org.jscience.ml.sbml
Class Species

java.lang.Object
  org.jscience.ml.sbml.SBase
      org.jscience.ml.sbml.SBaseId
          org.jscience.ml.sbml.Species

public class Species
extends SBaseId

This class represents an entity that takes part in Reactions. This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Field Summary

Fields inherited from class org.jscience.ml.sbml.SBaseId

id, name

Constructor Summary

Species()
Creates a new instance of Species

Species(java.lang.String id, java.lang.String name)
Creates a new Species object.

Method Summary

java.lang.String	getCharge() Getter for property charge.
java.lang.String	getCompartment() Getter for property compartment.
boolean	getHasOnlySubstanceUnits() Getter for property hasOnlySubstanceUnits.
double	getInitialAmount() Getter for property initialAmount.
double	getInitialConcentration() Getter for property initialConcentration.
java.lang.String	getSpatialSizeUnits() Getter for property spatialSizeUnits.
java.lang.String	getSubstanceUnits() Getter for property substanceUnits.
boolean	isBoundaryCondition() Getter for property boundaryCondition.
boolean	isConstant() Getter for property constant.
void	setBoundaryCondition(boolean boundaryCondition) Sets whether the species is on the boundary of the reaction system.
void	setCharge(java.lang.String charge) Setter for property charge.
void	setCompartment(Compartment ref) DOCUMENT ME!
void	setCompartment(java.lang.String compartment) Setter for property compartment.
void	setConstant(boolean constant) Setter for property constant.
void	setHasOnlySubstanceUnits(boolean hasOnlySubstanceUnits) Setter for property hasOnlySubstanceUnits.
void	setInitialAmount(double initialAmount) Setter for property initialAmount.
void	setInitialConcentration(double initialConcentration) Setter for property initialConcentration.
void	setSpatialSizeUnits(java.lang.String spatialSizeUnits) Setter for property spatialSizeUnits.
void	setSubstanceUnits(java.lang.String substanceUnits) Setter for property substanceUnits.
java.lang.String	toString() Get the SBML representation for this class.

Methods inherited from class org.jscience.ml.sbml.SBaseId

getId, getName, setId, setName

Methods inherited from class org.jscience.ml.sbml.SBase

getAnnotations, getMetaid, getNotes, getRDF, printList, printShortForm, setMetaid, setRDF, setRDF

Methods inherited from class java.lang.Object

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

Constructor Detail

Species

public Species(java.lang.String id,
               java.lang.String name)

Creates a new Species object.

Parameters:

id - DOCUMENT ME!

name - DOCUMENT ME!

Species

public Species()

Creates a new instance of Species

Method Detail

getCharge

public java.lang.String getCharge()

Getter for property charge.

Returns:

Value of property charge.

getCompartment

public java.lang.String getCompartment()

Getter for property compartment.

Returns:

Value of property compartment.

getHasOnlySubstanceUnits

public boolean getHasOnlySubstanceUnits()

Getter for property hasOnlySubstanceUnits.

Returns:

Value of property hasOnlySubstanceUnits.

getInitialAmount

public double getInitialAmount()

Getter for property initialAmount.

Returns:

Value of property initialAmount.

getInitialConcentration

public double getInitialConcentration()

Getter for property initialConcentration.

Returns:

Value of property initialConcentration.

getSpatialSizeUnits

public java.lang.String getSpatialSizeUnits()

Getter for property spatialSizeUnits.

Returns:

Value of property spatialSizeUnits.

getSubstanceUnits

public java.lang.String getSubstanceUnits()

Getter for property substanceUnits.

Returns:

Value of property substanceUnits.

isBoundaryCondition

public boolean isBoundaryCondition()

Getter for property boundaryCondition.

Returns:

Value of property boundaryCondition.

isConstant

public boolean isConstant()

Getter for property constant.

Returns:

Value of property constant.

setBoundaryCondition

public void setBoundaryCondition(boolean boundaryCondition)

Sets whether the species is on the boundary of the reaction system.

Parameters:

boundaryCondition - New value of property boundaryCondition.

setCharge

public void setCharge(java.lang.String charge)

Setter for property charge.

Parameters:

charge - New value of property charge.

setCompartment

public void setCompartment(Compartment ref)

DOCUMENT ME!

Parameters:

ref - DOCUMENT ME!

setCompartment

public void setCompartment(java.lang.String compartment)

Setter for property compartment.

Parameters:

compartment - New value of property compartment.

setConstant

public void setConstant(boolean constant)

Setter for property constant.

Parameters:

constant - New value of property constant.

setHasOnlySubstanceUnits

public void setHasOnlySubstanceUnits(boolean hasOnlySubstanceUnits)

Setter for property hasOnlySubstanceUnits.

Parameters:

hasOnlySubstanceUnits - New value of property hasOnlySubstanceUnits.

setInitialAmount

public void setInitialAmount(double initialAmount)

Setter for property initialAmount.

Parameters:

initialAmount - New value of property initialAmount.

setInitialConcentration

public void setInitialConcentration(double initialConcentration)

Setter for property initialConcentration.

Parameters:

initialConcentration - New value of property initialConcentration.

setSpatialSizeUnits

public void setSpatialSizeUnits(java.lang.String spatialSizeUnits)

Setter for property spatialSizeUnits.

Parameters:

spatialSizeUnits - New value of property spatialSizeUnits.

setSubstanceUnits

public void setSubstanceUnits(java.lang.String substanceUnits)

Setter for property substanceUnits.

Parameters:

substanceUnits - New value of property substanceUnits.

toString

public java.lang.String toString()

Get the SBML representation for this class.

Overrides:

toString in class SBase

Returns:

The class's SBML representation