IsoDec incorporation

MetaMorpheus/EngineLayer/CommonParameters.cs

@@ -139,8 +139,8 @@ public int DeconvolutionMaxAssumedChargeState
             get => PrecursorDeconvolutionParameters.MaxAssumedChargeState;
             private set => PrecursorDeconvolutionParameters.MaxAssumedChargeState = value;
         }
-        [TomlIgnore] public DeconvolutionParameters PrecursorDeconvolutionParameters { get; private set; }
-        [TomlIgnore] public DeconvolutionParameters ProductDeconvolutionParameters { get; private set; }
+        public DeconvolutionParameters PrecursorDeconvolutionParameters { get; private set; }
+        public DeconvolutionParameters ProductDeconvolutionParameters { get; private set; }
         [TomlIgnore] public Tolerance DeconvolutionMassTolerance { get; private set; }
         public int TotalPartitions { get; set; }
         public Tolerance ProductMassTolerance { get; set; } // public setter required for calibration task

MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs

@@ -263,7 +263,9 @@ private void ProteaseSpecificUpdate(object sender, SelectionChangedEventArgs e)
                         if (UpdateGUISettings.UseTopDownRecommendedSettings())
                         {
                             DeconHostViewModel.UseProvidedPrecursors = false;
-                            DeconHostViewModel.PrecursorDeconvolutionParameters.MaxAssumedChargeState = 60;
+                            DeconHostViewModel.DoPrecursorDeconvolution = true;
+                            DeconHostViewModel.SetAllPrecursorMaxChargeState(60);
+                            DeconHostViewModel.SetAllProductMaxChargeState(20);
                             TrimMsMs.IsChecked = false;
                             //uncheck all variable mods
                             foreach (var mod in VariableModTypeForTreeViewObservableCollection)

MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs

@@ -299,6 +299,7 @@ private void UpdateFieldsFromTask(SearchTask task)
             DeconHostViewModel = new DeconHostViewModel(TheTask.CommonParameters.PrecursorDeconvolutionParameters,
                 TheTask.CommonParameters.ProductDeconvolutionParameters,
                 TheTask.CommonParameters.UseProvidedPrecursorInfo, TheTask.CommonParameters.DoPrecursorDeconvolution);
+            DeisotopingControl.DataContext = DeconHostViewModel;
 
             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);
@@ -428,7 +429,6 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             CleavageSpecificity searchModeType = GetSearchModeType(); //change search type to semi or non if selected
             SnesUpdates(searchModeType); //decide on singleN/C, make comp ion changes
 
-            // TODO: Reconcile Isodec params with Mass difference acceptor
             if (!GlobalGuiSettings.CheckTaskSettingsValidity(
                 PrecursorMassToleranceTextBox.Text, 
                 ProductMassToleranceTextBox.Text, 
@@ -892,7 +892,9 @@ private void ProteaseSpecificUpdate(object sender, SelectionChangedEventArgs e)
                         if (UpdateGUISettings.UseTopDownRecommendedSettings())
                         {
                             DeconHostViewModel.DoPrecursorDeconvolution = true;
-                            DeconHostViewModel.PrecursorDeconvolutionParameters.MaxAssumedChargeState = 60;
+                            DeconHostViewModel.UseProvidedPrecursors = false;
+                            DeconHostViewModel.SetAllPrecursorMaxChargeState(60);
+                            DeconHostViewModel.SetAllProductMaxChargeState(20);
                             TrimMsMs.IsChecked = false;
                             CheckBoxNoQuant.IsChecked = true;
                             MassDiffAccept3mm.IsChecked = true;

MetaMorpheus/GUI/Util/Converters/DeconvolutionTypeToControlConverter.cs

@@ -29,6 +29,8 @@ public override object Convert(object value, Type targetType, object parameter,
             {
                 case DeconvolutionType.ClassicDeconvolution:
                     return new ClassicDeconParamsControl() { DataContext = value as ClassicDeconParamsViewModel };
+                case DeconvolutionType.IsoDecDeconvolution:
+                    return new IsoDecDeconParamControl() { DataContext = value as IsoDecDeconParamsViewModel };
 
                 case DeconvolutionType.ExampleNewDeconvolutionTemplate:
                 default:

MetaMorpheus/GUI/Views/Deconvolution/HostDeconParamControl.xaml

@@ -25,7 +25,7 @@
         </Style>
     </UserControl.Resources>
 
-    <GroupBox Header="Deisotoping" > 
+    <GroupBox Header="MS1 Deconvolution" > 
         <Grid d:DataContext="{x:Static guiFunctions:DeconHostModel.Instance}">
 
             <Grid.RowDefinitions>
@@ -66,7 +66,7 @@
                     </StackPanel>
 
                     <!-- Deconvolute precursors -->
-                    <StackPanel Orientation="Horizontal" Margin="10,5,5,5">
+                    <StackPanel Orientation="Horizontal" Margin="10,10,5,5">
                         <CheckBox x:Name="DeconvolutePrecursors" Content="Deconvolute Precursors"
                                   IsChecked="{Binding DoPrecursorDeconvolution}" ToolTipService.ShowDuration="999999"
                                   ToolTipService.InitialShowDelay="500">
@@ -79,13 +79,13 @@
                     </StackPanel>
                 </StackPanel>
 
-                <!-- Decon Type ComboBox -->
-                <ComboBox Grid.Column="1" x:Name="DeconvolutionTypeComboBox" Width="140" Height="35"
+                <!-- Precursor Decon Type ComboBox -->
+                <ComboBox Grid.Column="1" x:Name="DeconvolutionTypeComboBox" Width="100" Height="35"
                           VerticalContentAlignment="Center" HorizontalContentAlignment="Center"
                           ItemsSource="{Binding PrecursorDeconvolutionParametersList}"
                           SelectedItem="{Binding PrecursorDeconvolutionParameters}"
-                          ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"
-                          Visibility="{Binding DisplayDeconSelectionComboBox, Converter={StaticResource BooleanToVisibilityConverter}}">
+                          Visibility="{Binding DisplayDeconSelectionComboBox, Converter={StaticResource BooleanToVisibilityConverter}}"
+                          ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
                     <ComboBox.ToolTip>
                         <TextBlock>
                             The type of deconvolution to perform.
@@ -95,18 +95,34 @@
             </Grid>
 
             <!-- Specific Precursor Parameters -->
-            <ItemsControl Grid.Row="1" Margin="5"
-                          ItemsSource="{Binding PrecursorDeconvolutionParametersList}">
-                <ItemsControl.ItemTemplate>
-                    <DataTemplate>
-                        <ContentControl
-                            Content="{
-                        Binding RelativeSource={RelativeSource AncestorType=Grid, Mode=FindAncestor}, 
-                        Path=DataContext.PrecursorDeconvolutionParameters,
+            <ContentControl Grid.Row="1" Margin="5" Content="{
+                        Binding PrecursorDeconvolutionParameters,
                         Converter={StaticResource DeconTypeToControlConverter }}" />
-                    </DataTemplate>
-                </ItemsControl.ItemTemplate>
-            </ItemsControl>
+
+            <!-- Specific Product Parameters -->
+            <Expander Grid.Row="2" Header="MS2 Deconvolution" >
+                <Border BorderBrush="{StaticResource BorderColor}" BorderThickness="1" CornerRadius="10">
+                    <StackPanel>
+                        <ComboBox  x:Name="ProductDeconvolutionTypeComboBox" Width="100" Height="35" Margin="5 5 5 -5"
+                                   VerticalContentAlignment="Center" HorizontalContentAlignment="Center" HorizontalAlignment="Right"
+                                   ItemsSource="{Binding ProductDeconvolutionParametersList}"
+                                   SelectedItem="{Binding ProductDeconvolutionParameters}"
+                                   Visibility="{Binding DisplayDeconSelectionComboBox, Converter={StaticResource BooleanToVisibilityConverter}}"
+                                   ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" >
+                            <ComboBox.ToolTip>
+                                <TextBlock>
+                                    The type of deconvolution to perform.
+                                </TextBlock>
+                            </ComboBox.ToolTip>
+                        </ComboBox>
+
+                        <ContentControl Margin="5"  Content="{
+                        Binding ProductDeconvolutionParameters,
+                        Converter={StaticResource DeconTypeToControlConverter }}" />
+                    </StackPanel>
+
+                </Border>
+            </Expander>
         </Grid>
     </GroupBox>
 </UserControl>