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Changelog

Source: NEWS.md

glyrepr 1.1.0

New features

  • New canonicalize_glycan_graphs() validates and canonicalizes a batch of glycan graphs, returning aligned canonical graphs, IUPAC keys, statuses, and failure reasons while preserving source attributes. (#94)
  • canonicalize_glycan_graphs() and structure_from_arrays() support per-element recovery with on_failure = "na"; their warning conditions expose failed positions and reasons for programmatic handling. (#94)
  • New structure_from_arrays() constructs glycan vectors directly from residue, edge, and floating-metadata records, preserving names and missing values while deduplicating canonical graphs. (#94)

Performance improvements

  • as_glycan_structure() converts IUPAC-condensed strings faster, including strings with modified residues or floating structures, while preserving on_failure = "error" and on_failure = "na" behavior. Source installation now requires Rcpp and a C++17 compiler. (#94)
  • as_glycan_structure() and glycan_structure() construct vectors from graphs faster while preserving validation and canonical ordering; glycan_structure() also uses less temporary memory for large vectors. (#92)

Bug fixes

  • Floating structure canonicalization now removes occupied candidate parents after singleton localization, preserving valid graphs and canonical-string round-trips. (#95)

glyrepr 1.0.0

CRAN release: 2026-08-22

Breaking changes

  • get_mono_type() now returns one value per structure or composition instead of one scalar for the whole vector and may return "mixed"; callers that assume a scalar result must handle aligned per-element values. Generic and concrete residues can now coexist within structures, compositions, and their vectors. (#90)
  • Structure levels now depend only on linkage and anomer information. get_structure_level() returns one "intact", "partial", or "topological" value per structure; the former "basic" level and reduce_structure_level() have been removed. Use remove_linkages() to remove linkage information and convert_to_generic() to convert residue identities. (#90)

New features

  • Generic and concrete residues can now coexist within structures, compositions, and their vectors; use aligned get_mono_type() results to inspect each element. (#90)
  • Glycan structures now support alditols through reducing-end -ol IUPAC syntax, such as Gal(b1-4)GlcNAc-ol(a1-. New get_alditol() inspects the graph-level status, and structure_from_tibbles() gains an alditols argument for lossless table round-trips; legacy graphs without the attribute remain non-alditols. (#88)
  • Concrete monosaccharides now support explicit unusual absolute configurations using a leading D- or L-, such as D-Fuc, L-Gul, and D-Fucf; unprefixed names retain their natural configurations. (#85, #86)
  • Concrete monosaccharides now support explicit furanose forms such as Galf and GlcfNAc; generic conversion remains unchanged, so these become Hex and HexNAc, respectively. (#82)
  • as_glycan_structure() and glycan_structure() now support floating glycan substructures with optional candidate-parent indices using {<floating>} and {<floating>|<parents>} syntax. Floating structures retain component-node and candidate-parent metadata through validation, canonicalization, transformations, and graph-table round-trips. (#80)
  • as_glycan_structure() and glycan_structure() now support floating substituents with unresolved parent residues using {<substituent>} and {<substituent>|<parents>} syntax, including unknown carbon positions such as {?S}. (#87)
  • Floating candidate-parent indices follow complete IUPAC-condensed residue order. Floating parts may attach to other floating components or the main tree, floating substituents may target any residue node, and localization retains only conflict-free acyclic assignments that connect every component to the main tree. (#89)
  • New enumerate_floating_graph_localizations() and enumerate_floating_localizations() return conflict-free floating-part and floating-substituent assignments with provenance, while localize_floating_parts() attaches selected floating parts; graph-level results retain original vertex IDs, and deduplicate = FALSE retains assignments that canonicalize to the same structure. (#80)
  • print() gains an n argument for glyrepr_structure and glyrepr_composition vectors. (#77)
  • New structure_candidate_edges(), structure_component_membership(), and structure_floating_candidates() helpers expose floating-part membership and virtual edges plus floating-part and floating-substituent candidate parents for inspection, drawing, and constraint-aware graph operations. (#80)
  • Structure inspection, transformation, graph-table, composition, and IUPAC APIs now accept individual glycan igraph objects directly while preserving existing glyrepr_structure vector behavior and vertex IDs. (#81)

Minor improvements and fixes

  • as_glycan_structure() and glycan_structure() now support ambiguous substituent positions such as Gal4/6S(a1- and preserve them during graph and IUPAC conversion. (#84)
  • as_glycan_structure() now accepts omitted reducing-end annotations by inferring the anomer position, normalizes (?-?) to (??-?), and collapses linkage-position choices containing ? to a single unknown position. (#83)
  • get_structure_level() treats floating candidate-parent ambiguity independently from linkage resolution; fully specified floating structures can be intact. (#80)
  • IUPAC-condensed sequence generation from glycan graphs is now faster. (#78)
  • validate_glycan_graph() and as_glycan_structure() are faster through bulk linkage-position validation. (#79)

glyrepr 0.14.0

CRAN release: 2026-07-21

New features

Minor improvements and bug fixes

  • Glycan structures now allow multiple substituents with unknown positions. (#67)
  • as_glycan_structure() gains on_failure = "na" to preserve valid elements, replace element-local failures with NA, and report one aggregated warning. (#73)
  • convert_to_generic() now converts concrete monosaccharides in mixed concrete/generic character vectors. (#68)
  • fill_anomer_pos() now accepts glycan structures with generic monosaccharides. (#70)

glyrepr 0.13.0

CRAN release: 2026-07-05

Breaking changes

  • Remove the .parallel argument from smap(), smap2(), spmap(), and their variants, and drop the unused furrr and future dependencies. (#62)

New features

Minor improvements and bug fixes

glyrepr 0.12.1

CRAN release: 2026-06-19

Minor improvements and bug fixes

  • Performance optimization for glycan structure vector creation. (#46)

glyrepr 0.12.0

CRAN release: 2026-05-14

New features

  • Add get_anomer_pos() helper to get the anomer position of a monosaccharide.
  • Add fill_anomer_pos() function to fill the anomer position of a glycan structure with missing anomer information.

glyrepr 0.11.0

CRAN release: 2026-04-26

Breaking changes

  • get_structure_level() now returns one character scalar for a glyrepr_structure vector instead of one value per element. The vector-wide level is “intact”, “partial”, “topological”, or “basic” according to the combined residue and linkage detail of the non-missing structures in the vector (#42).

New features

  • as_glycan_composition() now supports parsing “E” and “L” in the input composition strings as “NeuAc”. For example, as_glycan_composition("H5N4F1L1E1") is now correctly parsed as Hex(5)HexNAc(4)Fuc(1)NeuAc(2), with a warning about dropping the sialic acid linkage information (#41).

Minor improvements and bug fixes

  • Fix the bug that glycan_composition() and as_glycan_composition() cannot handle duplications in the input. For example, as_glycan_composition("Hex(2)Hex(1)HexNAc(2)") is correctly regared as Hex(3)HexNAc(2) now (#40).
  • as_glycan_structure(NA_character_) now creates a missing structure instead of erroring.
  • get_structure_level() now ignores missing structures when determining the vector-wide level, and returns NA_character_ for empty or all-missing structure vectors.
  • reduce_structure_level() preserves missing structures in output.
  • simap() and `simap_structure() now skip missing structures like the other smap variants.
  • get_mono_type.glyrepr_composition() now ignores missing composition elements and returns NA_character_ for all-NA composition vectors.
  • Rewrite the Getting Started vignette for better readability and adopt a calmer tone for all vignettes.

glyrepr 0.10.1

CRAN release: 2026-02-13

Minor improvements and bug fixes

glyrepr 0.10.0

CRAN release: 2026-01-24

We have redesigned the internal implementation of glyrepr_composition and glyrepr_structure. This brought native support for names to glyrepr_structure, and NA values to both glyrepr_structure and glyrepr_composition.

New features

  • smap(), smap2(), spmap(), simap() and their variants now preserve names from input glyrepr_structure vectors in their output.
  • glyrepr_structure now formally supports names. All operations on a named glyrepr_structure vectors preserve the names.
  • NA values are supported for glyrepr_structure and glyrepr_composition. Any operation on a glyrepr_structure or glyrepr_composition vector with NA values behave intuitively. is.na() now works for these two classes.
  • glycan_composition() now accepts another glyrepr_composition vector as input, returning it as-is.

Breaking changes

  • glyrepr_composition and glyrepr_structure now enforce the same monosaccharide type (“concrete” or “generic”) within a vector. Mixed types are not allowed anymore. This invariant is enforced both when creating new vectors and when combining existing vectors.
  • glycan_structure() now does not support multiple glyrepr_structure vectors as input anymore. For example, glycan_structure(o_glycan_core_1(), o_glycan_core_2()) is not valid anymore. Please use c(o_glycan_core_1(), o_glycan_core_2()) instead.
  • get_mono_type() now returns a character scalar instead of a character vector for glyrepr_structure and glyrepr_composition.

Minor improvements and bug fixes

  • Subsetting glyrepr_structure with integer(0) and NULL correctly removes all underlying graphs.
  • [[<- is forbidden on glyrepr_structure vectors. Previously, the operation could be performed silently, but resulted in an invalid object.

glyrepr 0.9.0

CRAN release: 2025-11-23

New features

  • Update the monosaccharides table, ensuring all monosaccharides having generic names:
    • Add generic monosaccharides to Ara, Lyx, Xyl, Rib, Api, Neu, Kdn, Pse, Leg, Aci, 4eLeg, Bac, LDmanHep, DDmanHep, Kdo, Dha, MurNAc, MurNGc, Mur, Fru, Tag, Sor, Psi.
    • Rename “Pent” to “Pen”.
    • Delete “Sia” from the table.
  • count_mono() now supports counting substituents, with a new argument include_subs.
  • Add reduce_structure_level() to reduce a glycan structure to a lower resolution level.

Minor improvements and bug fixes

glyrepr 0.8.0

CRAN release: 2025-11-09

Breaking changes

  • Remove normalize_substituents(). This function does not help outside of glyrepr so we make it an internal function.
  • glycan_composition() cannot accept empty integer vectors now. Therefore, glycan_composition(integer(0)) is not valid anymore.
  • glycan_composition() now checks input types more strictly.
  • as_glycan_composition() handles NA values and empty strings (““) more strictly. Now an error will be raised if NA values or empty strings are passed instead of dropping them silently. This update makes as_glycan_composition() size-stable and consistent with as_glycan_structure().

New features

  • Add get_structure_level() to get the structure resolution levels of a glycan structure vector.
  • as_glycan_composition() now supports simple composition strings like “H5N2”, “H5N4F1S2”, “H5N4A1G1”, etc.
  • count_mono() now returns total number of monosaccharides when mono is NULL.
  • has_linkages() now has a strict parameter to control the strictness of the check.

Minor improvements and bug fixes

glyrepr 0.7.5

CRAN release: 2025-10-29

Minor improvements and bug fixes

  • IUPAC sequence generation is deterministic now for tie branches.
  • Glycan structures are now truncated when printed to console as a column in a tibble.
  • Glycan compositions are now colored when printed to console as a column in a tibble.

glyrepr 0.7.4

CRAN release: 2025-09-23

Minor improvements and bug fixes

  • Update package title and description.
  • Remove parallel examples in smap().

glyrepr 0.7.3

Minor improvements and bug fixes

  • Fix some typos in the documentation.
  • Add examples to some functions.
  • Prepare for release on CRAN.

glyrepr 0.7.2

Minor improvements and bug fixes

  • Fix the bug that structure_to_iupac() returns incorrect sequences with incorrect backbone or branch order.

glyrepr 0.7.1

Minor improvements and bug fixes

  • Fix the bug that smap2(), spmap(), and related functions return unexpected results when the input y is a list.
  • Improve the documentation of glycan_structure(), including the new behavior of vertex and edge order introduced in 0.7.0.

glyrepr 0.7.0

Breaking changes

  • convert_mono_type() is now replaced by convert_to_generic(). convert_mono_type() was created when three monosaccharide types existed: “concrete”, “generic”, and “simple”. When “simple” was removed, the old convert_mono_type() seems redundant, as the only valid conversion is from “concrete” to “generic” now. Therefore, we remove this function now and add a more straightforward convert_to_generic().
  • get_structure_graphs() is redesigned.
    • The i parameter is removed, as indexing can be done manually on the input glyrepr_structure vector or on the returned list easily.
    • Add a return_list parameter to control the return type. This parameter makes this function “type-stable”.
  • glycan_structure() and as_glycan_structure() now reorder the underlying graphs to be in line with the IUPAC-style sequence. For example, the vertex order of “Gal(b1-3)[GlcNAc(b1-6)]GalNAc(b1-” is always 1. Gal, 2. GlcNAc, 3. GalNAc, and edges b1-3, b1-6, no matter what the original graphs are. Users can assign the indices of vertices and edges easily by printing the structure to console. This update makes glymotif::match_motif() more meaningful.

New features

  • glyrepr_structure has colors now in tibbles when printed to console.

Minor improvements and bug fixes

  • Fix the bug that monosaccharides with substituents are not colored when a glycan_structure() is printed in the console. For example, the “Neu5Ac” part in “Neu5Ac9Ac(a2-” was printed in black. Now it is printed in purple, while the “9Ac” part remains in black.
  • Fix the bug that Neu5Ac and Neu5Gc with substituents at position 2, 3, or 4 could not be correctly parsed. Now, complex patterns like “Neu4Ac5Ac9Ac” can be properly handled, into a “Neu5Ac” monosaccharide with “4Ac,9Ac” as substituents.

glyrepr 0.6.1

Minor improvements and bug fixes

glyrepr 0.6.0

Breaking changes

  • Remove the “alditol” attribute from glycan_structure() objects. This information is rarely used in glycomics and glycoproteomics data analysis. It is removed according to the razor principle.
  • as_glycan_structure() now doesn’t allow the input IUPAC-condensed strings to omit the anomer information. Previously, something like “Glc(a1-3)GlcNAc” is valid. as_glycan_structure() assumed that the core “GlcNAc” has a “?1-” anomer and added it automatically. The problem is that this behavior was not easily awared by users and might cause confusion. Again, less is more, so we remove it.

glyrepr 0.5.2

Minor improvements and bug fixes

  • Fix some error message format errors.
  • Update the abbreviated type name of glyrepr_structure from structure to struct.

glyrepr 0.5.0

Major changes

  • Glycan structures now support multiple substituents on a single monosaccharide. Substituents are stored as comma-separated strings internally and concatenated in IUPAC format for display.
  • Glycan compositions now support substituents. The glycan_composition class can now represent and count substituents alongside monosaccharides.