From f8d02b128ea9456716a44ee940f552eefd1bed3a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=B0=E7=8E=AE=20=E7=8E=8B?= <wfw2310165722@outlook.com>
Date: Mon, 17 Apr 2023 13:37:36 -0500
Subject: [PATCH 01/20] Begin implementing GUI save preset settings

---
 GUI/MainWindow.xaml                           |  21 +--
 GUI/TaskWindows/SearchTaskWindow.xaml         |  18 ++
 GUI/TaskWindows/SearchTaskWindow.xaml.cs      |  44 ++++-
 GUI/Views/SaveSettingsWindow.xaml             |  42 +++++
 GUI/Views/SaveSettingsWindow.xaml.cs          |  31 ++++
 GuiFunctions/DelegateCommand.cs               |  64 +++++++
 GuiFunctions/GuiFunctions.csproj              |   1 +
 GuiFunctions/RelayCommand.cs                  |  64 +++++++
 GuiFunctions/TomlFileFolderSerializer.cs      | 143 +++++++++++++++
 .../ViewModels/TaskSettingViewModel.cs        | 169 ++++++++++++++++++
 Test/SaveSettingsTests.cs                     |  81 +++++++++
 11 files changed, 659 insertions(+), 19 deletions(-)
 create mode 100644 GUI/Views/SaveSettingsWindow.xaml
 create mode 100644 GUI/Views/SaveSettingsWindow.xaml.cs
 create mode 100644 GuiFunctions/DelegateCommand.cs
 create mode 100644 GuiFunctions/RelayCommand.cs
 create mode 100644 GuiFunctions/TomlFileFolderSerializer.cs
 create mode 100644 GuiFunctions/ViewModels/TaskSettingViewModel.cs
 create mode 100644 Test/SaveSettingsTests.cs

diff --git a/GUI/MainWindow.xaml b/GUI/MainWindow.xaml
index 64b1998e7..ddd9321c8 100644
--- a/GUI/MainWindow.xaml
+++ b/GUI/MainWindow.xaml
@@ -432,32 +432,33 @@
                         <RowDefinition Height="50"/>
                         <RowDefinition Height="50"/>
                         <RowDefinition Height="25"/>
-                        <RowDefinition Height="1*"/>
+                        <RowDefinition Height="41*"/>
+                        <RowDefinition Height="153*"/>
                     </Grid.RowDefinitions>
 
                     <!--Header label-->
                     <Label Content="Spectra" Grid.Row="0" Style="{StaticResource HeaderLabelStyle}" />
 
                     <!--Detail text-->
-                    <TextBlock Grid.Row="1" Style="{StaticResource TextBlockStyle}">
+                    <TextBlock Grid.Row="1" Style="{StaticResource TextBlockStyle}" Margin="15,0,10,0">
                         Add spectra file(s) in .mzML, .mgf, or Thermo .raw format.
                     </TextBlock>
 
                     <!--Button to add spectra files-->
-                    <Button Name="AddSpectraButton" Grid.Row="2" Content="+ADD SPECTRA" Click="AddSpectraFile_Click" HorizontalAlignment="Right" 
-                            Style="{StaticResource ImportantButtonStyle}" Margin="0,0,10,0"/>
+                    <Button Name="AddSpectraButton" Grid.Row="2" Content="+ADD SPECTRA" Click="AddSpectraFile_Click" HorizontalAlignment="Left" 
+                            Style="{StaticResource ImportantButtonStyle}" Margin="634,0,0,0"/>
 
                     <Button Name="SetFileSpecificSettingsButton" Grid.Row="2" Content="SET FILE-SPECIFIC SETTINGS" Click="SetFileSpecificParameters_Click" 
-                            HorizontalAlignment="Right" Style="{StaticResource ImportantButtonStyle}"
-                        Margin="0,0,211,0"/>
+                            HorizontalAlignment="Left" Style="{StaticResource ImportantButtonStyle}"
+                        Margin="433,0,0,0"/>
 
                     <Button Name="SetExperimentalDesignButton" Grid.Row="2" Content="SET EXPERIMENTAL DESIGN" Click="SetExperimentalDesign_Click" 
-                            HorizontalAlignment="Right" Style="{StaticResource ImportantButtonStyle}"
-                        Margin="0,0,412,0"/>
+                            HorizontalAlignment="Left" Style="{StaticResource ImportantButtonStyle}"
+                        Margin="232,0,0,0"/>
 
                     <!--The list of spectra files-->
                     <DataGrid Name="dataGridSpectraFiles" ItemsSource="{Binding}" Grid.Row="3" Style="{StaticResource x:DataGridStyle}"
-                              ColumnHeaderStyle="{StaticResource DataGridColumnHeaderStyle}" PreviewKeyDown="Window_PreviewKeyDown">
+                              ColumnHeaderStyle="{StaticResource DataGridColumnHeaderStyle}" PreviewKeyDown="Window_PreviewKeyDown" Margin="10,0,10,10" Grid.RowSpan="2">
                         <DataGrid.RowStyle>
                             <Style TargetType="{x:Type DataGridRow}" BasedOn="{StaticResource SpectraFileDataGridItemStyle}" />
                         </DataGrid.RowStyle>
@@ -475,7 +476,7 @@
             </TabItem>
 
             <!--Workflow tab-->
-            <TabItem Name="TasksTab" Header="Tasks" TabIndex="0" Style="{StaticResource TabItemStyle}">
+            <TabItem Name="TasksTab" Header="Tasks" TabIndex="0" Style="{StaticResource TabItemStyle}" Height="35" Margin="0,0,2,0" VerticalAlignment="Bottom">
                 <Grid Style="{StaticResource PageGridStyle}">
                     <Grid.RowDefinitions>
                         <RowDefinition Height="50"/>
diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml b/GUI/TaskWindows/SearchTaskWindow.xaml
index 908587e90..6c9608495 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml
@@ -7,6 +7,7 @@
         xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
         mc:Ignorable="d"
         KeyDown="KeyPressed"
+        d:Height="1500"
         Title="Search Task" Width="750" Height="725" WindowStartupLocation="CenterScreen">
     <Window.Resources>
         <local:BooleanInverter x:Key="InvertedBooleanConverter" />
@@ -79,6 +80,23 @@
                 <!-- BASIC SETTINGS -->
                 <StackPanel DockPanel.Dock="Top" Margin="10">
 
+                    <!-- save settings -->
+                    <StackPanel  x:Name="TaskSettingsCtrl" Height="Auto" DataContext="{Binding TaskSettingsViewModel}"
+                                 Background="{StaticResource BackgroundColor}" Orientation="Horizontal" HorizontalAlignment="Right">
+
+                        <ComboBox Name="TaskSettingsComboBox" Width="200" Height="20" VerticalAlignment="Center" 
+                                  HorizontalAlignment="Left" IsSynchronizedWithCurrentItem="True"
+                                  ItemsSource="{Binding Path=DataContext.AllSettings, ElementName=TaskSettingsCtrl}" 
+                                  SelectedItem="{Binding Path=DataContext.SelectedSettings, ElementName=TaskSettingsCtrl}">
+                        </ComboBox> 
+                        <Button x:Name="Save" Content="Save" FontSize="10" 
+                                Width="60" Margin="5,5,2.5,5" Command="{Binding SaveSettingsCommand}"/>
+                        <Button x:Name="SaveAs" Content="Save as" FontSize="10" 
+                                Width="60" Margin="5,5,2.5,5" Click="SaveAs_Click"/>
+                        <Button x:Name="Delete"  Content="Delete" FontSize="10" Width="60" Margin="5,5,2.5,5"
+                                Command="{Binding DeleteSettingsCommand}"/>
+                    </StackPanel>
+
                     <!-- Search Parameters -->
                     <GroupBox Header="Search Parameters" DockPanel.Dock="Top" >
                         <StackPanel>
diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index 4ef9b71a4..c1d5fcc6a 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -17,6 +17,7 @@
 using TaskLayer;
 using UsefulProteomicsDatabases;
 using GuiFunctions;
+using static System.Net.WebRequestMethods;
 
 namespace MetaMorpheusGUI
 {
@@ -34,6 +35,7 @@ public partial class SearchTaskWindow : Window
         private readonly ObservableCollection<SilacInfoForDataGrid> StaticSilacLabelsObservableCollection = new ObservableCollection<SilacInfoForDataGrid>();
         private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
         private CustomFragmentationWindow CustomFragmentationWindow;
+        public TaskSettingViewModel TaskSettingViewModel { get; set; }
 
         internal SearchTask TheTask { get; private set; }
 
@@ -42,6 +44,9 @@ public SearchTaskWindow(SearchTask task)
             InitializeComponent();
             TheTask = task ?? new SearchTask();
 
+            TaskSettingViewModel = new(TheTask);
+            TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+            
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
             PopulateChoices();
             UpdateFieldsFromTask(TheTask);
@@ -408,6 +413,16 @@ private void CancelButton_Click(object sender, RoutedEventArgs e)
         }
 
         private void SaveButton_Click(object sender, RoutedEventArgs e)
+        {
+            SearchTask task =  GetTaskFromGui();
+            if (task == null)
+                return;
+
+            TheTask = task;
+            DialogResult = true;
+        }
+
+        private SearchTask GetTaskFromGui()
         {
             CleavageSpecificity searchModeType = GetSearchModeType(); //change search type to semi or non if selected
             SnesUpdates(searchModeType); //decide on singleN/C, make comp ion changes
@@ -415,10 +430,10 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecursorMassToleranceTextBox.Text, ProductMassToleranceTextBox.Text, MissedCleavagesTextBox.Text,
                 maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, MaxThreadsTextBox.Text, MinScoreAllowed.Text,
                 PeakFindingToleranceTextBox.Text, HistogramBinWidthTextBox.Text, DeconvolutionMaxAssumedChargeStateTextBox.Text, NumberOfPeaksToKeepPerWindowTextBox.Text,
-                MinimumAllowedIntensityRatioToBasePeakTexBox.Text, WindowWidthThomsonsTextBox.Text, NumberOfWindowsTextBox.Text, NumberOfDatabaseSearchesTextBox.Text, 
+                MinimumAllowedIntensityRatioToBasePeakTexBox.Text, WindowWidthThomsonsTextBox.Text, NumberOfWindowsTextBox.Text, NumberOfDatabaseSearchesTextBox.Text,
                 MaxModNumTextBox.Text, MaxFragmentMassTextBox.Text, QValueTextBox.Text, PepQValueTextBox.Text, InternalIonsCheckBox.IsChecked.Value ? MinInternalFragmentLengthTextBox.Text : null))
             {
-                return;
+                return null;
             }
 
             Protease protease = (Protease)ProteaseComboBox.SelectedItem;
@@ -436,7 +451,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
                 if (silacError.Length != 0)
                 {
                     MessageBox.Show(silacError);
-                    return;
+                    return null;
                 }
             }
             else
@@ -502,7 +517,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
 
             if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
             {
-                return;
+                return null;
             }
 
             bool TrimMs1Peaks = TrimMs1.IsChecked.Value;
@@ -585,7 +600,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             if (TheTask.SearchParameters.SearchType != SearchType.Classic && dissociationType == DissociationType.Autodetect)
             {
                 MessageBox.Show("Autodetection of dissociation type from scan headers is only available for classic search. Please choose a different dissociation type or search mode");
-                return;
+                return null;
             }
 
             TheTask.SearchParameters.MinAllowedInternalFragmentLength = InternalIonsCheckBox.IsChecked.Value ? Convert.ToInt32(MinInternalFragmentLengthTextBox.Text) : 0;
@@ -673,7 +688,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
                 catch (Exception ex)
                 {
                     MessageBox.Show("Could not parse custom mass difference acceptor: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Error);
-                    return;
+                    return null;
                 }
 
                 TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Custom;
@@ -703,7 +718,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
 
                 if (result == MessageBoxResult.Cancel)
                 {
-                    return;
+                    return null;
                 }
             }
 
@@ -715,9 +730,9 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             SetModSelectionForPrunedDB();
 
             TheTask.CommonParameters = commonParamsToSave;
-
-            DialogResult = true;
+            return TheTask;
         }
+        
 
         private void ApmdExpander_Collapsed(object sender, RoutedEventArgs e)
         {
@@ -1311,6 +1326,17 @@ private void InternalIonsCheckBox_Checked(object sender, RoutedEventArgs e)
         {
             MinInternalFragmentLengthTextBox.Text = "4";
         }
+
+        /// <summary>
+        /// Open the SaveSettings Window
+        /// </summary>
+        /// <param name="sender"></param>
+        /// <param name="e"></param>
+        private void SaveAs_Click(object sender, RoutedEventArgs e)
+        {
+            SaveSettingsWindow newWindow = new SaveSettingsWindow(TaskSettingViewModel);
+            newWindow.ShowDialog();
+        }
     }
 
     public class DataContextForSearchTaskWindow : INotifyPropertyChanged
diff --git a/GUI/Views/SaveSettingsWindow.xaml b/GUI/Views/SaveSettingsWindow.xaml
new file mode 100644
index 000000000..6c15733ae
--- /dev/null
+++ b/GUI/Views/SaveSettingsWindow.xaml
@@ -0,0 +1,42 @@
+<Window x:Class="MetaMorpheusGUI.SaveSettingsWindow"
+        xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
+        xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+        xmlns:d="http://schemas.microsoft.com/expression/blend/2008"
+        xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
+        xmlns:local="clr-namespace:MetaMorpheusGUI"
+        xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
+        mc:Ignorable="d"
+        Title="SaveSettingsWindow" Height="350" Width="600">
+    <d:UserControl.DataContext>
+        <guiFunctions:TaskSettingViewModel/>
+    </d:UserControl.DataContext>
+    
+   
+
+    <Grid >
+        <Grid.RowDefinitions>
+            <RowDefinition Height="2*"/>
+            <RowDefinition Height="6*"/>
+            <RowDefinition Height="*"/>
+        </Grid.RowDefinitions>
+
+        <ListBox Grid.Row="1" x:Name="SavedSettingsListBox" IsSynchronizedWithCurrentItem="True"
+                 ItemsSource="{Binding Path=AllSettings}" SelectedItem="{Binding SelectedSettings,Mode=TwoWay}" 
+                 VerticalAlignment="Stretch"  HorizontalAlignment="Stretch" 
+                 Margin="10" FontSize="15" 
+                 d:ItemsSource="{d:SampleData ItemCount=15}">
+        </ListBox>
+
+        <TextBox Grid.Row="0" Text="{Binding TypedSettingsName}" Height="40"
+                 HorizontalAlignment="Stretch"  VerticalAlignment="Top"
+                 Margin="10" FontSize="25" x:Name="NameTextBox">
+        </TextBox>
+
+        <Button x:Name="Delete"  Grid.Row="2" Content="Delete" FontSize="20" Height="30" 
+                Width="200" VerticalAlignment="Center"  HorizontalAlignment="Left"
+                Command="{Binding DeleteSettingsCommand}"/>
+        <Button x:Name="Save" Grid.Row="2" Content="Save" FontSize="20" Height="30" 
+                Width="200" VerticalAlignment="Center" HorizontalAlignment="Right"
+                Command="{Binding SaveSettingsFromWindowCommand}" CommandParameter="{Binding TypedSettingsName}"/>
+    </Grid>
+</Window>
diff --git a/GUI/Views/SaveSettingsWindow.xaml.cs b/GUI/Views/SaveSettingsWindow.xaml.cs
new file mode 100644
index 000000000..649ea6cc2
--- /dev/null
+++ b/GUI/Views/SaveSettingsWindow.xaml.cs
@@ -0,0 +1,31 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using System.Windows;
+using System.Windows.Controls;
+using System.Windows.Data;
+using System.Windows.Documents;
+using System.Windows.Input;
+using System.Windows.Media;
+using System.Windows.Media.Imaging;
+using System.Windows.Shapes;
+using GuiFunctions;
+
+namespace MetaMorpheusGUI
+{
+    /// <summary>
+    /// Interaction logic for SaveSettingsWindow.xaml
+    /// </summary>
+    public partial class SaveSettingsWindow : Window
+    {
+        public SaveSettingsWindow(TaskSettingViewModel viewModel)
+        {
+            InitializeComponent();
+            this.DataContext = viewModel;
+            SavedSettingsListBox.ItemsSource = viewModel.AllSettings;
+            SavedSettingsListBox.SelectedItem = viewModel.SelectedSettings;
+        }
+    }
+}
diff --git a/GuiFunctions/DelegateCommand.cs b/GuiFunctions/DelegateCommand.cs
new file mode 100644
index 000000000..c91e75265
--- /dev/null
+++ b/GuiFunctions/DelegateCommand.cs
@@ -0,0 +1,64 @@
+using System;
+using System.Windows.Input;
+
+namespace GuiFunctions
+{
+    /// <summary>
+    /// A basic command that runs an Action
+    /// </summary>
+    public class DelegateCommand : ICommand
+    {
+        #region Private Members
+
+        /// <summary>
+        /// The action to run
+        /// </summary>
+        private Action<object> mAction;
+
+        #endregion
+
+        #region Public Events
+
+        /// <summary>
+        /// The event thats fired when the <see cref="CanExecute(object)"/> value has changed
+        /// </summary>
+        public event EventHandler CanExecuteChanged = (sender, e) => { };
+
+        #endregion
+
+        #region Constructor
+
+        /// <summary>
+        /// Default constructor
+        /// </summary>
+        public DelegateCommand(Action<object> action)
+        {
+            mAction = action;
+        }
+
+        #endregion
+
+        #region Command Methods
+
+        /// <summary>
+        /// A relay command can always execute
+        /// </summary>
+        /// <param name="parameter"></param>
+        /// <returns></returns>
+        public bool CanExecute(object parameter)
+        {
+            return true;
+        }
+
+        /// <summary>
+        /// Executes the commands Action
+        /// </summary>
+        /// <param name="parameter"></param>
+        public void Execute(object parameter)
+        {
+            mAction(parameter);
+        }
+
+        #endregion
+    }
+}
\ No newline at end of file
diff --git a/GuiFunctions/GuiFunctions.csproj b/GuiFunctions/GuiFunctions.csproj
index 9b9d0d43e..e0a55462a 100644
--- a/GuiFunctions/GuiFunctions.csproj
+++ b/GuiFunctions/GuiFunctions.csproj
@@ -21,6 +21,7 @@
 
   <ItemGroup>
     <ProjectReference Include="..\EngineLayer\EngineLayer.csproj" />
+    <ProjectReference Include="..\TaskLayer\TaskLayer.csproj" />
   </ItemGroup>
 
 </Project>
diff --git a/GuiFunctions/RelayCommand.cs b/GuiFunctions/RelayCommand.cs
new file mode 100644
index 000000000..b7f8488b6
--- /dev/null
+++ b/GuiFunctions/RelayCommand.cs
@@ -0,0 +1,64 @@
+using System;
+using System.Windows.Input;
+
+namespace GuiFunctions
+{
+    /// <summary>
+    /// A basic command that runs an Action
+    /// </summary>
+    public class RelayCommand : ICommand
+    {
+        #region Private Members
+
+        /// <summary>
+        /// The action to run
+        /// </summary>
+        private Action mAction;
+
+        #endregion
+
+        #region Public Events
+
+        /// <summary>
+        /// The event thats fired when the <see cref="CanExecute(object)"/> value has changed
+        /// </summary>
+        public event EventHandler CanExecuteChanged = (sender, e) => { };
+
+        #endregion
+
+        #region Constructor
+
+        /// <summary>
+        /// Default constructor
+        /// </summary>
+        public RelayCommand(Action action)
+        {
+            mAction = action;
+        }
+
+        #endregion
+
+        #region Command Methods
+
+        /// <summary>
+        /// A relay command can always execute
+        /// </summary>
+        /// <param name="parameter"></param>
+        /// <returns></returns>
+        public bool CanExecute(object parameter)
+        {
+            return true;
+        }
+
+        /// <summary>
+        /// Executes the commands Action
+        /// </summary>
+        /// <param name="parameter"></param>
+        public void Execute(object parameter)
+        {
+            mAction();
+        }
+
+        #endregion
+    }
+}
diff --git a/GuiFunctions/TomlFileFolderSerializer.cs b/GuiFunctions/TomlFileFolderSerializer.cs
new file mode 100644
index 000000000..cb62491a1
--- /dev/null
+++ b/GuiFunctions/TomlFileFolderSerializer.cs
@@ -0,0 +1,143 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using System.Diagnostics.CodeAnalysis;
+using System.IO;
+using System.Xml.Linq;
+using Newtonsoft.Json;
+using Proteomics;
+using Nett;
+using TaskLayer;
+
+namespace GuiFunctions
+
+{
+    /// <summary>
+    /// This class is about the implementation of inputs and outputs. 
+    /// </summary>
+    /// 
+    public static class TomlFileFolderSerializer
+    {
+        public static string PathToCheck = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "SettingsDataFiles");
+        /// <summary>
+        /// Create a file that contains the serialized object. 
+        /// </summary>
+        /// <typeparam name="T"></typeparam>
+        /// <param name="path">The path the file will be created</param>
+        /// <param name="objectToSerialize">The object to serialize</param>
+        public static void Serialize<T>(string path, T objectToSerialize)
+        {
+            Toml.WriteFile<T>(objectToSerialize, path, MetaMorpheusTask.tomlConfig);
+        }
+
+        /// <summary>
+        /// Return a json deserialized object
+        /// </summary>
+        /// <typeparam name="T"></typeparam>
+        /// <param name="path">The path of file that will be deserialized</param>
+        /// <returns>The deserialized object</returns>
+        /// <exception cref="ArgumentNullException"></exception>
+        public static T Deserialize<T>(string path)
+        {
+            T toml = Toml.ReadFile<T>(path, MetaMorpheusTask.tomlConfig);
+            return toml;
+        }
+
+        /// <summary>
+        /// Check if the type exist
+        /// </summary>
+        /// <param name="type">The type to check</param>
+        /// <returns>True if it exist, false if it does not</returns>
+        public static bool CheckforTypeFolder(Type type)
+        {
+            string path = Path.Combine(PathToCheck, type.ToString());
+            return Directory.Exists(path);
+        }
+
+        /// <summary>
+        /// Return the path of the folder (type)
+        /// </summary>
+        /// <param name="folder">The type to check</param>
+        /// <param name="name">The name of the type</param>
+        /// <returns></returns>
+        public static string GetFilePath(Type folder, string name)
+        {
+            string txtFilePath = folder.ToString() + "/" + name + ".toml";
+            string path = Path.Combine(PathToCheck, txtFilePath);
+            return path;
+        }
+
+        /// <summary>
+        /// Create the type's folder if it does not exist, save it if it exists. 
+        /// </summary>
+        /// <typeparam name="T"></typeparam>
+        /// <param name="name">name of the object to save</param>
+        /// <param name="o">object to save</param>
+        public static void Save<T>(string name, T o)
+        {
+            if (!CheckforTypeFolder(o.GetType()))
+            {
+                string pathOfFolder = Path.Combine(PathToCheck, o.GetType().ToString());
+                Directory.CreateDirectory(pathOfFolder);
+            }
+            string path = GetFilePath(o.GetType(), name);
+            Serialize<T>(path, o);
+        }
+
+        /// <summary>
+        /// Return an Dictionary of all deserialized file
+        /// </summary>
+        /// <typeparam name="T"></typeparam>
+        /// <param name="folder">The folder to check</param>
+        /// <returns>Dictionary of all deserialized file</returns>
+        public static Dictionary<string, T> LoadAllOfTypeT<T>(T obj)
+        {
+            Dictionary<string, T> dictionary = new Dictionary<string, T>();
+            Type folder = obj.GetType();
+            if (CheckforTypeFolder(folder))
+            {
+                string pathOfFolder = Path.Combine(PathToCheck, folder.ToString());
+                string[] contentsInFolder = Directory.GetFiles(pathOfFolder);
+                foreach (string path in contentsInFolder)
+                {
+                   dictionary.Add(Path.GetFileNameWithoutExtension(path), Deserialize<T>(path));
+                }                
+            }
+            return dictionary;
+        }
+
+
+        /// <summary>
+        /// Delete file
+        /// </summary>
+        /// <typeparam name="T"></typeparam>m 
+        /// <param name="type">type of file to delete</param>
+        /// <param name="name">name of the file</param>
+        public static void Delete(Type type, string name)
+        {
+            if (CheckforTypeFolder(type))
+            {
+                string filePath = GetFilePath(type, name);
+                if (File.Exists(filePath))
+                {
+                    File.Delete(filePath);
+                }
+            }
+        }
+
+        /// <summary>
+        /// Returns the names of each saved object of Type passed
+        /// </summary>
+        /// <param name="type">Type of object to load names for</param>
+        /// <returns></returns>
+        public static string[] LoadAllNamesOfType(Type type)
+        {
+            string path = Path.Combine(PathToCheck, type.ToString());
+            var folders = Directory.GetFiles(path)
+                .Select(p => Path.GetFileNameWithoutExtension(p)).ToArray();
+            return folders;
+        }        
+    }
+}
\ No newline at end of file
diff --git a/GuiFunctions/ViewModels/TaskSettingViewModel.cs b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
new file mode 100644
index 000000000..59606f51e
--- /dev/null
+++ b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
@@ -0,0 +1,169 @@
+using System;
+using System.Collections;
+using System.Collections.Generic;
+using System.Collections.ObjectModel;
+using System.Linq;
+using System.Reflection;
+using System.Text;
+using System.Threading.Tasks;
+using System.Windows;
+using System.Windows.Input;
+using Easy.Common.Extensions;
+using OxyPlot;
+using TaskLayer;
+
+namespace GuiFunctions
+{
+    public class TaskSettingViewModel : BaseViewModel
+    {
+        #region Private Properties
+
+        private string selectedSettings;
+        private string typedSettingsName;
+
+        #endregion
+
+        #region Public Properties
+
+        public ObservableCollection<string> AllSettings;
+        public string SelectedSettings
+        {
+            get { return selectedSettings; }
+            set { selectedSettings = value; OnPropertyChanged(nameof(SelectedSettings)); }
+        }
+
+        public string TypedSettingsName
+        {
+            get { return typedSettingsName; }
+            set { typedSettingsName = value; OnPropertyChanged(nameof(TypedSettingsName)); }
+        }
+
+        public Dictionary<string, MetaMorpheusTask> AllSettingsDict { get; set; }
+
+        //public String AllSettingNames {get; set; }
+
+        public ICommand SaveSettingsCommand { get; set; }
+        public ICommand SaveSettingsFromWindowCommand { get; set; }
+
+        public ICommand DeleteSettingsCommand { get; set; }
+
+        public MetaMorpheusTask TheTask { get; set; }
+
+
+        #endregion
+
+        #region Constructor
+
+        public TaskSettingViewModel(MetaMorpheusTask task)
+        {
+            TheTask = task;
+            var temp = typeof(SearchTask);
+            var type = task.GetType();
+            MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("LoadAllOfTypeT");
+            MethodInfo genericMethod = method.MakeGenericMethod(type);
+            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] {TheTask}));
+
+            var keys = result.Keys.Cast<string>().ToList();
+            var values = result.Values.Cast<MetaMorpheusTask>().ToList();
+            Dictionary<string, MetaMorpheusTask> tempDict = new();
+            for(int i = 0; i < keys.Count; i++)
+            {
+                tempDict.Add(keys[i], values[i]);
+            }
+            AllSettingsDict = tempDict;
+
+            AllSettings = new ObservableCollection<string>(AllSettingsDict.Select(p=>p.Key));
+            SaveSettingsCommand = new RelayCommand(() => SaveSettings());
+            DeleteSettingsCommand = new RelayCommand(() => DeleteSettings());
+            SaveSettingsFromWindowCommand = new DelegateCommand((param) => SaveSettingsFromWindow(param));
+
+        }
+
+        public TaskSettingViewModel()
+        {
+            MetaMorpheusTask task = new SearchTask();
+            TheTask = task;
+            var temp = typeof(SearchTask);
+            var type = task.GetType();
+            MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("LoadAllOfTypeT");
+            MethodInfo genericMethod = method.MakeGenericMethod(type);
+            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] { TheTask }));
+
+            var keys = result.Keys.Cast<string>().ToList();
+            var values = result.Values.Cast<MetaMorpheusTask>().ToList();
+            Dictionary<string, MetaMorpheusTask> tempDict = new();
+            for (int i = 0; i < keys.Count; i++)
+            {
+                tempDict.Add(keys[i], values[i]);
+            }
+            AllSettingsDict = tempDict;
+
+            AllSettings = new ObservableCollection<string>(AllSettingsDict.Select(p => p.Key));
+            SaveSettingsCommand = new RelayCommand(() => SaveSettings());
+            DeleteSettingsCommand = new RelayCommand(() => DeleteSettings());
+            SaveSettingsFromWindowCommand = new DelegateCommand((param) => SaveSettingsFromWindow(param));
+        }
+
+
+            #endregion
+
+            #region Command Methods
+
+        public void SaveSettings()
+        {
+            if (SelectedSettings == null)
+            {
+                return;
+            }
+            AllSettingsDict.Add(SelectedSettings, TheTask);
+            AllSettings.Add(SelectedSettings);
+            OnPropertyChanged(nameof(AllSettingsDict));
+            TomlFileFolderSerializer.Save(SelectedSettings, TheTask);
+        }
+
+        public void SaveSettingsFromWindow(object name)
+        {
+
+            if (name is null || name.ToString().IsNullOrEmptyOrWhiteSpace())
+            {
+                MessageBox.Show("The name cannot be empty", "Save Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                return;
+            }
+
+            string settingsName = name.ToString();
+
+            if (AllSettingsDict.ContainsKey(settingsName))
+            {
+                MessageBox.Show("The name already exists", "Repeated Name Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                return;
+            }
+
+            AllSettingsDict.Add(settingsName, TheTask);
+            AllSettings.Add(settingsName);
+            OnPropertyChanged(nameof(AllSettingsDict));
+            TomlFileFolderSerializer.Save(settingsName, TheTask);
+            
+        }
+
+        public void DeleteSettings()
+        {
+            if(SelectedSettings == null)
+            {
+                return;
+            }
+            AllSettingsDict.Remove(SelectedSettings);
+            AllSettings.Remove(SelectedSettings);
+            OnPropertyChanged(nameof(AllSettingsDict));
+            TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings);
+        }
+
+        #endregion
+
+        #region Helpers
+
+   
+
+        #endregion
+
+    }
+}
diff --git a/Test/SaveSettingsTests.cs b/Test/SaveSettingsTests.cs
new file mode 100644
index 000000000..d611a60f6
--- /dev/null
+++ b/Test/SaveSettingsTests.cs
@@ -0,0 +1,81 @@
+using System;
+using System.Collections.Generic;
+using System.Diagnostics.CodeAnalysis;
+using System.IO;
+using System.Linq;
+using System.Security.AccessControl;
+using System.Text;
+using System.Threading.Tasks;
+using GuiFunctions;
+using Nett;
+using NUnit.Framework;
+using TaskLayer;
+
+namespace Test
+{
+
+    [TestFixture]
+    [ExcludeFromCodeCoverage]
+    public class SaveSettingsTests
+    {
+        [OneTimeSetUp]
+        public static void OneTimeSetup()
+        {
+            Directory.CreateDirectory(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"));
+            var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory,@"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
+            var tomlFile2 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"), MetaMorpheusTask.tomlConfig);
+            var tomlFile3 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"), MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBCZ.toml", tomlFile1);
+            TomlFileFolderSerializer.Save("customBY.toml", tomlFile2);
+            TomlFileFolderSerializer.Save("customCZ.toml", tomlFile3);
+        }
+
+        [OneTimeTearDown]
+        public static void OneTimeTearDown()
+        {
+            //Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"), true);
+        }
+
+        [Test]
+        public void test1()
+        {
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask());
+            var a = testTaskSettingViewModel.AllSettings;
+            string[] testArrayOfKeys = testTaskSettingViewModel.AllSettingsDict.Keys.ToArray();
+            Assert.That(testArrayOfKeys[0].Equals("customBCZ.toml"));
+            Assert.That(testArrayOfKeys[1].Equals("customBY.toml"));
+            Assert.That(testArrayOfKeys[2].Equals("customCZ.toml"));
+            Assert.That(false);
+        }
+
+
+        [Test]
+        public void testDeleteGetFilePath()
+        {
+            var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
+            var tomlFile2 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"), MetaMorpheusTask.tomlConfig);
+            var tomlFile3 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"), MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBCZ.toml", tomlFile1);
+            TomlFileFolderSerializer.Save("customBY.toml", tomlFile2);
+            TomlFileFolderSerializer.Save("customCZ.toml", tomlFile3);
+            Type deletedFileType = tomlFile1.GetType();
+            String path = TomlFileFolderSerializer.GetFilePath(deletedFileType, "customBCZ.toml");
+            TomlFileFolderSerializer.Delete(deletedFileType, "customBCZ.toml");
+            Assert.That(!File.Exists(path),Is.True);                        
+        }
+
+        [Test]
+        public void testLoadAllNamesOfType()
+        {
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask());
+            var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
+            Type testFolder = tomlFile1.GetType();
+            String[] testStringArray = TomlFileFolderSerializer.LoadAllNamesOfType(testFolder);
+            Assert.That(testStringArray[0].Equals("customBCZ.toml"));
+            Assert.That(testStringArray[1].Equals("customBY.toml"));
+            Assert.That(testStringArray[2].Equals("customCZ.toml"));
+        }
+
+        //TODO:TestGetFilePath returns toml file
+    }
+}

From 4ebfdade2ef1aad411f1482c484136b9cc5edfd3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=B0=E7=8E=AE=20=E7=8E=8B?= <wfw2310165722@outlook.com>
Date: Mon, 17 Apr 2023 14:57:29 -0500
Subject: [PATCH 02/20] Change the Save button in the SaveSettingsWindow

---
 GUI/TaskWindows/SearchTaskWindow.xaml         |  6 ++--
 GUI/TaskWindows/SearchTaskWindow.xaml.cs      | 27 ++++++++++++++++-
 GUI/Views/SaveSettingsWindow.xaml             | 25 +++++++---------
 GUI/Views/SaveSettingsWindow.xaml.cs          | 19 ++++++++++--
 .../ViewModels/TaskSettingViewModel.cs        | 30 ++++++++++++++-----
 5 files changed, 78 insertions(+), 29 deletions(-)

diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml b/GUI/TaskWindows/SearchTaskWindow.xaml
index 6c9608495..ebaf38cc5 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml
@@ -87,14 +87,14 @@
                         <ComboBox Name="TaskSettingsComboBox" Width="200" Height="20" VerticalAlignment="Center" 
                                   HorizontalAlignment="Left" IsSynchronizedWithCurrentItem="True"
                                   ItemsSource="{Binding Path=DataContext.AllSettings, ElementName=TaskSettingsCtrl}" 
-                                  SelectedItem="{Binding Path=DataContext.SelectedSettings, ElementName=TaskSettingsCtrl}">
+                                  SelectedItem="{Binding Path=DataContext.SelectedSettings, ElementName=TaskSettingsCtrl}" SelectionChanged="TaskSettingsComboBox_SelectionChanged">
                         </ComboBox> 
                         <Button x:Name="Save" Content="Save" FontSize="10" 
-                                Width="60" Margin="5,5,2.5,5" Command="{Binding SaveSettingsCommand}"/>
+                                Width="60" Margin="5,5,2.5,5" Command="{Binding SaveSettingsCommand}" Click="Save_Click"/>
                         <Button x:Name="SaveAs" Content="Save as" FontSize="10" 
                                 Width="60" Margin="5,5,2.5,5" Click="SaveAs_Click"/>
                         <Button x:Name="Delete"  Content="Delete" FontSize="10" Width="60" Margin="5,5,2.5,5"
-                                Command="{Binding DeleteSettingsCommand}"/>
+                                Command="{Binding DeleteSettingsCommand}" Click="Delete_Click"/>
                     </StackPanel>
 
                     <!-- Search Parameters -->
diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index c1d5fcc6a..c6a0b9a1d 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -1335,7 +1335,32 @@ private void InternalIonsCheckBox_Checked(object sender, RoutedEventArgs e)
         private void SaveAs_Click(object sender, RoutedEventArgs e)
         {
             SaveSettingsWindow newWindow = new SaveSettingsWindow(TaskSettingViewModel);
-            newWindow.ShowDialog();
+
+            // if user hit save button
+            if (newWindow.ShowDialog() == true)
+            {
+                TaskSettingViewModel.SaveSettingsFromWindow();
+            }
+            // if user hit cancel
+            else
+            {
+                this.Close();
+            }
+        }
+
+        private void TaskSettingsComboBox_SelectionChanged(object sender, SelectionChangedEventArgs e)
+        {
+
+        }
+
+        private void Delete_Click(object sender, RoutedEventArgs e)
+        {
+
+        }
+
+        private void Save_Click(object sender, RoutedEventArgs e)
+        {
+
         }
     }
 
diff --git a/GUI/Views/SaveSettingsWindow.xaml b/GUI/Views/SaveSettingsWindow.xaml
index 6c15733ae..aa38a3812 100644
--- a/GUI/Views/SaveSettingsWindow.xaml
+++ b/GUI/Views/SaveSettingsWindow.xaml
@@ -6,7 +6,7 @@
         xmlns:local="clr-namespace:MetaMorpheusGUI"
         xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
         mc:Ignorable="d"
-        Title="SaveSettingsWindow" Height="350" Width="600">
+        Title="SaveSettingsWindow" Height="135" Width="600">
     <d:UserControl.DataContext>
         <guiFunctions:TaskSettingViewModel/>
     </d:UserControl.DataContext>
@@ -16,27 +16,22 @@
     <Grid >
         <Grid.RowDefinitions>
             <RowDefinition Height="2*"/>
-            <RowDefinition Height="6*"/>
             <RowDefinition Height="*"/>
         </Grid.RowDefinitions>
 
-        <ListBox Grid.Row="1" x:Name="SavedSettingsListBox" IsSynchronizedWithCurrentItem="True"
-                 ItemsSource="{Binding Path=AllSettings}" SelectedItem="{Binding SelectedSettings,Mode=TwoWay}" 
-                 VerticalAlignment="Stretch"  HorizontalAlignment="Stretch" 
-                 Margin="10" FontSize="15" 
-                 d:ItemsSource="{d:SampleData ItemCount=15}">
-        </ListBox>
-
-        <TextBox Grid.Row="0" Text="{Binding TypedSettingsName}" Height="40"
+        <TextBox Grid.Row="0" Text="{Binding TypedSettingsName}" Height="35"
                  HorizontalAlignment="Stretch"  VerticalAlignment="Top"
                  Margin="10" FontSize="25" x:Name="NameTextBox">
         </TextBox>
 
-        <Button x:Name="Delete"  Grid.Row="2" Content="Delete" FontSize="20" Height="30" 
-                Width="200" VerticalAlignment="Center"  HorizontalAlignment="Left"
-                Command="{Binding DeleteSettingsCommand}"/>
+        <Button x:Name="Cancel"  Grid.Row="2" Content="Cancel" 
+                FontSize="20" Height="30" IsCancel="true" Click="CloseWindow"
+                Width="200" VerticalAlignment="Center"  HorizontalAlignment="Right"/>
+        
         <Button x:Name="Save" Grid.Row="2" Content="Save" FontSize="20" Height="30" 
-                Width="200" VerticalAlignment="Center" HorizontalAlignment="Right"
-                Command="{Binding SaveSettingsFromWindowCommand}" CommandParameter="{Binding TypedSettingsName}"/>
+                Width="200" VerticalAlignment="Center" HorizontalAlignment="Left"
+                 Click="Save_Click"/>
+        <!--Command="{Binding SaveSettingsFromWindowCommand}" 
+                CommandParameter="{Binding TypedSettingsName}"-->
     </Grid>
 </Window>
diff --git a/GUI/Views/SaveSettingsWindow.xaml.cs b/GUI/Views/SaveSettingsWindow.xaml.cs
index 649ea6cc2..a7dd4f4d9 100644
--- a/GUI/Views/SaveSettingsWindow.xaml.cs
+++ b/GUI/Views/SaveSettingsWindow.xaml.cs
@@ -24,8 +24,23 @@ public SaveSettingsWindow(TaskSettingViewModel viewModel)
         {
             InitializeComponent();
             this.DataContext = viewModel;
-            SavedSettingsListBox.ItemsSource = viewModel.AllSettings;
-            SavedSettingsListBox.SelectedItem = viewModel.SelectedSettings;
+        }
+
+        private void Save_Click(object sender, RoutedEventArgs e)
+        {
+            DialogResult = true;
+            this.Close();
+        }
+
+        private void CloseWindow(object sender, RoutedEventArgs e)
+        {
+            DialogResult = false;
+            this.Close();
+        }
+
+        private void Save_Click_1(object sender, RoutedEventArgs e)
+        {
+
         }
     }
 }
diff --git a/GuiFunctions/ViewModels/TaskSettingViewModel.cs b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
index 59606f51e..0330087d7 100644
--- a/GuiFunctions/ViewModels/TaskSettingViewModel.cs
+++ b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
@@ -20,16 +20,30 @@ public class TaskSettingViewModel : BaseViewModel
 
         private string selectedSettings;
         private string typedSettingsName;
+        private ObservableCollection<string> allSettings;
 
         #endregion
 
         #region Public Properties
 
-        public ObservableCollection<string> AllSettings;
+        public ObservableCollection<string> AllSettings
+        {
+            get => allSettings;
+            set
+            {
+                allSettings = value;
+                OnPropertyChanged(nameof(AllSettings));
+            }
+        }
+
         public string SelectedSettings
         {
-            get { return selectedSettings; }
-            set { selectedSettings = value; OnPropertyChanged(nameof(SelectedSettings)); }
+            get => selectedSettings; 
+            set
+            { 
+                selectedSettings = value; 
+                OnPropertyChanged(nameof(SelectedSettings)); 
+            }
         }
 
         public string TypedSettingsName
@@ -75,7 +89,7 @@ public TaskSettingViewModel(MetaMorpheusTask task)
             AllSettings = new ObservableCollection<string>(AllSettingsDict.Select(p=>p.Key));
             SaveSettingsCommand = new RelayCommand(() => SaveSettings());
             DeleteSettingsCommand = new RelayCommand(() => DeleteSettings());
-            SaveSettingsFromWindowCommand = new DelegateCommand((param) => SaveSettingsFromWindow(param));
+            SaveSettingsFromWindowCommand = new DelegateCommand((param) => SaveSettingsFromWindow());
 
         }
 
@@ -101,7 +115,7 @@ public TaskSettingViewModel()
             AllSettings = new ObservableCollection<string>(AllSettingsDict.Select(p => p.Key));
             SaveSettingsCommand = new RelayCommand(() => SaveSettings());
             DeleteSettingsCommand = new RelayCommand(() => DeleteSettings());
-            SaveSettingsFromWindowCommand = new DelegateCommand((param) => SaveSettingsFromWindow(param));
+            SaveSettingsFromWindowCommand = new DelegateCommand((param) => SaveSettingsFromWindow());
         }
 
 
@@ -121,16 +135,16 @@ public void SaveSettings()
             TomlFileFolderSerializer.Save(SelectedSettings, TheTask);
         }
 
-        public void SaveSettingsFromWindow(object name)
+        public void SaveSettingsFromWindow()
         {
 
-            if (name is null || name.ToString().IsNullOrEmptyOrWhiteSpace())
+            if (TypedSettingsName is null || TypedSettingsName.IsNullOrEmptyOrWhiteSpace())
             {
                 MessageBox.Show("The name cannot be empty", "Save Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
                 return;
             }
 
-            string settingsName = name.ToString();
+            string settingsName = TypedSettingsName.ToString();
 
             if (AllSettingsDict.ContainsKey(settingsName))
             {

From bc81a2f7bb6fb84cb88a6d76af5d53c287abe6fc Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Mon, 17 Apr 2023 14:58:08 -0500
Subject: [PATCH 03/20] Attached ViewModel to main task window

---
 GUI/TaskWindows/SearchTaskWindow.xaml         | 42 ++++++++-------
 GUI/Views/SaveSettingsWindow.xaml.cs          |  2 -
 .../ViewModels/TaskSettingViewModel.cs        | 52 +++++++++++++------
 3 files changed, 58 insertions(+), 38 deletions(-)

diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml b/GUI/TaskWindows/SearchTaskWindow.xaml
index 6c9608495..0c521da75 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml
@@ -4,7 +4,7 @@
         xmlns:d="http://schemas.microsoft.com/expression/blend/2008"
         xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
         xmlns:local="clr-namespace:MetaMorpheusGUI"
-        xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
+        xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions" 
         mc:Ignorable="d"
         KeyDown="KeyPressed"
         d:Height="1500"
@@ -16,7 +16,7 @@
         <BooleanToVisibilityConverter x:Key="bool2VisConverter" />
         <guiFunctions:BooleanOrConverter x:Key="boolOrConverter"/>
 
-            <!-- Style GroupBoxes -->
+        <!-- Style GroupBoxes -->
         <Style TargetType="GroupBox">
             <Setter Property="BorderThickness" Value="3 1 1 1"/>
             <Setter Property="Padding" Value="5"/>
@@ -81,14 +81,15 @@
                 <StackPanel DockPanel.Dock="Top" Margin="10">
 
                     <!-- save settings -->
-                    <StackPanel  x:Name="TaskSettingsCtrl" Height="Auto" DataContext="{Binding TaskSettingsViewModel}"
+                    <StackPanel  x:Name="TaskSettingsCtrl" Height="Auto" 
+                                 DataContext="{Binding TaskSettingViewModel}"
                                  Background="{StaticResource BackgroundColor}" Orientation="Horizontal" HorizontalAlignment="Right">
 
                         <ComboBox Name="TaskSettingsComboBox" Width="200" Height="20" VerticalAlignment="Center" 
                                   HorizontalAlignment="Left" IsSynchronizedWithCurrentItem="True"
-                                  ItemsSource="{Binding Path=DataContext.AllSettings, ElementName=TaskSettingsCtrl}" 
-                                  SelectedItem="{Binding Path=DataContext.SelectedSettings, ElementName=TaskSettingsCtrl}">
-                        </ComboBox> 
+                                  ItemsSource="{Binding Path=.AllSettings}" 
+                                  SelectedItem="{Binding Path=SelectedSettings}">
+                        </ComboBox>
                         <Button x:Name="Save" Content="Save" FontSize="10" 
                                 Width="60" Margin="5,5,2.5,5" Command="{Binding SaveSettingsCommand}"/>
                         <Button x:Name="SaveAs" Content="Save as" FontSize="10" 
@@ -255,11 +256,12 @@
                         <StackPanel Height="115">
                             <Grid>
                                 <Grid.ColumnDefinitions>
-                                    <ColumnDefinition Width="1*" />
-                                    <ColumnDefinition Width="1*" />
+                                    <ColumnDefinition Width="118*" />
+                                    <ColumnDefinition Width="21*" />
+                                    <ColumnDefinition Width="97*"/>
 
                                 </Grid.ColumnDefinitions>
-                                <StackPanel Margin="5 0 5 0">
+                                <StackPanel Margin="5,0,5,0">
                                     <Label Content="Fixed:" />
                                     <TreeView x:Name="FixedModsTreeView" ItemsSource="{Binding}" DataContext="{x:Type guiFunctions:ModTypeForTreeViewModel}" Height="85">
                                         <TreeView.Resources>
@@ -283,7 +285,7 @@
                                         </TreeView.ItemContainerStyle>
                                     </TreeView>
                                 </StackPanel>
-                                <StackPanel Grid.Column="1" Margin="5 0 3 0">
+                                <StackPanel Grid.Column="1" Margin="5,0,3,0" Grid.ColumnSpan="2">
                                     <Label Content="Variable:"  ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
                                         <Label.ToolTip>
                                             <TextBlock>
@@ -341,7 +343,7 @@
                                         </Style>
                                     </TextBox.Style>
                                 </TextBox>
-                                <TextBox x:Name="SearchVarMod" TextChanged="TextChanged_Var" Grid.Column="1" HorizontalAlignment="Left" Margin="82,4,0,410" TextWrapping="Wrap" Width="140">
+                                <TextBox x:Name="SearchVarMod" TextChanged="TextChanged_Var" Grid.Column="2" HorizontalAlignment="Left" Margin="19,4,0,410" TextWrapping="Wrap" Width="140">
                                     <TextBox.Style>
                                         <Style TargetType="TextBox" xmlns:sys="clr-namespace:System;assembly=mscorlib">
                                             <Style.Resources>
@@ -500,7 +502,7 @@
                                 <ColumnDefinition Width="*" />
 
                             </Grid.ColumnDefinitions>
-                            
+
                             <!-- writing options -->
                             <StackPanel Orientation="Vertical" Margin="5" Grid.Column="0">
                                 <CheckBox x:Name="CkbMzId" Content="Write .mzID" IsEnabled="{Binding IsChecked, ElementName=CheckBoxParsimony}" ToolTipService.ShowOnDisabled="True">
@@ -515,9 +517,9 @@
                                 <CheckBox x:Name="WriteSpectralLibraryCheckBox" Content="Write spectral library" />
                                 <CheckBox x:Name="UpdateSpectralLibraryCheckBox" Content="Update SpectralLibrary" />
                                 <CheckBox x:Name="CompressIndividualResultsCheckBox" Content="Compress individual file results" IsEnabled="{Binding IsChecked, ElementName=WriteIndividualResultsCheckBox}"/>
-                                
+
                             </StackPanel>
-                            
+
                             <!-- filtering options -->
                             <StackPanel Orientation="Vertical" Margin="5" Grid.Column="1">
 
@@ -538,14 +540,14 @@
                                     <TextBox x:Name="PepQValueTextBox" PreviewTextInput="CheckIfNumber" Margin="10,0,0,0" 
                                              IsEnabled="{Binding IsChecked, ElementName=PepQValueRadioButton}" Width="45" Height="23" />
                                 </Grid>
-                                
+
                                 <!-- q value button -->
                                 <Grid>
                                     <Grid.ColumnDefinitions>
                                         <ColumnDefinition Width="400" />
                                         <ColumnDefinition Width="50" />
                                     </Grid.ColumnDefinitions>
-                                    
+
                                     <RadioButton x:Name="QValueRadioButton" Content="Filter results to q-value:" 
                                                  IsChecked="False" GroupName="Filtering" Checked="QValueRadioButton_Checked">
                                         <ToolTipService.ToolTip>
@@ -557,7 +559,7 @@
                                     <TextBox x:Name="QValueTextBox" PreviewTextInput="CheckIfNumber" Margin="10,0,0,0" 
                                              IsEnabled="{Binding IsChecked, ElementName=QValueRadioButton}" Width="45" Height="23" />
                                 </Grid>
-                                
+
                                 <!-- min score allowed box -->
                                 <Grid>
                                     <Grid.ColumnDefinitions>
@@ -577,10 +579,10 @@
                                     </TextBox>
                                 </Grid>
                             </StackPanel>
-                            
+
                         </Grid>
-                        
-                        
+
+
                         <!--</Expander>-->
                     </GroupBox>
                 </StackPanel>
diff --git a/GUI/Views/SaveSettingsWindow.xaml.cs b/GUI/Views/SaveSettingsWindow.xaml.cs
index 649ea6cc2..fdf31cc56 100644
--- a/GUI/Views/SaveSettingsWindow.xaml.cs
+++ b/GUI/Views/SaveSettingsWindow.xaml.cs
@@ -24,8 +24,6 @@ public SaveSettingsWindow(TaskSettingViewModel viewModel)
         {
             InitializeComponent();
             this.DataContext = viewModel;
-            SavedSettingsListBox.ItemsSource = viewModel.AllSettings;
-            SavedSettingsListBox.SelectedItem = viewModel.SelectedSettings;
         }
     }
 }
diff --git a/GuiFunctions/ViewModels/TaskSettingViewModel.cs b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
index 59606f51e..dd5c98415 100644
--- a/GuiFunctions/ViewModels/TaskSettingViewModel.cs
+++ b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
@@ -20,25 +20,47 @@ public class TaskSettingViewModel : BaseViewModel
 
         private string selectedSettings;
         private string typedSettingsName;
+        private Dictionary<string, MetaMorpheusTask> allSettingsDict;
+        private ObservableCollection<string> allSettings => new ObservableCollection<string>(allSettingsDict.Keys);
 
         #endregion
 
         #region Public Properties
 
-        public ObservableCollection<string> AllSettings;
-        public string SelectedSettings
+        public ObservableCollection<string> AllSettings
         {
-            get { return selectedSettings; }
-            set { selectedSettings = value; OnPropertyChanged(nameof(SelectedSettings)); }
+            get => allSettings;
         }
 
         public string TypedSettingsName
         {
-            get { return typedSettingsName; }
-            set { typedSettingsName = value; OnPropertyChanged(nameof(TypedSettingsName)); }
+            get => typedSettingsName;
+            set
+            {
+                typedSettingsName = value;
+                OnPropertyChanged(nameof(TypedSettingsName));
+            }
         }
 
-        public Dictionary<string, MetaMorpheusTask> AllSettingsDict { get; set; }
+        public string SelectedSettings
+        {
+            get => selectedSettings;
+            set
+            {
+                selectedSettings = value;
+                OnPropertyChanged(nameof(SelectedSettings));
+            }
+        }
+
+        public Dictionary<string, MetaMorpheusTask> AllSettingsDict
+        {
+            get => allSettingsDict;
+            set
+            {
+                allSettingsDict = value;
+                OnPropertyChanged(nameof(AllSettingsDict));
+            }
+    }
 
         //public String AllSettingNames {get; set; }
 
@@ -72,9 +94,8 @@ public TaskSettingViewModel(MetaMorpheusTask task)
             }
             AllSettingsDict = tempDict;
 
-            AllSettings = new ObservableCollection<string>(AllSettingsDict.Select(p=>p.Key));
-            SaveSettingsCommand = new RelayCommand(() => SaveSettings());
-            DeleteSettingsCommand = new RelayCommand(() => DeleteSettings());
+            SaveSettingsCommand = new RelayCommand(SaveSettings);
+            DeleteSettingsCommand = new RelayCommand(DeleteSettings);
             SaveSettingsFromWindowCommand = new DelegateCommand((param) => SaveSettingsFromWindow(param));
 
         }
@@ -98,9 +119,8 @@ public TaskSettingViewModel()
             }
             AllSettingsDict = tempDict;
 
-            AllSettings = new ObservableCollection<string>(AllSettingsDict.Select(p => p.Key));
-            SaveSettingsCommand = new RelayCommand(() => SaveSettings());
-            DeleteSettingsCommand = new RelayCommand(() => DeleteSettings());
+            SaveSettingsCommand = new RelayCommand(SaveSettings);
+            DeleteSettingsCommand = new RelayCommand(DeleteSettings);
             SaveSettingsFromWindowCommand = new DelegateCommand((param) => SaveSettingsFromWindow(param));
         }
 
@@ -116,7 +136,7 @@ public void SaveSettings()
                 return;
             }
             AllSettingsDict.Add(SelectedSettings, TheTask);
-            AllSettings.Add(SelectedSettings);
+            OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
             TomlFileFolderSerializer.Save(SelectedSettings, TheTask);
         }
@@ -139,7 +159,7 @@ public void SaveSettingsFromWindow(object name)
             }
 
             AllSettingsDict.Add(settingsName, TheTask);
-            AllSettings.Add(settingsName);
+            OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
             TomlFileFolderSerializer.Save(settingsName, TheTask);
             
@@ -152,7 +172,7 @@ public void DeleteSettings()
                 return;
             }
             AllSettingsDict.Remove(SelectedSettings);
-            AllSettings.Remove(SelectedSettings);
+            OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
             TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings);
         }

From 0e49b6dce24b9f83074f8f48fd334a9aa8e85c83 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 19 Apr 2023 15:06:03 -0500
Subject: [PATCH 04/20] Added ability for view model to communicate selected
 item with gui and get task from gui

---
 GUI/TaskWindows/SearchTaskWindow.xaml.cs      | 21 +++-
 .../ViewModels/TaskSettingViewModel.cs        | 96 ++++++++++---------
 2 files changed, 71 insertions(+), 46 deletions(-)

diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index c6a0b9a1d..d45a775bf 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -37,6 +37,7 @@ public partial class SearchTaskWindow : Window
         private CustomFragmentationWindow CustomFragmentationWindow;
         public TaskSettingViewModel TaskSettingViewModel { get; set; }
 
+
         internal SearchTask TheTask { get; private set; }
 
         public SearchTaskWindow(SearchTask task)
@@ -44,9 +45,10 @@ public SearchTaskWindow(SearchTask task)
             InitializeComponent();
             TheTask = task ?? new SearchTask();
 
-            TaskSettingViewModel = new(TheTask);
+            var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as SearchTask);
+            TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
             TaskSettingsCtrl.DataContext = TaskSettingViewModel;
-            
+
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
             PopulateChoices();
             UpdateFieldsFromTask(TheTask);
@@ -152,6 +154,17 @@ private void PopulateChoices()
             }
         }
 
+
+        ///// <summary>
+        ///// Calls the UpdateFieldsFromTask Method from an event
+        ///// </summary>
+        ///// <param name="sender"></param>
+        ///// <param name="args"></param>
+        //private void UpdateFieldsFromTask(object sender, MetaMorpheusTaskEventArgs args)
+        //{
+        //    UpdateFieldsFromTask(args.TheTask as SearchTask);
+        //}
+
         /// <summary>
         /// Initializes the fields in the search task window upon opening to the settings of the param Task
         /// </summary>
@@ -422,6 +435,8 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             DialogResult = true;
         }
 
+
+
         private SearchTask GetTaskFromGui()
         {
             CleavageSpecificity searchModeType = GetSearchModeType(); //change search type to semi or non if selected
@@ -1344,7 +1359,7 @@ private void SaveAs_Click(object sender, RoutedEventArgs e)
             // if user hit cancel
             else
             {
-                this.Close();
+           
             }
         }
 
diff --git a/GuiFunctions/ViewModels/TaskSettingViewModel.cs b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
index e8a9fd6a2..7d41fb6d6 100644
--- a/GuiFunctions/ViewModels/TaskSettingViewModel.cs
+++ b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
@@ -48,6 +48,7 @@ public string SelectedSettings
             set
             {
                 selectedSettings = value;
+                UpdateFieldsInGuiWithNewTask.Invoke(AllSettingsDict[SelectedSettings]);
                 OnPropertyChanged(nameof(SelectedSettings));
             }
         }
@@ -60,23 +61,27 @@ public Dictionary<string, MetaMorpheusTask> AllSettingsDict
                 allSettingsDict = value;
                 OnPropertyChanged(nameof(AllSettingsDict));
             }
-    }
+        }
 
       
         public ICommand SaveSettingsCommand { get; set; }
         public ICommand DeleteSettingsCommand { get; set; }
 
         public MetaMorpheusTask TheTask { get; set; }
-
+        public Func<MetaMorpheusTask> GetTaskFromGui { get; set; }
+        public Action<MetaMorpheusTask> UpdateFieldsInGuiWithNewTask { get; set; }
 
         #endregion
 
         #region Constructor
 
-        public TaskSettingViewModel(MetaMorpheusTask task)
+        public TaskSettingViewModel(MetaMorpheusTask task, Action<MetaMorpheusTask> updateFieldsInGuiEventHandler, Func<MetaMorpheusTask> getTaskFromGui)
         {
+            
             TheTask = task;
-            var temp = typeof(SearchTask);
+            UpdateFieldsInGuiWithNewTask = updateFieldsInGuiEventHandler;
+            GetTaskFromGui = getTaskFromGui;
+
             var type = task.GetType();
             MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("LoadAllOfTypeT");
             MethodInfo genericMethod = method.MakeGenericMethod(type);
@@ -118,60 +123,65 @@ public TaskSettingViewModel()
             DeleteSettingsCommand = new RelayCommand(DeleteSettings);
         }
 
+        
+        #endregion
+
 
-            #endregion
 
-            #region Command Methods
+        #region Command Methods
 
-        public void SaveSettings()
+    public void SaveSettings()
+    {
+   
+        if (SelectedSettings == null)
         {
-            if (SelectedSettings == null)
-            {
-                return;
-            }
-            AllSettingsDict.Add(SelectedSettings, TheTask);
-            OnPropertyChanged(nameof(AllSettings));
-            OnPropertyChanged(nameof(AllSettingsDict));
-            TomlFileFolderSerializer.Save(SelectedSettings, TheTask);
+            return;
         }
+        AllSettingsDict.Add(SelectedSettings, TheTask);
+        OnPropertyChanged(nameof(AllSettings));
+        OnPropertyChanged(nameof(AllSettingsDict));
+        TomlFileFolderSerializer.Save(SelectedSettings, TheTask);
 
-        public void SaveSettingsFromWindow()
-        {
 
-            if (TypedSettingsName is null || TypedSettingsName.IsNullOrEmptyOrWhiteSpace())
-            {
-                MessageBox.Show("The name cannot be empty", "Save Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
-                return;
-            }
+    }
 
-            string settingsName = TypedSettingsName.ToString();
+    public void SaveSettingsFromWindow()
+    {
 
-            if (AllSettingsDict.ContainsKey(settingsName))
-            {
-                MessageBox.Show("The name already exists", "Repeated Name Error", MessageBoxButton.OK, MessageBoxImage.Warning);
-                return;
-            }
+        if (TypedSettingsName is null || TypedSettingsName.IsNullOrEmptyOrWhiteSpace())
+        {
+            MessageBox.Show("The name cannot be empty", "Save Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+            return;
+        }
 
-            AllSettingsDict.Add(settingsName, TheTask);
-            OnPropertyChanged(nameof(AllSettings));
-            OnPropertyChanged(nameof(AllSettingsDict));
-            TomlFileFolderSerializer.Save(settingsName, TheTask);
-            
+        string settingsName = TypedSettingsName.ToString();
+
+        if (AllSettingsDict.ContainsKey(settingsName))
+        {
+            MessageBox.Show("The name already exists", "Repeated Name Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+            return;
         }
 
-        public void DeleteSettings()
+        AllSettingsDict.Add(settingsName, TheTask);
+        OnPropertyChanged(nameof(AllSettings));
+        OnPropertyChanged(nameof(AllSettingsDict));
+        TomlFileFolderSerializer.Save(settingsName, TheTask);
+        
+    }
+
+    public void DeleteSettings()
+    {
+        if(SelectedSettings == null)
         {
-            if(SelectedSettings == null)
-            {
-                return;
-            }
-            AllSettingsDict.Remove(SelectedSettings);
-            OnPropertyChanged(nameof(AllSettings));
-            OnPropertyChanged(nameof(AllSettingsDict));
-            TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings);
+            return;
         }
+        AllSettingsDict.Remove(SelectedSettings);
+        OnPropertyChanged(nameof(AllSettings));
+        OnPropertyChanged(nameof(AllSettingsDict));
+        TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings);
+    }
 
-        #endregion
+    #endregion
 
         #region Helpers
 

From b24aafc90c70ffb37351ab300b580ca3f19d7dfc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=B0=E7=8E=AE=20=E7=8E=8B?= <wfw2310165722@outlook.com>
Date: Wed, 19 Apr 2023 15:07:06 -0500
Subject: [PATCH 05/20] Default Settings updated.

---
 GUI/TaskWindows/SearchTaskWindow.xaml         |  4 +-
 GUI/TaskWindows/SearchTaskWindow.xaml.cs      |  7 ++-
 .../ViewModels/TaskSettingViewModel.cs        | 22 ++++++-
 Test/SaveSettingsTests.cs                     | 13 ++++-
 Test/TaskSettingViewModelTests.cs             | 57 +++++++++++++++++++
 5 files changed, 95 insertions(+), 8 deletions(-)
 create mode 100644 Test/TaskSettingViewModelTests.cs

diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml b/GUI/TaskWindows/SearchTaskWindow.xaml
index 0d1d72fcb..0d963148a 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml
@@ -87,8 +87,8 @@
 
                         <ComboBox Name="TaskSettingsComboBox" Width="200" Height="20" VerticalAlignment="Center" 
                                   HorizontalAlignment="Left" IsSynchronizedWithCurrentItem="True"
-                                  ItemsSource="{Binding Path=.AllSettings}" 
-                                  SelectedItem="{Binding Path=SelectedSettings}">
+                                  ItemsSource="{Binding Path=AllSettings}" 
+                                  SelectedItem="{Binding Path=SelectedSettings}" SelectionChanged="TaskSettingsComboBox_SelectionChanged_1">
                         </ComboBox>
                         <Button x:Name="Save" Content="Save" FontSize="10" 
                                 Width="60" Margin="5,5,2.5,5" Command="{Binding SaveSettingsCommand}" Click="Save_Click"/>
diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index c6a0b9a1d..27854b379 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -1344,7 +1344,7 @@ private void SaveAs_Click(object sender, RoutedEventArgs e)
             // if user hit cancel
             else
             {
-                this.Close();
+
             }
         }
 
@@ -1362,6 +1362,11 @@ private void Save_Click(object sender, RoutedEventArgs e)
         {
 
         }
+
+        private void TaskSettingsComboBox_SelectionChanged_1(object sender, SelectionChangedEventArgs e)
+        {
+
+        }
     }
 
     public class DataContextForSearchTaskWindow : INotifyPropertyChanged
diff --git a/GuiFunctions/ViewModels/TaskSettingViewModel.cs b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
index e8a9fd6a2..bd6db910d 100644
--- a/GuiFunctions/ViewModels/TaskSettingViewModel.cs
+++ b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
@@ -129,10 +129,19 @@ public void SaveSettings()
             {
                 return;
             }
+
+            if (SelectedSettings.Contains("(Default)"))
+            {
+                MessageBox.Show("Default Setting cannot be modified. Please use \"Save as Default\" button", "Modifying Default Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                return;
+            }
+
+            TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings);
+            TomlFileFolderSerializer.Save(SelectedSettings, TheTask);
+            AllSettingsDict.Remove(SelectedSettings);
             AllSettingsDict.Add(SelectedSettings, TheTask);
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
-            TomlFileFolderSerializer.Save(SelectedSettings, TheTask);
         }
 
         public void SaveSettingsFromWindow()
@@ -141,6 +150,7 @@ public void SaveSettingsFromWindow()
             if (TypedSettingsName is null || TypedSettingsName.IsNullOrEmptyOrWhiteSpace())
             {
                 MessageBox.Show("The name cannot be empty", "Save Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                TypedSettingsName = "";
                 return;
             }
 
@@ -149,6 +159,7 @@ public void SaveSettingsFromWindow()
             if (AllSettingsDict.ContainsKey(settingsName))
             {
                 MessageBox.Show("The name already exists", "Repeated Name Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                TypedSettingsName = "";
                 return;
             }
 
@@ -156,6 +167,7 @@ public void SaveSettingsFromWindow()
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
             TomlFileFolderSerializer.Save(settingsName, TheTask);
+            TypedSettingsName = "";
             
         }
 
@@ -165,10 +177,16 @@ public void DeleteSettings()
             {
                 return;
             }
+            if (SelectedSettings.Contains("(Default)"))
+            {
+                MessageBox.Show("Default Setting cannot be deleted", "Deleting Default Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                return;
+            }
+
+            TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings);
             AllSettingsDict.Remove(SelectedSettings);
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
-            TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings);
         }
 
         #endregion
diff --git a/Test/SaveSettingsTests.cs b/Test/SaveSettingsTests.cs
index d611a60f6..86dd46d94 100644
--- a/Test/SaveSettingsTests.cs
+++ b/Test/SaveSettingsTests.cs
@@ -33,11 +33,11 @@ public static void OneTimeSetup()
         [OneTimeTearDown]
         public static void OneTimeTearDown()
         {
-            //Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"), true);
+            Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"), true);
         }
 
         [Test]
-        public void test1()
+        public void testConstructor()
         {
             TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask());
             var a = testTaskSettingViewModel.AllSettings;
@@ -76,6 +76,13 @@ public void testLoadAllNamesOfType()
             Assert.That(testStringArray[2].Equals("customCZ.toml"));
         }
 
-        //TODO:TestGetFilePath returns toml file
+        [Test]
+        public void testGetFilePath()
+        {
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask());
+            var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
+            string testPath = TomlFileFolderSerializer.GetFilePath(tomlFile1.GetType(), "customBCZ.toml");
+            Assert.That(testPath.Contains("toml"));
+        }
     }
 }
diff --git a/Test/TaskSettingViewModelTests.cs b/Test/TaskSettingViewModelTests.cs
new file mode 100644
index 000000000..c82be21e1
--- /dev/null
+++ b/Test/TaskSettingViewModelTests.cs
@@ -0,0 +1,57 @@
+using System;
+using System.Collections.Generic;
+using System.Diagnostics.CodeAnalysis;
+using System.IO;
+using System.Linq;
+using System.Security.AccessControl;
+using System.Text;
+using System.Threading.Tasks;
+using EngineLayer;
+using GuiFunctions;
+using MassSpectrometry;
+using Nett;
+using NUnit.Framework;
+using TaskLayer;
+
+namespace Test
+{
+    public class TaskSettingViewModelTests
+    {
+        [OneTimeSetUp]
+        public static void OneTimeSetup()
+        {
+            Directory.CreateDirectory(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"));
+            var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
+            var tomlFile2 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"), MetaMorpheusTask.tomlConfig);
+            var tomlFile3 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"), MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBCZ.toml", tomlFile1);
+            TomlFileFolderSerializer.Save("customBY.toml", tomlFile2);
+            TomlFileFolderSerializer.Save("customCZ.toml", tomlFile3);
+        }
+
+        [OneTimeTearDown]
+        public static void OneTimeTearDown()
+        {
+            Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"), true);
+        }
+
+        [Test]
+        public void testSaveSettings()
+        {
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask());
+
+            var paramsOne = new CommonParameters(null, DissociationType.CID);
+            var paramsTwo = new CommonParameters(null, DissociationType.HCD);
+            var paramsThree = new CommonParameters(null, DissociationType.PD);
+
+            var one = new SearchTask();
+            var two = new SearchTask();
+            var three = new SearchTask();
+
+            one.CommonParameters = paramsOne;
+            two.CommonParameters = paramsTwo;
+            three.CommonParameters = paramsThree;
+
+        }
+    }
+}

From 79a2a0fe62397c64ff2f5dc02f8fdcc0444d9703 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 19 Apr 2023 15:07:19 -0500
Subject: [PATCH 06/20] Removed dead method

---
 GUI/TaskWindows/SearchTaskWindow.xaml.cs | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index d45a775bf..9dca01215 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -155,16 +155,6 @@ private void PopulateChoices()
         }
 
 
-        ///// <summary>
-        ///// Calls the UpdateFieldsFromTask Method from an event
-        ///// </summary>
-        ///// <param name="sender"></param>
-        ///// <param name="args"></param>
-        //private void UpdateFieldsFromTask(object sender, MetaMorpheusTaskEventArgs args)
-        //{
-        //    UpdateFieldsFromTask(args.TheTask as SearchTask);
-        //}
-
         /// <summary>
         /// Initializes the fields in the search task window upon opening to the settings of the param Task
         /// </summary>

From 8d0c428d9ded52fc2d8de108600775655dcfa74f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=B0=E7=8E=AE=20=E7=8E=8B?= <wfw2310165722@outlook.com>
Date: Wed, 26 Apr 2023 13:57:42 -0500
Subject: [PATCH 07/20] SaveAsDefautSettings and SaveSettings buttons updated.

---
 GUI/TaskWindows/SearchTaskWindow.xaml         |  10 +-
 GUI/TaskWindows/SearchTaskWindow.xaml.cs      |  18 +--
 GuiFunctions/GuiFunctions.csproj              |   6 +
 GuiFunctions/TomlFileFolderSerializer.cs      |   2 +-
 .../ViewModels/TaskSettingViewModel.cs        | 130 ++++++++++++++++--
 5 files changed, 137 insertions(+), 29 deletions(-)

diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml b/GUI/TaskWindows/SearchTaskWindow.xaml
index 0d963148a..73496d3db 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml
@@ -88,14 +88,14 @@
                         <ComboBox Name="TaskSettingsComboBox" Width="200" Height="20" VerticalAlignment="Center" 
                                   HorizontalAlignment="Left" IsSynchronizedWithCurrentItem="True"
                                   ItemsSource="{Binding Path=AllSettings}" 
-                                  SelectedItem="{Binding Path=SelectedSettings}" SelectionChanged="TaskSettingsComboBox_SelectionChanged_1">
+                                  SelectedItem="{Binding Path=SelectedSettings}">
                         </ComboBox>
                         <Button x:Name="Save" Content="Save" FontSize="10" 
-                                Width="60" Margin="5,5,2.5,5" Command="{Binding SaveSettingsCommand}" Click="Save_Click"/>
+                                Width="60" Margin="5,5,2.5,5" Command="{Binding SaveSettingsCommand}" />
                         <Button x:Name="SaveAs" Content="Save as" FontSize="10" 
                                 Width="60" Margin="5,5,2.5,5" Click="SaveAs_Click"/>
                         <Button x:Name="Delete"  Content="Delete" FontSize="10" Width="60" Margin="5,5,2.5,5"
-                                Command="{Binding DeleteSettingsCommand}" Click="Delete_Click"/>
+                                Command="{Binding DeleteSettingsCommand}" />
                     </StackPanel>
 
                     <!-- Search Parameters -->
@@ -1197,7 +1197,9 @@
         <StackPanel  Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1" Margin="5">
             <Button x:Name="cancelButton" Content="Cancel" Click="CancelButton_Click" />
             <Button x:Name="saveButton" Content="Save Search Task" Click="SaveButton_Click" FontSize="24" />
-            <Button x:Name="setDefaultbutton" Click="SaveAsDefault_Click" Width="100" >
+            <Button x:Name="setDefaultbutton"  Width="100" 
+                    Command="{Binding Path=TaskSettingViewModel.SaveAsDefaultSettingsCommand, 
+                RelativeSource={RelativeSource FindAncestor, AncestorType={x:Type Window}}}">
                 <TextBlock Text="Save As Default" TextWrapping="Wrap" TextAlignment="Center"/>
                 <ToolTipService.ToolTip>
                     <ToolTip Content="Save these parameters as the default. MetaMorpheus can return to original defaults by deleting the folder 'DefaultParameters'" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index 9dca01215..716059a17 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -43,6 +43,7 @@ public partial class SearchTaskWindow : Window
         public SearchTaskWindow(SearchTask task)
         {
             InitializeComponent();
+            PopulateChoices();
             TheTask = task ?? new SearchTask();
 
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as SearchTask);
@@ -50,7 +51,7 @@ public SearchTaskWindow(SearchTask task)
             TaskSettingsCtrl.DataContext = TaskSettingViewModel;
 
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
-            PopulateChoices();
+            
             UpdateFieldsFromTask(TheTask);
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
 
@@ -1352,21 +1353,6 @@ private void SaveAs_Click(object sender, RoutedEventArgs e)
            
             }
         }
-
-        private void TaskSettingsComboBox_SelectionChanged(object sender, SelectionChangedEventArgs e)
-        {
-
-        }
-
-        private void Delete_Click(object sender, RoutedEventArgs e)
-        {
-
-        }
-
-        private void Save_Click(object sender, RoutedEventArgs e)
-        {
-
-        }
     }
 
     public class DataContextForSearchTaskWindow : INotifyPropertyChanged
diff --git a/GuiFunctions/GuiFunctions.csproj b/GuiFunctions/GuiFunctions.csproj
index e0a55462a..c1acfd624 100644
--- a/GuiFunctions/GuiFunctions.csproj
+++ b/GuiFunctions/GuiFunctions.csproj
@@ -24,4 +24,10 @@
     <ProjectReference Include="..\TaskLayer\TaskLayer.csproj" />
   </ItemGroup>
 
+	<ItemGroup>
+		<AssemblyAttribute Include="System.Runtime.CompilerServices.InternalsVisibleTo">
+			<_Parameter1>Test</_Parameter1>
+		</AssemblyAttribute>
+	</ItemGroup>
+
 </Project>
diff --git a/GuiFunctions/TomlFileFolderSerializer.cs b/GuiFunctions/TomlFileFolderSerializer.cs
index cb62491a1..23baa4e4e 100644
--- a/GuiFunctions/TomlFileFolderSerializer.cs
+++ b/GuiFunctions/TomlFileFolderSerializer.cs
@@ -64,7 +64,7 @@ public static bool CheckforTypeFolder(Type type)
         /// <returns></returns>
         public static string GetFilePath(Type folder, string name)
         {
-            string txtFilePath = folder.ToString() + "/" + name + ".toml";
+            string txtFilePath = Path.Combine(folder.FullName, $"{name}.toml");
             string path = Path.Combine(PathToCheck, txtFilePath);
             return path;
         }
diff --git a/GuiFunctions/ViewModels/TaskSettingViewModel.cs b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
index f3cdcf46d..058df155e 100644
--- a/GuiFunctions/ViewModels/TaskSettingViewModel.cs
+++ b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
@@ -2,6 +2,7 @@
 using System.Collections;
 using System.Collections.Generic;
 using System.Collections.ObjectModel;
+using System.IO;
 using System.Linq;
 using System.Reflection;
 using System.Text;
@@ -9,6 +10,7 @@
 using System.Windows;
 using System.Windows.Input;
 using Easy.Common.Extensions;
+using Org.BouncyCastle.Asn1.X509.Qualified;
 using OxyPlot;
 using TaskLayer;
 
@@ -48,7 +50,8 @@ public string SelectedSettings
             set
             {
                 selectedSettings = value;
-                UpdateFieldsInGuiWithNewTask.Invoke(AllSettingsDict[SelectedSettings]);
+                if (UpdateFieldsInGuiWithNewTask is not null)
+                    UpdateFieldsInGuiWithNewTask.Invoke(AllSettingsDict[SelectedSettings]);
                 OnPropertyChanged(nameof(SelectedSettings));
             }
         }
@@ -66,9 +69,21 @@ public Dictionary<string, MetaMorpheusTask> AllSettingsDict
       
         public ICommand SaveSettingsCommand { get; set; }
         public ICommand DeleteSettingsCommand { get; set; }
+        public ICommand SaveAsDefaultSettingsCommand { get; set; }
 
+        /// <summary>
+        /// 
+        /// </summary>
         public MetaMorpheusTask TheTask { get; set; }
+
+        /// <summary>
+        /// 
+        /// </summary>
         public Func<MetaMorpheusTask> GetTaskFromGui { get; set; }
+
+        /// <summary>
+        /// 
+        /// </summary>
         public Action<MetaMorpheusTask> UpdateFieldsInGuiWithNewTask { get; set; }
 
         #endregion
@@ -96,10 +111,44 @@ public TaskSettingViewModel(MetaMorpheusTask task, Action<MetaMorpheusTask> upda
             }
             AllSettingsDict = tempDict;
 
+            
             SaveSettingsCommand = new RelayCommand(SaveSettings);
             DeleteSettingsCommand = new RelayCommand(DeleteSettings);
+            SaveAsDefaultSettingsCommand = new RelayCommand(SaveAsDefaultSettings);
+            SelectDefaultAuto();
         }
 
+        /// <summary>
+        /// ONLY USED FOR TESTING
+        /// </summary>
+        /// <param name="task"></param>
+        internal TaskSettingViewModel(MetaMorpheusTask task)
+        {
+            TheTask = task;
+
+            var type = task.GetType();
+            MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("LoadAllOfTypeT");
+            MethodInfo genericMethod = method.MakeGenericMethod(type);
+            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] { TheTask }));
+
+            var keys = result.Keys.Cast<string>().ToList();
+            var values = result.Values.Cast<MetaMorpheusTask>().ToList();
+            Dictionary<string, MetaMorpheusTask> tempDict = new();
+            for (int i = 0; i < keys.Count; i++)
+            {
+                tempDict.Add(keys[i], values[i]);
+            }
+            AllSettingsDict = tempDict;
+
+            SaveSettingsCommand = new RelayCommand(SaveSettings);
+            DeleteSettingsCommand = new RelayCommand(DeleteSettings);
+            SaveAsDefaultSettingsCommand = new RelayCommand(SaveAsDefaultSettings);
+            SelectDefaultAuto();
+        }
+
+        /// <summary>
+        ///  Used only for design time viewing of data 
+        /// </summary>
         public TaskSettingViewModel()
         {
             MetaMorpheusTask task = new SearchTask();
@@ -121,6 +170,8 @@ public TaskSettingViewModel()
 
             SaveSettingsCommand = new RelayCommand(SaveSettings);
             DeleteSettingsCommand = new RelayCommand(DeleteSettings);
+            SaveAsDefaultSettingsCommand = new RelayCommand(SaveAsDefaultSettings);
+            SelectDefaultAuto();
         }
 
         
@@ -142,13 +193,17 @@ public void SaveSettings()
                 MessageBox.Show("Default Setting cannot be modified. Please use \"Save as Default\" button", "Modifying Default Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
                 return;
             }
-
+            
             TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings);
-            TomlFileFolderSerializer.Save(SelectedSettings, TheTask);
             AllSettingsDict.Remove(SelectedSettings);
+
+            TheTask = GetTaskFromGui.Invoke();
+
+            TomlFileFolderSerializer.Save(SelectedSettings, TheTask);
             AllSettingsDict.Add(SelectedSettings, TheTask);
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
+            SelectDefaultAuto();
         }
 
     public void SaveSettingsFromWindow()
@@ -156,12 +211,12 @@ public void SaveSettingsFromWindow()
 
             if (TypedSettingsName is null || TypedSettingsName.IsNullOrEmptyOrWhiteSpace())
             {
-                MessageBox.Show("The name cannot be empty", "Save Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                MessageBox.Show("The name cannot be empty", "Empty Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
                 TypedSettingsName = "";
                 return;
             }
 
-        string settingsName = TypedSettingsName.ToString();
+            string settingsName = TypedSettingsName.ToString();
 
             if (AllSettingsDict.ContainsKey(settingsName))
             {
@@ -170,12 +225,27 @@ public void SaveSettingsFromWindow()
                 return;
             }
 
+            // get current gui representation
+            TheTask = GetTaskFromGui.Invoke();
             AllSettingsDict.Add(settingsName, TheTask);
+
+            // revert modified settings before saving
+            string settingsThatWereModifiedButNotMeantToBeSavedPath = TomlFileFolderSerializer.GetFilePath(TheTask.GetType(), SelectedSettings);
+            var type = TheTask.GetType();
+            MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("Deserialize");
+            MethodInfo genericMethod = method.MakeGenericMethod(type);
+            var reloadedModifiedSettings = genericMethod.Invoke(null, new object[] { settingsThatWereModifiedButNotMeantToBeSavedPath });
+            AllSettingsDict[SelectedSettings] = reloadedModifiedSettings as MetaMorpheusTask;
+
+            // save modified settings with new name
+            SelectedSettings = settingsName;
+            TomlFileFolderSerializer.Save(settingsName, TheTask);
+
+            // update gui representation
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
-            TomlFileFolderSerializer.Save(settingsName, TheTask);
             TypedSettingsName = "";
-            
+            SelectDefaultAuto();
         }
 
         public void DeleteSettings()
@@ -184,6 +254,7 @@ public void DeleteSettings()
             {
                 return;
             }
+
             if (SelectedSettings.Contains("(Default)"))
             {
                 MessageBox.Show("Default Setting cannot be deleted", "Deleting Default Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
@@ -194,12 +265,55 @@ public void DeleteSettings()
             AllSettingsDict.Remove(SelectedSettings);
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
+            SelectDefaultAuto();
         }
 
+        public void SaveAsDefaultSettings()
+        {
+            if (SelectedSettings == null)
+            {
+                return;
+            }
+
+            if (SelectedSettings.Contains("(Default)"))
+            {
+                MessageBox.Show("It's already a default setting", "Repeatted Setting Default Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                return;
+            }
+
+            // if there is currently a default
+            if (AllSettingsDict.Any(p => p.Key.Contains("(Default)")))
+            {
+                var oldDefault = AllSettingsDict.First(p => p.Key.Contains("(Default)"));
+                string oldDefaultName = oldDefault.Key;
+                string changedOldDefaultName = oldDefaultName.Remove(oldDefaultName.Length - 9);
+                var oldDefaultValue = oldDefault.Value;
+                TomlFileFolderSerializer.Delete(oldDefaultValue.GetType(), oldDefaultName);
+                AllSettingsDict.Remove(oldDefaultName);
+                TomlFileFolderSerializer.Save(changedOldDefaultName, oldDefaultValue);
+                AllSettingsDict.Add(changedOldDefaultName, oldDefaultValue);               
+            }
+
+            var temp = TheTask;
+            TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings); 
+            AllSettingsDict.Remove(SelectedSettings);
+            TomlFileFolderSerializer.Save(SelectedSettings + "(Default)", temp);
+            AllSettingsDict.Add(SelectedSettings + "(Default)", temp);
+            OnPropertyChanged(nameof(AllSettings));
+            OnPropertyChanged(nameof(AllSettingsDict));
+            SelectDefaultAuto();
+        }
+
+        
+
     #endregion
 
         #region Helpers
-
+        private void SelectDefaultAuto()
+        {
+            var defaultSetting = AllSettingsDict.First(p => p.Key.Contains("(Default)"));
+            SelectedSettings = defaultSetting.Key;
+        }
    
 
         #endregion

From aa3ce6d1bb21e8d5def5adeb87b751df05e9510d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=B0=E7=8E=AE=20=E7=8E=8B?= <wfw2310165722@outlook.com>
Date: Wed, 26 Apr 2023 15:08:48 -0500
Subject: [PATCH 08/20] Some Gui bugs fixed.

---
 GUI/TaskWindows/SearchTaskWindow.xaml.cs      |  2 +-
 .../ViewModels/TaskSettingViewModel.cs        | 98 +++++++------------
 2 files changed, 34 insertions(+), 66 deletions(-)

diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index 716059a17..a87fce9dc 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -52,7 +52,7 @@ public SearchTaskWindow(SearchTask task)
 
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
             
-            UpdateFieldsFromTask(TheTask);
+            //UpdateFieldsFromTask(TheTask);
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
 
             if (task == null)
diff --git a/GuiFunctions/ViewModels/TaskSettingViewModel.cs b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
index 058df155e..9116995db 100644
--- a/GuiFunctions/ViewModels/TaskSettingViewModel.cs
+++ b/GuiFunctions/ViewModels/TaskSettingViewModel.cs
@@ -74,7 +74,7 @@ public Dictionary<string, MetaMorpheusTask> AllSettingsDict
         /// <summary>
         /// 
         /// </summary>
-        public MetaMorpheusTask TheTask { get; set; }
+        public MetaMorpheusTask TheTask => AllSettingsDict[SelectedSettings];
 
         /// <summary>
         /// 
@@ -92,72 +92,41 @@ public Dictionary<string, MetaMorpheusTask> AllSettingsDict
 
         public TaskSettingViewModel(MetaMorpheusTask task, Action<MetaMorpheusTask> updateFieldsInGuiEventHandler, Func<MetaMorpheusTask> getTaskFromGui)
         {
-            
-            TheTask = task;
+            // initial construction
+            var type = task.GetType();
             UpdateFieldsInGuiWithNewTask = updateFieldsInGuiEventHandler;
             GetTaskFromGui = getTaskFromGui;
-
-            var type = task.GetType();
-            MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("LoadAllOfTypeT");
-            MethodInfo genericMethod = method.MakeGenericMethod(type);
-            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] {TheTask}));
-
-            var keys = result.Keys.Cast<string>().ToList();
-            var values = result.Values.Cast<MetaMorpheusTask>().ToList();
-            Dictionary<string, MetaMorpheusTask> tempDict = new();
-            for(int i = 0; i < keys.Count; i++)
-            {
-                tempDict.Add(keys[i], values[i]);
-            }
-            AllSettingsDict = tempDict;
-
-            
             SaveSettingsCommand = new RelayCommand(SaveSettings);
             DeleteSettingsCommand = new RelayCommand(DeleteSettings);
             SaveAsDefaultSettingsCommand = new RelayCommand(SaveAsDefaultSettings);
-            SelectDefaultAuto();
-        }
-
-        /// <summary>
-        /// ONLY USED FOR TESTING
-        /// </summary>
-        /// <param name="task"></param>
-        internal TaskSettingViewModel(MetaMorpheusTask task)
-        {
-            TheTask = task;
 
-            var type = task.GetType();
+            // load in all settings from directory of specific object type
             MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("LoadAllOfTypeT");
             MethodInfo genericMethod = method.MakeGenericMethod(type);
-            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] { TheTask }));
+            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] {task}));
 
             var keys = result.Keys.Cast<string>().ToList();
             var values = result.Values.Cast<MetaMorpheusTask>().ToList();
             Dictionary<string, MetaMorpheusTask> tempDict = new();
-            for (int i = 0; i < keys.Count; i++)
+            for(int i = 0; i < keys.Count; i++)
             {
                 tempDict.Add(keys[i], values[i]);
             }
             AllSettingsDict = tempDict;
 
-            SaveSettingsCommand = new RelayCommand(SaveSettings);
-            DeleteSettingsCommand = new RelayCommand(DeleteSettings);
-            SaveAsDefaultSettingsCommand = new RelayCommand(SaveAsDefaultSettings);
             SelectDefaultAuto();
         }
 
         /// <summary>
-        ///  Used only for design time viewing of data 
+        /// ONLY USED FOR TESTING
         /// </summary>
-        public TaskSettingViewModel()
+        /// <param name="task"></param>
+        internal TaskSettingViewModel(MetaMorpheusTask task = null)
         {
-            MetaMorpheusTask task = new SearchTask();
-            TheTask = task;
-            var temp = typeof(SearchTask);
-            var type = task.GetType();
+            var type = task.GetType() ?? typeof(SearchTask);
             MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("LoadAllOfTypeT");
             MethodInfo genericMethod = method.MakeGenericMethod(type);
-            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] { TheTask }));
+            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] { task ?? new SearchTask() }));
 
             var keys = result.Keys.Cast<string>().ToList();
             var values = result.Values.Cast<MetaMorpheusTask>().ToList();
@@ -173,7 +142,6 @@ public TaskSettingViewModel()
             SaveAsDefaultSettingsCommand = new RelayCommand(SaveAsDefaultSettings);
             SelectDefaultAuto();
         }
-
         
         #endregion
 
@@ -193,14 +161,12 @@ public void SaveSettings()
                 MessageBox.Show("Default Setting cannot be modified. Please use \"Save as Default\" button", "Modifying Default Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
                 return;
             }
-            
+
+            var taskFromGUI = GetTaskFromGui.Invoke();
             TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings);
             AllSettingsDict.Remove(SelectedSettings);
-
-            TheTask = GetTaskFromGui.Invoke();
-
-            TomlFileFolderSerializer.Save(SelectedSettings, TheTask);
-            AllSettingsDict.Add(SelectedSettings, TheTask);
+            TomlFileFolderSerializer.Save(SelectedSettings, taskFromGUI);
+            AllSettingsDict.Add(SelectedSettings, taskFromGUI);
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
             SelectDefaultAuto();
@@ -226,12 +192,12 @@ public void SaveSettingsFromWindow()
             }
 
             // get current gui representation
-            TheTask = GetTaskFromGui.Invoke();
-            AllSettingsDict.Add(settingsName, TheTask);
+            var taskFromGUI = GetTaskFromGui.Invoke();
+            AllSettingsDict.Add(settingsName, taskFromGUI);
 
             // revert modified settings before saving
-            string settingsThatWereModifiedButNotMeantToBeSavedPath = TomlFileFolderSerializer.GetFilePath(TheTask.GetType(), SelectedSettings);
-            var type = TheTask.GetType();
+            string settingsThatWereModifiedButNotMeantToBeSavedPath = TomlFileFolderSerializer.GetFilePath(taskFromGUI.GetType(), SelectedSettings);
+            var type = taskFromGUI.GetType();
             MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("Deserialize");
             MethodInfo genericMethod = method.MakeGenericMethod(type);
             var reloadedModifiedSettings = genericMethod.Invoke(null, new object[] { settingsThatWereModifiedButNotMeantToBeSavedPath });
@@ -239,7 +205,7 @@ public void SaveSettingsFromWindow()
 
             // save modified settings with new name
             SelectedSettings = settingsName;
-            TomlFileFolderSerializer.Save(settingsName, TheTask);
+            TomlFileFolderSerializer.Save(settingsName, taskFromGUI);
 
             // update gui representation
             OnPropertyChanged(nameof(AllSettings));
@@ -281,24 +247,26 @@ public void SaveAsDefaultSettings()
                 return;
             }
 
-            // if there is currently a default
+            var temp = TheTask;
+            string currentName = SelectedSettings;
+
+            // if there is currently a default, remove "(Default)" and save with new name
             if (AllSettingsDict.Any(p => p.Key.Contains("(Default)")))
             {
                 var oldDefault = AllSettingsDict.First(p => p.Key.Contains("(Default)"));
-                string oldDefaultName = oldDefault.Key;
-                string changedOldDefaultName = oldDefaultName.Remove(oldDefaultName.Length - 9);
-                var oldDefaultValue = oldDefault.Value;
-                TomlFileFolderSerializer.Delete(oldDefaultValue.GetType(), oldDefaultName);
-                AllSettingsDict.Remove(oldDefaultName);
-                TomlFileFolderSerializer.Save(changedOldDefaultName, oldDefaultValue);
-                AllSettingsDict.Add(changedOldDefaultName, oldDefaultValue);               
+                string newOldDefaultName = oldDefault.Key.Remove(oldDefault.Key.Length - 9); // TODO
+                TomlFileFolderSerializer.Delete(oldDefault.Value.GetType(), oldDefault.Key);
+                AllSettingsDict.Remove(oldDefault.Key);
+                TomlFileFolderSerializer.Save(newOldDefaultName, oldDefault.Value);
+                AllSettingsDict.Add(newOldDefaultName, oldDefault.Value);
             }
 
-            var temp = TheTask;
+            // save currently selected settings as new default
             TomlFileFolderSerializer.Delete(TheTask.GetType(), SelectedSettings); 
             AllSettingsDict.Remove(SelectedSettings);
-            TomlFileFolderSerializer.Save(SelectedSettings + "(Default)", temp);
-            AllSettingsDict.Add(SelectedSettings + "(Default)", temp);
+            TomlFileFolderSerializer.Save(currentName + "(Default)", temp);
+            AllSettingsDict.Add(currentName + "(Default)", temp);
+
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
             SelectDefaultAuto();

From 4d0e2cb95f0fb3c7062be0a7e040cd3fb485b684 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 26 Apr 2023 15:17:25 -0500
Subject: [PATCH 09/20] Developed ability to test with actions and methods

---
 GUI/TaskWindows/GPTMDTaskWindow.xaml.cs  |  7 +++++--
 GUI/TaskWindows/SearchTaskWindow.xaml.cs |  2 --
 Test/SaveSettingsTests.cs                | 13 ++++++++++++-
 3 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs b/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
index fa0270c33..ede739e62 100644
--- a/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
@@ -29,15 +29,18 @@ public partial class GptmdTaskWindow : Window
         private readonly ObservableCollection<ModTypeForTreeViewModel> GptmdModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForTreeViewModel>();
         private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
         private CustomFragmentationWindow CustomFragmentationWindow;
+        public TaskSettingViewModel TaskSettingViewModel { get; set; }
 
         public GptmdTaskWindow(GptmdTask myGPTMDtask)
         {
             InitializeComponent();
+            PopulateChoices();
             TheTask = myGPTMDtask ?? new GptmdTask();
 
+            var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as GptmdTask);
+
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
-            PopulateChoices();
-            UpdateFieldsFromTask(TheTask);
+            //UpdateFieldsFromTask(TheTask);
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
 
             if (myGPTMDtask == null)
diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index 716059a17..e77470d48 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -426,8 +426,6 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             DialogResult = true;
         }
 
-
-
         private SearchTask GetTaskFromGui()
         {
             CleavageSpecificity searchModeType = GetSearchModeType(); //change search type to semi or non if selected
diff --git a/Test/SaveSettingsTests.cs b/Test/SaveSettingsTests.cs
index 86dd46d94..cac483f60 100644
--- a/Test/SaveSettingsTests.cs
+++ b/Test/SaveSettingsTests.cs
@@ -36,10 +36,21 @@ public static void OneTimeTearDown()
             Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"), true);
         }
 
+        private MetaMorpheusTask GetFakeSearchTaskFromGui() => new SearchTask();
+        private MetaMorpheusTask GetFakeGptmdTaskFromGui() => new GptmdTask();
+        private MetaMorpheusTask GetFakeCalibrationTaskFromGui() => new CalibrationTask();
+        private MetaMorpheusTask GetFakeXLSearchTaskFromGui() => new XLSearchTask();
+        private MetaMorpheusTask GetFakeGlycoSearchTaskFromGui() => new GlycoSearchTask();
+
+        private void UpdateFieldsFromNewTask(MetaMorpheusTask task)
+        {
+
+        }
+        
         [Test]
         public void testConstructor()
         {
-            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask());
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), UpdateFieldsFromNewTask, GetFakeSearchTaskFromGui);
             var a = testTaskSettingViewModel.AllSettings;
             string[] testArrayOfKeys = testTaskSettingViewModel.AllSettingsDict.Keys.ToArray();
             Assert.That(testArrayOfKeys[0].Equals("customBCZ.toml"));

From f421159be18dc97d38e9c0bafc97fd81429558e8 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 27 Apr 2023 15:59:08 -0500
Subject: [PATCH 10/20] Added testing class for window operations

---
 Test/SaveSettingsTests.cs | 42 ++++++++++++++++++++++++++++++---------
 1 file changed, 33 insertions(+), 9 deletions(-)

diff --git a/Test/SaveSettingsTests.cs b/Test/SaveSettingsTests.cs
index cac483f60..aec141927 100644
--- a/Test/SaveSettingsTests.cs
+++ b/Test/SaveSettingsTests.cs
@@ -36,21 +36,45 @@ public static void OneTimeTearDown()
             Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"), true);
         }
 
-        private MetaMorpheusTask GetFakeSearchTaskFromGui() => new SearchTask();
-        private MetaMorpheusTask GetFakeGptmdTaskFromGui() => new GptmdTask();
-        private MetaMorpheusTask GetFakeCalibrationTaskFromGui() => new CalibrationTask();
-        private MetaMorpheusTask GetFakeXLSearchTaskFromGui() => new XLSearchTask();
-        private MetaMorpheusTask GetFakeGlycoSearchTaskFromGui() => new GlycoSearchTask();
-
-        private void UpdateFieldsFromNewTask(MetaMorpheusTask task)
+        private class FakeGuiWindow
         {
+            public MetaMorpheusTask TheTask { get; private set; }
+            public FakeGuiWindow(MyTask taskType)
+            {
+                TheTask = taskType switch
+                {
+                    MyTask.Search => new SearchTask(),
+                    MyTask.Gptmd => new GptmdTask(),
+                    MyTask.Calibrate => new CalibrationTask(),
+                    MyTask.XLSearch => new XLSearchTask(),
+                    MyTask.GlycoSearch => new GlycoSearchTask(),
+                    _ => throw new ArgumentOutOfRangeException(nameof(taskType), taskType, null)
+                };
+            }
+
+            public MetaMorpheusTask GetTaskFromGui()
+            {
+                return TheTask;
+            }
 
+            public void UpdateFieldsFromNewTask(MetaMorpheusTask task)
+            {
+                TheTask = task;
+            }
         }
-        
+
+        [Test]
+        public void ExampleTest()
+        {
+            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+        }
+
         [Test]
         public void testConstructor()
         {
-            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), UpdateFieldsFromNewTask, GetFakeSearchTaskFromGui);
+            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
             var a = testTaskSettingViewModel.AllSettings;
             string[] testArrayOfKeys = testTaskSettingViewModel.AllSettingsDict.Keys.ToArray();
             Assert.That(testArrayOfKeys[0].Equals("customBCZ.toml"));

From 957185fc6bf608b1cf594c3750356fc9310fdc8f Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 27 Apr 2023 18:17:47 -0500
Subject: [PATCH 11/20] Got the other windows ready

---
 GUI/TaskWindows/CalibrateTaskWindow.xaml.cs   | 26 ++++++++++++----
 GUI/TaskWindows/GPTMDTaskWindow.xaml.cs       | 30 ++++++++++++-------
 GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs | 25 ++++++++++++----
 GUI/TaskWindows/SearchTaskWindow.xaml.cs      |  6 ++--
 GUI/TaskWindows/XLSearchTaskWindow.xaml.cs    | 26 +++++++++++-----
 5 files changed, 80 insertions(+), 33 deletions(-)

diff --git a/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs b/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
index 68aa2fc4c..4b385e0e0 100644
--- a/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
@@ -28,15 +28,19 @@ public partial class CalibrateTaskWindow : Window
         private readonly ObservableCollection<ModTypeForLoc> LocalizeModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForLoc>();
         private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
         private CustomFragmentationWindow CustomFragmentationWindow;
+        private TaskSettingViewModel TaskSettingViewModel;
 
         public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
         {
             InitializeComponent();
+            PopulateChoices();
             TheTask = myCalibrateTask ?? new CalibrationTask();
 
+            var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as CalibrationTask);
+            TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
+            //TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
-            PopulateChoices();
-            UpdateFieldsFromTask(TheTask);
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
 
             if (myCalibrateTask == null)
@@ -187,15 +191,25 @@ private void CancelButton_Click(object sender, RoutedEventArgs e)
         }
 
         private void SaveButton_Click(object sender, RoutedEventArgs e)
+        {
+            CalibrationTask task = GetTaskFromGui();
+            if (task == null)
+                return;
+
+            TheTask = task;
+            DialogResult = true;
+        }
+
+        private CalibrationTask GetTaskFromGui()
         {
             string fieldNotUsed = "1";
 
             if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecursorMassToleranceTextBox.Text, ProductMassToleranceTextBox.Text, MissedCleavagesTextBox.Text,
                  MaxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, MaxThreadsTextBox.Text, MinScoreAllowed.Text,
-                 fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, null, null, fieldNotUsed, MaxModsPerPeptideTextBox.Text, fieldNotUsed, 
+                 fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, null, null, fieldNotUsed, MaxModsPerPeptideTextBox.Text, fieldNotUsed,
                  null, null, null))
             {
-                return;
+                return null;
             }
 
             Protease protease = (Protease)ProteaseComboBox.SelectedItem;
@@ -226,7 +240,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
 
             if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
             {
-                return;
+                return null;
             }
 
             var listOfModsFixed = new List<(string, string)>();
@@ -296,7 +310,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             }
 
             TheTask.CalibrationParameters.WriteIndexedMzml = writeIndexMzmlCheckbox.IsChecked.Value;
-            DialogResult = true;
+            return TheTask;
         }
 
         private void CheckIfNumber(object sender, TextCompositionEventArgs e)
diff --git a/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs b/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
index ede739e62..f5d4347dd 100644
--- a/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
@@ -29,7 +29,7 @@ public partial class GptmdTaskWindow : Window
         private readonly ObservableCollection<ModTypeForTreeViewModel> GptmdModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForTreeViewModel>();
         private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
         private CustomFragmentationWindow CustomFragmentationWindow;
-        public TaskSettingViewModel TaskSettingViewModel { get; set; }
+        private TaskSettingViewModel TaskSettingViewModel;
 
         public GptmdTaskWindow(GptmdTask myGPTMDtask)
         {
@@ -38,9 +38,10 @@ public GptmdTaskWindow(GptmdTask myGPTMDtask)
             TheTask = myGPTMDtask ?? new GptmdTask();
 
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as GptmdTask);
+            TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
+            //TaskSettingsCtrl.DataContext = TaskSettingViewModel;
 
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
-            //UpdateFieldsFromTask(TheTask);
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
 
             if (myGPTMDtask == null)
@@ -352,15 +353,25 @@ private void ProteaseSpecificUpdate(object sender, TextChangedEventArgs e)
         }
 
         private void SaveButton_Click(object sender, RoutedEventArgs e)
+        {
+            GptmdTask task = GetTaskFromGui();
+            if (task is null)
+                return;
+
+            TheTask = task;
+            DialogResult = true;
+        }
+
+        public GptmdTask GetTaskFromGui()
         {
             string fieldNotUsed = "1";
 
             if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecursorMassToleranceTextBox.Text, ProductMassToleranceTextBox.Text, MissedCleavagesTextBox.Text,
                  MaxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, MaxThreadsTextBox.Text, MinScoreAllowed.Text,
-                fieldNotUsed, fieldNotUsed, DeconvolutionMaxAssumedChargeStateTextBox.Text, NumberOfPeaksToKeepPerWindowTextBox.Text, MinimumAllowedIntensityRatioToBasePeakTexBox.Text, 
+                fieldNotUsed, fieldNotUsed, DeconvolutionMaxAssumedChargeStateTextBox.Text, NumberOfPeaksToKeepPerWindowTextBox.Text, MinimumAllowedIntensityRatioToBasePeakTexBox.Text,
                 null, null, fieldNotUsed, fieldNotUsed, fieldNotUsed, null, null, null))
             {
-                return;
+                return null;
             }
 
             Protease protease = (Protease)ProteaseComboBox.SelectedItem;
@@ -403,7 +414,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
 
             if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
             {
-                return;
+                return null;
             }
 
             bool TrimMs1Peaks = TrimMs1.IsChecked.Value;
@@ -419,7 +430,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
                 else
                 {
                     MessageBox.Show("The value that you entered for number of peaks to keep is not acceptable. Try again.");
-                    return;
+                    return null;
                 }
             }
 
@@ -433,7 +444,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
                 else
                 {
                     MessageBox.Show("The value that you entered for minimum allowed intensity ratio to keep is not acceptable. Try again.");
-                    return;
+                    return null;
                 }
             }
 
@@ -461,7 +472,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
                     dissociationType: dissociationType,
                     scoreCutoff: double.Parse(MinScoreAllowed.Text, CultureInfo.InvariantCulture),
                     precursorMassTolerance: precursorMassTolerance,
-                    productMassTolerance: productMassTolerance,                    
+                    productMassTolerance: productMassTolerance,
                     trimMs1Peaks: TrimMs1Peaks,
                     trimMsMsPeaks: TrimMsMsPeaks,
                     numberOfPeaksToKeepPerWindow: numPeaksToKeep,
@@ -480,8 +491,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             }
 
             TheTask.CommonParameters = commonParamsToSave;
-
-            DialogResult = true;
+            return TheTask;
         }
 
         private void CheckIfNumber(object sender, TextCompositionEventArgs e)
diff --git a/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs b/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
index 866cbc2b8..3ed169cba 100644
--- a/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
@@ -30,7 +30,7 @@ public partial class GlycoSearchTaskWindow : Window
         private readonly ObservableCollection<ModTypeForTreeViewModel> FixedModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForTreeViewModel>();
         private readonly ObservableCollection<ModTypeForTreeViewModel> VariableModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForTreeViewModel>();
         private CustomFragmentationWindow CustomFragmentationWindow;
-
+        private TaskSettingViewModel TaskSettingViewModel;
         public GlycoSearchTaskWindow() : this(null)
         {
         }
@@ -40,7 +40,11 @@ public GlycoSearchTaskWindow(GlycoSearchTask task)
             InitializeComponent();
             PopulateChoices();
             TheTask = task ?? new GlycoSearchTask();
-            UpdateFieldsFromTask(TheTask);
+
+            var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as GlycoSearchTask);
+            TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
+            //TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+            
 
             if (task == null)
             {
@@ -226,15 +230,25 @@ private void CancelButton_Click(object sender, RoutedEventArgs e)
         }
 
         private void SaveButton_Click(object sender, RoutedEventArgs e)
+        {
+            GlycoSearchTask task = GetTaskFromGui();
+            if (task is null)
+                return;
+
+            TheTask = task;
+            DialogResult = true;
+        }
+
+        private GlycoSearchTask GetTaskFromGui()
         {
             string fieldNotUsed = "1";
 
             if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecusorMsTlTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
                 maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
-                fieldNotUsed, fieldNotUsed, fieldNotUsed, TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text, TxtBoxMaxModPerPep.Text, 
+                fieldNotUsed, fieldNotUsed, fieldNotUsed, TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text, TxtBoxMaxModPerPep.Text,
                 fieldNotUsed, null, null, null))
             {
-                return;
+                return null;
             }
 
             DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[DissociationTypeComboBox.SelectedItem.ToString()];
@@ -353,8 +367,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
                 assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down");
 
             TheTask.CommonParameters = commonParamsToSave;
-
-            DialogResult = true;
+            return TheTask;
         }
 
         private void ApmdExpander_Collapsed(object sender, RoutedEventArgs e)
diff --git a/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index 7b8fc6f19..ba8a5eb41 100644
--- a/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -35,7 +35,7 @@ public partial class SearchTaskWindow : Window
         private readonly ObservableCollection<SilacInfoForDataGrid> StaticSilacLabelsObservableCollection = new ObservableCollection<SilacInfoForDataGrid>();
         private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
         private CustomFragmentationWindow CustomFragmentationWindow;
-        public TaskSettingViewModel TaskSettingViewModel { get; set; }
+        private TaskSettingViewModel TaskSettingViewModel;
 
 
         internal SearchTask TheTask { get; private set; }
@@ -51,8 +51,6 @@ public SearchTaskWindow(SearchTask task)
             TaskSettingsCtrl.DataContext = TaskSettingViewModel;
 
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
-            
-            //UpdateFieldsFromTask(TheTask);
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
 
             if (task == null)
@@ -418,7 +416,7 @@ private void CancelButton_Click(object sender, RoutedEventArgs e)
 
         private void SaveButton_Click(object sender, RoutedEventArgs e)
         {
-            SearchTask task =  GetTaskFromGui();
+            SearchTask task = GetTaskFromGui();
             if (task == null)
                 return;
 
diff --git a/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs b/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
index 0161e021c..e08dba3ec 100644
--- a/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
+++ b/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
@@ -29,13 +29,16 @@ public partial class XLSearchTaskWindow : Window
         private readonly ObservableCollection<ModTypeForTreeViewModel> FixedModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForTreeViewModel>();
         private readonly ObservableCollection<ModTypeForTreeViewModel> VariableModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForTreeViewModel>();
         private CustomFragmentationWindow CustomFragmentationWindow;
-
+        private TaskSettingViewModel TaskSettingViewModel;
         public XLSearchTaskWindow(XLSearchTask task)
         {
             InitializeComponent();
             PopulateChoices();
             TheTask = task ?? new XLSearchTask();
-            UpdateFieldsFromTask(TheTask);
+
+            var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as XLSearchTask);
+            TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
+            //TaskSettingsCtrl.DataContext = TaskSettingViewModel;
 
             if (task == null)
             {
@@ -234,15 +237,25 @@ private void CancelButton_Click(object sender, RoutedEventArgs e)
         }
 
         private void SaveButton_Click(object sender, RoutedEventArgs e)
+        {
+            XLSearchTask task = GetTaskFromGui();
+            if (task == null)
+                return;
+
+            TheTask = task;
+            DialogResult = true;
+        }
+
+        private XLSearchTask GetTaskFromGui()
         {
             string fieldNotUsed = "1";
 
             if (!GlobalGuiSettings.CheckTaskSettingsValidity(XLPrecusorMsTlTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
                 maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
-                fieldNotUsed, fieldNotUsed, fieldNotUsed, TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text, 
+                fieldNotUsed, fieldNotUsed, fieldNotUsed, TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text,
                 fieldNotUsed, fieldNotUsed, null, null, null))
             {
-                return;
+                return null;
             }
 
             DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[DissociationTypeComboBox.SelectedItem.ToString()];
@@ -260,7 +273,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
 
             CustomFragmentationWindow.Close();
 
-            TheTask.XlSearchParameters.CrosslinkSearchTopNum = int.Parse(txtXLTopNum.Text, CultureInfo.InvariantCulture);           
+            TheTask.XlSearchParameters.CrosslinkSearchTopNum = int.Parse(txtXLTopNum.Text, CultureInfo.InvariantCulture);
             TheTask.XlSearchParameters.CrosslinkAtCleavageSite = ckbCrosslinkAtCleavageSite.IsChecked.Value;
             TheTask.XlSearchParameters.Crosslinker = (Crosslinker)cbCrosslinkers.SelectedItem;
 
@@ -344,8 +357,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
                 assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down");
 
             TheTask.CommonParameters = commonParamsToSave;
-
-            DialogResult = true;
+            return TheTask;
         }
 
         private void ApmdExpander_Collapsed(object sender, RoutedEventArgs e)

From ffacfc64ec4c3f009eb81cc4852f154aca3e82ab Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=B0=E7=8E=AE=20=E7=8E=8B?= <wfw2310165722@outlook.com>
Date: Tue, 19 Sep 2023 14:16:36 -0500
Subject: [PATCH 12/20] Replace added files with what's in the old hard drive.

---
 .../GUI/TaskWindows/SearchTaskWindow.xaml     | 185 +++++++-----------
 .../GUI/TaskWindows/SearchTaskWindow.xaml.cs  | 125 ++++--------
 .../GUI/Views/SaveSettingsWindow.xaml         |   6 +-
 .../GuiFunctions/TomlFileFolderSerializer.cs  |   2 +-
 .../ViewModels/TaskSettingViewModel.cs        |  39 +++-
 MetaMorpheus/Test/SaveSettingsTests.cs        | 108 +++++++++-
 .../Test/TaskSettingViewModelTests.cs         |   2 +-
 7 files changed, 254 insertions(+), 213 deletions(-)

diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
index 9b46c524b..8b16380f1 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
@@ -14,8 +14,7 @@
 
         <!-- used in Quantifications -->
         <BooleanToVisibilityConverter x:Key="bool2VisConverter" />
-        <local:BooleanOrConverter x:Key="boolOrConverter"/>
-        <local:BooleanOrToVisibilityConverter x:Key="boolOr2VisConverter"/>
+        <guiFunctions:BooleanOrConverter x:Key="boolOrConverter"/>
 
         <!-- Style GroupBoxes -->
         <Style TargetType="GroupBox">
@@ -36,10 +35,6 @@
             <Setter Property="VerticalContentAlignment" Value="Center"/>
             <Setter Property="Padding" Value="3 0 0 0"/>
         </Style>
-        <Style TargetType="local:DoubleTextBoxControl">
-            <Setter Property="VerticalContentAlignment" Value="Center"/>
-            <Setter Property="Padding" Value="3 0 0 0"/>
-        </Style>
     </Window.Resources>
     <Grid>
         <Grid.RowDefinitions>
@@ -118,13 +113,12 @@
                                     <RowDefinition Height="1*"/>
                                     <RowDefinition Height="1*"/>
                                     <RowDefinition Height="1*"/>
-                                    <RowDefinition Height="1*"/>
                                 </Grid.RowDefinitions>
 
                                 <!-- Precursor Mass Tolerance -->
                                 <StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="1" Grid.Row="0">
                                     <Label Content="Precursor Mass Tolerance:" Width="150" />
-                                    <local:DoubleTextBoxControl x:Name="PrecursorMassToleranceTextBox" HorizontalAlignment="Left" TextWrapping="Wrap" Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
+                                    <TextBox x:Name="PrecursorMassToleranceTextBox" PreviewTextInput="CheckIfNumber" HorizontalAlignment="Left" TextWrapping="Wrap" Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
                                         <TextBox.ToolTip>
                                             <TextBlock>
                                             Accepted tolerance between experimental and theoretical MS1 peaks.
@@ -132,14 +126,14 @@
                                             This is a file specific parameter; calibration of spectra files will overwrite this value with the suggested tolerance(s).
                                             </TextBlock>
                                         </TextBox.ToolTip>
-                                    </local:DoubleTextBoxControl>
+                                    </TextBox>
                                     <ComboBox x:Name="PrecursorMassToleranceComboBox" HorizontalAlignment="Left" />
                                 </StackPanel>
 
                                 <!-- Product Mass Tolerance -->
                                 <StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="1" Grid.Row="1">
                                     <Label Content="Product Mass Tolerance:" Width="150" />
-                                    <local:DoubleTextBoxControl x:Name="ProductMassToleranceTextBox" HorizontalAlignment="Left" TextWrapping="Wrap" Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
+                                    <TextBox x:Name="ProductMassToleranceTextBox" PreviewTextInput="CheckIfNumber" HorizontalAlignment="Left" TextWrapping="Wrap" Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
                                         <TextBox.ToolTip>
                                             <TextBlock>
                                             Accepted tolerance between experimental and theoretical MS2 peaks.
@@ -147,7 +141,7 @@
                                             This is a file specific parameter; calibration of spectra files will overwrite this value with the suggested tolerance(s).
                                             </TextBlock>
                                         </TextBox.ToolTip>
-                                    </local:DoubleTextBoxControl>
+                                    </TextBox>
                                     <ComboBox x:Name="ProductMassToleranceComboBox" HorizontalAlignment="Left" />
                                 </StackPanel>
 
@@ -253,41 +247,6 @@
                                         </TextBox.ToolTip>
                                     </TextBox>
                                 </StackPanel>
-
-                                <!-- Q-Value Filter -->
-                                <StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="0" Grid.Row="6">
-                                    <Label x:Name="QValueThreshold" Content="Q-Value Threshold:" Width="150" />
-                                    <local:DoubleTextBoxControl x:Name="QValueThresholdTextBox"  Width="45" 
-                                             ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"
-                                             IsEnabled="{Binding ElementName=PepQValueThresholdCheckbox, Path=IsChecked, Converter={StaticResource InvertedBooleanConverter}}">
-                                        <TextBox.ToolTip>
-                                            <TextBlock>
-                                                   The maximum q-value of peptides used for quantification and spectral library generation. Protein group construction is not affected by this threshold.
-                                                <LineBreak />
-                                                    If the q-value threshold is set, PEP q-value filtering will not be performed.
-                                            </TextBlock>
-                                        </TextBox.ToolTip>
-                                    </local:DoubleTextBoxControl>
-                                </StackPanel>
-
-                                <!-- PEP Q-Value Filter -->
-                                <StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="1" Grid.Row="6">
-                                    <!-- pep 1-value button -->
-                                    <CheckBox x:Name="PepQValueThresholdCheckbox" Content="PEP Q-Value Threshold:" 
-                                                 IsChecked="False" Margin="5,5,5,0" />
-                                    <local:DoubleTextBoxControl x:Name="PepQValueThresholdTextBox"
-                                             IsEnabled="{Binding IsChecked, ElementName=PepQValueThresholdCheckbox}" Width="45"
-                                             Height="23" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
-                                        <TextBox.ToolTip>
-                                            <TextBlock>
-                                                    The maximum q-value of peptides used for quantification and spectral library generation. Protein group construction is not affected by this threshold.
-                                                    <LineBreak />
-                                                    If the PEP q-value threshold is set, traditional q-value filtering will not be performed.
-                                            </TextBlock>
-                                        </TextBox.ToolTip>
-                                    </local:DoubleTextBoxControl>
-                                </StackPanel>
-
                             </Grid>
                         </StackPanel>
                     </GroupBox>
@@ -319,6 +278,11 @@
                                                 </StackPanel>
                                             </DataTemplate>
                                         </TreeView.Resources>
+                                        <TreeView.ItemContainerStyle>
+                                            <Style TargetType="TreeViewItem">
+                                                <Setter Property="IsExpanded" Value="{Binding Expanded}" />
+                                            </Style>
+                                        </TreeView.ItemContainerStyle>
                                     </TreeView>
                                 </StackPanel>
                                 <StackPanel Grid.Column="1" Margin="5,0,3,0" Grid.ColumnSpan="2">
@@ -348,6 +312,11 @@
                                                 </StackPanel>
                                             </DataTemplate>
                                         </TreeView.Resources>
+                                        <TreeView.ItemContainerStyle>
+                                            <Style TargetType="TreeViewItem">
+                                                <Setter Property="IsExpanded" Value="{Binding Expanded}" />
+                                            </Style>
+                                        </TreeView.ItemContainerStyle>
                                     </TreeView>
                                 </StackPanel>
                                 <TextBox x:Name="SearchFixMod" TextChanged="TextChanged_Fixed" HorizontalAlignment="Left" Margin="82,4,0,410" TextWrapping="Wrap" Width="140">
@@ -405,7 +374,7 @@
                     <!-- Protein parsimony options -->
                     <GroupBox Header="Protein Parsimony" DockPanel.Dock="Top">
                         <StackPanel Margin="5">
-                            <CheckBox x:Name="CheckBoxParsimony" Content="Apply protein parsimony and construct protein groups" IsEnabled="{Binding IsChecked, ElementName=CheckBoxParsimony}">
+                            <CheckBox x:Name="CheckBoxParsimony" Content="Apply protein parsimony and construct protein groups">
                                 <ToolTipService.ToolTip>
                                     <ToolTip Content="Constructs protein groups according to the rule of maximum parsimony (Occam's razor)"  ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
@@ -425,7 +394,6 @@
 
                     <!-- Quantification options -->
                     <GroupBox Header="Quantification" DockPanel.Dock="Top">
-                        <!-- Radio Buttons for Quant Method -->
                         <StackPanel Margin="5">
                             <RadioButton x:Name="CheckBoxNoQuant" Content="No quantification" GroupName="QuantType">
                                 <ToolTipService.ToolTip>
@@ -437,24 +405,17 @@
                                     <ToolTip Content="Label-free quantification is performed with FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
                             </RadioButton>
-                            <RadioButton x:Name="CheckBoxSILAC" Content="SILAC/SILAM: Quantify peptides/proteins with stable isotope labels" GroupName="QuantType" Click="CheckBoxSILAC_Checked">
-                                <ToolTipService.ToolTip>
-                                    <ToolTip Content="SILAC quantification is performed using FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"/>
-                                </ToolTipService.ToolTip>
-                            </RadioButton>
-                            <RadioButton x:Name="CheckBoxMultiplex" Content="Multiplex Quantification: Quantify peptides labeled with isobaric tags" GroupName="QuantType" Unchecked="MultiplexUpdate" Checked="MultiplexUpdate">
+                            <RadioButton x:Name="CheckBoxLFQwMBR" Content="LFQ + MBR Analysis: FlashLFQ quantification with enhanced match between runs" 
+                                         GroupName="QuantType" Click="MbrAnalysisUpdate">
                                 <ToolTipService.ToolTip>
-                                    <ToolTip Content="Intensity of reporter ions are reported as additional columns in AllPeptides.psmtsv and AllPSMs.psmtsv" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"/>
+                                    <ToolTip Content="Match between runs analysis via spectral library search" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
                             </RadioButton>
-                            <RadioButton x:Name="CheckBoxLFQwSpectralRecovery" Content="LFQ + Spectral Recovery: Spectral recovery finds misidentified MS/MS spectra common in single-cell proteomics data" 
-                                         GroupName="QuantType" Click="SpectralRecoveryUpdate">
+                            <RadioButton x:Name="CheckBoxSILAC" Content="SILAC/SILAM: Quantify peptides/proteins with stable isotope labels" GroupName="QuantType" Click="CheckBoxSILAC_Checked">
                                 <ToolTipService.ToolTip>
-                                    <ToolTip Content="Match between runs analysis via spectral library search" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
+                                    <ToolTip Content="SILAC quantification is performed using FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"/>
                                 </ToolTipService.ToolTip>
                             </RadioButton>
-
-                            <!-- SILAC Options -->
                             <CheckBox x:Name="CheckBoxQuantifyUnlabeledForSilac" 
                                       Content="Quantify unlabeled peptides/proteins" 
                                       IsEnabled="{Binding IsChecked, ElementName=CheckBoxSILAC}"
@@ -482,22 +443,14 @@
                                     <Button x:Name="ClearSilac" Content="Clear" Click="ClearSilac_Click" IsEnabled="{Binding IsChecked, ElementName=CheckBoxSILAC}"/>
                                 </StackPanel>
                             </Grid>
-
-                            <!-- LFQ Options -->
                             <StackPanel Orientation="Horizontal">
                                 <TextBox x:Name="PeakFindingToleranceTextBox"  PreviewTextInput="CheckIfNumber" Width="30" Height="20">
                                     <TextBox.IsEnabled>
                                         <MultiBinding Converter="{StaticResource boolOrConverter}">
                                             <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                            <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
+                                            <Binding  ElementName="CheckBoxLFQwMBR" Path ="IsChecked"/>
                                         </MultiBinding>
                                     </TextBox.IsEnabled>
-                                    <TextBox.Visibility>
-                                        <MultiBinding Converter="{StaticResource boolOr2VisConverter}">
-                                            <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                            <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
-                                        </MultiBinding>
-                                    </TextBox.Visibility>
                                     <ToolTipService.ToolTip>
                                         <ToolTip Content="PPM tolerance for MS1 (LFQ) peakfinding" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                     </ToolTipService.ToolTip>
@@ -506,26 +459,18 @@
                                     <Label.IsEnabled>
                                         <MultiBinding Converter="{StaticResource boolOrConverter}">
                                             <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                            <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
+                                            <Binding  ElementName="CheckBoxLFQwMBR" Path ="IsChecked"/>
                                         </MultiBinding>
                                     </Label.IsEnabled>
-                                    <Label.Visibility>
-                                        <MultiBinding Converter="{StaticResource boolOr2VisConverter}">
-                                            <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                            <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
-                                        </MultiBinding>
-                                    </Label.Visibility>
                                 </Label>
                             </StackPanel>
-                            <CheckBox x:Name="CheckBoxMatchBetweenRuns" 
-                                      Content="Match between runs"
-                                      IsEnabled ="{Binding IsChecked, ElementName=CheckBoxLFQ}">
-                                <CheckBox.Visibility>
-                                    <MultiBinding Converter="{StaticResource boolOr2VisConverter}">
+                            <CheckBox x:Name="CheckBoxMatchBetweenRuns" Content="Match between runs" >
+                                <CheckBox.IsEnabled>
+                                    <MultiBinding Converter="{StaticResource boolOrConverter}">
                                         <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                        <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
+                                        <Binding  ElementName="CheckBoxLFQwMBR" Path ="IsChecked"/>
                                     </MultiBinding>
-                                </CheckBox.Visibility>
+                                </CheckBox.IsEnabled>
                                 <ToolTipService.ToolTip>
                                     <ToolTip Content="(LFQ) Use MS2 identifications from one run to quantify those same peptides in other runs where they were not identified&#x0a;Selecting &quot;Write Spectral Library&quot; in the Output Options below will enable additional MBR analysis" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
@@ -534,38 +479,13 @@
                                 <CheckBox.IsEnabled>
                                     <MultiBinding Converter="{StaticResource boolOrConverter}">
                                         <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                        <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
+                                        <Binding  ElementName="CheckBoxLFQwMBR" Path ="IsChecked"/>
                                     </MultiBinding>
                                 </CheckBox.IsEnabled>
-                                <CheckBox.Visibility>
-                                    <MultiBinding Converter="{StaticResource boolOr2VisConverter}">
-                                        <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                        <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
-                                    </MultiBinding>
-                                </CheckBox.Visibility>
                                 <ToolTipService.ToolTip>
                                     <ToolTip Content="Use the 'Experimental Design' to normalize intensity values from FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
                             </CheckBox>
-
-                            <!-- Multiplex Options -->
-                            <StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="0" Grid.Row="0">
-                                <Label x:Name="MultiplexTag" Content="Label Type:" Width="75" 
-                                       Visibility="{Binding IsChecked, ElementName=CheckBoxMultiplex, Converter={StaticResource bool2VisConverter}}"/>
-                                <ComboBox x:Name="MultiplexComboBox" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" 
-                                          SelectionChanged="MultiplexUpdate"
-                                          IsEnabled="{Binding IsChecked, ElementName=CheckBoxMultiplex}"
-                                          Visibility="{Binding IsChecked, ElementName=CheckBoxMultiplex, Converter={StaticResource bool2VisConverter}}">
-                                    <ComboBox.ToolTip>
-                                        <TextBlock>
-                                            Isobaric label used for multiplexing
-                                            <LineBreak />
-                                            Labels can be added/modified by the user at "Data -> Open folder with mods/data files -> Mods -> tmt.txt"
-                                        </TextBlock>
-                                    </ComboBox.ToolTip>
-                                </ComboBox>
-                            </StackPanel>
-
                         </StackPanel>
                     </GroupBox>
 
@@ -593,10 +513,9 @@
                                 <!--<CheckBox x:Name="ckbPepXML" Content="Write .pep.XML" />-->
                                 <CheckBox x:Name="WriteDecoyCheckBox" Content="Write decoys" />
                                 <CheckBox x:Name="WriteContaminantCheckBox" Content="Write contaminants" />
-                                <CheckBox x:Name="WriteHighQPsmsCheckBox" Content="Write PSMs &amp; peptides with q-value above threshold"/>
                                 <CheckBox x:Name="WriteIndividualResultsCheckBox" Content="Write individual file results" />
-                                <CheckBox x:Name="WriteSpectralLibraryCheckBox" Content="Write spectral library" IsEnabled="{Binding IsChecked, Converter={local:BooleanInverter}, ElementName=CheckBoxLFQwSpectralRecovery }"/>
-                                <CheckBox x:Name="UpdateSpectralLibraryCheckBox" Content="Update spectral library" />
+                                <CheckBox x:Name="WriteSpectralLibraryCheckBox" Content="Write spectral library" />
+                                <CheckBox x:Name="UpdateSpectralLibraryCheckBox" Content="Update SpectralLibrary" />
                                 <CheckBox x:Name="CompressIndividualResultsCheckBox" Content="Compress individual file results" IsEnabled="{Binding IsChecked, ElementName=WriteIndividualResultsCheckBox}"/>
 
                             </StackPanel>
@@ -604,6 +523,43 @@
                             <!-- filtering options -->
                             <StackPanel Orientation="Vertical" Margin="5" Grid.Column="1">
 
+                                <!-- pep 1-value button -->
+                                <Grid>
+                                    <Grid.ColumnDefinitions>
+                                        <ColumnDefinition Width="400" />
+                                        <ColumnDefinition Width="50" />
+                                    </Grid.ColumnDefinitions>
+
+                                    <RadioButton x:Name="PepQValueRadioButton" Content="Filter results to pep q-value:" 
+                                                 IsChecked="False" GroupName="Filtering" Checked="PepQValueRadioButton_Checked">
+                                        <ToolTipService.ToolTip>
+                                            Removes PSM and protein results from the written output below the input pep q-value.
+                                            Mutually exclusive with filter results to q-value
+                                        </ToolTipService.ToolTip>
+                                    </RadioButton>
+                                    <TextBox x:Name="PepQValueTextBox" PreviewTextInput="CheckIfNumber" Margin="10,0,0,0" 
+                                             IsEnabled="{Binding IsChecked, ElementName=PepQValueRadioButton}" Width="45" Height="23" />
+                                </Grid>
+
+                                <!-- q value button -->
+                                <Grid>
+                                    <Grid.ColumnDefinitions>
+                                        <ColumnDefinition Width="400" />
+                                        <ColumnDefinition Width="50" />
+                                    </Grid.ColumnDefinitions>
+
+                                    <RadioButton x:Name="QValueRadioButton" Content="Filter results to q-value:" 
+                                                 IsChecked="False" GroupName="Filtering" Checked="QValueRadioButton_Checked">
+                                        <ToolTipService.ToolTip>
+                                            Removes PSM and protein results from the written output below the input q-value.
+                                            Mutually exclusive with filter results to pep q-value
+                                        </ToolTipService.ToolTip>
+                                    </RadioButton>
+
+                                    <TextBox x:Name="QValueTextBox" PreviewTextInput="CheckIfNumber" Margin="10,0,0,0" 
+                                             IsEnabled="{Binding IsChecked, ElementName=QValueRadioButton}" Width="45" Height="23" />
+                                </Grid>
+
                                 <!-- min score allowed box -->
                                 <Grid>
                                     <Grid.ColumnDefinitions>
@@ -1242,12 +1198,11 @@
             <Button x:Name="cancelButton" Content="Cancel" Click="CancelButton_Click" />
             <Button x:Name="saveButton" Content="Save Search Task" Click="SaveButton_Click" FontSize="24" />
             <Button x:Name="setDefaultbutton"  Width="100" 
-                    Command="{Binding Path=TaskSettingViewModel.SaveAsDefaultSettingsCommand, 
-                RelativeSource={RelativeSource FindAncestor, AncestorType={x:Type Window}}}">
-                <TextBlock Text="Save As Default" TextWrapping="Wrap" TextAlignment="Center"/>
+                    Command="{Binding TaskSettingViewModel.SaveAsDefaultSettingsCommand, RelativeSource={RelativeSource FindAncestor, AncestorType={x:Type Window}}}">
                 <ToolTipService.ToolTip>
                     <ToolTip Content="Save these parameters as the default. MetaMorpheus can return to original defaults by deleting the folder 'DefaultParameters'" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                 </ToolTipService.ToolTip>
+                <TextBlock Text="Save As Default" TextWrapping="Wrap" TextAlignment="Center"/>
             </Button>
         </StackPanel>
     </Grid>
diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index 0dac20e54..ba8a5eb41 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -17,8 +17,6 @@
 using TaskLayer;
 using UsefulProteomicsDatabases;
 using GuiFunctions;
-using Proteomics;
-using System.Threading.Tasks;
 using static System.Net.WebRequestMethods;
 
 namespace MetaMorpheusGUI
@@ -37,7 +35,6 @@ public partial class SearchTaskWindow : Window
         private readonly ObservableCollection<SilacInfoForDataGrid> StaticSilacLabelsObservableCollection = new ObservableCollection<SilacInfoForDataGrid>();
         private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
         private CustomFragmentationWindow CustomFragmentationWindow;
-        private string _defaultMultiplexType = "TMT10";
         private TaskSettingViewModel TaskSettingViewModel;
 
 
@@ -154,13 +151,6 @@ private void PopulateChoices()
             {
                 LocalizeModTypeForTreeViewObservableCollection.Add(new ModTypeForLoc(hm.Key));
             }
-
-            foreach (string labelModType in GlobalVariables.AllModsKnown.Where(m => m.ModificationType.Equals("Multiplex Label"))
-                         .Select(m => m.OriginalId).Distinct())
-            {
-                MultiplexComboBox.Items.Add(labelModType);
-            }
-            MultiplexComboBox.SelectedItem = _defaultMultiplexType;
         }
 
 
@@ -192,15 +182,8 @@ private void UpdateFieldsFromTask(SearchTask task)
             }
             CheckBoxParsimony.IsChecked = task.SearchParameters.DoParsimony;
             CheckBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
-            CheckBoxNoQuant.IsChecked = !task.SearchParameters.DoLabelFreeQuantification;
-            CheckBoxLFQ.IsChecked = task.SearchParameters.DoLabelFreeQuantification;
-            CheckBoxMultiplex.IsChecked = task.SearchParameters.DoMultiplexQuantification;
-            MultiplexComboBox.SelectedItem = task.SearchParameters.MultiplexModId ?? _defaultMultiplexType;
-            // If Spectral Recovery is enabled
-            if (task.SearchParameters.WriteSpectralLibrary & task.SearchParameters.MatchBetweenRuns)
-            {
-                CheckBoxLFQwSpectralRecovery.IsChecked = task.SearchParameters.DoSpectralRecovery;
-            }
+            CheckBoxNoQuant.IsChecked = !task.SearchParameters.DoQuantification;
+            CheckBoxLFQ.IsChecked = task.SearchParameters.DoQuantification;
             //If SILAC turnover
             if (task.SearchParameters.StartTurnoverLabel != null || task.SearchParameters.EndTurnoverLabel != null)
             {
@@ -319,28 +302,28 @@ private void UpdateFieldsFromTask(SearchTask task)
             MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
             CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
 
-            if (task.CommonParameters.QValueThreshold < 1)
+            if (task.CommonParameters.QValueOutputFilter < 1)
             {
-                QValueThresholdTextBox.Text = task.CommonParameters.QValueThreshold.ToString(CultureInfo.InvariantCulture);
+                QValueTextBox.Text = task.CommonParameters.QValueOutputFilter.ToString(CultureInfo.InvariantCulture);
+                QValueRadioButton.IsChecked = true;
             }
             else
             {
-                QValueThresholdTextBox.Text = "0.01";
+                QValueTextBox.Text = "0.01";
             }
 
-            if (task.CommonParameters.PepQValueThreshold < 1)
+            if (task.CommonParameters.PepQValueOutputFilter < 1)
             {
-                PepQValueThresholdTextBox.Text = task.CommonParameters.PepQValueThreshold.ToString(CultureInfo.InvariantCulture);
-                PepQValueThresholdCheckbox.IsChecked = true;
+                PepQValueTextBox.Text = task.CommonParameters.QValueOutputFilter.ToString(CultureInfo.InvariantCulture);
+                PepQValueRadioButton.IsChecked = true;
             }
             else
             {
-                PepQValueThresholdTextBox.Text = "0.01";
+                PepQValueTextBox.Text = "0.01";  
             }
 
             OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
             CkbMzId.IsChecked = task.SearchParameters.WriteMzId;
-            WriteHighQPsmsCheckBox.IsChecked = task.SearchParameters.WriteHighQValuePsms;
             WriteDecoyCheckBox.IsChecked = task.SearchParameters.WriteDecoys;
             WriteContaminantCheckBox.IsChecked = task.SearchParameters.WriteContaminants;
             WriteIndividualResultsCheckBox.IsChecked = task.SearchParameters.WriteIndividualFiles;
@@ -446,28 +429,11 @@ private SearchTask GetTaskFromGui()
             CleavageSpecificity searchModeType = GetSearchModeType(); //change search type to semi or non if selected
             SnesUpdates(searchModeType); //decide on singleN/C, make comp ion changes
 
-            if (!GlobalGuiSettings.CheckTaskSettingsValidity(
-                PrecursorMassToleranceTextBox.Text, 
-                ProductMassToleranceTextBox.Text, 
-                MissedCleavagesTextBox.Text,
-                maxModificationIsoformsTextBox.Text, 
-                MinPeptideLengthTextBox.Text, 
-                MaxPeptideLengthTextBox.Text,
-                MaxThreadsTextBox.Text, 
-                MinScoreAllowed.Text,
-                PeakFindingToleranceTextBox.Text, 
-                HistogramBinWidthTextBox.Text, 
-                DeconvolutionMaxAssumedChargeStateTextBox.Text, 
-                NumberOfPeaksToKeepPerWindowTextBox.Text,
-                MinimumAllowedIntensityRatioToBasePeakTexBox.Text, 
-                WindowWidthThomsonsTextBox.Text, 
-                NumberOfWindowsTextBox.Text, 
-                NumberOfDatabaseSearchesTextBox.Text, 
-                MaxModNumTextBox.Text, 
-                MaxFragmentMassTextBox.Text, 
-                QValueThresholdTextBox.Text, 
-                PepQValueThresholdTextBox.Text, 
-                InternalIonsCheckBox.IsChecked.Value ? MinInternalFragmentLengthTextBox.Text : null))
+            if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecursorMassToleranceTextBox.Text, ProductMassToleranceTextBox.Text, MissedCleavagesTextBox.Text,
+                maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, MaxThreadsTextBox.Text, MinScoreAllowed.Text,
+                PeakFindingToleranceTextBox.Text, HistogramBinWidthTextBox.Text, DeconvolutionMaxAssumedChargeStateTextBox.Text, NumberOfPeaksToKeepPerWindowTextBox.Text,
+                MinimumAllowedIntensityRatioToBasePeakTexBox.Text, WindowWidthThomsonsTextBox.Text, NumberOfWindowsTextBox.Text, NumberOfDatabaseSearchesTextBox.Text,
+                MaxModNumTextBox.Text, MaxFragmentMassTextBox.Text, QValueTextBox.Text, PepQValueTextBox.Text, InternalIonsCheckBox.IsChecked.Value ? MinInternalFragmentLengthTextBox.Text : null))
             {
                 return null;
             }
@@ -597,8 +563,6 @@ private SearchTask GetTaskFromGui()
                 totalPartitions: int.Parse(NumberOfDatabaseSearchesTextBox.Text, CultureInfo.InvariantCulture),
                 doPrecursorDeconvolution: DeconvolutePrecursors.IsChecked.Value,
                 useProvidedPrecursorInfo: UseProvidedPrecursor.IsChecked.Value,
-                qValueThreshold: !PepQValueThresholdCheckbox.IsChecked.Value ? double.Parse(QValueThresholdTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
-                pepQValueThreshold: PepQValueThresholdCheckbox.IsChecked.Value ? double.Parse(PepQValueThresholdTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
                 scoreCutoff: double.Parse(MinScoreAllowed.Text, CultureInfo.InvariantCulture),
                 listOfModsFixed: listOfModsFixed,
                 listOfModsVariable: listOfModsVariable,
@@ -616,6 +580,8 @@ private SearchTask GetTaskFromGui()
                 numberOfWindows: numberOfWindows,//maybe change this some day
                 normalizePeaksAccrossAllWindows: normalizePeaksAccrossAllWindows,//maybe change this some day
                 addCompIons: AddCompIonCheckBox.IsChecked.Value,
+                qValueOutputFilter: QValueRadioButton.IsChecked.Value ? double.Parse(QValueTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
+                pepQValueOutputFilter: PepQValueRadioButton.IsChecked.Value ? double.Parse(PepQValueTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
                 assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
                 minVariantDepth: MinVariantDepth,
                 maxHeterozygousVariants: MaxHeterozygousVariants);
@@ -642,22 +608,17 @@ private SearchTask GetTaskFromGui()
             TheTask.SearchParameters.MinAllowedInternalFragmentLength = InternalIonsCheckBox.IsChecked.Value ? Convert.ToInt32(MinInternalFragmentLengthTextBox.Text) : 0;
             TheTask.SearchParameters.DoParsimony = CheckBoxParsimony.IsChecked.Value;
             TheTask.SearchParameters.NoOneHitWonders = CheckBoxNoOneHitWonders.IsChecked.Value;
-            TheTask.SearchParameters.DoLabelFreeQuantification = !CheckBoxNoQuant.IsChecked.Value;
-            TheTask.SearchParameters.DoSpectralRecovery = CheckBoxLFQwSpectralRecovery.IsChecked.Value;
-            TheTask.SearchParameters.DoMultiplexQuantification = CheckBoxMultiplex.IsChecked.Value;
-            TheTask.SearchParameters.MultiplexModId = (string)MultiplexComboBox.SelectedItem;
+            TheTask.SearchParameters.DoQuantification = !CheckBoxNoQuant.IsChecked.Value;
             TheTask.SearchParameters.Normalize = CheckBoxNormalize.IsChecked.Value;
             TheTask.SearchParameters.MatchBetweenRuns = CheckBoxMatchBetweenRuns.IsChecked.Value;
             TheTask.SearchParameters.ModPeptidesAreDifferent = ModPepsAreUnique.IsChecked.Value;
             TheTask.SearchParameters.QuantifyPpmTol = double.Parse(PeakFindingToleranceTextBox.Text, CultureInfo.InvariantCulture);
             TheTask.SearchParameters.SearchTarget = CheckBoxTarget.IsChecked.Value;
             TheTask.SearchParameters.WriteMzId = CkbMzId.IsChecked.Value;
-            TheTask.SearchParameters.WriteHighQValuePsms = WriteHighQPsmsCheckBox.IsChecked.Value;
             TheTask.SearchParameters.WriteDecoys = WriteDecoyCheckBox.IsChecked.Value;
             TheTask.SearchParameters.WriteContaminants = WriteContaminantCheckBox.IsChecked.Value;
             TheTask.SearchParameters.WriteIndividualFiles = WriteIndividualResultsCheckBox.IsChecked.Value;
             TheTask.SearchParameters.WriteSpectralLibrary = WriteSpectralLibraryCheckBox.IsChecked.Value;
-            TheTask.SearchParameters.UpdateSpectralLibrary = UpdateSpectralLibraryCheckBox.IsChecked.Value;
             TheTask.SearchParameters.CompressIndividualFiles = CompressIndividualResultsCheckBox.IsChecked.Value;
             TheTask.SearchParameters.IncludeModMotifInMzid = IncludeMotifInModNamesCheckBox.IsChecked.Value;
 
@@ -861,25 +822,6 @@ private void NonSpecificUsingNonSpecific(object sender, RoutedEventArgs e)
             }
         }
 
-        /// <summary>
-        /// When a new multiplex label is selected from the drop-down menu (MultiplexComboBox),
-        /// the fixed mod tree view is updated so that only those mods are selected. 
-        /// </summary>
-        private void MultiplexUpdate(object sender, RoutedEventArgs routedEventArgs)
-        {
-            ModTypeForTreeViewModel multiplexModType = FixedModTypeForTreeViewObservableCollection
-                .FirstOrDefault(b => b.DisplayName.Equals("Multiplex Label"));
-            string selectedModId = CheckBoxMultiplex.IsChecked.Value
-                ? (string)MultiplexComboBox.SelectedItem
-                : "NoMatchingMod";
-
-            foreach (ModForTreeViewModel mod in multiplexModType.Children)
-            {
-                mod.Use = mod.DisplayName.Contains(selectedModId);
-            }
-            UpdateModSelectionGrid();
-        }
-
         //this one is used by the GUI
         private void ProteaseSpecificUpdate(object sender, SelectionChangedEventArgs e)
         {
@@ -1008,11 +950,11 @@ private void SemiSpecificUpdate(object sender, RoutedEventArgs e)
             }
         }
 
-        private void SpectralRecoveryUpdate(object sender, RoutedEventArgs e)
+        private void MbrAnalysisUpdate(object sender, RoutedEventArgs e)
         {
-            if (CheckBoxLFQwSpectralRecovery.IsChecked.Value)
+            if (CheckBoxLFQwMBR.IsChecked.Value)
             {
-                if (UpdateGUISettings.UseSpectralRecoveryMandatorySettings())
+                if (UpdateGUISettings.UseMBRAnalysisMandatorySettings())
                 {
                     CheckBoxMatchBetweenRuns.IsChecked = true;
                     WriteSpectralLibraryCheckBox.IsChecked = true;
@@ -1336,15 +1278,32 @@ private void CheckBoxSILAC_Checked(object sender, RoutedEventArgs e)
             CheckBoxQuantifyUnlabeledForSilac_Checked(sender, e);
         }
 
-        private void CheckBoxMultiplex_Checked(object sender, RoutedEventArgs e)
+        private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
         {
+            SaveButton_Click(sender, e);
+            Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"SearchTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
+        }
 
+        /// <summary>
+        /// Event Handler for when the pepQvalue radio button is checked. Sets value to default then uncecks and clears qValue
+        /// </summary>
+        /// <param name="sender"></param>
+        /// <param name="e"></param>
+        private void PepQValueRadioButton_Checked(object sender, RoutedEventArgs e)
+        {
+            QValueTextBox.Clear();
+            PepQValueTextBox.Text = "0.01";
         }
 
-        private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
+        /// <summary>
+        /// Event Handler for when the qvalue radio button is checked. Sets value to default then unchecks and clears pepQvalue.
+        /// </summary>
+        /// <param name="sender"></param>
+        /// <param name="e"></param>
+        private void QValueRadioButton_Checked(object sender, RoutedEventArgs e)
         {
-            SaveButton_Click(sender, e);
-            Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"SearchTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
+            PepQValueTextBox.Clear();
+            QValueTextBox.Text = "0.01";
         }
 
         /// <summary>
diff --git a/MetaMorpheus/GUI/Views/SaveSettingsWindow.xaml b/MetaMorpheus/GUI/Views/SaveSettingsWindow.xaml
index aa38a3812..e1b72bf1c 100644
--- a/MetaMorpheus/GUI/Views/SaveSettingsWindow.xaml
+++ b/MetaMorpheus/GUI/Views/SaveSettingsWindow.xaml
@@ -7,11 +7,7 @@
         xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
         mc:Ignorable="d"
         Title="SaveSettingsWindow" Height="135" Width="600">
-    <d:UserControl.DataContext>
-        <guiFunctions:TaskSettingViewModel/>
-    </d:UserControl.DataContext>
-    
-   
+
 
     <Grid >
         <Grid.RowDefinitions>
diff --git a/MetaMorpheus/GuiFunctions/TomlFileFolderSerializer.cs b/MetaMorpheus/GuiFunctions/TomlFileFolderSerializer.cs
index 23baa4e4e..39170d86f 100644
--- a/MetaMorpheus/GuiFunctions/TomlFileFolderSerializer.cs
+++ b/MetaMorpheus/GuiFunctions/TomlFileFolderSerializer.cs
@@ -33,7 +33,7 @@ public static void Serialize<T>(string path, T objectToSerialize)
         }
 
         /// <summary>
-        /// Return a json deserialized object
+        /// Return a toml deserialized object
         /// </summary>
         /// <typeparam name="T"></typeparam>
         /// <param name="path">The path of file that will be deserialized</param>
diff --git a/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs
index 9116995db..2450814b9 100644
--- a/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs
@@ -12,6 +12,7 @@
 using Easy.Common.Extensions;
 using Org.BouncyCastle.Asn1.X509.Qualified;
 using OxyPlot;
+using pepXML.Generated;
 using TaskLayer;
 
 namespace GuiFunctions
@@ -114,6 +115,24 @@ public TaskSettingViewModel(MetaMorpheusTask task, Action<MetaMorpheusTask> upda
             }
             AllSettingsDict = tempDict;
 
+            //When there is no default setting, create a default called "Default(Default)"
+            string[] keysInDict = AllSettingsDict.Keys.Cast<string>().ToArray();
+            for (int j = 0; j < keysInDict.Length; j++)
+            {
+                if (keysInDict[j].Contains("(Default)"))
+                {
+                    break;
+                }
+                else
+                {
+                    if (j == keysInDict.Length - 1)
+                    {
+                        AllSettingsDict.Add("DefaultSetting(Default)", task);
+                        TomlFileFolderSerializer.Save("DefaultSetting(Default)", task);
+                    }
+                }
+            }
+
             SelectDefaultAuto();
         }
 
@@ -279,12 +298,26 @@ public void SaveAsDefaultSettings()
         #region Helpers
         private void SelectDefaultAuto()
         {
+
             var defaultSetting = AllSettingsDict.First(p => p.Key.Contains("(Default)"));
             SelectedSettings = defaultSetting.Key;
         }
-   
-
-        #endregion
 
+        //private MetaMorpheusTask GetDefaultTask(MetaMorpheusTask taskTypeToGetDefault)
+        //{
+        //    return taskTypeToGetDefault.TaskType switch
+        //    {
+        //        MyTask.Search => new SearchTask(),
+        //        MyTask.Gptmd => new GptmdTask(),
+        //        MyTask.Calibrate => new CalibrationTask(),
+        //        MyTask.XLSearch => new XLSearchTask(),
+        //        MyTask.GlycoSearch => new GlycoSearchTask(),
+        //        _ => throw new ArgumentOutOfRangeException(nameof(taskTypeToGetDefault.TaskType), taskTypeToGetDefault.TaskType, null)
+        //    };
+        //}
     }
+       
+    #endregion
+
 }
+
diff --git a/MetaMorpheus/Test/SaveSettingsTests.cs b/MetaMorpheus/Test/SaveSettingsTests.cs
index aec141927..01c1c1c20 100644
--- a/MetaMorpheus/Test/SaveSettingsTests.cs
+++ b/MetaMorpheus/Test/SaveSettingsTests.cs
@@ -25,15 +25,21 @@ public static void OneTimeSetup()
             var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory,@"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
             var tomlFile2 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"), MetaMorpheusTask.tomlConfig);
             var tomlFile3 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"), MetaMorpheusTask.tomlConfig);
-            TomlFileFolderSerializer.Save("customBCZ.toml", tomlFile1);
-            TomlFileFolderSerializer.Save("customBY.toml", tomlFile2);
-            TomlFileFolderSerializer.Save("customCZ.toml", tomlFile3);
-        }
+            TomlFileFolderSerializer.Save("customBCZ", tomlFile1);
+            TomlFileFolderSerializer.Save("customBY", tomlFile2);
+            TomlFileFolderSerializer.Save("customCZ", tomlFile3);
+
+            // TODO: Repeat above for callibration task, without setting a default
+
+            // example code
+            var task = new CalibrationTask();
+            Toml.WriteFile<CalibrationTask>(task, "file out path.toml", MetaMorpheusTask.tomlConfig);
+        }   
 
         [OneTimeTearDown]
         public static void OneTimeTearDown()
         {
-            Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"), true);
+            //Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"), true);
         }
 
         private class FakeGuiWindow
@@ -63,11 +69,87 @@ public void UpdateFieldsFromNewTask(MetaMorpheusTask task)
             }
         }
 
+        // TODO: Test what happens when no default is set
+
+        [Test]
+        public void ConstructorTestWithoutDefaultSettings()
+        {
+            // set up directories
+
+
+
+            // test
+            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var testDictionary = testTaskSettingViewModel.AllSettingsDict;
+            Assert.That(testDictionary.ContainsKey("DefaultSetting(Default)"));
+            var testWindow = fakeTaskWindow.GetTaskFromGui();
+            var comparingWindow = testDictionary["DefaultSetting(Default)"];
+            Assert.That(testWindow.Equals(comparingWindow));
+            TomlFileFolderSerializer.Save("testFile", testWindow);
+            string pathOfTestFile = TomlFileFolderSerializer.GetFilePath(testWindow.GetType(), "testFile");
+            string pathOfComparingFile = TomlFileFolderSerializer.GetFilePath(comparingWindow.GetType(), "DefaultSetting(Default)");
+            var linesA = File.ReadAllLines(pathOfTestFile);
+            var linesB = File.ReadAllLines(pathOfComparingFile);
+
+            Assert.That(linesA.Length, Is.EqualTo(linesB.Length));
+            for (int i = 0; i < linesA.Length; i++)
+            {
+                //if (linesA[i].StartsWith("MaxMissedCleavages"))
+                //{
+                //    Assert.That(linesA[i], Is.Not.EqualTo(linesB[i]));
+                //    Assert.That(linesA[i].EndsWith('1'));
+                //    Assert.That(linesB[i].EndsWith('2'));
+                //}
+                //else
+                Assert.That(linesA[i], Is.EqualTo(linesB[i]));
+            }
+
+
+            // clean up directories
+        }
+
         [Test]
         public void ExampleTest()
         {
             var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
             TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+
+            // test everything is loaded correctly
+            // check task fake window is correct
+            // check serialized files is correct
+            // check dictionary is correct
+
+            // run a command
+
+
+            // test everything has changed as it should
+            // check task fake window is correct
+            // check serialized files is correct
+            // check dictionary is correct
+
+
+            // example read all lines comparison
+            string pathA = "";
+            string pathB = "";
+
+            var linesA = File.ReadAllLines(pathA);
+            var linesB = File.ReadAllLines(pathB);
+
+            Assert.That(linesA.Length, Is.EqualTo(linesB.Length));
+            for (int i = 0; i < linesA.Length; i++)
+            {
+                if (linesA[i].StartsWith("MaxMissedCleavages"))
+                {
+                    Assert.That(linesA[i], Is.Not.EqualTo(linesB[i]));
+                    Assert.That(linesA[i].EndsWith('1'));
+                    Assert.That(linesB[i].EndsWith('2'));
+                }
+                else
+                    Assert.That(linesA[i], Is.EqualTo(linesB[i]));
+            }
+            
+
         }
 
         [Test]
@@ -119,5 +201,21 @@ public void testGetFilePath()
             string testPath = TomlFileFolderSerializer.GetFilePath(tomlFile1.GetType(), "customBCZ.toml");
             Assert.That(testPath.Contains("toml"));
         }
+
+        [Test]
+        public void testSaveAs()
+        {
+            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var testDictionary = testTaskSettingViewModel.AllSettingsDict;
+
+            // TODO: Replace new search task with refernce B
+            var referenceA = TomlFileFolderSerializer.Deserialize<MetaMorpheusTask>("C:/Users/Administrator/source/repos/MetaMorpheus/Test/" +
+                "bin/Debug/net6.0-windows/TestData/SavedSettingsReferenceDirectory/a.toml");
+            testTaskSettingViewModel.UpdateFieldsInGuiWithNewTask.Invoke(referenceA as MetaMorpheusTask);
+            testTaskSettingViewModel.TypedSettingsName = "a";
+            testTaskSettingViewModel.SaveSettingsFromWindow();
+            Assert.That(false);
+        }
     }
 }
diff --git a/MetaMorpheus/Test/TaskSettingViewModelTests.cs b/MetaMorpheus/Test/TaskSettingViewModelTests.cs
index c82be21e1..b490a0218 100644
--- a/MetaMorpheus/Test/TaskSettingViewModelTests.cs
+++ b/MetaMorpheus/Test/TaskSettingViewModelTests.cs
@@ -38,7 +38,7 @@ public static void OneTimeTearDown()
         [Test]
         public void testSaveSettings()
         {
-            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask());
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel();
 
             var paramsOne = new CommonParameters(null, DissociationType.CID);
             var paramsTwo = new CommonParameters(null, DissociationType.HCD);

From f7f8772e17ae91492d6e3473d8efe720da405d60 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=B0=E7=8E=AE=20=E7=8E=8B?= <wfw2310165722@outlook.com>
Date: Tue, 28 Nov 2023 15:56:57 -0600
Subject: [PATCH 13/20] Add the TaskSettingViewModel to all task window except
 for Spectral Averaging.

---
 .../GUI/TaskWindows/CalibrateTaskWindow.xaml  |   7 +
 .../TaskWindows/CalibrateTaskWindow.xaml.cs   |   4 +-
 .../GUI/TaskWindows/GPTMDTaskWindow.xaml      |   8 +
 .../GUI/TaskWindows/GPTMDTaskWindow.xaml.cs   |   9 +-
 .../TaskWindows/GlycoSearchTaskWindow.xaml    |   8 +
 .../TaskWindows/GlycoSearchTaskWindow.xaml.cs |   5 +-
 .../GUI/TaskWindows/SearchTaskWindow.xaml     | 217 ++++----
 .../GUI/TaskWindows/SearchTaskWindow.xaml.cs  | 160 +++---
 .../SpectralAveragingTaskWindow.xaml          |   4 +-
 .../GUI/TaskWindows/XLSearchTaskWindow.xaml   |  10 +-
 .../TaskWindows/XLSearchTaskWindow.xaml.cs    |   9 +-
 .../GUI/Views/SaveSettingsControl.xaml        |  28 +
 .../GUI/Views/SaveSettingsControl.xaml.cs     |  54 ++
 .../GuiFunctions/TomlFileFolderSerializer.cs  |   7 +-
 .../ViewModels/TaskSettingViewModel.cs        | 199 +++++---
 MetaMorpheus/Test/MetaDrawTest.cs             |   1 +
 MetaMorpheus/Test/SaveSettingsTests.cs        | 482 +++++++++++++-----
 .../Test/TaskSettingViewModelTests.cs         |  57 ---
 18 files changed, 842 insertions(+), 427 deletions(-)
 create mode 100644 MetaMorpheus/GUI/Views/SaveSettingsControl.xaml
 create mode 100644 MetaMorpheus/GUI/Views/SaveSettingsControl.xaml.cs
 delete mode 100644 MetaMorpheus/Test/TaskSettingViewModelTests.cs

diff --git a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml
index 0769a279a..acbf86818 100644
--- a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml
@@ -45,6 +45,13 @@
                         </TextBox.Style>
                     </TextBox>
                 </StackPanel>
+
+                <StackPanel DockPanel.Dock="Top" Margin="10">
+                    <!-- save settings -->
+                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
+                        DataContext="{Binding TaskSettingViewModel}"/>
+                </StackPanel>
+                
                 <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
index 4b385e0e0..798456c9f 100644
--- a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
@@ -38,7 +38,7 @@ public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
 
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as CalibrationTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
-            //TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+            TaskSettingsCtrl.DataContext = TaskSettingViewModel;
 
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
@@ -371,7 +371,7 @@ private void OnClosing(object sender, CancelEventArgs e)
             // remove event handler from timer
             // keeping it will trigger an exception because the closed window stops existing
 
-            CustomFragmentationWindow.Close();
+            CustomFragmentationWindow?.Close();
         }
 
         private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
diff --git a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
index 48060ddd7..955f65e7a 100644
--- a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
@@ -45,6 +45,14 @@
                         </TextBox.Style>
                     </TextBox>
                 </StackPanel>
+
+                <StackPanel DockPanel.Dock="Top" Margin="10">
+
+                    <!-- save settings -->
+                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
+             DataContext="{Binding TaskSettingViewModel}"/>
+                </StackPanel>
+
                 <GroupBox Header="File Loading Parameters" DockPanel.Dock="Top">
                     <Expander x:Name="FileLoadExpander" >
                         <StackPanel>
diff --git a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
index f5d4347dd..428f86d6e 100644
--- a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
@@ -39,7 +39,7 @@ public GptmdTaskWindow(GptmdTask myGPTMDtask)
 
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as GptmdTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
-            //TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+            TaskSettingsCtrl.DataContext = TaskSettingViewModel;
 
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
@@ -564,7 +564,7 @@ private void OnClosing(object sender, CancelEventArgs e)
             // remove event handler from timer
             // keeping it will trigger an exception because the closed window stops existing
 
-            CustomFragmentationWindow.Close();
+            CustomFragmentationWindow?.Close();
         }
 
         private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
@@ -572,5 +572,10 @@ private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
             SaveButton_Click(sender, e);
             Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"GptmdTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
         }
+
+        private void TaskSettingsCtrl_Loaded(object sender, RoutedEventArgs e)
+        {
+
+        }
     }
 }
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
index 38b251cb7..59432f211 100644
--- a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
@@ -67,6 +67,14 @@
                         </TextBox.Style>
                     </TextBox>
                 </StackPanel>
+
+                <StackPanel DockPanel.Dock="Top" Margin="10">
+
+                    <!-- save settings -->
+                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
+             DataContext="{Binding TaskSettingViewModel}" />
+                </StackPanel>
+
                 <StackPanel DockPanel.Dock="Top">
                     <Grid>
                         
diff --git a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
index 74e58e06a..649098f68 100644
--- a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
@@ -41,9 +41,10 @@ public GlycoSearchTaskWindow(GlycoSearchTask task)
             PopulateChoices();
             TheTask = task ?? new GlycoSearchTask();
 
+           
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as GlycoSearchTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
-            //TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+            TaskSettingsCtrl.DataContext = TaskSettingViewModel;
             
 
             if (task == null)
@@ -474,7 +475,7 @@ private void OnClosing(object sender, CancelEventArgs e)
             // remove event handler from timer
             // keeping it will trigger an exception because the closed window stops existing
 
-            CustomFragmentationWindow.Close();
+            CustomFragmentationWindow?.Close();
         }
 
         private void NonSpecificUpdate(object sender, SelectionChangedEventArgs e)
diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
index 8b16380f1..499efb6ac 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
@@ -4,17 +4,17 @@
         xmlns:d="http://schemas.microsoft.com/expression/blend/2008"
         xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
         xmlns:local="clr-namespace:MetaMorpheusGUI"
-        xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions" 
+        xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
         mc:Ignorable="d"
         KeyDown="KeyPressed"
-        d:Height="1500"
         Title="Search Task" Width="750" Height="725" WindowStartupLocation="CenterScreen">
     <Window.Resources>
         <local:BooleanInverter x:Key="InvertedBooleanConverter" />
 
         <!-- used in Quantifications -->
         <BooleanToVisibilityConverter x:Key="bool2VisConverter" />
-        <guiFunctions:BooleanOrConverter x:Key="boolOrConverter"/>
+        <local:BooleanOrConverter x:Key="boolOrConverter"/>
+        <local:BooleanOrToVisibilityConverter x:Key="boolOr2VisConverter"/>
 
         <!-- Style GroupBoxes -->
         <Style TargetType="GroupBox">
@@ -35,6 +35,10 @@
             <Setter Property="VerticalContentAlignment" Value="Center"/>
             <Setter Property="Padding" Value="3 0 0 0"/>
         </Style>
+        <Style TargetType="local:DoubleTextBoxControl">
+            <Setter Property="VerticalContentAlignment" Value="Center"/>
+            <Setter Property="Padding" Value="3 0 0 0"/>
+        </Style>
     </Window.Resources>
     <Grid>
         <Grid.RowDefinitions>
@@ -81,22 +85,8 @@
                 <StackPanel DockPanel.Dock="Top" Margin="10">
 
                     <!-- save settings -->
-                    <StackPanel  x:Name="TaskSettingsCtrl" Height="Auto" 
-                                 DataContext="{Binding TaskSettingViewModel}"
-                                 Background="{StaticResource BackgroundColor}" Orientation="Horizontal" HorizontalAlignment="Right">
-
-                        <ComboBox Name="TaskSettingsComboBox" Width="200" Height="20" VerticalAlignment="Center" 
-                                  HorizontalAlignment="Left" IsSynchronizedWithCurrentItem="True"
-                                  ItemsSource="{Binding Path=AllSettings}" 
-                                  SelectedItem="{Binding Path=SelectedSettings}">
-                        </ComboBox>
-                        <Button x:Name="Save" Content="Save" FontSize="10" 
-                                Width="60" Margin="5,5,2.5,5" Command="{Binding SaveSettingsCommand}" />
-                        <Button x:Name="SaveAs" Content="Save as" FontSize="10" 
-                                Width="60" Margin="5,5,2.5,5" Click="SaveAs_Click"/>
-                        <Button x:Name="Delete"  Content="Delete" FontSize="10" Width="60" Margin="5,5,2.5,5"
-                                Command="{Binding DeleteSettingsCommand}" />
-                    </StackPanel>
+                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
+                                               DataContext="{Binding TaskSettingViewModel}" />
 
                     <!-- Search Parameters -->
                     <GroupBox Header="Search Parameters" DockPanel.Dock="Top" >
@@ -113,12 +103,13 @@
                                     <RowDefinition Height="1*"/>
                                     <RowDefinition Height="1*"/>
                                     <RowDefinition Height="1*"/>
+                                    <RowDefinition Height="1*"/>
                                 </Grid.RowDefinitions>
 
                                 <!-- Precursor Mass Tolerance -->
                                 <StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="1" Grid.Row="0">
                                     <Label Content="Precursor Mass Tolerance:" Width="150" />
-                                    <TextBox x:Name="PrecursorMassToleranceTextBox" PreviewTextInput="CheckIfNumber" HorizontalAlignment="Left" TextWrapping="Wrap" Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
+                                    <local:DoubleTextBoxControl x:Name="PrecursorMassToleranceTextBox" HorizontalAlignment="Left" TextWrapping="Wrap" Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
                                         <TextBox.ToolTip>
                                             <TextBlock>
                                             Accepted tolerance between experimental and theoretical MS1 peaks.
@@ -126,14 +117,14 @@
                                             This is a file specific parameter; calibration of spectra files will overwrite this value with the suggested tolerance(s).
                                             </TextBlock>
                                         </TextBox.ToolTip>
-                                    </TextBox>
+                                    </local:DoubleTextBoxControl>
                                     <ComboBox x:Name="PrecursorMassToleranceComboBox" HorizontalAlignment="Left" />
                                 </StackPanel>
 
                                 <!-- Product Mass Tolerance -->
                                 <StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="1" Grid.Row="1">
                                     <Label Content="Product Mass Tolerance:" Width="150" />
-                                    <TextBox x:Name="ProductMassToleranceTextBox" PreviewTextInput="CheckIfNumber" HorizontalAlignment="Left" TextWrapping="Wrap" Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
+                                    <local:DoubleTextBoxControl x:Name="ProductMassToleranceTextBox" HorizontalAlignment="Left" TextWrapping="Wrap" Width="45" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
                                         <TextBox.ToolTip>
                                             <TextBlock>
                                             Accepted tolerance between experimental and theoretical MS2 peaks.
@@ -141,7 +132,7 @@
                                             This is a file specific parameter; calibration of spectra files will overwrite this value with the suggested tolerance(s).
                                             </TextBlock>
                                         </TextBox.ToolTip>
-                                    </TextBox>
+                                    </local:DoubleTextBoxControl>
                                     <ComboBox x:Name="ProductMassToleranceComboBox" HorizontalAlignment="Left" />
                                 </StackPanel>
 
@@ -247,6 +238,41 @@
                                         </TextBox.ToolTip>
                                     </TextBox>
                                 </StackPanel>
+
+                                <!-- Q-Value Filter -->
+                                <StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="0" Grid.Row="6">
+                                    <Label x:Name="QValueThreshold" Content="Q-Value Threshold:" Width="150" />
+                                    <local:DoubleTextBoxControl x:Name="QValueThresholdTextBox"  Width="45" 
+                                             ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"
+                                             IsEnabled="{Binding ElementName=PepQValueThresholdCheckbox, Path=IsChecked, Converter={StaticResource InvertedBooleanConverter}}">
+                                        <TextBox.ToolTip>
+                                            <TextBlock>
+                                                   The maximum q-value of peptides used for quantification and spectral library generation. Protein group construction is not affected by this threshold.
+                                                <LineBreak />
+                                                    If the q-value threshold is set, PEP q-value filtering will not be performed.
+                                            </TextBlock>
+                                        </TextBox.ToolTip>
+                                    </local:DoubleTextBoxControl>
+                                </StackPanel>
+
+                                <!-- PEP Q-Value Filter -->
+                                <StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="1" Grid.Row="6">
+                                    <!-- pep 1-value button -->
+                                    <CheckBox x:Name="PepQValueThresholdCheckbox" Content="PEP Q-Value Threshold:" 
+                                                 IsChecked="False" Margin="5,5,5,0" />
+                                    <local:DoubleTextBoxControl x:Name="PepQValueThresholdTextBox"
+                                             IsEnabled="{Binding IsChecked, ElementName=PepQValueThresholdCheckbox}" Width="45"
+                                             Height="23" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
+                                        <TextBox.ToolTip>
+                                            <TextBlock>
+                                                    The maximum q-value of peptides used for quantification and spectral library generation. Protein group construction is not affected by this threshold.
+                                                    <LineBreak />
+                                                    If the PEP q-value threshold is set, traditional q-value filtering will not be performed.
+                                            </TextBlock>
+                                        </TextBox.ToolTip>
+                                    </local:DoubleTextBoxControl>
+                                </StackPanel>
+
                             </Grid>
                         </StackPanel>
                     </GroupBox>
@@ -256,12 +282,11 @@
                         <StackPanel Height="115">
                             <Grid>
                                 <Grid.ColumnDefinitions>
-                                    <ColumnDefinition Width="118*" />
-                                    <ColumnDefinition Width="21*" />
-                                    <ColumnDefinition Width="97*"/>
+                                    <ColumnDefinition Width="1*" />
+                                    <ColumnDefinition Width="1*" />
 
                                 </Grid.ColumnDefinitions>
-                                <StackPanel Margin="5,0,5,0">
+                                <StackPanel Margin="5 0 5 0">
                                     <Label Content="Fixed:" />
                                     <TreeView x:Name="FixedModsTreeView" ItemsSource="{Binding}" DataContext="{x:Type guiFunctions:ModTypeForTreeViewModel}" Height="85">
                                         <TreeView.Resources>
@@ -278,14 +303,9 @@
                                                 </StackPanel>
                                             </DataTemplate>
                                         </TreeView.Resources>
-                                        <TreeView.ItemContainerStyle>
-                                            <Style TargetType="TreeViewItem">
-                                                <Setter Property="IsExpanded" Value="{Binding Expanded}" />
-                                            </Style>
-                                        </TreeView.ItemContainerStyle>
                                     </TreeView>
                                 </StackPanel>
-                                <StackPanel Grid.Column="1" Margin="5,0,3,0" Grid.ColumnSpan="2">
+                                <StackPanel Grid.Column="1" Margin="5 0 3 0">
                                     <Label Content="Variable:"  ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
                                         <Label.ToolTip>
                                             <TextBlock>
@@ -312,11 +332,6 @@
                                                 </StackPanel>
                                             </DataTemplate>
                                         </TreeView.Resources>
-                                        <TreeView.ItemContainerStyle>
-                                            <Style TargetType="TreeViewItem">
-                                                <Setter Property="IsExpanded" Value="{Binding Expanded}" />
-                                            </Style>
-                                        </TreeView.ItemContainerStyle>
                                     </TreeView>
                                 </StackPanel>
                                 <TextBox x:Name="SearchFixMod" TextChanged="TextChanged_Fixed" HorizontalAlignment="Left" Margin="82,4,0,410" TextWrapping="Wrap" Width="140">
@@ -343,7 +358,7 @@
                                         </Style>
                                     </TextBox.Style>
                                 </TextBox>
-                                <TextBox x:Name="SearchVarMod" TextChanged="TextChanged_Var" Grid.Column="2" HorizontalAlignment="Left" Margin="19,4,0,410" TextWrapping="Wrap" Width="140">
+                                <TextBox x:Name="SearchVarMod" TextChanged="TextChanged_Var" Grid.Column="1" HorizontalAlignment="Left" Margin="82,4,0,410" TextWrapping="Wrap" Width="140">
                                     <TextBox.Style>
                                         <Style TargetType="TextBox" xmlns:sys="clr-namespace:System;assembly=mscorlib">
                                             <Style.Resources>
@@ -374,7 +389,7 @@
                     <!-- Protein parsimony options -->
                     <GroupBox Header="Protein Parsimony" DockPanel.Dock="Top">
                         <StackPanel Margin="5">
-                            <CheckBox x:Name="CheckBoxParsimony" Content="Apply protein parsimony and construct protein groups">
+                            <CheckBox x:Name="CheckBoxParsimony" Content="Apply protein parsimony and construct protein groups" IsEnabled="{Binding IsChecked, ElementName=CheckBoxParsimony}">
                                 <ToolTipService.ToolTip>
                                     <ToolTip Content="Constructs protein groups according to the rule of maximum parsimony (Occam's razor)"  ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
@@ -394,6 +409,7 @@
 
                     <!-- Quantification options -->
                     <GroupBox Header="Quantification" DockPanel.Dock="Top">
+                        <!-- Radio Buttons for Quant Method -->
                         <StackPanel Margin="5">
                             <RadioButton x:Name="CheckBoxNoQuant" Content="No quantification" GroupName="QuantType">
                                 <ToolTipService.ToolTip>
@@ -405,17 +421,24 @@
                                     <ToolTip Content="Label-free quantification is performed with FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
                             </RadioButton>
-                            <RadioButton x:Name="CheckBoxLFQwMBR" Content="LFQ + MBR Analysis: FlashLFQ quantification with enhanced match between runs" 
-                                         GroupName="QuantType" Click="MbrAnalysisUpdate">
+                            <RadioButton x:Name="CheckBoxSILAC" Content="SILAC/SILAM: Quantify peptides/proteins with stable isotope labels" GroupName="QuantType" Click="CheckBoxSILAC_Checked">
                                 <ToolTipService.ToolTip>
-                                    <ToolTip Content="Match between runs analysis via spectral library search" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
+                                    <ToolTip Content="SILAC quantification is performed using FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"/>
                                 </ToolTipService.ToolTip>
                             </RadioButton>
-                            <RadioButton x:Name="CheckBoxSILAC" Content="SILAC/SILAM: Quantify peptides/proteins with stable isotope labels" GroupName="QuantType" Click="CheckBoxSILAC_Checked">
+                            <RadioButton x:Name="CheckBoxMultiplex" Content="Multiplex Quantification: Quantify peptides labeled with isobaric tags" GroupName="QuantType" Unchecked="MultiplexUpdate" Checked="MultiplexUpdate">
                                 <ToolTipService.ToolTip>
-                                    <ToolTip Content="SILAC quantification is performed using FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"/>
+                                    <ToolTip Content="Intensity of reporter ions are reported as additional columns in AllPeptides.psmtsv and AllPSMs.psmtsv" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"/>
+                                </ToolTipService.ToolTip>
+                            </RadioButton>
+                            <RadioButton x:Name="CheckBoxLFQwSpectralRecovery" Content="LFQ + Spectral Recovery: Spectral recovery finds misidentified MS/MS spectra common in single-cell proteomics data" 
+                                         GroupName="QuantType" Click="SpectralRecoveryUpdate">
+                                <ToolTipService.ToolTip>
+                                    <ToolTip Content="Match between runs analysis via spectral library search" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
                             </RadioButton>
+
+                            <!-- SILAC Options -->
                             <CheckBox x:Name="CheckBoxQuantifyUnlabeledForSilac" 
                                       Content="Quantify unlabeled peptides/proteins" 
                                       IsEnabled="{Binding IsChecked, ElementName=CheckBoxSILAC}"
@@ -443,14 +466,22 @@
                                     <Button x:Name="ClearSilac" Content="Clear" Click="ClearSilac_Click" IsEnabled="{Binding IsChecked, ElementName=CheckBoxSILAC}"/>
                                 </StackPanel>
                             </Grid>
+
+                            <!-- LFQ Options -->
                             <StackPanel Orientation="Horizontal">
                                 <TextBox x:Name="PeakFindingToleranceTextBox"  PreviewTextInput="CheckIfNumber" Width="30" Height="20">
                                     <TextBox.IsEnabled>
                                         <MultiBinding Converter="{StaticResource boolOrConverter}">
                                             <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                            <Binding  ElementName="CheckBoxLFQwMBR" Path ="IsChecked"/>
+                                            <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
                                         </MultiBinding>
                                     </TextBox.IsEnabled>
+                                    <TextBox.Visibility>
+                                        <MultiBinding Converter="{StaticResource boolOr2VisConverter}">
+                                            <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
+                                            <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
+                                        </MultiBinding>
+                                    </TextBox.Visibility>
                                     <ToolTipService.ToolTip>
                                         <ToolTip Content="PPM tolerance for MS1 (LFQ) peakfinding" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                     </ToolTipService.ToolTip>
@@ -459,18 +490,26 @@
                                     <Label.IsEnabled>
                                         <MultiBinding Converter="{StaticResource boolOrConverter}">
                                             <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                            <Binding  ElementName="CheckBoxLFQwMBR" Path ="IsChecked"/>
+                                            <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
                                         </MultiBinding>
                                     </Label.IsEnabled>
+                                    <Label.Visibility>
+                                        <MultiBinding Converter="{StaticResource boolOr2VisConverter}">
+                                            <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
+                                            <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
+                                        </MultiBinding>
+                                    </Label.Visibility>
                                 </Label>
                             </StackPanel>
-                            <CheckBox x:Name="CheckBoxMatchBetweenRuns" Content="Match between runs" >
-                                <CheckBox.IsEnabled>
-                                    <MultiBinding Converter="{StaticResource boolOrConverter}">
+                            <CheckBox x:Name="CheckBoxMatchBetweenRuns" 
+                                      Content="Match between runs"
+                                      IsEnabled ="{Binding IsChecked, ElementName=CheckBoxLFQ}">
+                                <CheckBox.Visibility>
+                                    <MultiBinding Converter="{StaticResource boolOr2VisConverter}">
                                         <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                        <Binding  ElementName="CheckBoxLFQwMBR" Path ="IsChecked"/>
+                                        <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
                                     </MultiBinding>
-                                </CheckBox.IsEnabled>
+                                </CheckBox.Visibility>
                                 <ToolTipService.ToolTip>
                                     <ToolTip Content="(LFQ) Use MS2 identifications from one run to quantify those same peptides in other runs where they were not identified&#x0a;Selecting &quot;Write Spectral Library&quot; in the Output Options below will enable additional MBR analysis" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
@@ -479,13 +518,38 @@
                                 <CheckBox.IsEnabled>
                                     <MultiBinding Converter="{StaticResource boolOrConverter}">
                                         <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
-                                        <Binding  ElementName="CheckBoxLFQwMBR" Path ="IsChecked"/>
+                                        <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
                                     </MultiBinding>
                                 </CheckBox.IsEnabled>
+                                <CheckBox.Visibility>
+                                    <MultiBinding Converter="{StaticResource boolOr2VisConverter}">
+                                        <Binding  ElementName="CheckBoxLFQ" Path ="IsChecked"/>
+                                        <Binding  ElementName="CheckBoxLFQwSpectralRecovery" Path ="IsChecked"/>
+                                    </MultiBinding>
+                                </CheckBox.Visibility>
                                 <ToolTipService.ToolTip>
                                     <ToolTip Content="Use the 'Experimental Design' to normalize intensity values from FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
                             </CheckBox>
+
+                            <!-- Multiplex Options -->
+                            <StackPanel Orientation="Horizontal" Margin="5 5 5 0" Grid.Column="0" Grid.Row="0">
+                                <Label x:Name="MultiplexTag" Content="Label Type:" Width="75" 
+                                       Visibility="{Binding IsChecked, ElementName=CheckBoxMultiplex, Converter={StaticResource bool2VisConverter}}"/>
+                                <ComboBox x:Name="MultiplexComboBox" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" 
+                                          SelectionChanged="MultiplexUpdate"
+                                          IsEnabled="{Binding IsChecked, ElementName=CheckBoxMultiplex}"
+                                          Visibility="{Binding IsChecked, ElementName=CheckBoxMultiplex, Converter={StaticResource bool2VisConverter}}">
+                                    <ComboBox.ToolTip>
+                                        <TextBlock>
+                                            Isobaric label used for multiplexing
+                                            <LineBreak />
+                                            Labels can be added/modified by the user at "Data -> Open folder with mods/data files -> Mods -> tmt.txt"
+                                        </TextBlock>
+                                    </ComboBox.ToolTip>
+                                </ComboBox>
+                            </StackPanel>
+
                         </StackPanel>
                     </GroupBox>
 
@@ -513,9 +577,10 @@
                                 <!--<CheckBox x:Name="ckbPepXML" Content="Write .pep.XML" />-->
                                 <CheckBox x:Name="WriteDecoyCheckBox" Content="Write decoys" />
                                 <CheckBox x:Name="WriteContaminantCheckBox" Content="Write contaminants" />
+                                <CheckBox x:Name="WriteHighQPsmsCheckBox" Content="Write PSMs &amp; peptides with q-value above threshold"/>
                                 <CheckBox x:Name="WriteIndividualResultsCheckBox" Content="Write individual file results" />
-                                <CheckBox x:Name="WriteSpectralLibraryCheckBox" Content="Write spectral library" />
-                                <CheckBox x:Name="UpdateSpectralLibraryCheckBox" Content="Update SpectralLibrary" />
+                                <CheckBox x:Name="WriteSpectralLibraryCheckBox" Content="Write spectral library" IsEnabled="{Binding IsChecked, Converter={local:BooleanInverter}, ElementName=CheckBoxLFQwSpectralRecovery }"/>
+                                <CheckBox x:Name="UpdateSpectralLibraryCheckBox" Content="Update spectral library" />
                                 <CheckBox x:Name="CompressIndividualResultsCheckBox" Content="Compress individual file results" IsEnabled="{Binding IsChecked, ElementName=WriteIndividualResultsCheckBox}"/>
 
                             </StackPanel>
@@ -523,43 +588,6 @@
                             <!-- filtering options -->
                             <StackPanel Orientation="Vertical" Margin="5" Grid.Column="1">
 
-                                <!-- pep 1-value button -->
-                                <Grid>
-                                    <Grid.ColumnDefinitions>
-                                        <ColumnDefinition Width="400" />
-                                        <ColumnDefinition Width="50" />
-                                    </Grid.ColumnDefinitions>
-
-                                    <RadioButton x:Name="PepQValueRadioButton" Content="Filter results to pep q-value:" 
-                                                 IsChecked="False" GroupName="Filtering" Checked="PepQValueRadioButton_Checked">
-                                        <ToolTipService.ToolTip>
-                                            Removes PSM and protein results from the written output below the input pep q-value.
-                                            Mutually exclusive with filter results to q-value
-                                        </ToolTipService.ToolTip>
-                                    </RadioButton>
-                                    <TextBox x:Name="PepQValueTextBox" PreviewTextInput="CheckIfNumber" Margin="10,0,0,0" 
-                                             IsEnabled="{Binding IsChecked, ElementName=PepQValueRadioButton}" Width="45" Height="23" />
-                                </Grid>
-
-                                <!-- q value button -->
-                                <Grid>
-                                    <Grid.ColumnDefinitions>
-                                        <ColumnDefinition Width="400" />
-                                        <ColumnDefinition Width="50" />
-                                    </Grid.ColumnDefinitions>
-
-                                    <RadioButton x:Name="QValueRadioButton" Content="Filter results to q-value:" 
-                                                 IsChecked="False" GroupName="Filtering" Checked="QValueRadioButton_Checked">
-                                        <ToolTipService.ToolTip>
-                                            Removes PSM and protein results from the written output below the input q-value.
-                                            Mutually exclusive with filter results to pep q-value
-                                        </ToolTipService.ToolTip>
-                                    </RadioButton>
-
-                                    <TextBox x:Name="QValueTextBox" PreviewTextInput="CheckIfNumber" Margin="10,0,0,0" 
-                                             IsEnabled="{Binding IsChecked, ElementName=QValueRadioButton}" Width="45" Height="23" />
-                                </Grid>
-
                                 <!-- min score allowed box -->
                                 <Grid>
                                     <Grid.ColumnDefinitions>
@@ -1197,12 +1225,11 @@
         <StackPanel  Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1" Margin="5">
             <Button x:Name="cancelButton" Content="Cancel" Click="CancelButton_Click" />
             <Button x:Name="saveButton" Content="Save Search Task" Click="SaveButton_Click" FontSize="24" />
-            <Button x:Name="setDefaultbutton"  Width="100" 
-                    Command="{Binding TaskSettingViewModel.SaveAsDefaultSettingsCommand, RelativeSource={RelativeSource FindAncestor, AncestorType={x:Type Window}}}">
+            <Button x:Name="setDefaultbutton" Click="SaveAsDefault_Click" Width="100" >
+                <TextBlock Text="Save As Default" TextWrapping="Wrap" TextAlignment="Center"/>
                 <ToolTipService.ToolTip>
                     <ToolTip Content="Save these parameters as the default. MetaMorpheus can return to original defaults by deleting the folder 'DefaultParameters'" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                 </ToolTipService.ToolTip>
-                <TextBlock Text="Save As Default" TextWrapping="Wrap" TextAlignment="Center"/>
             </Button>
         </StackPanel>
     </Grid>
diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index ba8a5eb41..38e0c32b9 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -17,6 +17,8 @@
 using TaskLayer;
 using UsefulProteomicsDatabases;
 using GuiFunctions;
+using Proteomics;
+using System.Threading.Tasks;
 using static System.Net.WebRequestMethods;
 
 namespace MetaMorpheusGUI
@@ -36,6 +38,7 @@ public partial class SearchTaskWindow : Window
         private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
         private CustomFragmentationWindow CustomFragmentationWindow;
         private TaskSettingViewModel TaskSettingViewModel;
+        private string _defaultMultiplexType = "TMT10";
 
 
         internal SearchTask TheTask { get; private set; }
@@ -43,9 +46,11 @@ public partial class SearchTaskWindow : Window
         public SearchTaskWindow(SearchTask task)
         {
             InitializeComponent();
-            PopulateChoices();
+            
             TheTask = task ?? new SearchTask();
 
+            PopulateChoices();//
+
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as SearchTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
             TaskSettingsCtrl.DataContext = TaskSettingViewModel;
@@ -151,6 +156,14 @@ private void PopulateChoices()
             {
                 LocalizeModTypeForTreeViewObservableCollection.Add(new ModTypeForLoc(hm.Key));
             }
+
+            foreach (string labelModType in GlobalVariables.AllModsKnown.Where(m => m.ModificationType.Equals("Multiplex Label"))
+                         .Select(m => m.OriginalId).Distinct())
+            {
+                MultiplexComboBox.Items.Add(labelModType);
+            }
+            MultiplexComboBox.SelectedItem = _defaultMultiplexType;
+
         }
 
 
@@ -182,8 +195,17 @@ private void UpdateFieldsFromTask(SearchTask task)
             }
             CheckBoxParsimony.IsChecked = task.SearchParameters.DoParsimony;
             CheckBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
-            CheckBoxNoQuant.IsChecked = !task.SearchParameters.DoQuantification;
-            CheckBoxLFQ.IsChecked = task.SearchParameters.DoQuantification;
+            CheckBoxParsimony.IsChecked = task.SearchParameters.DoParsimony;
+            CheckBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
+            CheckBoxNoQuant.IsChecked = !task.SearchParameters.DoLabelFreeQuantification;
+            CheckBoxLFQ.IsChecked = task.SearchParameters.DoLabelFreeQuantification;
+            CheckBoxMultiplex.IsChecked = task.SearchParameters.DoMultiplexQuantification;
+            MultiplexComboBox.SelectedItem = task.SearchParameters.MultiplexModId ?? _defaultMultiplexType;
+            // If Spectral Recovery is enabled
+            if (task.SearchParameters.WriteSpectralLibrary & task.SearchParameters.MatchBetweenRuns)
+            {
+                CheckBoxLFQwSpectralRecovery.IsChecked = task.SearchParameters.DoSpectralRecovery;
+            }
             //If SILAC turnover
             if (task.SearchParameters.StartTurnoverLabel != null || task.SearchParameters.EndTurnoverLabel != null)
             {
@@ -302,28 +324,28 @@ private void UpdateFieldsFromTask(SearchTask task)
             MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
             CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
 
-            if (task.CommonParameters.QValueOutputFilter < 1)
+            if (task.CommonParameters.QValueThreshold < 1)
             {
-                QValueTextBox.Text = task.CommonParameters.QValueOutputFilter.ToString(CultureInfo.InvariantCulture);
-                QValueRadioButton.IsChecked = true;
+                QValueThresholdTextBox.Text = task.CommonParameters.QValueThreshold.ToString(CultureInfo.InvariantCulture);
             }
             else
             {
-                QValueTextBox.Text = "0.01";
+                QValueThresholdTextBox.Text = "0.01";
             }
 
-            if (task.CommonParameters.PepQValueOutputFilter < 1)
+            if (task.CommonParameters.PepQValueThreshold < 1)
             {
-                PepQValueTextBox.Text = task.CommonParameters.QValueOutputFilter.ToString(CultureInfo.InvariantCulture);
-                PepQValueRadioButton.IsChecked = true;
+                PepQValueThresholdTextBox.Text = task.CommonParameters.PepQValueThreshold.ToString(CultureInfo.InvariantCulture);
+                PepQValueThresholdCheckbox.IsChecked = true;
             }
             else
             {
-                PepQValueTextBox.Text = "0.01";  
+                PepQValueThresholdTextBox.Text = "0.01";
             }
 
             OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
             CkbMzId.IsChecked = task.SearchParameters.WriteMzId;
+            WriteHighQPsmsCheckBox.IsChecked = task.SearchParameters.WriteHighQValuePsms;
             WriteDecoyCheckBox.IsChecked = task.SearchParameters.WriteDecoys;
             WriteContaminantCheckBox.IsChecked = task.SearchParameters.WriteContaminants;
             WriteIndividualResultsCheckBox.IsChecked = task.SearchParameters.WriteIndividualFiles;
@@ -429,11 +451,28 @@ private SearchTask GetTaskFromGui()
             CleavageSpecificity searchModeType = GetSearchModeType(); //change search type to semi or non if selected
             SnesUpdates(searchModeType); //decide on singleN/C, make comp ion changes
 
-            if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecursorMassToleranceTextBox.Text, ProductMassToleranceTextBox.Text, MissedCleavagesTextBox.Text,
-                maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, MaxThreadsTextBox.Text, MinScoreAllowed.Text,
-                PeakFindingToleranceTextBox.Text, HistogramBinWidthTextBox.Text, DeconvolutionMaxAssumedChargeStateTextBox.Text, NumberOfPeaksToKeepPerWindowTextBox.Text,
-                MinimumAllowedIntensityRatioToBasePeakTexBox.Text, WindowWidthThomsonsTextBox.Text, NumberOfWindowsTextBox.Text, NumberOfDatabaseSearchesTextBox.Text,
-                MaxModNumTextBox.Text, MaxFragmentMassTextBox.Text, QValueTextBox.Text, PepQValueTextBox.Text, InternalIonsCheckBox.IsChecked.Value ? MinInternalFragmentLengthTextBox.Text : null))
+            if (!GlobalGuiSettings.CheckTaskSettingsValidity(
+                PrecursorMassToleranceTextBox.Text,
+                ProductMassToleranceTextBox.Text,
+                MissedCleavagesTextBox.Text,
+                maxModificationIsoformsTextBox.Text,
+                MinPeptideLengthTextBox.Text,
+                MaxPeptideLengthTextBox.Text,
+                MaxThreadsTextBox.Text,
+                MinScoreAllowed.Text,
+                PeakFindingToleranceTextBox.Text,
+                HistogramBinWidthTextBox.Text,
+                DeconvolutionMaxAssumedChargeStateTextBox.Text,
+                NumberOfPeaksToKeepPerWindowTextBox.Text,
+                MinimumAllowedIntensityRatioToBasePeakTexBox.Text,
+                WindowWidthThomsonsTextBox.Text,
+                NumberOfWindowsTextBox.Text,
+                NumberOfDatabaseSearchesTextBox.Text,
+                MaxModNumTextBox.Text,
+                MaxFragmentMassTextBox.Text,
+                QValueThresholdTextBox.Text,
+                PepQValueThresholdTextBox.Text,
+                InternalIonsCheckBox.IsChecked.Value ? MinInternalFragmentLengthTextBox.Text : null))
             {
                 return null;
             }
@@ -563,6 +602,8 @@ private SearchTask GetTaskFromGui()
                 totalPartitions: int.Parse(NumberOfDatabaseSearchesTextBox.Text, CultureInfo.InvariantCulture),
                 doPrecursorDeconvolution: DeconvolutePrecursors.IsChecked.Value,
                 useProvidedPrecursorInfo: UseProvidedPrecursor.IsChecked.Value,
+                qValueThreshold: !PepQValueThresholdCheckbox.IsChecked.Value ? double.Parse(QValueThresholdTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
+                pepQValueThreshold: PepQValueThresholdCheckbox.IsChecked.Value ? double.Parse(PepQValueThresholdTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
                 scoreCutoff: double.Parse(MinScoreAllowed.Text, CultureInfo.InvariantCulture),
                 listOfModsFixed: listOfModsFixed,
                 listOfModsVariable: listOfModsVariable,
@@ -580,8 +621,6 @@ private SearchTask GetTaskFromGui()
                 numberOfWindows: numberOfWindows,//maybe change this some day
                 normalizePeaksAccrossAllWindows: normalizePeaksAccrossAllWindows,//maybe change this some day
                 addCompIons: AddCompIonCheckBox.IsChecked.Value,
-                qValueOutputFilter: QValueRadioButton.IsChecked.Value ? double.Parse(QValueTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
-                pepQValueOutputFilter: PepQValueRadioButton.IsChecked.Value ? double.Parse(PepQValueTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
                 assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
                 minVariantDepth: MinVariantDepth,
                 maxHeterozygousVariants: MaxHeterozygousVariants);
@@ -608,20 +647,26 @@ private SearchTask GetTaskFromGui()
             TheTask.SearchParameters.MinAllowedInternalFragmentLength = InternalIonsCheckBox.IsChecked.Value ? Convert.ToInt32(MinInternalFragmentLengthTextBox.Text) : 0;
             TheTask.SearchParameters.DoParsimony = CheckBoxParsimony.IsChecked.Value;
             TheTask.SearchParameters.NoOneHitWonders = CheckBoxNoOneHitWonders.IsChecked.Value;
-            TheTask.SearchParameters.DoQuantification = !CheckBoxNoQuant.IsChecked.Value;
+            TheTask.SearchParameters.DoLabelFreeQuantification = !CheckBoxNoQuant.IsChecked.Value;
+            TheTask.SearchParameters.DoSpectralRecovery = CheckBoxLFQwSpectralRecovery.IsChecked.Value;
+            TheTask.SearchParameters.DoMultiplexQuantification = CheckBoxMultiplex.IsChecked.Value;
+            TheTask.SearchParameters.MultiplexModId = (string)MultiplexComboBox.SelectedItem;
             TheTask.SearchParameters.Normalize = CheckBoxNormalize.IsChecked.Value;
             TheTask.SearchParameters.MatchBetweenRuns = CheckBoxMatchBetweenRuns.IsChecked.Value;
             TheTask.SearchParameters.ModPeptidesAreDifferent = ModPepsAreUnique.IsChecked.Value;
             TheTask.SearchParameters.QuantifyPpmTol = double.Parse(PeakFindingToleranceTextBox.Text, CultureInfo.InvariantCulture);
             TheTask.SearchParameters.SearchTarget = CheckBoxTarget.IsChecked.Value;
             TheTask.SearchParameters.WriteMzId = CkbMzId.IsChecked.Value;
+            TheTask.SearchParameters.WriteHighQValuePsms = WriteHighQPsmsCheckBox.IsChecked.Value;
             TheTask.SearchParameters.WriteDecoys = WriteDecoyCheckBox.IsChecked.Value;
             TheTask.SearchParameters.WriteContaminants = WriteContaminantCheckBox.IsChecked.Value;
             TheTask.SearchParameters.WriteIndividualFiles = WriteIndividualResultsCheckBox.IsChecked.Value;
             TheTask.SearchParameters.WriteSpectralLibrary = WriteSpectralLibraryCheckBox.IsChecked.Value;
+            TheTask.SearchParameters.UpdateSpectralLibrary = UpdateSpectralLibraryCheckBox.IsChecked.Value;
             TheTask.SearchParameters.CompressIndividualFiles = CompressIndividualResultsCheckBox.IsChecked.Value;
             TheTask.SearchParameters.IncludeModMotifInMzid = IncludeMotifInModNamesCheckBox.IsChecked.Value;
 
+
             if (RemoveContaminantRadioBox.IsChecked.Value)
             {
                 TheTask.SearchParameters.TCAmbiguity = TargetContaminantAmbiguity.RemoveContaminant;
@@ -822,6 +867,25 @@ private void NonSpecificUsingNonSpecific(object sender, RoutedEventArgs e)
             }
         }
 
+        /// <summary>
+        /// When a new multiplex label is selected from the drop-down menu (MultiplexComboBox),
+        /// the fixed mod tree view is updated so that only those mods are selected. 
+        /// </summary>
+        private void MultiplexUpdate(object sender, RoutedEventArgs routedEventArgs)
+        {
+            ModTypeForTreeViewModel multiplexModType = FixedModTypeForTreeViewObservableCollection
+                .FirstOrDefault(b => b.DisplayName.Equals("Multiplex Label"));
+            string selectedModId = CheckBoxMultiplex.IsChecked.Value
+                ? (string)MultiplexComboBox.SelectedItem
+                : "NoMatchingMod";
+
+            foreach (ModForTreeViewModel mod in multiplexModType.Children)
+            {
+                mod.Use = mod.DisplayName.Contains(selectedModId);
+            }
+            UpdateModSelectionGrid();
+        }
+
         //this one is used by the GUI
         private void ProteaseSpecificUpdate(object sender, SelectionChangedEventArgs e)
         {
@@ -950,11 +1014,11 @@ private void SemiSpecificUpdate(object sender, RoutedEventArgs e)
             }
         }
 
-        private void MbrAnalysisUpdate(object sender, RoutedEventArgs e)
+        private void SpectralRecoveryUpdate(object sender, RoutedEventArgs e)
         {
-            if (CheckBoxLFQwMBR.IsChecked.Value)
+            if (CheckBoxLFQwSpectralRecovery.IsChecked.Value)
             {
-                if (UpdateGUISettings.UseMBRAnalysisMandatorySettings())
+                if (UpdateGUISettings.UseSpectralRecoveryMandatorySettings())
                 {
                     CheckBoxMatchBetweenRuns.IsChecked = true;
                     WriteSpectralLibraryCheckBox.IsChecked = true;
@@ -1049,7 +1113,7 @@ private void OnClosing(object sender, CancelEventArgs e)
             // remove event handler from timer
             // keeping it will trigger an exception because the closed window stops existing
 
-            CustomFragmentationWindow.Close();
+            CustomFragmentationWindow?.Close();
         }
 
         private static Proteomics.SilacLabel ConvertSilacDataGridInfoToSilacLabel(SilacInfoForDataGrid info)
@@ -1280,30 +1344,9 @@ private void CheckBoxSILAC_Checked(object sender, RoutedEventArgs e)
 
         private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
         {
-            SaveButton_Click(sender, e);
-            Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"SearchTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
-        }
-
-        /// <summary>
-        /// Event Handler for when the pepQvalue radio button is checked. Sets value to default then uncecks and clears qValue
-        /// </summary>
-        /// <param name="sender"></param>
-        /// <param name="e"></param>
-        private void PepQValueRadioButton_Checked(object sender, RoutedEventArgs e)
-        {
-            QValueTextBox.Clear();
-            PepQValueTextBox.Text = "0.01";
-        }
-
-        /// <summary>
-        /// Event Handler for when the qvalue radio button is checked. Sets value to default then unchecks and clears pepQvalue.
-        /// </summary>
-        /// <param name="sender"></param>
-        /// <param name="e"></param>
-        private void QValueRadioButton_Checked(object sender, RoutedEventArgs e)
-        {
-            PepQValueTextBox.Clear();
-            QValueTextBox.Text = "0.01";
+           // SaveButton_Click(sender, e);
+            //Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"SearchTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
+            TaskSettingViewModel.SaveAsDefaultSettings();
         }
 
         /// <summary>
@@ -1329,26 +1372,15 @@ private void InternalIonsCheckBox_Checked(object sender, RoutedEventArgs e)
             MinInternalFragmentLengthTextBox.Text = "4";
         }
 
-        /// <summary>
-        /// Open the SaveSettings Window
-        /// </summary>
-        /// <param name="sender"></param>
-        /// <param name="e"></param>
-        private void SaveAs_Click(object sender, RoutedEventArgs e)
+        private void TaskSettingsCtrl_Loaded(object sender, RoutedEventArgs e)
         {
-            SaveSettingsWindow newWindow = new SaveSettingsWindow(TaskSettingViewModel);
 
-            // if user hit save button
-            if (newWindow.ShowDialog() == true)
-            {
-                TaskSettingViewModel.SaveSettingsFromWindow();
-            }
-            // if user hit cancel
-            else
-            {
-           
-            }
         }
+
+        //private void TaskSettingsCtrl_Loaded(object sender, RoutedEventArgs e)
+        //{
+
+        //}
     }
 
     public class DataContextForSearchTaskWindow : INotifyPropertyChanged
diff --git a/MetaMorpheus/GUI/TaskWindows/SpectralAveragingTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/SpectralAveragingTaskWindow.xaml
index e2d1b76de..e5e74ca4f 100644
--- a/MetaMorpheus/GUI/TaskWindows/SpectralAveragingTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/SpectralAveragingTaskWindow.xaml
@@ -61,6 +61,8 @@
                             </TextBox.Style>
                         </TextBox>
                     </StackPanel>
+                    
+                    
 
                     <!-- Wiki Link -->
                     <TextBlock Grid.Column="1" FontSize="13" HorizontalAlignment="Right" VerticalAlignment="Center"
@@ -72,7 +74,7 @@
                         </Hyperlink>
                     </TextBlock>
                 </Grid>
-                
+
                 <!-- Averaging Parameters -->
                 <GroupBox DockPanel.Dock="Top">
                     <StackPanel>
diff --git a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
index 41c908021..47ef3a313 100644
--- a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
@@ -19,7 +19,7 @@
             <DockPanel>
                 <StackPanel DockPanel.Dock="Top" Orientation="Horizontal">
                     <Label Content="Task Name" />
-                    <TextBox x:Name="OutputFileNameTextBox" Width="150">
+                    <TextBox x:Name="OutputFileNameTextBox" Width="150" TextChanged="OutputFileNameTextBox_TextChanged">
                         <TextBox.Style>
                             <Style TargetType="TextBox" xmlns:sys="clr-namespace:System;assembly=mscorlib">
                                 <Style.Resources>
@@ -44,6 +44,14 @@
                         </TextBox.Style>
                     </TextBox>
                 </StackPanel>
+
+                <StackPanel DockPanel.Dock="Top" Margin="10">
+
+                    <!-- save settings -->
+                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
+             DataContext="{Binding TaskSettingViewModel}"/>
+                </StackPanel>
+
                 <StackPanel DockPanel.Dock="Top">
                     <Grid>
                         <Grid.ColumnDefinitions>
diff --git a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
index e08dba3ec..3a1ce930a 100644
--- a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
@@ -38,7 +38,7 @@ public XLSearchTaskWindow(XLSearchTask task)
 
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as XLSearchTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
-            //TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+            TaskSettingsCtrl.DataContext = TaskSettingViewModel;
 
             if (task == null)
             {
@@ -441,7 +441,7 @@ private void OnClosing(object sender, CancelEventArgs e)
             // remove event handler from timer
             // keeping it will trigger an exception because the closed window stops existing
 
-            CustomFragmentationWindow.Close();
+            CustomFragmentationWindow?.Close();
         }
 
         private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
@@ -487,5 +487,10 @@ private void NonSpecificUpdate(object sender, TextChangedEventArgs e)
                 }
             }
         }
+
+        private void OutputFileNameTextBox_TextChanged(object sender, TextChangedEventArgs e)
+        {
+
+        }
     }
 }
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/Views/SaveSettingsControl.xaml b/MetaMorpheus/GUI/Views/SaveSettingsControl.xaml
new file mode 100644
index 000000000..aa8e9b5e2
--- /dev/null
+++ b/MetaMorpheus/GUI/Views/SaveSettingsControl.xaml
@@ -0,0 +1,28 @@
+<UserControl x:Class="MetaMorpheusGUI.SaveSettingsControl"
+             xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
+             xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+             xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" 
+             xmlns:d="http://schemas.microsoft.com/expression/blend/2008" 
+             xmlns:local="clr-namespace:MetaMorpheusGUI"
+        xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
+             mc:Ignorable="d" 
+             d:DataContext="{x:Type guiFunctions:TaskSettingViewModel}"
+             d:DesignHeight="30" d:DesignWidth="800">
+    <Grid>
+        <StackPanel   Height="Auto" DataContext="{Binding}"
+             Background="{StaticResource BackgroundColor}" Orientation="Horizontal" HorizontalAlignment="Right">
+
+            <ComboBox Name="TaskSettingsComboBox" Width="200" Height="20" VerticalAlignment="Center" 
+              HorizontalAlignment="Left" IsSynchronizedWithCurrentItem="True"
+              ItemsSource="{Binding Path=AllSettings}" 
+              SelectedItem="{Binding Path=SelectedSettings}">
+            </ComboBox>
+            <Button x:Name="Save" Content="Save" FontSize="10" 
+            Width="60" Margin="5,5,2.5,5" Command="{Binding SaveSettingsCommand}" />
+         <Button x:Name="SaveAs" Content="Save as" FontSize="10" 
+            Width="60" Margin="5,5,2.5,5" Click="SaveAs_Click"/>
+         <Button x:Name="Delete"  Content="Delete" FontSize="10" Width="60" Margin="5,5,2.5,5"
+            Command="{Binding DeleteSettingsCommand}" />
+        </StackPanel>
+    </Grid>
+</UserControl>
diff --git a/MetaMorpheus/GUI/Views/SaveSettingsControl.xaml.cs b/MetaMorpheus/GUI/Views/SaveSettingsControl.xaml.cs
new file mode 100644
index 000000000..13c450992
--- /dev/null
+++ b/MetaMorpheus/GUI/Views/SaveSettingsControl.xaml.cs
@@ -0,0 +1,54 @@
+using GuiFunctions;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using System.Windows;
+using System.Windows.Controls;
+using System.Windows.Data;
+using System.Windows.Documents;
+using System.Windows.Input;
+using System.Windows.Media;
+using System.Windows.Media.Imaging;
+using System.Windows.Navigation;
+using System.Windows.Shapes;
+
+namespace MetaMorpheusGUI
+{
+    /// <summary>
+    /// Interaction logic for SaveSettingsControl.xaml
+    /// </summary>
+    public partial class SaveSettingsControl : UserControl
+    {
+        public SaveSettingsControl()
+        {
+            InitializeComponent();
+        }
+
+        /// <summary>
+        /// Open the SaveSettings Window
+        /// </summary>
+        /// <param name="sender"></param>
+        /// <param name="e"></param>
+        private void SaveAs_Click(object sender, RoutedEventArgs e)
+        {
+            var taskSettingsViewModel = DataContext as TaskSettingViewModel 
+                ?? throw new ArgumentException($"DataContext is of type {DataContext.GetType()}, TaskSettingsViewModel is reaquired.");
+
+
+            SaveSettingsWindow newWindow = new SaveSettingsWindow(taskSettingsViewModel);
+
+            // if user hit save button
+            if (newWindow.ShowDialog() == true)
+            {
+                taskSettingsViewModel.SaveSettingsFromWindow();
+            }
+            // if user hit cancel
+            else
+            {
+
+            }
+        }
+    }
+}
diff --git a/MetaMorpheus/GuiFunctions/TomlFileFolderSerializer.cs b/MetaMorpheus/GuiFunctions/TomlFileFolderSerializer.cs
index 39170d86f..a9aaefa69 100644
--- a/MetaMorpheus/GuiFunctions/TomlFileFolderSerializer.cs
+++ b/MetaMorpheus/GuiFunctions/TomlFileFolderSerializer.cs
@@ -10,6 +10,7 @@
 using Proteomics;
 using Nett;
 using TaskLayer;
+using EngineLayer;
 
 namespace GuiFunctions
 
@@ -20,7 +21,7 @@ namespace GuiFunctions
     /// 
     public static class TomlFileFolderSerializer
     {
-        public static string PathToCheck = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "SettingsDataFiles");
+        public static string PathToCheck = Path.Combine(GlobalVariables.DataDir, "DefaultParameters");
         /// <summary>
         /// Create a file that contains the serialized object. 
         /// </summary>
@@ -138,6 +139,8 @@ public static string[] LoadAllNamesOfType(Type type)
             var folders = Directory.GetFiles(path)
                 .Select(p => Path.GetFileNameWithoutExtension(p)).ToArray();
             return folders;
-        }        
+        }     
+        
+       
     }
 }
\ No newline at end of file
diff --git a/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs
index 2450814b9..bffa2f03d 100644
--- a/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs
@@ -10,10 +10,14 @@
 using System.Windows;
 using System.Windows.Input;
 using Easy.Common.Extensions;
+using EngineLayer;
+using Nett;
 using Org.BouncyCastle.Asn1.X509.Qualified;
 using OxyPlot;
 using pepXML.Generated;
 using TaskLayer;
+using ThermoFisher.CommonCore.Data;
+using TopDownProteomics.Chemistry;
 
 namespace GuiFunctions
 {
@@ -30,10 +34,7 @@ public class TaskSettingViewModel : BaseViewModel
 
         #region Public Properties
 
-        public ObservableCollection<string> AllSettings
-        {
-            get => allSettings;
-        }
+        public ObservableCollection<string> AllSettings => allSettings;
 
         public string TypedSettingsName
         {
@@ -73,17 +74,17 @@ public Dictionary<string, MetaMorpheusTask> AllSettingsDict
         public ICommand SaveAsDefaultSettingsCommand { get; set; }
 
         /// <summary>
-        /// 
+        /// The task that is currently working on
         /// </summary>
         public MetaMorpheusTask TheTask => AllSettingsDict[SelectedSettings];
 
         /// <summary>
-        /// 
+        /// Task from gui
         /// </summary>
         public Func<MetaMorpheusTask> GetTaskFromGui { get; set; }
 
         /// <summary>
-        /// 
+        /// update the gui from the task
         /// </summary>
         public Action<MetaMorpheusTask> UpdateFieldsInGuiWithNewTask { get; set; }
 
@@ -93,6 +94,49 @@ public Dictionary<string, MetaMorpheusTask> AllSettingsDict
 
         public TaskSettingViewModel(MetaMorpheusTask task, Action<MetaMorpheusTask> updateFieldsInGuiEventHandler, Func<MetaMorpheusTask> getTaskFromGui)
         {
+            // if directory does not exist, create new directory and default settings
+            if (!Directory.Exists(TomlFileFolderSerializer.PathToCheck))
+            {
+                Directory.CreateDirectory(Path.Combine(TomlFileFolderSerializer.PathToCheck));
+            }
+
+            // check if default is saved in previous location, if so, move to new location and rename
+            if (Directory.Exists(TomlFileFolderSerializer.PathToCheck))
+            {
+                string oldDefaultPathToCheck = task switch
+                {
+                    SearchTask search => "SearchTaskDefault.toml",
+                    CalibrationTask calibration => "CalibrationTaskDefault.toml",
+                    GptmdTask gptmd => "GptmdTaskDefault.toml",
+                    XLSearchTask xLSearch => "XLSearchTaskDefault.toml",
+                    GlycoSearchTask glycoSearch => "GlycoSearchTaskDefault.toml",
+                    SpectralAveragingTask spectralAverage => "SpectralAverageTaskDefault.toml",
+                    _ => "",
+                };
+
+                String finalPath = Path.Combine(GlobalVariables.DataDir, "DefaultParameters", oldDefaultPathToCheck);
+                if (File.Exists(finalPath))
+                {
+                    // load in
+                    MetaMorpheusTask previouslySavedDefaultTask = task switch
+                    {
+                        SearchTask search => Toml.ReadFile<SearchTask>(finalPath, MetaMorpheusTask.tomlConfig),
+                        CalibrationTask calibration => Toml.ReadFile<CalibrationTask>(finalPath, MetaMorpheusTask.tomlConfig),
+                        GptmdTask gptmd => Toml.ReadFile<GptmdTask>(finalPath, MetaMorpheusTask.tomlConfig),
+                        XLSearchTask xLSearch => Toml.ReadFile<XLSearchTask>(finalPath, MetaMorpheusTask.tomlConfig),
+                        GlycoSearchTask glycoSearch => Toml.ReadFile<GlycoSearchTask>(finalPath, MetaMorpheusTask.tomlConfig),
+                        SpectralAveragingTask spectralAverage => Toml.ReadFile<SpectralAveragingTask>(finalPath, MetaMorpheusTask.tomlConfig),
+                        _ => Toml.ReadFile<MetaMorpheusTask>(finalPath, MetaMorpheusTask.tomlConfig),
+                    };
+
+
+                    String s = oldDefaultPathToCheck.Substring(0, oldDefaultPathToCheck.Length - 5) + "(Default)";
+                    TomlFileFolderSerializer.Save(oldDefaultPathToCheck.Substring(0, oldDefaultPathToCheck.Length - 5) + "(Default)", previouslySavedDefaultTask);
+                    TomlFileFolderSerializer.Delete(previouslySavedDefaultTask.GetType(), oldDefaultPathToCheck);
+                    File.Delete(finalPath);
+                }
+            }
+
             // initial construction
             var type = task.GetType();
             UpdateFieldsInGuiWithNewTask = updateFieldsInGuiEventHandler;
@@ -104,63 +148,32 @@ public TaskSettingViewModel(MetaMorpheusTask task, Action<MetaMorpheusTask> upda
             // load in all settings from directory of specific object type
             MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("LoadAllOfTypeT");
             MethodInfo genericMethod = method.MakeGenericMethod(type);
-            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] {task}));
+            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] { task }));
 
+            // parse directory to get object type and MMTask from toml files
             var keys = result.Keys.Cast<string>().ToList();
             var values = result.Values.Cast<MetaMorpheusTask>().ToList();
             Dictionary<string, MetaMorpheusTask> tempDict = new();
-            for(int i = 0; i < keys.Count; i++)
+            for (int i = 0; i < keys.Count; i++)
             {
                 tempDict.Add(keys[i], values[i]);
             }
             AllSettingsDict = tempDict;
-
-            //When there is no default setting, create a default called "Default(Default)"
-            string[] keysInDict = AllSettingsDict.Keys.Cast<string>().ToArray();
-            for (int j = 0; j < keysInDict.Length; j++)
+            
+            if (!AllSettingsDict.Any())
             {
-                if (keysInDict[j].Contains("(Default)"))
-                {
-                    break;
-                }
-                else
-                {
-                    if (j == keysInDict.Length - 1)
-                    {
-                        AllSettingsDict.Add("DefaultSetting(Default)", task);
-                        TomlFileFolderSerializer.Save("DefaultSetting(Default)", task);
-                    }
-                }
+                string name = "DefaultSetting(Default)";
+                TomlFileFolderSerializer.Save("DefaultSetting(Default)", task);
+                AllSettingsDict.Add(name, task);
+                SelectedSettings = AllSettingsDict.First(p => p.Key.Contains("(Default)")).Key;
             }
 
-            SelectDefaultAuto();
-        }
-
-        /// <summary>
-        /// ONLY USED FOR TESTING
-        /// </summary>
-        /// <param name="task"></param>
-        internal TaskSettingViewModel(MetaMorpheusTask task = null)
-        {
-            var type = task.GetType() ?? typeof(SearchTask);
-            MethodInfo method = typeof(TomlFileFolderSerializer).GetMethod("LoadAllOfTypeT");
-            MethodInfo genericMethod = method.MakeGenericMethod(type);
-            System.Collections.IDictionary result = ((System.Collections.IDictionary)genericMethod.Invoke(null, new object[] { task ?? new SearchTask() }));
-
-            var keys = result.Keys.Cast<string>().ToList();
-            var values = result.Values.Cast<MetaMorpheusTask>().ToList();
-            Dictionary<string, MetaMorpheusTask> tempDict = new();
-            for (int i = 0; i < keys.Count; i++)
+            if (AllSettingsDict.Any(p => p.Key.Contains("(Default)")))
             {
-                tempDict.Add(keys[i], values[i]);
+                SelectedSettings = AllSettingsDict.First(p => p.Key.Contains("(Default)")).Key;
             }
-            AllSettingsDict = tempDict;
-
-            SaveSettingsCommand = new RelayCommand(SaveSettings);
-            DeleteSettingsCommand = new RelayCommand(DeleteSettings);
-            SaveAsDefaultSettingsCommand = new RelayCommand(SaveAsDefaultSettings);
-            SelectDefaultAuto();
         }
+
         
         #endregion
 
@@ -168,6 +181,9 @@ internal TaskSettingViewModel(MetaMorpheusTask task = null)
 
         #region Command Methods
 
+        /// <summary>
+        /// Modify a saved task
+        /// </summary>
         public void SaveSettings()
         {
             if (SelectedSettings == null)
@@ -177,7 +193,12 @@ public void SaveSettings()
 
             if (SelectedSettings.Contains("(Default)"))
             {
-                MessageBox.Show("Default Setting cannot be modified. Please use \"Save as Default\" button", "Modifying Default Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                if (!GlobalVariables.MetaMorpheusVersion.Contains("DEBUG"))
+                {
+                    MessageBox.Show("Default Setting cannot be modified. Please use \"Save as\" button",
+                        "Modifying Default Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                }
+
                 return;
             }
 
@@ -188,16 +209,24 @@ public void SaveSettings()
             AllSettingsDict.Add(SelectedSettings, taskFromGUI);
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
-            SelectDefaultAuto();
+            SelectedSettings = this.SelectedSettings;
         }
 
-    public void SaveSettingsFromWindow()
-    {
+        /// <summary>
+        /// Save a new task with a window popped up
+        /// </summary>
+        public void SaveSettingsFromWindow()
+        {
 
             if (TypedSettingsName is null || TypedSettingsName.IsNullOrEmptyOrWhiteSpace())
             {
-                MessageBox.Show("The name cannot be empty", "Empty Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
-                TypedSettingsName = "";
+                if (!GlobalVariables.MetaMorpheusVersion.Contains("DEBUG"))
+                {
+                    MessageBox.Show("The name cannot be empty", "Empty Settings Error", MessageBoxButton.OK,
+                        MessageBoxImage.Warning);
+                    TypedSettingsName = "";
+                }
+
                 return;
             }
 
@@ -205,8 +234,13 @@ public void SaveSettingsFromWindow()
 
             if (AllSettingsDict.ContainsKey(settingsName))
             {
-                MessageBox.Show("The name already exists", "Repeated Name Error", MessageBoxButton.OK, MessageBoxImage.Warning);
-                TypedSettingsName = "";
+                if (!GlobalVariables.MetaMorpheusVersion.Contains("DEBUG"))
+                {
+                    MessageBox.Show("The name already exists", "Repeated Name Error", MessageBoxButton.OK,
+                        MessageBoxImage.Warning);
+                    TypedSettingsName = "";
+                }
+
                 return;
             }
 
@@ -230,9 +264,12 @@ public void SaveSettingsFromWindow()
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
             TypedSettingsName = "";
-            SelectDefaultAuto();
+            //SelectDefaultAuto();
         }
 
+        /// <summary>
+        /// Delete the selected task
+        /// </summary>
         public void DeleteSettings()
         {
             if(SelectedSettings == null)
@@ -242,7 +279,11 @@ public void DeleteSettings()
 
             if (SelectedSettings.Contains("(Default)"))
             {
-                MessageBox.Show("Default Setting cannot be deleted", "Deleting Default Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                if(!GlobalVariables.MetaMorpheusVersion.Contains("DEBUG")){
+                    MessageBox.Show("Default Setting cannot be deleted", "Deleting Default Settings Error",
+                        MessageBoxButton.OK, MessageBoxImage.Warning);
+                }
+
                 return;
             }
 
@@ -250,9 +291,12 @@ public void DeleteSettings()
             AllSettingsDict.Remove(SelectedSettings);
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
-            SelectDefaultAuto();
+            //SelectDefaultAuto();
         }
 
+        /// <summary>
+        /// Set a saved set as a default setting
+        /// </summary>
         public void SaveAsDefaultSettings()
         {
             if (SelectedSettings == null)
@@ -262,7 +306,12 @@ public void SaveAsDefaultSettings()
 
             if (SelectedSettings.Contains("(Default)"))
             {
-                MessageBox.Show("It's already a default setting", "Repeatted Setting Default Settings Error", MessageBoxButton.OK, MessageBoxImage.Warning);
+                if (!GlobalVariables.MetaMorpheusVersion.Contains("DEBUG"))
+                {
+                    MessageBox.Show("It's already a default setting", "Repeatted Setting Default Settings Error",
+                        MessageBoxButton.OK, MessageBoxImage.Warning);
+                }
+
                 return;
             }
 
@@ -273,7 +322,7 @@ public void SaveAsDefaultSettings()
             if (AllSettingsDict.Any(p => p.Key.Contains("(Default)")))
             {
                 var oldDefault = AllSettingsDict.First(p => p.Key.Contains("(Default)"));
-                string newOldDefaultName = oldDefault.Key.Remove(oldDefault.Key.Length - 9); // TODO
+                string newOldDefaultName = oldDefault.Key.Remove(oldDefault.Key.Length - 9);
                 TomlFileFolderSerializer.Delete(oldDefault.Value.GetType(), oldDefault.Key);
                 AllSettingsDict.Remove(oldDefault.Key);
                 TomlFileFolderSerializer.Save(newOldDefaultName, oldDefault.Value);
@@ -288,7 +337,7 @@ public void SaveAsDefaultSettings()
 
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
-            SelectDefaultAuto();
+            //SelectDefaultAuto();
         }
 
         
@@ -296,27 +345,9 @@ public void SaveAsDefaultSettings()
     #endregion
 
         #region Helpers
-        private void SelectDefaultAuto()
-        {
-
-            var defaultSetting = AllSettingsDict.First(p => p.Key.Contains("(Default)"));
-            SelectedSettings = defaultSetting.Key;
-        }
-
-        //private MetaMorpheusTask GetDefaultTask(MetaMorpheusTask taskTypeToGetDefault)
-        //{
-        //    return taskTypeToGetDefault.TaskType switch
-        //    {
-        //        MyTask.Search => new SearchTask(),
-        //        MyTask.Gptmd => new GptmdTask(),
-        //        MyTask.Calibrate => new CalibrationTask(),
-        //        MyTask.XLSearch => new XLSearchTask(),
-        //        MyTask.GlycoSearch => new GlycoSearchTask(),
-        //        _ => throw new ArgumentOutOfRangeException(nameof(taskTypeToGetDefault.TaskType), taskTypeToGetDefault.TaskType, null)
-        //    };
-        //}
+        
     }
-       
+
     #endregion
 
 }
diff --git a/MetaMorpheus/Test/MetaDrawTest.cs b/MetaMorpheus/Test/MetaDrawTest.cs
index 0016c7318..7a7b6b90f 100644
--- a/MetaMorpheus/Test/MetaDrawTest.cs
+++ b/MetaMorpheus/Test/MetaDrawTest.cs
@@ -990,6 +990,7 @@ public static void TestMetaDrawErrors()
         }
 
         [Test]
+        [NonParallelizable]
         public static void TestMetaDrawLoadingWithWeirdFileNames()
         {
             // test loading when the file has a periods, commas, spaces in the name
diff --git a/MetaMorpheus/Test/SaveSettingsTests.cs b/MetaMorpheus/Test/SaveSettingsTests.cs
index 01c1c1c20..118b518c7 100644
--- a/MetaMorpheus/Test/SaveSettingsTests.cs
+++ b/MetaMorpheus/Test/SaveSettingsTests.cs
@@ -1,14 +1,13 @@
-using System;
+using EngineLayer;
+using GuiFunctions;
+using Nett;
+using NUnit.Framework;
+using System;
 using System.Collections.Generic;
 using System.Diagnostics.CodeAnalysis;
 using System.IO;
 using System.Linq;
-using System.Security.AccessControl;
-using System.Text;
-using System.Threading.Tasks;
-using GuiFunctions;
-using Nett;
-using NUnit.Framework;
+using MassSpectrometry;
 using TaskLayer;
 
 namespace Test
@@ -18,33 +17,41 @@ namespace Test
     [ExcludeFromCodeCoverage]
     public class SaveSettingsTests
     {
-        [OneTimeSetUp]
-        public static void OneTimeSetup()
+        static SaveSettingsTests()
         {
-            Directory.CreateDirectory(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"));
-            var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory,@"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
-            var tomlFile2 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"), MetaMorpheusTask.tomlConfig);
-            var tomlFile3 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"), MetaMorpheusTask.tomlConfig);
-            TomlFileFolderSerializer.Save("customBCZ", tomlFile1);
-            TomlFileFolderSerializer.Save("customBY", tomlFile2);
-            TomlFileFolderSerializer.Save("customCZ", tomlFile3);
-
-            // TODO: Repeat above for callibration task, without setting a default
+            GlobalVariables.SetUpGlobalVariables();
+        }
+        public static IEnumerable<MetaMorpheusTask> SwitchTestCases =>
+            new List<MetaMorpheusTask>
+            {
+                new SearchTask(),
+                new SpectralAveragingTask(),
+                new CalibrationTask(),
+                new GlycoSearchTask(),
+                new XLSearchTask(),
+                new GptmdTask()
+            };
 
-            // example code
-            var task = new CalibrationTask();
-            Toml.WriteFile<CalibrationTask>(task, "file out path.toml", MetaMorpheusTask.tomlConfig);
-        }   
+        [OneTimeSetUp]
+        public static void Setup() {}
 
-        [OneTimeTearDown]
-        public static void OneTimeTearDown()
+        [TearDown]
+        public static void TearDown()
         {
-            //Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"), true);
+            String path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DefaultParameters");
+            if (Directory.Exists(path))
+            {
+                Directory.Delete(path, true);
+            }
         }
 
+        /// <summary>
+        /// fake window for the test
+        /// </summary>
         private class FakeGuiWindow
         {
-            public MetaMorpheusTask TheTask { get; private set; }
+            public MetaMorpheusTask TheTask { get; internal set; }
+
             public FakeGuiWindow(MyTask taskType)
             {
                 TheTask = taskType switch
@@ -54,6 +61,7 @@ public FakeGuiWindow(MyTask taskType)
                     MyTask.Calibrate => new CalibrationTask(),
                     MyTask.XLSearch => new XLSearchTask(),
                     MyTask.GlycoSearch => new GlycoSearchTask(),
+                    MyTask.Average => new SpectralAveragingTask(),
                     _ => throw new ArgumentOutOfRangeException(nameof(taskType), taskType, null)
                 };
             }
@@ -69,153 +77,397 @@ public void UpdateFieldsFromNewTask(MetaMorpheusTask task)
             }
         }
 
-        // TODO: Test what happens when no default is set
-
+        /// <summary>
+        /// test the constructor without the defaultparameter directory
+        /// </summary>
+        /// <param name="task">task currenty working on</param>
         [Test]
-        public void ConstructorTestWithoutDefaultSettings()
+        [NonParallelizable]
+        [TestCaseSource(nameof(SwitchTestCases))]
+        public void ConstructorTestWithoutDefaultParameters(MetaMorpheusTask task)
         {
-            // set up directories
-
-
-
-            // test
-            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
-            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var fakeTaskWindow = new FakeGuiWindow(task.TaskType);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(task,
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
             var testDictionary = testTaskSettingViewModel.AllSettingsDict;
+            String pathToCheck = Path.Combine(GlobalVariables.DataDir, "DefaultParameters");
+            Assert.That(Directory.Exists(pathToCheck));
             Assert.That(testDictionary.ContainsKey("DefaultSetting(Default)"));
             var testWindow = fakeTaskWindow.GetTaskFromGui();
             var comparingWindow = testDictionary["DefaultSetting(Default)"];
-            Assert.That(testWindow.Equals(comparingWindow));
+            Assert.That(!testWindow.Equals(null));
             TomlFileFolderSerializer.Save("testFile", testWindow);
             string pathOfTestFile = TomlFileFolderSerializer.GetFilePath(testWindow.GetType(), "testFile");
-            string pathOfComparingFile = TomlFileFolderSerializer.GetFilePath(comparingWindow.GetType(), "DefaultSetting(Default)");
+            string pathOfComparingFile =
+                TomlFileFolderSerializer.GetFilePath(comparingWindow.GetType(), "DefaultSetting(Default)");
             var linesA = File.ReadAllLines(pathOfTestFile);
             var linesB = File.ReadAllLines(pathOfComparingFile);
 
             Assert.That(linesA.Length, Is.EqualTo(linesB.Length));
             for (int i = 0; i < linesA.Length; i++)
             {
-                //if (linesA[i].StartsWith("MaxMissedCleavages"))
-                //{
-                //    Assert.That(linesA[i], Is.Not.EqualTo(linesB[i]));
-                //    Assert.That(linesA[i].EndsWith('1'));
-                //    Assert.That(linesB[i].EndsWith('2'));
-                //}
-                //else
                 Assert.That(linesA[i], Is.EqualTo(linesB[i]));
             }
-
-
-            // clean up directories
         }
 
+        /// <summary>
+        /// test the constructor with the defaultparameter directory but nothing is in it
+        /// </summary>
+        /// <param name="task">task currenty working on</param>
         [Test]
-        public void ExampleTest()
+        [NonParallelizable]
+        public void ConstructorTestWithDefaultParametersWithoutDefaultSettings()
         {
+            //setup
+            Directory.CreateDirectory(Path.Combine(GlobalVariables.DataDir, "DefaultParameters"));
+            //test
             var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
-            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
-
-            // test everything is loaded correctly
-            // check task fake window is correct
-            // check serialized files is correct
-            // check dictionary is correct
-
-            // run a command
-
-
-            // test everything has changed as it should
-            // check task fake window is correct
-            // check serialized files is correct
-            // check dictionary is correct
-
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var testDictionary = testTaskSettingViewModel.AllSettingsDict;
+            Assert.That(testDictionary.ContainsKey("DefaultSetting(Default)"));
+            var testWindow = fakeTaskWindow.GetTaskFromGui();
+            var comparingWindow = testDictionary["DefaultSetting(Default)"];
+            Assert.That(!testWindow.Equals(null));
+            TomlFileFolderSerializer.Save("testFile", testWindow);
+            string pathOfTestFile = TomlFileFolderSerializer.GetFilePath(testWindow.GetType(), "testFile");
+            string pathOfComparingFile =
+                TomlFileFolderSerializer.GetFilePath(comparingWindow.GetType(), "DefaultSetting(Default)");
+            var linesA = File.ReadAllLines(pathOfTestFile);
+            var linesB = File.ReadAllLines(pathOfComparingFile);
 
-            // example read all lines comparison
-            string pathA = "";
-            string pathB = "";
+            Assert.That(linesA.Length, Is.EqualTo(linesB.Length));
+            for (int i = 0; i < linesA.Length; i++)
+            {
+                Assert.That(linesA[i], Is.EqualTo(linesB[i]));
+            }
+        }
 
-            var linesA = File.ReadAllLines(pathA);
-            var linesB = File.ReadAllLines(pathB);
+        /// <summary>
+        /// test the constructor with the defaultparameter tasks
+        /// </summary>
+        /// <param name="task">task currenty working on</param>
+        [Test]
+        [NonParallelizable]
+        [TestCaseSource(nameof(SwitchTestCases))]
+        public void ConstructorTestWithDefaultSettings(MetaMorpheusTask task)
+        {
+            Directory.CreateDirectory(Path.Combine(GlobalVariables.DataDir, "DefaultParameters"));
+            string oldDefaultName = task switch
+            {
+                SearchTask search => "SearchTaskDefault.toml",
+                CalibrationTask calibration => "CalibrationTaskDefault.toml",
+                GptmdTask gptmd => "GptmdTaskDefault.toml",
+                XLSearchTask xLSearch => "XLSearchTaskDefault.toml",
+                GlycoSearchTask glycoSearch => "GlycoSearchTaskDefault.toml",
+                SpectralAveragingTask spectralAverage => "SpectralAverageTaskDefault.toml",
+                _ => "",
+            };
+            String pathToCheck = Path.Combine(TestContext.CurrentContext.TestDirectory,
+                "DefaultParameters\\" + oldDefaultName);
+            Toml.WriteFile<MetaMorpheusTask>(task, pathToCheck, MetaMorpheusTask.tomlConfig);
+            var fakeTaskWindow = new FakeGuiWindow(task.TaskType);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(task,
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var testDictionary = testTaskSettingViewModel.AllSettingsDict;
+            String defaultName = task switch
+            {
+                SearchTask search => "SearchTaskDefault(Default)",
+                CalibrationTask calibration => "CalibrationTaskDefault(Default)",
+                GptmdTask gptmd => "GptmdTaskDefault(Default)",
+                XLSearchTask xLSearch => "XLSearchTaskDefault(Default)",
+                GlycoSearchTask glycoSearch => "GlycoSearchTaskDefault(Default)",
+                SpectralAveragingTask spectralAverage => "SpectralAverageTaskDefault(Default)",
+                _ => "",
+            };
+            Assert.That(testDictionary.Keys.Contains(defaultName));
+            var testWindow = fakeTaskWindow.GetTaskFromGui();
+            var comparingWindow = testDictionary[defaultName];
+            Assert.That(!testWindow.Equals(null));
+            TomlFileFolderSerializer.Save("testFile", testWindow);
+            string pathOfTestFile = TomlFileFolderSerializer.GetFilePath(testWindow.GetType(), "testFile");
+            string pathOfComparingFile =
+                TomlFileFolderSerializer.GetFilePath(comparingWindow.GetType(), defaultName);
+            var linesA = File.ReadAllLines(pathOfTestFile);
+            var linesB = File.ReadAllLines(pathOfComparingFile);
 
             Assert.That(linesA.Length, Is.EqualTo(linesB.Length));
             for (int i = 0; i < linesA.Length; i++)
             {
-                if (linesA[i].StartsWith("MaxMissedCleavages"))
-                {
-                    Assert.That(linesA[i], Is.Not.EqualTo(linesB[i]));
-                    Assert.That(linesA[i].EndsWith('1'));
-                    Assert.That(linesB[i].EndsWith('2'));
-                }
-                else
-                    Assert.That(linesA[i], Is.EqualTo(linesB[i]));
+                Assert.That(linesA[i], Is.EqualTo(linesB[i]));
             }
-            
+        }
 
+        /// <summary>
+        /// test the function of saveSettings when modifying non-default task
+        /// </summary>
+        [Test]
+        public void SaveSettingsTest()
+        {
+            //Directory Set up
+            var tomlFile1 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBCZ", tomlFile1);
+            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            testTaskSettingViewModel.SelectedSettings = "customBCZ";
+            testTaskSettingViewModel.SaveSettings();
+            var currentTask = testTaskSettingViewModel.AllSettingsDict[testTaskSettingViewModel.SelectedSettings];
+            Assert.That(currentTask.CommonParameters.TotalPartitions, Is.EqualTo(1));
+
+            // test change in window is reflected when saving settings
+            currentTask = testTaskSettingViewModel.AllSettingsDict[testTaskSettingViewModel.SelectedSettings];
+            Assert.That(currentTask.CommonParameters.TotalPartitions, Is.EqualTo(1));
+            fakeTaskWindow.TheTask.CommonParameters.TotalPartitions = 36;
+            testTaskSettingViewModel.SaveSettings();
+
+            currentTask = testTaskSettingViewModel.AllSettingsDict[testTaskSettingViewModel.SelectedSettings];
+            Assert.That(currentTask.CommonParameters.TotalPartitions, Is.EqualTo(36));
+
+            // read back in saved file and check if total partitions was saved
+            testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            testTaskSettingViewModel.SelectedSettings = "customBCZ";
+            currentTask = testTaskSettingViewModel.AllSettingsDict[testTaskSettingViewModel.SelectedSettings];
+            Assert.That(currentTask.CommonParameters.TotalPartitions, Is.EqualTo(36));
+        }
+
+        /// <summary>
+        /// test the function of saveSettings when modifying default task
+        /// </summary>
+        [Test]
+        public void SaveDefaultSettingsTest()
+        {
+            //Directory Set up
+            var tomlFile1 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBCZ", tomlFile1);
+            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+
+            //Try to save a default setting
+            fakeTaskWindow.TheTask.CommonParameters.TotalPartitions = 36;
+            testTaskSettingViewModel.SelectedSettings = "customBCZ";
+            testTaskSettingViewModel.SaveAsDefaultSettings();
+            testTaskSettingViewModel.SelectedSettings = "customBCZ(Default)";
+            testTaskSettingViewModel.SaveSettings();
+            testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var a = testTaskSettingViewModel.AllSettingsDict;
+            testTaskSettingViewModel.SelectedSettings = "customBCZ(Default)";
+            var currentTask = testTaskSettingViewModel.AllSettingsDict[testTaskSettingViewModel.SelectedSettings];
+            Assert.That(currentTask.CommonParameters.TotalPartitions, Is.EqualTo(1));
         }
 
+        /// <summary>
+        /// test the function of saveSettingsFromWindow
+        /// </summary>
         [Test]
-        public void testConstructor()
+        public void SaveSettingsFromWindowTest()
         {
+            //Directory Set up
+            var tomlFile1 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBCZ", tomlFile1);
             var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
-            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
-            var a = testTaskSettingViewModel.AllSettings;
-            string[] testArrayOfKeys = testTaskSettingViewModel.AllSettingsDict.Keys.ToArray();
-            Assert.That(testArrayOfKeys[0].Equals("customBCZ.toml"));
-            Assert.That(testArrayOfKeys[1].Equals("customBY.toml"));
-            Assert.That(testArrayOfKeys[2].Equals("customCZ.toml"));
-            Assert.That(false);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var testDictionary = testTaskSettingViewModel.AllSettingsDict;
+
+            //Save a task from the window popped up
+            testTaskSettingViewModel.SelectedSettings = "customBCZ";
+            testTaskSettingViewModel.SaveSettingsFromWindow();//
+            Assert.That(!testDictionary.ContainsKey("testTask"));
+            testTaskSettingViewModel.TypedSettingsName = "customBCZ";
+            testTaskSettingViewModel.SaveSettingsFromWindow();
+            Assert.That(!testDictionary.ContainsKey("testTask"));
+            testTaskSettingViewModel.TypedSettingsName = "testTask";
+            testTaskSettingViewModel.SaveSettingsFromWindow();
+            Assert.That(testDictionary.ContainsKey("testTask"));
         }
 
+        /// <summary>
+        /// test the function of saveAsDefaultSetting
+        /// </summary>
+        [Test]
+        public void SaveAsDefaultSettingsTest()
+        {
+            //Directory Set up
+            var tomlFile1 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBCZ", tomlFile1);
+            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var testDictionary = testTaskSettingViewModel.AllSettingsDict;
+
+            //When SelectedSettings == null
+            testTaskSettingViewModel.SaveAsDefaultSettings();
+            Assert.That(testDictionary.ContainsKey("customBCZ"));
+            testTaskSettingViewModel.SelectedSettings = "customBCZ";
+            testTaskSettingViewModel.SaveAsDefaultSettings();
+            Assert.That(testDictionary.ContainsKey("customBCZ(Default)"));
+
+            //Setting default when there is an existing default
+            var tomlFile2 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"),
+                MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBY", tomlFile2); 
+            fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            testDictionary = testTaskSettingViewModel.AllSettingsDict;
+            testTaskSettingViewModel.SelectedSettings = "customBY";
+            testTaskSettingViewModel.SaveAsDefaultSettings();
+            Assert.That(testDictionary.ContainsKey("customBY(Default)"));
+            Assert.That(!testDictionary.ContainsKey("customBCZ(Default)"));
+        }
 
+        /// <summary>
+        /// test the function of deleteSettings when nothing is selected
+        /// </summary>
         [Test]
-        public void testDeleteGetFilePath()
+        public void DeleteSettingsTestWithoutSelectedSettings()
         {
-            var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
-            var tomlFile2 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"), MetaMorpheusTask.tomlConfig);
-            var tomlFile3 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"), MetaMorpheusTask.tomlConfig);
+            //Directory Set up
+            var tomlFile1 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            var tomlFile2 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"),
+                MetaMorpheusTask.tomlConfig);
+            var tomlFile3 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
             TomlFileFolderSerializer.Save("customBCZ.toml", tomlFile1);
             TomlFileFolderSerializer.Save("customBY.toml", tomlFile2);
             TomlFileFolderSerializer.Save("customCZ.toml", tomlFile3);
+            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var testDictionary = testTaskSettingViewModel.AllSettingsDict;
+
+            var expected = new List<string>() { "customBCZ.toml", "customBY.toml", "customCZ.toml" };
+            CollectionAssert.AreEqual(expected, testTaskSettingViewModel.AllSettings);
+            testTaskSettingViewModel.TypedSettingsName = "Name";
+            Assert.That(testTaskSettingViewModel.TypedSettingsName, Is.EqualTo("Name"));
+
+            //test
             Type deletedFileType = tomlFile1.GetType();
             String path = TomlFileFolderSerializer.GetFilePath(deletedFileType, "customBCZ.toml");
-            TomlFileFolderSerializer.Delete(deletedFileType, "customBCZ.toml");
-            Assert.That(!File.Exists(path),Is.True);                        
+            testTaskSettingViewModel.DeleteSettings();
+            Assert.That(File.Exists(path), Is.True);
         }
 
+        /// <summary>
+        /// test the function of deleteSettings when default setting is selected
+        /// </summary>
         [Test]
-        public void testLoadAllNamesOfType()
+        public void DeleteSettingsTestSelectingDefault()
         {
-            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask());
-            var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
-            Type testFolder = tomlFile1.GetType();
-            String[] testStringArray = TomlFileFolderSerializer.LoadAllNamesOfType(testFolder);
-            Assert.That(testStringArray[0].Equals("customBCZ.toml"));
-            Assert.That(testStringArray[1].Equals("customBY.toml"));
-            Assert.That(testStringArray[2].Equals("customCZ.toml"));
+            //Directory Set up
+            var tomlFile1 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            var tomlFile2 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"),
+                MetaMorpheusTask.tomlConfig);
+            var tomlFile3 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBCZ", tomlFile1);
+            TomlFileFolderSerializer.Save("customBY", tomlFile2);
+            TomlFileFolderSerializer.Save("customCZ", tomlFile3);
+            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var testDictionary = testTaskSettingViewModel.AllSettingsDict;
+
+
+            // save customBCZ as default settings
+            testTaskSettingViewModel.SelectedSettings = "customBCZ";
+            testTaskSettingViewModel.SaveAsDefaultSettings();
+            testTaskSettingViewModel.SelectedSettings = "customBCZ(Default)";
+
+            // try to delete default settings
+            testTaskSettingViewModel.DeleteSettings();
+
+            // ensure default was not deleted
+            Assert.That(testDictionary.ContainsKey("customBCZ(Default)"));
         }
 
+        /// <summary>
+        /// test the function of deleteSettings when select a non-default task
+        /// </summary>
         [Test]
-        public void testGetFilePath()
+        public void DeleteSettingsTestWithSelectedSettingsAndNotDefault()
         {
-            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask());
-            var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
-            string testPath = TomlFileFolderSerializer.GetFilePath(tomlFile1.GetType(), "customBCZ.toml");
-            Assert.That(testPath.Contains("toml"));
+            //Directory Set up
+            var tomlFile1 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            var tomlFile2 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"),
+                MetaMorpheusTask.tomlConfig);
+            var tomlFile3 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBCZ.toml", tomlFile1);
+            TomlFileFolderSerializer.Save("customBY.toml", tomlFile2);
+            TomlFileFolderSerializer.Save("customCZ.toml", tomlFile3);
+            var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            var testDictionary = testTaskSettingViewModel.AllSettingsDict;
+
+            //test
+            Type deletedFileType = tomlFile1.GetType();
+            String path = TomlFileFolderSerializer.GetFilePath(deletedFileType, "customBCZ.toml");
+            testTaskSettingViewModel.SelectedSettings = "customBCZ.toml";
+            testTaskSettingViewModel.DeleteSettings();
+            Assert.That(!testDictionary.ContainsKey("customBCZ.toml"));
+            Assert.That(!File.Exists(path), Is.True);
         }
 
         [Test]
-        public void testSaveAs()
+        public void InstanceTest()
         {
+            //Directory Set up
+            var tomlFile1 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            var tomlFile2 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"),
+                MetaMorpheusTask.tomlConfig);
+            var tomlFile3 = Toml.ReadFile<SearchTask>(
+                Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"),
+                MetaMorpheusTask.tomlConfig);
+            TomlFileFolderSerializer.Save("customBCZ.toml", tomlFile1);
+            TomlFileFolderSerializer.Save("customBY.toml", tomlFile2);
+            TomlFileFolderSerializer.Save("customCZ.toml", tomlFile3);
             var fakeTaskWindow = new FakeGuiWindow(MyTask.Search);
-            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(), fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
+            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel(new SearchTask(),
+                fakeTaskWindow.UpdateFieldsFromNewTask, fakeTaskWindow.GetTaskFromGui);
             var testDictionary = testTaskSettingViewModel.AllSettingsDict;
-
-            // TODO: Replace new search task with refernce B
-            var referenceA = TomlFileFolderSerializer.Deserialize<MetaMorpheusTask>("C:/Users/Administrator/source/repos/MetaMorpheus/Test/" +
-                "bin/Debug/net6.0-windows/TestData/SavedSettingsReferenceDirectory/a.toml");
-            testTaskSettingViewModel.UpdateFieldsInGuiWithNewTask.Invoke(referenceA as MetaMorpheusTask);
-            testTaskSettingViewModel.TypedSettingsName = "a";
-            testTaskSettingViewModel.SaveSettingsFromWindow();
-            Assert.That(false);
+            //AllSettings
+            var expected = new List<string>() { "customBCZ.toml", "customBY.toml", "customCZ.toml" };
+            CollectionAssert.AreEqual(expected, testTaskSettingViewModel.AllSettings);
+            //TypedSettingsName
+            testTaskSettingViewModel.TypedSettingsName = "Name";
+            Assert.That(testTaskSettingViewModel.TypedSettingsName, Is.EqualTo("Name"));
+            //SelectedSettings
+            testTaskSettingViewModel.SelectedSettings = "customBCZ.toml";
+            Assert.That(testTaskSettingViewModel.SelectedSettings.Equals("customBCZ.toml"));
+            //AllSettingsDict
+            Assert.That(testTaskSettingViewModel.AllSettingsDict.Equals(testDictionary));
+            //TheTask
+            Assert.That(testTaskSettingViewModel.TheTask.Equals(testDictionary["customBCZ.toml"]));
         }
     }
 }
diff --git a/MetaMorpheus/Test/TaskSettingViewModelTests.cs b/MetaMorpheus/Test/TaskSettingViewModelTests.cs
deleted file mode 100644
index b490a0218..000000000
--- a/MetaMorpheus/Test/TaskSettingViewModelTests.cs
+++ /dev/null
@@ -1,57 +0,0 @@
-using System;
-using System.Collections.Generic;
-using System.Diagnostics.CodeAnalysis;
-using System.IO;
-using System.Linq;
-using System.Security.AccessControl;
-using System.Text;
-using System.Threading.Tasks;
-using EngineLayer;
-using GuiFunctions;
-using MassSpectrometry;
-using Nett;
-using NUnit.Framework;
-using TaskLayer;
-
-namespace Test
-{
-    public class TaskSettingViewModelTests
-    {
-        [OneTimeSetUp]
-        public static void OneTimeSetup()
-        {
-            Directory.CreateDirectory(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"));
-            var tomlFile1 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
-            var tomlFile2 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"), MetaMorpheusTask.tomlConfig);
-            var tomlFile3 = Toml.ReadFile<SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"), MetaMorpheusTask.tomlConfig);
-            TomlFileFolderSerializer.Save("customBCZ.toml", tomlFile1);
-            TomlFileFolderSerializer.Save("customBY.toml", tomlFile2);
-            TomlFileFolderSerializer.Save("customCZ.toml", tomlFile3);
-        }
-
-        [OneTimeTearDown]
-        public static void OneTimeTearDown()
-        {
-            Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, "SettingsDataFiles"), true);
-        }
-
-        [Test]
-        public void testSaveSettings()
-        {
-            TaskSettingViewModel testTaskSettingViewModel = new TaskSettingViewModel();
-
-            var paramsOne = new CommonParameters(null, DissociationType.CID);
-            var paramsTwo = new CommonParameters(null, DissociationType.HCD);
-            var paramsThree = new CommonParameters(null, DissociationType.PD);
-
-            var one = new SearchTask();
-            var two = new SearchTask();
-            var three = new SearchTask();
-
-            one.CommonParameters = paramsOne;
-            two.CommonParameters = paramsTwo;
-            three.CommonParameters = paramsThree;
-
-        }
-    }
-}

From c9c2a8cb519be21b3ce6116c9bf4ec5c9c25dee7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=B0=E7=8E=AE=20=E7=8E=8B?= <wfw2310165722@outlook.com>
Date: Tue, 5 Dec 2023 15:36:47 -0600
Subject: [PATCH 14/20] Clean up codes and spaces that are not used.
 Reformatting the Guis that are accidentally modified in previous codings.

---
 MetaMorpheus/GUI/MainWindow.xaml              | 21 +++++-----
 .../GUI/TaskWindows/CalibrateTaskWindow.xaml  | 18 +++++----
 .../TaskWindows/CalibrateTaskWindow.xaml.cs   |  2 +-
 .../GUI/TaskWindows/GPTMDTaskWindow.xaml      | 24 ++++++-----
 .../GUI/TaskWindows/GPTMDTaskWindow.xaml.cs   |  6 +--
 .../TaskWindows/GlycoSearchTaskWindow.xaml    | 24 ++++++-----
 .../GUI/TaskWindows/SearchTaskWindow.xaml     | 40 +++++++++++--------
 .../GUI/TaskWindows/SearchTaskWindow.xaml.cs  | 25 ++----------
 .../GUI/TaskWindows/XLSearchTaskWindow.xaml   | 24 ++++++-----
 .../TaskWindows/XLSearchTaskWindow.xaml.cs    |  5 ---
 .../GUI/Views/SaveSettingsControl.xaml.cs     |  2 +-
 .../GUI/Views/SaveSettingsWindow.xaml.cs      |  5 ---
 .../ViewModels/TaskSettingViewModel.cs        | 27 ++++++-------
 13 files changed, 105 insertions(+), 118 deletions(-)

diff --git a/MetaMorpheus/GUI/MainWindow.xaml b/MetaMorpheus/GUI/MainWindow.xaml
index f64fcbe45..22331bea8 100644
--- a/MetaMorpheus/GUI/MainWindow.xaml
+++ b/MetaMorpheus/GUI/MainWindow.xaml
@@ -450,33 +450,32 @@
                         <RowDefinition Height="50"/>
                         <RowDefinition Height="50"/>
                         <RowDefinition Height="25"/>
-                        <RowDefinition Height="41*"/>
-                        <RowDefinition Height="153*"/>
+                        <RowDefinition Height="1*"/>
                     </Grid.RowDefinitions>
 
                     <!--Header label-->
                     <Label Content="Spectra" Grid.Row="0" Style="{StaticResource HeaderLabelStyle}" />
 
                     <!--Detail text-->
-                    <TextBlock Grid.Row="1" Style="{StaticResource TextBlockStyle}" Margin="15,0,10,0">
+                    <TextBlock Grid.Row="1" Style="{StaticResource TextBlockStyle}">
                         Add spectra file(s) in .mzML, .mgf, or Thermo .raw format.
                     </TextBlock>
 
                     <!--Button to add spectra files-->
-                    <Button Name="AddSpectraButton" Grid.Row="2" Content="+ADD SPECTRA" Click="AddSpectraFile_Click" HorizontalAlignment="Left" 
-                            Style="{StaticResource ImportantButtonStyle}" Margin="634,0,0,0"/>
+                    <Button Name="AddSpectraButton" Grid.Row="2" Content="+ADD SPECTRA" Click="AddSpectraFile_Click" HorizontalAlignment="Right" 
+                             Style="{StaticResource ImportantButtonStyle}" Margin="0,0,10,0"/>
 
                     <Button Name="SetFileSpecificSettingsButton" Grid.Row="2" Content="SET FILE-SPECIFIC SETTINGS" Click="SetFileSpecificParameters_Click" 
-                            HorizontalAlignment="Left" Style="{StaticResource ImportantButtonStyle}"
-                        Margin="433,0,0,0"/>
+                            HorizontalAlignment="Right" Style="{StaticResource ImportantButtonStyle}"
+                            Margin="0,0,211,0"/>
 
                     <Button Name="SetExperimentalDesignButton" Grid.Row="2" Content="SET EXPERIMENTAL DESIGN" Click="SetExperimentalDesign_Click" 
-                            HorizontalAlignment="Left" Style="{StaticResource ImportantButtonStyle}"
-                        Margin="232,0,0,0"/>
+                            HorizontalAlignment="Right" Style="{StaticResource ImportantButtonStyle}"
+                            Margin="0,0,412,0"/>
 
                     <!--The list of spectra files-->
                     <DataGrid Name="dataGridSpectraFiles" ItemsSource="{Binding}" Grid.Row="3" Style="{StaticResource x:DataGridStyle}"
-                              ColumnHeaderStyle="{StaticResource DataGridColumnHeaderStyle}" PreviewKeyDown="Window_PreviewKeyDown" Margin="10,0,10,10" Grid.RowSpan="2">
+                              ColumnHeaderStyle="{StaticResource DataGridColumnHeaderStyle}" PreviewKeyDown="Window_PreviewKeyDown">
                         <DataGrid.RowStyle>
                             <Style TargetType="{x:Type DataGridRow}" BasedOn="{StaticResource SpectraFileDataGridItemStyle}" />
                         </DataGrid.RowStyle>
@@ -494,7 +493,7 @@
             </TabItem>
 
             <!--Workflow tab-->
-            <TabItem Name="TasksTab" Header="Tasks" TabIndex="0" Style="{StaticResource TabItemStyle}" Height="35" Margin="0,0,2,0" VerticalAlignment="Bottom">
+            <TabItem Name="TasksTab" Header="Tasks" TabIndex="0" Style="{StaticResource TabItemStyle}">
                 <Grid Style="{StaticResource PageGridStyle}">
                     <Grid.RowDefinitions>
                         <RowDefinition Height="50"/>
diff --git a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml
index acbf86818..35be89406 100644
--- a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml
@@ -18,9 +18,14 @@
         </Grid.RowDefinitions>
         <ScrollViewer VerticalScrollBarVisibility="Auto">
             <DockPanel>
-                <StackPanel DockPanel.Dock="Top" Orientation="Horizontal">
+                <Grid DockPanel.Dock="Top" Margin="5,0,0,0">
+                    <Grid.ColumnDefinitions>
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="*" />
+                    </Grid.ColumnDefinitions>
                     <Label Content="Task Name" />
-                    <TextBox x:Name="OutputFileNameTextBox" Width="150">
+                    <TextBox x:Name="OutputFileNameTextBox" Width="150" Grid.Column="1">
                         <TextBox.Style>
                             <Style TargetType="TextBox" xmlns:sys="clr-namespace:System;assembly=mscorlib">
                                 <Style.Resources>
@@ -44,13 +49,10 @@
                             </Style>
                         </TextBox.Style>
                     </TextBox>
-                </StackPanel>
-
-                <StackPanel DockPanel.Dock="Top" Margin="10">
                     <!-- save settings -->
-                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
-                        DataContext="{Binding TaskSettingViewModel}"/>
-                </StackPanel>
+                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" Grid.Column="2" HorizontalAlignment="Right"
+                                               DataContext="{Binding TaskSettingViewModel}" />
+                </Grid>
                 
                 <GroupBox Header="Search Parameters" DockPanel.Dock="Top">
                     <Expander x:Name="SearchModeExpander">
diff --git a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
index 798456c9f..e8d0f1de7 100644
--- a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
@@ -33,7 +33,6 @@ public partial class CalibrateTaskWindow : Window
         public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
         {
             InitializeComponent();
-            PopulateChoices();
             TheTask = myCalibrateTask ?? new CalibrationTask();
 
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as CalibrationTask);
@@ -42,6 +41,7 @@ public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
 
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
+            PopulateChoices();
 
             if (myCalibrateTask == null)
             {
diff --git a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
index 955f65e7a..42530bbd2 100644
--- a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
@@ -18,13 +18,19 @@
         </Grid.RowDefinitions>
         <ScrollViewer VerticalScrollBarVisibility="Auto">
             <DockPanel>
-                <StackPanel DockPanel.Dock="Top" Orientation="Horizontal">
+                <Grid DockPanel.Dock="Top" Margin="5,0,0,0">
+                    <Grid.ColumnDefinitions>
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="*" />
+                    </Grid.ColumnDefinitions>
                     <Label Content="Task Name" />
-                    <TextBox x:Name="OutputFileNameTextBox" Width="150">
+                    <TextBox x:Name="OutputFileNameTextBox" Width="150" Grid.Column="1">
                         <TextBox.Style>
-                            <Style TargetType="TextBox" xmlns:sys="clr-namespace:System;assembly=mscorlib">
+                            <Style TargetType="TextBox">
                                 <Style.Resources>
-                                    <VisualBrush x:Key="CueBannerBrush" AlignmentX="Left" AlignmentY="Center" Stretch="None">
+                                    <VisualBrush x:Key="CueBannerBrush" AlignmentX="Left" AlignmentY="Center"
+                                                 Stretch="None">
                                         <VisualBrush.Visual>
                                             <Label Content="GPTMDTask" Foreground="Gray" />
                                         </VisualBrush.Visual>
@@ -44,14 +50,12 @@
                             </Style>
                         </TextBox.Style>
                     </TextBox>
-                </StackPanel>
+                    <!-- save settings -->
+                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" Grid.Column="2" HorizontalAlignment="Right"
+                                               DataContext="{Binding TaskSettingViewModel}" />
 
-                <StackPanel DockPanel.Dock="Top" Margin="10">
+                </Grid>
 
-                    <!-- save settings -->
-                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
-             DataContext="{Binding TaskSettingViewModel}"/>
-                </StackPanel>
 
                 <GroupBox Header="File Loading Parameters" DockPanel.Dock="Top">
                     <Expander x:Name="FileLoadExpander" >
diff --git a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
index 428f86d6e..4eddb674e 100644
--- a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
@@ -34,7 +34,6 @@ public partial class GptmdTaskWindow : Window
         public GptmdTaskWindow(GptmdTask myGPTMDtask)
         {
             InitializeComponent();
-            PopulateChoices();
             TheTask = myGPTMDtask ?? new GptmdTask();
 
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as GptmdTask);
@@ -43,6 +42,7 @@ public GptmdTaskWindow(GptmdTask myGPTMDtask)
 
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
+            PopulateChoices();
 
             if (myGPTMDtask == null)
             {
@@ -573,9 +573,5 @@ private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
             Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"GptmdTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
         }
 
-        private void TaskSettingsCtrl_Loaded(object sender, RoutedEventArgs e)
-        {
-
-        }
     }
 }
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
index 59432f211..e1cdd93ae 100644
--- a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
@@ -40,13 +40,19 @@
         </Grid.RowDefinitions>
         <ScrollViewer VerticalScrollBarVisibility="Auto" Grid.ColumnSpan="2">
             <DockPanel>
-                <StackPanel DockPanel.Dock="Top" Orientation="Horizontal">
+                <Grid DockPanel.Dock="Top" Margin="5,0,0,0">
+                    <Grid.ColumnDefinitions>
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="*" />
+                    </Grid.ColumnDefinitions>
                     <Label Content="Task Name" />
-                    <TextBox x:Name="OutputFileNameTextBox" Width="150">
+                    <TextBox x:Name="OutputFileNameTextBox" Width="150" Grid.Column="1">
                         <TextBox.Style>
-                            <Style TargetType="TextBox" xmlns:sys="clr-namespace:System;assembly=mscorlib">
+                            <Style TargetType="TextBox">
                                 <Style.Resources>
-                                    <VisualBrush x:Key="CueBannerBrush" AlignmentX="Left" AlignmentY="Center" Stretch="None">
+                                    <VisualBrush x:Key="CueBannerBrush" AlignmentX="Left" AlignmentY="Center"
+                                                 Stretch="None">
                                         <VisualBrush.Visual>
                                             <Label Content="SearchTask" Foreground="Gray" />
                                         </VisualBrush.Visual>
@@ -66,14 +72,12 @@
                             </Style>
                         </TextBox.Style>
                     </TextBox>
-                </StackPanel>
-
-                <StackPanel DockPanel.Dock="Top" Margin="10">
 
                     <!-- save settings -->
-                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
-             DataContext="{Binding TaskSettingViewModel}" />
-                </StackPanel>
+                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" Grid.Column="2" HorizontalAlignment="Right"
+                                               DataContext="{Binding TaskSettingViewModel}" />
+
+                </Grid>
 
                 <StackPanel DockPanel.Dock="Top">
                     <Grid>
diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
index 499efb6ac..7e8f9ebb5 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
@@ -47,15 +47,22 @@
         </Grid.RowDefinitions>
         <ScrollViewer VerticalScrollBarVisibility="Auto">
             <DockPanel>
-                <StackPanel DockPanel.Dock="Top" Orientation="Horizontal" Margin="5,0,0,0">
-                    <Label Content="Enter Task Name:" />
-                    <TextBox x:Name="OutputFileNameTextBox" Width="150">
+                <Grid DockPanel.Dock="Top" Margin="5,0,0,0">
+                    <Grid.ColumnDefinitions>
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="*" />
+                    </Grid.ColumnDefinitions>
+
+                    <Label Content="Enter Task Name:" Grid.Column="0" />
+                    <TextBox x:Name="OutputFileNameTextBox" Width="150" Grid.Column="1">
                         <TextBox.Style>
                             <Style TargetType="TextBox" xmlns:sys="clr-namespace:System;assembly=mscorlib">
                                 <Style.Resources>
-                                    <VisualBrush x:Key="CueBannerBrush" AlignmentX="Left" AlignmentY="Center" Stretch="None">
+                                    <VisualBrush x:Key="CueBannerBrush" AlignmentX="Left" AlignmentY="Center"
+                                                 Stretch="None">
                                         <VisualBrush.Visual>
-                                            <Label Content="SearchTask" Foreground="Gray" Padding="5 0 0 0"/>
+                                            <Label Content="SearchTask" Foreground="Gray" Padding="5 0 0 0" />
                                         </VisualBrush.Visual>
                                     </VisualBrush>
                                 </Style.Resources>
@@ -68,25 +75,26 @@
                                     </Trigger>
                                     <Trigger Property="IsKeyboardFocused" Value="True">
                                         <Setter Property="Background" Value="White" />
-                                        <Setter Property="Padding" Value="5 0 0 0"/>
-                                        <Setter Property="VerticalContentAlignment" Value="Center"/>
+                                        <Setter Property="Padding" Value="5 0 0 0" />
+                                        <Setter Property="VerticalContentAlignment" Value="Center" />
                                     </Trigger>
                                     <Trigger Property="IsKeyboardFocused" Value="False">
-                                        <Setter Property="Padding" Value="5 0 0 0"/>
-                                        <Setter Property="VerticalContentAlignment" Value="Center"/>
+                                        <Setter Property="Padding" Value="5 0 0 0" />
+                                        <Setter Property="VerticalContentAlignment" Value="Center" />
                                     </Trigger>
                                 </Style.Triggers>
                             </Style>
                         </TextBox.Style>
                     </TextBox>
-                </StackPanel>
+
+                    <!-- save settings -->
+                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" Grid.Column="2" HorizontalAlignment="Right"
+                                               DataContext="{Binding TaskSettingViewModel}" />
+                </Grid>
 
                 <!-- BASIC SETTINGS -->
                 <StackPanel DockPanel.Dock="Top" Margin="10">
 
-                    <!-- save settings -->
-                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
-                                               DataContext="{Binding TaskSettingViewModel}" />
 
                     <!-- Search Parameters -->
                     <GroupBox Header="Search Parameters" DockPanel.Dock="Top" >
@@ -582,7 +590,6 @@
                                 <CheckBox x:Name="WriteSpectralLibraryCheckBox" Content="Write spectral library" IsEnabled="{Binding IsChecked, Converter={local:BooleanInverter}, ElementName=CheckBoxLFQwSpectralRecovery }"/>
                                 <CheckBox x:Name="UpdateSpectralLibraryCheckBox" Content="Update spectral library" />
                                 <CheckBox x:Name="CompressIndividualResultsCheckBox" Content="Compress individual file results" IsEnabled="{Binding IsChecked, ElementName=WriteIndividualResultsCheckBox}"/>
-
                             </StackPanel>
 
                             <!-- filtering options -->
@@ -1222,10 +1229,11 @@
 
             </DockPanel>
         </ScrollViewer>
-        <StackPanel  Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1" Margin="5">
+        <StackPanel  Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1" Margin="5" >
             <Button x:Name="cancelButton" Content="Cancel" Click="CancelButton_Click" />
             <Button x:Name="saveButton" Content="Save Search Task" Click="SaveButton_Click" FontSize="24" />
-            <Button x:Name="setDefaultbutton" Click="SaveAsDefault_Click" Width="100" >
+            <Button x:Name="setDefaultbutton" 
+                    Command="{Binding SaveAsDefaultSettingsCommand}"  Width="100" >
                 <TextBlock Text="Save As Default" TextWrapping="Wrap" TextAlignment="Center"/>
                 <ToolTipService.ToolTip>
                     <ToolTip Content="Save these parameters as the default. MetaMorpheus can return to original defaults by deleting the folder 'DefaultParameters'" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index 38e0c32b9..e9f0798cb 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -37,7 +37,7 @@ public partial class SearchTaskWindow : Window
         private readonly ObservableCollection<SilacInfoForDataGrid> StaticSilacLabelsObservableCollection = new ObservableCollection<SilacInfoForDataGrid>();
         private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
         private CustomFragmentationWindow CustomFragmentationWindow;
-        private TaskSettingViewModel TaskSettingViewModel;
+        public TaskSettingViewModel TaskSettingViewModel { get; init; }
         private string _defaultMultiplexType = "TMT10";
 
 
@@ -49,14 +49,14 @@ public SearchTaskWindow(SearchTask task)
             
             TheTask = task ?? new SearchTask();
 
-            PopulateChoices();//
-
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as SearchTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
             TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+            setDefaultbutton.DataContext = TaskSettingViewModel;
 
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
+            PopulateChoices();
 
             if (task == null)
             {
@@ -195,8 +195,6 @@ private void UpdateFieldsFromTask(SearchTask task)
             }
             CheckBoxParsimony.IsChecked = task.SearchParameters.DoParsimony;
             CheckBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
-            CheckBoxParsimony.IsChecked = task.SearchParameters.DoParsimony;
-            CheckBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
             CheckBoxNoQuant.IsChecked = !task.SearchParameters.DoLabelFreeQuantification;
             CheckBoxLFQ.IsChecked = task.SearchParameters.DoLabelFreeQuantification;
             CheckBoxMultiplex.IsChecked = task.SearchParameters.DoMultiplexQuantification;
@@ -1342,12 +1340,6 @@ private void CheckBoxSILAC_Checked(object sender, RoutedEventArgs e)
             CheckBoxQuantifyUnlabeledForSilac_Checked(sender, e);
         }
 
-        private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
-        {
-           // SaveButton_Click(sender, e);
-            //Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"SearchTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
-            TaskSettingViewModel.SaveAsDefaultSettings();
-        }
 
         /// <summary>
         /// Retained/Lost Methionine is best handled through truncation search when truncation search is selected.
@@ -1371,16 +1363,7 @@ private void InternalIonsCheckBox_Checked(object sender, RoutedEventArgs e)
         {
             MinInternalFragmentLengthTextBox.Text = "4";
         }
-
-        private void TaskSettingsCtrl_Loaded(object sender, RoutedEventArgs e)
-        {
-
-        }
-
-        //private void TaskSettingsCtrl_Loaded(object sender, RoutedEventArgs e)
-        //{
-
-        //}
+        
     }
 
     public class DataContextForSearchTaskWindow : INotifyPropertyChanged
diff --git a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
index 47ef3a313..d305eb119 100644
--- a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
@@ -17,13 +17,19 @@
         </Grid.RowDefinitions>
         <ScrollViewer VerticalScrollBarVisibility="Auto" Grid.ColumnSpan="2">
             <DockPanel>
-                <StackPanel DockPanel.Dock="Top" Orientation="Horizontal">
+                <Grid DockPanel.Dock="Top" Margin="5,0,0,0">
+                    <Grid.ColumnDefinitions>
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="*" />
+                    </Grid.ColumnDefinitions>
                     <Label Content="Task Name" />
-                    <TextBox x:Name="OutputFileNameTextBox" Width="150" TextChanged="OutputFileNameTextBox_TextChanged">
+                    <TextBox x:Name="OutputFileNameTextBox" Width="150" Grid.Column="1">
                         <TextBox.Style>
-                            <Style TargetType="TextBox" xmlns:sys="clr-namespace:System;assembly=mscorlib">
+                            <Style TargetType="TextBox">
                                 <Style.Resources>
-                                    <VisualBrush x:Key="CueBannerBrush" AlignmentX="Left" AlignmentY="Center" Stretch="None">
+                                    <VisualBrush x:Key="CueBannerBrush" AlignmentX="Left" AlignmentY="Center"
+                                                 Stretch="None">
                                         <VisualBrush.Visual>
                                             <Label Content="XLSearchTask" Foreground="Gray" />
                                         </VisualBrush.Visual>
@@ -43,14 +49,10 @@
                             </Style>
                         </TextBox.Style>
                     </TextBox>
-                </StackPanel>
-
-                <StackPanel DockPanel.Dock="Top" Margin="10">
-
                     <!-- save settings -->
-                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
-             DataContext="{Binding TaskSettingViewModel}"/>
-                </StackPanel>
+                    <local:SaveSettingsControl x:Name="TaskSettingsCtrl" Grid.Column="2" HorizontalAlignment="Right"
+                                               DataContext="{Binding TaskSettingViewModel}" />
+                </Grid>
 
                 <StackPanel DockPanel.Dock="Top">
                     <Grid>
diff --git a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
index 3a1ce930a..699671d8e 100644
--- a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
@@ -487,10 +487,5 @@ private void NonSpecificUpdate(object sender, TextChangedEventArgs e)
                 }
             }
         }
-
-        private void OutputFileNameTextBox_TextChanged(object sender, TextChangedEventArgs e)
-        {
-
-        }
     }
 }
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/Views/SaveSettingsControl.xaml.cs b/MetaMorpheus/GUI/Views/SaveSettingsControl.xaml.cs
index 13c450992..5132835c8 100644
--- a/MetaMorpheus/GUI/Views/SaveSettingsControl.xaml.cs
+++ b/MetaMorpheus/GUI/Views/SaveSettingsControl.xaml.cs
@@ -34,7 +34,7 @@ public SaveSettingsControl()
         private void SaveAs_Click(object sender, RoutedEventArgs e)
         {
             var taskSettingsViewModel = DataContext as TaskSettingViewModel 
-                ?? throw new ArgumentException($"DataContext is of type {DataContext.GetType()}, TaskSettingsViewModel is reaquired.");
+                ?? throw new ArgumentException($"DataContext is of type {DataContext.GetType()}, TaskSettingsViewModel is required.");
 
 
             SaveSettingsWindow newWindow = new SaveSettingsWindow(taskSettingsViewModel);
diff --git a/MetaMorpheus/GUI/Views/SaveSettingsWindow.xaml.cs b/MetaMorpheus/GUI/Views/SaveSettingsWindow.xaml.cs
index a7dd4f4d9..9944b40af 100644
--- a/MetaMorpheus/GUI/Views/SaveSettingsWindow.xaml.cs
+++ b/MetaMorpheus/GUI/Views/SaveSettingsWindow.xaml.cs
@@ -37,10 +37,5 @@ private void CloseWindow(object sender, RoutedEventArgs e)
             DialogResult = false;
             this.Close();
         }
-
-        private void Save_Click_1(object sender, RoutedEventArgs e)
-        {
-
-        }
     }
 }
diff --git a/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs
index bffa2f03d..1bfe157bb 100644
--- a/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/ViewModels/TaskSettingViewModel.cs
@@ -33,9 +33,14 @@ public class TaskSettingViewModel : BaseViewModel
         #endregion
 
         #region Public Properties
-
+        /// <summary>
+        /// All the settings that are saved
+        /// </summary>
         public ObservableCollection<string> AllSettings => allSettings;
 
+        /// <summary>
+        /// The name typed in the text box
+        /// </summary>
         public string TypedSettingsName
         {
             get => typedSettingsName;
@@ -46,6 +51,9 @@ public string TypedSettingsName
             }
         }
 
+        /// <summary>
+        /// The setting that is selected
+        /// </summary>
         public string SelectedSettings
         {
             get => selectedSettings;
@@ -58,6 +66,9 @@ public string SelectedSettings
             }
         }
 
+        /// <summary>
+        /// The dictionary that saves all the settings that are saved
+        /// </summary>
         public Dictionary<string, MetaMorpheusTask> AllSettingsDict
         {
             get => allSettingsDict;
@@ -264,7 +275,6 @@ public void SaveSettingsFromWindow()
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
             TypedSettingsName = "";
-            //SelectDefaultAuto();
         }
 
         /// <summary>
@@ -291,7 +301,6 @@ public void DeleteSettings()
             AllSettingsDict.Remove(SelectedSettings);
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
-            //SelectDefaultAuto();
         }
 
         /// <summary>
@@ -334,21 +343,11 @@ public void SaveAsDefaultSettings()
             AllSettingsDict.Remove(SelectedSettings);
             TomlFileFolderSerializer.Save(currentName + "(Default)", temp);
             AllSettingsDict.Add(currentName + "(Default)", temp);
-
+            SelectedSettings = currentName + "(Default)";
             OnPropertyChanged(nameof(AllSettings));
             OnPropertyChanged(nameof(AllSettingsDict));
-            //SelectDefaultAuto();
         }
-
-        
-
-    #endregion
-
-        #region Helpers
-        
     }
-
     #endregion
-
 }
 

From a83a1b1b5d484cd1e89d386fc3b05fc8e708d569 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=B0=E7=8E=AE=20=E7=8E=8B?= <wfw2310165722@outlook.com>
Date: Tue, 5 Dec 2023 16:32:51 -0600
Subject: [PATCH 15/20] Binding SaveAsDefault button for all task windows and
 manually test the functions.

---
 MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml  |  3 ++-
 .../GUI/TaskWindows/CalibrateTaskWindow.xaml.cs        |  7 ++++---
 MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml      |  3 ++-
 MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs   |  5 +++--
 .../GUI/TaskWindows/GlycoSearchTaskWindow.xaml         | 10 +++++++++-
 .../GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs      |  3 ++-
 MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs  |  6 ++----
 MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml   |  3 ++-
 .../GUI/TaskWindows/XLSearchTaskWindow.xaml.cs         |  1 +
 9 files changed, 27 insertions(+), 14 deletions(-)

diff --git a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml
index 35be89406..ae786081f 100644
--- a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml
@@ -431,7 +431,8 @@
         <StackPanel  Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1" Margin="5">
             <Button x:Name="CancelButton" Content="Cancel" Click="CancelButton_Click" />
             <Button x:Name="SaveButton" Content="Save Calibrate Task" Click="SaveButton_Click" FontSize="24" />
-            <Button x:Name="SetDefaultbutton" Click="SaveAsDefault_Click" Width="100" >
+            <Button x:Name="setDefaultbutton" 
+                    Command="{Binding SaveAsDefaultSettingsCommand}"  Width="100" >
                 <TextBlock Text="Save As Default" TextWrapping="Wrap" TextAlignment="Center"/>
                 <ToolTipService.ToolTip>
                     <ToolTip Content="Save these parameters as the default. MetaMorpheus can return to original defaults by deleting the folder 'DefaultParameters'" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
diff --git a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
index e8d0f1de7..8bebdc26e 100644
--- a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
@@ -35,13 +35,14 @@ public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
             InitializeComponent();
             TheTask = myCalibrateTask ?? new CalibrationTask();
 
+            AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
+            PopulateChoices();
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as CalibrationTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
             TaskSettingsCtrl.DataContext = TaskSettingViewModel;
-
-            AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
+            setDefaultbutton.DataContext = TaskSettingViewModel;
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
-            PopulateChoices();
+            
 
             if (myCalibrateTask == null)
             {
diff --git a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
index 42530bbd2..72f94a14b 100644
--- a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
@@ -511,7 +511,8 @@
         <StackPanel  Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1" Margin="5">
             <Button x:Name="cancelButton" Content="Cancel" Click="CancelButton_Click" />
             <Button x:Name="saveButton" Content="Save GPTMD task" Click="SaveButton_Click" FontSize="24" />
-            <Button x:Name="setDefaultbutton" Click="SaveAsDefault_Click" Width="100" >
+            <Button x:Name="setDefaultbutton" 
+                    Command="{Binding SaveAsDefaultSettingsCommand}"  Width="100" >
                 <TextBlock Text="Save As Default" TextWrapping="Wrap" TextAlignment="Center"/>
                 <ToolTipService.ToolTip>
                     <ToolTip Content="Save these parameters as the default. MetaMorpheus can return to original defaults by deleting the folder 'DefaultParameters'" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
diff --git a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
index 4eddb674e..0dc4ba1dc 100644
--- a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
@@ -36,11 +36,12 @@ public GptmdTaskWindow(GptmdTask myGPTMDtask)
             InitializeComponent();
             TheTask = myGPTMDtask ?? new GptmdTask();
 
+            AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
+            PopulateChoices();
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as GptmdTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
             TaskSettingsCtrl.DataContext = TaskSettingViewModel;
-
-            AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
+            setDefaultbutton.DataContext = TaskSettingViewModel;
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
             PopulateChoices();
 
diff --git a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
index a48c115d0..c6e995511 100644
--- a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
@@ -5,6 +5,7 @@
         xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
         xmlns:local="clr-namespace:MetaMorpheusGUI"
         xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
+        xmlns:sys="clr-namespace:System;assembly=System.Runtime"
         mc:Ignorable="d"
         KeyDown="KeyPressed"
         Title="Glyco Search Task" Height="750" Width="750" WindowStartupLocation="CenterScreen">
@@ -512,9 +513,16 @@
                 
             </DockPanel>
         </ScrollViewer>
-        <StackPanel  Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1"  Margin="188.333,5,261,5" Grid.Column="1">
+        <StackPanel  Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1"  Margin="5" Grid.Column="1">
             <Button x:Name="cancelButton" Content="Cancel" Click="CancelButton_Click" />
             <Button x:Name="saveButton" Content="Save GlycoSearch Task" Click="SaveButton_Click" FontSize="24" />
+            <Button x:Name="setDefaultbutton" 
+                    Command="{Binding SaveAsDefaultSettingsCommand}"  Width="100" >
+                <TextBlock Text="Save As Default" TextWrapping="Wrap" TextAlignment="Center"/>
+                <ToolTipService.ToolTip>
+                    <ToolTip Content="Save these parameters as the default. MetaMorpheus can return to original defaults by deleting the folder 'DefaultParameters'" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
+                </ToolTipService.ToolTip>
+            </Button>
         </StackPanel>
     </Grid>
 </Window>
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
index af50ea1fa..4b9aa9217 100644
--- a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml.cs
@@ -44,7 +44,8 @@ public GlycoSearchTaskWindow(GlycoSearchTask task)
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as GlycoSearchTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
             TaskSettingsCtrl.DataContext = TaskSettingViewModel;
-            
+            setDefaultbutton.DataContext = TaskSettingViewModel;
+
 
             if (task == null)
             {
diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index e9f0798cb..f8d35a67a 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -46,17 +46,15 @@ public partial class SearchTaskWindow : Window
         public SearchTaskWindow(SearchTask task)
         {
             InitializeComponent();
-            
             TheTask = task ?? new SearchTask();
 
+            AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
+            PopulateChoices();
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as SearchTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
             TaskSettingsCtrl.DataContext = TaskSettingViewModel;
             setDefaultbutton.DataContext = TaskSettingViewModel;
-
-            AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
-            PopulateChoices();
 
             if (task == null)
             {
diff --git a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
index d305eb119..7139a6e87 100644
--- a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
@@ -385,7 +385,8 @@
         <StackPanel  Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1" Grid.Column="1">
             <Button x:Name="cancelButton" Content="Cancel" Click="CancelButton_Click" />
             <Button x:Name="saveButton" Content="Save Search Task" Click="SaveButton_Click" FontSize="24" />
-            <Button x:Name="setDefaultbutton" Click="SaveAsDefault_Click" Width="100" >
+            <Button x:Name="setDefaultbutton" 
+                    Command="{Binding SaveAsDefaultSettingsCommand}"  Width="100" >
                 <TextBlock Text="Save As Default" TextWrapping="Wrap" TextAlignment="Center"/>
                 <ToolTipService.ToolTip>
                     <ToolTip Content="Save these parameters as the default. MetaMorpheus can return to original defaults by deleting the folder 'DefaultParameters'" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
diff --git a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
index 699671d8e..3e36fb83f 100644
--- a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
@@ -39,6 +39,7 @@ public XLSearchTaskWindow(XLSearchTask task)
             var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as XLSearchTask);
             TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
             TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+            setDefaultbutton.DataContext = TaskSettingViewModel;
 
             if (task == null)
             {

From 43a7336ae23633272c5d8e86fad58a3a806f131d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=B0=E7=8E=AE=20=E7=8E=8B?= <wfw2310165722@outlook.com>
Date: Tue, 12 Dec 2023 13:46:14 -0600
Subject: [PATCH 16/20] Change the columns of the labels in TaskWindows. Remove
 SaveAsDefault_Click methodn in the cs files of TaskWindows.

---
 MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs | 6 ------
 MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml        | 2 +-
 MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs     | 7 -------
 MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml  | 2 +-
 MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml     | 2 +-
 MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs  | 6 ------
 MetaMorpheus/Test/TestScanManagement.cs                  | 4 ++--
 7 files changed, 5 insertions(+), 24 deletions(-)

diff --git a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
index 8bebdc26e..269ded68f 100644
--- a/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs
@@ -375,12 +375,6 @@ private void OnClosing(object sender, CancelEventArgs e)
             CustomFragmentationWindow?.Close();
         }
 
-        private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
-        {
-            SaveButton_Click(sender, e);
-            Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"CalibrationTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
-        }
-
         private void ProteaseSpecificUpdate(object sender, SelectionChangedEventArgs e)
         {
             string proteaseName = ((Protease)ProteaseComboBox.SelectedItem).Name;
diff --git a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
index 72f94a14b..693234d5d 100644
--- a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml
@@ -24,7 +24,7 @@
                         <ColumnDefinition Width="Auto" />
                         <ColumnDefinition Width="*" />
                     </Grid.ColumnDefinitions>
-                    <Label Content="Task Name" />
+                    <Label Content="Task Name" Grid.Column="0"/>
                     <TextBox x:Name="OutputFileNameTextBox" Width="150" Grid.Column="1">
                         <TextBox.Style>
                             <Style TargetType="TextBox">
diff --git a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
index 0dc4ba1dc..0a978af2c 100644
--- a/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs
@@ -567,12 +567,5 @@ private void OnClosing(object sender, CancelEventArgs e)
 
             CustomFragmentationWindow?.Close();
         }
-
-        private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
-        {
-            SaveButton_Click(sender, e);
-            Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"GptmdTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
-        }
-
     }
 }
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
index c6e995511..8c725298c 100644
--- a/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/GlycoSearchTaskWindow.xaml
@@ -49,7 +49,7 @@
                         <ColumnDefinition Width="Auto" />
                         <ColumnDefinition Width="*" />
                     </Grid.ColumnDefinitions>
-                    <Label Content="Task Name" />
+                    <Label Content="Task Name" Grid.Column="0"/>
                     <TextBox x:Name="OutputFileNameTextBox" Width="150" Grid.Column="1">
                         <TextBox.Style>
                             <Style TargetType="TextBox">
diff --git a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
index 7139a6e87..5941093fb 100644
--- a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml
@@ -23,7 +23,7 @@
                         <ColumnDefinition Width="Auto" />
                         <ColumnDefinition Width="*" />
                     </Grid.ColumnDefinitions>
-                    <Label Content="Task Name" />
+                    <Label Content="Task Name" Grid.Column="0"/>
                     <TextBox x:Name="OutputFileNameTextBox" Width="150" Grid.Column="1">
                         <TextBox.Style>
                             <Style TargetType="TextBox">
diff --git a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
index 3e36fb83f..dbffc4fc7 100644
--- a/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/XLSearchTaskWindow.xaml.cs
@@ -445,12 +445,6 @@ private void OnClosing(object sender, CancelEventArgs e)
             CustomFragmentationWindow?.Close();
         }
 
-        private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
-        {
-            SaveButton_Click(sender, e);
-            Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"XLSearchTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
-        }
-
         private void NonSpecificUpdate(object sender, SelectionChangedEventArgs e)
         {
             const int maxLength = 25;
diff --git a/MetaMorpheus/Test/TestScanManagement.cs b/MetaMorpheus/Test/TestScanManagement.cs
index 537fc658c..b8dbbdeff 100644
--- a/MetaMorpheus/Test/TestScanManagement.cs
+++ b/MetaMorpheus/Test/TestScanManagement.cs
@@ -11,7 +11,7 @@ namespace Test
     [TestFixture]
     internal class TestScanManagement
     {
-        //[Test]
+        [Test]
         public static void TestGetCombinedMs2Scans()
         {
             var myMsDataFile = new TestDataFile(5);
@@ -70,7 +70,7 @@ public static void TestGetCombinedMs2Scans()
                 test.Add(new Ms2ScanWithSpecificMass(ms2scan, ms2scan.SelectedIonMonoisotopicGuessMz.Value, ms2scan.SelectedIonChargeStateGuess.Value, "", new CommonParameters()));
             }
             var testToArray = test.OrderBy(b => b.PrecursorMass).ToArray();
-
+            Assert.That(true);
         }
     }
 }
\ No newline at end of file

From 834851332e2a870f3398cd76993981991e732ea6 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Tue, 6 Feb 2024 15:27:59 -0600
Subject: [PATCH 17/20] removed extra solution file

---
 MetaMorpheus.sln | 134 -----------------------------------------------
 1 file changed, 134 deletions(-)
 delete mode 100644 MetaMorpheus.sln

diff --git a/MetaMorpheus.sln b/MetaMorpheus.sln
deleted file mode 100644
index 259f79a58..000000000
--- a/MetaMorpheus.sln
+++ /dev/null
@@ -1,134 +0,0 @@
-
-Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio Version 17
-VisualStudioVersion = 17.1.32228.430
-MinimumVisualStudioVersion = 10.0.40219.1
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "CMD", "CMD\CMD.csproj", "{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}"
-EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "GUI", "GUI\GUI.csproj", "{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}"
-EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "EngineLayer", "EngineLayer\EngineLayer.csproj", "{FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}"
-EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "TaskLayer", "TaskLayer\TaskLayer.csproj", "{9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}"
-EndProject
-Project("{930C7802-8A8C-48F9-8165-68863BCCD9DD}") = "MetaMorpheusSetup", "MetaMorpheusSetup\MetaMorpheusSetup.wixproj", "{BE72541A-66A4-4958-9D19-56ACC7D3876B}"
-	ProjectSection(ProjectDependencies) = postProject
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD} = {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}
-	EndProjectSection
-EndProject
-Project("{930C7802-8A8C-48F9-8165-68863BCCD9DD}") = "Bootstrapper1", "Bootstrapper1\Bootstrapper1.wixproj", "{FBA0315B-076D-4470-AFB0-64C8AB4A65A9}"
-EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "GuiFunctions", "GuiFunctions\GuiFunctions.csproj", "{653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}"
-EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Test", "Test\Test.csproj", "{7EE028A9-75A2-450F-A9A7-76559ED15419}"
-EndProject
-Global
-	GlobalSection(SolutionConfigurationPlatforms) = preSolution
-		Debug|Any CPU = Debug|Any CPU
-		Debug|x64 = Debug|x64
-		Debug|x86 = Debug|x86
-		Release|Any CPU = Release|Any CPU
-		Release|x64 = Release|x64
-		Release|x86 = Release|x86
-	EndGlobalSection
-	GlobalSection(ProjectConfigurationPlatforms) = postSolution
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|x64.ActiveCfg = Debug|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|x64.Build.0 = Debug|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|x86.ActiveCfg = Debug|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|x86.Build.0 = Debug|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|Any CPU.Build.0 = Release|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|x64.ActiveCfg = Release|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|x64.Build.0 = Release|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|x86.ActiveCfg = Release|Any CPU
-		{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|x86.Build.0 = Release|Any CPU
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|x64.ActiveCfg = Debug|Any CPU
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|x64.Build.0 = Debug|Any CPU
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|x86.ActiveCfg = Debug|Any CPU
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|x86.Build.0 = Debug|Any CPU
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|Any CPU.Build.0 = Release|Any CPU
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|x64.ActiveCfg = Release|Any CPU
-		{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|x64.Build.0 = Release|Any CPU
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-		HideSolutionNode = FALSE
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From 8306c7aafb263a11651c55fe5b1f3ff875005b90 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Tue, 6 Feb 2024 15:30:59 -0600
Subject: [PATCH 18/20] Reverted changes to testscan management

---
 MetaMorpheus/Test/TestScanManagement.cs | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/MetaMorpheus/Test/TestScanManagement.cs b/MetaMorpheus/Test/TestScanManagement.cs
index b8dbbdeff..64c147e8d 100644
--- a/MetaMorpheus/Test/TestScanManagement.cs
+++ b/MetaMorpheus/Test/TestScanManagement.cs
@@ -11,7 +11,7 @@ namespace Test
     [TestFixture]
     internal class TestScanManagement
     {
-        [Test]
+        //[Test]
         public static void TestGetCombinedMs2Scans()
         {
             var myMsDataFile = new TestDataFile(5);
@@ -70,7 +70,6 @@ public static void TestGetCombinedMs2Scans()
                 test.Add(new Ms2ScanWithSpecificMass(ms2scan, ms2scan.SelectedIonMonoisotopicGuessMz.Value, ms2scan.SelectedIonChargeStateGuess.Value, "", new CommonParameters()));
             }
             var testToArray = test.OrderBy(b => b.PrecursorMass).ToArray();
-            Assert.That(true);
         }
     }
 }
\ No newline at end of file

From 1fb9361b7a3fbbcab590ff0765f5eb115885bc10 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Tue, 6 Feb 2024 15:30:59 -0600
Subject: [PATCH 19/20] Reverted changes to testscan management

---
 MetaMorpheus/Test/TestScanManagement.cs | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/MetaMorpheus/Test/TestScanManagement.cs b/MetaMorpheus/Test/TestScanManagement.cs
index b8dbbdeff..537fc658c 100644
--- a/MetaMorpheus/Test/TestScanManagement.cs
+++ b/MetaMorpheus/Test/TestScanManagement.cs
@@ -11,7 +11,7 @@ namespace Test
     [TestFixture]
     internal class TestScanManagement
     {
-        [Test]
+        //[Test]
         public static void TestGetCombinedMs2Scans()
         {
             var myMsDataFile = new TestDataFile(5);
@@ -70,7 +70,7 @@ public static void TestGetCombinedMs2Scans()
                 test.Add(new Ms2ScanWithSpecificMass(ms2scan, ms2scan.SelectedIonMonoisotopicGuessMz.Value, ms2scan.SelectedIonChargeStateGuess.Value, "", new CommonParameters()));
             }
             var testToArray = test.OrderBy(b => b.PrecursorMass).ToArray();
-            Assert.That(true);
+
         }
     }
 }
\ No newline at end of file

From f930a39c6a1d2112644213b90c04258a7a8e69ba Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Tue, 6 Feb 2024 15:32:32 -0600
Subject: [PATCH 20/20] reverted change to TestScanManagement

---
 MetaMorpheus/Test/TestScanManagement.cs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/MetaMorpheus/Test/TestScanManagement.cs b/MetaMorpheus/Test/TestScanManagement.cs
index 64c147e8d..537fc658c 100644
--- a/MetaMorpheus/Test/TestScanManagement.cs
+++ b/MetaMorpheus/Test/TestScanManagement.cs
@@ -70,6 +70,7 @@ public static void TestGetCombinedMs2Scans()
                 test.Add(new Ms2ScanWithSpecificMass(ms2scan, ms2scan.SelectedIonMonoisotopicGuessMz.Value, ms2scan.SelectedIonChargeStateGuess.Value, "", new CommonParameters()));
             }
             var testToArray = test.OrderBy(b => b.PrecursorMass).ToArray();
+
         }
     }
 }
\ No newline at end of file