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deleted msrefmatch parameter for gcms alignmemt process #711

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

deleted msrefmatch parameter for gcms alignmemt process #711

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2 changes: 0 additions & 2 deletions src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsAlignmentProcessFactory.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,6 @@ public override IPeakJoiner CreatePeakJoiner() {
switch (GcmsParameter.AlignmentIndexType) {
case Common.Enum.AlignmentIndexType.RT:
return GcmsPeakJoiner.CreateRTJoiner(
GcmsParameter.MspSearchParam,
GcmsParameter,
_evaluator,
_refer,
Expand All @@ -58,7 +57,6 @@ public override IPeakJoiner CreatePeakJoiner() {
case Common.Enum.AlignmentIndexType.RI:
default:
return GcmsPeakJoiner.CreateRIJoiner(
GcmsParameter.MspSearchParam,
GcmsParameter.RetentionIndexAlignmentTolerance,
GcmsParameter,
_evaluator,
Expand Down
18 changes: 9 additions & 9 deletions src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs
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Expand Up @@ -22,12 +22,12 @@ namespace CompMs.MsdialGcMsApi.Algorithm.Alignment;

public abstract class GcmsPeakJoiner : IPeakJoiner
{
public static GcmsPeakJoiner CreateRTJoiner(MsRefSearchParameterBase msMatchParam, MsdialGcmsParameter parameter, IMatchResultEvaluator<MsScanMatchResult> evaluator, IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> refer, IFeatureAccessor<SpectrumFeature> accessor, IProgress<int> progress = null) {
return new GcmsRTPeakJoiner(parameter.RiCompoundType, msMatchParam, parameter, evaluator, refer, accessor, progress);
public static GcmsPeakJoiner CreateRTJoiner(MsdialGcmsParameter parameter, IMatchResultEvaluator<MsScanMatchResult> evaluator, IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> refer, IFeatureAccessor<SpectrumFeature> accessor, IProgress<int> progress = null) {
return new GcmsRTPeakJoiner(parameter.RiCompoundType, parameter, evaluator, refer, accessor, progress);
}

public static GcmsPeakJoiner CreateRIJoiner(MsRefSearchParameterBase msMatchParam, double riTol, MsdialGcmsParameter parameter, IMatchResultEvaluator<MsScanMatchResult> evaluator, IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> refer, IFeatureAccessor<SpectrumFeature> accessor, IProgress<int> progress = null) {
return new GcmsRIPeakJoiner(parameter.RiCompoundType, msMatchParam, riTol, parameter, evaluator, refer, accessor, progress);
public static GcmsPeakJoiner CreateRIJoiner(double riTol, MsdialGcmsParameter parameter, IMatchResultEvaluator<MsScanMatchResult> evaluator, IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> refer, IFeatureAccessor<SpectrumFeature> accessor, IProgress<int> progress = null) {
return new GcmsRIPeakJoiner(parameter.RiCompoundType, riTol, parameter, evaluator, refer, accessor, progress);
}

protected readonly AlignmentIndexType _indextype;
Expand All @@ -40,7 +40,7 @@ public static GcmsPeakJoiner CreateRIJoiner(MsRefSearchParameterBase msMatchPara
private readonly IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> _refer;
private readonly int _binPrecision;

protected GcmsPeakJoiner(AlignmentIndexType indextype, RiCompoundType riCompoundType, MsRefSearchParameterBase msMatchParam, IComparer<IMSScanProperty> comparer, MsdialGcmsParameter parameter, IMatchResultEvaluator<MsScanMatchResult> evaluator, IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> refer) {
protected GcmsPeakJoiner(AlignmentIndexType indextype, RiCompoundType riCompoundType, IComparer<IMSScanProperty> comparer, MsdialGcmsParameter parameter, IMatchResultEvaluator<MsScanMatchResult> evaluator, IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> refer) {
_indextype = indextype;
_comparer = comparer;
_alignmentParameter = parameter.AlignmentBaseParam;
Expand Down Expand Up @@ -201,8 +201,8 @@ internal sealed class GcmsRTPeakJoiner : GcmsPeakJoiner
private readonly IMatchResultEvaluator<MsScanMatchResult> _evaluator;
private readonly AlignmentBaseParameter _alignmentParameter;

public GcmsRTPeakJoiner(RiCompoundType riCompoundType, MsRefSearchParameterBase msMatchParam, MsdialGcmsParameter parameter, IMatchResultEvaluator<MsScanMatchResult> evaluator, IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> refer, IFeatureAccessor<SpectrumFeature> accessor, IProgress<int> progress = null)
: base(AlignmentIndexType.RT, riCompoundType, msMatchParam, ChromXsComparer.RTComparer, parameter, evaluator, refer) {
public GcmsRTPeakJoiner(RiCompoundType riCompoundType, MsdialGcmsParameter parameter, IMatchResultEvaluator<MsScanMatchResult> evaluator, IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> refer, IFeatureAccessor<SpectrumFeature> accessor, IProgress<int> progress = null)
: base(AlignmentIndexType.RT, riCompoundType, ChromXsComparer.RTComparer, parameter, evaluator, refer) {
_alignmentParameter = parameter.AlignmentBaseParam;
_rtTol = parameter.AlignmentBaseParam.RetentionTimeAlignmentTolerance;
_rtBucket = parameter.AlignmentBaseParam.RetentionTimeAlignmentTolerance * 2;
Expand Down Expand Up @@ -324,8 +324,8 @@ internal sealed class GcmsRIPeakJoiner : GcmsPeakJoiner
private readonly IMatchResultEvaluator<MsScanMatchResult> _evaluator;
private readonly AlignmentBaseParameter _alignmentParameter;

public GcmsRIPeakJoiner(RiCompoundType riCompoundType, MsRefSearchParameterBase msMatchParam, double riTol, MsdialGcmsParameter parameter, IMatchResultEvaluator<MsScanMatchResult> evaluator, IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> refer, IFeatureAccessor<SpectrumFeature> accessor, IProgress<int> progress = null)
: base(AlignmentIndexType.RI, riCompoundType, msMatchParam, ChromXsComparer.RIComparer, parameter, evaluator, refer) {
public GcmsRIPeakJoiner(RiCompoundType riCompoundType, double riTol, MsdialGcmsParameter parameter, IMatchResultEvaluator<MsScanMatchResult> evaluator, IMatchResultRefer<MoleculeMsReference, MsScanMatchResult> refer, IFeatureAccessor<SpectrumFeature> accessor, IProgress<int> progress = null)
: base(AlignmentIndexType.RI, riCompoundType, ChromXsComparer.RIComparer, parameter, evaluator, refer) {
_alignmentParameter = parameter.AlignmentBaseParam;
_evaluator = evaluator;
_riTol = riTol;
Expand Down
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