private void PerformSort(string title, Comparison <PeptideGroupDocNode> comparison, MessageType type)
{
ModifyDocument(title, doc =>
{
var listIrt = new List <PeptideGroupDocNode>();
var listProteins = new List <PeptideGroupDocNode>(doc.Children.Count);
var listDecoy = new List <PeptideGroupDocNode>();
foreach (var nodePepGroup in doc.MoleculeGroups)
{
if (nodePepGroup.IsDecoy)
{
listDecoy.Add(nodePepGroup);
}
else if (nodePepGroup.PeptideCount > 0 && nodePepGroup.Peptides.All(nodePep => nodePep.GlobalStandardType == StandardType.IRT))
{
listIrt.Add(nodePepGroup);
}
else
{
listProteins.Add(nodePepGroup);
}
}
listIrt.Sort(comparison);
listProteins.Sort(comparison);
listDecoy.Sort(comparison);
return((SrmDocument)doc.ChangeChildrenChecked(listIrt.Concat(listProteins).Concat(listDecoy).ToArray()));
}, docPair => AuditLogEntry.CreateSingleMessageEntry(new MessageInfo(type, docPair.NewDocumentType)));
}
public bool ShowGenerateDecoysDlg(IWin32Window owner = null)
{
using (var decoysDlg = new GenerateDecoysDlg(DocumentUI))
{
if (decoysDlg.ShowDialog(owner ?? SkylineWindow) == DialogResult.OK)
{
var refinementSettings = new RefinementSettings {
NumberOfDecoys = decoysDlg.NumDecoys, DecoysMethod = decoysDlg.DecoysMethod
};
ModifyDocument(Resources.SkylineWindow_ShowGenerateDecoysDlg_Generate_Decoys, refinementSettings.GenerateDecoys,
docPair =>
{
var plural = refinementSettings.NumberOfDecoys > 1;
return(AuditLogEntry.CreateSingleMessageEntry(new MessageInfo(
plural ? MessageType.added_peptide_decoys : MessageType.added_peptide_decoy,
DocumentUI.DocumentType,
refinementSettings.NumberOfDecoys, refinementSettings.DecoysMethod)));
});
var nodePepGroup = DocumentUI.PeptideGroups.First(nodePeptideGroup => nodePeptideGroup.IsDecoy);
SelectedPath = DocumentUI.GetPathTo((int)SrmDocument.Level.MoleculeGroups, DocumentUI.FindNodeIndex(nodePepGroup.Id));
return(true);
}
}
return(false);
}
public void RemovePeaks(SrmDocument.DOCUMENT_TYPE docType, BoundDataGridView dataGridView)
{
var parent = FormUtil.FindTopLevelOwner(dataGridView);
var selectedPeaks = GetSelectedPeaks(dataGridView).Distinct().ToArray();
if (selectedPeaks.Length == 0)
{
MessageDlg.Show(parent, Resources.RemovePeaksAction_RemovePeaks_No_peaks_are_selected);
return;
}
var lookup = selectedPeaks.ToLookup(tuple => tuple.Item1, tuple => tuple.Item2).ToArray();
string message = GetConfirmRemoveMessage(docType, selectedPeaks.Length, lookup.Length);
if (MultiButtonMsgDlg.Show(parent, message, MultiButtonMsgDlg.BUTTON_OK) != DialogResult.OK)
{
return;
}
var skylineWindow = GetSkylineWindow(dataGridView);
lock (skylineWindow.GetDocumentChangeLock())
{
skylineWindow.ModifyDocument(Resources.RemovePeaksAction_RemovePeaks_Remove_peaks,
doc =>
{
var longOperationRunner = new LongOperationRunner
{
ParentControl = parent,
JobTitle = Resources.RemovePeaksAction_RemovePeaks_Removing_Peaks
};
SrmDocument resultDocument = doc;
doc = doc.BeginDeferSettingsChanges();
longOperationRunner.Run(broker =>
{
for (int iGroup = 0; iGroup < lookup.Length; iGroup++)
{
broker.ProgressValue = iGroup * 100 / lookup.Length;
if (broker.IsCanceled)
{
return;
}
doc = RemovePeaks(doc, lookup[iGroup]);
}
resultDocument = doc.EndDeferSettingsChanges(resultDocument, null);
});
return(resultDocument);
},
docPair => AuditLogEntry.CreateSingleMessageEntry(
new MessageInfo(MessageType.removed_peaks, docPair.NewDocumentType, selectedPeaks.Length, lookup.Length)));
}
}
private ToolStripMenuItem MakeExcludeStandardMenuItem(int replicateIndex)
{
var document = DocumentUiContainer.DocumentUI;
if (!document.Settings.HasResults)
{
return(null);
}
ChromatogramSet chromatogramSet = null;
if (replicateIndex >= 0 &&
replicateIndex < document.Settings.MeasuredResults.Chromatograms.Count)
{
chromatogramSet = document.Settings.MeasuredResults.Chromatograms[replicateIndex];
}
if (chromatogramSet == null)
{
return(null);
}
if (!chromatogramSet.SampleType.AllowExclude)
{
return(null);
}
PeptideDocNode peptideDocNode;
PeptideGroupDocNode peptideGroupDocNode;
if (!TryGetSelectedPeptide(out peptideGroupDocNode, out peptideDocNode))
{
return(null);
}
bool isExcluded = peptideDocNode.IsExcludeFromCalibration(replicateIndex);
var menuItemText = isExcluded ? QuantificationStrings.CalibrationForm_MakeExcludeStandardMenuItem_Include_Standard
: QuantificationStrings.CalibrationForm_MakeExcludeStandardMenuItem_Exclude_Standard;
var peptideIdPath = new IdentityPath(peptideGroupDocNode.Id, peptideDocNode.Id);
var menuItem = new ToolStripMenuItem(menuItemText, null, (sender, args) =>
{
_skylineWindow.ModifyDocument(menuItemText,
doc => SetExcludeStandard(doc, peptideIdPath, replicateIndex, !isExcluded), docPair =>
{
var msgType = isExcluded
? MessageType.set_included_standard
: MessageType.set_excluded_standard;
return(AuditLogEntry.CreateSingleMessageEntry(docPair.OldDoc,
new MessageInfo(msgType, PeptideTreeNode.GetLabel(peptideDocNode, string.Empty), chromatogramSet.Name)));
});
});
return(menuItem);
}
