mod index fix

MetaMorpheus/EngineLayer/Gptmd/IGptmdFilter.cs

@@ -0,0 +1,161 @@
+#nullable enable
+using System;
+using Omics.Fragmentation;
+using System.Collections.Generic;
+using Omics;
+using System.Linq;
+using Omics.Modifications;
+
+namespace EngineLayer;
+
+public interface IGptmdFilter : IEquatable<IGptmdFilter>
+{
+    public static string GetFilterTypeName(IGptmdFilter filter) => filter.GetType().Name;
+
+    bool Passes(
+        IBioPolymerWithSetMods candidatePeptide,
+        SpectralMatch psm,
+        double newScore,
+        double originalScore,
+        List<MatchedFragmentIon> matchedIons,
+        int peptideOneBasedModSite,
+        int peptideLength, 
+        Modification modAttemptingToAdd);
+
+    bool IEquatable<IGptmdFilter>.Equals(IGptmdFilter? other)
+    {
+        return other != null && GetType() == other.GetType();
+    }
+}
+
+/// <summary>
+/// Requires that the new score is greater than the original score.
+/// </summary>
+public sealed class ImprovedScoreFilter : IGptmdFilter
+{
+    public bool Passes(
+        IBioPolymerWithSetMods candidatePeptide,
+        SpectralMatch psm,
+        double newScore,
+        double originalScore,
+        List<MatchedFragmentIon> matchedIons,
+        int peptideOneBasedModSite,
+        int peptideLength,
+        Modification modAttemptingToAdd)
+    {
+        return newScore > originalScore;
+    }
+}
+
+/// <summary>
+/// Requires the mod site to be covered by at least one N-terminal and one C-terminal ion.
+/// That is, ions from both directions must include the mod, even if not flanking it.
+/// </summary>
+public sealed class DualDirectionalIonCoverageFilter : IGptmdFilter
+{
+    public bool Passes(
+        IBioPolymerWithSetMods candidatePeptide,
+        SpectralMatch psm,
+        double newScore,
+        double originalScore,
+        List<MatchedFragmentIon> matchedIons,
+        int peptideOneBasedModSite,
+        int peptideLength,
+        Modification modAttemptingToAdd)
+    {
+        if (matchedIons == null || matchedIons.Count == 0)
+            return false;
+
+        int site = peptideOneBasedModSite;
+
+        bool coveredFromNTerm = matchedIons.Any(m =>
+           m.NeutralTheoreticalProduct.ProductType == ProductType.M ||
+           (m.NeutralTheoreticalProduct.Terminus is FragmentationTerminus.N or FragmentationTerminus.FivePrime &&
+            m.NeutralTheoreticalProduct.ResiduePosition >= site)
+        );
+
+        bool coveredFromCTerm = matchedIons.Any(m =>
+           m.NeutralTheoreticalProduct.ProductType == ProductType.M ||
+           (m.NeutralTheoreticalProduct.Terminus is FragmentationTerminus.C or FragmentationTerminus.ThreePrime &&
+            m.NeutralTheoreticalProduct.ResiduePosition < site)
+        );
+
+        if (modAttemptingToAdd.LocationRestriction.Contains("terminal", StringComparison.InvariantCultureIgnoreCase))
+            return coveredFromCTerm || coveredFromNTerm;
+
+        return coveredFromNTerm && coveredFromCTerm;
+    }
+}
+
+/// <summary>
+/// Requires the mod site to be covered by at least one N-terminal or one C-terminal ion.
+/// That is, ions from one direction must include the mod, even if not flanking it.
+/// </summary>
+public sealed class UniDirectionalIonCoverageFilter : IGptmdFilter
+{
+    public bool Passes(
+        IBioPolymerWithSetMods candidatePeptide,
+        SpectralMatch psm,
+        double newScore,
+        double originalScore,
+        List<MatchedFragmentIon> matchedIons,
+        int peptideOneBasedModSite,
+        int peptideLength,
+        Modification modAttemptingToAdd)
+    {
+        if (matchedIons == null || matchedIons.Count == 0)
+            return false;
+
+        int site = peptideOneBasedModSite;
+
+        bool coveredFromNTerm = matchedIons.Any(m =>
+            m.NeutralTheoreticalProduct.ProductType == ProductType.M ||
+            (m.NeutralTheoreticalProduct.Terminus is FragmentationTerminus.N or FragmentationTerminus.FivePrime &&
+             m.NeutralTheoreticalProduct.ResiduePosition >= site)
+        );
+
+        bool coveredFromCTerm = matchedIons.Any(m =>
+            m.NeutralTheoreticalProduct.ProductType == ProductType.M ||
+            (m.NeutralTheoreticalProduct.Terminus is FragmentationTerminus.C or FragmentationTerminus.ThreePrime &&
+             m.NeutralTheoreticalProduct.ResiduePosition < site)
+        );
+
+        return coveredFromNTerm || coveredFromCTerm;
+    }
+}
+
+/// <summary>
+/// Requires flanking ions — a fragment from *before* and one from *after* the mod site,
+/// regardless of fragmentation direction.
+/// </summary>
+public sealed class FlankingIonCoverageFilter : IGptmdFilter
+{
+    // TODO: Consider N-terminal and C-terminal mods as special cases, where the flanking ion not possible except for the M ion. 
+    public bool Passes(
+        IBioPolymerWithSetMods candidatePeptide,
+        SpectralMatch psm,
+        double newScore,
+        double originalScore,
+        List<MatchedFragmentIon> matchedIons,
+        int peptideOneBasedModSite,
+        int peptideLength,
+        Modification modAttemptingToAdd)
+    {
+        if (matchedIons == null || matchedIons.Count == 0)
+            return false;
+
+        int site = peptideOneBasedModSite;
+
+        bool leftFlank = matchedIons.Any(m =>
+            m.NeutralTheoreticalProduct.ResiduePosition == site - 1);
+
+        bool rightFlank = matchedIons.Any(m =>
+            m.NeutralTheoreticalProduct.ResiduePosition == site);
+
+        if (modAttemptingToAdd.LocationRestriction.Contains("terminal", StringComparison.InvariantCultureIgnoreCase))
+            return leftFlank || rightFlank;
+
+        return leftFlank && rightFlank;
+    }
+}
+

MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml

@@ -441,7 +441,21 @@
                                     </TextBox.Style>
                                 </TextBox>
                             </StackPanel>
-                            <StackPanel Grid.Column="0" Grid.Row="2">
+                            <GroupBox Grid.Column="1" Grid.Row="1" Header="G-PTM-D Filter Stringency" Margin="0,-10,0,24">
+                                <ListBox x:Name="FilterOptionsListBox" ItemsSource="{Binding FilterOptions}" SelectionMode="Multiple"
+                                         Margin="0,0,0,0" Padding="0" BorderThickness="0">
+                                    <ListBox.ItemTemplate>
+                                        <DataTemplate>
+                                            <StackPanel Orientation="Horizontal" Margin="0,0,0,0" VerticalAlignment="Center"
+                                                        ToolTip="{Binding Summary}">
+                                                <CheckBox IsChecked="{Binding IsSelected, Mode=TwoWay}" VerticalAlignment="Center"/>
+                                                <TextBlock Text="{Binding Name}" Margin="8,0,0,0" VerticalAlignment="Center"/>
+                                            </StackPanel>
+                                        </DataTemplate>
+                                    </ListBox.ItemTemplate>
+                                </ListBox>
+                            </GroupBox>
+                            <StackPanel Grid.Column="0" Grid.Row="1">
                                 <TreeView x:Name="gptmdModsTreeView" ItemsSource="{Binding}" DataContext="{x:Type guiFunctions:ModTypeForTreeViewModel}" Height="400">
                                     <TreeView.Resources>
                                         <HierarchicalDataTemplate DataType="{x:Type guiFunctions:ModTypeForTreeViewModel}" ItemsSource="{Binding Children}">

MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml.cs

@@ -15,6 +15,7 @@
 using System.Windows.Input;
 using TaskLayer;
 using GuiFunctions;
+using EngineLayer;
 
 namespace MetaMorpheusGUI
 {
@@ -23,6 +24,7 @@ namespace MetaMorpheusGUI
     /// </summary>
     public partial class GptmdTaskWindow : Window
     {
+        public ObservableCollection<GptmdFilterViewModel> FilterOptions { get; } = new();
         private readonly ObservableCollection<ModTypeForTreeViewModel> FixedModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForTreeViewModel>();
         private readonly ObservableCollection<ModTypeForTreeViewModel> VariableModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForTreeViewModel>();
         private readonly ObservableCollection<ModTypeForLoc> LocalizeModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForLoc>();
@@ -38,6 +40,7 @@ public GptmdTaskWindow(GptmdTask myGPTMDtask)
 
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
             PopulateChoices();
+            FilterOptionsListBox.ItemsSource = FilterOptions;
             UpdateFieldsFromTask(TheTask);
             AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
             DeisotopingControl.DataContext = DeconHostViewModel;
@@ -183,6 +186,11 @@ private void UpdateFieldsFromTask(GptmdTask task)
             {
                 ye.VerifyCheckState();
             }
+
+            foreach (var filter in FilterOptions)
+            {
+                filter.IsSelected = TheTask.GptmdParameters.GptmdFilters.Any(f => f.GetType() == filter.Filter.GetType());
+            }
         }
 
         private void PopulateChoices()
@@ -240,6 +248,28 @@ private void PopulateChoices()
                 }
             }
             gptmdModsTreeView.DataContext = GptmdModTypeForTreeViewObservableCollection;
+
+            FilterOptions.Clear();
+            FilterOptions.Add(new GptmdFilterViewModel(
+                new ImprovedScoreFilter(),
+                "Improved Score",
+                "Requires that the new score is greater than the original score."
+            ));
+            FilterOptions.Add(new GptmdFilterViewModel(
+                new DualDirectionalIonCoverageFilter(),
+                "Dual Directional Ion Coverage",
+                "Requires the mod site to be covered by at least one N-terminal and one C-terminal ion. That is, ions from both directions must include the mod, even if not flanking it."
+            ));
+            FilterOptions.Add(new GptmdFilterViewModel(
+                new UniDirectionalIonCoverageFilter(),
+                "Uni-Directional Ion Coverage",
+                "Requires the mod site to be covered by at least one N-terminal or one C-terminal ion. That is, ions from one direction must include the mod, even if not flanking it."
+            ));
+            FilterOptions.Add(new GptmdFilterViewModel(
+                new FlankingIonCoverageFilter(),
+                "Flanking Ion Coverage",
+                "Requires flanking ions — a fragment from *before* and one from *after* the mod site, regardless of fragmentation direction."
+            ));
         }
 
         private void CancelButton_Click(object sender, RoutedEventArgs e)
@@ -489,6 +519,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             {
                 TheTask.GptmdParameters.ListOfModsGptmd.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
             }
+            TheTask.GptmdParameters.GptmdFilters = FilterOptions.Where(f => f.IsSelected).Select(f => f.Filter).ToList();
 
             TheTask.CommonParameters = commonParamsToSave;
 

MetaMorpheus/GuiFunctions/ViewModels/GptmdFilterViewModel.cs

@@ -0,0 +1,25 @@
+using EngineLayer;
+
+namespace GuiFunctions;
+
+public class GptmdFilterViewModel : BaseViewModel
+{
+    private bool _isSelected = false;
+    public IGptmdFilter Filter { get; }
+    public string Name { get; }
+    public string Summary { get; }
+
+    public bool IsSelected
+    {
+        get => _isSelected;
+        set { _isSelected = value; OnPropertyChanged(nameof(IsSelected)); }
+    }
+
+    public GptmdFilterViewModel(IGptmdFilter filter, string name, string summary, bool isSelected = true)
+    {
+        Filter = filter;
+        Name = name;
+        Summary = summary;
+        _isSelected = isSelected;
+    }
+}

MetaMorpheus/TaskLayer/GPTMDTask/GPTMDParameters.cs

@@ -1,5 +1,6 @@
 using System.Collections.Generic;
 using System.Linq;
+using EngineLayer.Gptmd;
 
 namespace EngineLayer
 {
@@ -10,6 +11,7 @@ public class GptmdParameters
         /// </summary>
         public GptmdParameters()
         {
+            GptmdFilters = new();
             ListOfModsGptmd = GlobalVariables.AllModsKnown.Where(b =>
                 b.ModificationType.Equals("Common Artifact")
                 || b.ModificationType.Equals("Common Biological")
@@ -19,5 +21,6 @@ public GptmdParameters()
         }
 
         public List<(string, string)> ListOfModsGptmd { get; set; }
+        public List<IGptmdFilter> GptmdFilters { get; set; } 
     }
 }

MetaMorpheus/TaskLayer/GPTMDTask/GPTMDTask.cs

@@ -175,7 +175,7 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
             // GPTMD doesn't work as well if you do FDR on a file-by-file basis. Presumably this is because it takes multiple files to get enough PSMs for all the different notches
             new FdrAnalysisEngine(allPsms, tempSearchMode.NumNotches, CommonParameters, this.FileSpecificParameters, new List<string> { taskId }, doPEP: false).Run();
             Dictionary<string, HashSet<Tuple<int, Modification>>> allModDictionary = new();
-            new GptmdEngine(allPsms, gptmdModifications, combos, filePathToPrecursorMassTolerance, CommonParameters, this.FileSpecificParameters, new List<string> { taskId }, allModDictionary).Run();
+            new GptmdEngine(allPsms, gptmdModifications, combos, filePathToPrecursorMassTolerance, CommonParameters, this.FileSpecificParameters, new List<string> { taskId }, allModDictionary, GptmdParameters.GptmdFilters).Run();
 
             //Move this text after search because proteins don't get loaded until search begins.
             ProseCreatedWhileRunning.Append("The combined search database contained " + proteinList.Count(p => !p.IsDecoy) + $" non-decoy {GlobalVariables.AnalyteType.GetBioPolymerLabel().ToLower()} entries including " + proteinList.Where(p => p.IsContaminant).Count() + " contaminant sequences. ");

MetaMorpheus/TaskLayer/MetaMorpheusTask.cs

@@ -16,7 +16,6 @@
 using SpectralAveraging;
 using Omics;
 using Omics.Digestion;
-using Omics.Fragmentation.Peptide;
 using Omics.Modifications;
 using Omics.SpectrumMatch;
 using UsefulProteomicsDatabases;
@@ -25,8 +24,6 @@
 using Proteomics.ProteolyticDigestion;
 using Transcriptomics;
 using Transcriptomics.Digestion;
-using Easy.Common.Extensions;
-using Readers;
 
 namespace TaskLayer
 {
@@ -134,6 +131,24 @@ public abstract class MetaMorpheusTask
             .ConfigureType<OxyriboAveragine>(type => type
                 .WithConversionFor<TomlString>(convert => convert
                     .ToToml(custom => custom.GetType().Name)))
+            .ConfigureType<List<IGptmdFilter>>(type => type
+                .WithConversionFor<TomlString>(convert => convert
+                    .ToToml(filters => string.Join("\t", filters.Select(f => f.GetType().Name)))
+                    .FromToml(tmlString => tmlString.Value
+                        .Split('\t', StringSplitOptions.RemoveEmptyEntries)
+                        .Select(typeName =>
+                            // Find the type in the current AppDomain by name
+                            AppDomain.CurrentDomain.GetAssemblies()
+                                .SelectMany(a => a.GetTypes())
+                                .FirstOrDefault(t => t.Name == typeName && typeof(IGptmdFilter).IsAssignableFrom(t))
+                        )
+                        .Where(t => t != null)
+                        .Select(t => Activator.CreateInstance(t) as IGptmdFilter)
+                        .Where(f => f != null)
+                        .ToList()
+                    )
+                )
+            )
         );