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changed alignment mass tolearnce to 0.5 Da #710

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Merged
htsugawa merged 1 commit into from
Feb 23, 2026
Merged

changed alignment mass tolearnce to 0.5 Da #710

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2 changes: 1 addition & 1 deletion src/MSDIAL5/MsdialCore/Parameter/ParameterBase.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -1148,7 +1148,7 @@ public class AlignmentBaseParameter {
[Key(3)]
public float SpectrumSimilarityAlignmentFactor { get; set; } = 0.5F;
[Key(4)]
public float Ms1AlignmentTolerance { get; set; } = 0.015F;
public float Ms1AlignmentTolerance { get; set; } = 0.5F;
[Key(5)]
public float RetentionTimeAlignmentTolerance { get; set; } = 0.10F;
[Key(6)]
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2 changes: 1 addition & 1 deletion src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs
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Expand Up @@ -45,7 +45,7 @@ protected GcmsPeakJoiner(AlignmentIndexType indextype, RiCompoundType riCompound
_comparer = comparer;
_alignmentParameter = parameter.AlignmentBaseParam;
_riCompoundType = riCompoundType;
_msMatchParam = msMatchParam;
_msMatchParam = new MsRefSearchParameterBase() { Ms1Tolerance = 0.5F, Ms2Tolerance = 0.5F, MassRangeBegin = 0, MassRangeEnd = 2000 };
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Copilot AI Feb 23, 2026

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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 };

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_parameter = parameter;
_evaluator = evaluator;
_refer = refer;
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