The purpose of the Model class is to serve as a placeholder for an external computational model and provide additional meta-data to enable better reasoning about the contents of this model.
In this way, there is minimal duplication of standardization efforts and users of SBOL can formalize the function of a ModuleDefinition in the language of their choice.
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URIProperty | source |
| | The source property is REQUIRED and MUST contain a URI reference to the source file for a model.
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| URIProperty | language |
| | The language property is REQUIRED and MUST contain a URI that specifies the language in which the model is implemented. More...
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URIProperty | framework |
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URIProperty | persistentIdentity |
| | The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.
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TextProperty | displayId |
| | The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.
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VersionProperty | version |
| | If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters “.” and “-” and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.
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URIProperty | wasDerivedFrom |
| | The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain “ A was derived from B and B was derived from A” is cyclical.
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ReferencedObject | wasGeneratedBy |
| | An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.
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TextProperty | name |
| | The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the object’s displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.
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TextProperty | description |
| | The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.
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URIProperty | identity |
| | The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified object’s identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.
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| | Model (std::string uri="example", std::string source="", std::string language=EDAM_SBML, std::string framework=SBO_CONTINUOUS, std::string version=VERSION_STRING) |
| | Construct a Model. More...
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| | Model (rdf_type type, std::string uri, std::string source, std::string language, std::string framework, std::string version) |
| | Constructor used for defining extension classes. More...
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| template<class SBOLClass > |
| SBOLClass & | copy (Document *target_doc=NULL, std::string ns="", std::string version="") |
| | Recursively copies an object. More...
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| template<class SBOLClass > |
| SBOLClass & | simpleCopy (std::string uri) |
| | Copies an object. More...
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| template<class SBOLClass > |
| SBOLClass & | generate (std::string uri) |
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| template<class SBOLClass > |
| SBOLClass & | generate (std::string uri, Agent &agent, Plan &plan, std::vector< Identified *> usages={}) |
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| virtual rdf_type | getTypeURI () |
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| std::string | getClassName (std::string type) |
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| SBOLObject * | find (std::string uri) |
| | Search this object recursively to see if an object or any child object with URI already exists. More...
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| SBOLObject * | find_property (std::string uri) |
| | Search this object recursively to see if it contains a member property with the given RDF type. More...
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| std::vector< SBOLObject * > | find_property_value (std::string uri, std::string value, std::vector< SBOLObject *> matches={}) |
| | Search this object recursively to see if it contains a member property with the given RDF type and indicated property value. More...
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| std::vector< SBOLObject * > | find_reference (std::string uri) |
| | Search this object recursively to see if it contains a member property with the given RDF type and indicated property value. More...
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| int | compare (SBOLObject *comparand) |
| | Compare two SBOL objects or Documents. More...
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| std::string | getPropertyValue (std::string property_uri) |
| | Get the value of a custom annotation property by its URI. More...
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| std::vector< std::string > | getPropertyValues (std::string property_uri) |
| | Get all values of a custom annotation property by its URI. More...
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| std::vector< std::string > | getProperties () |
| | Gets URIs for all properties contained by this object. More...
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| void | setPropertyValue (std::string property_uri, std::string val) |
| | Set and overwrite the value for a user-defined annotation property. More...
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| void | addPropertyValue (std::string property_uri, std::string val) |
| | Append a value to a user-defined annotation property. More...
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| void | setAnnotation (std::string property_uri, std::string val) |
| | Set the value for a user-defined annotation property. More...
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| std::string | getAnnotation (std::string property_uri) |
| | Get the value of a custom annotation property by its URI. More...
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| virtual void | close () |
| | Use this method to destroy an SBOL object that is not contained by a parent Document. More...
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| SBOLClass & copy |
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Document * |
target_doc = NULL, |
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std::string |
ns = "", |
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std::string |
version = "" |
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inherited |
Recursively copies an object.
Use this to copy an object to a new document, a new namespace, or to increment its version recursively. An object be recursively copied into a new document and a new namespace, assuming compliant URIs. If the optional version argument is specified, it will be used instead of incrementing the copied object's version (this can be used when using a custom versioning scheme other than libSBOL's default).
- Template Parameters
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| SBOLClass | The type of SBOL object being copied |
- Parameters
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| new_doc | The new copies will be attached to this Document. NULL by default. |
| ns | This namespace will be substituted for the current namespace (as configured by setHomespace) in all SBOL-compliant URIs. |
| version | A new version |
- Returns
- The copied object.
