libSBML C# API
libSBML 5.8.0 C# API
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Implementation of SBML's Model construct.
In an SBML model definition, a single object of class Model serves as the overall container for the lists of the various model components. All of the lists are optional, but if a given list container is present within the model, the list must not be empty; that is, it must have length one or more. The following are the components and lists permitted in different Levels and Versions of SBML in version 5.8.0 of libSBML:
In SBML Level 1, the components are: UnitDefinition, Compartment, Species, Parameter, Rule, and Reaction. Instances of the classes are placed inside instances of classes ListOfUnitDefinitions, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfRules, and ListOfReactions.
In SBML Level 2 Version 1, the components are: FunctionDefinition, UnitDefinition, Compartment, Species, Parameter, Rule, Reaction and Event. Instances of the classes are placed inside instances of classes ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfRules, ListOfReactions, and ListOfEvents.
In SBML Level 2 Versions 2, 3 and 4, the components are: FunctionDefinition, UnitDefinition, CompartmentType, SpeciesType, Compartment, Species, Parameter, InitialAssignment, Rule, Constraint, Reaction and Event. Instances of the classes are placed inside instances of classes ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartmentTypes, ListOfSpeciesTypes, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules, ListOfConstraints, ListOfReactions, and ListOfEvents.
Although all the lists are optional, there are dependencies between SBML components such that defining some components requires defining others. An example is that defining a species requires defining a compartment, and defining a reaction requires defining a species. The dependencies are explained in more detail in the SBML specifications.
In addition to the above lists and attributes, the Model class in both SBML Level 2 and Level 3 has the usual two attributes of 'id' and 'name', and both are optional. As is the case for other SBML components with 'id' and 'name' attributes, they must be used according to the guidelines described in the SBML specifications. (Within the frameworks of SBML Level 2 and Level 3 Version 1 Core, a Model object identifier has no assigned meaning, but extension packages planned for SBML Level 3 are likely to make use of this identifier.)
Finally, SBML Level 3 has introduced a number of additional Model attributes. They are discussed in a separate section below.
LibSBML provides two main mechanisms for creating objects: class constructors (e.g., Species::Species() ), and createObject()
methods (such as Model::createSpecies()) provided by certain Object classes such as Model. These multiple mechanisms are provided by libSBML for flexibility and to support different use-cases, but they also have different implications for the overall model structure.
In general, the recommended approach is to use the createObject()
methods. These methods both create an object and link it to the parent in one step. Here is an example: // Create an SBMLDocument object in Level 3 Version 1 format:
SBMLDocument sbmlDoc = new SBMLDocument(3, 1);
// Create a Model object inside the SBMLDocument object and set // its identifier. The call returns a pointer to the Model object // created, and methods called on that object affect the attributes // of the object attached to the model (as expected).
Model model = sbmlDoc.createModel(); model.setId('BestModelEver');
// Create a Species object inside the Model and set its identifier. // Similar to the lines above, this call returns a pointer to the Species // object created, and methods called on that object affect the attributes // of the object attached to the model (as expected).
Species sp = model.createSpecies(); sp.setId('MySpecies');
The createObject()
methods return a pointer to the object created, but they also add the object to the relevant list of object instances contained in the parent. (These lists become the <listOfObjects>
elements in the finished XML rendition of SBML.) In the example above, Model::createSpecies() adds the created species directly to the <listOfSpecies>
list in the model. Subsequently, methods called on the species change the species in the model (which is what is expected in most situations).
To make it easier for applications to do whatever they need, libSBML version 5.8.0 is relatively lax when it comes to enforcing correctness and completeness of models during model construction and editing. Essentially, libSBML will not in most cases check automatically that a model's components have valid attribute values, or that the overall model is consistent and free of errors—even obvious errors such as duplication of identifiers. This allows applications great leeway in how they build their models, but it means that software authors must take deliberate steps to ensure that the model will be, in the end, valid SBML. These steps include such things as keeping track of the identifiers used in a model, manually performing updates in certain situations where an entity is referenced in more than one place (e.g., a species that is referenced by multiple SpeciesReference objects), and so on.
That said, libSBML does provide powerful features for deliberately performing validation of SBML when an application decides it is time to do so. The interfaces to these facilities are on the SBMLDocument class, in the form of SBMLDocument::checkInternalConsistency() and SBMLDocument::checkConsistency(). Please refer to the documentation for SBMLDocument for more information about this.
While applications may play fast and loose and live like free spirits during the construction and editing of SBML models, they should always make sure to call SBMLDocument::checkInternalConsistency() and/or SBMLDocument::checkConsistency() before writing out the final version of an SBML model.
As mentioned above, the Model class has a number of optional attributes in SBML Level 3 Version 1 Core. These are 'substanceUnits', 'timeUnits', 'volumeUnits', 'areaUnits', 'lengthUnits', 'extentUnits', and 'conversionFactor. The following provide more information about them.
The 'substanceUnits' attribute is used to specify the unit of measurement associated with substance quantities of Species objects that do not specify units explicitly. If a given Species object definition does not specify its unit of substance quantity via the 'substanceUnits' attribute on the Species object instance, then that species inherits the value of the Model 'substanceUnits' attribute. If the Model does not define a value for this attribute, then there is no unit to inherit, and all species that do not specify individual 'substanceUnits' attribute values then have no declared units for their quantities. The SBML Level 3 Version 1 Core specification provides more details.
Note that when the identifier of a species appears in a model's mathematical expressions, the unit of measurement associated with that identifier is not solely determined by setting 'substanceUnits' on Model or Species. Please see the discussion about units given in the documentation for the Species class.
The 'timeUnits' attribute on SBML Level 3's Model object is used to specify the unit in which time is measured in the model. This attribute on Model is the only way to specify a unit for time in a model. It is a global attribute; time is measured in the model everywhere in the same way. This is particularly relevant to Reaction and RateRule objects in a model: all Reaction and RateRule objects in SBML define per-time values, and the unit of time is given by the 'timeUnits' attribute on the Model object instance. If the Model 'timeUnits' attribute has no value, it means that the unit of time is not defined for the model's reactions and rate rules. Leaving it unspecified in an SBML model does not result in an invalid model in SBML Level 3; however, as a matter of best practice, we strongly recommend that all models specify units of measurement for time.
The attributes 'volumeUnits', 'areaUnits' and 'lengthUnits' together are used to set the units of measurements for the sizes of Compartment objects in an SBML Level 3 model when those objects do not otherwise specify units. The three attributes correspond to the most common cases of compartment dimensions: 'volumeUnits' for compartments having a 'spatialDimensions' attribute value of '3'
, 'areaUnits' for compartments having a 'spatialDimensions' attribute value of '2'
, and 'lengthUnits' for compartments having a 'spatialDimensions' attribute value of '1'
. The attributes are not applicable to compartments whose 'spatialDimensions' attribute values are not one of '1'
, '2'
or '3'
.
If a given Compartment object instance does not provide a value for its 'units' attribute, then the unit of measurement of that compartment's size is inherited from the value specified by the Model 'volumeUnits', 'areaUnits' or 'lengthUnits' attribute, as appropriate based on the Compartment object's 'spatialDimensions' attribute value. If the Model object does not define the relevant attribute, then there are no units to inherit, and all Compartment objects that do not set a value for their 'units' attribute then have no units associated with their compartment sizes.
The use of three separate attributes is a carry-over from SBML Level 2. Note that it is entirely possible for a model to define a value for two or more of the attributes 'volumeUnits', 'areaUnits' and 'lengthUnits' simultaneously, because SBML models may contain compartments with different numbers of dimensions.
Reactions are processes that occur over time. These processes involve events of some sort, where a single ``reaction event'' is one in which some set of entities (known as reactants, products and modifiers in SBML) interact, once. The extent of a reaction is a measure of how many times the reaction has occurred, while the time derivative of the extent gives the instantaneous rate at which the reaction is occurring. Thus, what is colloquially referred to as the 'rate of the reaction' is in fact equal to the rate of change of reaction extent.
In SBML Level 3, the combination of 'extentUnits' and 'timeUnits' defines the units of kinetic laws in SBML and establishes how the numerical value of each KineticLaw object's mathematical formula is meant to be interpreted in a model. The units of the kinetic laws are taken to be 'extentUnits' divided by 'timeUnits'.
Note that this embodies an important principle in SBML Level 3 models: all reactions in an SBML model must have the same units for the rate of change of extent. In other words, the units of all reaction rates in the model must be the same. There is only one global value for 'extentUnits' and one global value for 'timeUnits'.
The attribute 'conversionFactor' in SBML Level 3's Model object defines a global value inherited by all Species object instances that do not define separate values for their 'conversionFactor' attributes. The value of this attribute must refer to a Parameter object instance defined in the model. The Parameter object in question must be a constant; ie it must have its 'constant' attribute value set to 'true'
.
If a given Species object definition does not specify a conversion factor via the 'conversionFactor' attribute on Species, then the species inherits the conversion factor specified by the Model 'conversionFactor' attribute. If the Model does not define a value for this attribute, then there is no conversion factor to inherit. More information about conversion factors is provided in the SBML Level 3 Version 1 specification.
Public Member Functions | |
int | addCompartment (Compartment c) |
Adds a copy of the given Compartment object to this Model. More... | |
int | addCompartmentType (CompartmentType ct) |
Adds a copy of the given CompartmentType object to this Model. More... | |
void | addConstantAttribute () |
Predicate returning true if the given ASTNode is a bool. More... | |
int | addConstraint (Constraint c) |
Adds a copy of the given Constraint object to this Model. More... | |
int | addCVTerm (CVTerm term, bool newBag) |
Adds a copy of the given CVTerm object to this SBML object. More... | |
int | addCVTerm (CVTerm term) |
Adds a copy of the given CVTerm object to this SBML object. More... | |
void | addDefinitionsForDefaultUnits () |
Predicate returning true if the given ASTNode is a bool. More... | |
int | addEvent (Event e) |
Adds a copy of the given Event object to this Model. More... | |
int | addFunctionDefinition (FunctionDefinition fd) |
Adds a copy of the given FunctionDefinition object to this Model. More... | |
int | addInitialAssignment (InitialAssignment ia) |
Adds a copy of the given InitialAssignment object to this Model. More... | |
void | addModifiers () |
Predicate returning true if the given ASTNode is a bool. More... | |
int | addParameter (Parameter p) |
Adds a copy of the given Parameter object to this Model. More... | |
int | addReaction (Reaction r) |
Adds a copy of the given Reaction object to this Model. More... | |
int | addRule (Rule r) |
Adds a copy of the given Rule object to this Model. More... | |
int | addSpecies (Species s) |
Adds a copy of the given Species object to this Model. More... | |
int | addSpeciesType (SpeciesType st) |
Adds a copy of the given SpeciesType object to this Model. More... | |
int | addUnitDefinition (UnitDefinition ud) |
Adds a copy of the given UnitDefinition object to this Model. More... | |
new int | appendAnnotation (XMLNode annotation) |
Appends annotation content to any existing content in the 'annotation' subelement of this object. More... | |
new int | appendAnnotation (string annotation) |
Appends annotation content to any existing content in the 'annotation' subelement of this object. More... | |
int | appendFrom (Model model) |
Takes the contents of the passed-in Model, makes copies of everything, and appends those copies to the appropriate places in this Model. More... | |
int | appendNotes (XMLNode notes) |
Appends the given notes to the 'notes' subelement of this object. More... | |
int | appendNotes (string notes) |
Appends the given notes to the 'notes' subelement of this object. More... | |
void | assignRequiredValues () |
Predicate returning true if the given ASTNode is a bool. More... | |
int | checkCompatibility (SBase arg0) |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
string | checkMathMLNamespace (XMLToken elem) |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
new Model | clone () |
Creates and returns a deep copy of this Model object. More... | |
void | connectToParent (SBase parent) |
Sets the parent SBML object of this SBML object. More... | |
void | convertL1ToL2 () |
Predicate returning true if the given ASTNode is a bool. More... | |
void | convertL1ToL3 () |
Predicate returning true if the given ASTNode is a bool. More... | |
void | convertL2ToL1 (bool strict) |
Predicate returning true if the given ASTNode is a bool. More... | |
void | convertL2ToL1 () |
Predicate returning true if the given ASTNode is a bool. More... | |
void | convertL2ToL3 () |
Predicate returning true if the given ASTNode is a bool. More... | |
void | convertL3ToL1 () |
Predicate returning true if the given ASTNode is a bool. More... | |
void | convertL3ToL2 (bool strict) |
Predicate returning true if the given ASTNode is a bool. More... | |
void | convertL3ToL2 () |
Predicate returning true if the given ASTNode is a bool. More... | |
void | convertParametersToLocals (long level, long version) |
Predicate returning true if the given ASTNode is a bool. More... | |
void | convertStoichiometryMath () |
Predicate returning true if the given ASTNode is a bool. More... | |
AlgebraicRule | createAlgebraicRule () |
Creates a new AlgebraicRule inside this Model and returns it. More... | |
AssignmentRule | createAssignmentRule () |
Creates a new AssignmentRule inside this Model and returns it. More... | |
Compartment | createCompartment () |
Creates a new Compartment inside this Model and returns it. More... | |
CompartmentType | createCompartmentType () |
Creates a new CompartmentType inside this Model and returns it. More... | |
Constraint | createConstraint () |
Creates a new Constraint inside this Model and returns it. More... | |
Delay | createDelay () |
Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it. More... | |
Event | createEvent () |
Creates a new Event inside this Model and returns it. More... | |
EventAssignment | createEventAssignment () |
Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it. More... | |
FunctionDefinition | createFunctionDefinition () |
Creates a new FunctionDefinition inside this Model and returns it. More... | |
InitialAssignment | createInitialAssignment () |
Creates a new InitialAssignment inside this Model and returns it. More... | |
KineticLaw | createKineticLaw () |
Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it. More... | |
LocalParameter | createKineticLawLocalParameter () |
Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it. More... | |
Parameter | createKineticLawParameter () |
Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it. More... | |
ModifierSpeciesReference | createModifier () |
Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it. More... | |
Parameter | createParameter () |
Creates a new Parameter inside this Model and returns it. More... | |
SpeciesReference | createProduct () |
Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it. More... | |
RateRule | createRateRule () |
Creates a new RateRule inside this Model and returns it. More... | |
SpeciesReference | createReactant () |
Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it. More... | |
Reaction | createReaction () |
Creates a new Reaction inside this Model and returns it. More... | |
Species | createSpecies () |
Creates a new Species inside this Model and returns it. More... | |
SpeciesType | createSpeciesType () |
Creates a new SpeciesType inside this Model and returns it. More... | |
Trigger | createTrigger () |
Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it. More... | |
Unit | createUnit () |
Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it. More... | |
UnitDefinition | createUnitDefinition () |
Creates a new UnitDefinition inside this Model and returns it. More... | |
void | dealWithEvents (bool strict) |
Predicate returning true if the given ASTNode is a bool. More... | |
void | dealWithModelUnits () |
Predicate returning true if the given ASTNode is a bool. More... | |
void | dealWithStoichiometry () |
Predicate returning true if the given ASTNode is a bool. More... | |
int | disablePackage (string pkgURI, string pkgPrefix) |
Disables the given SBML Level 3 package. More... | |
override void | Dispose () |
void | divideAssignmentsToSIdByFunction (string id, ASTNode function) |
If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More... | |
int | enablePackage (string pkgURI, string pkgPrefix, bool flag) |
Enables or disables the given SBML Level 3 package. More... | |
override bool | Equals (Object sb) |
SBase | getAncestorOfType (int type, string pkgName) |
Returns the first ancestor object that has the given SBML type code. More... | |
SBase | getAncestorOfType (int type) |
Returns the first ancestor object that has the given SBML type code. More... | |
XMLNode | getAnnotation () |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More... | |
string | getAnnotationString () |
Returns the content of the 'annotation' subelement of this object as a character string. More... | |
string | getAreaUnits () |
Returns the value of the 'areaUnits' attribute of this Model. More... | |
long | getColumn () |
Returns the column number on which this object first appears in the XML representation of the SBML document. More... | |
Compartment | getCompartment (long n) |
Get the nth Compartment object in this Model. More... | |
Compartment | getCompartment (string sid) |
Get a Compartment object based on its identifier. More... | |
CompartmentType | getCompartmentType (long n) |
Get the nth CompartmentType object in this Model. More... | |
CompartmentType | getCompartmentType (string sid) |
Get a CompartmentType object based on its identifier. More... | |
Constraint | getConstraint (long n) |
Get the nth Constraint object in this Model. More... | |
string | getConversionFactor () |
Returns the value of the 'conversionFactor' attribute of this Model. More... | |
CVTerm | getCVTerm (long n) |
Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
CVTermList | getCVTerms () |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
SBase | getElementByMetaId (string metaid) |
Returns the first child element it can find with the given metaid , or null if no such object is found. More... | |
SBase | getElementBySId (string id) |
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found. More... | |
SBase | getElementFromPluginsByMetaId (string metaid) |
Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found. More... | |
SBase | getElementFromPluginsBySId (string id) |
Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found. More... | |
new string | getElementName () |
Returns the XML element name of this object, which for Model, is always 'model' . More... | |
Event | getEvent (long n) |
Get the nth Event object in this Model. More... | |
Event | getEvent (string sid) |
Get an Event object based on its identifier. More... | |
string | getExtentUnits () |
Returns the value of the 'extentUnits' attribute of this Model. More... | |
FunctionDefinition | getFunctionDefinition (long n) |
Get the nth FunctionDefinitions object in this Model. More... | |
FunctionDefinition | getFunctionDefinition (string sid) |
Get a FunctionDefinition object based on its identifier. More... | |
override int | GetHashCode () |
new string | getId () |
Returns the value of the 'id' attribute of this Model. More... | |
InitialAssignment | getInitialAssignment (long n) |
Get the nth InitialAssignment object in this Model. More... | |
InitialAssignment | getInitialAssignment (string symbol) |
Get an InitialAssignment object based on the symbol to which it assigns a value. More... | |
string | getLengthUnits () |
Returns the value of the 'lengthUnits' attribute of this Model. More... | |
long | getLevel () |
Returns the SBML Level of the SBMLDocument object containing this object. More... | |
long | getLine () |
Returns the line number on which this object first appears in the XML representation of the SBML document. More... | |
SBaseList | getListOfAllElements () |
SBaseList | getListOfAllElementsFromPlugins () |
ListOfCompartments | getListOfCompartments () |
Get the ListOfCompartments object in this Model. More... | |
ListOfCompartmentTypes | getListOfCompartmentTypes () |
Get the ListOfCompartmentTypes object in this Model. More... | |
ListOfConstraints | getListOfConstraints () |
Get the ListOfConstraints object in this Model. More... | |
ListOfEvents | getListOfEvents () |
Get the ListOfEvents object in this Model. More... | |
ListOfFunctionDefinitions | getListOfFunctionDefinitions () |
Get the ListOfFunctionDefinitions object in this Model. More... | |
ListOfInitialAssignments | getListOfInitialAssignments () |
Get the ListOfInitialAssignments object in this Model. More... | |
ListOfParameters | getListOfParameters () |
Get the ListOfParameters object in this Model. More... | |
ListOfReactions | getListOfReactions () |
Get the ListOfReactions object in this Model. More... | |
ListOfRules | getListOfRules () |
Get the ListOfRules object in this Model. More... | |
ListOfSpecies | getListOfSpecies () |
Get the ListOfSpecies object in this Model. More... | |
ListOfSpeciesTypes | getListOfSpeciesTypes () |
Get the ListOfSpeciesTypes object in this Model. More... | |
ListOfUnitDefinitions | getListOfUnitDefinitions () |
Get the ListOfUnitDefinitions object in this Model. More... | |
string | getMetaId () |
Returns the value of the 'metaid' attribute of this object. More... | |
Model | getModel () |
Returns the Model object in which the current object is located. More... | |
ModelHistory | getModelHistory () |
Returns the ModelHistory object, if any, attached to this object. More... | |
new string | getName () |
Returns the value of the 'name' attribute of this Model. More... | |
XMLNamespaces | getNamespaces () |
Returns a list of the XML Namespaces declared on this SBML document. More... | |
XMLNode | getNotes () |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More... | |
string | getNotesString () |
Returns the content of the 'notes' subelement of this object as a string. More... | |
long | getNumCompartments () |
Get the number of Compartment objects in this Model. More... | |
long | getNumCompartmentTypes () |
Get the number of CompartmentType objects in this Model. More... | |
long | getNumConstraints () |
Get the number of Constraint objects in this Model. More... | |
long | getNumCVTerms () |
Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
long | getNumEvents () |
Get the number of Event objects in this Model. More... | |
long | getNumFunctionDefinitions () |
Get the number of FunctionDefinition objects in this Model. More... | |
long | getNumInitialAssignments () |
Get the number of InitialAssignment objects in this Model. More... | |
long | getNumParameters () |
Get the number of Parameter objects in this Model. More... | |
long | getNumPlugins () |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
long | getNumReactions () |
Get the number of Reaction objects in this Model. More... | |
long | getNumRules () |
Get the number of Rule objects in this Model. More... | |
long | getNumSpecies () |
Get the number of Specie objects in this Model. More... | |
long | getNumSpeciesTypes () |
Get the number of SpeciesType objects in this Model. More... | |
long | getNumSpeciesWithBoundaryCondition () |
Get the number of Species in this Model having their 'boundaryCondition' attribute value set to true . More... | |
long | getNumUnitDefinitions () |
Get the number of UnitDefinition objects in this Model. More... | |
string | getPackageName () |
Returns the name of the SBML Level 3 package in which this element is defined. More... | |
long | getPackageVersion () |
Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
Parameter | getParameter (long n) |
Get the nth Parameter object in this Model. More... | |
Parameter | getParameter (string sid) |
Get a Parameter object based on its identifier. More... | |
SBase | getParentSBMLObject () |
Returns the parent SBML object containing this object. More... | |
SBasePlugin | getPlugin (string package) |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
SBasePlugin | getPlugin (long n) |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
Reaction | getReaction (long n) |
Get the nth Reaction object in this Model. More... | |
Reaction | getReaction (string sid) |
Get a Reaction object based on its identifier. More... | |
int | getResourceBiologicalQualifier (string resource) |
Returns the MIRIAM biological qualifier associated with the given resource. More... | |
int | getResourceModelQualifier (string resource) |
Returns the MIRIAM model qualifier associated with the given resource. More... | |
Rule | getRule (long n) |
Get the nth Rule object in this Model. More... | |
Rule | getRule (string variable) |
Get a Rule object based on the variable to which it assigns a value. More... | |
SBMLDocument | getSBMLDocument () |
Returns the SBMLDocument object containing this object instance. More... | |
SBMLNamespaces | getSBMLNamespaces () |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
int | getSBOTerm () |
Returns the integer portion of the value of the 'sboTerm' attribute of this object. More... | |
string | getSBOTermAsURL () |
Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object. More... | |
string | getSBOTermID () |
Returns the string representation of the 'sboTerm' attribute of this object. More... | |
Species | getSpecies (long n) |
Get the nth Species object in this Model. More... | |
Species | getSpecies (string sid) |
Get a Species object based on its identifier. More... | |
SpeciesReference | getSpeciesReference (string sid) |
Get a SpeciesReference object based on its identifier. More... | |
SpeciesType | getSpeciesType (long n) |
Get the nth SpeciesType object in this Model. More... | |
SpeciesType | getSpeciesType (string sid) |
Get a SpeciesType object based on its identifier. More... | |
string | getSubstanceUnits () |
Returns the value of the 'substanceUnits' attribute of this Model. More... | |
string | getTimeUnits () |
Returns the value of the 'timeUnits' attribute of this Model. More... | |
new int | getTypeCode () |
Returns the libSBML type code for this SBML object. More... | |
UnitDefinition | getUnitDefinition (long n) |
Get the nth UnitDefinition object in this Model. More... | |
UnitDefinition | getUnitDefinition (string sid) |
Get a UnitDefinition based on its identifier. More... | |
long | getVersion () |
Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
string | getVolumeUnits () |
Returns the value of the 'volumeUnits' attribute of this Model. More... | |
bool | hasNonstandardIdentifierBeginningWith (string prefix) |
Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid'). More... | |
bool | hasRequiredAttributes () |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
new bool | hasRequiredElements () |
Predicate returning true if all the required elements for this Model object have been set. More... | |
bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
bool | isPackageEnabled (string pkgName) |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPackageURIEnabled (string pkgURI) |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isPkgEnabled (string pkgName) |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPkgURIEnabled (string pkgURI) |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isPopulatedListFormulaUnitsData () |
Predicate returning true if the list of FormulaUnitsData is populated. More... | |
bool | isSetAnnotation () |
Predicate returning true if this object's 'annotation' subelement exists and has content. More... | |
bool | isSetAreaUnits () |
Predicate returning true if this Model's 'areaUnits' attribute is set. More... | |
bool | isSetConversionFactor () |
Predicate returning true if this Model's 'conversionFactor' attribute is set. More... | |
bool | isSetExtentUnits () |
Predicate returning true if this Model's 'extentUnits' attribute is set. More... | |
new bool | isSetId () |
Predicate returning true if this Model's 'id' attribute is set. More... | |
bool | isSetLengthUnits () |
Predicate returning true if this Model's 'lengthUnits' attribute is set. More... | |
bool | isSetMetaId () |
Predicate returning true if this object's 'metaid' attribute is set. More... | |
bool | isSetModelHistory () |
Predicate returning true if this object has a ModelHistory object attached to it. More... | |
new bool | isSetName () |
Predicate returning true if this Model's 'name' attribute is set. More... | |
bool | isSetNotes () |
Predicate returning true if this object's 'notes' subelement exists and has content. More... | |
bool | isSetSBOTerm () |
Predicate returning true if this object's 'sboTerm' attribute is set. More... | |
bool | isSetSubstanceUnits () |
Predicate returning true if this Model's 'substanceUnits' attribute is set. More... | |
bool | isSetTimeUnits () |
Predicate returning true if this Model's 'timeUnits' attribute is set. More... | |
bool | isSetVolumeUnits () |
Predicate returning true if this Model's 'volumeUnits' attribute is set. More... | |
bool | matchesRequiredSBMLNamespacesForAddition (SBase sb) |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
bool | matchesSBMLNamespaces (SBase sb) |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
Model (long level, long version) | |
Creates a new Model using the given SBML level and version values. More... | |
Model (SBMLNamespaces sbmlns) | |
Creates a new Model using the given SBMLNamespaces object sbmlns . More... | |
Model (Model orig) | |
Copy constructor; creates a (deep) copy of the given Model object. More... | |
void | multiplyAssignmentsToSIdByFunction (string id, ASTNode function) |
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More... | |
void | populateListFormulaUnitsData () |
Populates the list of FormulaDataUnits with the units derived for the model. More... | |
int | prependStringToAllIdentifiers (string prefix) |
Add the given string to all identifiers in the object. More... | |
Compartment | removeCompartment (long n) |
Removes the nth Compartment object from this Model object and returns a pointer to it. More... | |
Compartment | removeCompartment (string sid) |
Removes the Compartment object with the given identifier from this Model object and returns a pointer to it. More... | |
CompartmentType | removeCompartmentType (long n) |
Removes the nth CompartmentType object from this Model object and returns a pointer to it. More... | |
CompartmentType | removeCompartmentType (string sid) |
Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it. More... | |
Constraint | removeConstraint (long n) |
Removes the nth Constraint object from this Model object and returns a pointer to it. More... | |
Event | removeEvent (long n) |
Removes the nth Event object from this Model object and returns a pointer to it. More... | |
Event | removeEvent (string sid) |
Removes the Event object with the given identifier from this Model object and returns a pointer to it. More... | |
int | removeFromParentAndDelete () |
Finds this Model's parent SBMLDocument and calls setModel(null) on it, indirectly deleting itself. More... | |
FunctionDefinition | removeFunctionDefinition (long n) |
Removes the nth FunctionDefinition object from this Model object and returns a pointer to it. More... | |
FunctionDefinition | removeFunctionDefinition (string sid) |
Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it. More... | |
InitialAssignment | removeInitialAssignment (long n) |
Removes the nth InitialAssignment object from this Model object and returns a pointer to it. More... | |
InitialAssignment | removeInitialAssignment (string symbol) |
Removes the InitialAssignment object with the given 'symbol' attribute from this Model object and returns a pointer to it. More... | |
Parameter | removeParameter (long n) |
Removes the nth Parameter object from this Model object and returns a pointer to it. More... | |
Parameter | removeParameter (string sid) |
Removes the Parameter object with the given identifier from this Model object and returns a pointer to it. More... | |
void | removeParameterRuleUnits (bool strict) |
Predicate returning true if the given ASTNode is a bool. More... | |
Reaction | removeReaction (long n) |
Removes the nth Reaction object from this Model object and returns a pointer to it. More... | |
Reaction | removeReaction (string sid) |
Removes the Reaction object with the given identifier from this Model object and returns a pointer to it. More... | |
Rule | removeRule (long n) |
Removes the nth Rule object from this Model object and returns a pointer to it. More... | |
Rule | removeRule (string variable) |
Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it. More... | |
Species | removeSpecies (long n) |
Removes the nth Species object from this Model object and returns a pointer to it. More... | |
Species | removeSpecies (string sid) |
Removes the Species object with the given identifier from this Model object and returns a pointer to it. More... | |
SpeciesType | removeSpeciesType (long n) |
Removes the nth SpeciesType object from this Model object and returns a pointer to it. More... | |
SpeciesType | removeSpeciesType (string sid) |
Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it. More... | |
int | removeTopLevelAnnotationElement (string elementName, string elementURI) |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
int | removeTopLevelAnnotationElement (string elementName) |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
UnitDefinition | removeUnitDefinition (long n) |
Removes the nth UnitDefinition object from this Model object and returns a pointer to it. More... | |
UnitDefinition | removeUnitDefinition (string sid) |
Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it. More... | |
void | renameMetaIdRefs (string oldid, string newid) |
Renames all the MetaIdRef attributes on this element. More... | |
void | renameSIdRefs (string oldid, string newid) |
Renames all the SIdRef attributes on this element, including any found in MathML. More... | |
void | renameUnitSIdRefs (string oldid, string newid) |
Renames all the UnitSIdRef attributes on this element. More... | |
void | replaceSIDWithFunction (string id, ASTNode function) |
If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More... | |
int | replaceTopLevelAnnotationElement (XMLNode annotation) |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More... | |
int | replaceTopLevelAnnotationElement (string annotation) |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More... | |
new int | setAnnotation (XMLNode annotation) |
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation . More... | |
new int | setAnnotation (string annotation) |
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation . More... | |
int | setAreaUnits (string units) |
Sets the value of the 'areaUnits' attribute of this Model. More... | |
int | setConversionFactor (string units) |
Sets the value of the 'conversionFactor' attribute of this Model. More... | |
int | setExtentUnits (string units) |
Sets the value of the 'extentUnits' attribute of this Model. More... | |
new int | setId (string sid) |
Sets the value of the 'id' attribute of this Model. More... | |
int | setLengthUnits (string units) |
Sets the value of the 'lengthUnits' attribute of this Model. More... | |
int | setMetaId (string metaid) |
Sets the value of the 'metaid' attribute of this object. More... | |
int | setModelHistory (ModelHistory history) |
Sets the ModelHistory of this object. More... | |
new int | setName (string name) |
Sets the value of the 'name' attribute of this Model. More... | |
int | setNamespaces (XMLNamespaces xmlns) |
Sets the namespaces relevant of this SBML object. More... | |
int | setNotes (XMLNode notes) |
Sets the value of the 'notes' subelement of this SBML object. More... | |
int | setNotes (string notes, bool addXHTMLMarkup) |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes . More... | |
int | setNotes (string notes) |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes . More... | |
void | setSBMLNamespacesAndOwn (SBMLNamespaces sbmlns) |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
int | setSBOTerm (int value) |
Sets the value of the 'sboTerm' attribute. More... | |
int | setSBOTerm (string sboid) |
Sets the value of the 'sboTerm' attribute by string. More... | |
void | setSpatialDimensions (double dims) |
Predicate returning true if the given ASTNode is a bool. More... | |
void | setSpatialDimensions () |
Predicate returning true if the given ASTNode is a bool. More... | |
void | setSpeciesReferenceConstantValueAndStoichiometry () |
Predicate returning true if the given ASTNode is a bool. More... | |
int | setSubstanceUnits (string units) |
Sets the value of the 'substanceUnits' attribute of this Model. More... | |
int | setTimeUnits (string units) |
Sets the value of the 'timeUnits' attribute of this Model. More... | |
int | setVolumeUnits (string units) |
Sets the value of the 'volumeUnits' attribute of this Model. More... | |
string | toSBML () |
Returns a string consisting of a partial SBML corresponding to just this object. More... | |
int | unsetAnnotation () |
Unsets the value of the 'annotation' subelement of this SBML object. More... | |
int | unsetAreaUnits () |
Unsets the value of the 'areaUnits' attribute of this Model. More... | |
int | unsetConversionFactor () |
Unsets the value of the 'conversionFactor' attribute of this Model. More... | |
int | unsetCVTerms () |
Clears the list of CVTerm objects attached to this SBML object. More... | |
int | unsetExtentUnits () |
Unsets the value of the 'extentUnits' attribute of this Model. More... | |
new int | unsetId () |
Unsets the value of the 'id' attribute of this Model. More... | |
int | unsetLengthUnits () |
Unsets the value of the 'lengthUnits' attribute of this Model. More... | |
int | unsetMetaId () |
Unsets the value of the 'metaid' attribute of this SBML object. More... | |
int | unsetModelHistory () |
Unsets the ModelHistory object attached to this object. More... | |
new int | unsetName () |
Unsets the value of the 'name' attribute of this Model. More... | |
int | unsetNotes () |
Unsets the value of the 'notes' subelement of this SBML object. More... | |
int | unsetSBOTerm () |
Unsets the value of the 'sboTerm' attribute of this SBML object. More... | |
int | unsetSubstanceUnits () |
Unsets the value of the 'substanceUnits' attribute of this Model. More... | |
int | unsetTimeUnits () |
Unsets the value of the 'timeUnits' attribute of this Model. More... | |
int | unsetVolumeUnits () |
Unsets the value of the 'volumeUnits' attribute of this Model. More... | |
void | writeExtensionElements (XMLOutputStream stream) |
Writes out contained SBML objects of package extensions (if any) as XML elements. More... | |
Static Public Member Functions | |
static bool | operator!= (SBase lhs, SBase rhs) |
static bool | operator== (SBase lhs, SBase rhs) |
Protected Attributes | |
bool | swigCMemOwn |
libsbmlcs.Model.Model | ( | long | level, |
long | version | ||
) |
Creates a new Model using the given SBML level
and version
values.
level | a long integer, the SBML Level to assign to this Model |
version | a long integer, the SBML Version to assign to this Model |
SBMLConstructorException | Thrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object. |
libsbmlcs.Model.Model | ( | SBMLNamespaces | sbmlns | ) |
Creates a new Model using the given SBMLNamespaces object sbmlns
.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using this class constructor is to create an SBMLNamespaces object somewhere in a program, once, then pass it to object constructors such as this one when needed.
sbmlns | an SBMLNamespaces object. |
SBMLConstructorException | Thrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object. |
libsbmlcs.Model.Model | ( | Model | orig | ) |
Copy constructor; creates a (deep) copy of the given Model object.
orig | the object to copy. |
SBMLConstructorException | Thrown if the argument orig is null . |
int libsbmlcs.Model.addCompartment | ( | Compartment | c | ) |
Adds a copy of the given Compartment object to this Model.
c | the Compartment object to add |
int libsbmlcs.Model.addCompartmentType | ( | CompartmentType | ct | ) |
Adds a copy of the given CompartmentType object to this Model.
ct | the CompartmentType object to add |
void libsbmlcs.Model.addConstantAttribute | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
int libsbmlcs.Model.addConstraint | ( | Constraint | c | ) |
Adds a copy of the given Constraint object to this Model.
c | the Constraint object to add |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if true , creates a new RDF bag with the same identifier as a previous bag, and if false , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if true , creates a new RDF bag with the same identifier as a previous bag, and if false , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
void libsbmlcs.Model.addDefinitionsForDefaultUnits | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
int libsbmlcs.Model.addEvent | ( | Event | e | ) |
Adds a copy of the given Event object to this Model.
e | the Event object to add |
int libsbmlcs.Model.addFunctionDefinition | ( | FunctionDefinition | fd | ) |
Adds a copy of the given FunctionDefinition object to this Model.
fd | the FunctionDefinition to add |
int libsbmlcs.Model.addInitialAssignment | ( | InitialAssignment | ia | ) |
Adds a copy of the given InitialAssignment object to this Model.
ia | the InitialAssignment object to add |
void libsbmlcs.Model.addModifiers | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
int libsbmlcs.Model.addParameter | ( | Parameter | p | ) |
Adds a copy of the given Parameter object to this Model.
p | the Parameter object to add |
int libsbmlcs.Model.addReaction | ( | Reaction | r | ) |
Adds a copy of the given Reaction object to this Model.
r | the Reaction object to add |
int libsbmlcs.Model.addRule | ( | Rule | r | ) |
Adds a copy of the given Rule object to this Model.
r | the Rule object to add |
int libsbmlcs.Model.addSpecies | ( | Species | s | ) |
Adds a copy of the given Species object to this Model.
s | the Species object to add |
int libsbmlcs.Model.addSpeciesType | ( | SpeciesType | st | ) |
Adds a copy of the given SpeciesType object to this Model.
st | the SpeciesType object to add |
int libsbmlcs.Model.addUnitDefinition | ( | UnitDefinition | ud | ) |
Adds a copy of the given UnitDefinition object to this Model.
ud | the UnitDefinition object to add |
new int libsbmlcs.Model.appendAnnotation | ( | XMLNode | annotation | ) |
Appends annotation content to any existing content in the 'annotation' subelement of this object.
The content in annotation
is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object |
new int libsbmlcs.Model.appendAnnotation | ( | string | annotation | ) |
Appends annotation content to any existing content in the 'annotation' subelement of this object.
The content in annotation
is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object |
int libsbmlcs.Model.appendFrom | ( | Model | model | ) |
|
inherited |
Appends the given notes
to the 'notes' subelement of this object.
The content of notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML node structure that is to appended to the content of the 'notes' subelement of this object |
|
inherited |
Appends the given notes
to the 'notes' subelement of this object.
The content of the parameter notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML string that is to appended to the content of the 'notes' subelement of this object |
void libsbmlcs.Model.assignRequiredValues | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
new Model libsbmlcs.Model.clone | ( | ) |
|
inherited |
Sets the parent SBML object of this SBML object.
(Creates a child-parent relationship by the child) This function is called when a child element is set/added/created by its parent element (e.g. by setXXX, addXXX, createXXX, and connectToChild functions of the parent element).
parent | the SBML object to use |
void libsbmlcs.Model.convertL1ToL2 | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.convertL1ToL3 | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.convertL2ToL1 | ( | bool | strict | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.convertL2ToL1 | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.convertL2ToL3 | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.convertL3ToL1 | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.convertL3ToL2 | ( | bool | strict | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.convertL3ToL2 | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.convertParametersToLocals | ( | long | level, |
long | version | ||
) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.convertStoichiometryMath | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
AlgebraicRule libsbmlcs.Model.createAlgebraicRule | ( | ) |
Creates a new AlgebraicRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
AssignmentRule libsbmlcs.Model.createAssignmentRule | ( | ) |
Creates a new AssignmentRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
Compartment libsbmlcs.Model.createCompartment | ( | ) |
Creates a new Compartment inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
CompartmentType libsbmlcs.Model.createCompartmentType | ( | ) |
Creates a new CompartmentType inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
Constraint libsbmlcs.Model.createConstraint | ( | ) |
Creates a new Constraint inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
Delay libsbmlcs.Model.createDelay | ( | ) |
Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Delay is not created and null
is returned instead.
Event libsbmlcs.Model.createEvent | ( | ) |
EventAssignment libsbmlcs.Model.createEventAssignment | ( | ) |
Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new EventAssignment is not created and null
is returned instead.
FunctionDefinition libsbmlcs.Model.createFunctionDefinition | ( | ) |
Creates a new FunctionDefinition inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
InitialAssignment libsbmlcs.Model.createInitialAssignment | ( | ) |
Creates a new InitialAssignment inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
KineticLaw libsbmlcs.Model.createKineticLaw | ( | ) |
Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, or a Reaction exists but already has a KineticLaw, a new KineticLaw is not created and null
is returned instead.
LocalParameter libsbmlcs.Model.createKineticLawLocalParameter | ( | ) |
Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction::createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new Parameter is not created and null
is returned instead.
Parameter libsbmlcs.Model.createKineticLawParameter | ( | ) |
Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction::createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new Parameter is not created and null
is returned instead.
ModifierSpeciesReference libsbmlcs.Model.createModifier | ( | ) |
Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new ModifierSpeciesReference is not created and null
is returned instead.
Parameter libsbmlcs.Model.createParameter | ( | ) |
Creates a new Parameter inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
SpeciesReference libsbmlcs.Model.createProduct | ( | ) |
Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and null
is returned instead.
RateRule libsbmlcs.Model.createRateRule | ( | ) |
Creates a new RateRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
SpeciesReference libsbmlcs.Model.createReactant | ( | ) |
Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and null
is returned instead.
Reaction libsbmlcs.Model.createReaction | ( | ) |
Creates a new Reaction inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
Species libsbmlcs.Model.createSpecies | ( | ) |
Creates a new Species inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
SpeciesType libsbmlcs.Model.createSpeciesType | ( | ) |
Creates a new SpeciesType inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
Trigger libsbmlcs.Model.createTrigger | ( | ) |
Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Trigger is not created and null
is returned instead.
Unit libsbmlcs.Model.createUnit | ( | ) |
Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the UnitDefinition was created is not significant. If a UnitDefinition object does not exist in this model, a new Unit is not created and null
is returned instead.
UnitDefinition libsbmlcs.Model.createUnitDefinition | ( | ) |
Creates a new UnitDefinition inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
void libsbmlcs.Model.dealWithEvents | ( | bool | strict | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.dealWithModelUnits | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.dealWithStoichiometry | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
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inherited |
Disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
|
virtual |
Reimplemented from libsbmlcs.SBase.
Reimplemented in libsbmlcs.ModelDefinition.
|
inherited |
If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).
|
inherited |
Enables or disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (true ) or disable (false ) the package |
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inherited |
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inherited |
Returns the first ancestor object that has the given SBML type code.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_
.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
null
if no ancestor exists.
|
inherited |
Returns the first ancestor object that has the given SBML type code.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_
.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
null
if no ancestor exists.
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inherited |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
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inherited |
Returns the content of the 'annotation' subelement of this object as a character string.
Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form.
string libsbmlcs.Model.getAreaUnits | ( | ) |
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inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
Compartment libsbmlcs.Model.getCompartment | ( | long | n | ) |
Get the nth Compartment object in this Model.
Compartment libsbmlcs.Model.getCompartment | ( | string | sid | ) |
Get a Compartment object based on its identifier.
sid
or null
if no such Compartment exists. CompartmentType libsbmlcs.Model.getCompartmentType | ( | long | n | ) |
Get the nth CompartmentType object in this Model.
CompartmentType libsbmlcs.Model.getCompartmentType | ( | string | sid | ) |
Get a CompartmentType object based on its identifier.
sid
or null
if no such CompartmentType exists.Constraint libsbmlcs.Model.getConstraint | ( | long | n | ) |
Get the nth Constraint object in this Model.
string libsbmlcs.Model.getConversionFactor | ( | ) |
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
SBase libsbmlcs.Model.getElementByMetaId | ( | string | metaid | ) |
Returns the first child element it can find with the given metaid
, or null if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
. SBase libsbmlcs.Model.getElementBySId | ( | string | id | ) |
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
id | string representing the id of objects to find. |
id
.
|
inherited |
Returns the first child element it can find with the given metaid
from all plug-ins associated with this element, or null
if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
.
|
inherited |
Returns the first child element found that has the given id
in the model-wide SId namespace from all plug-ins associated with this element, or null
if no such object is found.
id | string representing the id of objects to find |
id
. new string libsbmlcs.Model.getElementName | ( | ) |
Returns the XML element name of this object, which for Model, is always 'model'
.
'model'
. Event libsbmlcs.Model.getEvent | ( | long | n | ) |
Event libsbmlcs.Model.getEvent | ( | string | sid | ) |
string libsbmlcs.Model.getExtentUnits | ( | ) |
FunctionDefinition libsbmlcs.Model.getFunctionDefinition | ( | long | n | ) |
Get the nth FunctionDefinitions object in this Model.
FunctionDefinition libsbmlcs.Model.getFunctionDefinition | ( | string | sid | ) |
Get a FunctionDefinition object based on its identifier.
sid
or null
if no such FunctionDefinition exists.
|
inherited |
new string libsbmlcs.Model.getId | ( | ) |
InitialAssignment libsbmlcs.Model.getInitialAssignment | ( | long | n | ) |
Get the nth InitialAssignment object in this Model.
InitialAssignment libsbmlcs.Model.getInitialAssignment | ( | string | symbol | ) |
Get an InitialAssignment object based on the symbol to which it assigns a value.
null
if no such InitialAssignment exists. string libsbmlcs.Model.getLengthUnits | ( | ) |
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Returns the line number on which this object first appears in the XML representation of the SBML document.
|
inherited |
|
inherited |
ListOfCompartments libsbmlcs.Model.getListOfCompartments | ( | ) |
Get the ListOfCompartments object in this Model.
ListOfCompartmentTypes libsbmlcs.Model.getListOfCompartmentTypes | ( | ) |
Get the ListOfCompartmentTypes object in this Model.
ListOfConstraints libsbmlcs.Model.getListOfConstraints | ( | ) |
Get the ListOfConstraints object in this Model.
ListOfEvents libsbmlcs.Model.getListOfEvents | ( | ) |
Get the ListOfEvents object in this Model.
ListOfFunctionDefinitions libsbmlcs.Model.getListOfFunctionDefinitions | ( | ) |
Get the ListOfFunctionDefinitions object in this Model.
ListOfInitialAssignments libsbmlcs.Model.getListOfInitialAssignments | ( | ) |
Get the ListOfInitialAssignments object in this Model.
ListOfParameters libsbmlcs.Model.getListOfParameters | ( | ) |
Get the ListOfParameters object in this Model.
ListOfReactions libsbmlcs.Model.getListOfReactions | ( | ) |
Get the ListOfReactions object in this Model.
ListOfRules libsbmlcs.Model.getListOfRules | ( | ) |
Get the ListOfRules object in this Model.
ListOfSpecies libsbmlcs.Model.getListOfSpecies | ( | ) |
Get the ListOfSpecies object in this Model.
ListOfSpeciesTypes libsbmlcs.Model.getListOfSpeciesTypes | ( | ) |
Get the ListOfSpeciesTypes object in this Model.
ListOfUnitDefinitions libsbmlcs.Model.getListOfUnitDefinitions | ( | ) |
Get the ListOfUnitDefinitions object in this Model.
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inherited |
Returns the value of the 'metaid' attribute of this object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
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inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
null
if none exist.new string libsbmlcs.Model.getName | ( | ) |
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inherited |
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.
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inherited |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
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inherited |
Returns the content of the 'notes' subelement of this object as a string.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
long libsbmlcs.Model.getNumCompartments | ( | ) |
Get the number of Compartment objects in this Model.
long libsbmlcs.Model.getNumCompartmentTypes | ( | ) |
Get the number of CompartmentType objects in this Model.
long libsbmlcs.Model.getNumConstraints | ( | ) |
Get the number of Constraint objects in this Model.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
long libsbmlcs.Model.getNumEvents | ( | ) |
long libsbmlcs.Model.getNumFunctionDefinitions | ( | ) |
Get the number of FunctionDefinition objects in this Model.
long libsbmlcs.Model.getNumInitialAssignments | ( | ) |
Get the number of InitialAssignment objects in this Model.
long libsbmlcs.Model.getNumParameters | ( | ) |
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
long libsbmlcs.Model.getNumReactions | ( | ) |
long libsbmlcs.Model.getNumRules | ( | ) |
long libsbmlcs.Model.getNumSpecies | ( | ) |
long libsbmlcs.Model.getNumSpeciesTypes | ( | ) |
Get the number of SpeciesType objects in this Model.
long libsbmlcs.Model.getNumSpeciesWithBoundaryCondition | ( | ) |
long libsbmlcs.Model.getNumUnitDefinitions | ( | ) |
Get the number of UnitDefinition objects in this Model.
|
inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
"core"
will be returned if this element is defined in SBML Level 3 Core. The string "unknown"
will be returned if this element is not defined in any SBML package.
|
inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
0
will be returned if this element belongs to the SBML Level 3 Core package.Parameter libsbmlcs.Model.getParameter | ( | long | n | ) |
Parameter libsbmlcs.Model.getParameter | ( | string | sid | ) |
|
inherited |
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
Reaction libsbmlcs.Model.getReaction | ( | long | n | ) |
Reaction libsbmlcs.Model.getReaction | ( | string | sid | ) |
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inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_
in the interface class libsbml.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose names begin with BQB_
in the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQB_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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inherited |
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQB_
in the interface class libsbml.
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose names begin with BQB_
in the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQM_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time. Rule libsbmlcs.Model.getRule | ( | long | n | ) |
Rule libsbmlcs.Model.getRule | ( | string | variable | ) |
|
inherited |
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
|
inherited |
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
-1
if the value is not set.
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inherited |
Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.
This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
|
inherited |
Returns the string representation of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
Species libsbmlcs.Model.getSpecies | ( | long | n | ) |
Species libsbmlcs.Model.getSpecies | ( | string | sid | ) |
SpeciesReference libsbmlcs.Model.getSpeciesReference | ( | string | sid | ) |
Get a SpeciesReference object based on its identifier.
sid
or null
if no such SpeciesReference exists. SpeciesType libsbmlcs.Model.getSpeciesType | ( | long | n | ) |
Get the nth SpeciesType object in this Model.
SpeciesType libsbmlcs.Model.getSpeciesType | ( | string | sid | ) |
Get a SpeciesType object based on its identifier.
sid
or null
if no such SpeciesType exists.string libsbmlcs.Model.getSubstanceUnits | ( | ) |
string libsbmlcs.Model.getTimeUnits | ( | ) |
new int libsbmlcs.Model.getTypeCode | ( | ) |
Returns the libSBML type code for this SBML object.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml. The names of the type codes all begin with the characters SBML_
.
UnitDefinition libsbmlcs.Model.getUnitDefinition | ( | long | n | ) |
Get the nth UnitDefinition object in this Model.
UnitDefinition libsbmlcs.Model.getUnitDefinition | ( | string | sid | ) |
Get a UnitDefinition based on its identifier.
sid
or null
if no such UnitDefinition exists.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
string libsbmlcs.Model.getVolumeUnits | ( | ) |
|
inherited |
Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid').
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
new bool libsbmlcs.Model.hasRequiredElements | ( | ) |
Predicate returning true
if all the required elements for this Model object have been set.
|
inherited |
Predicate returning true
if this object's level/version and namespace values correspond to a valid SBML specification.
The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
'http://www.sbml.org/sbml/level1'
'http://www.sbml.org/sbml/level2'
'http://www.sbml.org/sbml/level2/version2'
'http://www.sbml.org/sbml/level2/version3'
'http://www.sbml.org/sbml/level2/version4'
'http://www.sbml.org/sbml/level3/version1/core'
true
if the level, version and namespace values of this SBML object correspond to a valid set of values, false
otherwise.
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.bool libsbmlcs.Model.isPopulatedListFormulaUnitsData | ( | ) |
Predicate returning true
if the list of FormulaUnitsData is populated.
true
if the list of FormulaUnitsData is populated, false
otherwise.
|
inherited |
Predicate returning true
if this object's 'annotation' subelement exists and has content.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
true
if a 'annotation' subelement exists, false
otherwise.bool libsbmlcs.Model.isSetAreaUnits | ( | ) |
bool libsbmlcs.Model.isSetConversionFactor | ( | ) |
bool libsbmlcs.Model.isSetExtentUnits | ( | ) |
new bool libsbmlcs.Model.isSetId | ( | ) |
bool libsbmlcs.Model.isSetLengthUnits | ( | ) |
|
inherited |
Predicate returning true
if this object's 'metaid' attribute is set.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
true
if the 'metaid' attribute of this SBML object is set, false
otherwise.
|
inherited |
Predicate returning true
if this object has a ModelHistory object attached to it.
true
if the ModelHistory of this object is set, false
otherwise.new bool libsbmlcs.Model.isSetName | ( | ) |
|
inherited |
Predicate returning true
if this object's 'notes' subelement exists and has content.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
true
if a 'notes' subelement exists, false
otherwise.
|
inherited |
Predicate returning true
if this object's 'sboTerm' attribute is set.
true
if the 'sboTerm' attribute of this SBML object is set, false
otherwise. bool libsbmlcs.Model.isSetSubstanceUnits | ( | ) |
bool libsbmlcs.Model.isSetTimeUnits | ( | ) |
bool libsbmlcs.Model.isSetVolumeUnits | ( | ) |
|
inherited |
Returns true
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is a subset of sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are the same as the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is the same as sb's
, false
otherwise.
|
inherited |
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).
void libsbmlcs.Model.populateListFormulaUnitsData | ( | ) |
Populates the list of FormulaDataUnits with the units derived for the model.
The list contains elements of class FormulaUnitsData.
The first element of the list refers to the default units of 'substance per time' derived from the model and has the unitReferenceId 'subs_per_time'. This facilitates the comparison of units derived from mathematical formula with the expected units.
The next elements of the list record the units of the compartments and species established from either explicitly declared or default units.
The next elements record the units of any parameters.
Subsequent elements of the list record the units derived for each mathematical expression encountered within the model.
|
inherited |
Add the given string to all identifiers in the object.
If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.
Compartment libsbmlcs.Model.removeCompartment | ( | long | n | ) |
Removes the nth Compartment object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Compartment object to remove |
null
is returned if the given index is out of range. Compartment libsbmlcs.Model.removeCompartment | ( | string | sid | ) |
Removes the Compartment object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Compartment objects in this Model object have the identifier sid
, then null
is returned.
sid | the identifier of the Compartment object to remove |
null
is returned if no Compartment object with the identifier exists in this Model object. CompartmentType libsbmlcs.Model.removeCompartmentType | ( | long | n | ) |
Removes the nth CompartmentType object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the CompartmentType object to remove |
null
is returned if the given index is out of range. CompartmentType libsbmlcs.Model.removeCompartmentType | ( | string | sid | ) |
Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the CompartmentType objects in this Model object have the identifier sid
, then null
is returned.
sid | the identifier of the object to remove |
null
is returned if no CompartmentType object with the identifier exists in this Model object. Constraint libsbmlcs.Model.removeConstraint | ( | long | n | ) |
Removes the nth Constraint object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Constraint object to remove |
null
is returned if the given index is out of range. Event libsbmlcs.Model.removeEvent | ( | long | n | ) |
Removes the nth Event object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Event object to remove |
null
is returned if the given index is out of range. Event libsbmlcs.Model.removeEvent | ( | string | sid | ) |
Removes the Event object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Event objects in this Model object have the identifier sid
, then null
is returned.
sid | the identifier of the Event object to remove |
int libsbmlcs.Model.removeFromParentAndDelete | ( | ) |
Finds this Model's parent SBMLDocument and calls setModel(null) on it, indirectly deleting itself.
Overridden from the SBase function since the parent is not a ListOf.
FunctionDefinition libsbmlcs.Model.removeFunctionDefinition | ( | long | n | ) |
Removes the nth FunctionDefinition object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the FunctionDefinition object to remove |
null
is returned if the given index is out of range. FunctionDefinition libsbmlcs.Model.removeFunctionDefinition | ( | string | sid | ) |
Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the FunctionDefinition objects in this Model object have the identifier sid
, then null
is returned.
sid | the identifier of the FunctionDefinition object to remove |
null
is returned if no FunctionDefinition object with the identifier exists in this Model object. InitialAssignment libsbmlcs.Model.removeInitialAssignment | ( | long | n | ) |
Removes the nth InitialAssignment object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the InitialAssignment object to remove |
null
is returned if the given index is out of range. InitialAssignment libsbmlcs.Model.removeInitialAssignment | ( | string | symbol | ) |
Removes the InitialAssignment object with the given 'symbol' attribute from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the InitialAssignment objects in this Model object have the 'symbol' attribute symbol
, then null
is returned.
symbol | the 'symbol' attribute of the InitialAssignment object to remove |
null
is returned if no InitialAssignment object with the 'symbol' attribute exists in this Model object. Parameter libsbmlcs.Model.removeParameter | ( | long | n | ) |
Removes the nth Parameter object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Parameter object to remove |
null
is returned if the given index is out of range. Parameter libsbmlcs.Model.removeParameter | ( | string | sid | ) |
Removes the Parameter object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Parameter objects in this Model object have the identifier sid
, then null
is returned.
sid | the identifier of the Parameter object to remove |
void libsbmlcs.Model.removeParameterRuleUnits | ( | bool | strict | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
Reaction libsbmlcs.Model.removeReaction | ( | long | n | ) |
Removes the nth Reaction object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Reaction object to remove |
null
is returned if the given index is out of range. Reaction libsbmlcs.Model.removeReaction | ( | string | sid | ) |
Removes the Reaction object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Reaction objects in this Model object have the identifier sid
, then null
is returned.
sid | the identifier of the Reaction object to remove |
Rule libsbmlcs.Model.removeRule | ( | long | n | ) |
Removes the nth Rule object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Rule object to remove |
null
is returned if the given index is out of range. Rule libsbmlcs.Model.removeRule | ( | string | variable | ) |
Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Rule objects in this Model object have the 'variable' attribute variable
, then null
is returned.
variable | the 'variable' attribute of the Rule object to remove |
Species libsbmlcs.Model.removeSpecies | ( | long | n | ) |
Removes the nth Species object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Species object to remove |
null
is returned if the given index is out of range. Species libsbmlcs.Model.removeSpecies | ( | string | sid | ) |
Removes the Species object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Species objects in this Model object have the identifier sid
, then null
is returned.
sid | the identifier of the Species object to remove |
SpeciesType libsbmlcs.Model.removeSpeciesType | ( | long | n | ) |
Removes the nth SpeciesType object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the SpeciesType object to remove |
null
is returned if the given index is out of range. SpeciesType libsbmlcs.Model.removeSpeciesType | ( | string | sid | ) |
Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the SpeciesType objects in this Model object have the identifier sid
, then null
is returned.
sid | the identifier of the SpeciesType object to remove |
null
is returned if no SpeciesType object with the identifier exists in this Model object.
|
inherited |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
|
inherited |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
UnitDefinition libsbmlcs.Model.removeUnitDefinition | ( | long | n | ) |
Removes the nth UnitDefinition object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the UnitDefinition object to remove |
null
is returned if the given index is out of range. UnitDefinition libsbmlcs.Model.removeUnitDefinition | ( | string | sid | ) |
Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the UnitDefinition objects in this Model object have the identifier sid
, then null
is returned.
sid | the identifier of the UnitDefinition object to remove |
null
is returned if no UnitDefinition object with the identifier exists in this Model object.
|
inherited |
Renames all the MetaIdRef
attributes on this element.
This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid
. If any matches are found, the matching identifiers are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier |
newid | the new identifier |
void libsbmlcs.Model.renameSIdRefs | ( | string | oldid, |
string | newid | ||
) |
Renames all the SIdRef attributes on this element, including any found in MathML.
void libsbmlcs.Model.renameUnitSIdRefs | ( | string | oldid, |
string | newid | ||
) |
Renames all the UnitSIdRef attributes on this element.
|
inherited |
If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.
|
inherited |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name);
with the exception that the placement of the annotation element remains the same.
annotation | XMLNode representing the replacement top level annotation |
|
inherited |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name);
with the exception that the placement of the annotation element remains the same.
annotation | string representing the replacement top level annotation |
new int libsbmlcs.Model.setAnnotation | ( | XMLNode | annotation | ) |
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation
.
Any existing content of the 'annotation' subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().
annotation | an XML structure that is to be used as the content of the 'annotation' subelement of this object |
new int libsbmlcs.Model.setAnnotation | ( | string | annotation | ) |
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation
.
Any existing content of the 'annotation' subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().
annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object |
int libsbmlcs.Model.setAreaUnits | ( | string | units | ) |
Sets the value of the 'areaUnits' attribute of this Model.
The string in units
is copied.
units | the new areaUnits for the Model |
int libsbmlcs.Model.setConversionFactor | ( | string | units | ) |
Sets the value of the 'conversionFactor' attribute of this Model.
The string in units
is copied.
units | the new conversionFactor for the Model |
int libsbmlcs.Model.setExtentUnits | ( | string | units | ) |
Sets the value of the 'extentUnits' attribute of this Model.
The string in units
is copied.
units | the new extentUnits for the Model |
new int libsbmlcs.Model.setId | ( | string | sid | ) |
Sets the value of the 'id' attribute of this Model.
The string sid
is copied. Note that SBML has strict requirements for the syntax of identifiers. The following is a summary of the definition of the SBML identifier type
SId
, which defines the permitted syntax of identifiers. We
express the syntax using an extended form of BNF notation:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*The characters
(
and )
are used for grouping, the
character *
"zero or more times", and the character
|
indicates logical "or". The equality of SBML identifiers is
determined by an exact character sequence match; i.e., comparisons must be
performed in a case-sensitive manner. In addition, there are a few
conditions for the uniqueness of identifiers in an SBML model. Please
consult the SBML specifications for the exact formulations.
sid | the string to use as the identifier of this Model |
int libsbmlcs.Model.setLengthUnits | ( | string | units | ) |
Sets the value of the 'lengthUnits' attribute of this Model.
The string in units
is copied.
units | the new lengthUnits for the Model |
|
inherited |
Sets the value of the 'metaid' attribute of this object.
The string metaid
is copied. The value of metaid
must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement.
metaid | the identifier string to use as the value of the 'metaid' attribute |
|
inherited |
Sets the ModelHistory of this object.
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
new int libsbmlcs.Model.setName | ( | string | name | ) |
|
inherited |
Sets the namespaces relevant of this SBML object.
The content of xmlns
is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
xmlns | the namespaces to set |
|
inherited |
Sets the value of the 'notes' subelement of this SBML object.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML structure that is to be used as the content of the 'notes' subelement of this object |
|
inherited |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">
here is my note
</body>');
notes | an XML string that is to be used as the content of the 'notes' subelement of this object |
addXHTMLMarkup | a bool indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
|
inherited |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">
here is my note
</body>');
notes | an XML string that is to be used as the content of the 'notes' subelement of this object |
addXHTMLMarkup | a bool indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
|
inherited |
Sets the value of the 'sboTerm' attribute.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
value | the NNNNNNN integer portion of the SBO identifier |
|
inherited |
Sets the value of the 'sboTerm' attribute by string.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
void libsbmlcs.Model.setSpatialDimensions | ( | double | dims | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.setSpatialDimensions | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
void libsbmlcs.Model.setSpeciesReferenceConstantValueAndStoichiometry | ( | ) |
Predicate returning true
if the given ASTNode is a bool.
Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.
int libsbmlcs.Model.setSubstanceUnits | ( | string | units | ) |
Sets the value of the 'substanceUnits' attribute of this Model.
The string in units
is copied.
units | the new substanceUnits for the Model |
int libsbmlcs.Model.setTimeUnits | ( | string | units | ) |
Sets the value of the 'timeUnits' attribute of this Model.
The string in units
is copied.
units | the new timeUnits for the Model |
int libsbmlcs.Model.setVolumeUnits | ( | string | units | ) |
Sets the value of the 'volumeUnits' attribute of this Model.
The string in units
is copied.
units | the new volumeUnits for the Model |
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inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
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inherited |
Unsets the value of the 'annotation' subelement of this SBML object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
int libsbmlcs.Model.unsetAreaUnits | ( | ) |
int libsbmlcs.Model.unsetConversionFactor | ( | ) |
Unsets the value of the 'conversionFactor' attribute of this Model.
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inherited |
Clears the list of CVTerm objects attached to this SBML object.
int libsbmlcs.Model.unsetExtentUnits | ( | ) |
new int libsbmlcs.Model.unsetId | ( | ) |
Unsets the value of the 'id' attribute of this Model.
int libsbmlcs.Model.unsetLengthUnits | ( | ) |
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inherited |
Unsets the value of the 'metaid' attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
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inherited |
Unsets the ModelHistory object attached to this object.
new int libsbmlcs.Model.unsetName | ( | ) |
Unsets the value of the 'name' attribute of this Model.
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inherited |
Unsets the value of the 'notes' subelement of this SBML object.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
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inherited |
Unsets the value of the 'sboTerm' attribute of this SBML object.
int libsbmlcs.Model.unsetSubstanceUnits | ( | ) |
int libsbmlcs.Model.unsetTimeUnits | ( | ) |
int libsbmlcs.Model.unsetVolumeUnits | ( | ) |
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inherited |
Writes out contained SBML objects of package extensions (if any) as XML elements.
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protectedinherited |