* Version up

* Version up

* Add UseRefMatchedPeaksOnly property to alignment settings

Added UseRefMatchedPeaksOnly property to ParameterBase,
AlignmentParameterSettingModel, GcmsAlignmentParameterSettingModel,
AlignmentParameterSettingViewModel, and GcmsAlignmentParameterSettingViewModel
to control peak matching behavior. Updated constructors and methods to
initialize and synchronize this property.

* Implement IFeatureAccessor in DataAccessor class

Updated DataAccessor.cs to implement IFeatureAccessor<IMSScanProperty>. Added IFeatureAccessor<TScan> interface in IFeatureAccessor.cs with methods GetMSScanProperties and AccumulateChromatogram. Updated using statements in IFeatureAccessor.cs to include necessary namespaces.

* Refactor IPeakJoiner and fix syntax in PeakAligner

Removed unused using directives from IPeakJoiner.cs to clean up code. Simplified IPeakJoiner interface by removing nested interface declaration and making Join method directly part of the interface. Fixed syntax error in PeakAligner.cs by removing an extra closing brace.

* Refactor LCMS alignment and update tests

Refactored `LcmsPeakJoiner` and related classes to use `ChromatogramPeakFeature` instead of `IMSScanProperty`, improving type safety and maintainability. Updated `LcmsDataAccessor` to implement `IFeatureAccessor<ChromatogramPeakFeature>`. Enhanced `LcmsPeakJoiner` methods for better parameter handling and readability.

Reorganized and updated `LcmsPeakJoinerTests` to reflect these changes, including the introduction of `StubAccessor` and `FakeEvaluator` classes. Added a new test method `Join_OnlyRefMatched` to verify functionality with `UseRefMatchedPeaksOnly` parameter. Updated project file to use the latest C# language version.

* Refactor GCMS alignment and peak joining processes

Updated GcmsAlignmentProcessFactory to include new parameters in CreateRTJoiner and CreateRIJoiner methods. Modified GcmsPeakJoiner to accept additional parameters and updated methods for null checks and list initialization. Enhanced GcmsRTPeakJoiner and GcmsRIPeakJoiner with new fields and constructors. Refactored GcmsDataAccessor to implement new interfaces and use switch expressions. Improved methods for merging spectrum features, progress reporting, and handling chromatogram data.

* Add checkbox for ref.matched peaks alignment in UI

A new checkbox labeled "Do alignment for ref.matched peaks only:"
was added to `AlignmentParameterSettingView.xaml`. It is bound
to the `UseRefMatchedPeaksOnly.Value` property for its `IsChecked`
state and uses the `IsReadOnly` property with a `NegativeConverter`
to control its `IsEnabled` state. A tooltip explains its purpose:
"Alignment is performed for peaks annotated." The checkbox is
styled with properties like `HorizontalAlignment="Left"`,
`VerticalContentAlignment="Center"`, and `Height="24"`.

…art UI (#550)

* Refactor Ms2ChromatogramsView to use SimpleChartControl

Replaced MultiChart with SimpleChartControl in Ms2ChromatogramsView.xaml, simplifying the charting component. Removed MultiChart-specific properties, styles, and templates. Configured SimpleChartControl with bindings for titles and axes, applying a new BasicChart style. Retained and moved the chart's ContextMenu for saving/copying chromatograms.

Introduced a Grid layout and multiple ItemsControl elements for rendering chromatograms and legends. Updated tooltips for consistent formatting. Improved modularity, readability, and maintainability by adopting a simpler and more flexible charting approach.

* Refactor brush logic for efficiency and clarity

Replaced dynamic brush creation with a precomputed `cls2brsh`
dictionary mapping class names to observable brushes, improving
efficiency and simplifying logic. Updated `files.Zip(peaks, brushes)`
to use `files.ZipInternal(peaks)` for better alignment with code
requirements. Adjusted fallback brush logic to use
`ChartBrushes.GetChartBrush` for missing class names. These changes
enhance readability and reduce redundant brush creation.

…ew (#551)

* Improve chart interactivity and refactor focus handling

- Added a transparent rectangle to the chart area to ensure
  interactivity and visual consistency.
- Increased the `radius` constant from 3d to 4d, likely affecting
  visual element size or sensitivity.
- Refactored `FocusedItem` and `FocusedPoint` logic for better
  clarity and proper null handling.

* Add AxisTitles class and AxisTitlesTypeConverter

Introduce the AxisTitles class in the CompMs.Graphics.Base namespace,
providing a bindable representation of axis titles with change
notification support. Add the AxisTitlesTypeConverter class to enable
custom type conversion for AxisTitles, supporting conversions from
string and IEnumerable<string> to AxisTitles, and vice versa. Include
necessary using directives for required namespaces.

* Mark AxisValue methods as readonly for immutability

Updated the CompareTo, Equals, ToString, GetHashCode, and
IsNaN methods in the AxisValue class to be readonly. This
ensures these methods do not modify the object's state,
reinforcing immutability and improving code clarity.

* Add state management and AxisTitles support to charts

Enhanced `MultiChart` and `SimpleChartControl` with new private
boolean fields to manage state during property changes and prevent
recursive updates. Updated `HorizontalTitle` and `VerticalTitle`
dependency properties with change callbacks for synchronization.

Introduced `HorizontalTitles` and `VerticalTitles` dependency
properties to support `AxisTitles` objects for complex title
management. Implemented bidirectional synchronization between
single and multiple title properties. Updated constructors to
initialize `RenderAreaControlStateProperty` with a new instance.

* Improve null-safety and axis handling in models and views

Updated `AxisItemModel` properties to be nullable, added null-checks
and fallback values to prevent runtime errors, and enhanced
`AxisItemSelector` with new methods. Introduced `VerticalTitles`
property, marking `VerticalTitle` as obsolete. Improved error
handling, reactive property updates, and code consistency. Updated
view models and methods to align with these changes.

* Support multiple vertical axis titles in charts

Updated MsSpectrumView.xaml and ChartStyles.xaml to enable
dynamic support for multiple vertical axis titles using an
ItemsControl with a UniformGrid layout. Adjusted bindings
in RawPurifiedView.xaml to reflect the new multi-title
structure and improved axis title styling.

* Add "Absolute" axis type to CreateAxisPropertySelectors2

Introduce a new "Absolute" axis type in ObservableMsSpectrum.cs,
created using ToReactiveContinuousAxisManager with a ConstantMargin
of (0, 30) and initial values of 0d for min/max. Add it to
AxisItemSelector as an AxisItemModel with a label and description.
Ensure proper disposal by adding to the Disposables collection.

Corrected text in `TextBlock` elements within `DataTemplate`
for `RawDecSpectrumsViewModel` across multiple XAML files
(`DimsMainView.xaml`, `GcmsMainView.xaml`, `ImmsMainView.xaml`,
`LcimmsMainView.xaml`, and `LcmsMainView.xaml`). Ensures
consistency and resolves a typographical error in displayed text.

* Fix msp file parcer

* Add test for query check based on solvent type

* Fix typo MspFileParcer.cs

---------

Co-authored-by: YukiMatsuzawa <122433968+YukiMatsuzawa@users.noreply.github.com>

…Lists (#554)

* Add ItemSelectBehavior for WPF item selection management

Introduced a new static class `ItemSelectBehavior` in the
`CompMs.Graphics.Behavior` namespace to manage item selection
behavior in WPF controls using attached properties.

- Added `SelectedItemProperty` for two-way binding of selected items.
- Implemented `OnSelectedItemChanged` to track parent dependency objects.
- Added `ItemProperty` to associate items with controls and handle changes.
- Implemented `OnItemChanged` to manage `OnClick` event handlers.
- Added `OnClick` to update `SelectedItemProperty` on control interaction.

* Add ItemSelectBehaviorTest page and AreEqualsConverter.Default

Introduced a new `ItemSelectBehaviorTest` page to demonstrate item
selection behavior in a WPF application. The page includes a
`ComboBox`, `ItemsControl`, `Label`, and another `ItemsControl`,
showcasing the use of `ItemSelectBehavior` and `AreEqualsConverter`
for managing selection states.

Added a static `Default` instance to the `AreEqualsConverter` class
for convenient reuse without creating new instances.

Implemented `INotifyPropertyChanged` in the code-behind for
`ItemSelectBehaviorTest.xaml` to support data binding, with a
`SelectedItem` property and a collection of items (`Items`).

Updated `MainWindow.xaml.cs` to integrate the new page into the
application's navigation system.

* Refactor selection logic and improve event handling

Removed `_defaultSelectedItem`, `OnSelectedItemChanged`, and
`ParentDependencyObject`, shifting to a visual tree-based approach
for managing parent-child relationships. Introduced
`FindAncestorWithProperty` to replace `GetParentDependencyObject`,
leveraging `VisualTreeHelper` for ancestor traversal. Updated
`OnItemChanged` to use `WeakEventManager` for better memory
management when handling `Click` events.

* Refactor SelectedItem handling and event management

Replaced `OnItemChanged` with `OnSelectedItemChanged` and `OnClick`
methods for improved event handling. Removed unused methods
(`OnItemChanged`, `FindAncestorWithProperty`) and the
`using System.Windows.Media;` directive. Updated `ItemProperty`
metadata to remove obsolete callback.

* Refactor Grid layout and add nested ContextMenu

Replaced the original `<Label>` in the `Grid` with a new `<Grid>`
container featuring two rows. Moved the original `<Label>` with
its `ContextMenu` to the first row, preserving its functionality.
Added a second `<Label>` in the second row with a `ContextMenu`
that includes a nested `MenuItem` for hierarchical menu support.
The nested `MenuItem` uses `ItemsSource` and `behavior:ItemSelectBehavior.SelectedItem`
bindings, along with an `ItemContainerStyle` for child `MenuItem` elements.

* Enhance axis type selection in spectrum views

Added a new namespace for behavior functionality in XAML files.
Updated context menus in `AlignmentMs2SpectrumView.xaml`,
`MsSpectrumView.xaml`, and `RawPurifiedView.xaml` to improve
axis type selection using `behavior:ItemSelectBehavior.SelectedItem`.
Introduced custom `MenuItem.ItemContainerStyle` with `MultiBinding`
and `AreEquals` converter for better selection handling. Added
separators for improved menu organization. Retained compatibility
with existing spectrum saving features.

* Update tests/Common/ChartDrawingUiTest/Behavior/ItemSelectBehaviorTest.xaml.cs

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Bujee <147805482+Bujee415@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Co-authored-by: mikiko.takahashi <mikiko.takahashi@riken.jp>

* Corrected misspelling

* Add formula list filtering

* Unit correction

* Update adduct ion acquisition

* Update database reading

* Add error handling

* Add short message window for msfinder

* Typo fix

* Delete precursor filtering

* Change intensity to abundance

* Update single spot msfinder

* Add msfinder utility

* Add fragmentation score

* Update msfinder

* Add short message for substructure view loading

* Change axis label of reference spectrum

* Update src/MSDIAL5/MsdialGuiApp/ViewModel/Lcimms/LcimmsAlignmentViewModel.cs

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Fix bug

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

…onvolution (#560)

* Refactor AmplitudeCutoff into ChromDecBaseParam

Encapsulated the AmplitudeCutoff parameter within ChromDecBaseParam
to improve code organization and modularity. Updated all references
to use param.ChromDecBaseParam.AmplitudeCutoff across multiple files
and methods, including MSDecHandler.cs, ParameterBase.cs, and others.

This refactoring enhances maintainability and readability without
changing functionality. Developers must now access AmplitudeCutoff
via ChromDecBaseParam, ensuring consistency across the codebase.

* Add RelativeAmplitudeCutoff for dynamic intensity filtering

Introduced a new `RelativeAmplitudeCutoff` parameter to enable
dynamic intensity thresholding based on a spectrum's maximum
intensity. Updated logic across multiple files to calculate
thresholds as the maximum of `maxIntensity * RelativeAmplitudeCutoff`
and `AmplitudeCutoff`.

Key changes:
- Added `RelativeAmplitudeCutoff` to `ParameterBase`, `DeconvolutionSettingModel`, and `ParameterBaseVM`.
- Updated spectrum filtering logic in `MSDecHandler.cs`, `DataAccess.cs`, and `Ms2Dec.cs`.
- Enhanced configuration parsing in `ConfigParser.cs` to support the new parameter.
- Improved code readability with shorthand syntax for empty lists and removal of magic numbers.

These changes improve deconvolution flexibility and configurability,
adapting filtering to spectrum intensity distributions and exposing
the new parameter in the UI and configuration files.

* Add RelativeAmplitudeCutoff and improve validation

- Added a new "MS/MS relative abundance cut off" input in
  `DeconvolutionSettingView.xaml` with labels, tooltips, and
  binding to the `RelativeAmplitudeCutoff` property.
- Introduced `RelativeAmplitudeCutoff` in
  `DeconvolutionSettingViewModel.cs` as a validated `ReactiveProperty`
  with error handling and synchronization with the model.
- Updated `ObserveHasErrors` and `ObserveChanges` to include
  `RelativeAmplitudeCutoff` for validation and change tracking.
- Added validation attributes (`[Required]`, `[RegularExpression]`)
  for `RelativeAmplitudeCutoff` to ensure valid percentage input.
- Introduced `RemoveAfterPrecursor` as a new property in the view model
  with synchronization and change observation.
- Improved overall functionality and user experience for deconvolution
  settings with better validation and configurability.

* Update src/MSDIAL5/MsdialGuiApp/Model/Setting/DeconvolutionSettingModel.cs

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Bujee <147805482+Bujee415@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* fixed file generator in msfinder

* Update src/MSFINDER/MsfinderCommonStandard/Process/StructureFinder.cs

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Fix version update notification service

* Update Help>About window

* Version up

* Change logo

* Change window height

…kbench

* Increase digit of scores for result files

* Update test

* Update test

* Add smiles to substructure image converter

* Add MsSpectrumView with substructure image

* Update internal msfinder

* Add smiles to substructure image converter

* Add MsSpectrumView with substructure image

* Update internal msfinder

* Update msfinder batch processing view

* Delete unused namespaces

* Fix typing of formula generator

* Fix typing of structure finder

* Update msfinder batch view

* Add short message when loading

* Update msfinder single spot model

* Update msfinder batch processing

* Update msfinder batch view

* Update msfinder batch model

* Update typing of molecule converter

* Delete unused comment outs

* Update axis

* Update msfinder methods

* Change disposing

* Update list filtering of msfinder