floating-parts.md
In glyrepr: Representation for Glycan Compositions and Structures

malformed floating-part IUPAC is rejected

Code
  cat(paste0(invalid, "\n", purrr::map_chr(errors, conditionMessage), collapse = "\n\n"))
Output
  {Neu5Ac(a2-3)}
  i In index: 1.
  Caused by error in `split_floating_iupac()`:
  ! A floating glycan structure must have a main glycan.

  {}Gal(b1-3)GalNAc(a1-
  i In index: 1.
  Caused by error in `split_floating_iupac_part()`:
  ! A floating part cannot be empty.

  {Neu5Ac}Gal(b1-3)GalNAc(a1-
  i In index: 1.
  Caused by error in `purrr::map()`:
  i In index: 1.
  Caused by error in `.f()`:
  ! A floating part must end with its linkage to its unresolved parent.

  {Neu5Ac(a2-3)|}Gal(b1-3)GalNAc(a1-
  i In index: 1.
  Caused by error in `split_floating_iupac_part()`:
  ! Floating part parents must be comma-separated positive node indices.

  {Neu5Ac(a2-3)|0}Gal(b1-3)GalNAc(a1-
  i In index: 1.
  Caused by error in `split_floating_iupac_part()`:
  ! Floating part parents must be comma-separated positive node indices.

  {Neu5Ac(a2-3)|1,1}Gal(b1-3)GalNAc(a1-
  i In index: 1.
  Caused by error in `split_floating_iupac_part()`:
  ! Floating part parent indices must be unique.

  {Neu5Ac(a2-3)|4}Gal(b1-3)GalNAc(a1-
  i In index: 1.
  Caused by error in `purrr::map2()`:
  i In index: 1.
  Caused by error in `validate_floating_source_parents()`:
  ! Floating parent index is outside the complete glycan structure.
  i The complete structure has 3 nodes.

  {Neu5Ac(a2-3)|1|2}Gal(b1-3)GalNAc(a1-
  i In index: 1.
  Caused by error in `split_floating_iupac_part()`:
  ! A floating part can contain at most one parent-index separator.

  {{Neu5Ac(a2-3)}}Gal(b1-3)GalNAc(a1-
  i In index: 1.
  Caused by error in `split_floating_iupac()`:
  ! Floating parts cannot be nested.

  Gal(b1-3)GalNAc(a1-{Neu5Ac(a2-3)}
  i In index: 1.
  Caused by error in `value[[3L]]()`:
  ! Could not parse IUPAC-condensed string: "Gal(b1-3)GalNAc(a1-{Neu5Ac(a2-3)}"
  i Invalid characters or format in IUPAC-condensed string

invalid floating-part graph annotations are rejected

Code
  cat(paste0(names(errors), "\n", purrr::map_chr(errors, conditionMessage),
  collapse = "\n\n"))
Output
  unannotated
  i In index: 1.
  Caused by error in `validate_floating_graph_shape()`:
  ! Glycan structure must be an out tree.

  malformed_attr
  i In index: 1.
  Caused by error in `normalize_floating_parts()`:
  ! Graph attribute floating_parts must be a list.

  nonroot
  i In index: 1.
  Caused by error in `validate_floating_graph_shape()`:
  ! Each floating part root must be the root of its graph component.

  floating_parent
  i In index: 1.
  Caused by error in `validate_floating_graph_shape()`:
  ! Floating part parent indices cannot refer to its own component.

  duplicate_parents
  i In index: 1.
  Caused by error in `purrr::map()`:
  i In index: 1.
  Caused by error in `.f()`:
  ! Floating part parent indices must be unique.

  duplicate_component
  i In index: 1.
  Caused by error in `floating_graph_info()`:
  ! Each floating part must identify a different graph component.

  undeclared_component
  i In index: 1.
  Caused by error in `floating_graph_info()`:
  ! A floating glycan structure must contain exactly one main tree.

floating parent indices reject integer overflow

Code
  as_glycan_structure("{Neu5Ac(a2-3)|2147483648}Gal(a1-")
Condition
  Error in `purrr::map()`:
  i In index: 1.
  Caused by error in `split_floating_iupac_part()`:
  ! Floating part parent indices exceed the supported integer range.

Code
  glycan_structure(graph)
Condition
  Error in `purrr::map()`:
  i In index: 1.
  Caused by error in `purrr::map()`:
  i In index: 1.
  Caused by error in `.f()`:
  ! Floating part parents must contain valid vertex indices.