deleted msrefmatch parameter for gcms alignmemt process

[htsugawa]

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[Copilot]

Pull request overview

This PR removes the MsRefSearchParameterBase (“msrefmatch”) argument from the GC-MS alignment peak-joining API and updates the GC-MS alignment process factory accordingly.

Changes:

• Removed MsRefSearchParameterBase msMatchParam from GcmsPeakJoiner.CreateRTJoiner / CreateRIJoiner and the related joiner constructors.
• Updated GcmsAlignmentProcessFactory.CreatePeakJoiner() to call the new GcmsPeakJoiner factory method signatures.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs	Removes msMatchParam from factory/constructors and adjusts joiner construction accordingly.
src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsAlignmentProcessFactory.cs	Stops passing GcmsParameter.MspSearchParam into the peak joiner creation.

Comments suppressed due to low confidence (1)

src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs:49

• After removing msMatchParam from the factory/constructors, the joiner now always initializes _msMatchParam with hard-coded tolerances (0.5F, mass range 0–2000). This means GC-MS alignment similarity (CompareEIMSScanProperties) no longer respects the user/configured MsdialGcmsParameter.MspSearchParam values that were previously passed in, which can change alignment behavior unexpectedly. Consider wiring _msMatchParam to the parameter’s search settings (e.g., copy parameter.MspSearchParam) or otherwise making the new fixed defaults explicit via the API/config.

        _comparer = comparer;
        _alignmentParameter = parameter.AlignmentBaseParam;
        _riCompoundType = riCompoundType;
        _msMatchParam = new MsRefSearchParameterBase() { Ms1Tolerance = 0.5F, Ms2Tolerance = 0.5F, MassRangeBegin = 0, MassRangeEnd = 2000 };
        _parameter = parameter;

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