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.util | |
org.sbml.jsbml.ext.arrays.validator | |
org.sbml.jsbml.ext.arrays.validator.constraints | |
org.sbml.jsbml.ext.distrib | |
org.sbml.jsbml.ext.qual |
Provides classes for the Qualitative Models package.
|
org.sbml.jsbml.ext.spatial |
Provides classes for the
Spatial Geometries and Processes package.
|
org.sbml.jsbml.math | |
org.sbml.jsbml.util.converters | |
org.sbml.jsbml.validator.offline.constraints.helper | |
org.sbml.jsbml.xml.stax |
Contains classes that use the Streaming API for XML (StAX)
to read or write an SBML file.
|
Modifier and Type | Interface | Description |
---|---|---|
interface |
Assignment |
An
Assignment can be seen as a mathematical equation with a
Variable on the left hand side and an equation on the right hand side
that assigns a value to the Variable . |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractMathContainer |
Base class for all the SBML components which contain MathML nodes.
|
class |
AlgebraicRule |
Represents the algebraicRule XML element of a SBML file.
|
class |
AssignmentRule |
Represents the assignmentRule XML element of a SBML file.
|
class |
Constraint |
Represents the constraint XML element of a SBML file.
|
class |
Delay |
Represents the delay subnode of an event element.
|
class |
EventAssignment |
Represents the eventAssignment XML element of a SBML file.
|
class |
ExplicitRule |
An explicit
Rule is a rule that explicitly declares its variable
element. |
class |
FunctionDefinition |
Represents the functionDefinition XML element of a SBML file.
|
class |
InitialAssignment |
Represents the initialAssignment XML element of a SBML file.
|
class |
KineticLaw |
Represents the kineticLaw XML element of a SBML file.
|
class |
Priority |
This class represents the priority element in SBML.
|
class |
RateRule |
Represents the rateRule XML element of a SBML file.
|
class |
Rule |
|
class |
StoichiometryMath |
Deprecated.
Since SBML Level 3 Version 1 use
AssignmentRule with
instances of SpeciesReference as Variable
instead. |
class |
Trigger |
Represents the trigger XML element of a SBML file.
|
Modifier and Type | Method | Description |
---|---|---|
MathContainer |
ASTNode.getParentSBMLObject() |
This method is convenient when holding an object nested inside other
objects in an SBML model.
|
Modifier and Type | Method | Description |
---|---|---|
static ASTNode |
ASTNode.abs(double d,
MathContainer parent) |
Creates and returns an
ASTNode that computes the absolute value
of the given double value. |
static ASTNode |
ASTNode.abs(int integer,
MathContainer parent) |
Creates and returns an
ASTNode that computes the absolute value
of the given integer value. |
static ASTNode |
ASTNode.frac(MathContainer container,
java.lang.String numeratorId,
java.lang.String denominatorId) |
Returns a new
ASTNode that of type DIVIDE with the two entities as numerator and denominator. |
static ASTNode |
ASTNode.frac(MathContainer container,
CallableSBase numerator,
CallableSBase denominator) |
Creates a new
ASTNode that divides two CallableSBase objects. |
static ASTNode |
ASTNode.piecewise(MathContainer parentSBMLObject,
ASTNode[] nodes) |
|
static ASTNode |
ASTNode.pow(MathContainer container,
CallableSBase basis,
CallableSBase exponent) |
Raises the given basis by the power of the given exponent.
|
static void |
ASTNode.setParentSBMLObject(ASTNode node,
MathContainer parent) |
Sets the Parent of the node and its children to the given value
|
void |
ASTNode.setParentSBMLObject(MathContainer parent) |
Sets the Parent of the node to the given value
|
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(char operator,
MathContainer parent) |
Creates a new
ASTNode representing an operator, i.e., an internal
node. |
ASTNode(double mantissa,
int exponent,
MathContainer parent) |
Creates and returns a new
ASTNode . |
ASTNode(double real,
MathContainer parent) |
Creates and returns a new
ASTNode . |
ASTNode(int integer,
java.lang.String unitsID,
MathContainer parent) |
Creates and returns a new
ASTNode with the given integer value with
the given associated ASTNode.unitId for the
given MathContainer as its parent SBML object. |
ASTNode(int integer,
MathContainer parent) |
Creates and returns a new
ASTNode with the given integer value for
the
given MathContainer as its parent SBML object. |
ASTNode(java.lang.String name,
MathContainer parent) |
Creates and returns a new
ASTNode with the given name. |
ASTNode(ASTNode.Type type,
MathContainer parent) |
Creates and returns a new
ASTNode . |
ASTNode(CallableSBase nsb,
MathContainer parent) |
Creates and returns a new
ASTNode referring to the given CallableSBase . |
ASTNode(MathContainer parent) |
Creates and returns a new
ASTNode . |
Modifier and Type | Class | Description |
---|---|---|
class |
Index |
The
Index is used to referenced an arrayed element specified in
an attribute. |
Modifier and Type | Method | Description |
---|---|---|
static boolean |
ArraysMath.checkVectorAssignment(Model model,
MathContainer mathContainer) |
|
static boolean |
ArraysMath.checkVectorMath(Model model,
MathContainer mathContainer) |
|
static boolean |
ArraysMath.evaluateSelectorBounds(Model model,
MathContainer mathContainer) |
Checks if the arguments of a selector function does not go out of bounds.
|
static boolean |
ArraysMath.isStaticallyComputable(Model model,
MathContainer mathContainer) |
Determines whether a
MathContainer object is statically computable. |
static boolean |
ArraysMath.isStaticallyComputable(Model model,
MathContainer mathContainer,
java.lang.String... constantIds) |
Determines whether a
MathContainer object is statically computable given
a list of ids that can appear in the math. |
static boolean |
ArraysMath.isVectorBalanced(Model model,
MathContainer mathContainer) |
Modifier and Type | Method | Description |
---|---|---|
static java.util.List<SBMLError> |
ArraysMathValidator.validate(Model model,
MathContainer math) |
Validates the given
SBase object. |
Constructor | Description |
---|---|
ArraysMathCheck(Model model,
MathContainer mathContainer) |
Modifier and Type | Class | Description |
---|---|---|
class |
UncertParameter |
Defines one uncertainty statistic about the parent element.
|
class |
UncertSpan |
The
UncertSpan class defines a span of values that define an uncertainty statistic such as confidence interval or
range. |
Modifier and Type | Class | Description |
---|---|---|
class |
FunctionTerm |
Each
FunctionTerm is also associated with a result and in addition to a Boolean
function inside a Math element that can be used to set the conditions under which this term
is selected. |
Modifier and Type | Class | Description |
---|---|---|
class |
AnalyticVolume |
Modifier and Type | Method | Description |
---|---|---|
MathContainer |
AbstractASTNode.getParentSBMLObject() |
|
MathContainer |
ASTNode2.getParentSBMLObject() |
Return the parentSBMLObject of this
ASTNode2 |
MathContainer |
ASTUnknown.getParentSBMLObject() |
Modifier and Type | Method | Description |
---|---|---|
void |
AbstractASTNode.setParentSBMLObject(MathContainer container) |
|
static void |
ASTFactory.setParentSBMLObject(ASTNode2 node,
MathContainer parent) |
Sets the Parent of the node and its children to the given value
|
void |
ASTFunction.setParentSBMLObject(MathContainer container) |
|
void |
ASTNode2.setParentSBMLObject(MathContainer container) |
Sets the parentSBMLObject to container recursively
|
void |
ASTUnknown.setParentSBMLObject(MathContainer container) |
Constructor | Description |
---|---|
AbstractASTNode(MathContainer container) |
Creates an empty
AbstractTreeNode with a pointer
to the specified MathContainer . |
ASTArithmeticOperatorNode(ASTNode.Type type,
MathContainer container) |
|
ASTArithmeticOperatorNode(MathContainer container) |
Creates a new
ASTArithmeticOperatorNode with a pointer
to the specified MathContainer .. |
ASTFunction(MathContainer container) |
Creates a new
ASTFunction with a pointer
to the specified MathContainer . |
Modifier and Type | Method | Description |
---|---|---|
static void |
ExpandFunctionDefinitionConverter.expandFunctionDefinition(MathContainer mathcontainer) |
Expands the
FunctionDefinition used in the given MathContainer . |
Modifier and Type | Class | Description |
---|---|---|
class |
DuplicatedMathValidationFunction<T extends MathContainer> |
Class used to check if the 'math' mathML element is duplicated.
|
Modifier and Type | Method | Description |
---|---|---|
static UnitDefinition |
ValidationTools.getMathDerivedUnitDefinition(ValidationContext ctx,
MathContainer container) |
Returns the derived
UnitDefinition for the given MathContainer . |
Modifier and Type | Method | Description |
---|---|---|
ASTNode |
SBMLReader.readMathML(java.lang.String mathML,
TreeNodeChangeListener listener,
MathContainer parent) |
Reads a mathML
String into an ASTNode . |