Mirror

.omo/run-continuation/ses_11f53df9effeMffN1QwBnnQeDL.json

@@ -0,0 +1,10 @@
+{
+  "sessionID": "ses_11f53df9effeMffN1QwBnnQeDL",
+  "updatedAt": "2026-06-19T16:47:34.897Z",
+  "sources": {
+    "background-task": {
+      "state": "idle",
+      "updatedAt": "2026-06-19T16:47:34.897Z"
+    }
+  }
+}

MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml

@@ -1,4 +1,4 @@
-<Window x:Class="MetaMorpheusGUI.MetaDraw"
+<Window x:Class="MetaMorpheusGUI.MetaDraw"
         x:Name="MetaDrawWindow"
         xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
         xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
@@ -704,6 +704,13 @@
                 <local:ChimeraAnalysisTabView x:Name="ChimeraAnalysisTabView" />
             </TabItem>
 
+            <!-- Mirror Plot tab -->
+            <TabItem Header="{Binding TabHeader}" IsEnabled="{Binding IsTabEnabled}" Background="DarkGray"
+                     d:DataContext="{d:DesignInstance metaDraw:MirrorPlotTabViewModel, IsDesignTimeCreatable=True}"
+                     DataContext="{Binding MirrorPlotTabViewModel, RelativeSource={RelativeSource AncestorType=Window}}">
+                <local:MirrorPlotTabView x:Name="MirrorPlotTabView" />
+            </TabItem>
+
             <!--Deconvolution Exploration tab-->
             <TabItem Header="{Binding TabHeader}" IsEnabled="{Binding IsTabEnabled}" Background="DarkGray"
                      d:DataContext="{d:DesignInstance guiFunctions:DeconExplorationTabViewModel, IsDesignTimeCreatable=True}"

MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs

@@ -44,6 +44,7 @@ public partial class MetaDraw : Window
         private static List<string> AcceptedSpectralLibraryFormats = new List<string> { ".msp" };
         private FragmentationReanalysisViewModel FragmentationReanalysisViewModel;
         public ChimeraAnalysisTabViewModel ChimeraAnalysisTabViewModel { get; set; }
+        public MirrorPlotTabViewModel MirrorPlotTabViewModel { get; set; }
         public DeconExplorationTabViewModel DeconExplorationViewModel { get; set; }
         public BioPolymerTabViewModel BioPolymerTabViewModel { get; set; }
 
@@ -61,6 +62,7 @@ public MetaDraw(string[]? filesToLoad = null)
 
             BioPolymerTabViewModel = new BioPolymerTabViewModel(MetaDrawLogic);
             ChimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel();
+            MirrorPlotTabViewModel = new MirrorPlotTabViewModel();
             DeconExplorationViewModel = new DeconExplorationTabViewModel(MetaDrawLogic);
 
             propertyView = new DataTable();
@@ -305,25 +307,37 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
             double maxDisplayedPerRow = (int)Math.Round((UpperSequenceAnnotaiton.ActualWidth - 10) / MetaDrawSettings.AnnotatedSequenceTextSpacing, 0) + 7;
             MetaDrawSettings.SequenceAnnotationSegmentPerRow = (int)Math.Floor(maxDisplayedPerRow / (double)(MetaDrawSettings.SequenceAnnotaitonResiduesPerSegment + 1));
 
-            // draw the annotated spectrum
-            MetaDrawLogic.DisplaySequences(stationarySequenceCanvas, scrollableSequenceCanvas, sequenceAnnotationCanvas, psm);
-            MetaDrawLogic.DisplaySpectrumMatch(plotView, psm, itemsControlSampleViewModel, out var errors);
-
-            // add ptm legend if desired
-            if (MetaDrawSettings.ShowLegend)
+            List<string> errors = null;
+            try
             {
-                int descriptionLineCount = MetaDrawSettings.SpectrumDescription.Count(p => p.Value);
-                if (psm.Name.IsNotNullOrEmptyOrWhiteSpace())
+                // draw the annotated spectrum
+                MetaDrawLogic.DisplaySequences(stationarySequenceCanvas, scrollableSequenceCanvas,
+                    sequenceAnnotationCanvas, psm);
+                MetaDrawLogic.DisplaySpectrumMatch(plotView, psm, itemsControlSampleViewModel, out errors);
+
+                // add ptm legend if desired
+                if (MetaDrawSettings.ShowLegend)
                 {
-                    descriptionLineCount += (int)Math.Floor((psm.Name.Length - 20) / (double)SpectrumMatchPlot.MaxCharactersPerDescriptionLine);
+                    int descriptionLineCount = MetaDrawSettings.SpectrumDescription.Count(p => p.Value);
+                    if (psm.Name.IsNotNullOrEmptyOrWhiteSpace())
+                    {
+                        descriptionLineCount += (int)Math.Floor((psm.Name.Length - 20) /
+                                                                (double)SpectrumMatchPlot
+                                                                    .MaxCharactersPerDescriptionLine);
+                    }
+
+                    if (psm.Accession.Length > 10)
+                        descriptionLineCount++;
+                    double verticalOffset = descriptionLineCount * 1.7 * MetaDrawSettings.SpectrumDescriptionFontSize;
+
+                    PtmLegend = new PtmLegendViewModel(psm, verticalOffset);
+                    ChildScanPtmLegendControl.DataContext = PtmLegend;
+                    SequenceCoveragePtmLegendControl.DataContext = PtmLegend;
                 }
-                if (psm.Accession.Length > 10)
-                    descriptionLineCount++;
-                double verticalOffset = descriptionLineCount * 1.4 * MetaDrawSettings.SpectrumDescriptionFontSize;
-
-                PtmLegend = new PtmLegendViewModel(psm, verticalOffset);
-                ChildScanPtmLegendControl.DataContext = PtmLegend;
-                SequenceCoveragePtmLegendControl.DataContext = PtmLegend;
+            }
+            catch (Exception ex)
+            {
+                MessageBox.Show("Error drawing spectrum and sequence: " + ex.Message);
             }
 
             //draw the sequence coverage if not crosslinked
@@ -498,6 +512,7 @@ private void RefreshPlotsAfterSettingsChange(object sender, MetaDrawSettingsChan
             {
                 MetaDrawLogic.FilterPsms();
                 ChimeraAnalysisTabViewModel.ProcessChimeraData(MetaDrawLogic.FilteredListOfPsms.ToList(), MetaDrawLogic.MsDataFiles);
+                MirrorPlotTabViewModel.ProcessMirrorData(MetaDrawLogic.FilteredListOfPsms.ToList(), MetaDrawLogic.MsDataFiles);
 
                 foreach (var group in BioPolymerTabViewModel.AllGroups)
                 {
@@ -522,6 +537,11 @@ private void RefreshPlotsAfterSettingsChange(object sender, MetaDrawSettingsChan
                 ChimeraAnalysisTabViewModel.ChimeraSpectrumMatchPlot = new ChimeraSpectrumMatchPlot(ChimeraAnalysisTabView.ms2ChimeraPlot, selectedChimeraGroup);
                 ChimeraAnalysisTabViewModel.ChimeraDrawnSequence = new ChimeraDrawnSequence(ChimeraAnalysisTabView.chimeraSequenceCanvas, selectedChimeraGroup, ChimeraAnalysisTabViewModel);
             }
+
+            if (MirrorPlotTabViewModel.SelectedLeftPsm != null && MirrorPlotTabViewModel.SelectedRightPsm != null)
+            {
+                MirrorPlotTabViewModel.RefreshPlot();
+            }
         }
 
         private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
@@ -554,6 +574,7 @@ private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
                 loadPsms: true,
                 loadLibraries: true,
                 chimeraTabViewModel: ChimeraAnalysisTabViewModel,
+                mirrorPlotTabViewModel: MirrorPlotTabViewModel,
                 bioPolymerTabViewModel: BioPolymerTabViewModel,
                 deconExplorationTabViewModel: DeconExplorationViewModel,
                 fragmentationReanalysisViewModel: FragmentationReanalysisViewModel);

MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml

@@ -6,7 +6,7 @@
         xmlns:local="clr-namespace:MetaMorpheusGUI" 
         xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
         mc:Ignorable="d"
-        Title="Graphical Settings" Width="620" SizeToContent="Height" WindowStartupLocation="CenterScreen"
+        Title="Graphical Settings" Width="640" SizeToContent="Height" WindowStartupLocation="CenterScreen"
         Height="500" MaxHeight="700"
         d:DataContext="{x:Static guiFunctions:MetaDrawSettingsViewModel.Instance}">
 
@@ -30,7 +30,7 @@
                 <!-- main settings content -->
                 <Grid >
                     <Grid.ColumnDefinitions>
-                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="*" />
                         <ColumnDefinition Width="Auto" />
                         <ColumnDefinition Width="*" />
                     </Grid.ColumnDefinitions>
@@ -99,7 +99,7 @@
                         HorizontalAlignment="Center"
                         Background="Transparent"
                         Width="2"
-                        Margin="20,0,0,0"/>
+                        Margin="5, 0"/>
 
                     <!-- right column -->
                     <ScrollViewer Grid.Column="2" HorizontalAlignment="Stretch">
@@ -146,8 +146,11 @@
                                     <CheckBox Name="SubSuperScriptedIonAnnotations"
                                               IsChecked="{Binding SubAndSuperScriptIons}"
                                               Content="Sub/superscripted ion annotations" Margin="5" />
+                                            <CheckBox Name="UseShortIonAnnotationsWhenPossible"
+                                              IsChecked="{Binding UseShortIonAnnotationsWhenPossible}"
+                                              Content="Use short ion names (bWaterLoss -> b-H2O)" Margin="5" />
 
-                                    <StackPanel Orientation="Horizontal" Margin="5 0">
+                                            <StackPanel Orientation="Horizontal" Margin="5 0">
                                         <Label Content="Annotation text size:" Width="165" />
                                         <local:IntegerTexBoxControl x:Name="TextSizeBox" Width="80" Height="24"
                                                                     Text="{Binding AnnotatedFontSize}"
@@ -204,19 +207,33 @@
                                         <local:DoubleTextBoxControl x:Name ="SpectrumDescriptionFontSizeBox" Width="80" Height="24" 
                                                                     VerticalContentAlignment="Center" HorizontalContentAlignment="Center" />
                                     </StackPanel>
-                                    <ItemsControl ItemsSource="{Binding SpectrumDescriptors}">
-                                        <ItemsControl.ItemTemplate>
-                                            <DataTemplate>
-                                                <CheckBox Margin="3"
-                                                          IsChecked="{Binding IsSelected, Mode=TwoWay}"
-                                                          Content="{Binding DisplayName}">
-                                                    <CheckBox.ToolTip>
-                                                        <TextBlock Text="{Binding DisplayName, Converter={StaticResource SpectrumDescriptorToolTipConverter}}"/>
-                                                    </CheckBox.ToolTip>
-                                                </CheckBox>
-                                            </DataTemplate>
-                                        </ItemsControl.ItemTemplate>
-                                    </ItemsControl>
+                                    <Grid Margin="0 3 0 0">
+                                        <ItemsControl Grid.Column="0" ItemsSource="{Binding SpectrumDescriptors}">
+                                            <ItemsControl.ItemTemplate>
+                                                <DataTemplate>
+                                                    <CheckBox Margin="3"
+                                                              IsChecked="{Binding IsSelected, Mode=TwoWay}"
+                                                              Content="{Binding DisplayName}">
+                                                        <CheckBox.ToolTip>
+                                                            <TextBlock Text="{Binding DisplayName, Converter={StaticResource SpectrumDescriptorToolTipConverter}}"/>
+                                                        </CheckBox.ToolTip>
+                                                    </CheckBox>
+                                                </DataTemplate>
+                                            </ItemsControl.ItemTemplate>
+                                        </ItemsControl>
+
+                                        <StackPanel Grid.Column="0" HorizontalAlignment="Right" VerticalAlignment="Top">
+                                            <Button Content="Select All"
+                                                    Width="90"
+                                                    Margin="0 0 0 5"
+                                                    Command="{Binding SelectAllSpectrumDescriptorsCommand}"
+                                                    Style="{StaticResource MetaDrawButtonStyle}"/>
+                                            <Button Content="Deselect All"
+                                                    Width="90"
+                                                    Command="{Binding DeselectAllSpectrumDescriptorsCommand}"
+                                                    Style="{StaticResource MetaDrawButtonStyle}"/>
+                                        </StackPanel>
+                                    </Grid>
                                 </StackPanel>
 
                             </Expander>