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avcarr2
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Averaging task in MetaMorpheus (#2281)
* Implemented AveragingTask in MM * Fixed runtime notification boxes and added Option to the small add task button on the Run Page * Updated default loading in with preset settings * Expanded View Model Test Coverage * Added tool tips to preset parameters * Added tests to expand coverage of SpectralAveragingParametersViewModel * Expanded test coverage * Expanded test coverage and added links to wiki * Fixed broken Tests * Fixed bug with null coalescing operator that was okay in compile time, but caused an issue in runtime. * Test comment to force build in github --------- Co-authored-by: avcarr2 <[email protected]> Co-authored-by: avcarr2 <[email protected]>
1 parent 2729265 commit 2fc4f6e

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-36
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‎MetaMorpheus/GUI/App.xaml

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Original file line numberDiff line numberDiff line change
@@ -36,5 +36,26 @@
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<Style x:Key="DataGridCenteredCellStyle" TargetType="TextBlock">
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<Setter Property="HorizontalAlignment" Value="Center"></Setter>
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</Style>
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<!-- GroupBoxStyle -->
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<Style TargetType="{x:Type GroupBox}" x:Key="GroupBoxStyle">
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<Setter Property="BorderBrush" Value="{StaticResource ForegroundDarkBrush}"></Setter>
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<Setter Property="BorderThickness" Value="2"></Setter>
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<Setter Property="Margin" Value="5"></Setter>
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</Style>
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<!-- ValueEnteringStackPanel -->
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<Style TargetType="{x:Type StackPanel}" x:Key="ValueEnteringStackPanel">
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<Setter Property="Orientation" Value="Horizontal"></Setter>
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<Setter Property="Margin" Value="5"></Setter>
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<Setter Property="HorizontalAlignment" Value="Center"></Setter>
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</Style>
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<!-- TextBoxStyle -->
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<Style TargetType="{x:Type TextBox}" x:Key="TextBoxStyle">
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<Setter Property="HorizontalContentAlignment" Value="Center"></Setter>
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<Setter Property="VerticalContentAlignment" Value="Center"></Setter>
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<Setter Property="Width" Value="40"></Setter>
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</Style>
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</Application.Resources>
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</Application>

‎MetaMorpheus/GUI/MainWindow.xaml

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@@ -6,7 +6,7 @@
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xmlns:local="clr-namespace:MetaMorpheusGUI"
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mc:Ignorable="d"
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Drop="Window_Drop" AllowDrop="true" Background="{StaticResource BackgroundColor}" WindowStartupLocation="CenterScreen" MinHeight="400"
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MinWidth="800" Height="550" Width="950"
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MinWidth="800" Height="550" Width="1000"
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Loaded="MyWindow_Loaded">
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<Window.Resources>
@@ -122,6 +122,7 @@
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<!--Defines the context menu when "add task" button is clicked-->
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<ContextMenu x:Key="AddTaskMenu" Style="{StaticResource ContextMenuStyle}">
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<MenuItem Header="Add new calibration task" Click="AddCalibrateTaskButton_Click" />
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<MenuItem Header="Add new averaging task" Click="AddAveragingTaskButton_OnClick" />
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<MenuItem Header="Add new GPTMD task" Click="AddGPTMDTaskButton_Click" />
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<MenuItem Header="Add new search task" Click="AddSearchTaskButton_Click" />
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<MenuItem Header="Add new crosslink task" Click="AddCrosslinkTask_Click" />
@@ -298,9 +299,20 @@
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task performs mass calibration;
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<!-- TODO: Change link to averaging paper once published -->
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<LineBreak />
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● The
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<Hyperlink NavigateUri="https://github.com/smith-chem-wisc/MetaMorpheus/wiki/Averaging-Task" RequestNavigate="Hyperlink_RequestNavigate">
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averaging
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</Hyperlink>
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● the
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task averages spectra to refine isotopic distributions
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<LineBreak />
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● The
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<Hyperlink NavigateUri="https://pubs.acs.org/doi/10.1021/acs.jproteome.6b00034" RequestNavigate="Hyperlink_RequestNavigate">
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GPTMD
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</Hyperlink>
@@ -309,7 +321,7 @@
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<LineBreak />
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● the search task performs a proteomics database search, with
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● The search task performs a proteomics database search, with
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<Hyperlink NavigateUri="https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00608" RequestNavigate="Hyperlink_RequestNavigate">
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quantification
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<LineBreak />
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● the
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● The
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<Hyperlink NavigateUri="https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00141" RequestNavigate="Hyperlink_RequestNavigate">
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XL search
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<LineBreak />
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● the
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● The
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<Hyperlink NavigateUri="https://www.biorxiv.org/content/10.1101/2020.05.18.102327v1.abstract" RequestNavigate="Hyperlink_RequestNavigate">
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glycopeptide
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<!--Button to add tasks-->
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<Grid Grid.Row="2" Background="{StaticResource BackgroundColor}" Margin="0,0,10,0" HorizontalAlignment="Right">
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<Grid.ColumnDefinitions>
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<ColumnDefinition Width="150"/>
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<ColumnDefinition Width="150"/>
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<ColumnDefinition Width="150"/>
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<ColumnDefinition Width="150"/>
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<ColumnDefinition Width="150"/>
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<ColumnDefinition Width="140"/>
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<ColumnDefinition Width="140"/>
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<ColumnDefinition Width="140"/>
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<ColumnDefinition Width="140"/>
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<ColumnDefinition Width="140"/>
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<ColumnDefinition Width="140"/>
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</Grid.ColumnDefinitions>
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<Button Name="AddCalibTaskButton" Grid.Column="0" Content="+ADD CALIBRATION" HorizontalAlignment="Right" Click="AddCalibrateTaskButton_Click"
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Style="{StaticResource ImportantButtonStyle}" Margin="0,0,1,0" Width="150"/>
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<Button Name="AddGptmdTaskButton" Grid.Column="1" Content="+ADD PTM DISCOVERY" HorizontalAlignment="Right" Click="AddGPTMDTaskButton_Click"
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Style="{StaticResource ImportantButtonStyle}" Margin="0,0,1,0" Width="150"/>
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<Button Name="AddSearchTaskButton" Grid.Column="2" Content="+ADD SEARCH" HorizontalAlignment="Right" Click="AddSearchTaskButton_Click"
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Style="{StaticResource ImportantButtonStyle}" Margin="0,0,1,0" Width="150"/>
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<Button Name="AddXlTaskButton" Grid.Column="3" Content="+ADD XL SEARCH" HorizontalAlignment="Right" Click="AddCrosslinkTask_Click"
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Style="{StaticResource ImportantButtonStyle}" Margin="0,0,1,0" Width="150"/>
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<Button Name="AddGlycoTaskButton" Grid.Column="4" Content="+ADD GLYCO SEARCH" HorizontalAlignment="Right" Click="AddGlycoSearchTask_Click"
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Style="{StaticResource ImportantButtonStyle}" Margin="0,0,0,0" Width="150"/>
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Style="{StaticResource ImportantButtonStyle}" Margin="0,0,1,0" Width="140"/>
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<Button Name="AddAveragingTaskButton" Grid.Column="1" Content="+AVERAGE SPECTRA" HorizontalAlignment="Right" Click="AddAveragingTaskButton_OnClick"
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Style="{StaticResource ImportantButtonStyle}" Margin="0, 0, 1, 0" Width="140" FontSize="11" />
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<Button Name="AddGptmdTaskButton" Grid.Column="2" Content="+ADD PTM DISCOVERY" HorizontalAlignment="Right" Click="AddGPTMDTaskButton_Click"
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Style="{StaticResource ImportantButtonStyle}" Margin="0,0,1,0" Width="140"/>
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<Button Name="AddSearchTaskButton" Grid.Column="3" Content="+ADD SEARCH" HorizontalAlignment="Right" Click="AddSearchTaskButton_Click"
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Style="{StaticResource ImportantButtonStyle}" Margin="0,0,1,0" Width="140"/>
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<Button Name="AddXlTaskButton" Grid.Column="4" Content="+ADD XL SEARCH" HorizontalAlignment="Right" Click="AddCrosslinkTask_Click"
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Style="{StaticResource ImportantButtonStyle}" Margin="0,0,1,0" Width="140"/>
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<Button Name="AddGlycoTaskButton" Grid.Column="5" Content="+ADD GLYCO SEARCH" HorizontalAlignment="Right" Click="AddGlycoSearchTask_Click"
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Style="{StaticResource ImportantButtonStyle}" Margin="0,0,0,0" Width="140"/>
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</Grid>
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<!--List of tasks-->

‎MetaMorpheus/GUI/MainWindow.xaml.cs

+22-6
Original file line numberDiff line numberDiff line change
@@ -710,9 +710,13 @@ private void AddGlycoSearchTask_Click(object sender, RoutedEventArgs e)
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{
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OpenNewTaskWindow(MyTask.GlycoSearch);
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}
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private void AddAveragingTaskButton_OnClick(object sender, RoutedEventArgs e)
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{
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OpenNewTaskWindow(MyTask.Average);
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}
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/// <summary>
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/// Event fires when the "Add Task" button is clicked.
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/// Event fires when the "Add Task" button is clicked on the RunPage
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/// </summary>
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private void AddTask_Click(object sender, RoutedEventArgs e)
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{
@@ -905,10 +909,9 @@ private void RunAllTasks_Click(object sender, RoutedEventArgs e)
905909
NotificationHandler(null, new StringEventArgs("You need to add at least one spectra file!", null));
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return;
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}
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if (!ProteinDatabases.Any())
912+
if (!ProteinDatabases.Any() && PreRunTasks.Any(p => p.metaMorpheusTask.TaskType != MyTask.Average)) // will not throw this if averaging is the only task
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{
910914
NotificationHandler(null, new StringEventArgs("You need to add at least one protein database!", null));
911-
return;
912915
}
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914917
// check that experimental design is defined if normalization is enabled
@@ -1658,6 +1661,11 @@ private void AddPreRunFile(string filePath)
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var glyco = Toml.ReadFile<GlycoSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
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AddTaskToCollection(glyco);
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break;
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case "Average":
1666+
var average = Toml.ReadFile<SpectralAveragingTask>(filePath, MetaMorpheusTask.tomlConfig);
1667+
AddTaskToCollection(average);
1668+
break;
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}
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}
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catch (Exception e)
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17061714
case MyTask.Gptmd: defaultTomlName = "GptmdTaskDefault.toml"; break;
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case MyTask.XLSearch: defaultTomlName = "XLSearchTaskDefault.toml"; break;
17081716
case MyTask.GlycoSearch: defaultTomlName = "GlycoSearchTaskDefault.toml"; break;
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case MyTask.Average: defaultTomlName = "SpectralAverageTaskDefault.toml"; break;
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}
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17111720
string defaultTomlFilePath = Path.Combine(GlobalVariables.DataDir, "DefaultParameters", defaultTomlName);
@@ -1721,6 +1730,7 @@ private void OpenNewTaskWindow(MyTask taskType)
17211730
case MyTask.Gptmd: task = Toml.ReadFile<GptmdTask>(defaultTomlFilePath, MetaMorpheusTask.tomlConfig); break;
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case MyTask.XLSearch: task = Toml.ReadFile<XLSearchTask>(defaultTomlFilePath, MetaMorpheusTask.tomlConfig); break;
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case MyTask.GlycoSearch: task = Toml.ReadFile<GlycoSearchTask>(defaultTomlFilePath, MetaMorpheusTask.tomlConfig); break;
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case MyTask.Average: task = Toml.ReadFile<SpectralAveragingTask>(defaultTomlFilePath, MetaMorpheusTask.tomlConfig); break;
17241734
}
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}
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catch (Exception)
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17371747
case MyTask.Gptmd: dialog = new GptmdTaskWindow((GptmdTask)task); break;
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case MyTask.XLSearch: dialog = new XLSearchTaskWindow((XLSearchTask)task); break;
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case MyTask.GlycoSearch: dialog = new GlycoSearchTaskWindow((GlycoSearchTask)task); break;
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case MyTask.Average: dialog = new SpectralAveragingTaskWindow((SpectralAveragingTask)task); break;
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}
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17421753
// save the task to the task collection
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17481759
case MyTask.Calibrate: AddTaskToCollection(((CalibrateTaskWindow)dialog).TheTask); break;
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case MyTask.Gptmd: AddTaskToCollection(((GptmdTaskWindow)dialog).TheTask); break;
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case MyTask.XLSearch: AddTaskToCollection(((XLSearchTaskWindow)dialog).TheTask); break;
1751-
case MyTask.GlycoSearch: AddTaskToCollection(((GlycoSearchTaskWindow)dialog).TheTask); break;
1762+
case MyTask.GlycoSearch: AddTaskToCollection(((GlycoSearchTaskWindow)dialog).TheTask); break;
1763+
case MyTask.Average: AddTaskToCollection(((SpectralAveragingTaskWindow)dialog).TheTask); break;
17521764
}
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17541766
UpdateGuiOnPreRunChange();
@@ -1866,6 +1878,12 @@ private void OpenPreRunTaskForEditing(PreRunTask preRunTask)
18661878
var GlycoSearchdialog = new GlycoSearchTaskWindow(preRunTask.metaMorpheusTask as GlycoSearchTask);
18671879
GlycoSearchdialog.ShowDialog();
18681880
break;
1881+
1882+
case MyTask.Average:
1883+
var averagingDialog =
1884+
new SpectralAveragingTaskWindow(preRunTask.metaMorpheusTask as SpectralAveragingTask);
1885+
averagingDialog.ShowDialog();
1886+
break;
18691887
}
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18711889
UpdateGuiOnPreRunChange();
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19501968
{
19511969
OpenFolder(Path.Combine(GlobalVariables.DataDir, @"Proteomes"));
19521970
}
1953-
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19551971
}
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}

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