private void PopulateChoices()
{
foreach (Protease protease in ProteaseDictionary.Dictionary.Values)
{
proteaseComboBox.Items.Add(protease);
}
Protease trypsin = ProteaseDictionary.Dictionary["trypsin"];
proteaseComboBox.SelectedItem = trypsin;
foreach (string initiatior_methionine_behavior in Enum.GetNames(typeof(InitiatorMethionineBehavior)))
{
initiatorMethionineBehaviorComboBox.Items.Add(initiatior_methionine_behavior);
}
foreach (string dissassociationType in GlobalVariables.AllSupportedDissociationTypes.Keys)
{
dissociationTypeComboBox.Items.Add(dissassociationType);
}
productMassToleranceComboBox.Items.Add("Da");
productMassToleranceComboBox.Items.Add("ppm");
precursorMassToleranceComboBox.Items.Add("Da");
precursorMassToleranceComboBox.Items.Add("ppm");
foreach (var hm in GlobalVariables.AllModsKnown.Where(b => b.ValidModification == true).GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForGrid(hm.Key);
ModSelectionGridItems.Add(theModType);
}
ModSelectionGrid.ItemsSource = ModSelectionGridItems;
foreach (var hm in GlobalVariables.AllModsKnown.Where(b => b.ValidModification == true).GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
fixedModsTreeView.DataContext = FixedModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.Where(b => b.ValidModification == true).GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
variableModsTreeView.DataContext = VariableModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.Where(b => b.ValidModification == true).GroupBy(b => b.ModificationType))
{
LocalizeModTypeForTreeViewObservableCollection.Add(new ModTypeForLoc(hm.Key));
}
}
// filters and expands tree according to user mod search
public static void FilterTree(TextBox textbox, TreeView tree, ObservableCollection <ModTypeForTreeView> collection)
{
string key = textbox.Text.ToLower();
if (string.IsNullOrEmpty(key))
{
tree.DataContext = collection; // shows full tree if nothing is searched
return;
}
var modTypesWithMatchingMods = collection.Where(p => p.Children.Any(c => c.ModName.ToLower().Contains(key))); // parent of child mods that match key
var modsThatMatchSearchString = new ObservableCollection <ModTypeForTreeView>(); // new collection containing expanded mod types that match key
foreach (ModTypeForTreeView modType in modTypesWithMatchingMods)
{
var textFilteredModType = new ModTypeForTreeView(modType.DisplayName, false);
modsThatMatchSearchString.Add(textFilteredModType);
textFilteredModType.Expanded = true;
textFilteredModType.Use = modType.Use;
var matchingChildren = modType.Children.Where(p => p.ModName.ToLower().Contains(key));
foreach (ModForTreeView mod in matchingChildren)
{
textFilteredModType.Children.Add(mod);
}
}
tree.DataContext = modsThatMatchSearchString;
}
private void PopulateChoices()
{
foreach (string crosslinkerName in Enum.GetNames(typeof(CrosslinkerType)))
{
cbCrosslinker.Items.Add(crosslinkerName);
}
//foreach (string fragmentationType in Enum.GetNames(typeof(FragmentaionType)))
// cbFragmentation.Items.Add(fragmentationType);
cbbXLprecusorMsTl.Items.Add("Absolute");
cbbXLprecusorMsTl.Items.Add("ppm");
//cbbXLBetaprecusorMsTl.Items.Add("Absolute");
//cbbXLBetaprecusorMsTl.Items.Add("ppm");
foreach (Protease protease in GlobalVariables.ProteaseDictionary.Values)
{
proteaseComboBox.Items.Add(protease);
}
proteaseComboBox.SelectedIndex = 12;
foreach (string initiatior_methionine_behavior in Enum.GetNames(typeof(InitiatorMethionineBehavior)))
{
initiatorMethionineBehaviorComboBox.Items.Add(initiatior_methionine_behavior);
}
productMassToleranceComboBox.Items.Add("Absolute");
productMassToleranceComboBox.Items.Add("ppm");
//foreach (string toleranceUnit in Enum.GetNames(typeof(ToleranceUnit)))
// productMassToleranceComboBox.Items.Add(toleranceUnit);
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.modificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
fixedModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.id, false, theModType));
}
}
fixedModsTreeView.DataContext = fixedModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.modificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
variableModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.id, false, theModType));
}
}
variableModsTreeView.DataContext = variableModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.modificationType))
{
localizeModTypeForTreeViewObservableCollection.Add(new ModTypeForLoc(hm.Key));
}
localizeModsTreeView.DataContext = localizeModTypeForTreeViewObservableCollection;
}
private void PopulateChoices()
{
foreach (var crosslinker in GlobalVariables.Crosslinkers)
{
cbCrosslinkers.Items.Add(crosslinker);
}
Crosslinker DSSO = GlobalVariables.Crosslinkers.First();
cbCrosslinkers.SelectedItem = DSSO;
foreach (string dissassociationType in GlobalVariables.AllSupportedDissociationTypes.Keys)
{
DissociationTypeComboBox.Items.Add(dissassociationType);
ChildScanDissociationTypeComboBox.Items.Add(dissassociationType);
}
cbbXLprecusorMsTl.Items.Add("Da");
cbbXLprecusorMsTl.Items.Add("ppm");
foreach (Protease protease in ProteaseDictionary.Dictionary.Values)
{
proteaseComboBox.Items.Add(protease);
}
Protease trypsin = ProteaseDictionary.Dictionary["trypsin"];
proteaseComboBox.SelectedItem = trypsin;
foreach (string initiatior_methionine_behavior in Enum.GetNames(typeof(InitiatorMethionineBehavior)))
{
initiatorMethionineBehaviorComboBox.Items.Add(initiatior_methionine_behavior);
}
productMassToleranceComboBox.Items.Add("Da");
productMassToleranceComboBox.Items.Add("ppm");
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
fixedModsTreeView.DataContext = FixedModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
variableModsTreeView.DataContext = VariableModTypeForTreeViewObservableCollection;
}
private void PopulateChoices()
{
foreach (Protease protease in GlobalVariables.ProteaseDictionary.Values)
{
proteaseComboBox.Items.Add(protease);
}
proteaseComboBox.SelectedIndex = 12;
foreach (string initiatior_methionine_behavior in Enum.GetNames(typeof(InitiatorMethionineBehavior)))
{
initiatorMethionineBehaviorComboBox.Items.Add(initiatior_methionine_behavior);
}
productMassToleranceComboBox.Items.Add("Absolute");
productMassToleranceComboBox.Items.Add("ppm");
precursorMassToleranceComboBox.Items.Add("Absolute");
precursorMassToleranceComboBox.Items.Add("ppm");
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.modificationType))
{
var theModType = new ModTypeForGrid(hm.Key);
modSelectionGridItems.Add(theModType);
}
ModSelectionGrid.ItemsSource = modSelectionGridItems;
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.modificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
fixedModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.id, false, theModType));
}
}
fixedModsTreeView.DataContext = fixedModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.modificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
variableModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.id, false, theModType));
}
}
variableModsTreeView.DataContext = variableModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.modificationType))
{
localizeModTypeForTreeViewObservableCollection.Add(new ModTypeForLoc(hm.Key));
}
//localizeModsTreeView.DataContext = localizeModTypeForTreeViewObservableCollection;
}
private void PopulateChoices()
{
ChildScanDissociationTypeComboBox.Items.Add("Null");
foreach (var dissassociationType in GlobalVariables.AllSupportedDissociationTypes.Where(p => p.Value != DissociationType.Autodetect))
{
DissociationTypeComboBox.Items.Add(dissassociationType.Key);
ChildScanDissociationTypeComboBox.Items.Add(dissassociationType.Key);
}
cbbPrecusorMsTl.Items.Add("Da");
cbbPrecusorMsTl.Items.Add("ppm");
CmbOGlycanDatabase.ItemsSource = GlobalVariables.OGlycanLocations.Select(p => Path.GetFileName(p));
CmbNGlycanDatabase.ItemsSource = GlobalVariables.NGlycanLocations.Select(p => Path.GetFileName(p));
foreach (Protease protease in ProteaseDictionary.Dictionary.Values)
{
proteaseComboBox.Items.Add(protease);
}
Protease trypsin = ProteaseDictionary.Dictionary["trypsin"];
proteaseComboBox.SelectedItem = trypsin;
foreach (string initiatior_methionine_behavior in Enum.GetNames(typeof(InitiatorMethionineBehavior)))
{
initiatorMethionineBehaviorComboBox.Items.Add(initiatior_methionine_behavior);
}
productMassToleranceComboBox.Items.Add("Da");
productMassToleranceComboBox.Items.Add("ppm");
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
fixedModsTreeView.DataContext = FixedModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
variableModsTreeView.DataContext = VariableModTypeForTreeViewObservableCollection;
}
public ModForTreeView(string toolTip, bool use, string displayName, bool bad, ModTypeForTreeView parent)
{
ToolTipStuff = toolTip;
Parent = parent;
Use = use;
DisplayName = displayName;
if (bad)
{
Background = new SolidColorBrush(Colors.Red);
}
else
{
Background = new SolidColorBrush(Colors.Transparent);
}
}
public ModForTreeView(string toolTip, bool use, string modName, bool bad, ModTypeForTreeView parent)
{
ToolTipStuff = toolTip;
Parent = parent;
Use = use;
ModName = modName;
DisplayName = modName;
if (toolTip.ToLower().Contains("terminal"))
{
var split = toolTip.Split('\n');
string location = split.First(p => p.StartsWith("PP "));
location = location.Substring(5, location.Length - 5).Trim();
switch (location)
{
case "N-terminal.": DisplayName += " (Prot N-Term)"; break;
case "C-terminal.": DisplayName += " (Prot C-Term)"; break;
case "Peptide N-terminal.": DisplayName += " (Pep N-Term)"; break;
case "Peptide C-terminal.": DisplayName += " (Pep C-Term)"; break;
}
}
if (bad)
{
Background = new SolidColorBrush(Colors.Red);
}
else
{
Background = new SolidColorBrush(Colors.Transparent);
}
}
private void UpdateFieldsFromTask(GptmdTask task)
{
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
DeconvolutionMaxAssumedChargeStateTextBox.Text = task.CommonParameters.DeconvolutionMaxAssumedChargeState.ToString();
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
precursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
precursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
bCheckBox.IsChecked = task.CommonParameters.BIons;
yCheckBox.IsChecked = task.CommonParameters.YIons;
cCheckBox.IsChecked = task.CommonParameters.CIons;
zdotCheckBox.IsChecked = task.CommonParameters.ZdotIons;
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
maxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = fixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
fixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = variableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
variableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
foreach (var mod in task.GptmdParameters.ListOfModsGptmd)
{
var theModType = gptmdModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
gptmdModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var ye in variableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in fixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in gptmdModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(GptmdTask task)
{
UseProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
DeconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
DeconvolutionMaxAssumedChargeStateTextBox.Text = task.CommonParameters.DeconvolutionMaxAssumedChargeState.ToString();
MissedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
ProteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
MaxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
MaxModsPerPeptideTextBox.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
InitiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
ProductMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
ProductMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
PrecursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
PrecursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
MinScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
MaxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
AddCompIonCheckBox.IsChecked = task.CommonParameters.AddCompIons;
MinVariantDepthTextBox.Text = task.CommonParameters.MinVariantDepth.ToString(CultureInfo.InvariantCulture);
MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
TrimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
TrimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
NumberOfPeaksToKeepPerWindowTextBox.Text = task.CommonParameters.NumberOfPeaksToKeepPerWindow == int.MaxValue || !task.CommonParameters.NumberOfPeaksToKeepPerWindow.HasValue ? "" : task.CommonParameters.NumberOfPeaksToKeepPerWindow.Value.ToString(CultureInfo.InvariantCulture);
MinimumAllowedIntensityRatioToBasePeakTexBox.Text = task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak == double.MaxValue || !task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.HasValue ? "" : task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.Value.ToString(CultureInfo.InvariantCulture);
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = fixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
fixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
ModTypeForTreeView theModType = variableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
variableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
foreach (var mod in task.GptmdParameters.ListOfModsGptmd)
{
ModTypeForTreeView theModType = gptmdModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
gptmdModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var ye in variableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in fixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in gptmdModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(SearchTask task)
{
classicSearchRadioButton.IsChecked = task.SearchParameters.SearchType == SearchType.Classic;
modernSearchRadioButton.IsChecked = task.SearchParameters.SearchType == SearchType.Modern;
nonSpecificSearchRadioButton1.IsChecked = task.SearchParameters.SearchType == SearchType.NonSpecific && task.CommonParameters.DigestionParams.Protease.Name.Contains("non-specific");
semiSpecificSearchRadioButton.IsChecked = task.SearchParameters.SearchType == SearchType.NonSpecific && !task.CommonParameters.DigestionParams.Protease.Name.Contains("non-specific");
MaxFragmentMassTextBox.Text = task.SearchParameters.MaxFragmentSize.ToString(CultureInfo.InvariantCulture);
checkBoxParsimony.IsChecked = task.SearchParameters.DoParsimony;
checkBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
checkBoxQuantification.IsChecked = task.SearchParameters.DoQuantification;
peakFindingToleranceTextBox.Text = task.SearchParameters.QuantifyPpmTol.ToString(CultureInfo.InvariantCulture);
checkBoxMatchBetweenRuns.IsChecked = task.SearchParameters.MatchBetweenRuns;
checkBoxNormalize.IsChecked = task.SearchParameters.Normalize;
modPepsAreUnique.IsChecked = task.SearchParameters.ModPeptidesAreDifferent;
checkBoxHistogramAnalysis.IsChecked = task.SearchParameters.DoHistogramAnalysis;
histogramBinWidthTextBox.Text = task.SearchParameters.HistogramBinTolInDaltons.ToString(CultureInfo.InvariantCulture);
checkBoxTarget.IsChecked = task.SearchParameters.SearchTarget;
checkBoxDecoy.IsChecked = task.SearchParameters.DecoyType != DecoyType.None;
radioButtonReverseDecoy.IsChecked = task.SearchParameters.DecoyType == DecoyType.Reverse;
radioButtonSlideDecoy.IsChecked = task.SearchParameters.DecoyType == DecoyType.Slide;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
MaxModNumTextBox.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
precursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
precursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
addCompIonCheckBox.IsChecked = task.CommonParameters.AddCompIons;
bCheckBox.IsChecked = task.CommonParameters.BIons;
yCheckBox.IsChecked = task.CommonParameters.YIons;
cCheckBox.IsChecked = task.CommonParameters.CIons;
zdotCheckBox.IsChecked = task.CommonParameters.ZdotIons;
numberOfDatabaseSearchesTextBox.Text = task.CommonParameters.TotalPartitions.ToString(CultureInfo.InvariantCulture);
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
allAmbiguity.IsChecked = task.CommonParameters.ReportAllAmbiguity;
DeconvolutionMaxAssumedChargeStateTextBox.Text = task.CommonParameters.DeconvolutionMaxAssumedChargeState.ToString();
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
eValueCheckBox.IsChecked = task.CommonParameters.CalculateEValue;
deltaScoreCheckBox.IsChecked = task.CommonParameters.UseDeltaScore;
trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
TopNPeaksTextBox.Text = task.CommonParameters.TopNpeaks == int.MaxValue ? "" : task.CommonParameters.TopNpeaks.ToString(CultureInfo.InvariantCulture);
MinRatioTextBox.Text = task.CommonParameters.MinRatio.ToString(CultureInfo.InvariantCulture);
maxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
if (task.CommonParameters.QValueOutputFilter < 1)
{
QValueTextBox.Text = task.CommonParameters.QValueOutputFilter.ToString(CultureInfo.InvariantCulture);
QValueCheckBox.IsChecked = true;
}
else
{
QValueTextBox.Text = "0.01";
QValueCheckBox.IsChecked = false;
}
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
//ckbPepXML.IsChecked = task.SearchParameters.OutPepXML;
ckbMzId.IsChecked = task.SearchParameters.WriteMzId;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var heh in LocalizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
massDiffAcceptExact.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Exact;
massDiffAccept1mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.OneMM;
massDiffAccept2mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.TwoMM;
massDiffAccept3mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ThreeMM;
massDiffAccept187.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ModOpen;
massDiffAcceptOpen.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Open;
massDiffAcceptCustom.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Custom;
if (task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Custom)
{
customkMdacTextBox.Text = task.SearchParameters.CustomMdac;
}
writePrunedDBCheckBox.IsChecked = task.SearchParameters.WritePrunedDatabase;
UpdateModSelectionGrid();
}
private void UpdateFieldsFromTask(CalibrationTask task)
{
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
txtMinPeptideLength.Text = task.CommonParameters.DigestionParams.MinPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MinPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
txtMaxPeptideLength.Text = task.CommonParameters.DigestionParams.MaxPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MaxPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
precursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
precursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
bCheckBox.IsChecked = task.CommonParameters.BIons;
yCheckBox.IsChecked = task.CommonParameters.YIons;
//maxDegreesOfParallelism.Text = task.CommonParameters.MaxParallelFilesToAnalyze.ToString();
zdotCheckBox.IsChecked = task.CommonParameters.ZdotIons;
cCheckBox.IsChecked = task.CommonParameters.CIons;
//conserveMemoryCheckBox.IsChecked = task.CommonParameters.ConserveMemory;
//writeIntermediateFilesCheckBox.IsChecked = task.CalibrationParameters.WriteIntermediateFiles;
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = fixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
fixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = variableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
variableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
//localizeAllCheckBox.IsChecked = task.CommonParameters.LocalizeAll;
if (task.CommonParameters.LocalizeAll)
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
}
else
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
if (task.CommonParameters.ListOfModTypesLocalize.Contains(heh.DisplayName))
{
heh.Use = true;
}
else
{
heh.Use = false;
}
}
}
foreach (var ye in variableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in fixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(NeoSearchTask task)
{
calibrate.IsChecked = task.NeoParameters.Calibrate;
gptmd.IsChecked = task.NeoParameters.GPTMD;
searchTarget.IsChecked = task.NeoParameters.TargetSearch;
targetPath.Text = task.NeoParameters.TargetFilePath != null ? task.NeoParameters.TargetFilePath : "";
searchDecoy.IsChecked = task.NeoParameters.DecoySearch;
decoyPath.Text = task.NeoParameters.TargetFilePath != null ? task.NeoParameters.DecoyFilePath : "";
searchN.IsChecked = task.NeoParameters.SearchNTerminus;
NPath.Text = task.NeoParameters.NFilePath != null ? task.NeoParameters.NFilePath : "";
searchC.IsChecked = task.NeoParameters.SearchCTerminus;
CPath.Text = task.NeoParameters.CFilePath != null ? task.NeoParameters.CFilePath : "";
maxMissedConsecutiveTextBox.Text = task.NeoParameters.MaxMissedConsecutiveCleavages.ToString();
maxMissedTextBox.Text = task.NeoParameters.MaxMissedCleavages.ToString();
maxCandidatesPerSpectrumTextBox.Text = task.NeoParameters.MaxCandidatesPerSpectrum.ToString();
minCisLengthTextBox.Text = task.NeoParameters.MinDistanceAllowed.ToString();
maxCisLengthTextBox.Text = task.NeoParameters.MaxDistanceAllowed.ToString();
searchNormalCis.IsChecked = task.NeoParameters.NormalCis;
searchReverseCis.IsChecked = task.NeoParameters.ReverseCis;
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
txtMinPeptideLength.Text = task.CommonParameters.DigestionParams.MinPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MinPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
txtMaxPeptideLength.Text = task.CommonParameters.DigestionParams.MaxPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MaxPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
txtMaxModNum.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
if (task.CommonParameters.ProductMassTolerance != null)
{
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
}
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
if (task.CommonParameters.PrecursorMassTolerance != null)
{
precursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
}
precursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
bCheckBox.IsChecked = task.CommonParameters.BIons;
yCheckBox.IsChecked = task.CommonParameters.YIons;
cCheckBox.IsChecked = task.CommonParameters.CIons;
zdotCheckBox.IsChecked = task.CommonParameters.ZdotIons;
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = fixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
fixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = variableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
variableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
localizeAllCheckBox.IsChecked = task.CommonParameters.LocalizeAll;
if (task.CommonParameters.LocalizeAll)
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
heh.Use = true;
}
}
else
{
foreach (var mod in task.CommonParameters.ListOfModTypesLocalize)
{
var theModType = localizeModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod));
theModType.Use = true;
}
}
foreach (var ye in variableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in fixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in localizeModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(GlycoSearchTask task)
{
RbtOGlycoSearch.IsChecked = task._glycoSearchParameters.GlycoSearchType == EngineLayer.GlycoSearch.GlycoSearchType.OGlycanSearch;
RbtNGlycoSearch.IsChecked = task._glycoSearchParameters.GlycoSearchType == EngineLayer.GlycoSearch.GlycoSearchType.NGlycanSearch;
Rbt_N_O_GlycoSearch.IsChecked = task._glycoSearchParameters.GlycoSearchType == EngineLayer.GlycoSearch.GlycoSearchType.N_O_GlycanSearch;
TbMaxOGlycanNum.Text = task._glycoSearchParameters.MaximumOGlycanAllowed.ToString(CultureInfo.InvariantCulture);
CkbOxoniumIonFilt.IsChecked = task._glycoSearchParameters.OxoniumIonFilt;
txtTopNum.Text = task._glycoSearchParameters.GlycoSearchTopNum.ToString(CultureInfo.InvariantCulture);
CmbOGlycanDatabase.SelectedItem = task._glycoSearchParameters.OGlycanDatabasefile;
CmbNGlycanDatabase.SelectedItem = task._glycoSearchParameters.NGlycanDatabasefile;
cbbPrecusorMsTl.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
PrecusorMsTlTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
TopNPeaksTextBox.Text = task.CommonParameters.NumberOfPeaksToKeepPerWindow == int.MaxValue || !task.CommonParameters.NumberOfPeaksToKeepPerWindow.HasValue ? "" : task.CommonParameters.NumberOfPeaksToKeepPerWindow.Value.ToString(CultureInfo.InvariantCulture);
MinRatioTextBox.Text = task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak == double.MaxValue || !task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.HasValue ? "" : task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.Value.ToString(CultureInfo.InvariantCulture);
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
ChildScanDissociationTypeComboBox.SelectedItem = "Null";
if (task.CommonParameters.MS2ChildScanDissociationType != DissociationType.Unknown)
{
ChildScanDissociationTypeComboBox.SelectedItem = task.CommonParameters.MS2ChildScanDissociationType.ToString();
}
CheckBoxDecoy.IsChecked = task._glycoSearchParameters.DecoyType != DecoyType.None;
RadioButtonReverseDecoy.IsChecked = task._glycoSearchParameters.DecoyType == DecoyType.Reverse;
RadioButtonSlideDecoy.IsChecked = task._glycoSearchParameters.DecoyType == DecoyType.Slide;
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
TxtBoxMaxModPerPep.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
numberOfDatabaseSearchesTextBox.Text = task.CommonParameters.TotalPartitions.ToString(CultureInfo.InvariantCulture);
maxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(CalibrationTask task)
{
ProteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease; //protease needs to come first or recommended settings can overwrite the actual settings
MissedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxModsPerPeptideTextBox.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
MaxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
InitiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
MaxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
MinVariantDepthTextBox.Text = task.CommonParameters.MinVariantDepth.ToString(CultureInfo.InvariantCulture);
MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
ProductMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
ProductMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
PrecursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
PrecursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
writeIndexMzmlCheckbox.IsChecked = task.CalibrationParameters.WriteIndexedMzml;
//writeIntermediateFilesCheckBox.IsChecked = task.CalibrationParameters.WriteIntermediateFiles;
MinScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var heh in LocalizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(XLSearchTask task)
{
//Crosslink search para
//RbSearchCrosslink.IsChecked = !task.XlSearchParameters.SearchGlyco;
//RbSearchGlyco.IsChecked = task.XlSearchParameters.SearchGlyco;
cbCrosslinkers.SelectedItem = task.XlSearchParameters.Crosslinker;
ckbXLTopNum.IsChecked = task.XlSearchParameters.RestrictToTopNHits;
txtXLTopNum.Text = task.XlSearchParameters.CrosslinkSearchTopNum.ToString(CultureInfo.InvariantCulture);
ckbCrosslinkAtCleavageSite.IsChecked = task.XlSearchParameters.CrosslinkAtCleavageSite;
ckbQuenchH2O.IsChecked = task.XlSearchParameters.XlQuench_H2O;
ckbQuenchNH2.IsChecked = task.XlSearchParameters.XlQuench_NH2;
ckbQuenchTris.IsChecked = task.XlSearchParameters.XlQuench_Tris;
cbbXLprecusorMsTl.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
XLPrecusorMsTlTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
TopNPeaksTextBox.Text = task.CommonParameters.NumberOfPeaksToKeepPerWindow == int.MaxValue || !task.CommonParameters.NumberOfPeaksToKeepPerWindow.HasValue ? "" : task.CommonParameters.NumberOfPeaksToKeepPerWindow.Value.ToString(CultureInfo.InvariantCulture);
MinRatioTextBox.Text = task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak == double.MaxValue || !task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.HasValue ? "" : task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.Value.ToString(CultureInfo.InvariantCulture);
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
if (task.CommonParameters.ChildScanDissociationType != DissociationType.Unknown)
{
ChildScanDissociationTypeComboBox.SelectedItem = task.CommonParameters.ChildScanDissociationType.ToString();
}
checkBoxDecoy.IsChecked = task.XlSearchParameters.DecoyType != DecoyType.None;
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
numberOfDatabaseSearchesTextBox.Text = task.CommonParameters.TotalPartitions.ToString(CultureInfo.InvariantCulture);
maxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
ckbPercolator.IsChecked = task.XlSearchParameters.WriteOutputForPercolator;
ckbPepXML.IsChecked = task.XlSearchParameters.WritePepXml;
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(SearchTask task)
{
classicSearchRadioButton.IsChecked = task.SearchParameters.SearchType == SearchType.Classic;
modernSearchRadioButton.IsChecked = task.SearchParameters.SearchType == SearchType.Modern;
nonSpecificSearchRadioButton.IsChecked = task.SearchParameters.SearchType == SearchType.NonSpecific;
txtMaxFragmentSize.Text = task.SearchParameters.MaxFragmentSize.ToString(CultureInfo.InvariantCulture);
checkBoxParsimony.IsChecked = task.SearchParameters.DoParsimony;
checkBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
checkBoxQuantification.IsChecked = task.SearchParameters.DoQuantification;
quantPpmTolerance.Text = task.SearchParameters.QuantifyPpmTol.ToString(CultureInfo.InvariantCulture);
checkBoxMatchBetweenRuns.IsChecked = task.SearchParameters.MatchBetweenRuns;
modPepsAreUnique.IsChecked = task.SearchParameters.ModPeptidesAreDifferent;
checkBoxHistogramAnalysis.IsChecked = task.SearchParameters.DoHistogramAnalysis;
histogramBinWidthTextBox.Text = task.SearchParameters.HistogramBinTolInDaltons.ToString(CultureInfo.InvariantCulture);
checkBoxTarget.IsChecked = task.SearchParameters.SearchTarget;
checkBoxDecoy.IsChecked = task.SearchParameters.DecoyType != DecoyType.None;
radioButtonReverseDecoy.IsChecked = task.SearchParameters.DecoyType == DecoyType.Reverse;
radioButtonSlideDecoy.IsChecked = task.SearchParameters.DecoyType == DecoyType.Slide;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
txtMinPeptideLength.Text = task.CommonParameters.DigestionParams.MinPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MinPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
txtMaxPeptideLength.Text = task.CommonParameters.DigestionParams.MaxPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MaxPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
txtMaxModNum.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
precursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
precursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
addCompIonCheckBox.IsChecked = task.SearchParameters.AddCompIons;
bCheckBox.IsChecked = task.CommonParameters.BIons;
yCheckBox.IsChecked = task.CommonParameters.YIons;
cCheckBox.IsChecked = task.CommonParameters.CIons;
zdotCheckBox.IsChecked = task.CommonParameters.ZdotIons;
//conserveMemoryCheckBox.IsChecked = task.CommonParameters.ConserveMemory;
numberOfDatabaseSearchesTextBox.Text = task.CommonParameters.TotalPartitions.ToString(CultureInfo.InvariantCulture);
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
//maxDegreesOfParallelism.Text = task.CommonParameters.MaxParallelFilesToAnalyze.ToString();
//disposeOfFilesWhenDone.IsChecked = task.SearchParameters.DisposeOfFileWhenDone;
allAmbiguity.IsChecked = task.CommonParameters.ReportAllAmbiguity;
//DeconvolutionIntensityRatioTextBox.Text = task.CommonParameters.DeconvolutionIntensityRatio.ToString();
DeconvolutionMaxAssumedChargeStateTextBox.Text = task.CommonParameters.DeconvolutionMaxAssumedChargeState.ToString();
//DeconvolutionMassToleranceInPpmTextBox.Text = task.CommonParameters.DeconvolutionMassTolerance.Value.ToString();
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
eValueCheckBox.IsChecked = task.CommonParameters.CalculateEValue;
//trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
//trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
//TopNPeaksCheckBox.Text = task.CommonParameters.TopNpeaks.HasValue ? task.CommonParameters.TopNpeaks.Value.ToString(CultureInfo.InvariantCulture) : "";
//MinRatioCheckBox.Text = task.CommonParameters.MinRatio.HasValue ? task.CommonParameters.MinRatio.Value.ToString(CultureInfo.InvariantCulture) : "";
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = fixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
fixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = variableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
variableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
//localizeAllCheckBox.IsChecked = task.CommonParameters.LocalizeAll;
if (task.CommonParameters.LocalizeAll)
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
}
else
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
if (task.CommonParameters.ListOfModTypesLocalize.Contains(heh.DisplayName))
{
heh.Use = true;
}
else
{
heh.Use = false;
}
}
}
foreach (var ye in variableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in fixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
mdacExact.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Exact;
mdac1mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.OneMM;
mdac2mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.TwoMM;
mdac3mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ThreeMM;
mdac187.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ModOpen;
mdacOpen.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Open;
mdacCustom.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Custom;
if (task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Custom)
{
customkMdacTextBox.Text = task.SearchParameters.CustomMdac;
}
writePrunedDBCheckBox.IsChecked = task.SearchParameters.WritePrunedDatabase;
UpdateModSelectionGrid();
}
private void ProteaseSpecificUpdate(object sender, SelectionChangedEventArgs e)
{
string proteaseName = ((Protease)ProteaseComboBox.SelectedItem).Name;
MissedCleavagesTextBox.IsEnabled = !proteaseName.Equals("top-down");
if (AutomaticallyAskAndOrUpdateParametersBasedOnProtease)
{
switch (proteaseName)
{
case "non-specific":
if (UpdateGUISettings.UseNonSpecificRecommendedSettings())
{
MaxPeptideLengthTextBox.Text = "25";
}
break;
case "top-down":
if (UpdateGUISettings.UseTopDownRecommendedSettings())
{
UseProvidedPrecursor.IsChecked = false;
DeconvolutionMaxAssumedChargeStateTextBox.Text = "60";
TrimMsMs.IsChecked = false;
//uncheck all variable mods
foreach (var mod in VariableModTypeForTreeViewObservableCollection)
{
mod.Use = false;
}
//clear GPTMD mods and replace them with a subset
foreach (var mod in GptmdModTypeForTreeViewObservableCollection)
{
mod.Use = false;
}
//populate the recommended mods
foreach (var mod in UpdateGUISettings.TopDownModsForGPTMD)
{
ModTypeForTreeView theModType = GptmdModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
}
}
}
break;
case "Arg-C":
if (UpdateGUISettings.UseArgCRecommendedSettings())
{
ProteaseComboBox.SelectedItem = ProteaseDictionary.Dictionary["trypsin"];
}
break;
case "chymotrypsin (don't cleave before proline)":
case "chymotrypsin (cleave before proline)":
{
if (UpdateGUISettings.UseChymotrypsinRecommendedSettings())
{
MissedCleavagesTextBox.Text = "3";
}
}
break;
case "elastase":
{
if (UpdateGUISettings.UseElastaseRecommendedSettings())
{
MissedCleavagesTextBox.Text = "16";
}
}
break;
//nothing to change for semi-trypsin
default:
break;
}
}
}
private void UpdateFieldsFromTask(SearchTask task)
{
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.SpecificProtease; //needs to be first, so nonspecific can override if necessary
classicSearchRadioButton.IsChecked = task.SearchParameters.SearchType == SearchType.Classic;
modernSearchRadioButton.IsChecked = task.SearchParameters.SearchType == SearchType.Modern;
//do these in if statements so as not to trigger the change
if (task.SearchParameters.SearchType == SearchType.NonSpecific && task.CommonParameters.DigestionParams.SearchModeType == CleavageSpecificity.None)
{
nonSpecificSearchRadioButton.IsChecked = true; //when this is changed it overrides the protease
if (task.CommonParameters.DigestionParams.SpecificProtease.Name.Equals("singleC") || task.CommonParameters.DigestionParams.SpecificProtease.Name.Equals("singleN"))
{
Protease nonspecific = ProteaseDictionary.Dictionary["non-specific"];
proteaseComboBox.SelectedItem = nonspecific;
}
else
{
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.SpecificProtease;
}
}
if (task.SearchParameters.SearchType == SearchType.NonSpecific && task.CommonParameters.DigestionParams.SearchModeType != CleavageSpecificity.None)
{
semiSpecificSearchRadioButton.IsChecked = true;
}
checkBoxParsimony.IsChecked = task.SearchParameters.DoParsimony;
checkBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
checkBoxNoQuant.IsChecked = !task.SearchParameters.DoQuantification;
checkBoxLFQ.IsChecked = task.SearchParameters.DoQuantification;
if (task.SearchParameters.SilacLabels != null && task.SearchParameters.SilacLabels.Count != 0)
{
checkBoxSILAC.IsChecked = true;
List <Proteomics.SilacLabel> labels = task.SearchParameters.SilacLabels;
foreach (Proteomics.SilacLabel label in labels)
{
SilacInfoForDataGrid infoToAdd = new SilacInfoForDataGrid(label);
if (label.AdditionalLabels != null)
{
foreach (Proteomics.SilacLabel additionalLabel in label.AdditionalLabels)
{
infoToAdd.AddAdditionalLabel(new SilacInfoForDataGrid(additionalLabel));
}
}
StaticSilacLabelsObservableCollection.Add(infoToAdd);
}
}
CheckBoxQuantifyUnlabeledForSilac.IsChecked = task.CommonParameters.DigestionParams.GeneratehUnlabeledProteinsForSilac;
peakFindingToleranceTextBox.Text = task.SearchParameters.QuantifyPpmTol.ToString(CultureInfo.InvariantCulture);
checkBoxMatchBetweenRuns.IsChecked = task.SearchParameters.MatchBetweenRuns;
checkBoxNormalize.IsChecked = task.SearchParameters.Normalize;
modPepsAreUnique.IsChecked = task.SearchParameters.ModPeptidesAreDifferent;
checkBoxHistogramAnalysis.IsChecked = task.SearchParameters.DoHistogramAnalysis;
histogramBinWidthTextBox.Text = task.SearchParameters.HistogramBinTolInDaltons.ToString(CultureInfo.InvariantCulture);
checkBoxTarget.IsChecked = task.SearchParameters.SearchTarget;
checkBoxDecoy.IsChecked = task.SearchParameters.DecoyType != DecoyType.None;
radioButtonReverseDecoy.IsChecked = task.SearchParameters.DecoyType == DecoyType.Reverse;
radioButtonSlideDecoy.IsChecked = task.SearchParameters.DecoyType == DecoyType.Slide;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxFragmentMassTextBox.Text = task.SearchParameters.MaxFragmentSize.ToString(CultureInfo.InvariantCulture); //put after max peptide length to allow for override of auto
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
MaxModNumTextBox.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
dissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
nTerminalIons.IsChecked = task.CommonParameters.DigestionParams.FragmentationTerminus == FragmentationTerminus.Both || task.CommonParameters.DigestionParams.FragmentationTerminus == FragmentationTerminus.N;
cTerminalIons.IsChecked = task.CommonParameters.DigestionParams.FragmentationTerminus == FragmentationTerminus.Both || task.CommonParameters.DigestionParams.FragmentationTerminus == FragmentationTerminus.C;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
precursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
precursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
addCompIonCheckBox.IsChecked = task.CommonParameters.AddCompIons;
numberOfDatabaseSearchesTextBox.Text = task.CommonParameters.TotalPartitions.ToString(CultureInfo.InvariantCulture);
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
allAmbiguity.IsChecked = task.CommonParameters.ReportAllAmbiguity;
DeconvolutionMaxAssumedChargeStateTextBox.Text = task.CommonParameters.DeconvolutionMaxAssumedChargeState.ToString();
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
deltaScoreCheckBox.IsChecked = task.CommonParameters.UseDeltaScore;
trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
NumberOfPeaksToKeepPerWindowTextBox.Text = task.CommonParameters.NumberOfPeaksToKeepPerWindow == int.MaxValue || !task.CommonParameters.NumberOfPeaksToKeepPerWindow.HasValue ? "" : task.CommonParameters.NumberOfPeaksToKeepPerWindow.Value.ToString(CultureInfo.InvariantCulture);
MinimumAllowedIntensityRatioToBasePeakTexBox.Text = task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak == double.MaxValue || !task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.HasValue ? "" : task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.Value.ToString(CultureInfo.InvariantCulture);
WindowWidthThomsonsTextBox.Text = task.CommonParameters.WindowWidthThomsons == double.MaxValue || !task.CommonParameters.WindowWidthThomsons.HasValue ? "" : task.CommonParameters.WindowWidthThomsons.Value.ToString(CultureInfo.InvariantCulture);
NumberOfWindowsTextBox.Text = task.CommonParameters.NumberOfWindows == int.MaxValue || !task.CommonParameters.NumberOfWindows.HasValue ? "" : task.CommonParameters.NumberOfWindows.Value.ToString(CultureInfo.InvariantCulture);
normalizePeaksInWindowCheckBox.IsChecked = task.CommonParameters.NormalizePeaksAccrossAllWindows;
maxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
MinVariantDepthTextBox.Text = task.CommonParameters.MinVariantDepth.ToString(CultureInfo.InvariantCulture);
MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
if (task.CommonParameters.QValueOutputFilter < 1)
{
QValueTextBox.Text = task.CommonParameters.QValueOutputFilter.ToString(CultureInfo.InvariantCulture);
QValueCheckBox.IsChecked = true;
}
else
{
QValueTextBox.Text = "0.01";
QValueCheckBox.IsChecked = false;
}
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
ckbMzId.IsChecked = task.SearchParameters.WriteMzId;
writeDecoyCheckBox.IsChecked = task.SearchParameters.WriteDecoys;
writeContaminantCheckBox.IsChecked = task.SearchParameters.WriteContaminants;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var heh in LocalizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
massDiffAcceptExact.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Exact;
massDiffAccept1mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.OneMM;
massDiffAccept2mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.TwoMM;
massDiffAccept3mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ThreeMM;
massDiffAccept187.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ModOpen;
massDiffAcceptOpen.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Open;
massDiffAcceptCustom.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Custom;
if (task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Custom)
{
customkMdacTextBox.Text = task.SearchParameters.CustomMdac;
}
writePrunedDBCheckBox.IsChecked = task.SearchParameters.WritePrunedDatabase;
UpdateModSelectionGrid();
}
private void UpdateFieldsFromTask(XLSearchTask task)
{
//Crosslink search para
cbCrosslinker.SelectedIndex = (int)task.XlSearchParameters.CrosslinkerType;
//cbFragmentation.SelectedIndex = (int)task.XlSearchParameters.FragmentationType;
ckbXLTopNum.IsChecked = task.XlSearchParameters.CrosslinkSearchTop;
txtXLTopNum.Text = task.XlSearchParameters.CrosslinkSearchTopNum.ToString(CultureInfo.InvariantCulture);
ckbQuenchH2O.IsChecked = task.XlSearchParameters.XlQuench_H2O;
ckbQuenchNH2.IsChecked = task.XlSearchParameters.XlQuench_NH2;
ckbQuenchTris.IsChecked = task.XlSearchParameters.XlQuench_Tris;
//ckbSearchWithXLAllBeta.IsChecked = task.XlSearchParameters.CrosslinkSearchWithAllBeta;
txtUdXLKerName.Text = task.XlSearchParameters.UdXLkerName;
ckbUdXLkerCleavable.IsChecked = task.XlSearchParameters.UdXLkerCleavable;
txtUdXLkerTotalMs.Text = task.XlSearchParameters.UdXLkerTotalMass.HasValue ? task.XlSearchParameters.UdXLkerTotalMass.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerShortMass.Text = task.XlSearchParameters.UdXLkerShortMass.HasValue ? task.XlSearchParameters.UdXLkerShortMass.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerLongMass.Text = task.XlSearchParameters.UdXLkerLongMass.HasValue ? task.XlSearchParameters.UdXLkerLongMass.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerLoopMass.Text = task.XlSearchParameters.UdXLkerLoopMass.HasValue ? task.XlSearchParameters.UdXLkerLoopMass.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerAminoAcid.Text = task.XlSearchParameters.UdXLkerResidue.ToString();
txtUdXLkerDeadendH2O.Text = task.XlSearchParameters.UdXLkerDeadendMassH2O.HasValue ? task.XlSearchParameters.UdXLkerDeadendMassH2O.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerDeadendNH2.Text = task.XlSearchParameters.UdXLkerDeadendMassNH2.HasValue ? task.XlSearchParameters.UdXLkerDeadendMassNH2.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerDeadendTris.Text = task.XlSearchParameters.UdXLkerDeadendMassTris.HasValue ? task.XlSearchParameters.UdXLkerDeadendMassTris.Value.ToString(CultureInfo.InvariantCulture) : "";
cbbXLprecusorMsTl.SelectedIndex = task.XlSearchParameters.XlPrecusorMsTl is AbsoluteTolerance ? 0 : 1;
txtXLPrecusorMsTl.Text = task.XlSearchParameters.XlPrecusorMsTl.Value.ToString(CultureInfo.InvariantCulture);
//cbbXLBetaprecusorMsTl.SelectedIndex = task.XlSearchParameters.XlPrecusorMsTl is AbsoluteTolerance ? 0 : 1;
//txtXLBetaPrecusorMsTl.Text = task.XlSearchParameters.XlPrecusorMsTl.Value.ToString(CultureInfo.InvariantCulture);
trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
TopNPeaksCheckBox.Text = task.CommonParameters.TopNpeaks.HasValue ? task.CommonParameters.TopNpeaks.Value.ToString(CultureInfo.InvariantCulture) : "";
MinRatioCheckBox.Text = task.CommonParameters.MinRatio.HasValue ? task.CommonParameters.MinRatio.Value.ToString(CultureInfo.InvariantCulture) : "";
ckbCharge_2_3.IsChecked = task.XlSearchParameters.XlCharge_2_3;
ckbCharge_2_3_PrimeFragments.IsChecked = task.XlSearchParameters.XlCharge_2_3_PrimeFragment;
checkBoxDecoy.IsChecked = task.XlSearchParameters.DecoyType != DecoyType.None;
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
txtMinPeptideLength.Text = task.CommonParameters.DigestionParams.MinPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MinPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
txtMaxPeptideLength.Text = task.CommonParameters.DigestionParams.MaxPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MaxPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
bCheckBox.IsChecked = task.CommonParameters.BIons;
yCheckBox.IsChecked = task.CommonParameters.YIons;
cCheckBox.IsChecked = task.CommonParameters.CIons;
zdotCheckBox.IsChecked = task.CommonParameters.ZdotIons;
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
ckbAllResults.IsChecked = task.XlSearchParameters.XlOutAll;
ckbPercolator.IsChecked = task.XlSearchParameters.XlOutPercolator;
ckbCrosslink.IsChecked = task.XlSearchParameters.XlOutCrosslink;
ckbPepXML.IsChecked = task.XlSearchParameters.XlOutPepXML;
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = fixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
fixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = variableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
variableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
localizeAllCheckBox.IsChecked = task.CommonParameters.LocalizeAll;
if (task.CommonParameters.LocalizeAll)
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
}
else
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
if (task.CommonParameters.ListOfModTypesLocalize.Contains(heh.DisplayName))
{
heh.Use = true;
}
else
{
heh.Use = false;
}
}
}
foreach (var ye in variableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in fixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
