Implement Raw Spectrum Overlay

src/Common/ChartDrawing/Chart/LineSpectrumControlSlim.cs

@@ -250,7 +250,7 @@ private static void OnLineBrushPropertyChanged(DependencyObject d, DependencyPro
 
         [System.Diagnostics.CodeAnalysis.SuppressMessage("Style", "IDE0060:Remove unused parameter", Justification = "<Pending>")]
         private void OnLineBrushPropertyChanged(IBrushMapper oldValue, IBrushMapper newValue) {
-            Selector.Update(newValue, LineThickness);
+            Selector.Update(newValue, LineThickness, StrokeDashArray);
         }
 
         public static readonly DependencyProperty HuePropertyProperty =
@@ -310,15 +310,40 @@ private static void OnLineThicknessChanged(DependencyObject d, DependencyPropert
 
         [System.Diagnostics.CodeAnalysis.SuppressMessage("Style", "IDE0060:Remove unused parameter", Justification = "<Pending>")]
         private void OnLineThicknessChanged(double oldValue, double newValue) {
-            Selector.Update(LineBrush, newValue);
+            Selector.Update(LineBrush, newValue, StrokeDashArray);
+        }
+
+        public static readonly DependencyProperty StrokeDashArrayProperty =
+            DependencyProperty.Register(
+                nameof(StrokeDashArray),
+                typeof(DoubleCollection),
+                typeof(LineSpectrumControlSlim),
+                new FrameworkPropertyMetadata(
+                    null,
+                    FrameworkPropertyMetadataOptions.AffectsRender,
+                    OnStrokeDashArrayChanged));
+
+        public DoubleCollection StrokeDashArray {
+            get => (DoubleCollection)GetValue(StrokeDashArrayProperty);
+            set => SetValue(StrokeDashArrayProperty, value);
+        }
+
+        private static void OnStrokeDashArrayChanged(DependencyObject d, DependencyPropertyChangedEventArgs e) {
+            var c = (LineSpectrumControlSlim)d;
+            c.OnStrokeDashArrayChanged((DoubleCollection)e.OldValue, (DoubleCollection)e.NewValue);
+        }
+
+        [System.Diagnostics.CodeAnalysis.SuppressMessage("Style", "IDE0060:Remove unused parameter", Justification = "<Pending>")]
+        private void OnStrokeDashArrayChanged(DoubleCollection oldValue, DoubleCollection newValue) {
+            Selector.Update(LineBrush, LineThickness, newValue);
         }
 
         private PenSelector Selector {
             get {
                 if (selector is null) {
                     selector = new PenSelector();
                     if (!(LineBrush is null)) {
-                        selector.Update(LineBrush, LineThickness);
+                        selector.Update(LineBrush, LineThickness, StrokeDashArray);
                     }
                 }
                 return selector;

src/Common/ChartDrawing/Design/PenSelector.cs

@@ -1,4 +1,5 @@
 using System.Collections.Generic;
+using System.Linq;
 using System.Windows.Media;
 using CompMs.Graphics.Base;
 
@@ -31,11 +32,15 @@ public void Update(Pen pen) {
         }
 
         public void Update(IBrushMapper mapper, double thickness) {
+            Update(mapper, thickness, null);
+        }
+
+        public void Update(IBrushMapper mapper, double thickness, DoubleCollection strokeDashArray) {
             if (mapper is null) {
                 Reset();
             }
             else {
-                strategy = new BrushMapStrategy(mapper, thickness);
+                strategy = new BrushMapStrategy(mapper, thickness, strokeDashArray);
             }
         }
 
@@ -62,13 +67,15 @@ public Pen Get(object o) {
 
         class BrushMapStrategy : ISelectStrategy
         {
-            public BrushMapStrategy(IBrushMapper mapper, double thickness) {
+            public BrushMapStrategy(IBrushMapper mapper, double thickness, DoubleCollection strokeDashArray) {
                 Mapper = mapper;
                 Thickness = thickness;
+                StrokeDashArray = strokeDashArray?.ToArray();
             }
 
             private readonly IBrushMapper Mapper;
             private readonly double Thickness;
+            private readonly double[] StrokeDashArray;
             private readonly Dictionary<object, Pen> cache = new Dictionary<object, Pen>();
 
             public Pen Get(object o) {
@@ -77,6 +84,9 @@ public Pen Get(object o) {
                 }
                 var brush = Mapper.Map(o);
                 var pen = new Pen(brush, Thickness);
+                if (StrokeDashArray is { Length: > 0 }) {
+                    pen.DashStyle = new DashStyle(new DoubleCollection(StrokeDashArray), 0d);
+                }
                 pen.Freeze();
                 if (cache.Count > 1_000_000) {
                     cache.Clear();

src/MSDIAL5/MsdialGuiApp/Model/Chart/RawDecSpectrumsModel.cs

@@ -1,8 +1,11 @@
 using CompMs.App.Msdial.Model.Loader;
 using CompMs.Common.Algorithm.Scoring;
 using CompMs.CommonMVVM;
+using CompMs.Graphics.Design;
+using Reactive.Bindings;
 using Reactive.Bindings.Extensions;
 using System;
+using System.Windows.Media;
 
 namespace CompMs.App.Msdial.Model.Chart
 {
@@ -37,17 +40,37 @@ public RawDecSpectrumsModel(SingleSpectrumModel rawSpectrumModel, SingleSpectrum
                 HorizontalTitle = "m/z",
                 VerticalTitle = "Relative abundance",
             }.AddTo(Disposables);
+
+            IsRawSpectrumOverlayVisible = new ReactivePropertySlim<bool>(true).AddTo(Disposables);
+
+
+            var decRawOverlaySpectrumModel = rawSpectrumModel.Clone().AddTo(Disposables);
+            decRawOverlaySpectrumModel.IsVisible.Value = false;
+            decRawOverlaySpectrumModel.IsAnnotationVisible.Value = false;
+            decRawOverlaySpectrumModel.LineThickness.Value = 1d;
+            decRawOverlaySpectrumModel.StrokeDashArray.Value = new DoubleCollection { 3d, 3d };
+            decRawOverlaySpectrumModel.Brush = new ConstantBrushMapper<object>(Brushes.DarkGray);
+
             DecRefSpectrumModels = new MsSpectrumModel(decSpectrumModel, referenceSpectrumModel, ms2ScanMatching)
             {
                 GraphTitle =  "Deconvolution vs. Reference",
                 HorizontalTitle = "m/z",
-                VerticalTitle = "Relative abundacne",
+                VerticalTitle = "Relative abundance",
             }.AddTo(Disposables);
+            DecRefSpectrumModels.UpperSpectraModel.Insert(0, decRawOverlaySpectrumModel);
+
+            IsRawSpectrumOverlayVisible
+                .Subscribe(isVisible => {
+                    decRawOverlaySpectrumModel.IsVisible.Value = isVisible;
+                })
+                .AddTo(Disposables);
+
             RawLoader = loader;
         }
 
         public MsSpectrumModel RawRefSpectrumModels { get; }
         public MsSpectrumModel DecRefSpectrumModels { get; }
+        public ReactivePropertySlim<bool> IsRawSpectrumOverlayVisible { get; }
         public MultiMsmsRawSpectrumLoader? RawLoader { get; }
     }
 }

src/MSDIAL5/MsdialGuiApp/Model/Chart/SingleSpectrumModel.cs

@@ -9,6 +9,7 @@
 using System.IO;
 using System.Linq;
 using System.Reactive.Linq;
+using System.Windows.Media;
 
 namespace CompMs.App.Msdial.Model.Chart
 {
@@ -24,10 +25,13 @@ public SingleSpectrumModel(ObservableMsSpectrum observableMsSpectrum, AxisProper
             HorizontalProperty = HorizontalPropertySelectors.GetSelector(typeof(SpectrumPeak))?.Property ?? throw new Exception("Valid PropertySelector is not found.");
             VerticalProperty = VerticalPropertySelectors.GetSelector(typeof(SpectrumPeak))?.Property ?? throw new Exception("Valid PropertySelector is not found.");
             _hueItem = hueItem;
+            Brush = hueItem.Brush;
             Labels = graphLabels;
 
             IsVisible = new ReactivePropertySlim<bool>(true).AddTo(Disposables);
+            IsAnnotationVisible = new ReactivePropertySlim<bool>(true).AddTo(Disposables);
             LineThickness = new ReactivePropertySlim<double>(2d).AddTo(Disposables);
+            StrokeDashArray = new ReactivePropertySlim<DoubleCollection?>(null).AddTo(Disposables);
         }
 
         public IObservable<MsSpectrum?> MsSpectrum => _observableMsSpectrum.MsSpectrum;
@@ -38,12 +42,14 @@ public SingleSpectrumModel(ObservableMsSpectrum observableMsSpectrum, AxisProper
         public IObservable<IAxisManager<double>> VerticalAxis => VerticalPropertySelectors.AxisItemSelector.GetAxisItemAsObservable().SkipNull().Select(item => item.AxisManager);
         public AxisItemSelector<double> VerticalAxisItemSelector => VerticalPropertySelectors.AxisItemSelector;
         public string VerticalProperty { get; }
-        public IBrushMapper Brush => _hueItem.Brush;
+        public IBrushMapper Brush { get; set; }
         public string HueProperty => _hueItem.Property;
         public GraphLabels Labels { get; }
         public ReadOnlyReactivePropertySlim<bool> SpectrumLoaded => _observableMsSpectrum.Loaded;
         public ReactivePropertySlim<bool> IsVisible { get; }
+        public ReactivePropertySlim<bool> IsAnnotationVisible { get; }
         public ReactivePropertySlim<double> LineThickness { get; }
+        public ReactivePropertySlim<DoubleCollection?> StrokeDashArray { get; }
 
         public IObservable<bool> CanSave => _observableMsSpectrum.CanSave;
 
@@ -81,5 +87,9 @@ private SingleSpectrumModel CreateFromMsSpectrum(ObservableMsSpectrum msSpectrum
             spectrumModel.Disposables.Add(msSpectrum);
             return spectrumModel;
         }
+
+        public SingleSpectrumModel Clone() {
+            return new SingleSpectrumModel(_observableMsSpectrum, HorizontalPropertySelectors, VerticalPropertySelectors, _hueItem, Labels);
+        }
     }
 }

src/MSDIAL5/MsdialGuiApp/View/Chart/ExpRefView.xaml

@@ -56,6 +56,12 @@
                          ToolTip="Show deconvoluted spectra vs. reference spectra"
                          Style="{StaticResource IconRadioButton}"/>
 
+            <CheckBox VerticalAlignment="Center"
+                      Margin="8,0,0,0"
+                      Content="Raw (dashed)"
+                      ToolTip="Overlay raw spectrum as dashed line on Q1Dec/Deconvolution views"
+                      IsChecked="{Binding RawDecSpectrumsViewModel.IsRawSpectrumOverlayVisible.Value, Mode=TwoWay}"/>
+
             <Button Name="Button_CompoundSearchPeakViewer"
                     Command="{Binding SearchCompoundCommand, Mode=OneTime}"
                     Content="/Resources/CompoundSearchIcon.ico"

src/MSDIAL5/MsdialGuiApp/View/Chart/MsSpectrumView.xaml

@@ -141,6 +141,7 @@
                                                            VerticalProperty="{Binding VerticalProperty}"
                                                            LineBrush="{Binding Brush.Value}"
                                                            LineThickness="{Binding LineThickness.Value}"
+                                                           StrokeDashArray="{Binding StrokeDashArray.Value}"
                                                            HueProperty="SpectrumComment">
                                 <chart:LineSpectrumControlSlim.ToolTip>
                                     <ToolTip DataContext="{Binding PlacementTarget, RelativeSource={RelativeSource Self}}"
@@ -162,7 +163,8 @@
                                              Brush="Black"
                                              Overlap="Horizontal, Direct"
                                              Format="F4"
-                                             ClipToBounds="True"/>
+                                             ClipToBounds="True"
+                                             Visibility="{Binding IsAnnotationVisible.Value, Converter={StaticResource BooleanToVisibility}}"/>
                         </Grid>
                     </DataTemplate>
                 </ItemsControl.ItemTemplate>
@@ -190,6 +192,7 @@
                                                HorizontalProperty="{Binding HorizontalProperty}"
                                                VerticalProperty="{Binding VerticalProperty}"
                                                LineBrush="{Binding Brush.Value}"
+                                               StrokeDashArray="{Binding StrokeDashArray.Value}"
                                                HueProperty="SpectrumComment">
                     <chart:LineSpectrumControlSlim.ToolTip>
                         <ToolTip DataContext="{Binding PlacementTarget, RelativeSource={RelativeSource Self}}"

src/MSDIAL5/MsdialGuiApp/ViewModel/Chart/RawDecSpectrumsViewModel.cs

@@ -34,6 +34,7 @@ public RawDecSpectrumsViewModel(RawDecSpectrumsModel model, Action focusAction,
 
         public MsSpectrumViewModel RawRefSpectrumViewModels { get; }
         public MsSpectrumViewModel DecRefSpectrumViewModels { get; }
+        public ReactivePropertySlim<bool> IsRawSpectrumOverlayVisible => _model.IsRawSpectrumOverlayVisible;
 
         public ReadOnlyReactivePropertySlim<List<MsSelectionItem>> Ms2IdList { get; }
         public ReactivePropertySlim<MsSelectionItem?> SelectedMs2Id { get; }

src/MSDIAL5/MsdialGuiApp/ViewModel/Chart/SingleSpectrumViewModel.cs

@@ -12,6 +12,7 @@
 using System.IO;
 using System.Linq;
 using System.Reactive.Linq;
+using System.Windows.Media;
 
 namespace CompMs.App.Msdial.ViewModel.Chart
 {
@@ -26,7 +27,9 @@ public SingleSpectrumViewModel(SingleSpectrumModel model, IMessageBroker? broker
             VerticalAxis = model.VerticalAxis.Cast<IAxisManager>().ToReadOnlyReactivePropertySlim().AddTo(Disposables);
             Brush = Observable.Return(model.Brush).ToReadOnlyReactivePropertySlim<IBrushMapper>().AddTo(Disposables);
             LineThickness = model.LineThickness;
+            StrokeDashArray = model.StrokeDashArray;
             IsVisible = model.IsVisible;
+            IsAnnotationVisible = model.IsAnnotationVisible;
             SelectedVerticalAxisItem = model.VerticalAxisItemSelector.GetAxisItemAsObservable().SkipNull().ToReadOnlyReactivePropertySlim().AddTo(Disposables);
             if (broker is not null) {
                 SaveCommand = model.CanSave.ToReactiveCommand().WithSubscribe(SaveSpectrum(model.Save, filter:  "NIST format(*.msp)|*.msp", broker)).AddTo(Disposables);
@@ -46,7 +49,9 @@ public SingleSpectrumViewModel(SingleSpectrumModel model, IMessageBroker? broker
         public string HueProperty => _model.HueProperty;
         public ReadOnlyReactivePropertySlim<bool> SpectrumLoaded => _model.SpectrumLoaded;
         public ReactivePropertySlim<double> LineThickness { get; }
+        public ReactivePropertySlim<DoubleCollection?> StrokeDashArray { get; }
         public ReactivePropertySlim<bool> IsVisible { get; }
+        public ReactivePropertySlim<bool> IsAnnotationVisible { get; }
         public ReactiveCommand? SaveCommand { get; }
 
         private Action SaveSpectrum(Action<Stream> handler, string filter, IMessageBroker broker) {