Package org.simulator.sbml.astnode

Class SpeciesValue

java.lang.Object

org.simulator.sbml.astnode.ASTNodeValue

org.simulator.sbml.astnode.SpeciesValue

public class SpeciesValue
extends ASTNodeValue

This class computes and stores values of ASTNodes that refer to a Species.

Since:

1.0

Version:

$Rev: 205 $

Author:

Roland Keller

Field Summary

Fields

Modifier and Type	Field	Description
protected int	compartmentPosition	The position of the compartment value of the species in the Y vector of the value holder
protected boolean	hasOnlySubstanceUnits	The hasOnlySubstanceUnits attribute of the species
protected String	id	The id of the species
protected boolean	isAmount	Is the Y value of the species referring to an amount?
protected boolean	isSetInitialConcentration	Has the species an initial concentration set?
protected int	position	The position of the species value in the Y vector of the value holder
protected org.sbml.jsbml.Species	s	The corresponding species
protected SBMLValueHolder	valueHolder	The value holder that stores the current simulation results
protected boolean	zeroSpatialDimensions	Has the compartment of the species no spatial dimensions?

Fields inherited from class org.simulator.sbml.astnode.ASTNodeValue

alreadyProcessed, booleanValue, children, denominator, doubleValue, exponent, interpreter, isConstant, isDouble, isInfinite, leftChild, logger, mantissa, name, node, nodeType, numChildren, numerator, real, rightChild, time, units

Constructor Summary

Constructors

Constructor	Description
SpeciesValue(ASTNodeInterpreter interpreter, org.sbml.jsbml.ASTNode node, org.sbml.jsbml.Species s, SBMLValueHolder valueHolder, int position, int compartmentPosition, String compartmentID, boolean zeroSpatialDimensions, boolean isAmount)

Method Summary

Modifier and Type	Method	Description
protected void	computeDoubleValue(double delay)	Computes the double value of the node.

Methods inherited from class org.simulator.sbml.astnode.ASTNodeValue

compileBoolean, compileDouble, computeBooleanValue, getConstant, getName, getNode, getTime, getValue, isName, reset, setTime

Methods inherited from class java.lang.Object

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

Field Detail

s

protected org.sbml.jsbml.Species s

The corresponding species

id

protected String id

The id of the species

valueHolder

protected SBMLValueHolder valueHolder

The value holder that stores the current simulation results

isAmount

protected boolean isAmount

Is the Y value of the species referring to an amount?

hasOnlySubstanceUnits

protected boolean hasOnlySubstanceUnits

The hasOnlySubstanceUnits attribute of the species

isSetInitialConcentration

protected boolean isSetInitialConcentration

Has the species an initial concentration set?

position

protected int position

The position of the species value in the Y vector of the value holder

compartmentPosition

protected int compartmentPosition

The position of the compartment value of the species in the Y vector of the value holder

zeroSpatialDimensions

protected boolean zeroSpatialDimensions

Has the compartment of the species no spatial dimensions?

Constructor Detail

SpeciesValue

public SpeciesValue(ASTNodeInterpreter interpreter,
                    org.sbml.jsbml.ASTNode node,
                    org.sbml.jsbml.Species s,
                    SBMLValueHolder valueHolder,
                    int position,
                    int compartmentPosition,
                    String compartmentID,
                    boolean zeroSpatialDimensions,
                    boolean isAmount)

Parameters:

interpreter -

node -

s -

valueHolder -

position -

compartmentPosition -

compartmentID -

zeroSpatialDimensions -

isAmount -

Method Detail

computeDoubleValue

protected void computeDoubleValue(double delay)

Description copied from class: ASTNodeValue

Computes the double value of the node.

Overrides:

computeDoubleValue in class ASTNodeValue