Package | Description |
---|---|
org.sbml.jsbml |
Pure Java™ implementation of the data structures to represent all SBML
constructs.
|
org.sbml.jsbml.ext.arrays | |
org.sbml.jsbml.ext.arrays.compiler | |
org.sbml.jsbml.ext.multi |
Provides classes for the Multi package.
|
org.sbml.jsbml.ext.qual |
Provides classes for the Qualitative Models package.
|
org.sbml.jsbml.math | |
org.sbml.jsbml.math.compiler | |
org.sbml.jsbml.util.compilers |
The classes in this package can be used to evaluate the information
represented by abstract syntax trees (ASTNode objects).
|
org.sbml.jsbml.validator.offline.constraints.helper |
Modifier and Type | Interface | Description |
---|---|---|
interface |
Quantity |
A quantity is an element that represents a value with an associated unit that
can be addressed through the identifier or name attribute of this element.
|
interface |
Variable |
A variable of the system is a
Quantity whose value may change during
a simulation. |
Modifier and Type | Class | Description |
---|---|---|
class |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
class |
FunctionDefinition |
Represents the functionDefinition XML element of a SBML file.
|
class |
LocalParameter |
A local parameter can only be used to specify a constant within a
KineticLaw . |
class |
Parameter |
Represents a globally valid parameter in the model, i.e., a variable that
may change during a simulation or that provides a constant value.
|
class |
QuantityWithUnit |
This object represents an element with identifier and name, a value, and a
defined unit.
|
class |
Reaction |
Represents the reaction XML element of a SBML file.
|
class |
Species |
Represents the species XML element of a SBML file.
|
class |
SpeciesReference |
Represents the speciesReference XML element of a SBML file.
|
class |
Symbol |
Modifier and Type | Method | Description |
---|---|---|
CallableSBase |
Model.findCallableSBase(java.lang.String id) |
Returns a
CallableSBase element of the Model that has the
given 'id' as identifier or null if no element is found. |
CallableSBase |
ASTNode.getVariable() |
Returns the variable of this node.
|
Modifier and Type | Method | Description |
---|---|---|
ASTNode |
ASTNode.divideBy(CallableSBase namedSBase) |
Divides this node by the given SBML element.
|
static ASTNode |
ASTNode.frac(MathContainer container,
CallableSBase numerator,
CallableSBase denominator) |
Creates a new
ASTNode that divides two CallableSBase objects. |
ASTNode |
ASTNode.multiplyWith(CallableSBase nsb) |
Multiplies this
ASTNode with the given SBML element. |
ASTNode |
ASTNode.plus(CallableSBase nsb) |
Adds an SBML element to this node.
|
static ASTNode |
ASTNode.pow(MathContainer container,
CallableSBase basis,
CallableSBase exponent) |
Raises the given basis by the power of the given exponent.
|
ASTNode |
ASTNode.raiseByThePowerOf(CallableSBase nsb) |
Raises this ASTNode by the power of the value of this named SBase object.
|
void |
ASTNode.setVariable(CallableSBase variable) |
Allows you to directly set an instance of
CallableSBase as the
variable of this ASTNode . |
static ASTNode |
ASTNode.sum(MathContainer parent,
CallableSBase... sbase) |
Sum of several NamedSBase objects.
|
static ASTNode |
ASTNode.times(MathContainer parent,
CallableSBase... sbase) |
Multiplies several
CallableSBase objects. |
static ASTNode |
ASTNode.uMinus(MathContainer container,
CallableSBase sbase) |
Creates a new
ASTNode that has exactly one child and which is of type
minus, i.e., this negates what is encoded in ast. |
Constructor | Description |
---|---|
ASTNode(CallableSBase nsb) |
Creates and returns a new
ASTNode referring to the given CallableSBase . |
ASTNode(CallableSBase nsb,
MathContainer parent) |
Creates and returns a new
ASTNode referring to the given CallableSBase . |
Modifier and Type | Class | Description |
---|---|---|
class |
Dimension |
Modifier and Type | Method | Description |
---|---|---|
ASTNodeValue |
ArraysCompiler.compile(CallableSBase variable) |
|
ASTNodeValue |
StaticallyComputableCompiler.compile(CallableSBase variable) |
|
ASTNodeValue |
VectorCompiler.compile(CallableSBase variable) |
Modifier and Type | Class | Description |
---|---|---|
class |
IntraSpeciesReaction |
Modifier and Type | Class | Description |
---|---|---|
class |
Input |
|
class |
Output |
Each
Output refers to a QualitativeSpecies that participates
in (is affected by) the corresponding Transition . |
Modifier and Type | Method | Description |
---|---|---|
CallableSBase |
ASTCiNumberNode.getReferenceInstance() |
Returns the variable (
CallableSBase ) of this ASTCiNumberNode . |
Modifier and Type | Method | Description |
---|---|---|
java.util.List<CallableSBase> |
ASTFunction.findReferencedCallableSBases() |
Goes through the formula and identifies all global parameters that are
referenced by this rate rule.
|
Modifier and Type | Method | Description |
---|---|---|
void |
ASTCiNumberNode.setReference(CallableSBase sbase) |
Set an instance of
CallableSBase as the variable of this
ASTCiNumberNode . |
Modifier and Type | Method | Description |
---|---|---|
CallableSBase |
ASTNode2Value.toCallableSBase() |
Modifier and Type | Method | Description |
---|---|---|
<T> ASTNode2Value<CallableSBase> |
UnitsCompiler.compile(CallableSBase variable) |
|
<T> ASTNode2Value<CallableSBase> |
UnitsCompiler.compile(Compartment c) |
Modifier and Type | Method | Description |
---|---|---|
<T> ASTNode2Value<?> |
ASTNode2Compiler.compile(CallableSBase variable) |
|
<T> ASTNode2Value<java.lang.String> |
FindUnitsCompiler.compile(CallableSBase variable) |
|
<T> ASTNode2Value<java.lang.String> |
FormulaCompiler.compile(CallableSBase variable) |
|
<T> ASTNode2Value<java.lang.String> |
LaTeXCompiler.compile(CallableSBase variable) |
|
<T> ASTNode2Value<CallableSBase> |
UnitsCompiler.compile(CallableSBase variable) |
Modifier and Type | Method | Description |
---|---|---|
CallableSBase |
ASTNodeValue.toCallableSBase() |
Modifier and Type | Method | Description |
---|---|---|
ASTNodeValue |
ASTNodeCompiler.compile(CallableSBase variable) |
|
ASTNodeValue |
FindUnitsCompiler.compile(CallableSBase variable) |
|
ASTNodeValue |
FormulaCompiler.compile(CallableSBase variable) |
|
ASTNodeValue |
LaTeXCompiler.compile(CallableSBase variable) |
|
ASTNodeValue |
MathMLCompiler.compile(CallableSBase variable) |
Deprecated.
|
ASTNodeValue |
UnitsCompiler.compile(CallableSBase variable) |
|
void |
ASTNodeValue.setValue(CallableSBase value) |
Constructor | Description |
---|---|
ASTNodeValue(CallableSBase value,
ASTNodeCompiler compiler) |
Modifier and Type | Method | Description |
---|---|---|
ASTNodeValue |
ValidationUnitsCompiler.compile(CallableSBase variable) |