public void OkDialog() { Entry = string.IsNullOrEmpty(logMessageTextBox.Text) ? AuditLogEntry.GetUndocumentedChangeEntry(_doc) : AuditLogEntry.CreateSimpleEntry(_doc, MessageType.modified_outside_of_skyline, logMessageTextBox.Text); DialogResult = DialogResult.OK; }
public void ModifyDocument(EditDescription editDescription, Func <SrmDocument, SrmDocument> action, Func <SrmDocumentPair, AuditLogEntry> logFunc = null) { if (_batchChangesOriginalDocument == null) { if (SkylineWindow != null) { SkylineWindow.ModifyDocument(editDescription.GetUndoText(DataSchemaLocalizer), action, logFunc ?? (docPair => AuditLogEntry.CreateSimpleEntry(MessageType.set_to_in_document_grid, docPair.NewDocumentType, editDescription.AuditLogParseString, editDescription.ElementRefName, CellValueToString(editDescription.Value)))); } else { var doc = _documentContainer.Document; if (!_documentContainer.SetDocument(action(doc), doc)) { throw new InvalidOperationException(Resources .SkylineDataSchema_VerifyDocumentCurrent_The_document_was_modified_in_the_middle_of_the_operation_); } } return; } VerifyDocumentCurrent(_batchChangesOriginalDocument, _documentContainer.Document); _batchEditDescriptions.Add(editDescription); _document = action(_document.BeginDeferSettingsChanges()); }
public void ClickCancel() { graphChromatograms.IsCanceled = IsUserCanceled = true; Program.MainWindow.ModifyDocument(Resources.AllChromatogramsGraph_btnCancel_Click_Cancel_import, doc => FilterFiles(doc, info => IsCachedFile(doc, info)), docPair => AuditLogEntry.CreateSimpleEntry(docPair.OldDoc, MessageType.canceled_import)); }
public void OkDialog() { Entry = string.IsNullOrEmpty(logMessageTextBox.Text) ? AuditLogEntry.CreateUndocumentedChangeEntry() : AuditLogEntry.CreateSimpleEntry(MessageType.modified_outside_of_skyline, SrmDocument.DOCUMENT_TYPE.none, logMessageTextBox.Text); DialogResult = DialogResult.OK; }
public void TestAuditLogSerialization() { const int entryCount = 20000; var document = new SrmDocument(SrmSettingsList.GetDefault()); var simpleEntry = AuditLogEntry.CreateSimpleEntry(document, MessageType.test_only, string.Empty); var entries = Enumerable.Range(0, entryCount).Select(index => simpleEntry).ToArray(); Array.Reverse(entries); AuditLogEntry headEntry = null; foreach (var entry in entries) { if (headEntry == null) { headEntry = entry; } else { headEntry = entry.ChangeParent(headEntry); } } Assert.IsNotNull(headEntry); Assert.AreEqual(entryCount, headEntry.Count); Assert.AreEqual(headEntry.Count, headEntry.Enumerate().Count()); var auditLogList = new AuditLogList(headEntry); var serializedAuditLog = new StringWriter(); var serializer = new XmlSerializer(typeof(AuditLogList)); serializer.Serialize(serializedAuditLog, auditLogList); var roundTrip = (AuditLogList)serializer.Deserialize(new StringReader(serializedAuditLog.ToString())); Assert.IsNotNull(roundTrip); Assert.AreEqual(auditLogList.AuditLogEntries.Count, roundTrip.AuditLogEntries.Count); }
public void RemoveMissingResults() { var refinementSettings = new RefinementSettings { RemoveMissingResults = true }; ModifyDocument(Resources.SkylineWindow_RemoveMissingResults_Remove_missing_results, refinementSettings.Refine, docPair => AuditLogEntry.CreateSimpleEntry(MessageType.removed_missing_results, docPair.NewDocumentType)); }
public AuditLogEntry LogEntryFromEditDescription(EditDescription editDescription, SrmDocumentPair docPair) { if (EqualExceptAuditLog(docPair.OldDoc, docPair.NewDoc)) { return(AuditLogEntry.SKIP); } return(AuditLogEntry.CreateSimpleEntry(MessageType.set_to_in_document_grid, docPair.NewDocumentType, editDescription.AuditLogParseString, editDescription.ElementRefName, CellValueToString(editDescription.Value))); }
public void ModifyDocument(EditDescription editDescription, Func <SrmDocument, SrmDocument> action, Func <SrmDocumentPair, AuditLogEntry> logFunc = null) { if (_batchChangesOriginalDocument == null) { SkylineWindow.ModifyDocument(editDescription.GetUndoText(DataSchemaLocalizer), action, logFunc ?? (docPair => AuditLogEntry.CreateSimpleEntry(docPair.OldDoc, MessageType.set_to_in_document_grid, editDescription.ColumnCaption.GetCaption(DataSchemaLocalizer), editDescription.ElementRefName, CellValueToString(editDescription.Value)))); return; } VerifyDocumentCurrent(_batchChangesOriginalDocument, _documentContainer.Document); _batchEditDescriptions.Add(editDescription); _document = action(_document.BeginDeferSettingsChanges()); }
public void RemoveBelowCutoffs() { var rows = _bindingListSource.OfType <RowItem>() .Select(rowItem => rowItem.Value) .OfType <FoldChangeBindingSource.FoldChangeRow>() .ToArray(); var foldchangeCutoff = Math.Abs(Settings.Default.Log2FoldChangeCutoff); var pvalueCutoff = Math.Pow(10, -Settings.Default.PValueCutoff); var indices = rows.Where(r => CutoffSettings.PValueCutoffValid && r.FoldChangeResult.AdjustedPValue >= pvalueCutoff || CutoffSettings.FoldChangeCutoffValid && r.FoldChangeResult.AbsLog2FoldChange <= foldchangeCutoff) .Select(GetGlobalIndex) .Distinct() .ToArray(); _skylineWindow.ModifyDocument(GroupComparisonStrings.FoldChangeVolcanoPlot_RemoveBelowCutoffs_Remove_peptides_below_cutoffs, document => (SrmDocument)document.RemoveAll(indices), docPair => AuditLogEntry.CreateSimpleEntry(indices.Length == 1 ? MessageType.removed_single_below_cutoffs : MessageType.removed_below_cutoffs, docPair.NewDocumentType, indices.Length, GroupComparisonDef.Name).Merge(CutoffSettings.EntryCreator.Create(docPair))); }
public void RemoveBelowCutoffs() { var rows = _bindingListSource.OfType <RowItem>() .Select(rowItem => rowItem.Value) .OfType <FoldChangeBindingSource.FoldChangeRow>() .ToArray(); var foldchangeCutoff = Math.Abs(Settings.Default.Log2FoldChangeCutoff); var pvalueCutoff = Math.Pow(10, -Settings.Default.PValueCutoff); var indices = new int[0]; if (CutoffSettings.PValueCutoffValid || CutoffSettings.FoldChangeCutoffValid) { indices = GroupComparisonRefinementData.IndicesBelowCutoff(CutoffSettings.PValueCutoffValid ? pvalueCutoff : double.NaN, CutoffSettings.FoldChangeCutoffValid ? foldchangeCutoff : double.NaN, double.NaN, rows).ToArray(); } _skylineWindow.ModifyDocument(GroupComparisonStrings.FoldChangeVolcanoPlot_RemoveBelowCutoffs_Remove_peptides_below_cutoffs, document => (SrmDocument)document.RemoveAll(indices), docPair => AuditLogEntry.CreateSimpleEntry(indices.Length == 1 ? MessageType.removed_single_below_cutoffs : MessageType.removed_below_cutoffs, docPair.NewDocumentType, indices.Length, GroupComparisonDef.Name).Merge(CutoffSettings.EntryCreator.Create(docPair))); }
private AuditLogEntry CreateRemoveNodesEntry(SrmDocumentPair docPair, MessageType singular, MessageType plural) { var count = SkylineWindow.CountNodeDiff(docPair); return(AuditLogEntry.CreateSimpleEntry(count == 1 ? singular : plural, docPair.NewDocumentType, count)); }
public AuditLogEntry GetAuditLogEntry(SrmDocumentPair docPair, StaticMod isotopeModification, bool simple) { return(AuditLogEntry.CreateSimpleEntry( simple ? MessageType.permuted_isotope_label_simple : MessageType.permuted_isotope_label_complete, docPair.NewDocumentType, isotopeModification.Name)); }