org.systemsbiology.chem
Class Compartment

java.lang.Object
  org.systemsbiology.math.SymbolValue
      org.systemsbiology.chem.Compartment

All Implemented Interfaces:

Comparable

public final class Compartment

extends SymbolValue

Represents a named, well-mixed reaction compartment, which has a numeric volume. In Model objects constructed using the ModelBuilderCommandLanguage, typically only a default Compartment object (with unit volume) is used, with the actual volume being absorbed into the values for the reaction parameters. However, Model objects constructed from SBML using the ModelBuilderMarkupLanguage are special, in that the symbol evaluator implicitly makes use of the Compartment volume when evaluating a Species symbol that appears in a kinticLaw formula.

Author:

Stephen Ramsey

Field Summary

static double

DEFAULT_VOLUME

Fields inherited from class org.systemsbiology.math.SymbolValue

mSymbol, mValue

Constructor Summary

Compartment(String pName)

Compartment(String pName, double pVolume)
Creates a compartment.

Compartment(SymbolValue pSymbolValue)

Method Summary

Object	clone()
boolean	equals(Compartment pCompartment)
String	getName()
void	setVolume(double pVolume)
void	setVolume(Expression pVolume)
String	toString()

Methods inherited from class org.systemsbiology.math.SymbolValue

addSymbolToMap, addSymbolToMap, compareTo, equals, getSymbol, getValue, setValue

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_VOLUME

public static final double DEFAULT_VOLUME

See Also:

Constant Field Values

Constructor Detail

Compartment

public Compartment(String pName,
                   double pVolume)

Creates a compartment. The compartment name may not contain the NAME_DELIMITER string, which is a single colon character.

Compartment

public Compartment(SymbolValue pSymbolValue)

Compartment

public Compartment(String pName)

Method Detail

setVolume

public void setVolume(double pVolume)

setVolume

public void setVolume(Expression pVolume)

getName

public String getName()

equals

public boolean equals(Compartment pCompartment)

toString

public String toString()

clone

public Object clone()

Overrides:

clone in class SymbolValue