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

Packages that use ASTNodeObject
org.simulator.sbml  
org.simulator.sbml.astnode Classes for efficient numerical treatment of equations in form of abstract syntax trees. 
 

Uses of ASTNodeObject in org.simulator.sbml
 

Fields in org.simulator.sbml declared as ASTNodeObject
protected  ASTNodeObject EventInProcess.delayObject
           
protected  ASTNodeObject EventInProcess.priorityObject
           
protected  ASTNodeObject EventInProcess.triggerObject
           
 

Methods in org.simulator.sbml that return ASTNodeObject
 ASTNodeObject EventInProcess.getDelayObject()
           
 ASTNodeObject EventInProcess.getPriorityObject()
           
 ASTNodeObject EventInProcess.getTriggerObject()
           
 

Methods in org.simulator.sbml with parameters of type ASTNodeObject
 void EventInProcess.setDelayObject(ASTNodeObject delayObject)
          Sets the math of the delay to a specific ASTNodeObject.
 void EventInProcess.setPriorityObject(ASTNodeObject priorityObject)
          Sets the math of the priority to a specific ASTNodeObject.
 void EventInProcess.setTriggerObject(ASTNodeObject triggerObject)
          Sets the math of the trigger to a specific ASTNodeObject.
 

Uses of ASTNodeObject in org.simulator.sbml.astnode
 

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

Fields in org.simulator.sbml.astnode with type parameters of type ASTNodeObject
protected  java.util.List<ASTNodeObject> ASTNodeObject.children
          The ASTNodeObjects of the child nodes of the corresponding ASTNode
 

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

Method parameters in org.simulator.sbml.astnode with type arguments of type ASTNodeObject
 boolean ASTNodeInterpreterWithTime.and(java.util.List<ASTNodeObject> nodes, int size, double time)
           
 boolean ASTNodeInterpreterWithTime.functionBoolean(ASTNodeObject rightChild, java.util.List<java.lang.String> variables, java.util.List<ASTNodeObject> arguments, double[] values, double time)
           
 boolean ASTNodeInterpreterWithTime.functionBoolean(java.lang.String name, java.util.List<ASTNodeObject> children)
           
 double ASTNodeInterpreterWithTime.functionDouble(ASTNodeObject rightChild, java.util.List<java.lang.String> variables, java.util.List<ASTNodeObject> arguments, int nArguments, double[] values, double time)
           
 double ASTNodeInterpreterWithTime.functionDouble(java.lang.String functionDefinitionName, java.util.List<ASTNodeObject> args, double time)
           
 boolean ASTNodeInterpreterWithTime.lambdaBoolean(java.util.List<ASTNodeObject> nodes, double time)
           
 double ASTNodeInterpreterWithTime.lambdaDouble(java.util.List<ASTNodeObject> nodes, double time)
           
 double ASTNodeInterpreterWithTime.minus(java.util.List<ASTNodeObject> nodes, int size, double time)
           
 boolean ASTNodeInterpreterWithTime.or(java.util.List<ASTNodeObject> nodes, double time)
           
 double ASTNodeInterpreterWithTime.piecewise(java.util.List<ASTNodeObject> nodes, double time)
           
 double ASTNodeInterpreterWithTime.plus(java.util.List<ASTNodeObject> nodes, int size, double time)
           
 double ASTNodeInterpreterWithTime.times(java.util.List<ASTNodeObject> nodes, int size, double time)
           
 boolean ASTNodeInterpreterWithTime.xor(java.util.List<ASTNodeObject> nodes, double time)
           
 

Constructors in org.simulator.sbml.astnode with parameters of type ASTNodeObject
AssignmentRuleObject(ASTNodeObject nodeObject, int index)
           
AssignmentRuleObject(ASTNodeObject nodeObject, int index, org.sbml.jsbml.Species sp, int compartmentIndex, boolean hasZeroSpatialDimensions, ValueHolder valueHolder)
          Constructor for rules that refer to a species
AssignmentRuleObject(ASTNodeObject nodeObject, java.lang.String speciesReferenceID, java.util.Map<java.lang.String,java.lang.Double> stoichiometricCoefHash)
          Constructor for rules that refer to a species reference
RateRuleObject(ASTNodeObject nodeObject, int index)
           
RateRuleObject(ASTNodeObject nodeObject, int index, java.util.List<java.lang.Integer> speciesIndices, ValueHolder valueHolder)
          Constructor for a rule with a compartment as variable
RateRuleObject(ASTNodeObject nodeObject, int index, org.sbml.jsbml.Species sp, int compartmentIndex, boolean hasZeroSpatialDimensions, ValueHolder valueHolder)
          Constructor for a rule with a species as variable
RuleObject(ASTNodeObject nodeObject, int index)
           
RuleObject(ASTNodeObject nodeObject, int index, org.sbml.jsbml.Species sp, int compartmentIndex, boolean hasZeroSpatialDimensions, ValueHolder valueHolder)
          Constructor for rules that refer to a species.
 

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