From cfaebaaa42f295e8541158ae3b89e94b5841796d Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 8 Jan 2025 18:41:28 -0600
Subject: [PATCH] include protein ambiguous gui component

---
 MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml   | 12 ++++++++++++
 .../GUI/TaskWindows/SearchTaskWindow.xaml.cs         |  3 +++
 .../TaskLayer/SearchTask/SearchParameters.cs         |  5 ++++-
 3 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
index 8ea672f1ad..f212d8bb2d 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
@@ -1146,6 +1146,18 @@
                                                     </TextBlock>
                                                 </ToolTipService.ToolTip>
                                             </CheckBox>
+                                            <CheckBox Margin="0 0 0 5" x:Name="IncludeProteinAmbiguousCheckbox" VerticalAlignment="Center"
+                                                      Content="Include Protein Ambiguous" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
+                                                <ToolTipService.ToolTip>
+                                                    <TextBlock>
+                                                        Ambiguous results are excluded from this analysis by default.
+                                                        <LineBreak/>
+                                                        If checked, search results with localized modifications that are ambiguous only in their protein of origin will be included.
+                                                        <LineBreak/>
+                                                        This can be used for the case of peptides that could come from more than one protein. 
+                                                    </TextBlock>
+                                                </ToolTipService.ToolTip>
+                                            </CheckBox>
                                             <StackPanel  Orientation="Horizontal"  VerticalAlignment="Center">
                                                 <local:IntegerTexBoxControl x:Name="PrunedDatabaseEvidenceTextBox" Width="30" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" >
                                                     <ToolTipService.ToolTip>
diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index 641bdc893c..8336ba3f36 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -304,6 +304,8 @@ private void UpdateFieldsFromTask(SearchTask task)
             NormalizePeaksInWindowCheckBox.IsChecked = task.CommonParameters.NormalizePeaksAccrossAllWindows;
 
             PrunedDatabaseEvidenceTextBox.Text = task.SearchParameters.EvidenceRequiredToWriteLocalizedMod.ToString(CultureInfo.InvariantCulture);
+            IncludeProteinAmbiguousCheckbox.IsChecked = task.SearchParameters.IncludeProteinAmbiguous;
+
             MaxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
             MinVariantDepthTextBox.Text = task.CommonParameters.MinVariantDepth.ToString(CultureInfo.InvariantCulture);
             MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
@@ -641,6 +643,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             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);
+            TheTask.SearchParameters.IncludeProteinAmbiguous = IncludeProteinAmbiguousCheckbox.IsChecked.Value;
 
             if (RemoveContaminantRadioBox.IsChecked.Value)
             {
diff --git a/MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs b/MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs
index e3a5f94a81..7fa9a74e13 100644
--- a/MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs
+++ b/MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs
@@ -87,7 +87,6 @@ public SearchParameters()
         public double MaxFragmentSize { get; set; }
         public int MinAllowedInternalFragmentLength { get; set; } //0 means "no internal fragments"
         public double HistogramBinTolInDaltons { get; set; } 
-        public uint EvidenceRequiredToWriteLocalizedMod { get; set; } = 1;
         public Dictionary<string, int> ModsToWriteSelection { get; set; }
         public double MaximumMassThatFragmentIonScoreIsDoubled { get; set; }
         public bool WriteMzId { get; set; }
@@ -104,5 +103,9 @@ public SearchParameters()
         public SilacLabel EndTurnoverLabel { get; set; } //used for SILAC turnover experiments
         public TargetContaminantAmbiguity TCAmbiguity { get; set; }
         public bool IncludeModMotifInMzid { get; set; }
+
+        // For writing localized mods to pruned database
+        public uint EvidenceRequiredToWriteLocalizedMod { get; set; } = 1;
+        public bool IncludeProteinAmbiguous { get; set; } = false; // if true, a 2D ambiguous result will be written to all possible proteins of origin. 
     }
 }
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