Revert MS1AlignmentTolerance default change and limit 0.5 tolerance to GCMS#719
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YukiMatsuzawa merged 2 commits intomasterfrom Mar 23, 2026
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This reverts commit 3b62d50.
GcmsPeakJoiner now always initializes _msMatchParam with default tolerances for MS1 and MS2, and MsdialGcmsParameter sets AlignmentBaseParam.Ms1AlignmentTolerance to 0.5f by default. This ensures consistent and appropriate default values for GCMS alignment and spectral matching.
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Pull request overview
This PR restores the original default MS1 alignment tolerance across the core parameter model and ensures the previously relaxed tolerance is applied only to GCMS-specific parameter instances.
Changes:
- Revert
AlignmentBaseParameter.Ms1AlignmentTolerancedefault from0.5Fback to0.015F. - Set
AlignmentBaseParam.Ms1AlignmentTolerance = 0.5finMsdialGcmsParameterconstructor to scope the relaxed tolerance to GCMS. - Minor cleanup of an object initializer in
GcmsPeakJoiner(no behavioral change intended).
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| src/MSDIAL5/MsdialGcMsApi/Parameter/MsdialGcmsParameter.cs | Applies GCMS-specific override for MS1 alignment tolerance. |
| src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs | Formatting/style-only update to MsRefSearchParameterBase initializer. |
| src/MSDIAL5/MsdialCore/Parameter/ParameterBase.cs | Restores core default MS1 alignment tolerance for non-GCMS workflows. |
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PR Classification
Bug fix / Parameter correction
PR Summary
This PR reverts an unintended change to the default MS1 alignment tolerance and scopes the relaxed tolerance specifically to GCMS workflows.
Background
In a previous PR, the default value of ParameterBase.Ms1AlignmentTolerance was unintentionally changed from 0.015 to 0.5. This broader tolerance negatively impacts non-GCMS workflows where stricter alignment is expected.
Purpose of this PR
Impact