MetaDraw Update - Data Loading Refactor, Chimera Tab, BioPolymer Tab

MetaMorpheus/EngineLayer/GlobalVariables.cs

@@ -70,7 +70,7 @@ public static class GlobalVariables
         public static void SetUpGlobalVariables()
         {
             AcceptedDatabaseFormats = new List<string> { ".fasta", ".fa", ".xml", ".msp" };
-            AcceptedSpectraFormats = new List<string> { ".raw", ".mzml", ".mgf", ".msalign" };
+            AcceptedSpectraFormats = new List<string> { ".raw", ".mzml", ".mgf", ".msalign", ".tdf", ".tdf_bin", ".d" };
             AnalyteType = AnalyteType.Peptide;
             _InvalidAminoAcids = new char[] { 'X', 'B', 'J', 'Z', ':', '|', ';', '[', ']', '{', '}', '(', ')', '+', '-' };
             ExperimentalDesignFileName = "ExperimentalDesign.tsv";

MetaMorpheus/GUI/App.xaml

@@ -9,7 +9,7 @@
         <SolidColorBrush x:Key="SideBarMainColor" Color="#353b48" />
         <SolidColorBrush x:Key="AccentColor" Color="#0097e6" />
         <SolidColorBrush x:Key="PurpleAccentColor" Color="#e6aeff" />
-        <SolidColorBrush x:Key="SecondaryButtonColor" Color="#2f3640" />
+        <SolidColorBrush x:Key="SecondaryButtonColor" Color="#504B59" />
         <SolidColorBrush x:Key="BackgroundColor" Color="#f5f6fa" />
         <SolidColorBrush x:Key="DataGridBackgroundColor" Color="#f5f6fa" />
         <SolidColorBrush x:Key="DataGridHeaderColor" Color="#dcdde1" />

MetaMorpheus/GUI/MainWindow.xaml.cs

@@ -301,7 +301,7 @@
             {
                 Dispatcher.BeginInvoke(new Action(() => NewoutLabelStatus(sender, s)));
             }
-            else
+            else if (InProgressTasks != null)
             {
                 // Find the task or the collection!!!
 
@@ -1080,7 +1080,7 @@
             }
         }
 
         private MetaMorpheusTask? _clipboard;
 
         /// <summary>
         /// Handles keyboard input.
@@ -1264,7 +1264,7 @@
 
         private void MenuItem_MetaDraw_Click(object sender, RoutedEventArgs e)
         {
             string[]? filesToLoad = null;
             try
             {
                 // get completed search tasks from in progress tasks. 
@@ -1279,11 +1279,11 @@
 
                 // Get search results
                 var searchResult = Directory.GetFiles(finalSearchTask.Task.OutputFolder)
-                    .First(p => p.EndsWith(".psmtsv") || p.EndsWith(".osmtsv"));
+                    .First(p => p.EndsWith("PSMs.psmtsv") || p.EndsWith("OSMs.osmtsv"));
 
                 filesToLoad = spectraFiles.Append(searchResult).ToArray();
             }
             catch (Exception ex)
             {
                 // Something went wrong in trying to find a completed search task. 
                 // This is expected when we do not have a completed search to parse. 

MetaMorpheus/GUI/MetaDraw/BioPolymerCoverageTabView.xaml

@@ -0,0 +1,164 @@
+<UserControl x:Class="MetaMorpheusGUI.BioPolymerCoverageTabView"
+             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"
+             xmlns:metaDraw="clr-namespace:GuiFunctions.MetaDraw;assembly=GuiFunctions"
+             mc:Ignorable="d" 
+             d:DataContext="{x:Static metaDraw:BioPolymerTabModel.Instance}"
+             d:DesignHeight="450" d:DesignWidth="800">
+    <DockPanel>
+        <Grid>
+            <Grid.ColumnDefinitions>
+                <ColumnDefinition Width="1*" />
+                <ColumnDefinition Width="Auto" />
+                <ColumnDefinition Width="3*" />
+            </Grid.ColumnDefinitions>
+
+            <!-- Left Side -->
+            <Grid Grid.Column="0">
+                <Grid.RowDefinitions>
+                    <RowDefinition Height="Auto"/>
+                    <RowDefinition Height="Auto"/>
+                    <RowDefinition Height="Auto"/>
+                    <RowDefinition Height="Auto"/>
+                    <RowDefinition Height="2*"/>
+                    <RowDefinition Height="25"/>
+                </Grid.RowDefinitions>
+
+                <!--Select database file-->
+                <DockPanel Grid.Row="0" LastChildFill="True" Grid.ColumnSpan="3" Margin="5 2">
+                    <Label Content="Database File: " Width="95" />
+
+                    <Button Content="Reset" HorizontalAlignment="Right" DockPanel.Dock="Right"
+                        VerticalAlignment="Center" Width="40" Height="26"
+                        IsEnabled="{Binding DatabasePath,  Converter={local:StringIsNotNullOrEmptyToBoolConverter}}"
+                        Command="{Binding ResetDatabaseCommand}" />
+
+                    <Button Name="SelectDatabaseButton"  Content="Select" HorizontalAlignment="Right" DockPanel.Dock="Right"
+                        VerticalAlignment="Center" Width="40" Height="26" Margin="5 0"
+                        IsEnabled="{Binding DatabasePath, Converter={local:StringIsNullOrEmptyToBoolConverter}}"
+                        Click="SelectDatabaseButton_OnClick" />
+
+                    <Label BorderThickness="1">
+                        <TextBlock TextTrimming="CharacterEllipsis">
+                            <TextBlock.Text>
+                                <Binding Path="DatabaseName" FallbackValue="None Selected" />
+                            </TextBlock.Text>
+                        </TextBlock>
+                    </Label>
+                </DockPanel>
+
+                <DockPanel Grid.Row ="1" Margin =" 5 2">
+                    <Label Content="Color By:" DockPanel.Dock="Left" />
+                    <ComboBox Width="120" Margin="5 0" DockPanel.Dock="Left" HorizontalAlignment="Left"
+                              SelectedValue="{Binding CoverageMapViewModel.ColorBy}" 
+                              ItemsSource="{Binding CoverageMapViewModel.AllColorByTypes}" />
+                </DockPanel>
+
+
+
+                <!-- Load Button and Search Bar -->
+                <Border Grid.Row="2" Grid.ColumnSpan="3" BorderBrush="Black" 
+                    BorderThickness="0,0,0,1" Margin="5 2" >
+                    <DockPanel  LastChildFill="True" Margin="0 0 0 2">
+                        <Button Name="LoadDatabase" Content="Load Files" Width="80" 
+                                Command="{Binding LoadDatabaseCommand}"/>
+
+                        <TextBox Width="140"  DockPanel.Dock="Right" VerticalContentAlignment="Center"
+                                 Text="{Binding SearchText, UpdateSourceTrigger=PropertyChanged}" />
+                        <Label HorizontalAlignment="Right" Height="28">Search</Label>
+                    </DockPanel>
+                </Border>
+
+                <!-- Data Table -->
+                <GroupBox Header="BioPolymer Groups" Grid.Row="4" Margin="0 2">
+                    <Grid>
+                        <Grid.RowDefinitions>
+                            <RowDefinition Height="1*"/>
+                        </Grid.RowDefinitions>
+
+                        <DataGrid x:Name="biopolymerDataGrid" Grid.Row="0" AutoGenerateColumns="False" VerticalAlignment="Stretch" ScrollViewer.CanContentScroll="True" IsReadOnly="True" 
+                              CanUserDeleteRows="false" CanUserAddRows="false" SelectionMode="Single"
+                              SelectionChanged="BioPolymerDataGrid_OnSelectionChanged"
+                              ItemsSource="{Binding FilteredGroups}" 
+                              SelectedItem="{Binding SelectedGroup}">
+                            <DataGrid.Columns>
+                                <DataGridTextColumn Header="Accession" Binding="{Binding Accession}" Width="90" 
+                                                ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                                <DataGridTextColumn Header="Unique Cov" Binding="{Binding UniqueSequenceCoverage, StringFormat={}{0:F2}}" Width="60" 
+                                                    ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                                <DataGridTextColumn Header="Max Cov" Binding="{Binding MaximumSequenceCoverage, StringFormat={}{0:F2}}" Width="60" 
+                                                    ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                                <DataGridTextColumn Header="Name" Binding="{Binding ProteinName}" Width="90" 
+                                                    ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                                <DataGridTextColumn Header="Count" Binding="{Binding GroupCount}" Width="70" 
+                                                ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                                <DataGridTextColumn Header="Length" Binding="{Binding Length}" Width="52" 
+                                                ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                            </DataGrid.Columns>
+                        </DataGrid>
+                    </Grid>
+                </GroupBox>
+
+                <!-- Loading overlay -->
+                <Grid x:Name="LoadOverlay" Grid.Row="4" Margin="2 16 2 4"
+                      Visibility="{Binding IsLoading, Converter={local:BooleanToVisibilityConverter}}"
+
+                      Background="#80000000"
+                      Panel.ZIndex="100">
+                    <StackPanel VerticalAlignment="Center" HorizontalAlignment="Center">
+                        <ProgressBar IsIndeterminate="True" Width="120" Height="18" Margin="0,0,0,8"/>
+                        <TextBlock Text="Loading..." Foreground="White" FontWeight="Bold" FontSize="16" HorizontalAlignment="Center"/>
+                    </StackPanel>
+                </Grid>
+
+                <!-- Export -->
+                <DockPanel Grid.Row="5" LastChildFill="True"  HorizontalAlignment="Center">
+                    <Label Content="Export As: "  DockPanel.Dock="Left"/>
+                    <Button Name="ExportBioPolymerCoverage" Width="40" HorizontalAlignment="Left"
+                            Style="{StaticResource MetaDrawButtonStyle}"
+                            Content="{Binding ExportType, Source={x:Static guiFunctions:MetaDrawSettingsViewModel.Instance}}"
+                            Command="{Binding ExportImageCommand}"/>
+                </DockPanel>
+            </Grid>
+
+            <!--Moveable splitter-->
+            <GridSplitter Grid.Column="1" 
+                      HorizontalAlignment="Center"
+                      VerticalAlignment="Stretch"
+                      Background="Silver"
+                      Width="3"/>
+
+            <!-- Right side -->
+            <Grid Grid.Column="2" Name="BioPolymerAnnotationGrid" Style="{StaticResource InternalGridStyle}">
+                <Grid.RowDefinitions>
+                    <RowDefinition Height="Auto" />
+                    <RowDefinition Height="4*" />
+                    <RowDefinition Height="Auto" MaxHeight="300" />
+                </Grid.RowDefinitions>
+
+                <local:SettingsButtonControl Grid.Row="0" Height="52" x:Name="SettingsButton"
+                                                 HorizontalAlignment="Left" VerticalAlignment="Top"
+                                                 Panel.ZIndex="1" SelectedTabIndex="4" />
+                <!-- BioPolymer coverage display -->
+                <ScrollViewer Grid.Row="1" Name="BioPolymerCoverageHorizontalScroll" Width="Auto" 
+                              CanContentScroll="True" VerticalScrollBarVisibility="Auto" Margin="0 10 ">
+                    <local:BioPolymerCoverageMapView DataContext="{Binding CoverageMapViewModel}" />
+                </ScrollViewer>
+
+                <!-- Individual Results -->
+                <Expander Grid.Row="2" Header="Individual Results">
+                    <DataGrid ScrollViewer.CanContentScroll="True" IsReadOnly="True" 
+                              CanUserDeleteRows="false" CanUserAddRows="false" SelectionMode="Single"
+                              SelectionChanged="BioPolymerDataGrid_OnSelectionChanged"
+                              ItemsSource="{Binding SelectedGroup.CoverageResults}" >
+
+                    </DataGrid>
+                </Expander>
+            </Grid>
+        </Grid>
+    </DockPanel>
+</UserControl>

MetaMorpheus/GUI/MetaDraw/BioPolymerCoverageTabView.xaml.cs

@@ -0,0 +1,55 @@
+using System.Linq;
+using EngineLayer;
+using System.Windows;
+using System.Windows.Controls;
+using GuiFunctions.MetaDraw;
+
+namespace MetaMorpheusGUI;
+
+/// <summary>
+/// Interaction logic for BioPolymerCoverageTabView.xaml
+/// </summary>
+public partial class BioPolymerCoverageTabView : UserControl
+{
+    public BioPolymerCoverageTabView()
+    {
+        InitializeComponent();
+    }
+
+    private void SelectDatabaseButton_OnClick(object sender, RoutedEventArgs e)
+    {
+        var dataContext = DataContext as BioPolymerTabViewModel;
+        if (sender == null || dataContext == null)
+        {
+            return;
+        }
+
+        string filterString = string.Join(";", GlobalVariables.AcceptedDatabaseFormats.Select(p => "*" + p));
+
+        Microsoft.Win32.OpenFileDialog openFileDialog1 = new Microsoft.Win32.OpenFileDialog
+        {
+            Filter = "Database Files(" + filterString + ")|" + filterString,
+            FilterIndex = 1,
+            RestoreDirectory = true,
+            Multiselect = false
+        };
+
+        if (openFileDialog1.ShowDialog() == true)
+        {
+            var toAdd = openFileDialog1.FileName;
+            if (GlobalVariables.AcceptedDatabaseFormats.Contains(GlobalVariables.GetFileExtension(toAdd).ToLowerInvariant()))
+            {
+                dataContext.DatabasePath = toAdd;
+            }
+            else
+            {
+                MessageBox.Show("Cannot read file type: " + GlobalVariables.GetFileExtension(toAdd).ToLowerInvariant());
+            }
+        }
+    }
+
+    private void BioPolymerDataGrid_OnSelectionChanged(object sender, SelectionChangedEventArgs e)
+    {
+        //throw new System.NotImplementedException();
+    }
+}

MetaMorpheus/GUI/MetaDraw/ChimeraAnalysisTabView.xaml.cs

@@ -105,11 +105,11 @@ private void AttachLegendCanvasEvents()
             if (legendCanvas != null)
             {
                 ChimeraLegend.Children.Add(dataContext?.LegendCanvas);
-
+                legendCanvas.UpdateLayout();
                 double parentWidth = ChimeraLegend.ActualWidth;
                 double parentHeight = ChimeraLegend.ActualHeight;
-                double legendWidth = legendCanvas.Width;
-                double legendHeight = legendCanvas.Height;
+                double legendWidth = legendCanvas.ActualWidth;
+                double legendHeight = legendCanvas.ActualHeight;
 
                 // Check if previous position is valid and within bounds
                 bool validLeft = !double.IsNaN(lastLeft) && lastLeft >= 0 && lastLeft + legendWidth <= parentWidth;