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Add parse_gwb() with branch, substituent, reducing-end, and uncertain-antenna support. Integrate automatic format detection and add corpus-derived regression coverage and documentation.
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Preserve the GWB ring marker and reject explicit open-chain residues unless they are representable as a reduced redEnd root. Add regressions for free-end and linked open-chain inputs.
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Up to standards ✅🟢 Issues
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Emit explicit candidate parents whenever occupied acceptor positions remove nodes from a GlycoWorkbench uncertain-antenna domain. Cover lone floating monosaccharide and substituent cases.
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Codex Review: Didn't find any major issues. Already looking forward to the next diff. Reviewed commit: ℹ️ About Codex in GitHubYour team has set up Codex to review pull requests in this repo. Reviews are triggered when you
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| feasible <- purrr::map_lgl(main_nodes, function(main_node) { | ||
| occupied <- gwb_node_occupied_positions(main_node) | ||
| any(!positions %in% occupied) | ||
| }) |
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When a GWB uncertain antenna has alternative positions, retaining a parent because any position is free leaves the occupied alternatives in the serialized linkage. For example, freeEnd--1b1D-Glc,p--3Ac}--3/6S$... has only one candidate parent whose position 3 is occupied, but this code keeps it and emits {3/6S}, so the parsed domain incorrectly still permits sulfate at position 3. Compute the feasible positions per retained parent and narrow the linkage when the resulting sets agree; reject parent-position combinations that cannot be represented without introducing impossible alternatives.
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Summary
parse_gwb()support for GWB/GWS sequences, including branches, substituents, furanose and configured residues, reducing-end alditols, legacy ulosonic markers, and uncertain antennae.freeEndandredEndinputs throughauto_parse()and update package documentation, pkgdown, and NEWS.Verification
Rscript -e 'devtools::test()'— 1,655 tests passed.Rscript -e 'pkgdown::check_pkgdown()'— no problems.Rscript -e 'devtools::check(error_on = "warning", args = c("--no-manual"))'— 0 errors, 0 warnings, one environment-only clock NOTE.