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(); } }