Input and output

close(model::HDF5Model)

Close (and un-cache) the HDF5Model data. This allows the associated file to be opened for writing again.

load_h5_model(file_name::String) -> HDF5Model

Return a HDF5Model associated with the given file. Does not actually load anything (for efficiency) – use precache! to start pulling data into the memory.

save_h5_model(model::MetabolicModel, file_name::String) -> HDF5Model

Converts and writes a metabolic model to disk in the HDF5 format.

Additionally returns an (uncached) HDF5Model that represents the contents of the saved file. Because all HDF5-based models need to be backed by disk storage, writing the data to disk (using this function) is the only way to make new HDF5 models.

load_model(file_name::String; extension) -> Any

Generic function for loading models that chooses a specific loader function based on the extension argument (e.g., ".xml" chooses loading of the SBML model format), or throws an error. By default the extension from file_name is used.

Currently, these model types are supported:

• SBML models (*.xml, loaded with load_sbml_model)
• JSON models (*.json, loaded with load_json_model)
• MATLAB models (*.mat, loaded with load_mat_model)
• HDF5 models (*.h5, loaded with load_h5_model)

load_model(type::Type{T<:MetabolicModel}, file_name::String; extension) -> MetabolicModel

Helper function that loads the model using load_model and returns it converted to type.

Example:

load_model(CoreModel, "mySBMLModel.xml")

save_model(model::MetabolicModel, file_name::String; extension) -> Maybe{HDF5Model}

Generic function for saving models that chooses a specific writer function from the extension argument (such as ".xml" for SBML format), or throws an error. By default the extension from file_name is used.

Currently, these model types are supported:

• SBML models (*.xml, saved with save_sbml_model)
• JSON models (*.json, saved with save_json_model)
• MATLAB models (*.mat, saved with save_mat_model)
• HDF5 models (*.h5, saved with save_h5_model)

load_json_model(filename::String) -> JSONModel

Load and return a JSON-formatted model that is stored in file_name.

save_json_model(model::MetabolicModel, file_name::String)

Save a JSONModel in model to a JSON file file_name.

In case the model is not JSONModel, it will be converted automatically.

load_mat_model(file_name::String) -> MATModel

Load and return a MATLAB file file_name that contains a COBRA-compatible model.

save_mat_model(model::MetabolicModel, file_path::String; model_name)

Save a MATModel in model to a MATLAB file file_name in a format compatible with other MATLAB-based COBRA software.

In case the model is not MATModel, it will be converted automatically.

model_name is the identifier name for the whole model written to the MATLAB file; defaults to just "model".

load_sbml_model(file_name::String) -> SBMLModel

Load and return a SBML XML model in file_name.

save_sbml_model(model::MetabolicModel, file_name::String)

Write a given SBML model to file_name.

show(io::IO, _::MIME{Symbol("text/plain")}, m::MetabolicModel)

Pretty printing of everything metabolic-modelish.

_pretty_substances(ss::Vector{String}) -> String

Nicely format a substance list.

show(io::IO, _::MIME{Symbol("text/plain")}, m::Serialized{M})

Show the Serialized model without unnecessarily loading it.

_pretty_print_keyvals(io, def::String, payload; kwargs...)

Nicely prints keys and values.

_pretty_print_keyvals(io, def::String, payload::Dict)

Specialization of _pretty_print_keyvals for dictionaries.

_pretty_print_keyvals(io, def::String, payload::String)

Specialization of _pretty_print_keyvals for plain strings.