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Try to fix gcms alignment processing bugs #708

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Merged
htsugawa merged 1 commit into from
Feb 18, 2026
Merged

Try to fix gcms alignment processing bugs #708

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4 changes: 2 additions & 2 deletions src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsAlignmentRefiner.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,10 @@ protected override List<AlignmentSpotProperty> GetCleanedSpots(List<AlignmentSpo
if (!(_param is MsdialGcmsParameter param)) return alignmentSpotList;

var cSpots = new List<AlignmentSpotProperty>();
cSpots.AddRange(alignmentSpotList.Where(spot => spot.IsReferenceMatched(evaluator)));
cSpots.AddRange(alignmentSpotList.Where(spot => spot.IsReferenceMatched(evaluator) && !spot.Name.StartsWith("Putative")));

//if both Quant mass and Retention is same, exclude the spot information.
foreach (var aSpot in alignmentSpotList.Where(spot => !spot.IsReferenceMatched(evaluator))) {
foreach (var aSpot in alignmentSpotList.Where(spot => !spot.IsReferenceMatched(evaluator) || spot.Name.StartsWith("Putative"))) {
var aSpotRt = aSpot.TimesCenter.RT.Value;
var aSpotRi = aSpot.TimesCenter.RI.Value;
var aSpotMass = aSpot.QuantMass;
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4 changes: 2 additions & 2 deletions src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs
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Expand Up @@ -137,15 +137,15 @@ private bool QuantMassExists(double quantMass, MSDecResult result) {

protected bool IsSimilarTo(SpectrumFeature x, SpectrumFeature y) {
var result = MsScanMatching.CompareEIMSScanProperties(x.AnnotatedMSDecResult.MSDecResult, y.AnnotatedMSDecResult.MSDecResult, _msMatchParam,
_alignmentParameter.Ms1AlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance,
_alignmentParameter.Ms1AlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance, _parameter.RetentionIndexAlignmentTolerance,
_alignmentParameter.Ms1AlignmentFactor, _alignmentParameter.RetentionTimeAlignmentFactor, _indextype == AlignmentIndexType.RI);
var isRetentionMatch = _indextype == AlignmentIndexType.RI ? result.IsRiMatch : result.IsRtMatch;
return result.IsSpectrumMatch && isRetentionMatch;
}

protected double GetSimilality(SpectrumFeature x, SpectrumFeature y) {
var result = MsScanMatching.CompareEIMSScanProperties(x.AnnotatedMSDecResult.MSDecResult, y.AnnotatedMSDecResult.MSDecResult, _msMatchParam,
_alignmentParameter.Ms1AlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance,
_alignmentParameter.Ms1AlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance, _parameter.RetentionIndexAlignmentTolerance,
_alignmentParameter.Ms1AlignmentFactor, _alignmentParameter.RetentionTimeAlignmentFactor, _indextype == AlignmentIndexType.RI);
return result.TotalScore;
}
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