out matchedPeaks in GetAllXics #958
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #958 +/- ##
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Files 269 269
Lines 38740 38740
Branches 4226 4226
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Hits 31371 31371
Misses 6639 6639
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Pull Request Overview
This PR modifies the GetAllXics method to expose matched peaks information by adding an out parameter. This allows callers to receive a dictionary mapping individual peaks to their corresponding XICs, improving visibility into the peak-matching process.
- Changed
GetAllXicsmethod signature to includeout Dictionary<IIndexedPeak, ExtractedIonChromatogram> matchedPeaksparameter - Updated all test cases to capture the new
outparameter - Added test assertion to verify the total count of matched peaks
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| mzLib/MassSpectrometry/PeakIndexing/IndexingEngine.cs | Modified GetAllXics method signature to expose matchedPeaks as an out parameter instead of keeping it internal |
| mzLib/Test/TestXic.cs | Updated all test calls to GetAllXics to capture the new out parameter and added validation for matched peaks count |
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| /// <param name="cutPeakDiscriminationFactor"> The discrimination factor to determine if a peak should be cut if we are doing peak cutting </param> | ||
| /// <returns> A list of ExtractedIonChromatogram objects representing all XICs that can be found in an indexingEngine </returns> | ||
| public virtual List<ExtractedIonChromatogram> GetAllXics(Tolerance peakFindingTolerance, int maxMissedScanAllowed, double maxRTRange, int numPeakThreshold, double? cutPeakDiscriminationFactor = null) | ||
| public virtual List<ExtractedIonChromatogram> GetAllXics(Tolerance peakFindingTolerance, int maxMissedScanAllowed, double maxRTRange, int numPeakThreshold, out Dictionary<IIndexedPeak, ExtractedIonChromatogram> matchedPeaks, double? cutPeakDiscriminationFactor = null) |
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The optional parameter cutPeakDiscriminationFactor should appear before the out parameter matchedPeaks. In C#, optional parameters must come after all required parameters, but out parameters are considered required. The current ordering violates this convention and could cause API confusion.
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