deleted msrefmatch parameter for gcms alignmemt process (#711)

Author: htsugawa

src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsAlignmentProcessFactory.cs

@@ -49,7 +49,6 @@ public override IPeakJoiner CreatePeakJoiner() {
         switch (GcmsParameter.AlignmentIndexType) {
             case Common.Enum.AlignmentIndexType.RT:
                 return GcmsPeakJoiner.CreateRTJoiner(
-                    GcmsParameter.MspSearchParam,
                     GcmsParameter,
                     _evaluator,
                     _refer,
@@ -58,7 +57,6 @@ public override IPeakJoiner CreatePeakJoiner() {
             case Common.Enum.AlignmentIndexType.RI:
             default:
                 return GcmsPeakJoiner.CreateRIJoiner(
-                    GcmsParameter.MspSearchParam,
                     GcmsParameter.RetentionIndexAlignmentTolerance,
                     GcmsParameter,
                     _evaluator,

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

@@ -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;
@@ -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;
@@ -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;
@@ -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;