diff --git a/docs/src/functions/types.md b/docs/src/functions/types.md index ad20573e3..c952444c3 100644 --- a/docs/src/functions/types.md +++ b/docs/src/functions/types.md @@ -12,3 +12,9 @@ Pages = map(file -> joinpath("base", "types", "abstract", file), readdir("../src Modules = [COBREXA] Pages = map(file -> joinpath("base", "types", file), readdir("../src/base/types")) ``` + +## Model type wrappers +```@autodocs +Modules = [COBREXA] +Pages = map(file -> joinpath("base", "types", "wrappers", file), readdir("../src/base/types/wrappers")) +``` diff --git a/src/base/types/MetabolicModel.jl b/src/base/types/MetabolicModel.jl index e9571b4e7..ee764cffe 100644 --- a/src/base/types/MetabolicModel.jl +++ b/src/base/types/MetabolicModel.jl @@ -31,7 +31,7 @@ end Return a vector of metabolite identifiers in a model. The vector precisely corresponds to the rows in [`stoichiometry`](@ref) matrix. -As with [`reaction`](@ref)s, some metabolites in models may be virtual, +As with [`reactions`](@ref)s, some metabolites in models may be virtual, representing purely technical equality constraints. """ function metabolites(a::MetabolicModel)::Vector{String} diff --git a/src/base/utils/enzymes.jl b/src/base/utils/enzymes.jl index 1d1278e0f..152437fb1 100644 --- a/src/base/utils/enzymes.jl +++ b/src/base/utils/enzymes.jl @@ -34,9 +34,10 @@ gene_product_mass_group_dict(model::GeckoModel, opt_model) = """ gene_product_mass_group_dict(model::GeckoModel) -A pipe-able variant of [`mass_group_dict`](@ref). +A pipe-able variant of [`gene_product_mass_group_dict`](@ref). """ -gene_product_mass_group_dict(model::GeckoModel) = x -> mass_group_dict(model, x) +gene_product_mass_group_dict(model::GeckoModel) = + x -> gene_product_mass_group_dict(model, x) """ gene_product_mass(model::SMomentModel) diff --git a/src/reconstruction/gapfill_minimum_reactions.jl b/src/reconstruction/gapfill_minimum_reactions.jl index c4b975a02..f6bced117 100644 --- a/src/reconstruction/gapfill_minimum_reactions.jl +++ b/src/reconstruction/gapfill_minimum_reactions.jl @@ -21,7 +21,7 @@ refining genome annotation." *Proceedings of the National Academy of Sciences* The function returns a solved JuMP optimization model, with the boolean reaction inclusion indicators in variable vector `y`. Use -[`mask`](@ref) or [`gapfilled_rids`](@ref) to collect the reaction +[`gapfilled_mask`](@ref) or [`gapfilled_rids`](@ref) to collect the reaction information in Julia datatypes. To reduce the uncertainty in the MILP solver (and likely reduce the