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Shared peptides tic box for lfq #2353

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Shared peptides tic box for lfq #2353

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3356784
added tic box plus other needed code
trishorts Feb 23, 2024
8cd8eea
add nics fix for custom fragmentation window xaml cs
trishorts Feb 23, 2024
6d7019f
seeems to work lets seee
trishorts Feb 23, 2024
95cf3f4
merge upstream
trishorts Feb 27, 2024
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2 changes: 2 additions & 0 deletions MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
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Original file line number Diff line number Diff line change
Expand Up @@ -417,6 +417,8 @@
<ToolTip Content="Label-free quantification is performed with FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
</ToolTipService.ToolTip>
</RadioButton>
<CheckBox x:Name="CheckBoxUseSharedPeptidesForQuant" Content="Use shared peptides for protein quantification" IsEnabled="True" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
</CheckBox>
<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"/>
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2 changes: 2 additions & 0 deletions MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
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Expand Up @@ -189,6 +189,7 @@ private void UpdateFieldsFromTask(SearchTask task)
CheckBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
CheckBoxNoQuant.IsChecked = !task.SearchParameters.DoLabelFreeQuantification;
CheckBoxLFQ.IsChecked = task.SearchParameters.DoLabelFreeQuantification;
CheckBoxUseSharedPeptidesForQuant.IsChecked = task.SearchParameters.UseSharedPeptidesForLFQ;
CheckBoxMultiplex.IsChecked = task.SearchParameters.DoMultiplexQuantification;
MultiplexComboBox.SelectedItem = task.SearchParameters.MultiplexModId ?? _defaultMultiplexType;
// If Spectral Recovery is enabled
Expand Down Expand Up @@ -626,6 +627,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
TheTask.SearchParameters.DoParsimony = CheckBoxParsimony.IsChecked.Value;
TheTask.SearchParameters.NoOneHitWonders = CheckBoxNoOneHitWonders.IsChecked.Value;
TheTask.SearchParameters.DoLabelFreeQuantification = !CheckBoxNoQuant.IsChecked.Value;
TheTask.SearchParameters.UseSharedPeptidesForLFQ = CheckBoxUseSharedPeptidesForQuant.IsChecked.Value;
TheTask.SearchParameters.DoSpectralRecovery = CheckBoxLFQwSpectralRecovery.IsChecked.Value;
TheTask.SearchParameters.DoMultiplexQuantification = CheckBoxMultiplex.IsChecked.Value;
TheTask.SearchParameters.MultiplexModId = (string)MultiplexComboBox.SelectedItem;
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10 changes: 5 additions & 5 deletions MetaMorpheus/GUI/Views/CustomFragmentationWindow.xaml.cs
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Expand Up @@ -32,10 +32,10 @@ public CustomFragmentationWindow(List<ProductType> list, bool isRna = false)
if (list != null)
{
var res = TheList.Where(n => list.Contains(n.Type));
foreach(var r in res)
foreach (var r in res)
{
r.IsSelected = true;
}
}
}

base.Closing += this.OnClosing;
Expand Down Expand Up @@ -126,17 +126,17 @@ private void OnClosing(object sender, CancelEventArgs e)
{
// this window only closes when task is added
if (this.Visibility == Visibility.Visible)
{
{
this.Visibility = Visibility.Hidden;
e.Cancel = true;
}
}
}

public class BoolStringClass
public class BoolStringClass
{
public ProductType Type { get; set; }
public bool IsSelected { get; set; }
public string ToolTip { get; set; }
}
}
}
1 change: 1 addition & 0 deletions MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs
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Expand Up @@ -588,6 +588,7 @@ private void QuantificationAnalysis()
ppmTolerance: Parameters.SearchParameters.QuantifyPpmTol,
matchBetweenRunsPpmTolerance: Parameters.SearchParameters.QuantifyPpmTol, // If these tolerances are not equivalent, then MBR will falsely classify peptides found in the initial search as MBR peaks
matchBetweenRuns: Parameters.SearchParameters.MatchBetweenRuns,
useSharedPeptidesForProteinQuant: Parameters.SearchParameters.UseSharedPeptidesForLFQ,
silent: true,
maxThreads: CommonParameters.MaxThreadsToUsePerFile);

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2 changes: 2 additions & 0 deletions MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs
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Expand Up @@ -16,6 +16,7 @@ public SearchParameters()
NoOneHitWonders = false;
ModPeptidesAreDifferent = false;
DoLabelFreeQuantification = true;
UseSharedPeptidesForLFQ = false;
DoSpectralRecovery = false;
QuantifyPpmTol = 5;
SearchTarget = true;
Expand Down Expand Up @@ -76,6 +77,7 @@ public SearchParameters()
public bool KeepAllUniprotMods { get; set; }
public bool DoLocalizationAnalysis { get; set; }
public bool DoLabelFreeQuantification { get; set; }
public bool UseSharedPeptidesForLFQ { get; set; }
public bool DoMultiplexQuantification { get; set; }
public string MultiplexModId { get; set; }
public bool DoSpectralRecovery { get; set; }
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