structure.md
In glyrepr: Representation for Glycan Compositions and Structures

as_glycan_structure can replace invalid graphs with NA

Code
  result <- as_glycan_structure(graphs, on_failure = "na")
Condition
  Warning:
  1 structure failed validation and was replaced with `NA`.
  x Position 3 (`invalid`): Unknown monosaccharide: NotAMonosaccharide

as_glycan_structure can replace invalid character input with NA

Code
  result <- as_glycan_structure(iupacs, on_failure = "na")
Condition
  Warning:
  1 structure failed validation and was replaced with `NA`.
  x Position 2 (`invalid`): Could not parse IUPAC-condensed string: "not-a-structure" i Invalid characters or format in IUPAC-condensed string

as_glycan_structure keeps strict failures as the default

Code
  as_glycan_structure(list(valid, invalid))
Condition
  Error in `purrr::map()`:
  i In index: 2.
  Caused by error in `validate_glycan_graph()`:
  ! Unknown monosaccharide: NotAMonosaccharide

as_glycan_structure validates on_failure

Code
  as_glycan_structure("Glc(?1-", on_failure = "skip")
Condition
  Error in `as_glycan_structure()`:
  ! `on_failure` must be one of "error" or "na", not "skip".

format.glyrepr_structure includes names with tab separation

Code
  format(glycans)
Output
  [1] "A\tGal(b1-3)GalNAc(a1-                                "
  [2] "B\tMan(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-"

format.glyrepr_structure without names works correctly

Code
  format(glycans)
Output
  [1] "Gal(b1-3)GalNAc(a1-                                "
  [2] "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-"

truncation works in tibble

Code
  print(tibble, width = 30)
Output
  # A tibble: 3 x 2
    struc                      a
    <struct>               <dbl>
  1 Man(a1-3)[Man(a1-6)]M~     1
  2 Man(a1-3)[Man(a1-6)]M~     1
  3 Man(a1-3)[Man(a1-6)]M~     1

print.glyrepr_structure supports n

<glycan_structure[11]>
[1] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[2] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[3] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[4] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[5] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[6] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[7] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[8] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[9] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[10] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
... (1 more not shown)
# Unique structures: 1

<glycan_structure[11]>
[1] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[2] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[3] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[4] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[5] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[6] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[7] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[8] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[9] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[10] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
[11] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
# Unique structures: 1

get_structure_graphs validates return_list parameter

Code
  get_structure_graphs(sv, return_list = FALSE)
Condition
  Error in `get_structure_graphs()`:
  ! `return_list` must be `TRUE` or `NULL` unless `x` has length 1.
  i Length of `x`: 2

Code
  get_structure_graphs(as_glycan_structure(character()), return_list = FALSE)
Condition
  Error in `get_structure_graphs()`:
  ! `return_list` must be `TRUE` or `NULL` unless `x` has length 1.
  i Length of `x`: 0