org.sbml.jsbml.ext.fbc
public class FBCModelPlugin extends AbstractSBasePlugin
Modifier and Type | Field and Description |
---|---|
private ListOf<FluxBound> |
listOfFluxBounds |
private ListOfObjectives |
listOfObjectives |
private static long |
serialVersionUID
Generated serial version identifier.
|
extendedSBase, packageVersion
listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS
Constructor and Description |
---|
FBCModelPlugin(FBCModelPlugin obj)
Clone constructor
|
FBCModelPlugin(Model model) |
Modifier and Type | Method and Description |
---|---|
boolean |
addFluxBound(FluxBound fluxBound)
Adds a new
FluxBound to the listOfFluxBounds. |
boolean |
addObjective(Objective objective)
Adds a new
Objective to the listOfObjectives. |
FBCModelPlugin |
clone() |
FluxBound |
createFluxBound()
Creates a new FluxBound element and adds it to the ListOfFluxBounds list
|
FluxBound |
createFluxBound(java.lang.String id)
Creates a new
FluxBound element and adds it to the ListOfFluxBounds list |
Objective |
createObjective()
Creates a new Objective element and adds it to the ListOfObjectives list
|
Objective |
createObjective(java.lang.String id)
Creates a new
Objective element and adds it to the ListOfObjectives list |
java.lang.String |
getActiveObjective()
Gets the
activeObjective . |
boolean |
getAllowsChildren() |
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.
|
FluxBound |
getFluxBound(int i)
Gets an element from the listOfFluxBounds at the given index.
|
ListOf<FluxBound> |
getListOfFluxBounds()
Returns the listOfFluxBounds.
|
ListOfObjectives |
getListOfObjectives()
Returns the
listOfObjectives . |
Objective |
getObjective(int i)
Gets an element from the listOfObjectives at the given index.
|
java.lang.String |
getPackageName()
Returns the package name of this plugin object.
|
Model |
getParent() |
Model |
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.
|
boolean |
isSetListOfFluxBounds()
Returns
true if listOfFluxBounds contains at least one element. |
boolean |
isSetListOfObjectives()
Returns
true if listOfObjectives is not null . |
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 . |
boolean |
removeFluxBound(FluxBound fluxBound)
Removes an element from the listOfFluxBounds.
|
void |
removeFluxBound(int i)
Removes an element from the listOfFluxBounds at the given index.
|
void |
removeObjective(int i)
Removes an element from the listOfObjectives at the given index.
|
boolean |
removeObjective(Objective objective)
Removes an element from the listOfObjectives.
|
void |
setActiveObjective(Objective objective) |
void |
setActiveObjective(java.lang.String activeObjective) |
void |
setListOfFluxBounds(ListOf<FluxBound> listOfFluxBounds)
Sets the given
ListOf<FluxBound> . |
void |
setListOfObjectives(ListOf<Objective> listOfObjectives)
Sets the given
ListOf<Objective> . |
void |
setListOfObjectives(ListOfObjectives listOfObjectives)
Sets the given
ListOfObjectives . |
boolean |
unsetListOfFluxBounds()
|
boolean |
unsetListOfObjectives()
Returns
true if listOfObjectives contain at least one element,
otherwise false |
java.util.Map<java.lang.String,java.lang.String> |
writeXMLAttributes()
Returns a
Map containing the XML attributes of this object. |
equals, getExtendedSBase, getLevel, getPackageVersion, getSBMLDocument, getVersion, hashCode, isSetExtendedSBase
addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, notifyChildChange, putUserObject, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, toString, userObjectKeySet
finalize, getClass, notify, notifyAll, wait, wait, wait
addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet
private static final long serialVersionUID
private ListOfObjectives listOfObjectives
public FBCModelPlugin(FBCModelPlugin obj)
public FBCModelPlugin(Model model)
model
- public java.lang.String getElementNamespace()
SBasePlugin
public java.lang.String getPackageName()
SBasePlugin
public java.lang.String getPrefix()
SBasePlugin
public java.lang.String getURI()
SBasePlugin
public Model getParent()
getParent
in interface javax.swing.tree.TreeNode
getParent
in class AbstractTreeNode
public Model getParentSBMLObject()
SBasePlugin
SBase
object to which this plugin object connected.getParentSBMLObject
in interface SBasePlugin
getParentSBMLObject
in class AbstractSBasePlugin
SBase
object to which this plugin object connected.public boolean addFluxBound(FluxBound fluxBound)
FluxBound
to the listOfFluxBounds.
The listOfFluxBounds is initialized if necessary.
fluxBound
- the element to add to the listtrue
(as specified by Collection.add
)public boolean addObjective(Objective objective)
Objective
to the listOfObjectives.
The listOfObjectives is initialized if necessary.
objective
- the element to add to the listtrue
(as specified by Collection.add
)public FBCModelPlugin clone()
clone
in interface SBasePlugin
clone
in class AbstractSBasePlugin
public FluxBound createFluxBound()
public FluxBound createFluxBound(java.lang.String id)
FluxBound
element and adds it to the ListOfFluxBounds listFluxBound
elementpublic Objective createObjective()
public Objective createObjective(java.lang.String id)
Objective
element and adds it to the ListOfObjectives listObjective
elementpublic java.lang.String getActiveObjective()
activeObjective
.
If the activeObjective
is not defined, an empty String is returned.
activeObjective
or "".public boolean getAllowsChildren()
public javax.swing.tree.TreeNode getChildAt(int index)
public int getChildCount()
public FluxBound getFluxBound(int i)
i
- the index where to get the FluxBound
java.lang.IndexOutOfBoundsException
- if the index is out of bound (index < 0 || index > list.size)public ListOf<FluxBound> getListOfFluxBounds()
public ListOfObjectives getListOfObjectives()
listOfObjectives
. Creates it if it is not already
existing.public Objective getObjective(int i)
i
- the index where to get the Objective
java.lang.IndexOutOfBoundsException
- if the index is out of bound (index < 0 || index > list.size)public boolean isSetListOfFluxBounds()
true
if listOfFluxBounds contains at least one element.true
if listOfFluxBounds contains at least one element,
otherwise false
public boolean isSetListOfObjectives()
true
if listOfObjectives is not null
.true
if listOfObjectives is not null,
otherwise false
public boolean readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
SBasePlugin
SBasePlugin
.attributeName
- localName of the XML attributeprefix
- prefix of the XML attributevalue
- value of the XML attributetrue
if the attribute has been successfully read.public boolean removeFluxBound(FluxBound fluxBound)
fluxBound
- the element to be removed from the listtrue
if the list contained the specified elementList.remove(Object)
public void removeFluxBound(int i)
i
- the index where to remove the FluxBound
java.lang.IndexOutOfBoundsException
- if the listOf is not set or
if the index is out of bound (index < 0 || index > list.size)public void removeObjective(int i)
i
- the index where to remove the Objective
java.lang.IndexOutOfBoundsException
- if the listOf is not set or
if the index is out of bound (index < 0 || index > list.size)public boolean removeObjective(Objective objective)
objective
- the element to be removed from the listtrue
if the list contained the specified elementList.remove(Object)
public void setActiveObjective(java.lang.String activeObjective)
activeObjective
- public void setActiveObjective(Objective objective)
objective
- public void setListOfFluxBounds(ListOf<FluxBound> listOfFluxBounds)
ListOf<FluxBound>
. If listOfFluxBounds was defined before and contained some elements, they are all unset.
listOfFluxBounds
- public void setListOfObjectives(ListOfObjectives listOfObjectives)
ListOfObjectives
. If listOfObjectives was defined before and contained some elements, they are all unset.
listOfObjectives
- public void setListOfObjectives(ListOf<Objective> listOfObjectives)
ListOf<Objective>
.
If the given list is an instance of ListOfObjectives
, a call of
this
method is identical to directly calling
setListOfObjectives(ListOfObjectives)
.
Otherwise, a new ListOfObjectives
will be created from the given
ListOf
.
Note that in the second case there is no active objective defined.
listOfObjectives
- public boolean unsetListOfFluxBounds()
true
if listOfFluxBounds
contain at least one
element, otherwise false
public boolean unsetListOfObjectives()
true
if listOfObjectives contain at least one element,
otherwise false
true
if listOfObjectives contain at least one element,
otherwise false
public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
SBasePlugin
Map
containing the XML attributes of this object.writeXMLAttributes
in interface SBasePlugin
writeXMLAttributes
in class AbstractSBasePlugin
Map
containing the XML attributes of this object.