From e03ff2ac46d1fbe09d784cd37cce9b2571831518 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Mon, 26 Aug 2024 16:55:46 -0400 Subject: [PATCH 1/6] - reworked DIA workflow radio button to work with and without DIA-Umpire - added checkboxes next to DIA workflow for DIA-Umpire and Gas Phase Fractionation * added faster TestDiaSearch test (sharing TestDiaSearch DiaUmpire code) * updated audit logs --- ...ildPeptideSearchLibraryControl.Designer.cs | 22 +- .../BuildPeptideSearchLibraryControl.cs | 40 +- .../BuildPeptideSearchLibraryControl.resx | 77 +++- .../PeptideSearch/ConverterSettingsControl.cs | 7 +- .../PeptideSearch/ImportPeptideSearchDlg.cs | 34 +- .../PeptideSearch/SearchSettingsControl.cs | 52 ++- .../Model/AuditLog/EnumNames.Designer.cs | 2 +- .../Skyline/Model/AuditLog/EnumNames.resx | 2 +- .../Model/AuditLog/PropertyNames.Designer.cs | 18 + .../Skyline/Model/AuditLog/PropertyNames.resx | 6 + .../DdaSearch/DdaSearchResources.designer.cs | 9 + .../Model/DdaSearch/DdaSearchResources.resx | 3 + .../Model/DdaSearch/MsFraggerSearchEngine.cs | 15 +- .../Model/DdaSearch/MsconvertDdaConverter.cs | 16 + .../Skyline/Model/ImportPeptideSearch.cs | 1 + .../Skyline/TestFunctional/DiaSearchTest.cs | 341 +++++++++++++++++- .../Skyline/TestPerf/DiaSearchTutorialTest.cs | 13 +- .../en/TestDiaSearchQeTutorial.log | 12 +- .../en/TestDiaSearchStellarTutorial.log | 12 +- .../fr/TestDiaSearchQeTutorial.log | 12 +- .../fr/TestDiaSearchStellarTutorial.log | 12 +- .../ja/TestDiaSearchQeTutorial.log | 12 +- .../ja/TestDiaSearchStellarTutorial.log | 12 +- .../tr/TestDiaSearchQeTutorial.log | 12 +- .../tr/TestDiaSearchStellarTutorial.log | 12 +- .../zh/TestDiaSearchQeTutorial.log | 12 +- .../zh/TestDiaSearchStellarTutorial.log | 12 +- 27 files changed, 667 insertions(+), 111 deletions(-) diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs index 77533ceadb..b22656a773 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs @@ -28,8 +28,11 @@ protected override void Dispose(bool disposing) /// private void InitializeComponent() { + this.components = new System.ComponentModel.Container(); System.ComponentModel.ComponentResourceManager resources = new System.ComponentModel.ComponentResourceManager(typeof(BuildPeptideSearchLibraryControl)); this.grpWorkflow = new System.Windows.Forms.GroupBox(); + this.cbGpf = new System.Windows.Forms.CheckBox(); + this.cbDiaUmpire = new System.Windows.Forms.CheckBox(); this.radioDIA = new System.Windows.Forms.RadioButton(); this.radioPRM = new System.Windows.Forms.RadioButton(); this.radioDDA = new System.Windows.Forms.RadioButton(); @@ -49,7 +52,7 @@ private void InitializeComponent() this.btnRemFile = new System.Windows.Forms.Button(); this.lblFileCaption = new System.Windows.Forms.Label(); this.btnAddFile = new System.Windows.Forms.Button(); - this.helpTip = new System.Windows.Forms.ToolTip(); + this.helpTip = new System.Windows.Forms.ToolTip(this.components); this.dataGridViewTextBoxColumn1 = new System.Windows.Forms.DataGridViewTextBoxColumn(); this.dataGridViewTextBoxColumn2 = new System.Windows.Forms.DataGridViewTextBoxColumn(); this.dataGridViewTextBoxColumn3 = new System.Windows.Forms.DataGridViewTextBoxColumn(); @@ -63,6 +66,8 @@ private void InitializeComponent() // // grpWorkflow // + this.grpWorkflow.Controls.Add(this.cbGpf); + this.grpWorkflow.Controls.Add(this.cbDiaUmpire); this.grpWorkflow.Controls.Add(this.radioDIA); this.grpWorkflow.Controls.Add(this.radioPRM); this.grpWorkflow.Controls.Add(this.radioDDA); @@ -70,6 +75,18 @@ private void InitializeComponent() this.grpWorkflow.Name = "grpWorkflow"; this.grpWorkflow.TabStop = false; // + // cbGpf + // + resources.ApplyResources(this.cbGpf, "cbGpf"); + this.cbGpf.Name = "cbGpf"; + this.cbGpf.UseVisualStyleBackColor = true; + // + // cbDiaUmpire + // + resources.ApplyResources(this.cbDiaUmpire, "cbDiaUmpire"); + this.cbDiaUmpire.Name = "cbDiaUmpire"; + this.cbDiaUmpire.UseVisualStyleBackColor = true; + // // radioDIA // resources.ApplyResources(this.radioDIA, "radioDIA"); @@ -255,6 +272,7 @@ private void InitializeComponent() this.Controls.Add(this.panel1); this.Name = "BuildPeptideSearchLibraryControl"; this.grpWorkflow.ResumeLayout(false); + this.grpWorkflow.PerformLayout(); this.panel1.ResumeLayout(false); this.panel1.PerformLayout(); this.panelChooseFile.ResumeLayout(false); @@ -292,5 +310,7 @@ private void InitializeComponent() private System.Windows.Forms.DataGridViewTextBoxColumn dataGridViewTextBoxColumn3; private System.Windows.Forms.DataGridViewTextBoxColumn dataGridViewTextBoxColumn4; private System.Windows.Forms.ToolTip helpTip; + private System.Windows.Forms.CheckBox cbDiaUmpire; + private System.Windows.Forms.CheckBox cbGpf; } } diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs index 2c48309177..b979dc6b0d 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs @@ -72,9 +72,10 @@ public BuildPeptideSearchLibraryControl(IModifyDocumentContainer documentContain if (_isRunPeptideSearch) { panel1.Hide(); - radioDIA.Text = SkylineResources.BuildPeptideSearchLibraryControl_RunPeptideSearchRadioDIAText_DIA_with_DIA_Umpire; - helpTip.SetToolTip(radioDIA, SkylineResources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibraryControl_Library_from_DIA_deconvoluted_to_single_precursor_MS_MS_spectra_and_chromatograms_from_raw_DIA_spectra_of_same_runs); - InputFileType = ImportPeptideSearchDlg.InputFile.dda_raw; + if (ImportPeptideSearch.IsDIASearch) + InputFileType = ImportPeptideSearchDlg.InputFile.dia_raw; + else + InputFileType = ImportPeptideSearchDlg.InputFile.dda_raw; } else { @@ -96,7 +97,7 @@ public class BuildPeptideSearchLibrarySettings : AuditLogOperationSettings files, IrtStandard standard, bool includeAmbiguousMatches, bool filterForDocumentPeptides, - ImportPeptideSearchDlg.Workflow workFlow, ImportPeptideSearchDlg.InputFile inputFileType, SrmDocument.DOCUMENT_TYPE docType) + ImportPeptideSearchDlg.Workflow workFlow, bool useDiaUmpire, bool isGpf, + ImportPeptideSearchDlg.InputFile inputFileType, SrmDocument.DOCUMENT_TYPE docType) { SearchFileNames = files?.ToArray() ?? Array.Empty(); Standard = standard; IncludeAmbiguousMatches = includeAmbiguousMatches; FilterForDocumentPeptides = filterForDocumentPeptides; WorkFlow = workFlow; + UseDiaUmpire = useDiaUmpire; + IsGpf = isGpf; InputFileType = inputFileType; _docType = docType; } @@ -137,6 +141,10 @@ public BuildPeptideSearchLibrarySettings(IEnumerable [Track(ignoreDefaultParent: true)] public ImportPeptideSearchDlg.Workflow WorkFlow { get; private set; } [Track(ignoreDefaultParent: true)] + public bool UseDiaUmpire { get; private set; } + [Track(ignoreDefaultParent: true)] + public bool IsGpf { get; private set; } + [Track(ignoreDefaultParent: true)] public ImportPeptideSearchDlg.InputFile InputFileType { get; private set; } public string LibraryName; // Name of the library being built @@ -218,9 +226,27 @@ public ImportPeptideSearchDlg.Workflow WorkflowType radioDDA.Checked = true; break; } + + cbDiaUmpire.Enabled = cbGpf.Enabled = radioDIA.Checked; } } + public bool UseDiaUmpire + { + get => cbDiaUmpire.Checked; + set => cbDiaUmpire.Checked = value; + } + + public bool IsGpf + { + get => cbGpf.Checked; + set => cbGpf.Checked = value; + } + + // for testing + public bool IsGpfEnabled => cbGpf.Enabled; + public bool IsDiaUmpireEnabled => cbDiaUmpire.Enabled; + public ImportPeptideSearchDlg.InputFile InputFileType { get => _inputFileType; @@ -669,7 +695,7 @@ public bool PerformDDASearch get { return InputFileType != ImportPeptideSearchDlg.InputFile.search_result; } } - public bool DIAConversionNeeded => InputFileType == ImportPeptideSearchDlg.InputFile.dia_raw; + public bool DIAConversionNeeded => InputFileType == ImportPeptideSearchDlg.InputFile.dia_raw && UseDiaUmpire; private void OnGridChange(object sender, EventArgs e) { diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx index 33f932d0ef..6b8ad699f2 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx @@ -117,21 +117,84 @@ System.Resources.ResXResourceWriter, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + + True + + + False + + + NoControl + + + + 201, 43 + + + 142, 17 + + + 4 + + + Gas Phase Fractionation + + + cbGpf + + + System.Windows.Forms.CheckBox, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + + grpWorkflow + + + 0 + + + True + + + False + + + 96, 43 + + + 80, 17 + + + 3 + + + DIA-Umpire + + + cbDiaUmpire + + + System.Windows.Forms.CheckBox, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + + grpWorkflow + + + 1 + Top, Left, Right NoControl - 6, 42 - 369, 17 + 84, 17 - 1 @@ -154,7 +217,7 @@ grpWorkflow - 0 + 2 Top, Left, Right @@ -187,7 +250,7 @@ grpWorkflow - 1 + 3 Top, Left, Right @@ -220,7 +283,7 @@ grpWorkflow - 2 + 4 Bottom @@ -468,7 +531,7 @@ like BiblioSpec .blib, EncyclopeDIA .elib, SpectraST .sqt gridSearchFiles - pwiz.Skyline.FileUI.PeptideSearch.BuildLibraryGridView, Skyline, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null + pwiz.Skyline.FileUI.PeptideSearch.BuildLibraryGridView, Skyline-daily, Version=24.1.1.214, Culture=neutral, PublicKeyToken=null panelPeptideSearch diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.cs index 0fc4cf389d..6d0371b7b0 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.cs @@ -314,11 +314,16 @@ public DiaUmpireDdaConverter GetDiaUmpireConverter() return new DiaUmpireDdaConverter(ImportPeptideSearch, _fullScanSettingsControlGetter().IsolationScheme, diaUmpireConfig); } - public MsconvertDdaConverter GetMsconvertConverter() + public MsconvertDdaConverter GetDdaConverter() { return new MsconvertDdaConverter(ImportPeptideSearch); } + public DiaConverter GetDiaConverter() + { + return new DiaConverter(ImportPeptideSearch); + } + public HardklorDdaConverter GetHardklorConverter() { return new HardklorDdaConverter(ImportPeptideSearch); diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs index aa20dae0c8..22eb6f01f3 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs @@ -74,7 +74,7 @@ public enum Workflow { dda, prm, - dia, // currently means deconvolution with DIA-Umpire + dia, feature_detection } @@ -552,7 +552,10 @@ private void NextPage() { _pagesToSkip.Clear(); ImportPeptideSearch.IsDDASearch = BuildPepSearchLibControl.PerformDDASearch && !IsFeatureDetectionWorkflow; - ImportPeptideSearch.IsDIASearch = WorkflowType == Workflow.prm; // DIA-Umpire is more like DDA search + ImportPeptideSearch.IsDIASearch = WorkflowType == Workflow.dia && + BuildPepSearchLibControl.PerformDDASearch && + !BuildPepSearchLibControl.UseDiaUmpire; + ImportPeptideSearch.IsGpfData = BuildPepSearchLibControl.IsGpf; ImportFastaControl.IsDDASearch = BuildPepSearchLibControl.PerformDDASearch && !IsFeatureDetectionWorkflow; if (!BuildPepSearchLibControl.UseExistingLibrary) { @@ -649,6 +652,7 @@ private void NextPage() _pagesToSkip.Add(Pages.converter_settings_page); ImportPeptideSearch.SpectrumSourceFiles.Clear(); + SearchSettingsControl.InitializeControls(); // in PerformDDA mode, set SpectrumSourceFiles and offer to remove prefix var uniqueNames = Helpers.EnsureUniqueNames(BuildPepSearchLibControl.DdaSearchDataSources.Select(s => s.GetFileName()).ToList()); @@ -768,7 +772,7 @@ private void NextPage() break; case Pages.import_fasta_page: // This is the last page (if there is no dda search) - if (ImportPeptideSearch.IsDDASearch) + if (ImportPeptideSearch.IsDDASearch || ImportPeptideSearch.IsDIASearch) { ImportPeptideSearch.CutoffScore = SearchSettingsControl.CutoffScore; @@ -988,27 +992,15 @@ private void InitiateSearch() IsFeatureDetectionWorkflow ? AbstractDdaConverter.MsdataFileFormat.mzML // Hardklor reads only mzML : AbstractDdaConverter.MsdataFileFormat.mz5; - if (ImportPeptideSearch.DdaConverter == null && - BuildPepSearchLibControl.DdaSearchDataSources.Any(f => - ImportPeptideSearch.SearchEngine.GetSearchFileNeedsConversion(f, out requiredFormat))) - { - ImportPeptideSearch.DdaConverter = IsFeatureDetectionWorkflow - ? ConverterSettingsControl.GetHardklorConverter() - : ConverterSettingsControl.GetMsconvertConverter(); - ImportPeptideSearch.DdaConverter.SetSpectrumFiles(BuildPepSearchLibControl.DdaSearchDataSources); - ImportPeptideSearch.DdaConverter.SetRequiredOutputFormat(requiredFormat); - } - else if (ImportPeptideSearch.DdaConverter != null && - ImportPeptideSearch.DdaConverter.ConvertedSpectrumSources.Any(f => - ImportPeptideSearch.SearchEngine.GetSearchFileNeedsConversion(f, out requiredFormat))) - { - ImportPeptideSearch.DdaConverter.SetRequiredOutputFormat(requiredFormat); - } - if (ImportPeptideSearch.DdaConverter == null && BuildPepSearchLibControl.DdaSearchDataSources.Any(f => ImportPeptideSearch.SearchEngine.GetSearchFileNeedsConversion(f, out requiredFormat))) { - ImportPeptideSearch.DdaConverter = ConverterSettingsControl.GetMsconvertConverter(); + if (IsFeatureDetectionWorkflow) + ImportPeptideSearch.DdaConverter = ConverterSettingsControl.GetHardklorConverter(); + else if (ImportPeptideSearch.IsDIASearch) + ImportPeptideSearch.DdaConverter = ConverterSettingsControl.GetDiaConverter(); + else + ImportPeptideSearch.DdaConverter = ConverterSettingsControl.GetDdaConverter(); ImportPeptideSearch.DdaConverter.SetSpectrumFiles(BuildPepSearchLibControl.DdaSearchDataSources); ImportPeptideSearch.DdaConverter.SetRequiredOutputFormat(requiredFormat); } diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchSettingsControl.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchSettingsControl.cs index 27963959b2..b5564aa3b4 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchSettingsControl.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchSettingsControl.cs @@ -41,6 +41,7 @@ public partial class SearchSettingsControl : UserControl private ImportPeptideSearch ImportPeptideSearch { get; set; } private readonly ImportPeptideSearchDlg _documentContainer; private readonly FullScanSettingsControl _hardklorInstrumentSettingsControl; + private SearchEngine? _searchEngine; public SearchSettingsControl(ImportPeptideSearchDlg documentContainer, ImportPeptideSearch importPeptideSearch) { @@ -48,7 +49,7 @@ public SearchSettingsControl(ImportPeptideSearchDlg documentContainer, ImportPep ImportPeptideSearch = importPeptideSearch; _documentContainer = documentContainer; - if (importPeptideSearch.IsFeatureDetection) + if (ImportPeptideSearch.IsFeatureDetection) { SearchEngineComboBox_SelectedIndexChanged(null, null); // Initialize // Hide all controls other than the logo picture box @@ -62,7 +63,7 @@ public SearchSettingsControl(ImportPeptideSearchDlg documentContainer, ImportPep // Add the Hardklor full scan settings control, used only when the user set FullScan analyzer to "Centroided" // Otherwise just displays the previously designated Full Scan settings - _hardklorInstrumentSettingsControl = new FullScanSettingsControl(documentContainer, ImportPeptideSearch.eFeatureDetectionPhase.hardklor_settings); + _hardklorInstrumentSettingsControl = new FullScanSettingsControl(_documentContainer, ImportPeptideSearch.eFeatureDetectionPhase.hardklor_settings); _hardklorInstrumentSettingsControl.ModifyOptionsForImportPeptideSearchWizard(ImportPeptideSearchDlg.Workflow.feature_detection, false, ImportPeptideSearch.eFeatureDetectionPhase.hardklor_settings); Controls.Add(_hardklorInstrumentSettingsControl); _hardklorInstrumentSettingsControl.Location = new System.Drawing.Point(0, 0); @@ -79,16 +80,36 @@ public SearchSettingsControl(ImportPeptideSearchDlg documentContainer, ImportPep searchEngineComboBox.SelectedIndexChanged += SearchEngineComboBox_SelectedIndexChanged; txtMS1Tolerance.LostFocus += txtMS1Tolerance_LostFocus; txtMS2Tolerance.LostFocus += txtMS2Tolerance_LostFocus; - - searchEngineComboBox.SelectedIndex = 0; groupBoxHardklor.Enabled = groupBoxHardklor.Visible = false; } + InitializeControls(); + } + + public void InitializeControls() + { LoadMassUnitEntries(); + + if (ImportPeptideSearch.IsFeatureDetection) + return; + + if (_searchEngine == null || ImportPeptideSearch.IsDIASearch && _searchEngine != SearchEngine.MSFragger) + searchEngineComboBox.SelectedIndex = ImportPeptideSearch.IsDIASearch ? 2 : 0; // currently only supported by MSFragger } private void SearchEngineComboBox_SelectedIndexChanged(object sender, EventArgs e) { + if (_searchEngine == SelectedSearchEngine) + return; // nothing to do + + if (ImportPeptideSearch.IsDIASearch && SelectedSearchEngine != SearchEngine.MSFragger) // currently only supported by MSFragger + { + MessageDlg.Show(Parent, DdaSearchResources.SearchSettingsControl_SelectedIndexChanged_Only_MSFragger_is_currently_supported); + SelectedSearchEngine = _searchEngine.Value; // go back to previous selection + return; + } + + _searchEngine = (SearchEngine) searchEngineComboBox.SelectedIndex; ImportPeptideSearch.SearchEngine?.Dispose(); ImportPeptideSearch.SearchEngine = InitSelectedSearchEngine(); InitializeEngine(); @@ -217,7 +238,12 @@ private AbstractDdaSearchEngine InitSelectedSearchEngine() case SearchEngine.MSFragger: if (!EnsureRequiredFilesDownloaded(MsFraggerSearchEngine.FilesToDownload, ShowDownloadMsFraggerDialog)) SelectedSearchEngine = SearchEngine.MSAmanda; - return new MsFraggerSearchEngine(CutoffScore, ImportPeptideSearch.IsDIASearch); + MsFraggerSearchEngine.DataType dataType; + if (!ImportPeptideSearch.IsDIASearch) + dataType = MsFraggerSearchEngine.DataType.dda; + else + dataType = ImportPeptideSearch.IsGpfData ? MsFraggerSearchEngine.DataType.dia_gpf : MsFraggerSearchEngine.DataType.dia; + return new MsFraggerSearchEngine(dataType); case SearchEngine.Hardklor: return new HardklorSearchEngine(ImportPeptideSearch); default: @@ -344,16 +370,20 @@ private void LoadComboboxEntries() CutoffScore = BiblioSpecLiteBuilder.GetDefaultScoreThreshold(ImportPeptideSearch.SearchEngine.CutoffScoreName) ?? ImportPeptideSearch.SearchEngine.DefaultCutoffScore; + ImportPeptideSearch.SearchEngine.SetCutoffScore(CutoffScore); } private void LoadMassUnitEntries() { - cbMS1TolUnit.Items.Clear(); - cbMS2TolUnit.Items.Clear(); - - string[] entries = {@"Da", @"ppm"}; - cbMS1TolUnit.Items.AddRange(entries); - cbMS2TolUnit.Items.AddRange(entries); + string[] entries = { @"Da", @"ppm" }; + foreach (var cb in new [] { cbMS1TolUnit, cbMS2TolUnit }) + { + int oldSelectedIndex = cb.SelectedIndex; + cb.Items.Clear(); + cb.Items.AddRange(entries); + if (oldSelectedIndex > -1) + cb.SelectedIndex = oldSelectedIndex; + } } private void LoadFragmentIonEntries() diff --git a/pwiz_tools/Skyline/Model/AuditLog/EnumNames.Designer.cs b/pwiz_tools/Skyline/Model/AuditLog/EnumNames.Designer.cs index 474dffdd94..3da03cddb8 100644 --- a/pwiz_tools/Skyline/Model/AuditLog/EnumNames.Designer.cs +++ b/pwiz_tools/Skyline/Model/AuditLog/EnumNames.Designer.cs @@ -574,7 +574,7 @@ public static string InputFile_dda_raw { } /// - /// Looks up a localized string similar to DIA raw (deconvolute, search, and build library). + /// Looks up a localized string similar to DIA raw (search and build library). /// public static string InputFile_dia_raw { get { diff --git a/pwiz_tools/Skyline/Model/AuditLog/EnumNames.resx b/pwiz_tools/Skyline/Model/AuditLog/EnumNames.resx index 70a93a5fcb..74f4ab9cc6 100644 --- a/pwiz_tools/Skyline/Model/AuditLog/EnumNames.resx +++ b/pwiz_tools/Skyline/Model/AuditLog/EnumNames.resx @@ -598,7 +598,7 @@ DDA raw (search and build library) - DIA raw (deconvolute, search, and build library) + DIA raw (search and build library) Search results (build library directly) diff --git a/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.Designer.cs b/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.Designer.cs index 6582b99b6a..ba1f185df5 100644 --- a/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.Designer.cs +++ b/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.Designer.cs @@ -348,6 +348,15 @@ public static string BuildPeptideSearchLibrarySettings_InputFileType { } } + /// + /// Looks up a localized string similar to Gas phase fractionation. + /// + public static string BuildPeptideSearchLibrarySettings_IsGpf { + get { + return ResourceManager.GetString("BuildPeptideSearchLibrarySettings_IsGpf", resourceCulture); + } + } + /// /// Looks up a localized string similar to Search files. /// @@ -366,6 +375,15 @@ public static string BuildPeptideSearchLibrarySettings_Standard { } } + /// + /// Looks up a localized string similar to Deconvolute spectra with DIA-Umpire. + /// + public static string BuildPeptideSearchLibrarySettings_UseDiaUmpire { + get { + return ResourceManager.GetString("BuildPeptideSearchLibrarySettings_UseDiaUmpire", resourceCulture); + } + } + /// /// Looks up a localized string similar to Workflow. /// diff --git a/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.resx b/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.resx index aa503d094c..dabc6dedcd 100644 --- a/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.resx +++ b/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.resx @@ -1808,4 +1808,10 @@ Spectrum Filter + + Gas phase fractionation + + + Deconvolute spectra with DIA-Umpire + \ No newline at end of file diff --git a/pwiz_tools/Skyline/Model/DdaSearch/DdaSearchResources.designer.cs b/pwiz_tools/Skyline/Model/DdaSearch/DdaSearchResources.designer.cs index e381afb41e..cc1efc4cd3 100644 --- a/pwiz_tools/Skyline/Model/DdaSearch/DdaSearchResources.designer.cs +++ b/pwiz_tools/Skyline/Model/DdaSearch/DdaSearchResources.designer.cs @@ -374,5 +374,14 @@ public static string MsconvertDdaConverter_Run_Starting_msconvert_conversion_ { return ResourceManager.GetString("MsconvertDdaConverter_Run_Starting_msconvert_conversion_", resourceCulture); } } + + /// + /// Looks up a localized string similar to Only MSFragger is currently supported for raw DIA searches. Enable DIA-Umpire to use other search engines.. + /// + public static string SearchSettingsControl_SelectedIndexChanged_Only_MSFragger_is_currently_supported { + get { + return ResourceManager.GetString("SearchSettingsControl_SelectedIndexChanged_Only_MSFragger_is_currently_supported", resourceCulture); + } + } } } diff --git a/pwiz_tools/Skyline/Model/DdaSearch/DdaSearchResources.resx b/pwiz_tools/Skyline/Model/DdaSearch/DdaSearchResources.resx index 4e0dd665f8..9a65ee5bc9 100644 --- a/pwiz_tools/Skyline/Model/DdaSearch/DdaSearchResources.resx +++ b/pwiz_tools/Skyline/Model/DdaSearch/DdaSearchResources.resx @@ -220,4 +220,7 @@ Waiting for next file + + Only MSFragger is currently supported for raw DIA searches. Enable DIA-Umpire to use other search engines. + \ No newline at end of file diff --git a/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs b/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs index 40ab58b44d..652327b089 100644 --- a/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs +++ b/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs @@ -54,23 +54,30 @@ public class MsFraggerSearchEngine : AbstractDdaSearchEngine, IProgressMonitor private const string KEEP_INTERMEDIATE_FILES = "keep-intermediate-files"; + public enum DataType + { + dda = 0, + dia = 1, + dia_gpf = 2 + } + private bool DataIsDIA { get; } - public MsFraggerSearchEngine(double percolatorQvalueCutoff, bool dataIsDIA) + public MsFraggerSearchEngine(DataType dataType) { - DataIsDIA = dataIsDIA; + DataIsDIA = dataType != DataType.dda; AdditionalSettings = new Dictionary { {CHECK_SPECTRAL_FILES, new Setting(CHECK_SPECTRAL_FILES, 1, 0, 1)}, {CALIBRATE_MASS, new Setting(CALIBRATE_MASS, 0, 0, 2)}, - {PERCOLATOR_TEST_QVALUE_CUTOFF, new Setting(PERCOLATOR_TEST_QVALUE_CUTOFF, percolatorQvalueCutoff, 0, 1)}, + {PERCOLATOR_TEST_QVALUE_CUTOFF, new Setting(PERCOLATOR_TEST_QVALUE_CUTOFF, 0.01, 0, 1)}, {PERCOLATOR_TRAIN_QVALUE_CUTOFF, new Setting(PERCOLATOR_TRAIN_QVALUE_CUTOFF, 0.01, 0, 1)}, {KEEP_INTERMEDIATE_FILES, new Setting(KEEP_INTERMEDIATE_FILES, false)}, }; // ReSharper disable LocalizableElement - AddAdditionalSetting(MSFRAGGER_SETTINGS, new Setting(@"data_type", DataIsDIA ? 1 : 0, 0, 3)); // Data type (0 for DDA, 1 for DIA, 2 for gas-phase fractionation DIA, 3 for DDA+). + AddAdditionalSetting(MSFRAGGER_SETTINGS, new Setting(@"data_type", (int) dataType, 0, 3)); // Data type (0 for DDA, 1 for DIA, 2 for gas-phase fractionation DIA, 3 for DDA+). AddAdditionalSetting(MSFRAGGER_SETTINGS, new Setting("precursor_true_tolerance", 20.0)); // True precursor mass tolerance (window is +/- this value). AddAdditionalSetting(MSFRAGGER_SETTINGS, new Setting("precursor_true_units", 1, 0, 1)); // True precursor mass tolerance units (0 for Da, 1 for ppm). diff --git a/pwiz_tools/Skyline/Model/DdaSearch/MsconvertDdaConverter.cs b/pwiz_tools/Skyline/Model/DdaSearch/MsconvertDdaConverter.cs index f76224c639..d541ce2676 100644 --- a/pwiz_tools/Skyline/Model/DdaSearch/MsconvertDdaConverter.cs +++ b/pwiz_tools/Skyline/Model/DdaSearch/MsconvertDdaConverter.cs @@ -208,6 +208,22 @@ public UpdateProgressResponse UpdateProgress(IProgressStatus status) } } + /// + /// An MsconvertDdaConverter with slightly different settings, for DIA search + /// + public class DiaConverter : MsconvertDdaConverter + { + public DiaConverter(ImportPeptideSearch importPeptideSearch) : base(importPeptideSearch) + { + } + + public override string FilterMslevel() + { + return ""; // DIA needs both levels + } + + } + /// /// Just an Msconvert caller with slightly different settings, for Hardklor purposes /// diff --git a/pwiz_tools/Skyline/Model/ImportPeptideSearch.cs b/pwiz_tools/Skyline/Model/ImportPeptideSearch.cs index 8ce7ba2921..bc4694507d 100644 --- a/pwiz_tools/Skyline/Model/ImportPeptideSearch.cs +++ b/pwiz_tools/Skyline/Model/ImportPeptideSearch.cs @@ -62,6 +62,7 @@ public enum eFeatureDetectionPhase public IrtStandard IrtStandard { get; set; } public bool IsDDASearch { get; set; } public bool IsDIASearch { get; set; } + public bool IsGpfData { get; set; } public bool IsFeatureDetection { get; set; } public int RemainingStepsInSearch { get; set; } // In the case of Hardklor+Bullseye there may be several steps public HardklorSettings SettingsHardklor { get; set; } diff --git a/pwiz_tools/Skyline/TestFunctional/DiaSearchTest.cs b/pwiz_tools/Skyline/TestFunctional/DiaSearchTest.cs index 3a2692a594..bf1a042655 100644 --- a/pwiz_tools/Skyline/TestFunctional/DiaSearchTest.cs +++ b/pwiz_tools/Skyline/TestFunctional/DiaSearchTest.cs @@ -29,6 +29,7 @@ using pwiz.Skyline.FileUI; using pwiz.Skyline.FileUI.PeptideSearch; using pwiz.Skyline.Model; +using pwiz.Skyline.Model.DdaSearch; using pwiz.Skyline.Model.DocSettings; using pwiz.Skyline.Model.Results; using pwiz.Skyline.Properties; @@ -80,6 +81,8 @@ public override string ToString() public DocumentCounts Final { get; set; } public Action EditIsolationSchemeAction { get; set; } + + public Action TestAction { get; set; } } private void SetupDiaSearchVariableWindows() @@ -105,7 +108,9 @@ private void SetupDiaSearchVariableWindows() importRangesDlg.SelectFile(importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources.First().GetFileName()); importRangesDlg.Open(); }); - } + }, + + TestAction = TestDiaUmpireSearch }; } @@ -153,6 +158,13 @@ public void TestDiaSearchVariableWindowsMsFragger() new KeyValuePair("remove_precursor_peak", "0") }; + _testDetails.TestAction = () => + { + // run it twice to make sure logic still works + TestDiaUmpireSearch(); + TestDiaUmpireSearch(); + }; + RunFunctionalTest(); } @@ -183,13 +195,6 @@ public void TestDiaSearchFixedWindows() EditIsolationSchemeAction = (importPeptideSearchDlg, isolationScheme) => { - /*RunDlg(isolationScheme.ImportRanges, importRangesDlg => - { - var diaSource = importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources[0]; - importRangesDlg.CurrentDirectory = new MsDataFilePath(Path.GetDirectoryName(diaSource.GetFilePath())); - importRangesDlg.SelectFile(importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources.First().GetFileName()); - importRangesDlg.Open(); - });*/ RunDlg(isolationScheme.Calculate, calculateIsolationSchemeDlg => { calculateIsolationSchemeDlg.Start = 400; @@ -197,8 +202,51 @@ public void TestDiaSearchFixedWindows() calculateIsolationSchemeDlg.WindowWidth = 25; calculateIsolationSchemeDlg.OkDialog(); }); - } + }, + + TestAction = TestDiaUmpireSearch + }; + + RunFunctionalTest(); + } + + [TestMethod, NoParallelTesting(TestExclusionReason.RESOURCE_INTENSIVE), NoUnicodeTesting(TestExclusionReason.MSFRAGGER_UNICODE_ISSUES)] + public void TestDiaSearch() + { + TestFilesZip = @"TestFunctional\DiaSearchTest.zip"; + + _testDetails = new TestDetails + { + DocumentPath = "TestVariableWindowMsFragger.sky", + SearchFiles = new[] + { + "collinsb_I180316_001_SW-A-subset.mz5", + "collinsb_I180316_002_SW-B-subset.mz5" + }, + FastaPath = "collinsb_I180316.fasta", + + EditIsolationSchemeAction = (importPeptideSearchDlg, editIsolationSchemeDlg) => + { + RunDlg(editIsolationSchemeDlg.ImportRanges, importRangesDlg => + { + var diaSource = importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources[0]; + importRangesDlg.CurrentDirectory = new MsDataFilePath(Path.GetDirectoryName(diaSource.GetFilePath())); + importRangesDlg.SelectFile(importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources.First().GetFileName()); + importRangesDlg.Open(); + }); + }, }; + _testDetails.SearchEngine = SearchSettingsControl.SearchEngine.MSFragger; + _testDetails.PrecursorMzTolerance = new MzTolerance(25, MzTolerance.Units.ppm); + _testDetails.FragmentMzTolerance = new MzTolerance(25, MzTolerance.Units.ppm); + _testDetails.Final = new TestDetails.DocumentCounts { ProteinCount = 229, PeptideCount = 254, PrecursorCount = 283, TransitionCount = 2547 }; + _testDetails.AdditionalSettings = new List> + { + new KeyValuePair("check_spectral_files", "0"), + //new KeyValuePair("keep-intermediate-files", "True") + }; + + _testDetails.TestAction = TestDiaSearchPredicate; RunFunctionalTest(); } @@ -215,10 +263,7 @@ private string GetTestPath(string path) protected override void DoTest() { - TestDiaUmpireSearch(_testDetails); - - if (_testDetails.SearchEngine == SearchSettingsControl.SearchEngine.MSFragger) - TestDiaUmpireSearch(_testDetails); + _testDetails.TestAction(); } private void ValidateTargets(TestDetails.DocumentCounts targetCounts, TestDetails.DocumentCounts actualCounts, string propName) @@ -245,8 +290,9 @@ private void ValidateTargets(TestDetails.DocumentCounts targetCounts, TestDetail /// /// Quick test that DDA search works with MSAmanda. /// - private void TestDiaUmpireSearch(TestDetails testDetails) + private void TestDiaUmpireSearch() { + var testDetails = _testDetails; PrepareDocument(testDetails.DocumentPath); // copy files from core to test location (otherwise Skyline's DiaUmpire output will overwrite core test reference files) @@ -273,6 +319,7 @@ private void TestDiaUmpireSearch(TestDetails testDetails) importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = testDetails.SearchFiles .Select(o => (MsDataFileUri) new MsDataFilePath(GetTestPath(o))).Take(1).ToArray(); importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia; + importPeptideSearchDlg.BuildPepSearchLibControl.UseDiaUmpire = true; Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); }); @@ -541,6 +588,272 @@ private void TestDiaUmpireSearch(TestDetails testDetails) RunUI(() => SkylineWindow.SaveDocument()); } + private void TestDiaSearchPredicate() + { + var testDetails = _testDetails; + PrepareDocument(testDetails.DocumentPath); + + // Launch the wizard + var importPeptideSearchDlg = ShowDialog(SkylineWindow.ShowRunPeptideSearchDlg); + + // We're on the "Build Spectral Library" page of the wizard. + + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page); + importPeptideSearchDlg.BuildPepSearchLibControl.InputFileType = ImportPeptideSearchDlg.InputFile.dia_raw; + importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = testDetails.SearchFiles + .Select(o => (MsDataFileUri)new MsDataFilePath(GetTestPath(o))).Take(1).ToArray(); + importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia; + //Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + }); + + SkylineWindow.BeginInvoke(new Action(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()))); + + if (testDetails.HasMissingDependencies) + { + if (testDetails.SearchEngine == SearchSettingsControl.SearchEngine.MSFragger) + { + var msfraggerDownloaderDlg = TryWaitForOpenForm(2000); + if (msfraggerDownloaderDlg != null) + { + RunUI(() => msfraggerDownloaderDlg.SetValues("Matt Chambers (testing download from Skyline)", "matt.chambers42@gmail.com", "UW")); + OkDialog(msfraggerDownloaderDlg, msfraggerDownloaderDlg.ClickAccept); + } + } + + if (testDetails.SearchEngine != SearchSettingsControl.SearchEngine.MSAmanda) + { + var downloaderDlg = TryWaitForOpenForm(2000); + if (downloaderDlg != null) + { + OkDialog(downloaderDlg, downloaderDlg.ClickYes); + var waitDlg = WaitForOpenForm(); + WaitForClosedForm(waitDlg); + } + } + } + + // With only 1 source, no add/remove prefix/suffix dialog + + // We're on the "Match Modifications" page. Add M+16 mod. + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page); + }); + + bool secondLoop = importPeptideSearchDlg.MatchModificationsControl.MatchedModifications.Contains(m => m == "Oxidation (M)"); + // In PerformDDASearch mode, ClickAddStructuralModification launches edit list dialog + if (!secondLoop) + { + var editListUI = + ShowDialog, StaticMod>>(importPeptideSearchDlg.MatchModificationsControl.ClickAddStructuralModification); + RunDlg(editListUI.AddItem, editModDlg => + { + editModDlg.SetModification("Oxidation (M)"); // Not L10N + editModDlg.OkDialog(); + }); + + // Test a non-Unimod mod that won't affect the search + RunDlg(editListUI.AddItem, editModDlg => + { + editModDlg.Modification = new StaticMod("NotUniModMod (U)", "U", null, "C3P1O1", LabelAtoms.None, null, null); + editModDlg.OkDialog(); + }); + OkDialog(editListUI, editListUI.OkDialog); + } + + // Test back/next buttons + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page); + + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + }); + + // We're on the transition settings page. + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.transition_settings_page); + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + }); + + // We're on the MS1 full scan settings page. + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page); + }); + + string isolationSchemeName = "TestDiaSearch"; + if (secondLoop) + { + RunUI(() => + { + importPeptideSearchDlg.FullScanSettingsControl.ComboIsolationSchemeSetFocus(); + importPeptideSearchDlg.FullScanSettingsControl.IsolationSchemeName = isolationSchemeName; + }); + } + else + { + RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.ComboIsolationSchemeSetFocus()); + var isolationScheme = ShowDialog(importPeptideSearchDlg.FullScanSettingsControl.AddIsolationScheme); + + RunUI(() => + { + isolationScheme.IsolationSchemeName = isolationSchemeName; + isolationScheme.UseResults = false; + }); + + if (testDetails.EditIsolationSchemeAction != null) + testDetails.EditIsolationSchemeAction(importPeptideSearchDlg, isolationScheme); + WaitForConditionUI(10000, () => isolationScheme.GetIsolationWindows().Any()); + + var isolationGraph = ShowDialog(isolationScheme.OpenGraph); + + OkDialog(isolationGraph, isolationGraph.CloseButton); + OkDialog(isolationScheme, isolationScheme.OkDialog); + } + + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + }); + + // We're on the "Import FASTA" page. + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page); + // Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled); + importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled = false; + importPeptideSearchDlg.ImportFastaControl.SetFastaContent(GetTestPath(testDetails.FastaPath)); + importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 0; + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + }); + + // We're on the Adjust search settings page + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.dda_search_settings_page); + + // MSFragger should be selected by default + Assert.AreEqual(SearchSettingsControl.SearchEngine.MSFragger, importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine); + }); + //SkylineWindow.BeginInvoke(new Action(() => importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine = testDetails.SearchEngine)); + + + // selecting something other than MSFragger should show an error + RunDlg(() => importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine = SearchSettingsControl.SearchEngine.MSAmanda, + messageDlg => + { + Assert.AreEqual(DdaSearchResources.SearchSettingsControl_SelectedIndexChanged_Only_MSFragger_is_currently_supported, messageDlg.Message); + messageDlg.ClickOk(); + }); + + RunUI(() => + { + importPeptideSearchDlg.SearchSettingsControl.PrecursorTolerance = testDetails.PrecursorMzTolerance; + importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance = testDetails.FragmentMzTolerance; + importPeptideSearchDlg.SearchSettingsControl.CutoffScore = 0.05; // default q value is 0.01 + if (_testDetails.AdditionalSettings != null) + foreach (var additionalSetting in testDetails.AdditionalSettings) + importPeptideSearchDlg.SearchSettingsControl.SetAdditionalSetting(additionalSetting.Key, additionalSetting.Value); + //importPeptideSearchDlg.SearchSettingsControl.FragmentIons = "b, y"; + }); + + WaitForConditionUI(() => testDetails.FragmentMzTolerance.Unit == importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance.Unit); + + bool? searchSucceeded = null; + RunUI(() => + { + // Run the search + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + + importPeptideSearchDlg.SearchControl.SearchFinished += (success) => searchSucceeded = success; + importPeptideSearchDlg.BuildPepSearchLibControl.IncludeAmbiguousMatches = true; + + // Cancel search + importPeptideSearchDlg.SearchControl.Cancel(); + }); + + WaitForConditionUI(60000, () => searchSucceeded.HasValue, + () => importPeptideSearchDlg.SearchControl.LogText); + RunUI(() => Assert.IsFalse(searchSucceeded.Value, importPeptideSearchDlg.SearchControl.LogText)); + searchSucceeded = null; + + // Go back and add another file + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on search settings + Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on import FASTA + Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on full scan settings + Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on transition settings + Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on modifications + Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on input files + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page); + + importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = testDetails.SearchFiles.Select(o => (MsDataFileUri)new MsDataFilePath(GetTestPath(o))).ToArray(); + }); + + + // With 2 sources, we get the remove prefix/suffix dialog; accept default behavior + if (testDetails.SearchFiles.Count() > 1) + { + var removeSuffix = ShowDialog(() => importPeptideSearchDlg.ClickNextButton()); // now on remove prefix/suffix dialog + OkDialog(removeSuffix, () => removeSuffix.YesDialog()); // now on modifications + WaitForDocumentLoaded(); + } + else + RunUI(() => importPeptideSearchDlg.ClickNextButton()); + + RunUI(() => + { + // We're on the "Match Modifications" page again. + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == + ImportPeptideSearchDlg.Pages.match_modifications_page); + importPeptideSearchDlg.MatchModificationsControl.ChangeItem(0, true); // uncheck C+57 + importPeptideSearchDlg.MatchModificationsControl.ChangeItem(1, true); // check M+16 + importPeptideSearchDlg.MatchModificationsControl.ChangeItem(2, true); // check U+C3P0 + + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on transition settings + importPeptideSearchDlg.TransitionSettingsControl.IonRangeFrom = TransitionFilter.StartFragmentFinder.ION_1.Label; + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on full scan settings + + // re-select isolation scheme after FullScanSettingsControl reset + importPeptideSearchDlg.FullScanSettingsControl.IsolationSchemeName = isolationSchemeName; + }); + + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on import FASTA + importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled = false; + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on search settings + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on search progress + }); + + WaitForConditionUI(120000, () => searchSucceeded.HasValue, () => importPeptideSearchDlg.SearchControl.LogText); + + RunUI(() => Assert.IsTrue(searchSucceeded.Value, importPeptideSearchDlg.SearchControl.LogText)); + + if (IsRecordMode) + Console.WriteLine(); + + var emptyProteinsDlg = ShowDialog(importPeptideSearchDlg.ClickNextButtonNoCheck); + WaitForConditionUI(() => emptyProteinsDlg.DocumentFinalCalculated); + RunUI(() => + { + var aic = new TestDetails.DocumentCounts(); + emptyProteinsDlg.NewTargetsFinalSync(out aic.ProteinCount, out aic.PeptideCount, out aic.PrecursorCount, out aic.TransitionCount); + ValidateTargets(testDetails.Final, aic, "_testDetails.Final"); + }); + OkDialog(emptyProteinsDlg, emptyProteinsDlg.OkDialog); + + WaitForDocumentLoaded(); + RunUI(() => SkylineWindow.SaveDocument()); + } + private void PrepareDocument(string documentFile) { RunUI(() => SkylineWindow.NewDocument(true)); diff --git a/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs b/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs index df950042e1..094a7a7881 100644 --- a/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs +++ b/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs @@ -62,6 +62,7 @@ private class AnalysisValues public string ZipPath; public string[] DiaFiles; + public bool IsGpfData; public string ProteinToSelect; public string PeptideToSelect; @@ -96,13 +97,14 @@ public void TestDiaSearchStellarTutorial() "P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML", "P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML", }, + IsGpfData = true, ProteinToSelect = "sp|P01591|IGJ_HUMAN", PeptideToSelect = "ENISDPTSPLR", AdditionalSettings = new Dictionary { - { "data_type", "2" } // set MSFragger to GPF mode + //{ "data_type", "2" } // set MSFragger to GPF mode }, }; @@ -241,7 +243,12 @@ private void TestMsFraggerSearch() Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page); importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = SearchFiles.Select(o => new MsDataFilePath(o)).ToArray(); importPeptideSearchDlg.BuildPepSearchLibControl.IncludeAmbiguousMatches = false; - importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.prm; + Assert.IsFalse(importPeptideSearchDlg.BuildPepSearchLibControl.IsGpfEnabled); + Assert.IsFalse(importPeptideSearchDlg.BuildPepSearchLibControl.IsDiaUmpireEnabled); + importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia; + Assert.IsTrue(importPeptideSearchDlg.BuildPepSearchLibControl.IsGpfEnabled); + Assert.IsTrue(importPeptideSearchDlg.BuildPepSearchLibControl.IsDiaUmpireEnabled); + importPeptideSearchDlg.BuildPepSearchLibControl.IsGpf = _analysisValues.IsGpfData; }); PauseForScreenShot("Import Peptide Search - After Selecting DIA Files page", tutorialPage++); @@ -358,7 +365,7 @@ private void TestMsFraggerSearch() RunUI(() => { Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page); - Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled); + //Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled); importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 1; importPeptideSearchDlg.ImportFastaControl.SetFastaContent(GetTestPath(_analysisValues.FastaPath)); }); diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchQeTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchQeTutorial.log index aa42752846..e90041854c 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchQeTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchQeTutorial.log @@ -12,8 +12,10 @@ Build Spectral Library > Search files : contains { File = "23aug2017_hela_serum_ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False -Build Spectral Library > Workflow is "PRM" -Build Spectral Library > Input File Type is "DDA raw (search and build library)" +Build Spectral Library > Workflow is "DIA" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is False +Build Spectral Library > Gas phase fractionation is False +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -25,8 +27,10 @@ Extra Info: Search files = iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, -Workflow = "PRM", -Input File Type = "DDA raw (search and build library)" +Workflow = "DIA", +Deconvolute spectra with DIA-Umpire = False, +Gas phase fractionation = False, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log index 6a4bcaba89..37cc03a557 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log @@ -13,8 +13,10 @@ Build Spectral Library > Search files : contains { File = "P2_202405_neo_150uID_ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False -Build Spectral Library > Workflow is "PRM" -Build Spectral Library > Input File Type is "DDA raw (search and build library)" +Build Spectral Library > Workflow is "DIA" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is False +Build Spectral Library > Gas phase fractionation is True +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -31,8 +33,10 @@ Extra Info: Search files = iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, -Workflow = "PRM", -Input File Type = "DDA raw (search and build library)" +Workflow = "DIA", +Deconvolute spectra with DIA-Umpire = False, +Gas phase fractionation = True, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchQeTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchQeTutorial.log index d18318b6a4..4cbba73ce8 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchQeTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchQeTutorial.log @@ -12,8 +12,10 @@ Build Spectral Library > Search files : contains { File = "23aug2017_hela_serum_ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False -Build Spectral Library > Workflow is "PRM" -Build Spectral Library > Input File Type is "DDA raw (search and build library)" +Build Spectral Library > Workflow is "DIA" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is False +Build Spectral Library > Gas phase fractionation is False +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -25,8 +27,10 @@ Extra Info: Search files = iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, -Workflow = "PRM", -Input File Type = "DDA raw (search and build library)" +Workflow = "DIA", +Deconvolute spectra with DIA-Umpire = False, +Gas phase fractionation = False, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log index b08715c4be..153835886d 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log @@ -13,8 +13,10 @@ Build Spectral Library > Search files : contains { File = "P2_202405_neo_150uID_ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False -Build Spectral Library > Workflow is "PRM" -Build Spectral Library > Input File Type is "DDA raw (search and build library)" +Build Spectral Library > Workflow is "DIA" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is False +Build Spectral Library > Gas phase fractionation is True +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -31,8 +33,10 @@ Extra Info: Search files = iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, -Workflow = "PRM", -Input File Type = "DDA raw (search and build library)" +Workflow = "DIA", +Deconvolute spectra with DIA-Umpire = False, +Gas phase fractionation = True, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchQeTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchQeTutorial.log index 7d529ad6d9..5576bd3035 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchQeTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchQeTutorial.log @@ -12,8 +12,10 @@ All Info : スペクトルライブラリを構築>iRT標準ペプチドはなしです スペクトルライブラリを構築>曖昧な一致を含むは偽です スペクトルライブラリを構築>ドキュメント内のペプチドをフィルタリングは偽です -スペクトルライブラリを構築>ワークフローは"PRM"です -スペクトルライブラリを構築>入力ファイルタイプは"DDA生データ (ライブラリの検索と構築)"です +スペクトルライブラリを構築>ワークフローは"DIA"です +スペクトルライブラリを構築>Deconvolute spectra with DIA-Umpireは偽です +スペクトルライブラリを構築>Gas phase fractionationは偽です +スペクトルライブラリを構築>入力ファイルタイプは"DIA生データ (ライブラリのデコンボリューション、検索、構築)"です Extra Info: ファイルを検索 = [ { @@ -25,8 +27,10 @@ Extra Info: ファイルを検索 = iRT標準ペプチド = なし, 曖昧な一致を含む = 偽, ドキュメント内のペプチドをフィルタリング = 偽, -ワークフロー = "PRM", -入力ファイルタイプ = "DDA生データ (ライブラリの検索と構築)" +ワークフロー = "DIA", +Deconvolute spectra with DIA-Umpire = 偽, +Gas phase fractionation = 偽, +入力ファイルタイプ = "DIA生データ (ライブラリのデコンボリューション、検索、構築)" Undo Redo : ペプチド検索がインポートされました Summary : ペプチド検索がインポートされました diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log index c65fa08d29..d7801ac33d 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log @@ -13,8 +13,10 @@ All Info : スペクトルライブラリを構築>iRT標準ペプチドはなしです スペクトルライブラリを構築>曖昧な一致を含むは偽です スペクトルライブラリを構築>ドキュメント内のペプチドをフィルタリングは偽です -スペクトルライブラリを構築>ワークフローは"PRM"です -スペクトルライブラリを構築>入力ファイルタイプは"DDA生データ (ライブラリの検索と構築)"です +スペクトルライブラリを構築>ワークフローは"DIA"です +スペクトルライブラリを構築>Deconvolute spectra with DIA-Umpireは偽です +スペクトルライブラリを構築>Gas phase fractionationは真です +スペクトルライブラリを構築>入力ファイルタイプは"DIA生データ (ライブラリのデコンボリューション、検索、構築)"です Extra Info: ファイルを検索 = [ { @@ -31,8 +33,10 @@ Extra Info: ファイルを検索 = iRT標準ペプチド = なし, 曖昧な一致を含む = 偽, ドキュメント内のペプチドをフィルタリング = 偽, -ワークフロー = "PRM", -入力ファイルタイプ = "DDA生データ (ライブラリの検索と構築)" +ワークフロー = "DIA", +Deconvolute spectra with DIA-Umpire = 偽, +Gas phase fractionation = 真, +入力ファイルタイプ = "DIA生データ (ライブラリのデコンボリューション、検索、構築)" Undo Redo : ペプチド検索がインポートされました Summary : ペプチド検索がインポートされました diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchQeTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchQeTutorial.log index d18318b6a4..4cbba73ce8 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchQeTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchQeTutorial.log @@ -12,8 +12,10 @@ Build Spectral Library > Search files : contains { File = "23aug2017_hela_serum_ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False -Build Spectral Library > Workflow is "PRM" -Build Spectral Library > Input File Type is "DDA raw (search and build library)" +Build Spectral Library > Workflow is "DIA" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is False +Build Spectral Library > Gas phase fractionation is False +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -25,8 +27,10 @@ Extra Info: Search files = iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, -Workflow = "PRM", -Input File Type = "DDA raw (search and build library)" +Workflow = "DIA", +Deconvolute spectra with DIA-Umpire = False, +Gas phase fractionation = False, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log index b08715c4be..153835886d 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log @@ -13,8 +13,10 @@ Build Spectral Library > Search files : contains { File = "P2_202405_neo_150uID_ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False -Build Spectral Library > Workflow is "PRM" -Build Spectral Library > Input File Type is "DDA raw (search and build library)" +Build Spectral Library > Workflow is "DIA" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is False +Build Spectral Library > Gas phase fractionation is True +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -31,8 +33,10 @@ Extra Info: Search files = iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, -Workflow = "PRM", -Input File Type = "DDA raw (search and build library)" +Workflow = "DIA", +Deconvolute spectra with DIA-Umpire = False, +Gas phase fractionation = True, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchQeTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchQeTutorial.log index 4062b396b7..d8b92d1aca 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchQeTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchQeTutorial.log @@ -12,8 +12,10 @@ All Info : 建立谱图库 > iRT 标准肽段 是 无 建立谱图库 > 包含不明确匹配项 是 假 建立谱图库 > 文档肽段筛选器 是 假 -建立谱图库 > 工作流程 是 "PRM（并行反应离子监测）" -建立谱图库 > 输入文件类型 是 "DDA 原始（搜索和构建库）" +建立谱图库 > 工作流程 是 "DIA（数据非依赖性采集）" +建立谱图库 > Deconvolute spectra with DIA-Umpire 是 假 +建立谱图库 > Gas phase fractionation 是 假 +建立谱图库 > 输入文件类型 是 "DIA 原始（去卷积、搜索和构建库）" Extra Info: 搜索文件 = [ { @@ -25,8 +27,10 @@ Extra Info: 搜索文件 = iRT 标准肽段 = 无, 包含不明确匹配项 = 假, 文档肽段筛选器 = 假, -工作流程 = "PRM（并行反应离子监测）", -输入文件类型 = "DDA 原始（搜索和构建库）" +工作流程 = "DIA（数据非依赖性采集）", +Deconvolute spectra with DIA-Umpire = 假, +Gas phase fractionation = 假, +输入文件类型 = "DIA 原始（去卷积、搜索和构建库）" Undo Redo : 已导入肽段搜索 Summary : 已导入肽段搜索 diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log index fd238524cc..f0438b94bb 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log @@ -13,8 +13,10 @@ All Info : 建立谱图库 > iRT 标准肽段 是 无 建立谱图库 > 包含不明确匹配项 是 假 建立谱图库 > 文档肽段筛选器 是 假 -建立谱图库 > 工作流程 是 "PRM（并行反应离子监测）" -建立谱图库 > 输入文件类型 是 "DDA 原始（搜索和构建库）" +建立谱图库 > 工作流程 是 "DIA（数据非依赖性采集）" +建立谱图库 > Deconvolute spectra with DIA-Umpire 是 假 +建立谱图库 > Gas phase fractionation 是 真 +建立谱图库 > 输入文件类型 是 "DIA 原始（去卷积、搜索和构建库）" Extra Info: 搜索文件 = [ { @@ -31,8 +33,10 @@ Extra Info: 搜索文件 = iRT 标准肽段 = 无, 包含不明确匹配项 = 假, 文档肽段筛选器 = 假, -工作流程 = "PRM（并行反应离子监测）", -输入文件类型 = "DDA 原始（搜索和构建库）" +工作流程 = "DIA（数据非依赖性采集）", +Deconvolute spectra with DIA-Umpire = 假, +Gas phase fractionation = 真, +输入文件类型 = "DIA 原始（去卷积、搜索和构建库）" Undo Redo : 已导入肽段搜索 Summary : 已导入肽段搜索 From f40cd3334198784539430c7bc1fc0a84018bd6b5 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Tue, 27 Aug 2024 13:28:12 -0400 Subject: [PATCH 2/6] * removed default value from audit log for IsGpf and UseDiaUmpire --- .../FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs | 4 ++-- pwiz_tools/Skyline/TestPerf/DiaUmpireTutorialTest.cs | 2 +- .../TutorialAuditLogs/en/TestDiaSearchQeTutorial.log | 4 ---- .../TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log | 2 -- .../TutorialAuditLogs/fr/TestDiaSearchQeTutorial.log | 4 ---- .../TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log | 2 -- .../TutorialAuditLogs/ja/TestDiaSearchQeTutorial.log | 4 ---- .../TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log | 2 -- .../TutorialAuditLogs/tr/TestDiaSearchQeTutorial.log | 4 ---- .../TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log | 2 -- .../TutorialAuditLogs/zh/TestDiaSearchQeTutorial.log | 4 ---- .../TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log | 2 -- 12 files changed, 3 insertions(+), 33 deletions(-) diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs index b979dc6b0d..e7ee75eb43 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs @@ -140,9 +140,9 @@ public BuildPeptideSearchLibrarySettings(IEnumerable public bool FilterForDocumentPeptides { get; private set; } [Track(ignoreDefaultParent: true)] public ImportPeptideSearchDlg.Workflow WorkFlow { get; private set; } - [Track(ignoreDefaultParent: true)] + [Track(defaultValues: typeof(DefaultValuesFalse))] public bool UseDiaUmpire { get; private set; } - [Track(ignoreDefaultParent: true)] + [Track(defaultValues: typeof(DefaultValuesFalse))] public bool IsGpf { get; private set; } [Track(ignoreDefaultParent: true)] public ImportPeptideSearchDlg.InputFile InputFileType { get; private set; } diff --git a/pwiz_tools/Skyline/TestPerf/DiaUmpireTutorialTest.cs b/pwiz_tools/Skyline/TestPerf/DiaUmpireTutorialTest.cs index d5fc91f948..872a3bcb59 100644 --- a/pwiz_tools/Skyline/TestPerf/DiaUmpireTutorialTest.cs +++ b/pwiz_tools/Skyline/TestPerf/DiaUmpireTutorialTest.cs @@ -394,7 +394,7 @@ protected override void DoTest() importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = searchFiles.Select(f => new MsDataFilePath(f)).ToArray(); importPeptideSearchDlg.BuildPepSearchLibControl.IrtStandards = IrtStandard.BIOGNOSYS_11; importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia; - importPeptideSearchDlg.BuildPepSearchLibControl.InputFileType = ImportPeptideSearchDlg.InputFile.dia_raw; + importPeptideSearchDlg.BuildPepSearchLibControl.UseDiaUmpire = true; // Check default settings shown in the tutorial Assert.IsFalse(importPeptideSearchDlg.BuildPepSearchLibControl.IncludeAmbiguousMatches); }); diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchQeTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchQeTutorial.log index e90041854c..af674dced4 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchQeTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchQeTutorial.log @@ -13,8 +13,6 @@ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is False -Build Spectral Library > Gas phase fractionation is False Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -28,8 +26,6 @@ iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = False, -Gas phase fractionation = False, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log index 37cc03a557..ad0e8549db 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is False Build Spectral Library > Gas phase fractionation is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = @@ -34,7 +33,6 @@ iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = False, Gas phase fractionation = True, Input File Type = "DIA raw (search and build library)" diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchQeTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchQeTutorial.log index 4cbba73ce8..bd3ccad907 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchQeTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchQeTutorial.log @@ -13,8 +13,6 @@ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is False -Build Spectral Library > Gas phase fractionation is False Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -28,8 +26,6 @@ iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = False, -Gas phase fractionation = False, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log index 153835886d..0946c0eccf 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is False Build Spectral Library > Gas phase fractionation is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = @@ -34,7 +33,6 @@ iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = False, Gas phase fractionation = True, Input File Type = "DIA raw (search and build library)" diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchQeTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchQeTutorial.log index 5576bd3035..ec475792a3 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchQeTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchQeTutorial.log @@ -13,8 +13,6 @@ All Info : スペクトルライブラリを構築>曖昧な一致を含むは偽です スペクトルライブラリを構築>ドキュメント内のペプチドをフィルタリングは偽です スペクトルライブラリを構築>ワークフローは"DIA"です -スペクトルライブラリを構築>Deconvolute spectra with DIA-Umpireは偽です -スペクトルライブラリを構築>Gas phase fractionationは偽です スペクトルライブラリを構築>入力ファイルタイプは"DIA生データ (ライブラリのデコンボリューション、検索、構築)"です Extra Info: ファイルを検索 = [ @@ -28,8 +26,6 @@ iRT標準ペプチド = なし, 曖昧な一致を含む = 偽, ドキュメント内のペプチドをフィルタリング = 偽, ワークフロー = "DIA", -Deconvolute spectra with DIA-Umpire = 偽, -Gas phase fractionation = 偽, 入力ファイルタイプ = "DIA生データ (ライブラリのデコンボリューション、検索、構築)" Undo Redo : ペプチド検索がインポートされました diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log index d7801ac33d..350b8d8eae 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log @@ -14,7 +14,6 @@ All Info : スペクトルライブラリを構築>曖昧な一致を含むは偽です スペクトルライブラリを構築>ドキュメント内のペプチドをフィルタリングは偽です スペクトルライブラリを構築>ワークフローは"DIA"です -スペクトルライブラリを構築>Deconvolute spectra with DIA-Umpireは偽です スペクトルライブラリを構築>Gas phase fractionationは真です スペクトルライブラリを構築>入力ファイルタイプは"DIA生データ (ライブラリのデコンボリューション、検索、構築)"です Extra Info: ファイルを検索 = @@ -34,7 +33,6 @@ iRT標準ペプチド = なし, 曖昧な一致を含む = 偽, ドキュメント内のペプチドをフィルタリング = 偽, ワークフロー = "DIA", -Deconvolute spectra with DIA-Umpire = 偽, Gas phase fractionation = 真, 入力ファイルタイプ = "DIA生データ (ライブラリのデコンボリューション、検索、構築)" diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchQeTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchQeTutorial.log index 4cbba73ce8..bd3ccad907 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchQeTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchQeTutorial.log @@ -13,8 +13,6 @@ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is False -Build Spectral Library > Gas phase fractionation is False Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -28,8 +26,6 @@ iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = False, -Gas phase fractionation = False, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log index 153835886d..0946c0eccf 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is False Build Spectral Library > Gas phase fractionation is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = @@ -34,7 +33,6 @@ iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = False, Gas phase fractionation = True, Input File Type = "DIA raw (search and build library)" diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchQeTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchQeTutorial.log index d8b92d1aca..cbf6bc013c 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchQeTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchQeTutorial.log @@ -13,8 +13,6 @@ All Info : 建立谱图库 > 包含不明确匹配项 是 假 建立谱图库 > 文档肽段筛选器 是 假 建立谱图库 > 工作流程 是 "DIA（数据非依赖性采集）" -建立谱图库 > Deconvolute spectra with DIA-Umpire 是 假 -建立谱图库 > Gas phase fractionation 是 假 建立谱图库 > 输入文件类型 是 "DIA 原始（去卷积、搜索和构建库）" Extra Info: 搜索文件 = [ @@ -28,8 +26,6 @@ iRT 标准肽段 = 无, 包含不明确匹配项 = 假, 文档肽段筛选器 = 假, 工作流程 = "DIA（数据非依赖性采集）", -Deconvolute spectra with DIA-Umpire = 假, -Gas phase fractionation = 假, 输入文件类型 = "DIA 原始（去卷积、搜索和构建库）" Undo Redo : 已导入肽段搜索 diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log index f0438b94bb..398914d2a8 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log @@ -14,7 +14,6 @@ All Info : 建立谱图库 > 包含不明确匹配项 是 假 建立谱图库 > 文档肽段筛选器 是 假 建立谱图库 > 工作流程 是 "DIA（数据非依赖性采集）" -建立谱图库 > Deconvolute spectra with DIA-Umpire 是 假 建立谱图库 > Gas phase fractionation 是 真 建立谱图库 > 输入文件类型 是 "DIA 原始（去卷积、搜索和构建库）" Extra Info: 搜索文件 = @@ -34,7 +33,6 @@ iRT 标准肽段 = 无, 包含不明确匹配项 = 假, 文档肽段筛选器 = 假, 工作流程 = "DIA（数据非依赖性采集）", -Deconvolute spectra with DIA-Umpire = 假, Gas phase fractionation = 真, 输入文件类型 = "DIA 原始（去卷积、搜索和构建库）" From 26b99fd5665a871a879876486f24a6a690ceed66 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Thu, 29 Aug 2024 14:15:37 -0400 Subject: [PATCH 3/6] * fixed DdaSearchTest and updated audit logs --- pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs | 2 +- .../TutorialAuditLogs/en/TestDiaQeDiaUmpireTutorial.log | 6 ++++-- .../TutorialAuditLogs/en/TestDiaTtofDiaUmpireTutorial.log | 6 ++++-- .../TutorialAuditLogs/fr/TestDiaQeDiaUmpireTutorial.log | 6 ++++-- .../TutorialAuditLogs/fr/TestDiaTtofDiaUmpireTutorial.log | 6 ++++-- .../TutorialAuditLogs/ja/TestDiaQeDiaUmpireTutorial.log | 2 ++ .../TutorialAuditLogs/ja/TestDiaTtofDiaUmpireTutorial.log | 2 ++ .../TutorialAuditLogs/tr/TestDiaQeDiaUmpireTutorial.log | 6 ++++-- .../TutorialAuditLogs/tr/TestDiaTtofDiaUmpireTutorial.log | 6 ++++-- .../TutorialAuditLogs/zh/TestDiaQeDiaUmpireTutorial.log | 2 ++ .../TutorialAuditLogs/zh/TestDiaTtofDiaUmpireTutorial.log | 2 ++ 11 files changed, 33 insertions(+), 13 deletions(-) diff --git a/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs b/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs index ea57bfefed..4f10bf3fee 100644 --- a/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs +++ b/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs @@ -264,7 +264,7 @@ private void TestSearch() { Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page); importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = SearchFiles.Select(o => (MsDataFileUri)new MsDataFilePath(o)).Take(1).ToArray(); - importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia; // will go back and switch to DDA + importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.prm; // will go back and switch to DDA importPeptideSearchDlg.BuildPepSearchLibControl.IrtStandards = IrtStandard.AUTO; Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // With only 1 source, no add/remove prefix/suffix dialog diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaQeDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaQeDiaUmpireTutorial.log index 946481bf63..e9df59552c 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaQeDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaQeDiaUmpireTutorial.log @@ -14,7 +14,8 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Input File Type is "DIA raw (deconvolute, search, and build library)" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is True +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -32,7 +33,8 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Input File Type = "DIA raw (deconvolute, search, and build library)" +Deconvolute spectra with DIA-Umpire = True, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaTtofDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaTtofDiaUmpireTutorial.log index 4ba8ba019b..7ba6916a1f 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaTtofDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaTtofDiaUmpireTutorial.log @@ -14,7 +14,8 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Input File Type is "DIA raw (deconvolute, search, and build library)" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is True +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -32,7 +33,8 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Input File Type = "DIA raw (deconvolute, search, and build library)" +Deconvolute spectra with DIA-Umpire = True, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaQeDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaQeDiaUmpireTutorial.log index 9935782f3f..163f7eeb1d 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaQeDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaQeDiaUmpireTutorial.log @@ -14,7 +14,8 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Input File Type is "DIA raw (deconvolute, search, and build library)" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is True +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -32,7 +33,8 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Input File Type = "DIA raw (deconvolute, search, and build library)" +Deconvolute spectra with DIA-Umpire = True, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaTtofDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaTtofDiaUmpireTutorial.log index ec2650f2e5..dc5904f3e9 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaTtofDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaTtofDiaUmpireTutorial.log @@ -14,7 +14,8 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Input File Type is "DIA raw (deconvolute, search, and build library)" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is True +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -32,7 +33,8 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Input File Type = "DIA raw (deconvolute, search, and build library)" +Deconvolute spectra with DIA-Umpire = True, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaQeDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaQeDiaUmpireTutorial.log index a6a7f0b0a4..220ca8a7ed 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaQeDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaQeDiaUmpireTutorial.log @@ -14,6 +14,7 @@ All Info : スペクトルライブラリを構築>曖昧な一致を含むは真です スペクトルライブラリを構築>ドキュメント内のペプチドをフィルタリングは偽です スペクトルライブラリを構築>ワークフローは"DIA"です +スペクトルライブラリを構築>Deconvolute spectra with DIA-Umpireは真です スペクトルライブラリを構築>入力ファイルタイプは"DIA生データ (ライブラリのデコンボリューション、検索、構築)"です Extra Info: ファイルを検索 = [ @@ -32,6 +33,7 @@ iRT標準ペプチド = "Biognosys-11 (iRT-C18)", 曖昧な一致を含む = 真, ドキュメント内のペプチドをフィルタリング = 偽, ワークフロー = "DIA", +Deconvolute spectra with DIA-Umpire = 真, 入力ファイルタイプ = "DIA生データ (ライブラリのデコンボリューション、検索、構築)" Undo Redo : ペプチド検索がインポートされました diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaTtofDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaTtofDiaUmpireTutorial.log index 2f4fde8620..00dc9874e0 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaTtofDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaTtofDiaUmpireTutorial.log @@ -14,6 +14,7 @@ All Info : スペクトルライブラリを構築>曖昧な一致を含むは真です スペクトルライブラリを構築>ドキュメント内のペプチドをフィルタリングは偽です スペクトルライブラリを構築>ワークフローは"DIA"です +スペクトルライブラリを構築>Deconvolute spectra with DIA-Umpireは真です スペクトルライブラリを構築>入力ファイルタイプは"DIA生データ (ライブラリのデコンボリューション、検索、構築)"です Extra Info: ファイルを検索 = [ @@ -32,6 +33,7 @@ iRT標準ペプチド = "Biognosys-11 (iRT-C18)", 曖昧な一致を含む = 真, ドキュメント内のペプチドをフィルタリング = 偽, ワークフロー = "DIA", +Deconvolute spectra with DIA-Umpire = 真, 入力ファイルタイプ = "DIA生データ (ライブラリのデコンボリューション、検索、構築)" Undo Redo : ペプチド検索がインポートされました diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaQeDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaQeDiaUmpireTutorial.log index 9935782f3f..163f7eeb1d 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaQeDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaQeDiaUmpireTutorial.log @@ -14,7 +14,8 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Input File Type is "DIA raw (deconvolute, search, and build library)" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is True +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -32,7 +33,8 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Input File Type = "DIA raw (deconvolute, search, and build library)" +Deconvolute spectra with DIA-Umpire = True, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaTtofDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaTtofDiaUmpireTutorial.log index ec2650f2e5..dc5904f3e9 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaTtofDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaTtofDiaUmpireTutorial.log @@ -14,7 +14,8 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Input File Type is "DIA raw (deconvolute, search, and build library)" +Build Spectral Library > Deconvolute spectra with DIA-Umpire is True +Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ { @@ -32,7 +33,8 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Input File Type = "DIA raw (deconvolute, search, and build library)" +Deconvolute spectra with DIA-Umpire = True, +Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search Summary : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaQeDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaQeDiaUmpireTutorial.log index a9f5941242..b352570f26 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaQeDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaQeDiaUmpireTutorial.log @@ -14,6 +14,7 @@ All Info : 建立谱图库 > 包含不明确匹配项 是 真 建立谱图库 > 文档肽段筛选器 是 假 建立谱图库 > 工作流程 是 "DIA（数据非依赖性采集）" +建立谱图库 > Deconvolute spectra with DIA-Umpire 是 真 建立谱图库 > 输入文件类型 是 "DIA 原始（去卷积、搜索和构建库）" Extra Info: 搜索文件 = [ @@ -32,6 +33,7 @@ iRT 标准肽段 = "Biognosys-11 (iRT-C18)", 包含不明确匹配项 = 真, 文档肽段筛选器 = 假, 工作流程 = "DIA（数据非依赖性采集）", +Deconvolute spectra with DIA-Umpire = 真, 输入文件类型 = "DIA 原始（去卷积、搜索和构建库）" Undo Redo : 已导入肽段搜索 diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaTtofDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaTtofDiaUmpireTutorial.log index e520d93f8d..919107edee 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaTtofDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaTtofDiaUmpireTutorial.log @@ -14,6 +14,7 @@ All Info : 建立谱图库 > 包含不明确匹配项 是 真 建立谱图库 > 文档肽段筛选器 是 假 建立谱图库 > 工作流程 是 "DIA（数据非依赖性采集）" +建立谱图库 > Deconvolute spectra with DIA-Umpire 是 真 建立谱图库 > 输入文件类型 是 "DIA 原始（去卷积、搜索和构建库）" Extra Info: 搜索文件 = [ @@ -32,6 +33,7 @@ iRT 标准肽段 = "Biognosys-11 (iRT-C18)", 包含不明确匹配项 = 真, 文档肽段筛选器 = 假, 工作流程 = "DIA（数据非依赖性采集）", +Deconvolute spectra with DIA-Umpire = 真, 输入文件类型 = "DIA 原始（去卷积、搜索和构建库）" Undo Redo : 已导入肽段搜索 From 426036c13d450d954cfc7a6c4617e624ad4282be Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Fri, 30 Aug 2024 13:47:21 -0400 Subject: [PATCH 4/6] * fixed DIA search tutorial not handling download dialogs at the right time --- .../Skyline/TestPerf/DiaSearchTutorialTest.cs | 55 ++++++++++--------- 1 file changed, 29 insertions(+), 26 deletions(-) diff --git a/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs b/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs index 094a7a7881..c973c83f54 100644 --- a/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs +++ b/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs @@ -194,7 +194,7 @@ protected override void DoTest() /// private bool IsRecordMode => false; - private bool RedownloadTools => !IsRecordMode && !IsRecordAuditLogForTutorials && IsPass0; + private bool RedownloadTools => !IsRecordMode && !IsRecordAuditLogForTutorials; private bool HasMissingDependencies => !SearchSettingsControl.HasRequiredFilesDownloaded(SearchSettingsControl.SearchEngine.MSFragger); private Image _searchLogImage; @@ -250,18 +250,43 @@ private void TestMsFraggerSearch() Assert.IsTrue(importPeptideSearchDlg.BuildPepSearchLibControl.IsDiaUmpireEnabled); importPeptideSearchDlg.BuildPepSearchLibControl.IsGpf = _analysisValues.IsGpfData; }); + + SkylineWindow.BeginInvoke(new Action(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()))); + + // SearchEngine changed to MSFragger automatically due to changing to DIA workflow: handle download dialogs if necessary + if (RedownloadTools || HasMissingDependencies) + { + var msfraggerDownloaderDlg = TryWaitForOpenForm(2000); + if (msfraggerDownloaderDlg != null) + { + PauseForScreenShot("Import Peptide Search - Download MSFragger", + tutorialPage++); // Maybe someday + RunUI(() => msfraggerDownloaderDlg.SetValues("Matt Chambers (testing download from Skyline)", + "matt.chambers42@gmail.com", "UW")); + OkDialog(msfraggerDownloaderDlg, msfraggerDownloaderDlg.ClickAccept); + } + + var downloaderDlg = TryWaitForOpenForm(2000); + if (downloaderDlg != null) + { + PauseForScreenShot("Import Peptide Search - Download Java and Crux", + tutorialPage++); // Maybe someday + OkDialog(downloaderDlg, downloaderDlg.ClickYes); + var waitDlg = WaitForOpenForm(); + WaitForClosedForm(waitDlg); + } + } + PauseForScreenShot("Import Peptide Search - After Selecting DIA Files page", tutorialPage++); if (SearchFiles.Count() > 1) { // Remove prefix/suffix dialog pops up; accept default behavior - var removeSuffix = ShowDialog(() => importPeptideSearchDlg.ClickNextButton()); + var removeSuffix = WaitForOpenForm(); PauseForScreenShot("Import Results - Common prefix form", tutorialPage++); OkDialog(removeSuffix, () => removeSuffix.YesDialog()); WaitForDocumentLoaded(); } - else - RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton())); // We're on the "Match Modifications" page. Add M+16 WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page); @@ -376,28 +401,6 @@ private void TestMsFraggerSearch() bool? searchSucceeded = null; RunUI(() => Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.dda_search_settings_page)); - // switch SearchEngine and handle download dialogs if necessary - SkylineWindow.BeginInvoke(new Action(() => importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine = SearchSettingsControl.SearchEngine.MSFragger)); - if (RedownloadTools || HasMissingDependencies) - { - var msfraggerDownloaderDlg = TryWaitForOpenForm(2000); - if (msfraggerDownloaderDlg != null) - { - PauseForScreenShot("Import Peptide Search - Download MSFragger", tutorialPage++); // Maybe someday - RunUI(() => msfraggerDownloaderDlg.SetValues("Matt Chambers (testing download from Skyline)", "matt.chambers42@gmail.com", "UW")); - OkDialog(msfraggerDownloaderDlg, msfraggerDownloaderDlg.ClickAccept); - } - - var downloaderDlg = TryWaitForOpenForm(2000); - if (downloaderDlg != null) - { - PauseForScreenShot("Import Peptide Search - Download Java and Crux", tutorialPage++); // Maybe someday - OkDialog(downloaderDlg, downloaderDlg.ClickYes); - var waitDlg = WaitForOpenForm(); - WaitForClosedForm(waitDlg); - } - } - RunUI(() => { importPeptideSearchDlg.SearchSettingsControl.PrecursorTolerance = new MzTolerance(10, MzTolerance.Units.ppm); From 5a9ac83cbba0902f95db37c3ac9dd484f01cfbc3 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Tue, 1 Oct 2024 12:17:28 -0400 Subject: [PATCH 5/6] * added tooltips for new checkboxes * fixed MSFragger to look for correct pepXML file extension based on data_type parameter instead of workflow setting --- ...uildPeptideSearchLibraryControl.Designer.cs | 2 ++ .../BuildPeptideSearchLibraryControl.resx | 18 ++++++++++++------ .../Model/DdaSearch/MsFraggerSearchEngine.cs | 9 ++++----- 3 files changed, 18 insertions(+), 11 deletions(-) diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs index b22656a773..df3d61694e 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs @@ -79,12 +79,14 @@ private void InitializeComponent() // resources.ApplyResources(this.cbGpf, "cbGpf"); this.cbGpf.Name = "cbGpf"; + this.helpTip.SetToolTip(this.cbGpf, resources.GetString("cbGpf.ToolTip")); this.cbGpf.UseVisualStyleBackColor = true; // // cbDiaUmpire // resources.ApplyResources(this.cbDiaUmpire, "cbDiaUmpire"); this.cbDiaUmpire.Name = "cbDiaUmpire"; + this.helpTip.SetToolTip(this.cbDiaUmpire, resources.GetString("cbDiaUmpire.ToolTip")); this.cbDiaUmpire.UseVisualStyleBackColor = true; // // radioDIA diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx index 6b8ad699f2..30fc6f3e44 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx @@ -133,13 +133,19 @@ 201, 43 - 142, 17 + 138, 17 4 - Gas Phase Fractionation + Gas phase fractionation + + + 17, 17 + + + Multiple narrow window DIA runs, each run covering a separate range of m/z (e.g. 400-500, 500-600, 600-700) cbGpf @@ -171,6 +177,9 @@ DIA-Umpire + + Create pseudo-DDA spectra with DIA-Umpire (allows using any DDA search engine) + cbDiaUmpire @@ -201,9 +210,6 @@ &DIA - - 17, 17 - Library spectra from DDA MS/MS with chromatograms from separate DIA runs @@ -531,7 +537,7 @@ like BiblioSpec .blib, EncyclopeDIA .elib, SpectraST .sqt gridSearchFiles - pwiz.Skyline.FileUI.PeptideSearch.BuildLibraryGridView, Skyline-daily, Version=24.1.1.214, Culture=neutral, PublicKeyToken=null + pwiz.Skyline.FileUI.PeptideSearch.BuildLibraryGridView, Skyline-daily, Version=24.1.1.263, Culture=neutral, PublicKeyToken=null panelPeptideSearch diff --git a/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs b/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs index 652327b089..f999d059f0 100644 --- a/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs +++ b/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs @@ -61,12 +61,11 @@ public enum DataType dia_gpf = 2 } - private bool DataIsDIA { get; } + private bool DataIsDIA => (DataType) AdditionalSettings[@"data_type"].Value != DataType.dda; + private string PepXmlSuffix => DataIsDIA ? @"_rank1.pepXML" : @".pepXML"; public MsFraggerSearchEngine(DataType dataType) { - DataIsDIA = dataType != DataType.dda; - AdditionalSettings = new Dictionary { {CHECK_SPECTRAL_FILES, new Setting(CHECK_SPECTRAL_FILES, 1, 0, 1)}, @@ -293,7 +292,7 @@ void RunInner() foreach (var spectrumFilename in SpectrumFileNames) { string msfraggerPepXmlFilepath = Path.Combine(Path.GetDirectoryName(spectrumFilename.GetFilePath()) ?? "", - spectrumFilename.GetFileNameWithoutExtension() + (DataIsDIA ? @"_rank1.pepXML" : @".pepXML")); + spectrumFilename.GetFileNameWithoutExtension() + PepXmlSuffix); string cruxInputFilepath = Path.ChangeExtension(spectrumFilename.GetFilePath(), ".pin"); string cruxFixedInputFilepath = Path.ChangeExtension(spectrumFilename.GetFilePath(), "fixed.pin"); _intermediateFiles.Add(cruxInputFilepath); @@ -325,7 +324,7 @@ void RunInner() foreach (var spectrumFilename in SpectrumFileNames) { string msfraggerPepXmlFilepath = Path.Combine(Path.GetDirectoryName(spectrumFilename.GetFilePath()) ?? "", - spectrumFilename.GetFileNameWithoutExtension() + (DataIsDIA ? @"_rank1.pepXML" : @".pepXML")); + spectrumFilename.GetFileNameWithoutExtension() + PepXmlSuffix); string finalOutputFilepath = GetSearchResultFilepath(spectrumFilename); _intermediateFiles.Add(msfraggerPepXmlFilepath); FixPercolatorPepXml(msfraggerPepXmlFilepath, finalOutputFilepath, spectrumFilename, qvalueByPsmId, this); From 0e942e0210b70235619476c4d4a90f876f9f910d Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Thu, 24 Oct 2024 15:01:17 -0400 Subject: [PATCH 6/6] * moved DIA-Umpire checkbox to converter settings page * moved GPF checkbox to extract chromatograms page, which is now always shown for DIA workflow --- .../CommonUtil/SystemUtil/ProcessRunner.cs | 4 +- ...ildPeptideSearchLibraryControl.Designer.cs | 39 +-- .../BuildPeptideSearchLibraryControl.cs | 32 +-- .../BuildPeptideSearchLibraryControl.resx | 85 +------ .../ConverterSettingsControl.Designer.cs | 78 ++++-- .../PeptideSearch/ConverterSettingsControl.cs | 23 +- .../ConverterSettingsControl.ja.resx | 2 +- .../ConverterSettingsControl.resx | 227 +++++++++++++----- .../PeptideSearch/IImportResultsControl.cs | 11 +- .../PeptideSearch/ImportPeptideSearchDlg.cs | 86 ++++--- .../ImportResultsDIAControl.Designer.cs | 9 + .../PeptideSearch/ImportResultsDIAControl.cs | 12 + .../ImportResultsDIAControl.resx | 53 +++- .../PeptideSearch/SearchSettingsControl.cs | 25 +- .../Skyline/Model/AbstractDdaSearchEngine.cs | 7 +- .../Model/AuditLog/PropertyNames.Designer.cs | 18 +- .../Skyline/Model/AuditLog/PropertyNames.resx | 2 +- .../Model/DdaSearch/HardklorSearchEngine.cs | 1 + .../Model/DdaSearch/MSAmandaSearchWrapper.cs | 1 + .../Model/DdaSearch/MsFraggerSearchEngine.cs | 1 + .../Model/DdaSearch/MsgfPlusSearchEngine.cs | 4 - .../Skyline/Model/DiaUmpireDdaConverter.cs | 2 +- pwiz_tools/Skyline/Skyline.csproj | 1 + .../Skyline/TestFunctional/DdaSearchTest.cs | 39 +-- .../Skyline/TestFunctional/DiaSearchTest.cs | 138 ++++++----- .../Skyline/TestPerf/DiaSearchTutorialTest.cs | 76 +++--- .../Skyline/TestPerf/DiaUmpireTutorialTest.cs | 23 +- .../en/TestDiaQeDiaUmpireTutorial.log | 2 - .../en/TestDiaSearchStellarTutorial.log | 4 +- .../en/TestDiaTtofDiaUmpireTutorial.log | 2 - .../fr/TestDiaQeDiaUmpireTutorial.log | 2 - .../fr/TestDiaSearchStellarTutorial.log | 4 +- .../fr/TestDiaTtofDiaUmpireTutorial.log | 2 - .../ja/TestDiaQeDiaUmpireTutorial.log | 2 - .../ja/TestDiaSearchStellarTutorial.log | 4 +- .../ja/TestDiaTtofDiaUmpireTutorial.log | 2 - .../tr/TestDiaQeDiaUmpireTutorial.log | 2 - .../tr/TestDiaSearchStellarTutorial.log | 4 +- .../tr/TestDiaTtofDiaUmpireTutorial.log | 2 - .../zh/TestDiaQeDiaUmpireTutorial.log | 2 - .../zh/TestDiaSearchStellarTutorial.log | 4 +- .../zh/TestDiaTtofDiaUmpireTutorial.log | 2 - 42 files changed, 605 insertions(+), 434 deletions(-) diff --git a/pwiz_tools/Shared/CommonUtil/SystemUtil/ProcessRunner.cs b/pwiz_tools/Shared/CommonUtil/SystemUtil/ProcessRunner.cs index 2ee0c103de..e53df52a56 100644 --- a/pwiz_tools/Shared/CommonUtil/SystemUtil/ProcessRunner.cs +++ b/pwiz_tools/Shared/CommonUtil/SystemUtil/ProcessRunner.cs @@ -221,10 +221,10 @@ public void Run(ProcessStartInfo psi, string stdin, IProgressMonitor progress, r ? Path.Combine(Environment.CurrentDirectory, psi.FileName) : psi.FileName; // ReSharper disable LocalizableElement - sbError.AppendFormat("\r\nCommand-line: {0} {1}\r\nWorking directory: {2}{3}", processPath, + sbError.AppendFormat("\r\nCommand-line: {0} {1}\r\nWorking directory: {2}{3}\r\nExit code: {4}", processPath, // ReSharper restore LocalizableElement string.Join(" ", proc.StartInfo.Arguments), psi.WorkingDirectory, - stdin != null ? "\r\nStandard input:\r\n" + stdin : ""); + stdin != null ? "\r\nStandard input:\r\n" + stdin : "", exit); throw new IOException(sbError.ToString()); } diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs index df3d61694e..967007c9ea 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.Designer.cs @@ -31,8 +31,6 @@ private void InitializeComponent() this.components = new System.ComponentModel.Container(); System.ComponentModel.ComponentResourceManager resources = new System.ComponentModel.ComponentResourceManager(typeof(BuildPeptideSearchLibraryControl)); this.grpWorkflow = new System.Windows.Forms.GroupBox(); - this.cbGpf = new System.Windows.Forms.CheckBox(); - this.cbDiaUmpire = new System.Windows.Forms.CheckBox(); this.radioDIA = new System.Windows.Forms.RadioButton(); this.radioPRM = new System.Windows.Forms.RadioButton(); this.radioDDA = new System.Windows.Forms.RadioButton(); @@ -44,7 +42,6 @@ private void InitializeComponent() this.btnBrowse = new System.Windows.Forms.Button(); this.lblLibraryPath = new System.Windows.Forms.Label(); this.panelPeptideSearch = new System.Windows.Forms.Panel(); - this.gridSearchFiles = new pwiz.Skyline.FileUI.PeptideSearch.BuildLibraryGridView(); this.lblStandardPeptides = new System.Windows.Forms.Label(); this.comboStandards = new System.Windows.Forms.ComboBox(); this.cbIncludeAmbiguousMatches = new System.Windows.Forms.CheckBox(); @@ -53,6 +50,7 @@ private void InitializeComponent() this.lblFileCaption = new System.Windows.Forms.Label(); this.btnAddFile = new System.Windows.Forms.Button(); this.helpTip = new System.Windows.Forms.ToolTip(this.components); + this.gridSearchFiles = new pwiz.Skyline.FileUI.PeptideSearch.BuildLibraryGridView(); this.dataGridViewTextBoxColumn1 = new System.Windows.Forms.DataGridViewTextBoxColumn(); this.dataGridViewTextBoxColumn2 = new System.Windows.Forms.DataGridViewTextBoxColumn(); this.dataGridViewTextBoxColumn3 = new System.Windows.Forms.DataGridViewTextBoxColumn(); @@ -66,8 +64,6 @@ private void InitializeComponent() // // grpWorkflow // - this.grpWorkflow.Controls.Add(this.cbGpf); - this.grpWorkflow.Controls.Add(this.cbDiaUmpire); this.grpWorkflow.Controls.Add(this.radioDIA); this.grpWorkflow.Controls.Add(this.radioPRM); this.grpWorkflow.Controls.Add(this.radioDDA); @@ -75,20 +71,6 @@ private void InitializeComponent() this.grpWorkflow.Name = "grpWorkflow"; this.grpWorkflow.TabStop = false; // - // cbGpf - // - resources.ApplyResources(this.cbGpf, "cbGpf"); - this.cbGpf.Name = "cbGpf"; - this.helpTip.SetToolTip(this.cbGpf, resources.GetString("cbGpf.ToolTip")); - this.cbGpf.UseVisualStyleBackColor = true; - // - // cbDiaUmpire - // - resources.ApplyResources(this.cbDiaUmpire, "cbDiaUmpire"); - this.cbDiaUmpire.Name = "cbDiaUmpire"; - this.helpTip.SetToolTip(this.cbDiaUmpire, resources.GetString("cbDiaUmpire.ToolTip")); - this.cbDiaUmpire.UseVisualStyleBackColor = true; - // // radioDIA // resources.ApplyResources(this.radioDIA, "radioDIA"); @@ -179,14 +161,6 @@ private void InitializeComponent() resources.ApplyResources(this.panelPeptideSearch, "panelPeptideSearch"); this.panelPeptideSearch.Name = "panelPeptideSearch"; // - // gridSearchFiles - // - this.gridSearchFiles.AllowUserToAddRows = false; - resources.ApplyResources(this.gridSearchFiles, "gridSearchFiles"); - this.gridSearchFiles.ColumnHeadersHeightSizeMode = System.Windows.Forms.DataGridViewColumnHeadersHeightSizeMode.AutoSize; - this.gridSearchFiles.Name = "gridSearchFiles"; - this.gridSearchFiles.SelectionChanged += new System.EventHandler(this.gridSearchFiles_SelectedIndexChanged); - // // lblStandardPeptides // resources.ApplyResources(this.lblStandardPeptides, "lblStandardPeptides"); @@ -234,6 +208,14 @@ private void InitializeComponent() this.btnAddFile.UseVisualStyleBackColor = true; this.btnAddFile.Click += new System.EventHandler(this.btnAddFile_Click); // + // gridSearchFiles + // + this.gridSearchFiles.AllowUserToAddRows = false; + resources.ApplyResources(this.gridSearchFiles, "gridSearchFiles"); + this.gridSearchFiles.ColumnHeadersHeightSizeMode = System.Windows.Forms.DataGridViewColumnHeadersHeightSizeMode.AutoSize; + this.gridSearchFiles.Name = "gridSearchFiles"; + this.gridSearchFiles.SelectionChanged += new System.EventHandler(this.gridSearchFiles_SelectedIndexChanged); + // // dataGridViewTextBoxColumn1 // this.dataGridViewTextBoxColumn1.Frozen = true; @@ -274,7 +256,6 @@ private void InitializeComponent() this.Controls.Add(this.panel1); this.Name = "BuildPeptideSearchLibraryControl"; this.grpWorkflow.ResumeLayout(false); - this.grpWorkflow.PerformLayout(); this.panel1.ResumeLayout(false); this.panel1.PerformLayout(); this.panelChooseFile.ResumeLayout(false); @@ -312,7 +293,5 @@ private void InitializeComponent() private System.Windows.Forms.DataGridViewTextBoxColumn dataGridViewTextBoxColumn3; private System.Windows.Forms.DataGridViewTextBoxColumn dataGridViewTextBoxColumn4; private System.Windows.Forms.ToolTip helpTip; - private System.Windows.Forms.CheckBox cbDiaUmpire; - private System.Windows.Forms.CheckBox cbGpf; } } diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs index e7ee75eb43..8349574933 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.cs @@ -97,7 +97,7 @@ public class BuildPeptideSearchLibrarySettings : AuditLogOperationSettings files, IrtStandard standard, bool includeAmbiguousMatches, bool filterForDocumentPeptides, - ImportPeptideSearchDlg.Workflow workFlow, bool useDiaUmpire, bool isGpf, + ImportPeptideSearchDlg.Workflow workFlow, ImportPeptideSearchDlg.InputFile inputFileType, SrmDocument.DOCUMENT_TYPE docType) { SearchFileNames = files?.ToArray() ?? Array.Empty(); @@ -124,8 +124,6 @@ public BuildPeptideSearchLibrarySettings(IEnumerable IncludeAmbiguousMatches = includeAmbiguousMatches; FilterForDocumentPeptides = filterForDocumentPeptides; WorkFlow = workFlow; - UseDiaUmpire = useDiaUmpire; - IsGpf = isGpf; InputFileType = inputFileType; _docType = docType; } @@ -140,10 +138,6 @@ public BuildPeptideSearchLibrarySettings(IEnumerable public bool FilterForDocumentPeptides { get; private set; } [Track(ignoreDefaultParent: true)] public ImportPeptideSearchDlg.Workflow WorkFlow { get; private set; } - [Track(defaultValues: typeof(DefaultValuesFalse))] - public bool UseDiaUmpire { get; private set; } - [Track(defaultValues: typeof(DefaultValuesFalse))] - public bool IsGpf { get; private set; } [Track(ignoreDefaultParent: true)] public ImportPeptideSearchDlg.InputFile InputFileType { get; private set; } @@ -226,27 +220,9 @@ public ImportPeptideSearchDlg.Workflow WorkflowType radioDDA.Checked = true; break; } - - cbDiaUmpire.Enabled = cbGpf.Enabled = radioDIA.Checked; } } - public bool UseDiaUmpire - { - get => cbDiaUmpire.Checked; - set => cbDiaUmpire.Checked = value; - } - - public bool IsGpf - { - get => cbGpf.Checked; - set => cbGpf.Checked = value; - } - - // for testing - public bool IsGpfEnabled => cbGpf.Enabled; - public bool IsDiaUmpireEnabled => cbDiaUmpire.Enabled; - public ImportPeptideSearchDlg.InputFile InputFileType { get => _inputFileType; @@ -695,8 +671,6 @@ public bool PerformDDASearch get { return InputFileType != ImportPeptideSearchDlg.InputFile.search_result; } } - public bool DIAConversionNeeded => InputFileType == ImportPeptideSearchDlg.InputFile.dia_raw && UseDiaUmpire; - private void OnGridChange(object sender, EventArgs e) { if (!PerformDDASearch) diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx index 30fc6f3e44..938d6d109e 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/BuildPeptideSearchLibraryControl.resx @@ -117,99 +117,30 @@ System.Resources.ResXResourceWriter, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 - - - True - - - False - - - NoControl - - - - 201, 43 - - - 138, 17 - - - 4 - - - Gas phase fractionation - - - 17, 17 - - - Multiple narrow window DIA runs, each run covering a separate range of m/z (e.g. 400-500, 500-600, 600-700) - - - cbGpf - - - System.Windows.Forms.CheckBox, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 - - - grpWorkflow - - - 0 - - - True - - - False - - - 96, 43 - - - 80, 17 - - - 3 - - - DIA-Umpire - - - Create pseudo-DDA spectra with DIA-Umpire (allows using any DDA search engine) - - - cbDiaUmpire - - - System.Windows.Forms.CheckBox, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 - - - grpWorkflow - - - 1 - Top, Left, Right NoControl + 6, 42 84, 17 + 1 &DIA + + 17, 17 + Library spectra from DDA MS/MS with chromatograms from separate DIA runs @@ -223,7 +154,7 @@ grpWorkflow - 2 + 0 Top, Left, Right @@ -256,7 +187,7 @@ grpWorkflow - 3 + 1 Top, Left, Right @@ -289,7 +220,7 @@ grpWorkflow - 4 + 2 Bottom diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.Designer.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.Designer.cs index d5a58a2381..5fe235c43e 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.Designer.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.Designer.cs @@ -34,13 +34,19 @@ private void InitializeComponent() this.converterTabControl = new pwiz.Skyline.Controls.WizardPages(); this.msconvertTabPage = new System.Windows.Forms.TabPage(); this.diaUmpireTabPage = new System.Windows.Forms.TabPage(); + this.diaUmpireSettingsPanel = new System.Windows.Forms.Panel(); + this.lblInstrumentPreset = new System.Windows.Forms.Label(); + this.cbInstrumentPreset = new System.Windows.Forms.ComboBox(); this.cbEstimateBg = new System.Windows.Forms.CheckBox(); + this.label2 = new System.Windows.Forms.Label(); + this.cbDiaUmpire = new System.Windows.Forms.CheckBox(); this.label1 = new System.Windows.Forms.Label(); - this.cbInstrumentPreset = new System.Windows.Forms.ComboBox(); - this.lblInstrumentPreset = new System.Windows.Forms.Label(); this.toolTip = new System.Windows.Forms.ToolTip(this.components); + this.diaUmpireDescriptionPanel = new System.Windows.Forms.FlowLayoutPanel(); this.converterTabControl.SuspendLayout(); this.diaUmpireTabPage.SuspendLayout(); + this.diaUmpireSettingsPanel.SuspendLayout(); + this.diaUmpireDescriptionPanel.SuspendLayout(); this.SuspendLayout(); // // btnAdditionalSettings @@ -66,15 +72,33 @@ private void InitializeComponent() // // diaUmpireTabPage // - this.diaUmpireTabPage.Controls.Add(this.cbEstimateBg); - this.diaUmpireTabPage.Controls.Add(this.label1); - this.diaUmpireTabPage.Controls.Add(this.btnAdditionalSettings); - this.diaUmpireTabPage.Controls.Add(this.cbInstrumentPreset); - this.diaUmpireTabPage.Controls.Add(this.lblInstrumentPreset); + this.diaUmpireTabPage.Controls.Add(this.diaUmpireDescriptionPanel); + this.diaUmpireTabPage.Controls.Add(this.diaUmpireSettingsPanel); resources.ApplyResources(this.diaUmpireTabPage, "diaUmpireTabPage"); this.diaUmpireTabPage.Name = "diaUmpireTabPage"; this.diaUmpireTabPage.UseVisualStyleBackColor = true; // + // diaUmpireSettingsPanel + // + this.diaUmpireSettingsPanel.Controls.Add(this.btnAdditionalSettings); + this.diaUmpireSettingsPanel.Controls.Add(this.lblInstrumentPreset); + this.diaUmpireSettingsPanel.Controls.Add(this.cbInstrumentPreset); + this.diaUmpireSettingsPanel.Controls.Add(this.cbEstimateBg); + resources.ApplyResources(this.diaUmpireSettingsPanel, "diaUmpireSettingsPanel"); + this.diaUmpireSettingsPanel.Name = "diaUmpireSettingsPanel"; + // + // lblInstrumentPreset + // + resources.ApplyResources(this.lblInstrumentPreset, "lblInstrumentPreset"); + this.lblInstrumentPreset.Name = "lblInstrumentPreset"; + // + // cbInstrumentPreset + // + this.cbInstrumentPreset.DropDownStyle = System.Windows.Forms.ComboBoxStyle.DropDownList; + this.cbInstrumentPreset.FormattingEnabled = true; + resources.ApplyResources(this.cbInstrumentPreset, "cbInstrumentPreset"); + this.cbInstrumentPreset.Name = "cbInstrumentPreset"; + // // cbEstimateBg // resources.ApplyResources(this.cbEstimateBg, "cbEstimateBg"); @@ -82,22 +106,33 @@ private void InitializeComponent() this.toolTip.SetToolTip(this.cbEstimateBg, resources.GetString("cbEstimateBg.ToolTip")); this.cbEstimateBg.UseVisualStyleBackColor = true; // + // label2 + // + resources.ApplyResources(this.label2, "label2"); + this.label2.Name = "label2"; + // + // cbDiaUmpire + // + this.diaUmpireDescriptionPanel.SetFlowBreak(this.cbDiaUmpire, true); + resources.ApplyResources(this.cbDiaUmpire, "cbDiaUmpire"); + this.cbDiaUmpire.Name = "cbDiaUmpire"; + this.toolTip.SetToolTip(this.cbDiaUmpire, resources.GetString("cbDiaUmpire.ToolTip")); + this.cbDiaUmpire.UseVisualStyleBackColor = true; + this.cbDiaUmpire.CheckedChanged += new System.EventHandler(this.cbDiaUmpire_CheckedChanged); + // // label1 // resources.ApplyResources(this.label1, "label1"); + this.diaUmpireDescriptionPanel.SetFlowBreak(this.label1, true); this.label1.Name = "label1"; // - // cbInstrumentPreset - // - this.cbInstrumentPreset.DropDownStyle = System.Windows.Forms.ComboBoxStyle.DropDownList; - this.cbInstrumentPreset.FormattingEnabled = true; - resources.ApplyResources(this.cbInstrumentPreset, "cbInstrumentPreset"); - this.cbInstrumentPreset.Name = "cbInstrumentPreset"; + // diaUmpireDescriptionPanel // - // lblInstrumentPreset - // - resources.ApplyResources(this.lblInstrumentPreset, "lblInstrumentPreset"); - this.lblInstrumentPreset.Name = "lblInstrumentPreset"; + resources.ApplyResources(this.diaUmpireDescriptionPanel, "diaUmpireDescriptionPanel"); + this.diaUmpireDescriptionPanel.Controls.Add(this.label1); + this.diaUmpireDescriptionPanel.Controls.Add(this.cbDiaUmpire); + this.diaUmpireDescriptionPanel.Controls.Add(this.label2); + this.diaUmpireDescriptionPanel.Name = "diaUmpireDescriptionPanel"; // // ConverterSettingsControl // @@ -107,7 +142,10 @@ private void InitializeComponent() this.Name = "ConverterSettingsControl"; this.converterTabControl.ResumeLayout(false); this.diaUmpireTabPage.ResumeLayout(false); - this.diaUmpireTabPage.PerformLayout(); + this.diaUmpireSettingsPanel.ResumeLayout(false); + this.diaUmpireSettingsPanel.PerformLayout(); + this.diaUmpireDescriptionPanel.ResumeLayout(false); + this.diaUmpireDescriptionPanel.PerformLayout(); this.ResumeLayout(false); } @@ -122,5 +160,9 @@ private void InitializeComponent() private System.Windows.Forms.Label label1; private System.Windows.Forms.CheckBox cbEstimateBg; private System.Windows.Forms.ToolTip toolTip; + private System.Windows.Forms.CheckBox cbDiaUmpire; + private System.Windows.Forms.Label label2; + private System.Windows.Forms.Panel diaUmpireSettingsPanel; + private System.Windows.Forms.FlowLayoutPanel diaUmpireDescriptionPanel; } } \ No newline at end of file diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.cs index 6d0371b7b0..98b3bc71b2 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.cs @@ -121,7 +121,7 @@ public void InitializeProtocol(Protocol protocol) public DdaConverterSettings ConverterSettings { - get { return CurrentProtocol != Protocol.none ? new DdaConverterSettings(this) : null; } + get { return DdaConverterSettings.GetSettings(this); } } public class DdaConverterSettings @@ -130,6 +130,14 @@ public static DdaConverterSettings GetDefault() { return new DdaConverterSettings(); } + public static DdaConverterSettings GetSettings(ConverterSettingsControl control) + { + if (control.CurrentProtocol == Protocol.none) + return null; + if (control.CurrentProtocol == Protocol.dia_umpire && !control.UseDiaUmpire) + return null; + return new DdaConverterSettings(control); + } public DdaConverterSettings() { @@ -149,7 +157,7 @@ public DdaConverterSettings(ConverterSettingsControl control) public Protocol Protocol { get; } [Track] public DiaUmpire.Config.InstrumentPreset InstrumentPreset { get; } - [Track] + [Track(defaultValues:typeof(DefaultValuesNullOrEmpty))] public IEnumerable NonDefaultAdditionalSettings { get; } } @@ -290,6 +298,12 @@ private void ApplyVisibleAdditionalSettings() } } + public bool UseDiaUmpire + { + get => cbDiaUmpire.Checked; + set => cbDiaUmpire.Checked = value; + } + public DiaUmpire.Config.InstrumentPreset InstrumentPreset { get { return (DiaUmpire.Config.InstrumentPreset) cbInstrumentPreset.SelectedIndex; } @@ -328,5 +342,10 @@ public HardklorDdaConverter GetHardklorConverter() { return new HardklorDdaConverter(ImportPeptideSearch); } + + private void cbDiaUmpire_CheckedChanged(object sender, EventArgs e) + { + diaUmpireSettingsPanel.Enabled = cbDiaUmpire.Checked; + } } } diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.ja.resx b/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.ja.resx index fe4954303c..f995f8bfc5 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.ja.resx +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.ja.resx @@ -196,7 +196,7 @@ 17, 17 - 推定バックグラウンド信号は、精度を多少犠牲にしてDIA-Umpireプロセスを大幅に高速にします。（EstimageBG） + 推定バックグラウンド信号は、精度を多少犠牲にしてDIA-Umpireプロセスを大幅に高速にします。（EstimateBG） cbEstimateBg diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.resx b/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.resx index b70ecfea70..69b2dd647b 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.resx +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ConverterSettingsControl.resx @@ -123,7 +123,7 @@ - 6, 335 + 3, 221 107, 23 @@ -142,10 +142,10 @@ System.Windows.Forms.Button, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 - diaUmpireTabPage + diaUmpireSettingsPanel - 2 + 0 Top, Bottom, Left, Right @@ -177,50 +177,23 @@ 0 - - True - - - 9, 119 - - - 126, 17 - - - 13 - - - &Estimate background - - - 17, 17 - - - Estimating background signal will make the DIA-Umpire process significantly faster, at a moderate penalty to accuracy. (EstimateBG) - - - cbEstimateBg - - - System.Windows.Forms.CheckBox, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 - - - diaUmpireTabPage - - - 0 + + Top, Left, Right Top, Left, Right + + True + NoControl - 3, 3 + 3, 0 - 360, 44 + 359, 39 12 @@ -235,31 +208,100 @@ System.Windows.Forms.Label, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 - diaUmpireTabPage + diaUmpireDescriptionPanel + 0 + + + NoControl + + + 3, 45 + + + 3, 6, 3, 6 + + + 184, 17 + + + 7 + + + Run DIA files through DIA-Umpire + + + 17, 17 + + + Create pseudo-DDA spectra with DIA-Umpire (allows using any DDA search engine) + + + cbDiaUmpire + + + System.Windows.Forms.CheckBox, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + + diaUmpireDescriptionPanel + + 1 - - 6, 79 + + Top, Left, Right - - 210, 21 + + True - - 8 + + NoControl - - cbInstrumentPreset + + 3, 68 - - System.Windows.Forms.ComboBox, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + 347, 39 - + + 15 + + + Running DIA-Umpire on your DIA files allows you to use any of the available DDA search engines. Only MSFragger supports searching raw DIA spectra. + + + label2 + + + System.Windows.Forms.Label, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + + diaUmpireDescriptionPanel + + + 2 + + + 0, 0 + + + 367, 111 + + + 17 + + + diaUmpireDescriptionPanel + + + System.Windows.Forms.FlowLayoutPanel, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + diaUmpireTabPage - - 3 + + 0 True @@ -268,7 +310,7 @@ NoControl - 6, 63 + 6, 22 91, 13 @@ -286,10 +328,85 @@ System.Windows.Forms.Label, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 - diaUmpireTabPage + diaUmpireSettingsPanel - 4 + 1 + + + 6, 38 + + + 210, 21 + + + 8 + + + cbInstrumentPreset + + + System.Windows.Forms.ComboBox, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + + diaUmpireSettingsPanel + + + 2 + + + True + + + 3, 78 + + + 126, 17 + + + 13 + + + &Estimate background + + + Estimating background signal will make the DIA-Umpire process significantly faster, at a moderate penalty to accuracy. (EstimateBG) + + + cbEstimateBg + + + System.Windows.Forms.CheckBox, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + + diaUmpireSettingsPanel + + + 3 + + + False + + + 0, 117 + + + 367, 247 + + + 16 + + + diaUmpireSettingsPanel + + + System.Windows.Forms.Panel, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + + diaUmpireTabPage + + + 1 4, 22 @@ -331,7 +448,7 @@ converterTabControl - System.Windows.Forms.TabControl, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + pwiz.Skyline.Controls.WizardPages, Skyline-daily, Version=24.1.1.277, Culture=neutral, PublicKeyToken=null $this diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/IImportResultsControl.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/IImportResultsControl.cs index 55c60a1623..d7bcf8aab0 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/IImportResultsControl.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/IImportResultsControl.cs @@ -29,18 +29,19 @@ namespace pwiz.Skyline.FileUI.PeptideSearch public class ImportResultsSettings { public static readonly ImportResultsSettings DEFAULT = new ImportResultsSettings(false, - MultiFileLoader.ImportResultsSimultaneousFileOptions.one_at_a_time, false, null, null, null); + MultiFileLoader.ImportResultsSimultaneousFileOptions.one_at_a_time, false, null, null, null, false); public ImportResultsSettings(bool excludeSpectrumSourceFiles, IImportResultsControl control) : this( excludeSpectrumSourceFiles, (MultiFileLoader.ImportResultsSimultaneousFileOptions) control.SimultaneousFiles, control.DoAutoRetry, - control.Prefix, control.Suffix, control.FoundResultsFiles.Select(file => file.Path).ToList()) + control.Prefix, control.Suffix, control.FoundResultsFiles.Select(file => file.Path).ToList(), + (control as ImportResultsDIAControl)?.IsGpf ?? false) { } public ImportResultsSettings(bool excludeSpectrumSourceFiles, MultiFileLoader.ImportResultsSimultaneousFileOptions fileImportOption, bool retryAfterImportFailure, - string prefix, string suffix, List foundResultsFiles) + string prefix, string suffix, List foundResultsFiles, bool isGpf) { ExcludeSpectrumSourceFiles = excludeSpectrumSourceFiles; FileImportOption = fileImportOption; @@ -50,11 +51,15 @@ public ImportResultsSettings(bool excludeSpectrumSourceFiles, FoundResultsFiles = foundResultsFiles != null ? foundResultsFiles.Select(AuditLogPath.Create).ToList() : null; + IsGpf = isGpf; } [Track] public List FoundResultsFiles { get; private set; } + [Track(defaultValues:typeof(DefaultValuesFalse))] + public bool IsGpf { get; private set; } + [Track] public bool ExcludeSpectrumSourceFiles { get; private set; } [Track] diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs index 22eb6f01f3..f8a3e9a2b3 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs @@ -420,9 +420,10 @@ public ImportPeptideSearchDlg(SkylineWindow skylineWindow, LibraryManager librar _pagesToSkip.Add(Pages.match_modifications_page); } + private bool _heightAdjusted; public void AdjustHeightForFullScanSettings() { - if (IsDdaWorkflow) + if (IsDdaWorkflow || _heightAdjusted) return; var tab = Controls.OfType().First().TabPages[(int) Pages.full_scan_settings_page]; @@ -437,6 +438,7 @@ public void AdjustHeightForFullScanSettings() { Height += change; } + _heightAdjusted = true; } private SkylineWindow SkylineWindow { get; set; } @@ -471,6 +473,7 @@ public Workflow WorkflowType get { return BuildPepSearchLibControl.WorkflowType; } } + public bool IsImportingSearchResults => InputFileType == InputFile.search_result; public bool IsDdaWorkflow => WorkflowType == Workflow.dda || WorkflowType == Workflow.feature_detection; public bool IsFeatureDetectionWorkflow => WorkflowType == Workflow.feature_detection; @@ -552,10 +555,7 @@ private void NextPage() { _pagesToSkip.Clear(); ImportPeptideSearch.IsDDASearch = BuildPepSearchLibControl.PerformDDASearch && !IsFeatureDetectionWorkflow; - ImportPeptideSearch.IsDIASearch = WorkflowType == Workflow.dia && - BuildPepSearchLibControl.PerformDDASearch && - !BuildPepSearchLibControl.UseDiaUmpire; - ImportPeptideSearch.IsGpfData = BuildPepSearchLibControl.IsGpf; + ImportPeptideSearch.IsDIASearch = BuildPepSearchLibControl.PerformDDASearch && WorkflowType == Workflow.dia; ImportFastaControl.IsDDASearch = BuildPepSearchLibControl.PerformDDASearch && !IsFeatureDetectionWorkflow; if (!BuildPepSearchLibControl.UseExistingLibrary) { @@ -585,9 +585,6 @@ private void NextPage() // the rest of the wizard pages. ShowEarlyFinish(false); - if (BuildPepSearchLibControl.PerformDDASearch) - _pagesToSkip.Add(Pages.chromatograms_page); - lblFasta.Text = FastaOptional ? PeptideSearchResources.ImportPeptideSearchDlg_NextPage_Import_FASTA__optional_ : PeptideSearchResources.ImportPeptideSearchDlg_NextPage_Import_FASTA__required_; @@ -620,23 +617,23 @@ private void NextPage() _pagesToSkip.Add(Pages.import_fasta_page); } } - else + else + { + // DIA workflow, replace old ImportResultsControl + if (!(ImportResultsControl is ImportResultsDIAControl)) { - // DIA workflow, replace old ImportResultsControl - if (!(ImportResultsControl is ImportResultsDIAControl)) + ImportResultsDIAControl = new ImportResultsDIAControl(this) { - ImportResultsDIAControl = new ImportResultsDIAControl(this) - { - Anchor = oldImportResultsControl.Anchor, - Location = oldImportResultsControl.Location, - Size = oldImportResultsControl.Size - }; - ImportResultsControl = ImportResultsDIAControl; - } + Anchor = oldImportResultsControl.Anchor, + Location = oldImportResultsControl.Location, + Size = oldImportResultsControl.Size + }; + ImportResultsControl = ImportResultsDIAControl; + } - if (BuildPepSearchLibControl.PerformDDASearch) - ImportResultsDIAControl.FoundResultsFiles = BuildPepSearchLibControl.DdaSearchDataSources.Select(o => - new ImportPeptideSearch.FoundResultsFile(o.GetFileName(), o.GetFilePath())).ToList(); + if (BuildPepSearchLibControl.PerformDDASearch) + ImportResultsDIAControl.FoundResultsFiles = BuildPepSearchLibControl.DdaSearchDataSources.Select(o => + new ImportPeptideSearch.FoundResultsFile(o.GetFileName(), o.GetFilePath())).ToList(); } getChromatogramsPage.Controls.Add((Control)ImportResultsControl); @@ -648,21 +645,27 @@ private void NextPage() } else { - if (IsDdaWorkflow || !BuildPepSearchLibControl.DIAConversionNeeded) + if (!IsImportingSearchResults && WorkflowType != Workflow.dia) + { + _pagesToSkip.Add(Pages.chromatograms_page); _pagesToSkip.Add(Pages.converter_settings_page); + } + + //ImportResultsDIAControl.HideFileAddRemoveButtons = true; ImportPeptideSearch.SpectrumSourceFiles.Clear(); - SearchSettingsControl.InitializeControls(); // in PerformDDA mode, set SpectrumSourceFiles and offer to remove prefix - var uniqueNames = Helpers.EnsureUniqueNames(BuildPepSearchLibControl.DdaSearchDataSources.Select(s => s.GetFileName()).ToList()); + var uniqueNames = Helpers.EnsureUniqueNames(BuildPepSearchLibControl.DdaSearchDataSources.Select(s => s.GetFileName()).ToList()); for (var i = 0; i < BuildPepSearchLibControl.DdaSearchDataSources.Length; i++) { var source = BuildPepSearchLibControl.DdaSearchDataSources[i]; ImportPeptideSearch.SpectrumSourceFiles.Add(uniqueNames[i], new ImportPeptideSearch.FoundResultsFilePossibilities(uniqueNames[i]) {ExactMatch = source.ToString()}); } - ShowRemovePrefixDialog(); + + if (IsDdaWorkflow) + ShowRemovePrefixDialog(); } // Set up full scan settings page @@ -689,7 +692,7 @@ private void NextPage() case Pages.chromatograms_page: { - if (!ImportPeptideSearch.VerifyRetentionTimes(ImportResultsControl.FoundResultsFiles.Select(f => f.Path))) + if (IsImportingSearchResults && !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_)); @@ -721,10 +724,15 @@ private void NextPage() } } + if (ImportResultsControl is ImportResultsDIAControl diaControl) + { + ImportPeptideSearch.IsGpfData = diaControl.IsGpf; + } + ShowRemovePrefixDialog(); ImportFastaControl.IsImportingResults = anyResults; - if (ImportFastaControl.DecoyGenerationEnabled) + if (ImportFastaControl.DecoyGenerationEnabled && WorkflowType != Workflow.dia) { if (anyResults) { @@ -782,7 +790,7 @@ private void NextPage() return; } - if (WorkflowType == Workflow.dia && BuildPepSearchLibControl.DIAConversionNeeded) + if (ImportPeptideSearch.IsDIASearch) ConverterSettingsControl.InitializeProtocol(ConverterSettingsControl.Protocol.dia_umpire); break; } @@ -795,16 +803,20 @@ private void NextPage() return; } case Pages.converter_settings_page: - if (WorkflowType == Workflow.dia && BuildPepSearchLibControl.DIAConversionNeeded) + if (WorkflowType == Workflow.dia) { - if (FullScanSettingsControl.IsolationScheme.PrespecifiedIsolationWindows.Count == 0) + if (ConverterSettingsControl.UseDiaUmpire) { - MessageDlg.Show(this, PeptideSearchResources.ImportPeptideSearchDlg_NextPage_No_isolation_windows_are_configured__); - - return; - } - else + if (FullScanSettingsControl.IsolationScheme.PrespecifiedIsolationWindows.Count == 0) + { + MessageDlg.Show(this, PeptideSearchResources.ImportPeptideSearchDlg_NextPage_No_isolation_windows_are_configured__); + return; + } ImportPeptideSearch.DdaConverter = ConverterSettingsControl.GetDiaUmpireConverter(); + } + + ImportPeptideSearch.IsDIASearch = !ConverterSettingsControl.UseDiaUmpire; + SearchSettingsControl.InitializeControls(); } break; case Pages.dda_search_settings_page: @@ -1135,7 +1147,7 @@ private void PreviousPage() private void UpdateButtons() { - if (CurrentPage <= Pages.chromatograms_page) + if (IsImportingSearchResults && CurrentPage <= Pages.chromatograms_page) { btnBack.Hide(); btnEarlyFinish.Location = btnBack.Location; diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.Designer.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.Designer.cs index 706e2f6602..0870530dac 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.Designer.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.Designer.cs @@ -36,6 +36,7 @@ private void InitializeComponent() this.cbAutoRetry = new System.Windows.Forms.CheckBox(); this.comboSimultaneousFiles = new System.Windows.Forms.ComboBox(); this.label1 = new System.Windows.Forms.Label(); + this.cbGpf = new System.Windows.Forms.CheckBox(); this.SuspendLayout(); // // labelResultsFiles @@ -86,11 +87,18 @@ private void InitializeComponent() resources.ApplyResources(this.label1, "label1"); this.label1.Name = "label1"; // + // cbGpf + // + resources.ApplyResources(this.cbGpf, "cbGpf"); + this.cbGpf.Name = "cbGpf"; + this.cbGpf.UseVisualStyleBackColor = true; + // // ImportResultsDIAControl // resources.ApplyResources(this, "$this"); this.AutoScaleMode = System.Windows.Forms.AutoScaleMode.Font; this.BackColor = System.Drawing.Color.Transparent; + this.Controls.Add(this.cbGpf); this.Controls.Add(this.cbAutoRetry); this.Controls.Add(this.comboSimultaneousFiles); this.Controls.Add(this.label1); @@ -113,5 +121,6 @@ private void InitializeComponent() private System.Windows.Forms.CheckBox cbAutoRetry; private System.Windows.Forms.ComboBox comboSimultaneousFiles; private System.Windows.Forms.Label label1; + private System.Windows.Forms.CheckBox cbGpf; } } diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.cs index 18b16b0997..8149f78c6a 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.cs @@ -63,6 +63,18 @@ public bool DoAutoRetry set { cbAutoRetry.Checked = value; } } + public bool IsGpf + { + get => cbGpf.Checked; + set => cbGpf.Checked = value; + } + + public bool HideFileAddRemoveButtons + { + get => btnBrowse.Visible; + set => btnBrowse.Visible = btnRemove.Visible = value; + } + public string Prefix { get; set; } public string Suffix { get; set; } diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.resx b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.resx index 3a6c951c5c..955ecb40cd 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.resx +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportResultsDIAControl.resx @@ -148,7 +148,7 @@ $this - 6 + 7 Top, Bottom, Left, Right @@ -157,7 +157,7 @@ 19, 26 - 345, 290 + 345, 277 1 @@ -172,7 +172,7 @@ $this - 5 + 6 Bottom, Left @@ -181,7 +181,7 @@ NoControl - 19, 322 + 19, 332 75, 23 @@ -202,7 +202,7 @@ $this - 4 + 5 Bottom, Left @@ -211,7 +211,7 @@ NoControl - 100, 322 + 100, 332 75, 23 @@ -232,7 +232,7 @@ $this - 3 + 4 Bottom, Left @@ -265,7 +265,7 @@ $this - 0 + 1 Bottom, Left @@ -298,7 +298,7 @@ $this - 1 + 2 Bottom, Left @@ -331,7 +331,40 @@ $this - 2 + 3 + + + Bottom, Left + + + True + + + NoControl + + + 19, 309 + + + 138, 17 + + + 8 + + + &Gas phase fractionation + + + cbGpf + + + System.Windows.Forms.CheckBox, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089 + + + $this + + + 0 True diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchSettingsControl.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchSettingsControl.cs index b5564aa3b4..673779744d 100644 --- a/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchSettingsControl.cs +++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchSettingsControl.cs @@ -99,7 +99,7 @@ public void InitializeControls() private void SearchEngineComboBox_SelectedIndexChanged(object sender, EventArgs e) { - if (_searchEngine == SelectedSearchEngine) + if (_searchEngine == SelectedSearchEngine && ImportPeptideSearch.SearchEngine?.IsDisposed != true) return; // nothing to do if (ImportPeptideSearch.IsDIASearch && SelectedSearchEngine != SearchEngine.MSFragger) // currently only supported by MSFragger @@ -203,6 +203,22 @@ private bool EnsureRequiredFilesDownloaded(IEnumerable require return !SimpleFileDownloader.FilesNotAlreadyDownloaded(filesNotAlreadyDownloaded).Any(); } + private bool EnsureRequiredFilesDownloaded() + { + switch (_searchEngine) + { + case SearchEngine.MSGFPlus: + return EnsureRequiredFilesDownloaded(MsgfPlusSearchEngine.FilesToDownload); + case SearchEngine.MSFragger: + return EnsureRequiredFilesDownloaded(MsFraggerSearchEngine.FilesToDownload, ShowDownloadMsFraggerDialog); + case SearchEngine.Hardklor: + case SearchEngine.MSAmanda: + return true; + default: + throw new NotImplementedException(); + } + } + public static bool HasRequiredFilesDownloaded(SearchEngine searchEngine) { FileDownloadInfo[] fileDownloadInfo; @@ -232,12 +248,8 @@ private AbstractDdaSearchEngine InitSelectedSearchEngine() case SearchEngine.MSAmanda: return new MSAmandaSearchWrapper(); case SearchEngine.MSGFPlus: - if (!EnsureRequiredFilesDownloaded(MsgfPlusSearchEngine.FilesToDownload)) - SelectedSearchEngine = SearchEngine.MSAmanda; return new MsgfPlusSearchEngine(); case SearchEngine.MSFragger: - if (!EnsureRequiredFilesDownloaded(MsFraggerSearchEngine.FilesToDownload, ShowDownloadMsFraggerDialog)) - SelectedSearchEngine = SearchEngine.MSAmanda; MsFraggerSearchEngine.DataType dataType; if (!ImportPeptideSearch.IsDIASearch) dataType = MsFraggerSearchEngine.DataType.dda; @@ -434,6 +446,9 @@ public bool SaveAllSettings(bool interactive) if (!valid) return false; + if (!EnsureRequiredFilesDownloaded()) + return false; + var modSettings = _documentContainer.Document.Settings.PeptideSettings.Modifications; var allMods = modSettings.StaticModifications.Union(modSettings.AllHeavyModifications); ImportPeptideSearch.SearchEngine.SetModifications(allMods, Convert.ToInt32(cbMaxVariableMods.SelectedItem)); diff --git a/pwiz_tools/Skyline/Model/AbstractDdaSearchEngine.cs b/pwiz_tools/Skyline/Model/AbstractDdaSearchEngine.cs index 0340b3de4e..2e6fe46b91 100644 --- a/pwiz_tools/Skyline/Model/AbstractDdaSearchEngine.cs +++ b/pwiz_tools/Skyline/Model/AbstractDdaSearchEngine.cs @@ -224,6 +224,11 @@ public void SetFastaFiles(string fastFile) public abstract void SetModifications(IEnumerable modifications, int maxVariableMods_); - public abstract void Dispose(); + public bool IsDisposed; + + public virtual void Dispose() + { + IsDisposed = true; + } } } diff --git a/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.Designer.cs b/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.Designer.cs index ba1f185df5..beaa00c8e1 100644 --- a/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.Designer.cs +++ b/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.Designer.cs @@ -348,15 +348,6 @@ public static string BuildPeptideSearchLibrarySettings_InputFileType { } } - /// - /// Looks up a localized string similar to Gas phase fractionation. - /// - public static string BuildPeptideSearchLibrarySettings_IsGpf { - get { - return ResourceManager.GetString("BuildPeptideSearchLibrarySettings_IsGpf", resourceCulture); - } - } - /// /// Looks up a localized string similar to Search files. /// @@ -1968,6 +1959,15 @@ public static string ImportResultsSettings_FoundResultsFiles { } } + /// + /// Looks up a localized string similar to Gas phase fractionation. + /// + public static string ImportResultsSettings_IsGpf { + get { + return ResourceManager.GetString("ImportResultsSettings_IsGpf", resourceCulture); + } + } + /// /// Looks up a localized string similar to Add multi-injection replicates in directories. /// diff --git a/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.resx b/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.resx index dabc6dedcd..06cf619089 100644 --- a/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.resx +++ b/pwiz_tools/Skyline/Model/AuditLog/PropertyNames.resx @@ -1808,7 +1808,7 @@ Spectrum Filter - + Gas phase fractionation diff --git a/pwiz_tools/Skyline/Model/DdaSearch/HardklorSearchEngine.cs b/pwiz_tools/Skyline/Model/DdaSearch/HardklorSearchEngine.cs index 2f4837fa6d..1110501fec 100644 --- a/pwiz_tools/Skyline/Model/DdaSearch/HardklorSearchEngine.cs +++ b/pwiz_tools/Skyline/Model/DdaSearch/HardklorSearchEngine.cs @@ -785,6 +785,7 @@ public override void Dispose() { DeleteIntermediateFiles(); } + base.Dispose(); } public void DeleteIntermediateFiles() diff --git a/pwiz_tools/Skyline/Model/DdaSearch/MSAmandaSearchWrapper.cs b/pwiz_tools/Skyline/Model/DdaSearch/MSAmandaSearchWrapper.cs index 69fb04d9ab..b545678cfc 100644 --- a/pwiz_tools/Skyline/Model/DdaSearch/MSAmandaSearchWrapper.cs +++ b/pwiz_tools/Skyline/Model/DdaSearch/MSAmandaSearchWrapper.cs @@ -119,6 +119,7 @@ public override void Dispose() amandaInputParser?.Dispose(); _baseDir.Dispose(); //AvailableSettings = new SettingsFile(null, Settings, mzID); + base.Dispose(); } private void Helper_SearchProgressChanged(string message) diff --git a/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs b/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs index f999d059f0..d4ca41eab3 100644 --- a/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs +++ b/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs @@ -1031,6 +1031,7 @@ public override void Dispose() { DeleteIntermediateFiles(); // In case cancel came at an awkward time } + base.Dispose(); } } } diff --git a/pwiz_tools/Skyline/Model/DdaSearch/MsgfPlusSearchEngine.cs b/pwiz_tools/Skyline/Model/DdaSearch/MsgfPlusSearchEngine.cs index f43a07a06c..41b44bf85e 100644 --- a/pwiz_tools/Skyline/Model/DdaSearch/MsgfPlusSearchEngine.cs +++ b/pwiz_tools/Skyline/Model/DdaSearch/MsgfPlusSearchEngine.cs @@ -339,9 +339,5 @@ public UpdateProgressResponse UpdateProgress(IProgressStatus status) } public bool HasUI => false; - - public override void Dispose() - { - } } } diff --git a/pwiz_tools/Skyline/Model/DiaUmpireDdaConverter.cs b/pwiz_tools/Skyline/Model/DiaUmpireDdaConverter.cs index b80feb9327..5073008ad5 100644 --- a/pwiz_tools/Skyline/Model/DiaUmpireDdaConverter.cs +++ b/pwiz_tools/Skyline/Model/DiaUmpireDdaConverter.cs @@ -77,7 +77,7 @@ public override void SetSpectrumFiles(MsDataFileUri[] spectrumFiles) for (int i = 0; i < OriginalSpectrumSources.Length; ++i) { string outputDirectory = Path.GetDirectoryName(OriginalSpectrumSources[i].GetFilePath()) ?? string.Empty; - if (Program.FunctionalTest || !DirectoryEx.IsWritable(outputDirectory)) + if (!DirectoryEx.IsWritable(outputDirectory)) outputDirectory = Path.GetDirectoryName(Program.MainWindow.DocumentFilePath) ?? string.Empty; var outputFilepath = Path.Combine(outputDirectory, OriginalSpectrumSources[i].GetFileNameWithoutExtension() + DiaUmpireFileSuffix); diff --git a/pwiz_tools/Skyline/Skyline.csproj b/pwiz_tools/Skyline/Skyline.csproj index 2cb35121ca..51b16584b7 100644 --- a/pwiz_tools/Skyline/Skyline.csproj +++ b/pwiz_tools/Skyline/Skyline.csproj @@ -3113,6 +3113,7 @@ ConverterSettingsControl.cs + Designer ConverterSettingsControl.cs diff --git a/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs b/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs index 4f10bf3fee..350a3232e6 100644 --- a/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs +++ b/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs @@ -355,8 +355,28 @@ private void TestSearch() Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.dda_search_settings_page); }); - SkylineWindow.BeginInvoke(new Action(() => importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine = TestSettings.SearchEngine)); + + // delete the FASTA to cause the error + if (errorExpected) + File.Delete(GetTestPath(TestSettings.FastaFilename)); + + RunUI(() => + { + importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine = TestSettings.SearchEngine; + foreach (var setting in TestSettings.AdditionalSettings) + importPeptideSearchDlg.SearchSettingsControl.SetAdditionalSetting(setting.Key, setting.Value); + importPeptideSearchDlg.SearchSettingsControl.PrecursorTolerance = TestSettings.PrecursorTolerance; + importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance = TestSettings.FragmentTolerance; + importPeptideSearchDlg.SearchSettingsControl.FragmentIons = TestSettings.FragmentIons; + importPeptideSearchDlg.SearchSettingsControl.Ms2Analyzer = TestSettings.Ms2Analyzer; + importPeptideSearchDlg.SearchSettingsControl.CutoffScore = 0.1; + + // Run the search + //Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + }); + + SkylineWindow.BeginInvoke(new Action(() => importPeptideSearchDlg.ClickNextButton())); if (RedownloadTools || TestSettings.HasMissingDependencies) { if (TestSettings.SearchEngine == SearchSettingsControl.SearchEngine.MSFragger) @@ -381,23 +401,6 @@ private void TestSearch() } } - // delete the FASTA to cause the error - if (errorExpected) - File.Delete(GetTestPath(TestSettings.FastaFilename)); - - RunUI(() => - { - foreach (var setting in TestSettings.AdditionalSettings) - importPeptideSearchDlg.SearchSettingsControl.SetAdditionalSetting(setting.Key, setting.Value); - importPeptideSearchDlg.SearchSettingsControl.PrecursorTolerance = TestSettings.PrecursorTolerance; - importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance = TestSettings.FragmentTolerance; - importPeptideSearchDlg.SearchSettingsControl.FragmentIons = TestSettings.FragmentIons; - importPeptideSearchDlg.SearchSettingsControl.Ms2Analyzer = TestSettings.Ms2Analyzer; - importPeptideSearchDlg.SearchSettingsControl.CutoffScore = 0.1; - - // Run the search - Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); - }); TryWaitForOpenForm(typeof(ImportPeptideSearchDlg.DDASearchPage)); // Stop to show this form during form testing RunUI(() => { diff --git a/pwiz_tools/Skyline/TestFunctional/DiaSearchTest.cs b/pwiz_tools/Skyline/TestFunctional/DiaSearchTest.cs index bf1a042655..52bab737f1 100644 --- a/pwiz_tools/Skyline/TestFunctional/DiaSearchTest.cs +++ b/pwiz_tools/Skyline/TestFunctional/DiaSearchTest.cs @@ -44,26 +44,15 @@ public class DiaSearchTest : AbstractFunctionalTest { private class TestDetails { - private SearchSettingsControl.SearchEngine _searchEngine; public string DocumentPath { get; set; } public IEnumerable SearchFiles { get; set; } public string FastaPath { get; set; } - - public SearchSettingsControl.SearchEngine SearchEngine - { - get => _searchEngine; - set - { - _searchEngine = value; - HasMissingDependencies = !SearchSettingsControl.HasRequiredFilesDownloaded(value); - } - } - + public SearchSettingsControl.SearchEngine SearchEngine { get; set; } public MzTolerance PrecursorMzTolerance { get; set; } public MzTolerance FragmentMzTolerance { get; set; } public List> AdditionalSettings { get; set; } - public bool HasMissingDependencies { get; private set; } + public bool HasMissingDependencies => !SearchSettingsControl.HasRequiredFilesDownloaded(SearchEngine); public class DocumentCounts { @@ -309,9 +298,6 @@ private void TestDiaUmpireSearch() var importPeptideSearchDlg = ShowDialog(SkylineWindow.ShowRunPeptideSearchDlg); // We're on the "Build Spectral Library" page of the wizard. - // Add the test xml file to the search files list and try to - // build the document library. - RunUI(() => { Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page); @@ -319,7 +305,12 @@ private void TestDiaUmpireSearch() importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = testDetails.SearchFiles .Select(o => (MsDataFileUri) new MsDataFilePath(GetTestPath(o))).Take(1).ToArray(); importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia; - importPeptideSearchDlg.BuildPepSearchLibControl.UseDiaUmpire = true; + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + }); + + RunUI(() => + { + Assert.AreEqual(ImportPeptideSearchDlg.Pages.chromatograms_page, importPeptideSearchDlg.CurrentPage); Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); }); @@ -426,7 +417,7 @@ private void TestDiaUmpireSearch() RunUI(() => { Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.converter_settings_page); - + importPeptideSearchDlg.ConverterSettingsControl.UseDiaUmpire = true; importPeptideSearchDlg.ConverterSettingsControl.InstrumentPreset = DiaUmpire.Config.InstrumentPreset.TripleTOF; importPeptideSearchDlg.ConverterSettingsControl.EstimateBackground = false; importPeptideSearchDlg.ConverterSettingsControl.UseMzMlSpillFile = true; // mz5 spill file leaks @@ -450,7 +441,21 @@ private void TestDiaUmpireSearch() Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.dda_search_settings_page); }); - SkylineWindow.BeginInvoke(new Action(() => importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine = testDetails.SearchEngine)); + RunUI(() => + { + importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine = testDetails.SearchEngine; + importPeptideSearchDlg.SearchSettingsControl.PrecursorTolerance = testDetails.PrecursorMzTolerance; + importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance = testDetails.FragmentMzTolerance; + if (_testDetails.AdditionalSettings != null) + foreach(var additionalSetting in testDetails.AdditionalSettings) + importPeptideSearchDlg.SearchSettingsControl.SetAdditionalSetting(additionalSetting.Key, additionalSetting.Value); + //importPeptideSearchDlg.SearchSettingsControl.FragmentIons = "b, y"; + }); + + WaitForConditionUI(() => testDetails.FragmentMzTolerance.Unit == importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance.Unit); + + // Run the search + SkylineWindow.BeginInvoke(new Action(() => importPeptideSearchDlg.ClickNextButton())); if (testDetails.HasMissingDependencies) { @@ -476,24 +481,9 @@ private void TestDiaUmpireSearch() } } - RunUI(() => - { - importPeptideSearchDlg.SearchSettingsControl.PrecursorTolerance = testDetails.PrecursorMzTolerance; - importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance = testDetails.FragmentMzTolerance; - if (_testDetails.AdditionalSettings != null) - foreach(var additionalSetting in testDetails.AdditionalSettings) - importPeptideSearchDlg.SearchSettingsControl.SetAdditionalSetting(additionalSetting.Key, additionalSetting.Value); - //importPeptideSearchDlg.SearchSettingsControl.FragmentIons = "b, y"; - }); - - WaitForConditionUI(() => testDetails.FragmentMzTolerance.Unit == importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance.Unit); - bool? searchSucceeded = null; RunUI(() => { - // Run the search - Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); - importPeptideSearchDlg.SearchControl.SearchFinished += (success) => searchSucceeded = success; importPeptideSearchDlg.BuildPepSearchLibControl.IncludeAmbiguousMatches = true; @@ -515,10 +505,13 @@ private void TestDiaUmpireSearch() Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on full scan settings Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on transition settings Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on modifications + Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on extract chromatograms Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on input files Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page); importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = testDetails.SearchFiles.Select(o => (MsDataFileUri) new MsDataFilePath(GetTestPath(o))).ToArray(); + + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on extract chromatograms }); @@ -608,31 +601,12 @@ private void TestDiaSearchPredicate() //Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); }); - SkylineWindow.BeginInvoke(new Action(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()))); - - if (testDetails.HasMissingDependencies) + RunUI(() => { - if (testDetails.SearchEngine == SearchSettingsControl.SearchEngine.MSFragger) - { - var msfraggerDownloaderDlg = TryWaitForOpenForm(2000); - if (msfraggerDownloaderDlg != null) - { - RunUI(() => msfraggerDownloaderDlg.SetValues("Matt Chambers (testing download from Skyline)", "matt.chambers42@gmail.com", "UW")); - OkDialog(msfraggerDownloaderDlg, msfraggerDownloaderDlg.ClickAccept); - } - } - - if (testDetails.SearchEngine != SearchSettingsControl.SearchEngine.MSAmanda) - { - var downloaderDlg = TryWaitForOpenForm(2000); - if (downloaderDlg != null) - { - OkDialog(downloaderDlg, downloaderDlg.ClickYes); - var waitDlg = WaitForOpenForm(); - WaitForClosedForm(waitDlg); - } - } - } + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page); + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + }); // With only 1 source, no add/remove prefix/suffix dialog @@ -733,6 +707,15 @@ private void TestDiaSearchPredicate() Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); }); + // We're on the DIA-Umpire settings page + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.converter_settings_page); + Assert.IsFalse(importPeptideSearchDlg.ConverterSettingsControl.UseDiaUmpire); + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + }); + + // We're on the Adjust search settings page RunUI(() => { @@ -741,8 +724,6 @@ private void TestDiaSearchPredicate() // MSFragger should be selected by default Assert.AreEqual(SearchSettingsControl.SearchEngine.MSFragger, importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine); }); - //SkylineWindow.BeginInvoke(new Action(() => importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine = testDetails.SearchEngine)); - // selecting something other than MSFragger should show an error RunDlg(() => importPeptideSearchDlg.SearchSettingsControl.SelectedSearchEngine = SearchSettingsControl.SearchEngine.MSAmanda, @@ -765,12 +746,36 @@ private void TestDiaSearchPredicate() WaitForConditionUI(() => testDetails.FragmentMzTolerance.Unit == importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance.Unit); + // Run the search + SkylineWindow.BeginInvoke(new Action(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()))); + + if (testDetails.HasMissingDependencies) + { + if (testDetails.SearchEngine == SearchSettingsControl.SearchEngine.MSFragger) + { + var msfraggerDownloaderDlg = TryWaitForOpenForm(2000); + if (msfraggerDownloaderDlg != null) + { + RunUI(() => msfraggerDownloaderDlg.SetValues("Matt Chambers (testing download from Skyline)", "matt.chambers42@gmail.com", "UW")); + OkDialog(msfraggerDownloaderDlg, msfraggerDownloaderDlg.ClickAccept); + } + } + + if (testDetails.SearchEngine != SearchSettingsControl.SearchEngine.MSAmanda) + { + var downloaderDlg = TryWaitForOpenForm(2000); + if (downloaderDlg != null) + { + OkDialog(downloaderDlg, downloaderDlg.ClickYes); + var waitDlg = WaitForOpenForm(); + WaitForClosedForm(waitDlg); + } + } + } + bool? searchSucceeded = null; RunUI(() => { - // Run the search - Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); - importPeptideSearchDlg.SearchControl.SearchFinished += (success) => searchSucceeded = success; importPeptideSearchDlg.BuildPepSearchLibControl.IncludeAmbiguousMatches = true; @@ -787,14 +792,18 @@ private void TestDiaSearchPredicate() RunUI(() => { Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on search settings + Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on converter settings Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on import FASTA Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on full scan settings Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on transition settings Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on modifications + Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on extract chromatograms Assert.IsTrue(importPeptideSearchDlg.ClickBackButton()); // now on input files - Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page); + Assert.AreEqual(ImportPeptideSearchDlg.Pages.spectra_page, importPeptideSearchDlg.CurrentPage); importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = testDetails.SearchFiles.Select(o => (MsDataFileUri)new MsDataFilePath(GetTestPath(o))).ToArray(); + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on extract chromatograms + Assert.AreEqual(ImportPeptideSearchDlg.Pages.chromatograms_page, importPeptideSearchDlg.CurrentPage); }); @@ -829,6 +838,7 @@ private void TestDiaSearchPredicate() { Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on import FASTA importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled = false; + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on converter settings Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on search settings Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); // now on search progress }); diff --git a/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs b/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs index c973c83f54..89dd6d5fe2 100644 --- a/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs +++ b/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs @@ -243,41 +243,19 @@ private void TestMsFraggerSearch() Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page); importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = SearchFiles.Select(o => new MsDataFilePath(o)).ToArray(); importPeptideSearchDlg.BuildPepSearchLibControl.IncludeAmbiguousMatches = false; - Assert.IsFalse(importPeptideSearchDlg.BuildPepSearchLibControl.IsGpfEnabled); - Assert.IsFalse(importPeptideSearchDlg.BuildPepSearchLibControl.IsDiaUmpireEnabled); importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia; - Assert.IsTrue(importPeptideSearchDlg.BuildPepSearchLibControl.IsGpfEnabled); - Assert.IsTrue(importPeptideSearchDlg.BuildPepSearchLibControl.IsDiaUmpireEnabled); - importPeptideSearchDlg.BuildPepSearchLibControl.IsGpf = _analysisValues.IsGpfData; }); + PauseForScreenShot("Import Peptide Search - After Selecting DIA Files page", tutorialPage++); - SkylineWindow.BeginInvoke(new Action(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()))); - - // SearchEngine changed to MSFragger automatically due to changing to DIA workflow: handle download dialogs if necessary - if (RedownloadTools || HasMissingDependencies) + RunUI(() => { - var msfraggerDownloaderDlg = TryWaitForOpenForm(2000); - if (msfraggerDownloaderDlg != null) - { - PauseForScreenShot("Import Peptide Search - Download MSFragger", - tutorialPage++); // Maybe someday - RunUI(() => msfraggerDownloaderDlg.SetValues("Matt Chambers (testing download from Skyline)", - "matt.chambers42@gmail.com", "UW")); - OkDialog(msfraggerDownloaderDlg, msfraggerDownloaderDlg.ClickAccept); - } - - var downloaderDlg = TryWaitForOpenForm(2000); - if (downloaderDlg != null) - { - PauseForScreenShot("Import Peptide Search - Download Java and Crux", - tutorialPage++); // Maybe someday - OkDialog(downloaderDlg, downloaderDlg.ClickYes); - var waitDlg = WaitForOpenForm(); - WaitForClosedForm(waitDlg); - } - } + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page); + importPeptideSearchDlg.ImportResultsDIAControl.IsGpf = _analysisValues.IsGpfData; + }); + PauseForScreenShot("Import Peptide Search - Extract Chromatograms page", tutorialPage++); - PauseForScreenShot("Import Peptide Search - After Selecting DIA Files page", tutorialPage++); + SkylineWindow.BeginInvoke(new Action(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()))); if (SearchFiles.Count() > 1) { @@ -397,6 +375,16 @@ private void TestMsFraggerSearch() PauseForScreenShot("Import Peptide Search - Import FASTA page", tutorialPage++); RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton())); + // We're on the DIA-Umpire settings page + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.converter_settings_page); + Assert.IsFalse(importPeptideSearchDlg.ConverterSettingsControl.UseDiaUmpire); + }); + PauseForScreenShot("Import Peptide Search - DIA-Umpire Settings page", tutorialPage++); + + RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton())); + // We're on the "Adjust Search Settings" page bool? searchSucceeded = null; RunUI(() => Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.dda_search_settings_page)); @@ -418,11 +406,37 @@ private void TestMsFraggerSearch() }); PauseForScreenShot("Import Peptide Search - Search Settings page", tutorialPage++); + WaitForConditionUI(() => MzTolerance.Units.ppm == importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance.Unit); // Run the search + SkylineWindow.BeginInvoke(new Action(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()))); + + // SearchEngine changed to MSFragger automatically due to changing to DIA workflow: handle download dialogs if necessary + if (RedownloadTools || HasMissingDependencies) + { + var msfraggerDownloaderDlg = TryWaitForOpenForm(2000); + if (msfraggerDownloaderDlg != null) + { + PauseForScreenShot("Import Peptide Search - Download MSFragger", + tutorialPage++); // Maybe someday + RunUI(() => msfraggerDownloaderDlg.SetValues("Matt Chambers (testing download from Skyline)", + "matt.chambers42@gmail.com", "UW")); + OkDialog(msfraggerDownloaderDlg, msfraggerDownloaderDlg.ClickAccept); + } + + var downloaderDlg = TryWaitForOpenForm(2000); + if (downloaderDlg != null) + { + PauseForScreenShot("Import Peptide Search - Download Java and Crux", + tutorialPage++); // Maybe someday + OkDialog(downloaderDlg, downloaderDlg.ClickYes); + var waitDlg = WaitForOpenForm(); + WaitForClosedForm(waitDlg); + } + } + try { - RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton())); WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.dda_search_page); PauseForScreenShot("Import Peptide Search - Search Progress page", tutorialPage++); diff --git a/pwiz_tools/Skyline/TestPerf/DiaUmpireTutorialTest.cs b/pwiz_tools/Skyline/TestPerf/DiaUmpireTutorialTest.cs index 872a3bcb59..2d352958b6 100644 --- a/pwiz_tools/Skyline/TestPerf/DiaUmpireTutorialTest.cs +++ b/pwiz_tools/Skyline/TestPerf/DiaUmpireTutorialTest.cs @@ -394,18 +394,28 @@ protected override void DoTest() importPeptideSearchDlg.BuildPepSearchLibControl.DdaSearchDataSources = searchFiles.Select(f => new MsDataFilePath(f)).ToArray(); importPeptideSearchDlg.BuildPepSearchLibControl.IrtStandards = IrtStandard.BIOGNOSYS_11; importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia; - importPeptideSearchDlg.BuildPepSearchLibControl.UseDiaUmpire = true; // Check default settings shown in the tutorial Assert.IsFalse(importPeptideSearchDlg.BuildPepSearchLibControl.IncludeAmbiguousMatches); }); PauseForScreenShot("Import Peptide Search - Build Spectral Library populated page", 4); - //WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled); + RunUI(() => + { + Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page); + }); + PauseForScreenShot("Import Peptide Search - Extract chromatograms page", 4); - var removeSuffix = ShowDialog(() => importPeptideSearchDlg.ClickNextButton()); // now on remove prefix/suffix dialog - PauseForScreenShot("Import Peptide Search - Remove shared prefix/suffix page", 5); - OkDialog(removeSuffix, () => removeSuffix.YesDialog()); // now on modifications - WaitForDocumentLoaded(); + // With 2 sources, we get the remove prefix/suffix dialog; accept default behavior + if (searchFiles.Length > 1) + { + var removeSuffix = ShowDialog(() => importPeptideSearchDlg.ClickNextButton()); // now on remove prefix/suffix dialog + PauseForScreenShot("Import Peptide Search - Remove shared prefix/suffix page", 5); + OkDialog(removeSuffix, () => removeSuffix.YesDialog()); // now on modifications + WaitForDocumentLoaded(); + } + else + RunUI(() => importPeptideSearchDlg.ClickNextButton()); RunUI(() => Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page)); @@ -533,6 +543,7 @@ protected override void DoTest() { Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()); + importPeptideSearchDlg.ConverterSettingsControl.UseDiaUmpire = true; importPeptideSearchDlg.ConverterSettingsControl.InstrumentPreset = _instrumentValues.InstrumentPreset; importPeptideSearchDlg.ConverterSettingsControl.EstimateBackground = true; //importPeptideSearchDlg.ConverterSettingsControl.AdditionalSettings = _instrumentValues.AdditionalSettings; diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaQeDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaQeDiaUmpireTutorial.log index e9df59552c..c3af3dca1f 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaQeDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaQeDiaUmpireTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -33,7 +32,6 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = True, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log index ad0e8549db..0f90210513 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Gas phase fractionation is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -33,7 +32,6 @@ iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, Workflow = "DIA", -Gas phase fractionation = True, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search @@ -42,6 +40,7 @@ All Info : Imported a peptide search Import Peptide Search > Extract Chromatograms > Found results files : contains "P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML" Import Peptide Search > Extract Chromatograms > Found results files : contains "P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML" +Import Peptide Search > Extract Chromatograms > Gas phase fractionation is True Import Peptide Search > Extract Chromatograms > Files to import simultaneously is "Many" Import Peptide Search > Extract Chromatograms > Removed prefix is "P2_202405_neo_150uID_CSF_GPF_2ThDIA_" Import Peptide Search > Add Modifications > Added modifications : contains "Carbamidomethyl (C) = C[57] (fixed)" @@ -72,6 +71,7 @@ Extra Info: Extract Chromatograms = "P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML", "P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML" ], + Gas phase fractionation = True, Files to import simultaneously = "Many", Removed prefix = "P2_202405_neo_150uID_CSF_GPF_2ThDIA_" }, diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaTtofDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaTtofDiaUmpireTutorial.log index 7ba6916a1f..c2fc0b90f7 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaTtofDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaTtofDiaUmpireTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -33,7 +32,6 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = True, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaQeDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaQeDiaUmpireTutorial.log index 163f7eeb1d..c9728d2886 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaQeDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaQeDiaUmpireTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -33,7 +32,6 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = True, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log index 0946c0eccf..4379639d9f 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Gas phase fractionation is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -33,7 +32,6 @@ iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, Workflow = "DIA", -Gas phase fractionation = True, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search @@ -42,6 +40,7 @@ All Info : Imported a peptide search Import Peptide Search > Extract Chromatograms > Found results files : contains "P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML" Import Peptide Search > Extract Chromatograms > Found results files : contains "P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML" +Import Peptide Search > Extract Chromatograms > Gas phase fractionation is True Import Peptide Search > Extract Chromatograms > Files to import simultaneously is "Many" Import Peptide Search > Extract Chromatograms > Removed prefix is "P2_202405_neo_150uID_CSF_GPF_2ThDIA_" Import Peptide Search > Add Modifications > Added modifications : contains "Carbamidomethyl (C) = C[57] (fixed)" @@ -72,6 +71,7 @@ Extra Info: Extract Chromatograms = "P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML", "P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML" ], + Gas phase fractionation = True, Files to import simultaneously = "Many", Removed prefix = "P2_202405_neo_150uID_CSF_GPF_2ThDIA_" }, diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaTtofDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaTtofDiaUmpireTutorial.log index dc5904f3e9..37dcb75280 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaTtofDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaTtofDiaUmpireTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -33,7 +32,6 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = True, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaQeDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaQeDiaUmpireTutorial.log index 220ca8a7ed..a6a7f0b0a4 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaQeDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaQeDiaUmpireTutorial.log @@ -14,7 +14,6 @@ All Info : スペクトルライブラリを構築>曖昧な一致を含むは真です スペクトルライブラリを構築>ドキュメント内のペプチドをフィルタリングは偽です スペクトルライブラリを構築>ワークフローは"DIA"です -スペクトルライブラリを構築>Deconvolute spectra with DIA-Umpireは真です スペクトルライブラリを構築>入力ファイルタイプは"DIA生データ (ライブラリのデコンボリューション、検索、構築)"です Extra Info: ファイルを検索 = [ @@ -33,7 +32,6 @@ iRT標準ペプチド = "Biognosys-11 (iRT-C18)", 曖昧な一致を含む = 真, ドキュメント内のペプチドをフィルタリング = 偽, ワークフロー = "DIA", -Deconvolute spectra with DIA-Umpire = 真, 入力ファイルタイプ = "DIA生データ (ライブラリのデコンボリューション、検索、構築)" Undo Redo : ペプチド検索がインポートされました diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log index 350b8d8eae..797a5f6d7e 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log @@ -14,7 +14,6 @@ All Info : スペクトルライブラリを構築>曖昧な一致を含むは偽です スペクトルライブラリを構築>ドキュメント内のペプチドをフィルタリングは偽です スペクトルライブラリを構築>ワークフローは"DIA"です -スペクトルライブラリを構築>Gas phase fractionationは真です スペクトルライブラリを構築>入力ファイルタイプは"DIA生データ (ライブラリのデコンボリューション、検索、構築)"です Extra Info: ファイルを検索 = [ @@ -33,7 +32,6 @@ iRT標準ペプチド = なし, 曖昧な一致を含む = 偽, ドキュメント内のペプチドをフィルタリング = 偽, ワークフロー = "DIA", -Gas phase fractionation = 真, 入力ファイルタイプ = "DIA生データ (ライブラリのデコンボリューション、検索、構築)" Undo Redo : ペプチド検索がインポートされました @@ -42,6 +40,7 @@ All Info : ペプチド検索がインポートされました ペプチド検索のインポート>クロマトグラムを抽出>結果ファイルが見つかりました："P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML"が含まれています ペプチド検索のインポート>クロマトグラムを抽出>結果ファイルが見つかりました："P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML"が含まれています +ペプチド検索のインポート>クロマトグラムを抽出>Gas phase fractionationは真です ペプチド検索のインポート>クロマトグラムを抽出>同時にインポートするファイルは"多く"です ペプチド検索のインポート>クロマトグラムを抽出>削除したプリフィックスは"P2_202405_neo_150uID_CSF_GPF_2ThDIA_"です ペプチド検索のインポート>修飾を追加>修飾が追加されました："Carbamidomethyl (C) = C[57] （固定）"が含まれています @@ -72,6 +71,7 @@ Extra Info: クロマトグラムを抽出 = "P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML", "P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML" ], + Gas phase fractionation = 真, 同時にインポートするファイル = "多く", 削除したプリフィックス = "P2_202405_neo_150uID_CSF_GPF_2ThDIA_" }, diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaTtofDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaTtofDiaUmpireTutorial.log index 00dc9874e0..2f4fde8620 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaTtofDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaTtofDiaUmpireTutorial.log @@ -14,7 +14,6 @@ All Info : スペクトルライブラリを構築>曖昧な一致を含むは真です スペクトルライブラリを構築>ドキュメント内のペプチドをフィルタリングは偽です スペクトルライブラリを構築>ワークフローは"DIA"です -スペクトルライブラリを構築>Deconvolute spectra with DIA-Umpireは真です スペクトルライブラリを構築>入力ファイルタイプは"DIA生データ (ライブラリのデコンボリューション、検索、構築)"です Extra Info: ファイルを検索 = [ @@ -33,7 +32,6 @@ iRT標準ペプチド = "Biognosys-11 (iRT-C18)", 曖昧な一致を含む = 真, ドキュメント内のペプチドをフィルタリング = 偽, ワークフロー = "DIA", -Deconvolute spectra with DIA-Umpire = 真, 入力ファイルタイプ = "DIA生データ (ライブラリのデコンボリューション、検索、構築)" Undo Redo : ペプチド検索がインポートされました diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaQeDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaQeDiaUmpireTutorial.log index 163f7eeb1d..c9728d2886 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaQeDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaQeDiaUmpireTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -33,7 +32,6 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = True, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log index 0946c0eccf..4379639d9f 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is None Build Spectral Library > Include ambiguous matches is False Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Gas phase fractionation is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -33,7 +32,6 @@ iRT standard peptides = None, Include ambiguous matches = False, Filter for document peptides = False, Workflow = "DIA", -Gas phase fractionation = True, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search @@ -42,6 +40,7 @@ All Info : Imported a peptide search Import Peptide Search > Extract Chromatograms > Found results files : contains "P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML" Import Peptide Search > Extract Chromatograms > Found results files : contains "P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML" +Import Peptide Search > Extract Chromatograms > Gas phase fractionation is True Import Peptide Search > Extract Chromatograms > Files to import simultaneously is "Many" Import Peptide Search > Extract Chromatograms > Removed prefix is "P2_202405_neo_150uID_CSF_GPF_2ThDIA_" Import Peptide Search > Add Modifications > Added modifications : contains "Carbamidomethyl (C) = C[57] (fixed)" @@ -72,6 +71,7 @@ Extra Info: Extract Chromatograms = "P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML", "P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML" ], + Gas phase fractionation = True, Files to import simultaneously = "Many", Removed prefix = "P2_202405_neo_150uID_CSF_GPF_2ThDIA_" }, diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaTtofDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaTtofDiaUmpireTutorial.log index dc5904f3e9..37dcb75280 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaTtofDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaTtofDiaUmpireTutorial.log @@ -14,7 +14,6 @@ Build Spectral Library > iRT standard peptides is "Biognosys-11 (iRT-C18)" Build Spectral Library > Include ambiguous matches is True Build Spectral Library > Filter for document peptides is False Build Spectral Library > Workflow is "DIA" -Build Spectral Library > Deconvolute spectra with DIA-Umpire is True Build Spectral Library > Input File Type is "DIA raw (search and build library)" Extra Info: Search files = [ @@ -33,7 +32,6 @@ iRT standard peptides = "Biognosys-11 (iRT-C18)", Include ambiguous matches = True, Filter for document peptides = False, Workflow = "DIA", -Deconvolute spectra with DIA-Umpire = True, Input File Type = "DIA raw (search and build library)" Undo Redo : Imported a peptide search diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaQeDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaQeDiaUmpireTutorial.log index b352570f26..a9f5941242 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaQeDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaQeDiaUmpireTutorial.log @@ -14,7 +14,6 @@ All Info : 建立谱图库 > 包含不明确匹配项 是 真 建立谱图库 > 文档肽段筛选器 是 假 建立谱图库 > 工作流程 是 "DIA（数据非依赖性采集）" -建立谱图库 > Deconvolute spectra with DIA-Umpire 是 真 建立谱图库 > 输入文件类型 是 "DIA 原始（去卷积、搜索和构建库）" Extra Info: 搜索文件 = [ @@ -33,7 +32,6 @@ iRT 标准肽段 = "Biognosys-11 (iRT-C18)", 包含不明确匹配项 = 真, 文档肽段筛选器 = 假, 工作流程 = "DIA（数据非依赖性采集）", -Deconvolute spectra with DIA-Umpire = 真, 输入文件类型 = "DIA 原始（去卷积、搜索和构建库）" Undo Redo : 已导入肽段搜索 diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log index 398914d2a8..f9b007f64b 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log @@ -14,7 +14,6 @@ All Info : 建立谱图库 > 包含不明确匹配项 是 假 建立谱图库 > 文档肽段筛选器 是 假 建立谱图库 > 工作流程 是 "DIA（数据非依赖性采集）" -建立谱图库 > Gas phase fractionation 是 真 建立谱图库 > 输入文件类型 是 "DIA 原始（去卷积、搜索和构建库）" Extra Info: 搜索文件 = [ @@ -33,7 +32,6 @@ iRT 标准肽段 = 无, 包含不明确匹配项 = 假, 文档肽段筛选器 = 假, 工作流程 = "DIA（数据非依赖性采集）", -Gas phase fractionation = 真, 输入文件类型 = "DIA 原始（去卷积、搜索和构建库）" Undo Redo : 已导入肽段搜索 @@ -42,6 +40,7 @@ All Info : 已导入肽段搜索 导入肽段搜索 > 提取色谱图 > 查找到结果文件 : 包含 "P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML" 导入肽段搜索 > 提取色谱图 > 查找到结果文件 : 包含 "P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML" +导入肽段搜索 > 提取色谱图 > Gas phase fractionation 是 真 导入肽段搜索 > 提取色谱图 > 要同步导入的文件 是 "许多个" 导入肽段搜索 > 提取色谱图 > 已删除前缀 是 "P2_202405_neo_150uID_CSF_GPF_2ThDIA_" 导入肽段搜索 > 添加修饰 > 已添加修饰 : 包含 "Carbamidomethyl (C) = C[57] （固定）" @@ -72,6 +71,7 @@ Extra Info: 提取色谱图 = "P2_202405_neo_150uID_CSF_GPF_2ThDIA_500-600_30m_14.mzML", "P2_202405_neo_150uID_CSF_GPF_2ThDIA_600-700_30m_15.mzML" ], + Gas phase fractionation = 真, 要同步导入的文件 = "许多个", 已删除前缀 = "P2_202405_neo_150uID_CSF_GPF_2ThDIA_" }, diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaTtofDiaUmpireTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaTtofDiaUmpireTutorial.log index 919107edee..e520d93f8d 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaTtofDiaUmpireTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaTtofDiaUmpireTutorial.log @@ -14,7 +14,6 @@ All Info : 建立谱图库 > 包含不明确匹配项 是 真 建立谱图库 > 文档肽段筛选器 是 假 建立谱图库 > 工作流程 是 "DIA（数据非依赖性采集）" -建立谱图库 > Deconvolute spectra with DIA-Umpire 是 真 建立谱图库 > 输入文件类型 是 "DIA 原始（去卷积、搜索和构建库）" Extra Info: 搜索文件 = [ @@ -33,7 +32,6 @@ iRT 标准肽段 = "Biognosys-11 (iRT-C18)", 包含不明确匹配项 = 真, 文档肽段筛选器 = 假, 工作流程 = "DIA（数据非依赖性采集）", -Deconvolute spectra with DIA-Umpire = 真, 输入文件类型 = "DIA 原始（去卷积、搜索和构建库）" Undo Redo : 已导入肽段搜索