changed alignment mass tolearnce to 0.5 Da

[htsugawa]

No description provided.

[Copilot]

Pull request overview

This PR aims to increase the mass tolerance used during alignment (notably to 0.5 Da), presumably to better fit nominal-mass GCMS alignment behavior.

Changes:

• Replaced the GcmsPeakJoiner constructor’s use of the provided MsRefSearchParameterBase with a newly constructed parameter fixed at 0.5 tolerances and a 0–2000 mass range.
• Updated the default AlignmentBaseParameter.Ms1AlignmentTolerance from 0.015F to 0.5F in the shared parameter model.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs	Forces a fixed MsRefSearchParameterBase for GCMS alignment comparisons, overriding caller-provided search parameters.
src/MSDIAL5/MsdialCore/Parameter/ParameterBase.cs	Raises the default MS1 alignment tolerance globally via AlignmentBaseParameter.

Comments suppressed due to low confidence (3)

src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs:48

• Hard-coded matching tolerances and mass range (0.5F, 0..2000) here bypass user/project settings (e.g., GcmsParameter.MspSearchParam and/or peak-pick mass range). Consider deriving these values from the passed search parameter and/or parameter.PeakPickBaseParam so alignment behavior stays consistent with the rest of the pipeline.

        _msMatchParam = new MsRefSearchParameterBase() { Ms1Tolerance = 0.5F, Ms2Tolerance = 0.5F, MassRangeBegin = 0, MassRangeEnd = 2000 };

src/MSDIAL5/MsdialCore/Parameter/ParameterBase.cs:1151

• Changing the default Ms1AlignmentTolerance from 0.015F to 0.5F in AlignmentBaseParameter affects all MSDIAL5 workflows (LCMS/IMMS/DIMS/GCMS), not just GCMS alignment. If the intent is GCMS-specific nominal-mass behavior, consider setting this default in MsdialGcmsParameter initialization (or UI preset logic) instead of the shared base parameter to avoid widening tolerances for high-resolution modes by default.

        public float Ms1AlignmentTolerance { get; set; } = 0.5F;

src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs:48

• This change alters GCMS alignment matching behavior by overriding the search parameter at construction time, but there doesn't appear to be unit coverage validating that GcmsPeakJoiner respects configured MsRefSearchParameterBase settings. Adding a test in tests/MSDIAL5/MsdialGcMsApiTests that exercises GcmsAlignmentProcessFactory.CreatePeakJoiner() and asserts the joiner uses the provided search parameter (e.g., Ms1Tolerance/MassRange) would help prevent regressions.

        _msMatchParam = new MsRefSearchParameterBase() { Ms1Tolerance = 0.5F, Ms2Tolerance = 0.5F, MassRangeBegin = 0, MassRangeEnd = 2000 };

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[Copilot]

The constructor ignores the provided msMatchParam argument and always replaces it with a new MsRefSearchParameterBase. This makes CreateRTJoiner/CreateRIJoiner's msMatchParam parameter ineffective and prevents callers from configuring spectrum matching behavior. Use the passed-in parameter (or a copy of it) and only override specific fields if needed.

Suggested change

	_msMatchParam = new MsRefSearchParameterBase() { Ms1Tolerance = 0.5F, Ms2Tolerance = 0.5F, MassRangeBegin = 0, MassRangeEnd = 2000 };
	_msMatchParam = msMatchParam ?? new MsRefSearchParameterBase() { Ms1Tolerance = 0.5F, Ms2Tolerance = 0.5F, MassRangeBegin = 0, MassRangeEnd = 2000 };