Optimize MS2 value peak extraction

[YukiMatsuzawa]

Summary

• eliminate the preliminary full scan used only to count matching MS2 spectra
• collect value peaks during the existing extraction pass
• preserve the returned per-m/z arrays and ordering

Performance audit: 10 opportunities

1. Implemented — DataAccess.GetMs2ValuePeaks: remove the duplicate provider traversal used to pre-count results; high impact for large raw-data ranges and low implementation risk.
2. DataAccess.GetMs2Peaklist: cache/reuse spectrum eligibility checks when multiple product ions are extracted from the same precursor window instead of reloading and filtering the same scans for every product m/z.
3. DataAccess.GetMs2ValuePeaks: compute intensities for sorted target m/z values with a shared monotonic peak cursor and avoid repeated setup when target lists are reused across files.
4. DataAccess.GetDriftChromatogramByRtMz: replace repeated ContainsKey plus indexer lookups in nested dictionaries with TryGetValue to reduce hash lookups in the inner peak loop.
5. DataAccess.GetDriftChromatogramByRtMz: replace per-peak double[] allocations with a value-oriented accumulator to reduce GC pressure during ion-mobility extraction.
6. SpectrumViewModel and SplitSpectrumsViewModel: maintain a membership set for drag/drop duplicate checks instead of linear Contains scans as displayed scan counts grow.
7. SpectrumViewModel and SplitSpectrumsViewModel: combine the repeated spectrum min/max enumerations per collection-change event so each spectrum is traversed once per axis update.
8. DataAccess.IsSWATH: perform one pass over MS2 spectra rather than materializing multiple LINQ sequences and enumerating them repeatedly.
9. DataAccess.GetBaselineCorrectedPeaklistByMassAccuracy: reserve output capacity from the input peak count to avoid repeated list growth during chromatogram construction.
10. DataAccess.GetDriftChromatogramByScanRtMz: use the existing RT index lookup to bound both directional scans before loading spectra, reducing provider calls outside the requested RT window.

Validation

• dotnet test tests\\MSDIAL5\\MsdialCoreTests\\MsdialCoreTests.csproj --no-restore --filter FullyQualifiedName~DataAccessTests

[Copilot]

🟢 Approval recommended

The behavioral shape of the returned data remains consistent while eliminating a redundant provider traversal, and the remaining feedback is limited to minor allocation overhead reductions.

Pull request overview

This PR optimizes MS2 value-peak extraction by removing a preliminary full provider scan that previously existed only to count eligible MS2 spectra, and instead collecting peaks during the existing extraction traversal while preserving the per-target-m/z output structure.

Changes:

• Removed the pre-counting pass (GetTargetArrayLength) that duplicated provider traversal work.
• Switched MS2 value peak collection to build per-target lists during the main scan loop and materialize them to arrays at the end.

File summaries

File	Description
src/MSDIAL5/MsdialCore/Utility/DataAccess.cs	Removes a redundant scan pass in GetMs2ValuePeaks and collects value peaks in a single traversal while returning the same per-m/z array structure.

Review details

• Files reviewed: 1/1 changed files
• Comments generated: 2
• Review effort level: Lite

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