skyline: Stopped inferring a Waters lockmass function from waters_connect mzML - #4498

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bspratt wants to merge 36 commits into

Skyline/work/20260727_Waters_dataconvert_mzml_import

Commits on Jul 28, 2026

Tagged Waters lockmass scans as calibration spectra (MS:1000928)

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162dbbf
Regenerated the Waters reference mzMLs affected by the calibration spectrum tag

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249389c
Stopped guessing at the Waters lockmass function for waters_connect mzML

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5753f6b
Restored the original source file paths in the regenerated Waters references

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38d8115
Regenerated the LockmassRefiner references affected by the calibration tag

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33062ad
Made the msLevel filter independent of spectrum type cvParam order

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b91cd88
Stopped UpdateMseLevel latching _mseLevel to zero

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4f811eb
Forwarded calibrationSpectraAreOmitted through SpectrumListWrapper

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579351f
Read the Waters function number from the merged DDA nativeID layout

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497cb26
Covered the MS:1000928 branch that the lockmass test could not detect

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87d22f1
Removed the waters_connect nativeID check, which had no effect

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a85e176
Resolved the Waters lockmass function once at construction

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48f63c2
Stopped parsing Waters nativeIDs for every vendor's spectra

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2909928

Commits on Jul 29, 2026

Used hasCVParamChild rather than cvParamChildren in the msLevel filter

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9a23cda
Confined IsWatersLockmassSpectrum to Waters files

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c7c96d3
Corrected comments that overstated what the code guarantees

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4df5021
Covered ignoreCalibrationScans against a file that has a lockspray function

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4945a60
Merge remote-tracking branch 'origin/master' into Skyline/work/20260727_Waters_dataconvert_mzml_import
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18b0084
Scrubbed absolute paths from the Waters lockmass test fixtures

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8f20b37
Kept the lockmass function out of the global TIC when its scans are excluded

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887bf25
Addressed review feedback on PR #4498

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df90ce8

Commits on Jul 30, 2026

Commits on Jul 31, 2026

Commits on Aug 4, 2026

Commits on Aug 11, 2026

Merge branch 'master' into Skyline/work/20260727_Waters_dataconvert_mzml_import
bspratt
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0ad9391

Commits on Aug 20, 2026

Merge branch 'master' into Skyline/work/20260727_Waters_dataconvert_mzml_import
bspratt
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feea902

Commits on Aug 24, 2026

Merge branch 'master' into Skyline/work/20260727_Waters_dataconvert_mzml_import
bspratt
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3bebf25