org.jscience.ml.sbml
Class SpeciesReference

java.lang.Object
  extended by org.jscience.ml.sbml.SBase
      extended by org.jscience.ml.sbml.SpeciesReference

public class SpeciesReference
extends SBase

A class defining a reference to a Species for use in a Reaction. This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.


Constructor Summary
SpeciesReference()
          Creates a new instance of SpeciesReference
SpeciesReference(Species species)
          Creates a new SpeciesReference object.
 
Method Summary
 java.lang.String getSpecies()
          Getter for property species.
 java.lang.String getStoichiometry()
          Getter for property stoichiometry.
 StoichiometryMath getStoichiometryMath()
          Getter for property stoichiometryMath.
 void setSpecies(Species ref)
          DOCUMENT ME!
 void setSpecies(java.lang.String species)
          Setter for property species.
 void setStoichiometry(double stoichiometry)
          Sets the rational stoichiometry of a reaction.
 void setStoichiometryMath(StoichiometryMath stoichiometryMath)
          Sets the stoichiometry of a reaction.
 java.lang.String toString()
          Get the SBML representation for this class.
 
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

SpeciesReference

public SpeciesReference()
Creates a new instance of SpeciesReference


SpeciesReference

public SpeciesReference(Species species)
Creates a new SpeciesReference object.

Parameters:
species - DOCUMENT ME!
Method Detail

getSpecies

public java.lang.String getSpecies()
Getter for property species.

Returns:
Value of property species.

getStoichiometry

public java.lang.String getStoichiometry()
Getter for property stoichiometry.

Returns:
Value of property stoichiometry.

getStoichiometryMath

public StoichiometryMath getStoichiometryMath()
Getter for property stoichiometryMath.

Returns:
Value of property stoichiometryMath.

setSpecies

public void setSpecies(Species ref)
DOCUMENT ME!

Parameters:
ref - DOCUMENT ME!

setSpecies

public void setSpecies(java.lang.String species)
Setter for property species.

Parameters:
species - Setter for property species.

setStoichiometry

public void setStoichiometry(double stoichiometry)
Sets the rational stoichiometry of a reaction. NaN indicates that the stoichiometry is not set. If the stoichiometry is not NaN, the stoichiometry math will be cleared. Stoichiometries must be non-negative. For maximum compatibility with other software, the stoichiometry should be an integer.

Parameters:
stoichiometry - Stoichiometry
Throws:
java.lang.IllegalArgumentException - DOCUMENT ME!

setStoichiometryMath

public void setStoichiometryMath(StoichiometryMath stoichiometryMath)
Sets the stoichiometry of a reaction. If the stoichiometry math is not null, the rational stoichiometry will be cleared. For maximum compatibility with other software, use a rational stoichiometry instead of stoichiometry math.

Parameters:
stoichiometryMath - Stoichiometry math

toString

public java.lang.String toString()
Get the SBML representation for this class.

Overrides:
toString in class SBase
Returns:
The class's SBML representation