[WIP] Enable saving of multiple settings for tasks

MetaMorpheus/GUI/MainWindow.xaml

@@ -463,15 +463,15 @@
 
  <!--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"/>
+  Style="{StaticResource ImportantButtonStyle}" Margin="0,0,10,0"/>
 
  <Button Name="SetFileSpecificSettingsButton" Grid.Row="2" Content="SET FILE-SPECIFIC SETTINGS" Click="SetFileSpecificParameters_Click" 
  HorizontalAlignment="Right" Style="{StaticResource ImportantButtonStyle}"
- Margin="0,0,211,0"/>
+  Margin="0,0,211,0"/>
 
  <Button Name="SetExperimentalDesignButton" Grid.Row="2" Content="SET EXPERIMENTAL DESIGN" Click="SetExperimentalDesign_Click" 
  HorizontalAlignment="Right" Style="{StaticResource ImportantButtonStyle}"
- Margin="0,0,412,0"/>
+  Margin="0,0,412,0"/>
 
  <!--The list of spectra files-->
  <DataGrid Name="dataGridSpectraFiles" ItemsSource="{Binding}" Grid.Row="3" Style="{StaticResource x:DataGridStyle}"

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>
@@ -44,7 +49,11 @@
  </Style>
  </TextBox.Style>
  </TextBox>
- </StackPanel>
+ <!-- save settings -->
+ <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">
  <StackPanel>
@@ -422,7 +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" />

MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs

@@ -28,6 +28,7 @@ public partial class CalibrateTaskWindow : Window
  private readonly ObservableCollection<ModTypeForLoc> LocalizeModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForLoc>();
  private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
  private CustomFragmentationWindow CustomFragmentationWindow;
+ private TaskSettingViewModel TaskSettingViewModel;
 
  public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
  {
@@ -36,8 +37,12 @@ public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
 
  AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
  PopulateChoices();
- UpdateFieldsFromTask(TheTask);
+ var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as CalibrationTask);
+ TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
+ TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+ setDefaultbutton.DataContext = TaskSettingViewModel;
  AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
+
 
  if (myCalibrateTask == null)
  {
@@ -187,15 +192,25 @@ 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 +241,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
 
  if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
  {
- return;
+ return null;
  }
 
  var listOfModsFixed = new List<(string, string)>();
@@ -296,7 +311,7 @@ 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)
@@ -357,13 +372,7 @@ 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();
- }
-
- private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
- {
- SaveButton_Click(sender, e);
- Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"CalibrationTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
+ CustomFragmentationWindow?.Close();
  }
 
  private void ProteaseSpecificUpdate(object sender, SelectionChangedEventArgs e)

MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml

@@ -18,13 +18,19 @@
  </Grid.RowDefinitions>
  <ScrollViewer VerticalScrollBarVisibility="Auto">
  <DockPanel>
- <StackPanel DockPanel.Dock="Top" Orientation="Horizontal">
- <Label Content="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="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 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>
@@ -44,7 +50,13 @@
  </Style>
  </TextBox.Style>
  </TextBox>
- </StackPanel>
+ <!-- save settings -->
+ <local:SaveSettingsControl x:Name="TaskSettingsCtrl" Grid.Column="2" HorizontalAlignment="Right"
+ DataContext="{Binding TaskSettingViewModel}" />
+
+ </Grid>
+
+
  <GroupBox Header="File Loading Parameters" DockPanel.Dock="Top">
  <Expander x:Name="FileLoadExpander" >
  <StackPanel>
@@ -499,7 +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" />

MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs

@@ -29,6 +29,7 @@ public partial class GptmdTaskWindow : Window
  private readonly ObservableCollection<ModTypeForTreeViewModel> GptmdModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForTreeViewModel>();
  private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
  private CustomFragmentationWindow CustomFragmentationWindow;
+ private TaskSettingViewModel TaskSettingViewModel;
 
  public GptmdTaskWindow(GptmdTask myGPTMDtask)
  {
@@ -37,8 +38,12 @@ public GptmdTaskWindow(GptmdTask myGPTMDtask)
 
  AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
  PopulateChoices();
- UpdateFieldsFromTask(TheTask);
+ var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as GptmdTask);
+ TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
+ TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+ setDefaultbutton.DataContext = TaskSettingViewModel;
  AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
+ PopulateChoices();
 
  if (myGPTMDtask == null)
  {
@@ -349,15 +354,25 @@ 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;
@@ -400,7 +415,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
 
  if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
  {
- return;
+ return null;
  }
 
  bool TrimMs1Peaks = TrimMs1.IsChecked.Value;
@@ -416,7 +431,7 @@ 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;
  }
  }
 
@@ -430,7 +445,7 @@ 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;
  }
  }
 
@@ -458,7 +473,7 @@ 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,
@@ -477,8 +492,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
  }
 
  TheTask.CommonParameters = commonParamsToSave;
-
- DialogResult = true;
+ return TheTask;
  }
 
  private void CheckIfNumber(object sender, TextCompositionEventArgs e)
@@ -551,13 +565,7 @@ 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();
- }
-
- private void SaveAsDefault_Click(object sender, RoutedEventArgs e)
- {
- SaveButton_Click(sender, e);
- Toml.WriteFile(TheTask, Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"GptmdTaskDefault.toml"), MetaMorpheusTask.tomlConfig);
+ CustomFragmentationWindow?.Close();
  }
  }
 }

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">
@@ -42,13 +43,19 @@
  </Grid.RowDefinitions>
  <ScrollViewer VerticalScrollBarVisibility="Auto" Grid.ColumnSpan="2">
  <DockPanel>
- <StackPanel DockPanel.Dock="Top" Orientation="Horizontal">
- <Label Content="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="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 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>
@@ -68,7 +75,13 @@
  </Style>
  </TextBox.Style>
  </TextBox>
- </StackPanel>
+
+ <!-- save settings -->
+ <local:SaveSettingsControl x:Name="TaskSettingsCtrl" Grid.Column="2" HorizontalAlignment="Right"
+ DataContext="{Binding TaskSettingViewModel}" />
+
+ </Grid>
+
  <StackPanel DockPanel.Dock="Top">
  <Grid>
 
@@ -500,9 +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>