Added Decon Parameters to Calibration Window (#2459)

* Added decon choice to calibration * Add DetermineAnalyteType call in UpdateFieldsFromTask Added MetaMorpheusTask.DetermineAnalyteType(TheTask.CommonParameters) at the beginning of the UpdateFieldsFromTask method in task windows. This ensures analyte type is determined before updating fields from the task. * Refactor charge state settings in CalibrateTaskWindow Replaced method calls for setting max charge states with direct assignment to PrecursorDeconvolutionParameters.MaxAssumedChargeState. This change simplifies the configuration of deconvolution parameters. * Removed Peak Filtering from calibration * oof
smith-chem-wisc · Feb 3, 2025 · b48a3f6 · b48a3f6
1 parent e6cf8e7
commit b48a3f6
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Showing 6 changed files with 35 additions and 4 deletions.
diff --git a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml
@@ -45,6 +45,13 @@
                         </TextBox.Style>
                     </TextBox>
                 </StackPanel>
+                <GroupBox Header="File Loading Parameters" DockPanel.Dock="Top">
+                    <Expander x:Name="FileLoadExpander" >
+                        <StackPanel>
+                            <local:HostDeconParamControl x:Name="DeisotopingControl" DataContext="{Binding}"/>
+                        </StackPanel>
+                    </Expander>
+                </GroupBox>
                 <GroupBox Header="Search Parameters" DockPanel.Dock="Top">
                     <Expander x:Name="SearchModeExpander">
                         <StackPanel>

diff --git a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
@@ -28,6 +28,7 @@ public partial class CalibrateTaskWindow : Window
         private readonly ObservableCollection<ModTypeForLoc> LocalizeModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForLoc>();
         private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
         private CustomFragmentationWindow CustomFragmentationWindow;
+        private DeconHostViewModel DeconHostViewModel;
 
         public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
         {
@@ -38,6 +39,7 @@ public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
             PopulateChoices();
             UpdateFieldsFromTask(TheTask);
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
+            DeisotopingControl.DataContext = DeconHostViewModel;
 
             if (myCalibrateTask == null)
             {
@@ -51,6 +53,10 @@ public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
 
         private void UpdateFieldsFromTask(CalibrationTask task)
         {
+            MetaMorpheusTask.DetermineAnalyteType(TheTask.CommonParameters);
+            DeconHostViewModel = new DeconHostViewModel(TheTask.CommonParameters.PrecursorDeconvolutionParameters,
+                TheTask.CommonParameters.ProductDeconvolutionParameters,
+                TheTask.CommonParameters.UseProvidedPrecursorInfo, TheTask.CommonParameters.DoPrecursorDeconvolution);
             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);
@@ -255,6 +261,10 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             }
 
             bool parseMaxThreadsPerFile = int.Parse(MaxThreadsTextBox.Text, CultureInfo.InvariantCulture) <= Environment.ProcessorCount && int.Parse(MaxThreadsTextBox.Text, CultureInfo.InvariantCulture) > 0;
+            DeconvolutionParameters precursorDeconvolutionParameters = DeconHostViewModel.PrecursorDeconvolutionParameters.Parameters;
+            DeconvolutionParameters productDeconvolutionParameters = DeconHostViewModel.ProductDeconvolutionParameters.Parameters;
+            bool useProvidedPrecursorInfo = DeconHostViewModel.UseProvidedPrecursors;
+            bool doPrecursorDeconvolution = DeconHostViewModel.DoPrecursorDeconvolution;
 
             //the below parameters are optimized for top-down but do not exist in the GUI as of Nov. 13, 2019
             if (((Protease)ProteaseComboBox.SelectedItem).Name.Contains("top-down"))
@@ -272,9 +282,11 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
                     assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
                     minVariantDepth: minVariantDepth,
                     maxHeterozygousVariants: maxHeterozygousVariants,
-                    useProvidedPrecursorInfo: false, //Updated
-                    deconvolutionMaxAssumedChargeState: 60, //Updated
-                    trimMsMsPeaks: false); //Updated
+                    trimMsMsPeaks: false,
+                    doPrecursorDeconvolution: doPrecursorDeconvolution,
+                    precursorDeconParams: precursorDeconvolutionParameters,
+                    productDeconParams: productDeconvolutionParameters,
+                    useProvidedPrecursorInfo: useProvidedPrecursorInfo); 
                 TheTask.CommonParameters = commonParamsToSave;
             }
             else //bottom-up
@@ -291,7 +303,11 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
                     precursorMassTolerance: precursorMassTolerance,
                     assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
                     minVariantDepth: minVariantDepth,
-                    maxHeterozygousVariants: maxHeterozygousVariants);
+                    maxHeterozygousVariants: maxHeterozygousVariants,
+                    useProvidedPrecursorInfo: useProvidedPrecursorInfo,
+                    doPrecursorDeconvolution: doPrecursorDeconvolution,
+                    precursorDeconParams: precursorDeconvolutionParameters,
+                    productDeconParams: productDeconvolutionParameters);
                 TheTask.CommonParameters = commonParamsToSave;
             }
 
@@ -381,6 +397,10 @@ private void ProteaseSpecificUpdate(object sender, SelectionChangedEventArgs e)
                         {
                             //many variables are not present in the calibrate task gui, but we modify them when saving
                             //uncheck all variable mods
+                            DeconHostViewModel.UseProvidedPrecursors = false;
+                            DeconHostViewModel.DoPrecursorDeconvolution = true;
+                            DeconHostViewModel.PrecursorDeconvolutionParameters.MaxAssumedChargeState = 60;
+
                             foreach (var mod in VariableModTypeForTreeViewObservableCollection)
                             {
                                 mod.Use = false;

diff --git a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
@@ -64,6 +64,7 @@ private void Row_DoubleClick(object sender, MouseButtonEventArgs e)
 
         private void UpdateFieldsFromTask(GptmdTask task)
         {
+            MetaMorpheusTask.DetermineAnalyteType(TheTask.CommonParameters);
             DeconHostViewModel = new DeconHostViewModel(TheTask.CommonParameters.PrecursorDeconvolutionParameters,
                 TheTask.CommonParameters.ProductDeconvolutionParameters,
                 TheTask.CommonParameters.UseProvidedPrecursorInfo, TheTask.CommonParameters.DoPrecursorDeconvolution);

diff --git a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
@@ -114,6 +114,7 @@ private void PopulateChoices()
 
         private void UpdateFieldsFromTask(GlycoSearchTask task)
         {
+            MetaMorpheusTask.DetermineAnalyteType(TheTask.CommonParameters);
             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;

diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -161,6 +161,7 @@ private void PopulateChoices()
         /// <param name="task"></param>
         private void UpdateFieldsFromTask(SearchTask task)
         {
+            MetaMorpheusTask.DetermineAnalyteType(TheTask.CommonParameters);
             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;

diff --git a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
@@ -121,6 +121,7 @@ private void PopulateChoices()
 
         private void UpdateFieldsFromTask(XLSearchTask task)
         {
+            MetaMorpheusTask.DetermineAnalyteType(TheTask.CommonParameters);
             cbCrosslinkers.SelectedItem = task.XlSearchParameters.Crosslinker;
             txtXLTopNum.Text = task.XlSearchParameters.CrosslinkSearchTopNum.ToString(CultureInfo.InvariantCulture);
             ckbAddCompIon.IsChecked = task.CommonParameters.AddCompIons;