modified isotope analysis in alignment process#642
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YukiMatsuzawa merged 2 commits intomasterfrom Oct 7, 2025
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Pull Request Overview
This PR modifies the isotope analysis logic in the alignment process by simplifying the initialization of isotope properties for alignment spots. The change removes conditional logic and isotope estimation processing.
- Simplified isotope property initialization to set all spots as their own parent with weight number 0
- Commented out the original conditional isotope analysis logic and isotope estimation processing
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| spot.PeakCharacter.IsotopeParentPeakID = spot.AlignmentID; | ||
| spot.PeakCharacter.IsotopeWeightNumber = 0; | ||
| } | ||
| if (_param.TrackingIsotopeLabels) return; | ||
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| IsotopeEstimator.Process(alignmentSpots, _param, _iupac); | ||
| //foreach (var spot in alignmentSpots) { | ||
| // spot.PeakCharacter.IsotopeParentPeakID = -1; | ||
| // spot.PeakCharacter.IsotopeWeightNumber = -1; | ||
| // if (_param.TrackingIsotopeLabels || spot.IsReferenceMatched(evaluator)) { | ||
| // spot.PeakCharacter.IsotopeParentPeakID = spot.AlignmentID; | ||
| // spot.PeakCharacter.IsotopeWeightNumber = 0; | ||
| // } | ||
| // if (!spot.IsReferenceMatched(evaluator) && !spot.IsAnnotationSuggested(evaluator)) { | ||
| // spot.SetAdductType(AdductIon.Default); | ||
| // } | ||
| //} | ||
| //if (_param.TrackingIsotopeLabels) return; | ||
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| //IsotopeEstimator.Process(alignmentSpots, _param, _iupac); |
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The simplified logic unconditionally sets all spots as their own isotope parent with weight 0, potentially breaking isotope relationship tracking. The original conditional logic appears to handle different cases based on reference matching and isotope label tracking parameters.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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