MetaDraw Bug Fix(es) and QOL Update

MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs

@@ -191,14 +191,16 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
             // Chimera plotter
             if (MetaDrawTabControl.SelectedContent is Grid { Name: "chimeraPlotGrid" })
             {
+                ClearPresentationArea();
+                chimeraPlot.Visibility = Visibility.Visible;
                 List<PsmFromTsv> chimericPsms = MetaDrawLogic.FilteredListOfPsms
                     .Where(p => p.Ms2ScanNumber == psm.Ms2ScanNumber && p.FileNameWithoutExtension == psm.FileNameWithoutExtension).ToList();
                 MetaDrawLogic.DisplayChimeraSpectra(chimeraPlot, chimericPsms, out List<string> error);
                 if (error != null && error.Count > 0)
                     Debugger.Break();
-                ClearPresentationArea();
                 wholeSequenceCoverageHorizontalScroll.Visibility = Visibility.Collapsed;
-
+                AmbiguousWarningTextBlocks.Visibility = Visibility.Collapsed;
+                AmbiguousSequenceOptionBox.Visibility = Visibility.Collapsed;
 
                 if (MetaDrawSettings.ShowLegend)
                 {
@@ -217,7 +219,27 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
             // 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;
+                // From chimeric scan view to child scan view with ambiguous selected
+                if (AmbiguousSequenceOptionBox.SelectedItem == null) 
+                {
+                    // set to first and break the loop if casted successfully
+                    foreach (var ambiguousResult in AmbiguousSequenceOptionBox.Items)
+                    {
+                        psm = ambiguousResult as PsmFromTsv;
+                        if (psm != null)
+                            break;
+                    }
+
+                    AmbiguousWarningTextBlocks.Visibility = Visibility.Collapsed;
+                    AmbiguousSequenceOptionBox.Visibility = Visibility.Visible;
+                    AmbiguousSequenceOptionBox.SelectedItem = psm;
+                }
+                // selecting a different ambiguous result from the combobox in child scan view
+                else
+                {
+                    psm = (PsmFromTsv)AmbiguousSequenceOptionBox.SelectedItem;
+                }
+
                 if (FragmentationReanalysisViewModel.Persist || sender is FragmentationReanalysisViewModel)
                 {
                     oldMatchedIons = psm.MatchedIons;
@@ -918,8 +940,15 @@ private void AmbiguousSequenceOptionBox_SelectionChanged(object sender, Selectio
             SetSequenceDrawingPositionSettings(true);
             object obj = new object();
             if (AmbiguousSequenceOptionBox.Items.Count > 0)
+            {
                 dataGridScanNums_SelectedCellsChanged(obj, null);
-            MetaDrawLogic.DisplaySequences(stationarySequenceCanvas, scrollableSequenceCanvas, sequenceAnnotationCanvas, psm);
+                MetaDrawLogic.DisplaySequences(stationarySequenceCanvas, scrollableSequenceCanvas,
+                    sequenceAnnotationCanvas, psm);
+            }
+            else
+            {
+                AmbiguousSequenceOptionBox.Visibility = Visibility.Hidden;
+            }
         }
 
         /// <summary>
@@ -1033,6 +1062,7 @@ private void MetaDrawTabControl_OnSelectionChanged(object sender, SelectionChang
             if (e.RemovedItems.Count > 0 && ((TabItem)e.RemovedItems[0]).Name == "ChimeraScanPlot")
             {
                 MetaDrawLogic.FilterPsms();
+                ClearPresentationArea();
 
                 // reselect what was selected
                 if (selectedPsm != null && MetaDrawLogic.FilteredListOfPsms.Contains(selectedPsm))
@@ -1047,12 +1077,15 @@ private void MetaDrawTabControl_OnSelectionChanged(object sender, SelectionChang
             if (e.AddedItems.Count > 0 && ((TabItem)e.AddedItems[0]).Name == "ChimeraScanPlot")
             {
                 MetaDrawLogic.FilterPsmsToChimerasOnly();
+                ClearPresentationArea();
 
-                // reselect what was selected
-                if (selectedPsm == null || !MetaDrawLogic.FilteredListOfPsms.Contains(selectedPsm)) return;
-                int psmIndex = MetaDrawLogic.FilteredListOfPsms.IndexOf(selectedPsm);
-                dataGridScanNums.SelectedIndex = psmIndex;
-                dataGridScanNums_SelectedCellsChanged(new object(), null);
+                // reselect what was selected if possible
+                if (selectedPsm != null && MetaDrawLogic.FilteredListOfPsms.Contains(selectedPsm))
+                {
+                    int psmIndex = MetaDrawLogic.FilteredListOfPsms.IndexOf(selectedPsm);
+                    dataGridScanNums.SelectedIndex = psmIndex;
+                    dataGridScanNums_SelectedCellsChanged(new object(), null);
+                }
             }
         }
 
@@ -1066,11 +1099,11 @@ private void ClearPresentationArea()
             DrawnSequence.ClearCanvas(map);
             DrawnSequence.ClearCanvas(sequenceText);
             DrawnSequence.ClearCanvas(sequenceAnnotationCanvas);
-            plotView.Visibility = Visibility.Hidden;
             GrayBox.Opacity = 0;
             wholeSequenceCoverageHorizontalScroll.Visibility = Visibility.Collapsed;
             AmbiguousSequenceOptionBox.Items.Clear();
             plotView.Visibility = Visibility.Hidden;
+            chimeraPlot.Visibility = Visibility.Hidden;
 
             if (ChimeraLegend != null)
                 ChimeraLegend.Visibility = false;

MetaMorpheus/GUI/Views/FragmentReanalysisControl.xaml

@@ -18,34 +18,46 @@
 
         <!-- 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="*"/>
+                <ColumnDefinition Width="2*"/>
+                <ColumnDefinition Width="3*"/>
+                <ColumnDefinition Width="3*"/>
+                <ColumnDefinition Width="3*"/>
             </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"/>
+            <Button Grid.Row="0" Grid.Column="0" x:Name="SearchButton" Content="Search"
+                    VerticalAlignment="Center" Margin="5 3"
+                    VerticalContentAlignment="Center" Click="SearchWithNewIons_OnClick" />
 
-            <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" />
+            <CheckBox Grid.Row="0" Grid.Column="1" 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" HorizontalAlignment="Left">
+                <TextBlock Text="Set Dissociation Type: " VerticalAlignment="Center" />
+                <ComboBox x:Name="DissociationTypeComboBox" ItemsSource="{Binding DissociationTypes}"
+                          SelectedItem="{Binding SelectedDissociationType}"
+                          Margin="5 3" VerticalContentAlignment="Center" Width="80"
+                          HorizontalContentAlignment="Center"/>
+            </StackPanel>
+
+            <StackPanel Grid.Row="0" Grid.Column="3" Orientation="Horizontal" VerticalAlignment="Center" HorizontalAlignment="Left">
+                <TextBlock Text="Mass Tolerance (ppm): " VerticalAlignment="Center" />
+                <local:DoubleTextBoxControl Text="{Binding ProductIonMassTolerance, FallbackValue=20}"
+                                            HorizontalAlignment="Center" HorizontalContentAlignment="Center"
+                                            VerticalAlignment="Center" VerticalContentAlignment="Center"
+                                            BorderThickness="1" />
             </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.Row="0" Grid.Column="4" Orientation="Horizontal" VerticalAlignment="Center" HorizontalAlignment="Left">
+                <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>
 

MetaMorpheus/GuiFunctions/MetaDraw/FragmentResearching/FragmentationReanalysisViewModel.cs

@@ -8,6 +8,7 @@
 using EngineLayer;
 using iText.StyledXmlParser.Jsoup;
 using MassSpectrometry;
+using MzLibUtil;
 using Omics;
 using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
@@ -26,6 +27,7 @@
             _isProtein = isProtein;
             UseInternalIons = false;
             MinInternalIonLength = 10;
+            ProductIonMassTolerance = 20;
             if (isProtein)
             {
                 DissociationTypes = new ObservableCollection<DissociationType>(Enum.GetValues<DissociationType>()
@@ -91,6 +93,14 @@
             set { _useInternalIons = value; OnPropertyChanged(nameof(UseInternalIons)); }
         }
 
+        private double _productIonMassTolerance;
+
+        public double ProductIonMassTolerance
+        {
+            get => _productIonMassTolerance;
+            set { _productIonMassTolerance = value; OnPropertyChanged(nameof(ProductIonMassTolerance)); }
+        }
+
         private IEnumerable<FragmentViewModel> GetPossibleProducts(bool isProtein)
         {
             foreach (var product in Enum.GetValues<ProductType>())
@@ -177,7 +187,7 @@
                     Omics.Fragmentation.Peptide.DissociationTypeCollection.ProductsFromDissociationType[dissociationType].ToArray()
                     : Omics.Fragmentation.Oligo.DissociationTypeCollection.GetRnaProductTypesFromDissociationType(dissociationType).ToArray();
             }
             catch (Exception e)
             {
                 _selectedDissociationType = DissociationType.HCD;
                 dissociationTypeProducts = isProtein ?
@@ -211,13 +221,15 @@
 
             // TODO: Adjust decon params for when RNA gets incorporated
             var commonParams = new CommonParameters();
+            if (Math.Abs(commonParams.ProductMassTolerance.Value - ProductIonMassTolerance) > 0.00001)
+                commonParams.ProductMassTolerance = new PpmTolerance(ProductIonMassTolerance);
+
             var specificMass = new Ms2ScanWithSpecificMass(ms2Scan, psmToRematch.PrecursorMz,
                 psmToRematch.PrecursorCharge, psmToRematch.FileNameWithoutExtension, commonParams);
 
             return MetaMorpheusEngine.MatchFragmentIons(specificMass, allProducts, commonParams, false)
                 .Union(psmToRematch.MatchedIons.Where(p => _productsToUse.Contains(p.NeutralTheoreticalProduct.ProductType)))
                 .ToList();
-
         }
     }
 }

MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs

@@ -781,7 +781,7 @@ public void FilterPsmsToChimerasOnly()
             {
                 FilteredListOfPsms.Clear();
 
-                var filteredChimericPsms = ChimericPsms.Where(p => MetaDrawSettings.FilterAcceptsPsm(p));
+                var filteredChimericPsms = ChimericPsms.Where(MetaDrawSettings.FilterAcceptsPsm);
                 foreach (var psm in filteredChimericPsms)
                 {
                     if (filteredChimericPsms.Count(p => p.Ms2ScanNumber == psm.Ms2ScanNumber && p.FileNameWithoutExtension == psm.FileNameWithoutExtension) > 1)

MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs

@@ -452,8 +452,9 @@
         /// <summary>
         /// Loads in settings based upon SettingsSnapshot parameter
         /// </summary>
-        public static void LoadSettings(MetaDrawSettingsSnapshot settings)
+        public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flaggedErrorOnRead)
         {
+            flaggedErrorOnRead = false;
             DisplayIonAnnotations = settings.DisplayIonAnnotations;
             AnnotateMzValues = settings.AnnotateMzValues;
             AnnotateCharges = settings.AnnotateCharges;
@@ -504,11 +505,15 @@
 
                         break;
                     }
+                    default:
+                        throw new MetaMorpheusException("Cannot parse Product Ion Color values");
                 }
             }
             catch (Exception e)
             {
                 Debugger.Break();
+                SetDefaultProductTypeColors();
+                flaggedErrorOnRead = true;
             }
 
             try // Beta Product Type Colors
@@ -537,11 +542,15 @@
 
                         break;
                     }
+                    default:
+                        throw new MetaMorpheusException("Cannot parse Beta Product Ion Color values");
                 }
             }
             catch (Exception e)
             {
                 Debugger.Break();
+                SetDefaultBetaProductTypeColors();
+                flaggedErrorOnRead = true;
             }
 
             try // Modification Type Colors
@@ -569,11 +578,15 @@
 
                         break;
                     }
+                    default:
+                        throw new MetaMorpheusException("Cannot parse Modification Color values");
                 }
             }
             catch (Exception e)
             {
                 Debugger.Break();
+                SetDefaultModificationColors();
+                flaggedErrorOnRead = true;
             }
 
             try // Coverage Type Colors
@@ -598,18 +611,25 @@
                             if (CoverageTypeToColor.ContainsKey(key))
                                 CoverageTypeToColor[key] = DrawnSequence.ParseOxyColorFromName(savedProductType.Split(',')[1]);
                         }
-
                         break;
                     }
+                    default:
+                        throw new MetaMorpheusException("Cannot parse Sequence Coverage color values");
+
                 }
             }
             catch (Exception e)
             {
-                Debugger.Break();
+                Debugger.Break(); 
+                SetDefaultCoverageTypeColors();
+                flaggedErrorOnRead = true;
             }
 
             try // Spectrum Descriptors
             {
+                if (!settings.SpectrumDescriptionValues.Any())
+                    throw new MetaMorpheusException("Cannot parse Spectrum Descriptor values");
+
                 var firstSplit = settings.SpectrumDescriptionValues.First().Split(',');
                 switch (firstSplit.Length)
                 {
@@ -633,11 +653,15 @@
 
                         break;
                     }
+                    default:
+                        throw new MetaMorpheusException("Cannot parse Spectrum Descriptor values");
                 }
             }
             catch (Exception e)
             {
                 Debugger.Break();
+                SetDefaultProductTypeColors();
+                flaggedErrorOnRead = true;
             }
         }
 

MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs

@@ -182,7 +182,10 @@ public void LoadSettings()
         {
             MetaDrawSettingsSnapshot settings = null;
             settings = XmlReaderWriter.ReadFromXmlFile<MetaDrawSettingsSnapshot>(SettingsPath);
-            MetaDrawSettings.LoadSettings(settings);
+            MetaDrawSettings.LoadSettings(settings, out bool flaggedErrorOnRead);
+
+            if (flaggedErrorOnRead)
+                SaveAsDefault();
         }
 
 

MetaMorpheus/Test/MetaDraw/105MetaDrawSettingsSavedEditedForTestCoverageFailures.xml

@@ -24,6 +24,7 @@
 	<string>true</string>
     <string>true</string>
     <string>true</string>
+    <string>gobbledygook</string>
   </SpectrumDescriptionValues>
   <ProductTypeToColorValues>
     <string>Aqua</string>
@@ -3823,6 +3824,7 @@
     <string>Hullabaloo</string>
     <string>Aqua</string>
     <string>Aqua</string>
+    <string>Claptrap</string>
   </CoverageTypeToColorValues>
   <UnannotatedPeakColor>LightGray</UnannotatedPeakColor>
   <InternalIonColor>Purple</InternalIonColor>