Implement SRM/PRM chromatogram traces for mzML export#30
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Wire the remaining piece of iter_chromatograms scoped out of Sigilweaver#26: one SRM-shaped ChromatogramRecord ("selected reaction monitoring chromatogram", MS:1001473) per scheduled PrmTarget, built on top of the TIC/BPC traces Sigilweaver#26 already wired up. For each PrmTarget, walk every msms_type == 10 (prm-PASEF) frame, decode its peak payload via the same per-frame decode path iter_spectra already uses (Reader::decode_peaks), sum the decoded intensity restricted to that target's PrmFrameMsMsInfo scan-number range, and append one point per frame. A target with a genuine zero-intensity frame keeps that point (real data, unlike a frame missing a Frames column); a target absent from every PrmFrameMsMsInfo row is omitted rather than emitted with an empty trace, matching the TIC/BPC no-empty-chromatogram contract. precursor_mz is the target's scheduled PrmTargets.MonoisotopicMz. product_mz is left unset: prm-PASEF records a full fragment-ion scan per precursor rather than a discrete triple-quadrupole product-ion transition, and the TDF schema has no product-ion m/z field to report - populating one would mean inventing a value with no schema backing, which the clean-room policy in CONTRIBUTING.md rules out. New pure helpers (sum_intensity_in_range, build_srm_record) are unit tested directly; the frame-walking orchestration (srm_chromatograms_for) follows the same shape as the existing spectra_for_frame and isn't unit tested in isolation for the same reason that one isn't - it's thin glue over already-tested pieces and a live Reader/bundle. The existing cache-gated prm_pasef_pxd028279 test in tests/roundtrip.rs already exercises the metadata this relies on (PrmFrameMsMsInfo/PrmTargets shape) and continues to pass. Distinct from Sigilweaver#13 (prm-PASEF frames skipped in the mzML *spectrum* projection): that issue is about spectra, this is about the chromatogram trace. Addresses the remaining SRM/PRM scope of Sigilweaver#25 (TIC/BPC portion done in Sigilweaver#26). Claude-Session: https://claude.ai/code/session_018ijUinjq3SKNZXFNWqTTmV
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Summary
Issue #25 originally described three pieces of
iter_chromatogramswork (TIC, BPC, SRM/PRM). PR #26 already implemented and merged the TIC and BPC pieces, and the issue was retitled to track only the remaining SRM/PRM chromatogram work (it was also briefly auto-closed by an accidental "Closes #25" keyword match in #26's original commit message, then manually reopened for this remaining scope).This PR implements only that remaining SRM/PRM piece, built on top of #26 rather than duplicating it (branched from current
mainpost-#26-merge; confirmed viagh pr view 26and readingmzml.rsthat TIC/BPC were already present and left untouched). Addssrm_chromatograms_for: for eachPrmTarget, walksmsms_type == 10frames, looks upPrmFrameMsMsInforows, decodes peaks via the samedecode_peakspathiter_spectrauses, sums intensity within the target's scan range, and accumulates one point per frame per target. Emits aChromatogramRecordper target withchromatogram_type=MS:1001473("selected reaction monitoring chromatogram") andprecursor_mzfromPrmTarget::monoisotopic_mz. A new combining wrapper concatenates TIC/BPC with the new SRM records and renumbersindexcontiguously, since mzML requires unique/contiguous indices across the whole<chromatogramList>; bothTdfSource/OwnedTdfSourceiter_chromatogramsimpls now point at this wrapper.product_mzis deliberately leftNone: the TDF schema has no discrete product-ion m/z field for prm-PASEF (a full fragment-ion scan per precursor, not a triple-quadrupole transition) - populating it would mean inventing an unbacked value, which the clean-room policy forbids. Genuine zero-intensity frames are kept as real points; targets never appearing inPrmFrameMsMsInfoare omitted rather than emitted empty. Correctness is argued from self-consistency and the PSI-MS mzML schema only, per CONTRIBUTING.md's clean-room note - no vendor software was used.Addresses the remaining SRM/PRM scope of #25.
Test plan
cargo fmt --all -- --checkcargo clippy --workspace --all-targets -- -D warningscargo test --workspace(26 unit tests including 5 new ones for the SRM helpers, 1 conformance test, 10 roundtrip tests; cache-gated ones skip cleanly since/corpus/isn't present here, matching existing CI behavior)Contributed by @Nabejo.