Changelog

glyanno 0.6.1

• comp_to_struc(), enhance_comp(), and enhance_struc() now support mixed generic and concrete residues with element-wise structure levels; structure matching excludes unresolved floating inputs and database candidates with a warning, and enhance_struc_denovo() now requires generic topological inputs. (#24)

• mz_to_comp(), enhance_comp(), comp_to_struc(), and enhance_struc() now include a confidence column in expanded results for customized prioritization. (#23)

glyanno 0.6.0

New features

• New enhance_struc_denovo() reconstructs topological N-glycans and falls back to the topological database when reconstruction is not possible. (#16, #17, #18)

Breaking changes

• Remove fill_anomer_pos() from the exported namespace. Use glyrepr::fill_anomer_pos() instead. (#15)

Minor improvements and bug fixes

• enhance_struc() now accepts duplicated input structures, preserves their order and per-occurrence results, and matches each unique non-missing structure only once. (#21)
• calculate_mz(), comp_to_struc(), enhance_comp(), and mz_to_comp() now process vector inputs substantially faster by reusing prepared databases and direct lookups. (#20)
• struc_to_glytoucan() now looks up accessions from glydb::glydb_data first and only falls back to the online GlycanFormatConverter API for missing structures. (#14)

glyanno 0.5.0

New features

• Add struc_to_glytoucan() to map glycan structures to GlyTouCan accessions (#11).
• Add fill_anomer_pos() to fill in missing anomeric position information in glycan structures (#13).

glyanno 0.4.2

Minor improvements and bug fixes

• Fix a bug in enhance_struc() introduced by the breaking change in glyrepr 0.11.0 (#9).
• Update vignette to mention that you can use a structure database with different structure levels.

glyanno 0.4.1

Minor improvements and bug fixes

• comp_to_struc() now explicitly returns when the output is empty.

glyanno 0.4.0

Breaking changes

• return_best = TRUE now returns a vector with the same length as input (with NA for unmatched glycans) instead of a tibble with potentially fewer rows. Affected functions: enhance_comp(), comp_to_struc(), mz_to_comp(), enhance_struc().

Minor improvements and bug fixes

• comp_to_struc() now errors when concrete compositions are matched against a generic structure database, instead of silently returning empty results.
• db paramter cannot be of zero length now, in which case an error will be raised.

glyanno 0.3.0

Breaking changes

• Remove to_level parameter from enhance_struc().

glyanno 0.2.0

New features

• Add return_best parameter to keep the most cited match when multiple compositions or structures are possible.

glyanno 0.1.2

Minor improvements and bug fixes

• Update dependency strategy to use the r-universe repo.

glyanno 0.1.1

Minor improvements and bug fixes

• Adapt to glyrepr 0.10.0.

glyanno 0.1.0

• First GitHub release.