org.jscience.ml.sbml
Class Reaction

java.lang.Object
  extended by org.jscience.ml.sbml.SBase
      extended by org.jscience.ml.sbml.SBaseId
          extended by org.jscience.ml.sbml.Reaction

public class Reaction
extends SBaseId

This class represents a reaction, which is some transformation, transport or binding process that can change the amount of one or more Species. 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
Reaction()
          Creates a new instance of Reaction
Reaction(java.lang.String id, java.lang.String name)
          Creates a new Reaction object.
 
Method Summary
 void addProduct(Species ref)
          DOCUMENT ME!
 void addProduct(SpeciesReference ref)
          DOCUMENT ME!
 void addReactant(Species ref)
          DOCUMENT ME!
 void addReactant(SpeciesReference ref)
          DOCUMENT ME!
 KineticLaw getKineticLaw()
          Getter for property kineticLaw.
 java.util.Vector getModifier()
          Getter for property modifier.
 SBase getModifiersElement()
          Getter for property modifiersElement.
 java.util.Vector getProduct()
          Getter for property product.
 SBase getProductsElement()
          Getter for property productsElement.
 java.util.Vector getReactant()
          Getter for property reactant.
 SBase getReactantsElement()
          Getter for property reactantsElement.
 boolean isFast()
          Getter for property fast.
 boolean isReversible()
          Getter for property reversible.
 void setFast(boolean fast)
          Setter for property fast.
 void setKineticLaw(KineticLaw kineticLaw)
          Setter for property kineticLaw.
 void setModifiersElement(SBase modifiersElement)
          Setter for property modifiersElement.
 void setProductsElement(SBase productsElement)
          Setter for property productsElement.
 void setReactantsElement(SBase reactantsElement)
          Setter for property reactantsElement.
 void setReversible(boolean reversible)
          Sets whether the reaction is reversible.
 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

Reaction

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

Parameters:
id - DOCUMENT ME!
name - DOCUMENT ME!

Reaction

public Reaction()
Creates a new instance of Reaction

Method Detail

addProduct

public void addProduct(Species ref)
DOCUMENT ME!

Parameters:
ref - DOCUMENT ME!

addProduct

public void addProduct(SpeciesReference ref)
DOCUMENT ME!

Parameters:
ref - DOCUMENT ME!

addReactant

public void addReactant(Species ref)
DOCUMENT ME!

Parameters:
ref - DOCUMENT ME!

addReactant

public void addReactant(SpeciesReference ref)
DOCUMENT ME!

Parameters:
ref - DOCUMENT ME!

getKineticLaw

public KineticLaw getKineticLaw()
Getter for property kineticLaw.

Returns:
Value of property kineticLaw.

getModifier

public java.util.Vector getModifier()
Getter for property modifier.

Returns:
Value of property modifier.

getModifiersElement

public SBase getModifiersElement()
Getter for property modifiersElement.

Returns:
Value of property modifiersElement.

getProduct

public java.util.Vector getProduct()
Getter for property product.

Returns:
Value of property product.

getProductsElement

public SBase getProductsElement()
Getter for property productsElement.

Returns:
Value of property productsElement.

getReactant

public java.util.Vector getReactant()
Getter for property reactant.

Returns:
Value of property reactant.

getReactantsElement

public SBase getReactantsElement()
Getter for property reactantsElement.

Returns:
Value of property reactantsElement.

isFast

public boolean isFast()
Getter for property fast.

Returns:
Value of property fast.

isReversible

public boolean isReversible()
Getter for property reversible.

Returns:
Value of property reversible.

setFast

public void setFast(boolean fast)
Setter for property fast.

Parameters:
fast - New value of property fast.

setKineticLaw

public void setKineticLaw(KineticLaw kineticLaw)
Setter for property kineticLaw.

Parameters:
kineticLaw - New value of property kineticLaw.

setModifiersElement

public void setModifiersElement(SBase modifiersElement)
Setter for property modifiersElement.

Parameters:
modifiersElement - New value of property modifiersElement.

setProductsElement

public void setProductsElement(SBase productsElement)
Setter for property productsElement.

Parameters:
productsElement - New value of property productsElement.

setReactantsElement

public void setReactantsElement(SBase reactantsElement)
Setter for property reactantsElement.

Parameters:
reactantsElement - New value of property reactantsElement.

setReversible

public void setReversible(boolean reversible)
Sets whether the reaction is reversible.

Parameters:
reversible - New value of property reversible.

toString

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

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