glyrepr 0.7.4

Minor improvements and bug fixes

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

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.

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.

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.

n_glycan_core() now has a “b1” reducing end anomer, not “?1”.
Add validation to glycan_structure() to ensure no duplicated linkage positions. For example, “Gal(b1-3)[Fuc(a1-3)]GalNAc(b1-” is invalid now becuase both “Gal” and “Fuc” are linked to “GalNAc” at position 3.
Add descriptions about ambiguous linkages and anomers in glycan_structure() documentation.
remove_linkages() now also removes reducing end anomers.
n_glycan_core(), o_glycan_core_1(), and o_glycan_core_2() now have “??” anomers when linkage = FALSE.
Fix a bug in smap_structure(), smap2_structure(), spmap_structure(), and simap_structure() where modifying the structures can create identical structures, but the unique structures are not updated correctly. This automatically fixes a similar bug in remove_linkages().

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.

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

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.