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Neutral Mass Spectrum #806

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Commits on Oct 11, 2024

  1. began neutral mz spectrum

    nbollis authored and Nic Bollis committed Oct 11, 2024
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  2. Refactor visibility and clean up deconvolution code

    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.
    Nic Bollis committed Oct 11, 2024
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  3. Finish NeutralMassSpectrum

    - 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`.
    Nic Bollis committed Oct 11, 2024
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  4. Refactor Deconvoluter and rename NeutralMzSpectrum

    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.
    Nic Bollis committed Oct 11, 2024
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  5. added neutral mass file bool

    Nic Bollis committed Oct 11, 2024
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Commits on Oct 12, 2024

  1. Refactor Deconvoluter and add new tests

    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.
    nbollis committed Oct 12, 2024
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  2. Make FirstX and LastX properties virtual; update tests

    - 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.
    nbollis committed Oct 12, 2024
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  3. fixed nuspec

    nbollis committed Oct 12, 2024
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  4. Update mzLib.nuspec

    nbollis authored Oct 12, 2024
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Commits on Oct 17, 2024

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