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Require More Evidence to Write mod to Pruned Database #2444

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Require More Evidence to Write mod to Pruned Database #2444

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a1eccce
Broke PrunedDB writing into distinct methods
nbollis Nov 26, 2024
5c7b81c
Async database writing and tests to cover it
nbollis Nov 27, 2024
eff4c66
Revised the parsing code to be much cleaner and added first round of …
nbollis Nov 27, 2024
e2109ef
Built Evidence requirement into search parameters and gui
nbollis Nov 27, 2024
fc6a5e5
Genera cleanup
nbollis Nov 27, 2024
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2 changes: 2 additions & 0 deletions MetaMorpheus/CMD/Program.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -150,6 +150,8 @@ private static int Run(CommandLineSettings settings)
MetaMorpheusTask.FinishedSingleTaskHandler += MyTaskEngine_finishedSingleTaskHandler;
MetaMorpheusTask.FinishedWritingFileHandler += MyTaskEngine_finishedWritingFileHandler;

PrunedDatabaseWriter.FinishedWritingFileHandler += MyTaskEngine_finishedWritingFileHandler;

bool containsRawFiles = settings.Spectra.Select(v => Path.GetExtension(v).ToLowerInvariant()).Any(v => v == ".raw");
if (containsRawFiles && !GlobalVariables.GlobalSettings.UserHasAgreedToThermoRawFileReaderLicence)
{
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18 changes: 18 additions & 0 deletions MetaMorpheus/EngineLayer/Util/DictionaryExtensions.cs
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Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
using System.Collections.Generic;

namespace EngineLayer;

public static class DictionaryExtensions
{
public static void AddOrCreate<TKey, TValue>(this IDictionary<TKey, List<TValue>> dictionary, TKey key, TValue value)
{
if (dictionary.TryGetValue(key, out var list))
{
list.Add(value);
}
else
{
dictionary[key] = [value];
}
}
}
2 changes: 2 additions & 0 deletions MetaMorpheus/GUI/MainWindow.xaml.cs
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Expand Up @@ -73,6 +73,8 @@ public MainWindow()
MetaMorpheusEngine.OutLabelStatusHandler += NewoutLabelStatus;
MetaMorpheusEngine.WarnHandler += NotificationHandler;

PrunedDatabaseWriter.FinishedWritingFileHandler += FinishedWritingFile;

MyFileManager.WarnHandler += NotificationHandler;
Application.Current.MainWindow.Closing += new CancelEventHandler(MainWindow_Closing);
}
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33 changes: 23 additions & 10 deletions MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
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Expand Up @@ -1130,21 +1130,34 @@
</GroupBox>
<GroupBox Header="Pruned Database Writing">
<StackPanel Margin="5">
<CheckBox Margin="0 0 0 5" x:Name="WritePrunedDBCheckBox" Content="Write Two Pruned Databases (Mod and Mod+Protein pruned)" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
<CheckBox Margin="0 0 0 5" x:Name="WritePrunedDBCheckBox" VerticalAlignment="Center"
Content="Write Two Pruned Databases (Mod and Mod+Protein pruned)" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
<ToolTipService.ToolTip>
<TextBlock>
This is very uncommon and not recommended for the typical user.
<LineBreak />
This option writes two databases:
<LineBreak />
1) Retain all proteins but only keeps modifications found at a 1% FDR.
<LineBreak />
2) Retain only proteins and modifications found at a 1% FDR.
<LineBreak />
This is intended for further analysis, such as importing into Proteoform Suite to analyse top-down and intact-mass data.
This is very uncommon and not recommended for the typical user.
<LineBreak />
This option writes two databases:
<LineBreak />
1) Retain all proteins but only keeps modifications found at a 1% FDR.
<LineBreak />
2) Retain only proteins and modifications found at a 1% FDR.
<LineBreak />
This is intended for further analysis, such as importing into Proteoform Suite to analyse top-down and intact-mass data.
</TextBlock>
</ToolTipService.ToolTip>
</CheckBox>
<StackPanel Orientation="Horizontal" VerticalAlignment="Center">
<local:IntegerTexBoxControl x:Name="PrunedDatabaseEvidenceTextBox" Width="30" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" >
<ToolTipService.ToolTip>
<TextBlock>
Only Retain a modified residue position if there is n pieces of unique information supporting it.
<LineBreak />
Unique information here is defined by the following criteria: Dissociation Type, Digestion Agent, and Missed Cleavage Product.
</TextBlock>
</ToolTipService.ToolTip>
</local:IntegerTexBoxControl>
<Label Content="Unique observations required to write modifications to pruned database" />
</StackPanel>
<DataGrid x:Name="ModSelectionGrid" AutoGenerateColumns = "false" ItemsSource="{Binding UpdateSourceTrigger=LostFocus, Mode=OneWay}" Visibility="{Binding prunedVisible, UpdateSourceTrigger=LostFocus}" IsEnabled="{Binding IsChecked, ElementName=WritePrunedDBCheckBox}" IsReadOnly="False" AlternatingRowBackground="LightGray" AlternationCount="2">
<DataGrid.Columns>
<DataGridTextColumn Header="Mod Type" Width="1*" Binding="{Binding ModName}" />
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2 changes: 2 additions & 0 deletions MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
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Expand Up @@ -303,6 +303,7 @@ private void UpdateFieldsFromTask(SearchTask task)
NumberOfWindowsTextBox.Text = task.CommonParameters.NumberOfWindows == int.MaxValue || !task.CommonParameters.NumberOfWindows.HasValue ? "" : task.CommonParameters.NumberOfWindows.Value.ToString(CultureInfo.InvariantCulture);
NormalizePeaksInWindowCheckBox.IsChecked = task.CommonParameters.NormalizePeaksAccrossAllWindows;

PrunedDatabaseEvidenceTextBox.Text = task.SearchParameters.EvidenceRequiredToWriteLocalizedMod.ToString(CultureInfo.InvariantCulture);
MaxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
MinVariantDepthTextBox.Text = task.CommonParameters.MinVariantDepth.ToString(CultureInfo.InvariantCulture);
MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
Expand Down Expand Up @@ -639,6 +640,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
TheTask.SearchParameters.UpdateSpectralLibrary = UpdateSpectralLibraryCheckBox.IsChecked.Value;
TheTask.SearchParameters.CompressIndividualFiles = CompressIndividualResultsCheckBox.IsChecked.Value;
TheTask.SearchParameters.IncludeModMotifInMzid = IncludeMotifInModNamesCheckBox.IsChecked.Value;
TheTask.SearchParameters.EvidenceRequiredToWriteLocalizedMod = PrunedDatabaseEvidenceTextBox.Text.Equals("") ? 1 : uint.Parse(PrunedDatabaseEvidenceTextBox.Text, CultureInfo.InvariantCulture);

if (RemoveContaminantRadioBox.IsChecked.Value)
{
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