org.sbml.jsbml.ext.fbc

Class FBCSpeciesPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, SBasePlugin, TreeNodeWithChangeSupport

public class FBCSpeciesPlugin
extends AbstractSBasePlugin

FBCSpeciesPlugin is the extended Species class with the additional attributes charge and chemicalFormula

Since:

1.0

Version:

$Rev: 1706 $

Author:

Nicolas Rodriguez, Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private int	charge
private java.lang.String	chemicalFormula
private boolean	isSetCharge
private static long	serialVersionUID Generated serial version identifier.

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

extendedSBase, packageVersion

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
FBCSpeciesPlugin	clone() Creates a new instance of SBasePlugin from this SBasePlugin.
boolean	getAllowsChildren()
int	getCharge() Returns the value of charge
java.lang.String	getChemicalFormula() Returns the value of chemicalFormula
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
java.lang.String	getElementNamespace() Returns the XML namespace (URI) of the package extension of this plugin object.
java.lang.String	getPackageName() Returns the package name of this plugin object.
ListOf<Species>	getParent()
ListOf<Species>	getParentSBMLObject() Returns the parent SBase object to which this plugin object connected.
java.lang.String	getPrefix() Returns the prefix of the package extension of this plugin object.
java.lang.String	getURI() Gets the URI to which this element belongs to.
void	initDefaults() Initializes the default values.
boolean	isSetCharge() Returns whether charge is set
boolean	isSetChemicalFormula() Returns whether chemicalFormula is set
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Reads and sets the attribute if it is know from this SBasePlugin.
void	setCharge(int charge) Sets the value of charge.
void	setChemicalFormula(java.lang.String chemicalFormula) Sets the value of chemicalFormula.
boolean	unsetCharge() Unsets the variable charge
boolean	unsetChemicalFormula() Unsets the variable chemicalFormula
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes() Returns a Map containing the XML attributes of this object.

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

equals, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getExtendedSBase, getLevel, getPackageVersion, getSBMLDocument, getVersion, hashCode, isSetExtendedSBase, removeFromParent, setExtendedSBase

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, isLeaf, 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

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

charge

private int charge

chemicalFormula

private java.lang.String chemicalFormula

isSetCharge

private boolean isSetCharge

Constructor Detail

FBCSpeciesPlugin

public FBCSpeciesPlugin(FBCSpeciesPlugin obj)

Clone constructor

FBCSpeciesPlugin

public FBCSpeciesPlugin(Species species)

Creates an FBCSpeciesPlugin instance

Method Detail

getElementNamespace

public java.lang.String getElementNamespace()

Description copied from interface: SBasePlugin

Returns the XML namespace (URI) of the package extension of this plugin object.

Returns:

the URI of the package extension of this plugin object.

getPackageName

public java.lang.String getPackageName()

Description copied from interface: SBasePlugin

Returns the package name of this plugin object.

Returns:

the package name of this plugin object.

getPrefix

public java.lang.String getPrefix()

Description copied from interface: SBasePlugin

Returns the prefix of the package extension of this plugin object.

Returns:

the prefix of the package extension of this plugin object.

getURI

public java.lang.String getURI()

Description copied from interface: SBasePlugin

Gets the URI to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/' Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found it will return the result of getElementNamespace

Returns:

the URI for this element

getParent

public ListOf<Species> getParent()

Specified by:

getParent in interface javax.swing.tree.TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public ListOf<Species> getParentSBMLObject()

Description copied from interface: SBasePlugin

Returns the parent SBase object to which this plugin object connected.

Specified by:

getParentSBMLObject in interface SBasePlugin

Overrides:

getParentSBMLObject in class AbstractSBasePlugin

Returns:

the parent SBase object to which this plugin object connected.

clone

public FBCSpeciesPlugin clone()

Description copied from interface: SBasePlugin

Creates a new instance of SBasePlugin from this SBasePlugin.

Specified by:

clone in interface SBasePlugin

Specified by:

clone in class AbstractSBasePlugin

Returns:

a new instance of SBasePlugin from this SBasePlugin.

getAllowsChildren

public boolean getAllowsChildren()

getCharge

public int getCharge()

Returns the value of charge

Returns:

the value of charge

getChemicalFormula

public java.lang.String getChemicalFormula()

Returns the value of chemicalFormula

Returns:

the value of chemicalFormula

getChildAt

public javax.swing.tree.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(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)

Description copied from interface: SBasePlugin

Reads and sets the attribute if it is know from this SBasePlugin.

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

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.

setChemicalFormula

public void setChemicalFormula(java.lang.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 inter-operability) it is recommended to use the Hill system order (Hill 1900, 2012).

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 java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBasePlugin

Returns a Map containing the XML attributes of this object.

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin

Returns:

a Map containing the XML attributes of this object.