org.sbml.jsbml.ext.fbc

Class FBCSpeciesPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBasePlugin, TreeNodeWithChangeSupport

public class FBCSpeciesPlugin
extends AbstractFBCSBasePlugin

Extends the SBML core Species class with the additional attributes charge and chemicalFormula.

Since:

1.0

Author:

Nicolas Rodriguez, Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.ext.AbstractSBasePlugin

elementNamespace, extendedSBase, packageVersion

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
FBCSpeciesPlugin(FBCSpeciesPlugin obj) Clone constructor
FBCSpeciesPlugin(Species species) Creates an FBCSpeciesPlugin instance

Method Summary

Modifier and Type	Method and Description
FBCSpeciesPlugin	clone()
boolean	getAllowsChildren()
int	getCharge() Returns the value of charge.
String	getChemicalFormula() Returns the value of chemicalFormula.
TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<Species>	getParent()
ListOf<Species>	getParentSBMLObject()
void	initDefaults() Initializes the default values.
boolean	isSetCharge() Returns whether charge is set.
boolean	isSetChemicalFormula() Returns whether chemicalFormula is set.
boolean	readAttribute(String attributeName, String prefix, String value)
void	setCharge(int charge) Sets the value of charge.
void	setChemicalFormula(String chemicalFormula) Sets the value of chemicalFormula.
boolean	unsetCharge() Unsets the variable charge
boolean	unsetChemicalFormula() Unsets the variable chemicalFormula
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

getPackageName, getPrefix, getURI

Methods inherited from class org.sbml.jsbml.ext.AbstractSBasePlugin

equals, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getElementNamespace, getExtendedSBase, getLevel, getPackageVersion, getSBMLDocument, getVersion, hashCode, isSetExtendedSBase, isSetPackageVersion, removeFromParent, setExtendedSBase, setNamespace, setPackageVersion

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, notifyChildChange, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, toString, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, isLeaf

Constructor Detail

FBCSpeciesPlugin

public FBCSpeciesPlugin(FBCSpeciesPlugin obj)

Clone constructor

Parameters:

obj - the instance to clone

FBCSpeciesPlugin

public FBCSpeciesPlugin(Species species)

Creates an FBCSpeciesPlugin instance

Parameters:

species - the core Species that is extended.

Method Detail

getParent

public ListOf<Species> getParent()

Specified by:

getParent in interface TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public ListOf<Species> getParentSBMLObject()

Specified by:

getParentSBMLObject in interface SBasePlugin

Overrides:

getParentSBMLObject in class AbstractSBasePlugin

clone

public FBCSpeciesPlugin clone()

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

getAllowsChildren

public boolean getAllowsChildren()

getCharge

public int getCharge()

Returns the value of charge.

Returns:

the value of charge.

getChemicalFormula

public String getChemicalFormula()

Returns the value of chemicalFormula.

Returns:

the value of chemicalFormula.

getChildAt

public TreeNode getChildAt(int index)

getChildCount

public int getChildCount()

initDefaults

public void initDefaults()

Initializes the default values.

isSetCharge

public boolean isSetCharge()

Returns whether charge is set.

Returns:

whether charge is set.

isSetChemicalFormula

public boolean isSetChemicalFormula()

Returns whether chemicalFormula is set.

Returns:

whether chemicalFormula is set.

readAttribute

public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)

setCharge

public void setCharge(int charge)

Sets the value of charge.

The optional field charge takes an integer indicating the charge on the species (in terms of electrons, not the SI unit coulombs).
This attribute can be used for charge balancing.

Parameters:

charge - the value of charge.

setChemicalFormula

public void setChemicalFormula(String chemicalFormula)

Sets the value of chemicalFormula.

The format of chemical formula must consist only of atomic names (as in the Periodic Table) or user defined compounds either of which take the form of a single capital letter followed by zero or more lower-case letters. Where there is more than a single atom present, this is indicated with an integer. With regards to order (and enhance interoperability) it is recommended to use the Hill system order (Hill 1900, 2012).

Parameters:

chemicalFormula - the chemical formula

unsetCharge

public boolean unsetCharge()

Unsets the variable charge

Returns:

true, if charge was set before, otherwise false

unsetChemicalFormula

public boolean unsetChemicalFormula()

Unsets the variable chemicalFormula

Returns:

true if chemicalFormula was set before, otherwise false

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin