Package | Description |
---|---|
org.sbml.jsbml |
Pure Java™ implementation of the data structures to represent all SBML
constructs.
|
org.sbml.jsbml.ext.fbc |
Provides classes for the
Flux Balance Constraints package (FBC).
|
org.sbml.jsbml.ext.spatial |
Provides classes for the
Spatial Geometries and Processes package.
|
org.sbml.jsbml.util |
A collection of handy utilities when working with JSBML classes,
such as classes for String manipulation or mathematical operations.
|
Modifier and Type | Method | Description |
---|---|---|
Parameter |
Parameter.clone() |
|
Parameter |
Model.createParameter() |
|
Parameter |
Model.createParameter(java.lang.String id) |
Creates a new
Parameter . |
Parameter |
Model.getConversionFactorInstance() |
Returns the Parameter instance which has the conversionFactorID of this
Model as id.
|
Parameter |
Species.getConversionFactorInstance() |
Returns the conversionFactor of this Species as a
Parameter instance. |
Parameter |
Model.getParameter(int n) |
|
Parameter |
Model.getParameter(java.lang.String id) |
Returns the
Parameter of the Model.listOfParameters which has
'id' as id |
Parameter |
Model.removeParameter(int n) |
|
Parameter |
Model.removeParameter(java.lang.String id) |
Modifier and Type | Method | Description |
---|---|---|
java.util.List<Parameter> |
ASTNode.findReferencedGlobalParameters() |
Goes through the formula and identifies all global parameters that are
referenced by this rate equation.
|
ListOf<Parameter> |
Model.getListOfParameters() |
Returns the
Model.listOfParameters of this Model . |
Modifier and Type | Method | Description |
---|---|---|
void |
KineticLaw.addParameter(Parameter p) |
Deprecated.
A
KineticLaw can only contain instances of
LocalParameter s. Please use
KineticLaw.addLocalParameter(LocalParameter) and create an
instance of LocalParameter for your purposes. |
boolean |
Model.addParameter(Parameter parameter) |
Adds a Parameter instance to the listOfParameters of this Model.
|
boolean |
KineticLaw.removeParameter(Parameter p) |
Deprecated.
|
boolean |
Model.removeParameter(Parameter parameter) |
Removes the Parameter 'parameter' from this Model.
|
void |
Model.setConversionFactor(Parameter conversionFactor) |
|
void |
Species.setConversionFactor(Parameter conversionFactor) |
Sets the conversionFactor of this
Species to the id of
'conversionFactor'. |
Modifier and Type | Method | Description |
---|---|---|
void |
Model.setListOfParameters(ListOf<Parameter> listOfParameters) |
Sets the
Model.listOfParameters of this Model to
'listOfParameters'. |
Constructor | Description |
---|---|
AssignmentRule(ASTNode math,
Parameter parameter) |
Creates an AssignmentRule instance from a given math and Parameter.
|
AssignmentRule(Parameter parameter) |
Creates an AssignmentRule instance from a given Parameter.
|
AssignmentRule(Parameter parameter,
ASTNode math) |
Creates an AssignmentRule instance from a given math and Parameter.
|
ExplicitRule(Parameter parameter) |
Creates a new
ExplicitRule |
ExplicitRule(Parameter parameter,
ASTNode math) |
Creates a new
ExplicitRule |
LocalParameter(Parameter parameter) |
Creates a new local parameter that will have the same properties than the
given global parameter.
|
Parameter(Parameter p) |
|
RateRule(ASTNode math,
Parameter parameter) |
Creates a new
RateRule instance. |
RateRule(Parameter parameter) |
Creates a new
RateRule instance. |
RateRule(Parameter parameter,
ASTNode math) |
Creates a new
RateRule instance. |
Modifier and Type | Method | Description |
---|---|---|
Parameter |
FBCReactionPlugin.getLowerFluxBoundInstance() |
|
Parameter |
FBCReactionPlugin.getUpperFluxBoundInstance() |
Modifier and Type | Method | Description |
---|---|---|
void |
FBCReactionPlugin.setLowerFluxBound(Parameter boundParameter) |
|
void |
FBCReactionPlugin.setUpperFluxBound(Parameter boundParameter) |
Modifier and Type | Method | Description |
---|---|---|
Parameter |
SpatialParameterPlugin.getExtendedSBase() |
|
Parameter |
ParameterType.getParameterInstance() |
Returns the
Parameter instance associated with ParameterType.variable . |
Constructor | Description |
---|---|
SpatialParameterPlugin(Parameter parameter) |
Modifier and Type | Method | Description |
---|---|---|
Parameter |
ModelBuilder.buildParameter(java.lang.String id,
java.lang.String name,
double value,
boolean constant,
java.lang.String units) |
|
Parameter |
ModelBuilder.buildParameter(java.lang.String id,
java.lang.String name,
double value,
boolean constant,
Unit.Kind units) |
|
Parameter |
ModelBuilder.buildParameter(java.lang.String id,
java.lang.String name,
double value,
boolean constant,
UnitDefinition units) |