Neutral Mass Spectrum #806
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Changed `ClassicDeconvolutionAlgorithm`, `DeconvolutionAlgorithm`, and `ExampleNewDeconvolutionAlgorithmTemplate` classes and their members from `public` to `internal` to restrict visibility within the assembly. Added summary comment to `DeconvolutionAlgorithm` class. Refactored `Deconvoluter` class to remove unnecessary `using` directives and simplify the `Deconvolute` method by removing switch-case logic. Updated `IsotopicEnvelope` class by removing `MassIndex` and `StDev` properties, and modified constructor and `ScoreIsotopeEnvelope` method accordingly. Updated `MzSpectrum` class to use `StandardDeviation` extension method from `Easy.Common.Extensions`. Removed various unnecessary `using` directives from multiple files.
- Added `InternalsVisibleTo` entries for "Development" and "Test" in `MassSpectrometry.csproj`. - Changed `MostAbundantObservedIsotopicMass` to `internal` in `IsotopicEnvelope.cs`. - Added a new constructor to `IsotopicEnvelope` with monoisotopic mass, intensity, and charge. - Added XML documentation and changed `GeneratePeak` to `protected virtual` in `MzSpectrum.cs`. - Removed unused `using` directives in `MzSpectrum.cs` and `NeutralMzSpectrum.cs`. - Modified `NeutralMzSpectrum` constructor to validate array lengths. - Added `Charges` property to `NeutralMzSpectrum` and initialized it in the constructor. - Overrode `GeneratePeak` in `NeutralMzSpectrum` to convert to a charged spectrum using `Charges`.
Added necessary using directives in Deconvoluter.cs. Modified Deconvoluter class for short-circuit deconvolution. Removed redundant lines in Deconvoluter.cs. Renamed NeutralMzSpectrum to NeutralMassSpectrum. Updated constructor and references accordingly.
Refactored Deconvoluter.cs to use a foreach loop for yielding IsotopicEnvelopes. Reformatted multiple test methods in TestDeconvolution.cs for better readability. Added new test methods to validate Deconvolute with NeutralMassSpectrum, ensuring correct processing of spectra with various charge states and ranges.
- Changed FirstX and LastX properties in MzSpectrum to virtual. - Included MzLibUtil namespace in NeutralMassSpectrum class. - Updated NeutralMassSpectrum constructor to set FirstX and LastX. - Overrode FirstX and LastX in NeutralMassSpectrum class. - Added test NeutralMassSpectrum_MzRange to validate m/z range.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #806 +/- ##
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+ Coverage 76.48% 76.55% +0.06%
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Files 211 212 +1
Lines 31960 32011 +51
Branches 3286 3297 +11
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+ Hits 24446 24507 +61
+ Misses 6954 6945 -9
+ Partials 560 559 -1
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| @@ -79,7 +58,22 @@ public static IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, | |||
| default: throw new MzLibException("DeconvolutionType not yet supported"); | |||
| } | |||
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| return deconAlgorithm.Deconvolute(spectrum, rangeToGetPeaksFrom); | |||
| // Short circuit deconvolution if it is called on a neutral mass spectrum | |||
| if (spectrum is NeutralMassSpectrum newt) | |||
Alexander-Sol
approved these changes
Oct 16, 2024
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Created a 'NeutralMassSpectrum' class to represent a spectrum read off of a deconvoluted file by deriving the MzSpectrum. This allows it to be easily swapped into an MsDataScan.
If this scan is deconvoltuted. Deconvolution will short circuit and return the neutral masses.
PR Summary
This pull request refines code visibility, improves readability, and adds new test cases to enhance code maintainability and functionality.
ClassicDeconvolutionAlgorithm,DeconvolutionAlgorithm, andExampleNewDeconvolutionAlgorithmTemplateclasses changed frompublictointernal.Deconvoluterclass refactored to streamline deconvolution logic and handleNeutralMassSpectrum.TestDeconvolution.csreformatted and new test cases added forNeutralMassSpectrum.Deconvolute.TestSpectra.csupdated with new test methods forNeutralMassSpectrumconstructor and properties.MassSpectrometry.csprojupdated withInternalsVisibleToattributes for "Development" and "Test" assemblies.