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));
}
