IsoDec Deconvolution Algorithm #791
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #791 +/- ##
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+ Coverage 77.26% 77.36% +0.09%
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Files 218 220 +2
Lines 33027 33187 +160
Branches 3426 3441 +15
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+ Hits 25519 25674 +155
- Misses 6938 6940 +2
- Partials 570 573 +3
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maybe we can add something for each new decon method about which of the two camps it falls into. |
…testing environment
trishorts
reviewed
Aug 6, 2024
trishorts
reviewed
Aug 6, 2024
mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.cs
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added 2 commits
August 6, 2024 08:59
…y correct charge states
…ect charge at least.
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What mass range and resolution will this method apply to? |
nbollis
commented
Oct 4, 2024
mzLib/Development/DeconvolutionDevelopment/StandardDeconvolutionTest.cs
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Patch coverage will need to be >= 90% |
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.
Updated IsoDecAlgorithm to use generic DeconvolutionParameters. Enhanced IsoDecDeconvolutionParameters with new properties. Refactored constructor to use camelCase parameter names. Removed unused using directives from IsoDecAlgorithm.cs. Ensured correct casting in IsoDecAlgorithm. Renamed Css_Threshold to CssThreshold for consistency.
Updated the `MassSpectrometry` namespace in `IsoDecAlgorithm.cs` and `IsoDecDeconvolutionParameters.cs`. In `IsoDecAlgorithm.cs`, added a type check for `DeconvolutionParameters` and replaced redundant type casting with `deconParams`. In `IsoDecDeconvolutionParameters.cs`, removed unnecessary `using` directives, moved the class under the `MassSpectrometry` namespace, added user-accessible and hard-coded parameters with comments, updated the constructor to initialize new parameters, and removed the nested class declaration.
- Change `_phaseModelPath` to readonly static string to prevent modification after initial set. - Remove `process_spectrum` method declaration from the class. - Add `try-finally` block in `Deconvolute` to ensure `matchedPeaksPtr` memory is freed even if an exception occurs. - Move allocation of `matchedPeaksPtr` inside `try` block to allocate only if needed. - Invert check for `process_spectrum` result to return empty enumerable if result is <= 0. - Reformat loop processing matched peaks for better readability. - Ensure `Marshal.FreeHGlobal` is called in `finally` block to free `matchedPeaksPtr` if not zero.
Removed unused using directives from IsoDecAlgorithm.cs and Deconvoluter.cs. Updated IsoSettings namespace in IsoDecAlgorithm.cs. Simplified NUnit assertions in TestDeconvolution.cs. Updated MassSpectrometry.csproj with HintPath and PackagePath for DLLs. Replaced phase_model.bin with isogenmass.dll. Incremented version number in mzLib.nuspec to 5.2.35. Added isogenmass.dll to mzLib.nuspec for net8.0 and net8.0-windows7.0 targets.
nbollis
requested review from
trishorts,
Alexander-Sol,
jgpavek,
zhuoxinshi and
RayMSMS
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Added Isodec to mzlib and incorporated into existing deconvolution structure. Isodec has the capability to return up to
IsoDecDeconvolutionParameters.MaxShiftmissed monoisotopic results that pass the envelope quality thresholds if theIsoDecDeconvolutionParameters.ReportMultipleMonoisosis set to true.Isodec Deconvolution Algorithm:
Introduced
IsoDecAlgorithmclass inmzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.csto support a new deconvolution methodAdded four new dlls to support isodec. They must be located in the main MassSpectrometery directory or else we run into a nightmare of nuget packing issues and dll reference mismatches when using mzlib as a nuget package
isodeclib.dll,isogenmass.dll,libmmd.dll,svml_dispmd.dllCode cleanup:
usingdirectives inDeconvolutionAlgorithm.cs.DeconvolutionTypeenum fromDeconvoluter.csand moved it toDeconvolutionType.csDeconvoluter.Deconvoluter()had a clean IEnumerable return by breaking out private method for neutral mass case and returning the IEnumerable instead of using yield return directly.Development test case developments:
StandardDeconvolutionTestinmzLib/Development/DeconvolutionDevelopment/StandardDeconvolutionTest.csto include test cases for the new IsoDec deconvolution parameters and refactored the test setup to iterate over multiple deconvolution parameters.DeconvolutionParametersproperty initialization in theSinglePeakDeconvolutionTestCaseconstructor inSinglePeakDeconvolutionTestCase.cs.StandardDeconvolutionTest.csandDevelopment.csprojto reflect the new directory structure (DeconvolutionDevelopment). [1] [2]