Model

class Model

A Component is any element of an SBML or CellML model. It can represent an SBML species, reaction, or compartment.

Subclassed by semsim::SBMLModel

Public Types

typedef std::vector<ComponentPtr> Components

The type used to store the collection of Components. Treat as opaque.

Public Functions

virtual ~Model()

Virtual destructor.

Component *addComponent(const Component &component)

Add a new component to the model (copy)

const Components &getComponents() const

Get the collection of components contained in this model. The return type is guaranteed to be iterable. Otherwise, treat it as opaque.

Components &getComponents()

Get the collection of components contained in this model. The return type is guaranteed to be iterable. Otherwise, treat it as opaque.

std::size_t getNumComponents() const

Get the number of components in the model.

virtual std::string getRDF(const URI &sbml_base_uri, const std::string &format = "rdfxml") const = 0

Get the RDF serialization of this model. The serialized RDF will always need to refer back to the original SBML or CellML model using a URI. Usually, the RDF will be written to a COMBINE archive along with the model, in which case the sbml_base_uri argument should be the relative path to the model file in the COMBINE archive.

Return

A string representation of the RDF for model using the desired RDF serialization format.

Parameters

• format: The RDF serialization format. Choices include “rdfxml”, “ntriples”, “turtle”, “trig”, “rss-tag-soup”, “grddl”, “rdfa”, “json”, and “nquads”.

• sbml_base_uri: A URI that points to the original model file. Usually a relative path in a COMBINE archive.

std::string humanize() const

Return a humanreadable representation of the annotation information. Ontology terms will be replaced with human-readable names.