Simulation Core Library

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
          The delay math of the event
protected  ASTNodeValue SBMLEventInProgress.priorityObject
          The priority math of the event
protected  ASTNodeValue SBMLEventInProgress.triggerObject
          The trigger of the event
 

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 DivideValue
          This class computes and stores values of ASTNodes that refer to a division object.
 class FunctionValue
          This class computes and stores values of ASTNodes that refer to the application of a FunctionDefinition.
 class IntegerValue
          This class can compute and store the value of an integer node.
 class LocalParameterValue
          This class computes and stores values of ASTNodes that refer to a LocalParameter.
 class MinusValue
          This class can compute and store the value of a minus node.
 class NamedValue
          This class computes and stores values of variables occurring in a function.
 class PlusValue
          This class can compute and store the value of a plus node.
 class PowerValue
          This class can compute and store the value of a power expression.
 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 SpeciesReference.
 class SpeciesValue
          This class computes and stores values of ASTNodes that refer to a Species.
 class TimesValue
          This class can compute and store the value of times nodes.
 

Fields in org.simulator.sbml.astnode declared as ASTNodeValue
protected  ASTNodeValue[] ASTNodeValue.children
          The ASTNodeObjects of the child nodes of the corresponding ASTNode
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
 

Methods in org.simulator.sbml.astnode with parameters of type ASTNodeValue
 double ASTNodeInterpreter.abs(ASTNodeValue userObject, double time, double delay)
           
 boolean ASTNodeInterpreter.and(ASTNodeValue[] children, int size, double time)
           
 double ASTNodeInterpreter.arccos(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arccosh(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arccot(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arccoth(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arccsc(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arccsch(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arcsec(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arcsech(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arcsin(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arcsinh(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arctan(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.arctanh(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.ceiling(ASTNodeValue userObject, double time, double delay)
           
 String ASTNodeInterpreter.compileString(ASTNodeValue child)
           
 double ASTNodeInterpreter.cos(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.cosh(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.cot(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.coth(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.csc(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.csch(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.delay(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 delay)
           
 double ASTNodeInterpreter.factorial(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.floor(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.frac(ASTNodeValue left, ASTNodeValue right, double time, double delay)
           
 boolean ASTNodeInterpreter.functionBoolean(ASTNodeValue rightChild, List<String> variables, ASTNodeValue[] children, double[] values, double time)
           
 boolean ASTNodeInterpreter.functionBoolean(ASTNodeValue rightChild, List<String> variables, ASTNodeValue[] children, double[] values, double time)
           
 double ASTNodeInterpreter.functionDouble(ASTNodeValue rightChild, List<String> variables, ASTNodeValue[] children, int nArguments, double[] values, double time)
           
 double ASTNodeInterpreter.functionDouble(ASTNodeValue rightChild, List<String> variables, ASTNodeValue[] children, 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.lambdaBoolean(ASTNodeValue[] children, double time)
           
 double ASTNodeInterpreter.lambdaDouble(ASTNodeValue[] children, double time)
           
 boolean ASTNodeInterpreter.leq(ASTNodeValue left, ASTNodeValue right, double time)
           
 double ASTNodeInterpreter.ln(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.log(ASTNodeValue left, ASTNodeValue right, double time, double delay)
           
 double ASTNodeInterpreter.log(ASTNodeValue userObject, double time, double delay)
           
 boolean ASTNodeInterpreter.lt(ASTNodeValue left, ASTNodeValue right, double time)
           
 double ASTNodeInterpreter.minus(ASTNodeValue[] children, int size, double time, double delay)
           
 boolean ASTNodeInterpreter.neq(ASTNodeValue left, ASTNodeValue right, double time)
           
 boolean ASTNodeInterpreter.not(ASTNodeValue node, double time)
           
 boolean ASTNodeInterpreter.or(ASTNodeValue[] children, double time)
           
 double ASTNodeInterpreter.piecewise(ASTNodeValue[] children, double time, double delay)
           
 double ASTNodeInterpreter.plus(ASTNodeValue[] children, int size, double time, double delay)
           
 double ASTNodeInterpreter.pow(ASTNodeValue left, ASTNodeValue right, double time, double delay)
           
 double ASTNodeInterpreter.root(ASTNodeValue rootExponent, ASTNodeValue radiant, double time, double delay)
           
 double ASTNodeInterpreter.root(double rootExponent, ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.sec(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.sech(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.sin(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.sinh(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.sqrt(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.tan(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.tanh(ASTNodeValue userObject, double time, double delay)
           
 double ASTNodeInterpreter.times(ASTNodeValue[] children, int size, double time, double delay)
           
 double ASTNodeInterpreter.uMinus(ASTNodeValue userObject, double time, double delay)
           
 boolean ASTNodeInterpreter.xor(ASTNodeValue[] children, double time)
           
 

Method parameters in org.simulator.sbml.astnode with type arguments of type ASTNodeValue
 boolean ASTNodeInterpreter.functionBoolean(String name, List<ASTNodeValue> children)
           
 double ASTNodeInterpreter.functionDouble(String functionDefinitionName, List<ASTNodeValue> args, 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 speciesRefIndex, Map<String,Double> stoichiometricCoefHash, double[] Y, ASTNodeValue stoichiometryMathValue)
           
 


Generated at March 17 2014
Version 1.4 Revision 453