MetaDraw Fragmentation Reanalysis

MetaMorpheus/EngineLayer/PsmTsv/PsmFromTsv.cs

@@ -33,7 +33,7 @@ public class PsmFromTsv
         public double Score { get; }
         public string ProteinAccession { get; }
         public double? SpectralAngle { get; }
-        public List<MatchedFragmentIon> MatchedIons { get; }
+        public List<MatchedFragmentIon> MatchedIons { get; set; }
         public Dictionary<int, List<MatchedFragmentIon>> ChildScanMatchedIons { get; } // this is only used in crosslink for now, but in the future will be used for other experiment types
         public double QValue { get; }
 

MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml

@@ -208,7 +208,8 @@
                                     </TabItem.Header>
                                     <Grid Name="PsmAnnotationGrid">
                                         <Grid.RowDefinitions>
-                                            <RowDefinition/>
+                                            <RowDefinition Height="*"/>
+                                            <RowDefinition Height="Auto"/>
                                         </Grid.RowDefinitions>
 
                                         <!--Spectrum annotation-->
@@ -248,8 +249,16 @@
                                                 <!-- actual ptm legend -->
                                                 <local:PtmLegendControl x:Name="ChildScanPtmLegendControl"   DataContext="{Binding}" />
                                             </StackPanel>
-
                                         </Grid>
+
+                                        <!-- Refragment analysis -->
+                                        <Expander Grid.Row="1" VerticalAlignment="Bottom" IsExpanded="False" x:Name="AdditionalFragmentIonDisplay"
+                                                   DataContext="{x:Type guiFunctions:FragmentationReanalysisViewModel}" Header="Fragment Reanalysis">
+                                            <Expander.ToolTip>
+                                                Research the spectra file against the sequence with different fragment ions. 
+                                            </Expander.ToolTip>
+                                            <local:FragmentReanalysisControl x:Name="AdditionalFragmentIonControl" DataContext="{Binding }" />
+                                        </Expander>
                                     </Grid>
                                 </TabItem>
 

MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs

@@ -1,6 +1,7 @@
 using Easy.Common.Extensions;
 using EngineLayer;
 using GuiFunctions;
+using MassSpectrometry;
 using OxyPlot;
 using System;
 using System.Collections.Generic;
@@ -16,6 +17,7 @@
 using System.Windows;
 using System.Windows.Controls;
 using System.Windows.Data;
+using Omics.Fragmentation;
 
 namespace MetaMorpheusGUI
 {
@@ -36,6 +38,7 @@ public partial class MetaDraw : Window
         private static List<string> AcceptedResultsFormats = new List<string> { ".psmtsv", ".tsv" };
         private static List<string> AcceptedSpectralLibraryFormats = new List<string> { ".msp" };
         private MetaDrawSettingsViewModel SettingsView;
+        private FragmentationReanalysisViewModel FragmentationReanalysisViewModel;
 
         public MetaDraw()
         {
@@ -52,6 +55,8 @@ public MetaDraw()
 
             itemsControlSampleViewModel = new ParentChildScanPlotsView();
             ParentChildScanViewPlots.DataContext = itemsControlSampleViewModel;
+            AdditionalFragmentIonControl.DataContext = FragmentationReanalysisViewModel ??= new FragmentationReanalysisViewModel();
+            AdditionalFragmentIonControl.LinkMetaDraw(this);
 
             propertyView = new DataTable();
             propertyView.Columns.Add("Name", typeof(string));
@@ -60,6 +65,7 @@ public MetaDraw()
 
             dataGridScanNums.DataContext = MetaDrawLogic.PeptideSpectralMatchesView;
 
+
             Title = "MetaDraw: version " + GlobalVariables.MetaMorpheusVersion;
             base.Closing += this.OnClosing;
 
@@ -71,7 +77,7 @@ public MetaDraw()
             SetUpPlots();
             plotsListBox.ItemsSource = plotTypes;
 
-            exportPdfs.Content = MetaDrawSettings.ExportType; ;
+            exportPdfs.Content = MetaDrawSettings.ExportType;
         }
 
         private void Window_Drop(object sender, DragEventArgs e)
@@ -156,6 +162,9 @@ private void AddFile(string filePath)
 
         /// <summary>
         /// Event triggers when a different cell is selected in the PSM data grid
+        /// <remarks>
+        ///  if sender is FragmentationReanalysisViewModel, then this method was run by clicking the search button on the FragmentationReanalysisViewModel
+        /// </remarks>
         /// </summary>
         private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
         {
@@ -172,6 +181,13 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
             plotView.Visibility = Visibility.Visible;
             PsmFromTsv psm = (PsmFromTsv)dataGridScanNums.SelectedItem;
 
+            List<MatchedFragmentIon> oldMatchedIons = null;
+            if (FragmentationReanalysisViewModel.Persist && sender is DataGrid)
+            {
+                oldMatchedIons = psm.MatchedIons;
+                ReplaceFragmentIonsOnPsmFromFragmentReanalysisViewModel(psm);
+            }
+
             // Chimera plotter
             if (MetaDrawTabControl.SelectedContent is Grid { Name: "chimeraPlotGrid" })
             {
@@ -197,8 +213,19 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
             }
 
             SetSequenceDrawingPositionSettings(true);
+            // Psm selected from ambiguous dropdown => adjust the psm to be drawn
+            // Clicking the research button on an ambiguous psm => research with new ions
+            if (psm.FullSequence.Contains('|') && (sender.ToString() == "System.Object" || sender is FragmentationReanalysisViewModel))
+            {
+                psm = (PsmFromTsv)AmbiguousSequenceOptionBox.SelectedItem;
+                if (FragmentationReanalysisViewModel.Persist || sender is FragmentationReanalysisViewModel)
+                {
+                    oldMatchedIons = psm.MatchedIons;
+                    ReplaceFragmentIonsOnPsmFromFragmentReanalysisViewModel(psm);
+                }
+            }
             // Selection of ambiguous psm => clean up the canvases and show the option box
-            if (psm.FullSequence.Contains('|') && sender.ToString() != "System.Object")
+            else if(psm.FullSequence.Contains('|') && sender.ToString() != "System.Object")
             {
                 // clear all drawings of the previous non-ambiguous psm
                 ClearPresentationArea();
@@ -215,11 +242,7 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
                 }
                 return;
             }
-            // Psm selected from ambiguous dropdown => adjust the psm to be drawn
-            else if (psm.FullSequence.Contains('|') && sender.ToString() == "System.Object")
-            {
-                psm = (PsmFromTsv)AmbiguousSequenceOptionBox.SelectedItem;
-            }
+
             // Selection of non-ambiguous psm => clear items in the drop down
             else if (!psm.FullSequence.Contains('|'))
             {
@@ -307,6 +330,10 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
                     propertyView.Rows.Add(temp[i].Name, temp[i].GetValue(psm, null));
                 }
             }
+
+            // put the original ions back in place if they were altered
+            if (oldMatchedIons != null && !psm.MatchedIons.SequenceEqual(oldMatchedIons))
+                psm.MatchedIons = oldMatchedIons;
         }
 
         private void selectSpectraFileButton_Click(object sender, RoutedEventArgs e)
@@ -990,6 +1017,9 @@ private void MetaDrawTabControl_OnSelectionChanged(object sender, SelectionChang
         {
             PsmFromTsv selectedPsm = (PsmFromTsv)dataGridScanNums.SelectedItem;
 
+            if (e.OriginalSource is not TabControl) // only clicking on different MetaDrawTabs will trigger this event
+                return;
+
             // switch from chimera to other views
             if (e.RemovedItems.Count > 0 && ((TabItem)e.RemovedItems[0]).Name == "ChimeraScanPlot")
             {
@@ -1056,6 +1086,38 @@ private void ToggleButtonsEnabled(bool value)
             exportSpectrumLibrary.IsEnabled = value;
         }
 
-
+        /// <summary>
+        /// Method to fire the plotting method with new fragment ions
+        /// </summary>
+        /// <param name="sender"></param>
+        /// <param name="e"></param>
+        /// <exception cref="NotImplementedException"></exception>
+        internal void SearchWithNewIons_OnClick(object sender, RoutedEventArgs e)
+        {
+            // find currently selected psm
+            var psm = dataGridScanNums.SelectedItem as PsmFromTsv;
+            if (psm is null)
+                return;
+
+            // replace the ions and replot
+            var oldIons = psm.MatchedIons;
+            ReplaceFragmentIonsOnPsmFromFragmentReanalysisViewModel(psm);
+            dataGridScanNums.SelectedItem = psm;
+            dataGridScanNums_SelectedCellsChanged(FragmentationReanalysisViewModel, null);
+
+            // put the old ions back
+            psm.MatchedIons = oldIons;
+        }
+
+        /// <summary>
+        /// Replaces matched fragment ions on a psm with new ion types after a quick search
+        /// </summary>
+        /// <param name="psm"></param>
+        private void ReplaceFragmentIonsOnPsmFromFragmentReanalysisViewModel(PsmFromTsv psm)
+        {
+            var scan = MetaDrawLogic.GetMs2ScanFromPsm(psm);
+            var newIons = FragmentationReanalysisViewModel.MatchIonsWithNewTypes(scan, psm);
+            psm.MatchedIons = newIons;
+        }
     }
 }

MetaMorpheus/GUI/Views/FragmentReanalysisControl.xaml

@@ -0,0 +1,70 @@
+<UserControl x:Class="MetaMorpheusGUI.FragmentReanalysisControl"
+             xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
+             xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+             xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" 
+             xmlns:d="http://schemas.microsoft.com/expression/blend/2008" 
+             xmlns:local="clr-namespace:MetaMorpheusGUI"
+             xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
+             mc:Ignorable="d" 
+             d:DesignHeight="450" d:DesignWidth="800">
+    <Grid d:DataContext="{x:Type guiFunctions:FragmentationReanalysisViewModel}" >
+        <Grid.RowDefinitions>
+            <RowDefinition Height="Auto"/>
+            <RowDefinition Height="*"/>
+        </Grid.RowDefinitions>
+        <Grid.ColumnDefinitions>
+            <ColumnDefinition Width="*"/>
+        </Grid.ColumnDefinitions>
+
+        <!-- All options in the header -->
+        <Grid Grid.Row="0">
+            <Grid.RowDefinitions>
+                <RowDefinition Height="*"/>
+            </Grid.RowDefinitions>
+            <Grid.ColumnDefinitions>
+                <ColumnDefinition Width="Auto"/>
+                <ColumnDefinition Width="*"/>
+                <ColumnDefinition Width="*"/>
+                <ColumnDefinition Width="*"/>
+            </Grid.ColumnDefinitions>
+
+            <Button Grid.Row="0" Grid.Column="0" x:Name="SearchButton"  Grid.RowSpan="2" Content="Search"  VerticalAlignment="Center" Margin="5 3" 
+            VerticalContentAlignment="Center" Click="SearchWithNewIons_OnClick"/>
+            <CheckBox Grid.Row="0" Grid.Column="1" Grid.RowSpan="2" Content="Persist?" VerticalAlignment="Center" 
+              IsChecked="{Binding Persist}"
+              Margin="5 3" ToolTip="Research each identification as they are selected"/>
+
+            <StackPanel Grid.Row="0" Grid.Column="2" Orientation="Horizontal" VerticalAlignment="Center">
+                <TextBlock Text="Set Dissociation Type: " VerticalAlignment="Center"/>
+                <ComboBox x:Name="DissociationTypeComboBox" ItemsSource="{Binding DissociationTypes}" 
+                  SelectedItem="{Binding SelectedDissociationType}" 
+                  Margin="5 3" VerticalContentAlignment="Center" Width="80" />
+            </StackPanel>
+            <StackPanel Grid.Row="0" Grid.Column="3" Orientation="Horizontal" VerticalAlignment="Center">
+                <CheckBox Content="Use internal ions of minimum length " IsChecked="{Binding UseInternalIons}" 
+                  HorizontalContentAlignment="Right" VerticalAlignment="Center" />
+                <local:IntegerTexBoxControl Text="{Binding MinInternalIonLength, FallbackValue=10}" 
+            HorizontalAlignment="Center" HorizontalContentAlignment="Center"  IsEnabled="{Binding UseInternalIons}"
+            VerticalAlignment="Center" VerticalContentAlignment="Center" BorderThickness="1" />
+            </StackPanel>
+        </Grid>
+
+        <!-- Fragment ion type display -->
+        <ListView Grid.Row="1" Grid.Column="0" Background="{StaticResource BackgroundColor}"
+          ItemsSource="{Binding PossibleProducts}" BorderThickness="0">
+            <ListView.ItemTemplate>
+                <DataTemplate>
+                    <StackPanel Orientation="Horizontal">
+                        <CheckBox IsChecked="{Binding Use}" />
+                        <TextBlock Text="{Binding TypeString}"></TextBlock>
+                    </StackPanel>
+                </DataTemplate>
+            </ListView.ItemTemplate>
+            <ListView.ItemsPanel>
+                <ItemsPanelTemplate>
+                    <UniformGrid Columns="6"/>
+                </ItemsPanelTemplate>
+            </ListView.ItemsPanel>
+        </ListView>
+    </Grid>
+</UserControl>

MetaMorpheus/GUI/Views/FragmentReanalysisControl.xaml.cs

@@ -0,0 +1,39 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using System.Windows;
+using System.Windows.Controls;
+using System.Windows.Data;
+using System.Windows.Documents;
+using System.Windows.Input;
+using System.Windows.Media;
+using System.Windows.Media.Imaging;
+using System.Windows.Navigation;
+using System.Windows.Shapes;
+
+namespace MetaMorpheusGUI
+{
+    /// <summary>
+    /// Interaction logic for FragmentReanalysisControl.xaml
+    /// </summary>
+    public partial class FragmentReanalysisControl : UserControl
+    {
+        private MetaDraw parent;
+        public FragmentReanalysisControl()
+        {
+            InitializeComponent();
+        }
+
+        internal void LinkMetaDraw(MetaDraw metaDraw)
+        {
+            parent = metaDraw;
+        }
+
+        private void SearchWithNewIons_OnClick(object sender, RoutedEventArgs e)
+        {
+            parent.SearchWithNewIons_OnClick(sender, e);
+        }
+    }
+}

MetaMorpheus/GuiFunctions/MetaDraw/FragmentResearching/FragmentViewModel.cs

@@ -0,0 +1,23 @@
+using Omics.Fragmentation;
+
+namespace GuiFunctions
+{
+    public class FragmentViewModel : BaseViewModel
+    {
+        public ProductType ProductType { get; }
+        public string TypeString => ProductType.ToString();
+        private bool use;
+
+        public bool Use
+        {
+            get => use;
+            set { use = value; OnPropertyChanged(nameof(Use)); }
+        }
+
+        public FragmentViewModel(bool use, ProductType type)
+        {
+            Use = use;
+            ProductType = type;
+        }
+    }
+}