
proteomeDb.Dispose();
}
}
}
else
{
btnAddFastaFile.Enabled = false;
tbxStatus.Text = Resources.BuildBackgroundProteomeDlg_RefreshStatus_Click_the_Open_button_to_choose_an_existing_proteome_file_or_click_the_Create_button_to_create_a_new_proteome_file;
}
}
private MsDataFilePath[] GetWiffSubPaths(string filePath)
{
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.ImportResultsDlg_GetWiffSubPaths_Sample_Names,
Message = string.Format(Resources.ImportResultsDlg_GetWiffSubPaths_Reading_sample_names_from__0__,
Path.GetFileName(filePath))
})
{
string[] dataIds = null;
try
{
longWaitDlg.PerformWork(this, 800, () => dataIds = MsDataFileImpl.ReadIds(filePath));
}
catch (Exception x)
{
string message = TextUtil.LineSeparate(
string.Format(Resources.ImportResultsDlg_GetWiffSubPaths_An_error_occurred_attempting_to_read_sample_information_from_the_file__0__, filePath),
Resources.ImportResultsDlg_GetWiffSubPaths_The_file_may_be_corrupted_missing_or_the_correct_libraries_may_not_be_installed,
x.Message);
MessageDlg.ShowWithException(this, message, x);
}
return DataSourceUtil.GetWiffSubPaths(filePath, dataIds, ChooseSamples);
}
}
private bool GetPackages()
{
try
{
using (var dlg = new LongWaitDlg(null, false) {Message = Resources.RInstaller_GetPAckages_Installing_Packages})
{
dlg.PerformWork(this, 1000, InstallPackages);
}
}
catch(TargetInvocationException ex)
{
//Win32Exception is thrown when the user does not ok Administrative Privileges
if (ex.InnerException is ToolExecutionException || ex.InnerException is System.ComponentModel.Win32Exception)
{
MessageDlg.ShowException(this, ex);
return false;
}
else
throw;
}
return true;
}
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 docNew = ImportPeptideSearch.AddDocumentSpectralLibrary(SkylineWindow.Document, docLibSpec);
if (docNew == null)
return false;
SkylineWindow.ModifyDocument(Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Add_document_spectral_library, doc => docNew);
if (!string.IsNullOrEmpty(builder.AmbiguousMatchesMessage))
{
MessageDlg.Show(WizardForm, builder.AmbiguousMatchesMessage);
}
return true;
}
public void DownloadSelectedTool()
{
try
{
string identifier = _tools[listBoxTools.SelectedIndex].Identifier;
using (var dlg = new LongWaitDlg {ProgressValue = 0, Message = string.Format(Resources.ToolStoreDlg_DownloadSelectedTool_Downloading__0_, _tools[listBoxTools.SelectedIndex].Name)})
{
dlg.PerformWork(this, 500, progressMonitor => DownloadPath = _toolStoreClient.GetToolZipFile(progressMonitor, identifier, Path.GetTempPath()));
if (!dlg.IsCanceled)
DialogResult = DialogResult.OK;
}
}
catch (TargetInvocationException ex)
{
var exceptionType = ex.InnerException.GetType();
if (exceptionType == typeof (ToolExecutionException) || exceptionType == typeof(WebException))
MessageDlg.ShowException(this, ex);
else
{
throw;
}
}
}
private bool LoadPeptideSearchLibrary(LibrarySpec docLibSpec)
{
if (docLibSpec == null)
return false;
using (var longWait = new LongWaitDlg
{
Text = Resources.BuildPeptideSearchLibraryControl_LoadPeptideSearchLibrary_Loading_Library
})
{
try
{
var status = longWait.PerformWork(WizardForm, 800, monitor => ImportPeptideSearch.LoadPeptideSearchLibrary(LibraryManager, docLibSpec, monitor));
if (status.IsError)
{
MessageDlg.ShowException(WizardForm, status.ErrorException);
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(WizardForm,
TextUtil.LineSeparate(string.Format(Resources.BuildPeptideSearchLibraryControl_LoadPeptideSearchLibrary_An_error_occurred_attempting_to_import_the__0__library_,
docLibSpec.Name), x.Message), x);
}
}
return ImportPeptideSearch.HasDocLib;
}
public Database GetDatabase(Control owner)
{
if (_database == null)
{
var status = new ProgressStatus(Resources.ExportReportDlg_GetDatabase_Generating_Report_Data);
using (var longWait = new LongWaitDlg
{
Text = status.Message,
Message = Resources.ExportReportDlg_GetDatabase_Analyzing_document
})
{
longWait.PerformWork(owner, 1500, broker => EnsureDatabase(broker, 100, ref status));
}
}
return _database;
}
private bool ExportReport(string fileName, char separator)
{
try
{
using (var saver = new FileSaver(fileName))
{
if (!saver.CanSave(this))
return false;
using (var writer = new StreamWriter(saver.SafeName))
{
Report report = GetReport();
bool success = false;
using (var longWait = new LongWaitDlg { Text = Resources.ExportReportDlg_ExportReport_Generating_Report })
{
longWait.PerformWork(this, 1500, broker =>
{
var status = new ProgressStatus(Resources.ExportReportDlg_GetDatabase_Analyzing_document);
broker.UpdateProgress(status);
Database database = EnsureDatabase(broker, 80, ref status);
if (broker.IsCanceled)
return;
broker.UpdateProgress(status = status.ChangeMessage(Resources.ExportReportDlg_ExportReport_Building_report));
ResultSet resultSet = report.Execute(database);
if (broker.IsCanceled)
return;
broker.UpdateProgress(status = status.ChangePercentComplete(95)
.ChangeMessage(Resources.ExportReportDlg_ExportReport_Writing_report));
ResultSet.WriteReportHelper(resultSet, separator, writer, CultureInfo);
writer.Flush();
writer.Close();
if (broker.IsCanceled)
return;
broker.UpdateProgress(status.Complete());
saver.Commit();
success = true;
});
}
return success;
}
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.ExportReportDlg_ExportReport_Failed_exporting_to, fileName, GetExceptionDisplayMessage(x)), x);
return false;
}
}
public void OkDialog()
{
MessageBoxHelper helper = new MessageBoxHelper(this);
string serverName;
if (!helper.ValidateNameTextBox(textServerURL, out serverName))
return;
Uri uriServer = PanoramaUtil.ServerNameToUri(serverName);
if (uriServer == null)
{
helper.ShowTextBoxError(textServerURL, Resources.EditServerDlg_OkDialog_The_text__0__is_not_a_valid_server_name_, serverName);
return;
}
var panoramaClient = PanoramaClient ?? new WebPanoramaClient(uriServer);
using (var waitDlg = new LongWaitDlg { Text = Resources.EditServerDlg_OkDialog_Verifying_server_information })
{
try
{
waitDlg.PerformWork(this, 1000, () => PanoramaUtil.VerifyServerInformation( panoramaClient, Username, Password));
}
catch (Exception x)
{
helper.ShowTextBoxError(textServerURL, x.Message);
return;
}
}
Uri updatedUri = panoramaClient.ServerUri ?? uriServer;
if (_existing.Contains(server => !ReferenceEquals(_server, server) && Equals(updatedUri, server.URI)))
{
helper.ShowTextBoxError(textServerURL, Resources.EditServerDlg_OkDialog_The_server__0__already_exists_, uriServer.Host);
return;
}
_server = new Server(updatedUri, Username, Password);
DialogResult = DialogResult.OK;
}
public static void InstallZipFromWeb(Control parent, InstallProgram install)
{
try
{
IList<ToolStoreItem> toolStoreItems = null;
using (var dlg = new LongWaitDlg { Message = Resources.ConfigureToolsDlg_AddFromWeb_Contacting_the_server })
{
dlg.PerformWork(parent, 1000, () =>
{
toolStoreItems = ToolStoreUtil.ToolStoreClient.GetToolStoreItems();
});
}
if (toolStoreItems == null || toolStoreItems.Count == 0)
{
MessageDlg.Show(parent, Resources.ConfigureToolsDlg_AddFromWeb_Unknown_error_connecting_to_the_tool_store);
}
using (var dlg = new ToolStoreDlg(ToolStoreUtil.ToolStoreClient, toolStoreItems))
{
if (dlg.ShowDialog(parent) == DialogResult.OK)
InstallZipTool(parent, dlg.DownloadPath, install);
}
}
catch (TargetInvocationException x)
{
if (x.InnerException.GetType() == typeof(ToolExecutionException) || x.InnerException is WebException)
MessageDlg.Show(parent, String.Format(Resources.ConfigureToolsDlg_GetZipFromWeb_Error_connecting_to_the_Tool_Store___0_, x.Message));
else
throw;
}
}