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Unverified Commit c9fb9e97 authored by St. Elmo's avatar St. Elmo
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implement some reviews

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src/reconstruction/CoreModel.jl
+ 23
− 72
View file @ c9fb9e97
......@@ -379,16 +379,9 @@ end
change_bounds!(
model::CoreModel,
reaction_idxs::Vector{Int};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
)
lower_bounds = fill(-_constants.default_reaction_bound, length(reaction_idxs)),
upper_bounds = fill(constants.default_reaction_bound, length(reaction_idxs)),
)
Change the bounds of all reactions with indices `reaction_idxs` in `model` in-place. Note
that if the bound argument is not supplied then a default (see
......@@ -407,14 +400,8 @@ change_bounds!(model, [2, 3]; upper_bounds=[10.2, 23])
function change_bounds!(
model::CoreModel,
rxns::Vector{Int};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
lower_bounds = fill(-_constants.default_reaction_bound, length(rxns)),
upper_bounds = fill(constants.default_reaction_bound, length(rxns)),
)
model.xl[rxns] .= lower_bounds
model.xu[rxns] .= upper_bounds
......@@ -455,18 +442,12 @@ end
"""
change_bounds!(
model::CoreModel,
reaction_ids::Vector{String};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
rxn_ids::Vector{String};
lower_bounds = fill(-_constants.default_reaction_bound, length(rxn_ids)),
upper_bounds = fill(constants.default_reaction_bound, length(rxn_ids)),
)
Change the bounds of all reactions with `reaction_ids` in `model` in-place. Note
Change the bounds of all reactions with `rxn_ids` in `model` in-place. Note
that if the bound argument is not supplied then a default (see
`_constants.default_reaction_bound`) is used. The same default bound argument is
used for each reaction bound if not supplied.
......@@ -483,14 +464,8 @@ change_bounds!(model, ["PFL", "FBA"]; upper_bounds=[10.2, 23])
function change_bounds!(
model::CoreModel,
rxn_ids::Vector{String};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
lower_bounds = fill(-_constants.default_reaction_bound, length(rxn_ids)),
upper_bounds = fill(constants.default_reaction_bound, length(rxn_ids)),
)
change_bounds!(model, Int.(indexin(rxn_ids, reactions(model))); lower_bounds = lower_bounds, upper_bounds = upper_bounds)
end
......@@ -528,19 +503,13 @@ end
"""
change_bounds(
model::CoreModel,
reaction_idxs::Vector{Int};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
)
rxns::Vector{Int};
lower_bounds = fill(-_constants.default_reaction_bound, length(rxns)),
upper_bounds = fill(constants.default_reaction_bound, length(rxns)),
)
Return a shallow copy of the `model` where the bounds of all reactions with
indices `reaction_idxs` in `model` have been changed. Note that if the bound
indices `rxns` in `model` have been changed. Note that if the bound
argument is not supplied then a default (see
`_constants.default_reaction_bound`) is used. The same default bound argument is
used for each reaction bound if not supplied.
......@@ -557,14 +526,8 @@ new_model = change_bounds(model, [2, 3]; upper_bounds=[10.2, 23])
function change_bounds(
model::CoreModel,
rxns::Vector{Int};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
lower_bounds = fill(-_constants.default_reaction_bound, length(rxns)),
upper_bounds = fill(constants.default_reaction_bound, length(rxns)),
)
m = copy(model)
m.xl = copy(model.xl)
......@@ -613,15 +576,9 @@ end
"""
change_bounds(
model::CoreModel,
reaction_ids::Vector{String};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
rxn_ids::Vector{String};
lower_bounds = fill(-_constants.default_reaction_bound, length(rxn_ids)),
upper_bounds = fill(constants.default_reaction_bound, length(rxn_ids)),
)
Change the bounds of all reactions with `reaction_ids` in `model` in-place. Note
......@@ -641,14 +598,8 @@ new_model = change_bounds(model, ["PFL", "FBA"]; upper_bounds=[10.2, 23])
function change_bounds(
model::CoreModel,
rxn_ids::Vector{String};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
lower_bounds = fill(-_constants.default_reaction_bound, length(rxn_ids)),
upper_bounds = fill(constants.default_reaction_bound, length(rxn_ids)),
)
change_bounds(model, Int.(indexin(rxn_ids, reactions(model))); lower_bounds = lower_bounds, upper_bounds = upper_bounds)
end
......
src/reconstruction/StandardModel.jl
+ 8
− 32
View file @ c9fb9e97
......@@ -249,14 +249,8 @@ end
change_bounds!(
model::StandardModel,
reaction_ids::Vector{String};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
lower_bounds = fill(-_constants.default_reaction_bound, length(reaction_ids)),
upper_bounds = fill(_constants.default_reaction_bound, length(reaction_ids)),
)
Change the bounds of all reactions with `reaction_ids` in `model` in-place. Note
......@@ -276,14 +270,8 @@ change_bounds!(model, ["PFL", "FBA"]; upper_bounds=[10.2, 23])
function change_bounds!(
model::StandardModel,
reaction_ids::Vector{String};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
lower_bounds = fill(-_constants.default_reaction_bound, length(reaction_ids)),
upper_bounds = fill(_constants.default_reaction_bound, length(reaction_ids)),
)
for (rid, lb, ub) in zip(reaction_ids, lower_bounds, upper_bounds)
change_bound!(model, rid; lower_bound = lb, upper_bound = ub)
......@@ -329,14 +317,8 @@ end
change_bounds(
model::StandardModel,
reaction_ids::Vector{String};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
lower_bounds = fill(-_constants.default_reaction_bound, length(reaction_ids)),
upper_bounds = fill(constants.default_reaction_bound, length(reaction_ids)),
)
Return a shallow copy of the `model` where the reaction bounds of all
......@@ -355,14 +337,8 @@ new_model = change_bounds(model, ["PFL", "FBA"]; ub=[10, 22])
function change_bounds(
model::StandardModel,
reaction_ids::Vector{String};
lower_bounds = repeat(
[-_constants.default_reaction_bound],
inner = length(reaction_ids),
),
upper_bounds = repeat(
[_constants.default_reaction_bound],
inner = length(reaction_ids),
),
lower_bounds = fill(-_constants.default_reaction_bound, length(reaction_ids)),
upper_bounds = fill(constants.default_reaction_bound, length(reaction_ids)),
)
m = copy(model)
m.reactions = copy(model.reactions)
......
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