Uses of Class
org.simulator.sbml.astnode.ASTNodeValue

Packages that use ASTNodeValue

org.simulator.sbml	Classes for storing and interpreting an SBML model.
org.simulator.sbml.astnode	Classes for efficient numerical treatment of equations in form of abstract syntax trees.

Uses of ASTNodeValue in org.simulator.sbml

Fields in org.simulator.sbml declared as ASTNodeValue

protected ASTNodeValue	SBMLEventInProgress.delayObject
protected ASTNodeValue	SBMLEventInProgress.priorityObject
protected ASTNodeValue	SBMLEventInProgress.triggerObject

Methods in org.simulator.sbml that return ASTNodeValue

ASTNodeValue	SBMLEventInProgress.getDelayObject()
ASTNodeValue	SBMLEventInProgress.getPriorityObject()
ASTNodeValue	SBMLEventInProgress.getTriggerObject()

Methods in org.simulator.sbml with parameters of type ASTNodeValue

void	SBMLEventInProgress.setDelayObject(ASTNodeValue delayObject) Sets the math of the delay to a specific ASTNodeObject.
void	SBMLEventInProgress.setPriorityObject(ASTNodeValue priorityObject) Sets the math of the priority to a specific ASTNodeObject.
void	SBMLEventInProgress.setTriggerObject(ASTNodeValue triggerObject) Sets the math of the trigger to a specific ASTNodeObject.

Uses of ASTNodeValue in org.simulator.sbml.astnode

Subclasses of ASTNodeValue in org.simulator.sbml.astnode

class	CompartmentOrParameterValue This class computes and stores values of ASTNodes that refer to a compartment or a parameter.
class	FunctionValue This class computes and stores values of ASTNodes that refer to the application of a FunctionDefinition.
class	LocalParameterValue This class computes and stores values of ASTNodes that refer to a local parameter.
class	NamedValue This class computes and stores values of variables occuring in a function.
class	ReactionValue This class computes and stores values of ASTNodes that refer to a reaction.
class	RootFunctionValue This class computes and stores values of ASTNodes that refer to a root function.
class	SpeciesReferenceValue This class computes and stores values of ASTNodes that refer to a species reference.
class	SpeciesValue This class computes and stores values of ASTNodes that refer to a species.

Fields in org.simulator.sbml.astnode declared as ASTNodeValue

protected ASTNodeValue	FunctionValue.evaluationBlock The value of the evaluation block of the function stored in an ASTNodeObject.
protected ASTNodeValue	ReactionValue.kineticLawUserObject The object hat refers to the kinetic law of the reaction
protected ASTNodeValue	ASTNodeValue.leftChild The ASTNodeObject of the left child of the corresponding ASTNode
protected ASTNodeValue	RuleValue.nodeObject Object that refers to the math of the rule
protected ASTNodeValue	ASTNodeValue.rightChild The ASTNodeObject of the right child of the corresponding ASTNode

Fields in org.simulator.sbml.astnode with type parameters of type ASTNodeValue

protected List<ASTNodeValue>

ASTNodeValue.children The ASTNodeObjects of the child nodes of the corresponding ASTNode

Methods in org.simulator.sbml.astnode with parameters of type ASTNodeValue

double	ASTNodeInterpreter.abs(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arccos(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arccosh(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arccot(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arccoth(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arccsc(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arccsch(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arcsec(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arcsech(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arcsin(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arcsinh(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arctan(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.arctanh(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.ceiling(ASTNodeValue userObject, double time)
String	ASTNodeInterpreter.compileString(ASTNodeValue child)
double	ASTNodeInterpreter.cos(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.cosh(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.cot(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.coth(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.csc(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.csch(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.delay(String delayName, ASTNodeValue x, ASTNodeValue delay, String timeUnits, double time)
boolean	ASTNodeInterpreter.eq(ASTNodeValue left, ASTNodeValue right, double time)
double	ASTNodeInterpreter.exp(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.factorial(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.floor(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.frac(ASTNodeValue left, ASTNodeValue right, double time)
boolean	ASTNodeInterpreter.functionBoolean(ASTNodeValue rightChild, List<String> variables, List<ASTNodeValue> arguments, double[] values, double time)
double	ASTNodeInterpreter.functionDouble(ASTNodeValue rightChild, List<String> variables, List<ASTNodeValue> arguments, int nArguments, double[] values, double time)
boolean	ASTNodeInterpreter.geq(ASTNodeValue left, ASTNodeValue right, double time)
boolean	ASTNodeInterpreter.gt(ASTNodeValue left, ASTNodeValue right, double time)
boolean	ASTNodeInterpreter.leq(ASTNodeValue left, ASTNodeValue right, double time)
double	ASTNodeInterpreter.ln(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.log(ASTNodeValue left, ASTNodeValue right, double time)
double	ASTNodeInterpreter.log(ASTNodeValue userObject, double time)
boolean	ASTNodeInterpreter.lt(ASTNodeValue left, ASTNodeValue right, double time)
boolean	ASTNodeInterpreter.neq(ASTNodeValue left, ASTNodeValue right, double time)
boolean	ASTNodeInterpreter.not(ASTNodeValue node, double time)
double	ASTNodeInterpreter.pow(ASTNodeValue left, ASTNodeValue right, double time)
double	ASTNodeInterpreter.root(ASTNodeValue rootExponent, ASTNodeValue radiant, double time)
double	ASTNodeInterpreter.root(double rootExponent, ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.sec(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.sech(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.sin(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.sinh(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.sqrt(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.tan(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.tanh(ASTNodeValue userObject, double time)
double	ASTNodeInterpreter.uMinus(ASTNodeValue userObject, double time)

Method parameters in org.simulator.sbml.astnode with type arguments of type ASTNodeValue

boolean	ASTNodeInterpreter.and(List<ASTNodeValue> nodes, int size, double time)
boolean	ASTNodeInterpreter.functionBoolean(ASTNodeValue rightChild, List<String> variables, List<ASTNodeValue> arguments, double[] values, double time)
boolean	ASTNodeInterpreter.functionBoolean(String name, List<ASTNodeValue> children)
double	ASTNodeInterpreter.functionDouble(ASTNodeValue rightChild, List<String> variables, List<ASTNodeValue> arguments, int nArguments, double[] values, double time)
double	ASTNodeInterpreter.functionDouble(String functionDefinitionName, List<ASTNodeValue> args, double time)
boolean	ASTNodeInterpreter.lambdaBoolean(List<ASTNodeValue> nodes, double time)
double	ASTNodeInterpreter.lambdaDouble(List<ASTNodeValue> nodes, double time)
double	ASTNodeInterpreter.minus(List<ASTNodeValue> nodes, int size, double time)
boolean	ASTNodeInterpreter.or(List<ASTNodeValue> nodes, double time)
double	ASTNodeInterpreter.piecewise(List<ASTNodeValue> nodes, double time)
double	ASTNodeInterpreter.plus(List<ASTNodeValue> nodes, int size, double time)
double	ASTNodeInterpreter.times(List<ASTNodeValue> nodes, int size, double time)
boolean	ASTNodeInterpreter.xor(List<ASTNodeValue> nodes, double time)

Constructors in org.simulator.sbml.astnode with parameters of type ASTNodeValue

AssignmentRuleValue(ASTNodeValue nodeObject, int index)

AssignmentRuleValue(ASTNodeValue nodeObject, int index, Species sp, int compartmentIndex, boolean hasZeroSpatialDimensions, SBMLValueHolder valueHolder)
Constructor for rules that refer to a species

AssignmentRuleValue(ASTNodeValue nodeObject, String speciesReferenceID, Map<String,Double> stoichiometricCoefHash)
Constructor for rules that refer to a species reference

RateRuleValue(ASTNodeValue nodeObject, int index)

RateRuleValue(ASTNodeValue nodeObject, int index, List<Integer> speciesIndices, SBMLValueHolder valueHolder)
Constructor for a rule with a compartment as variable

RateRuleValue(ASTNodeValue nodeObject, int index, Species sp, int compartmentIndex, boolean hasZeroSpatialDimensions, SBMLValueHolder valueHolder)
Constructor for a rule with a species as variable

RuleValue(ASTNodeValue nodeObject, int index)

RuleValue(ASTNodeValue nodeObject, int index, Species sp, int compartmentIndex, boolean hasZeroSpatialDimensions, SBMLValueHolder valueHolder)
Constructor for rules that refer to a species.

StoichiometryValue(SpeciesReference sr, int speciesIndex, int speciesRefIndex, int compartmentIndex, Map<String,Double> stoichiometricCoefHash, SBMLValueHolder valueHolder, double[] Y, ASTNodeValue stoichiometryMathValue, int reactionIndex, Set<String> inConcentrationSet, boolean isReactant)