Package org.simulator.sbml.astnode

Class RuleValue

java.lang.Object

org.simulator.sbml.astnode.RuleValue

Direct Known Subclasses:

AssignmentRuleValue, RateRuleValue

public class RuleValue
extends Object

This class can compute and store the value of a rule together with the variable of the rule.

Version:

$Rev$

Author:

Roland Keller

Field Summary

Fields

Modifier and Type	Field	Description
protected int	compartmentIndex	The index of the compartment of the species (if applicable)
protected boolean	hasOnlySubstanceUnits	The hasOnlySubstanceUnits attribute of the species (if applicable)
protected boolean	hasZeroSpatialDimensions	This flag is true if the variable is a species and its compartment has no spatial dimensions
protected int	index	The index of the variable in the Y vector of the value holder
protected boolean	isSetInitialAmount	The isSetInitialAmount attribute of the species (if applicable)
protected boolean	isSetInitialConcentration	The isSetInitialConcentration attribute of the species (if applicable)
protected boolean	isSpecies	Flag that is true if the variable is referring to a species, otherwise false
protected ASTNodeValue	nodeObject	Object that refers to the math of the rule
protected double	value	The calculated value of the rul
protected SBMLValueHolder	valueHolder	The value holder that stores the current simulation results

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
int	getIndex()	Returns the index of the variable in the Y vector of the value holder.
double	getValue()	Returns the value of the rule.
protected double	processAssignmentVariable(double time)	Calculates the math of the rule and returns the new value of the variable.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

nodeObject

protected ASTNodeValue nodeObject

Object that refers to the math of the rule

value

protected double value

The calculated value of the rul

isSpecies

protected boolean isSpecies

Flag that is true if the variable is referring to a species, otherwise false

valueHolder

protected SBMLValueHolder valueHolder

The value holder that stores the current simulation results

compartmentIndex

protected int compartmentIndex

The index of the compartment of the species (if applicable)

hasOnlySubstanceUnits

protected boolean hasOnlySubstanceUnits

The hasOnlySubstanceUnits attribute of the species (if applicable)

isSetInitialAmount

protected boolean isSetInitialAmount

The isSetInitialAmount attribute of the species (if applicable)

isSetInitialConcentration

protected boolean isSetInitialConcentration

The isSetInitialConcentration attribute of the species (if applicable)

hasZeroSpatialDimensions

protected boolean hasZeroSpatialDimensions

This flag is true if the variable is a species and its compartment has no spatial dimensions

index

protected int index

The index of the variable in the Y vector of the value holder

Constructor Detail

RuleValue

public RuleValue(ASTNodeValue nodeObject,
                 int index)

Parameters:

nodeObject -

index -

RuleValue

public RuleValue(ASTNodeValue nodeObject,
                 int index,
                 org.sbml.jsbml.Species sp,
                 int compartmentIndex,
                 boolean hasZeroSpatialDimensions,
                 SBMLValueHolder valueHolder)

Constructor for rules that refer to a species.

Parameters:

nodeObject -

index -

sp -

compartmentIndex -

hasZeroSpatialDimensions -

valueHolder -

Method Detail

processAssignmentVariable

protected double processAssignmentVariable(double time)

Calculates the math of the rule and returns the new value of the variable.

Parameters:

time -

Returns:

value the computed value of the variable

getValue

public double getValue()

Returns the value of the rule.

Returns:

value

getIndex

public int getIndex()

Returns the index of the variable in the Y vector of the value holder.

Returns:

index