IsoDec incorporation #2442
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IsoDec incorporation #2442
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* Updated to MzLib 1.0.548 and fixed custom ions in search tasks * reverted calibration task change * merged in master bbbyy * Enabled Library Loading from command line
Streamlined deconvolution parameter management by introducing `DeconHostViewModel` and custom control `HostDeconParamControl`. Updated `CommonParameters.cs` to change default `ProductDeconvolutionParameters` in negative mode from `-10` to `-20`. Modified `SearchTaskWindow.xaml` and `SearchTaskWindow.xaml.cs` to use the new view model, improving separation of concerns and maintainability. Updated `SaveButton_Click` and other relevant methods to retrieve parameters via the view model.
… set from the GUI with the new code structure
Refactored several XAML files to improve UI structure and readability: - Removed unnecessary `GroupBox` in `SearchTaskWindow.xaml` and added a new one for "Peak Trimming". - Adjusted layout in `ClassicDeconParamsControl.xaml` and `HostDeconParamControl.xaml`. Enhanced ViewModel logic: - Updated `DeconHostViewModel.cs` and `DeconParamsViewModel.cs` to include additional properties and validation logic. - Added `[ExcludeFromCodeCoverage]` attribute to `IsoDecDeconParamsViewModel.cs`. Expanded unit tests: - Removed obsolete `GuiFunctionsTest.cs`. - Added new test classes for `ClassicDeconParamsViewModel`, `DeconParamsViewModel`, `DeconHostViewModel`, and `MzLibExtensions`. - Included tests for property changes, validation logic, and conversion methods.
Updated mzLib package version from 5.2.10 to 5.2.15 in multiple project files. Added a new property `UseProvidedPrecursors` in `SearchTaskWindow.xaml.cs`. Introduced support for `IsoDecDeconvolution` in `DeconvolutionTypeToControlConverter.cs`. Refactored `HostDeconParamControl.xaml` for simpler binding. Removed `IsoDecDeconParamsControl.xaml` and its code-behind file. Added new `IsoDecDeconParamControl.xaml` and `IsoDecDeconParamControl.xaml.cs` for detailed UI and interaction logic. Enhanced `IsoDecDeconParamsViewModel` with new properties. Added `IsoDecDeconParamsViewModelTest` for validation. Updated `SearchTaskTest.cs` to include `IsoDecDeconvolutionParameters`.
- Updated DeconHostViewModel to use AnalyteType enum. - Removed IEquatable from DeconParamsViewModel; now uses UniqueIdentifier for hash code. - Minor formatting change in IsoDecDeconParamsViewModel. - Renamed and added assertions in DeconHostViewModelTests. - Updated DeconParamsViewModelTest with new and renamed tests.
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2442 +/- ##
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Coverage 93.89% 93.90%
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Files 146 147 +1
Lines 22206 22342 +136
Branches 3059 3066 +7
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+ Hits 20851 20980 +129
- Misses 906 911 +5
- Partials 449 451 +2
|
nbollis
changed the title
nbollis
requested review from
trishorts,
Alexander-Sol,
jgpavek,
zhuoxinshi and
RayMSMS
|
I'm wondering if there are different default parameters for bottom up and top down. I ran default isodec for bottom up and the results are less than classic. probably that makes sense. but i wonder if i make adjustments if isodec bottom up results can be improved. do we need explainers to help users? top down results are similar but not the same which make sense. not sure what to think about tha. |
trishorts
previously approved these changes
Jan 17, 2025
Default parameters for top down and bottom up are found in DeconHostViewModel. Your results are similar to what I get for top-down. I simply copied the default bottom-up parameters from classic deconvolution, so there is likely a more optimal default. |
trishorts
previously approved these changes
Jan 17, 2025
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Added Isodec deconvolution to MetaMorpheus.
Allowed customization of MS2 deconvoltuion parameters.
Isodec Decon can be switched out for classic decon in the GUI without the Search Task needing to know which decon type it is using.
PR Summary
Enhances deconvolution parameter handling by making them serializable, adding new UI controls, and improving view model management.
CommonParameters.cs: Removed[TomlIgnore]attribute fromDeconvolutionParametersproperties to ensure decon params get saved with each task ranIsoDecDeconParamControluser control and updatedHostDeconParamControl.xamlfor new UI elements.DeconHostViewModel.csandDeconParamsViewModel.cs: Updated to manageIsoDecDeconvolutionParameters.IsoDecDeconvolutionParametersand related view models.