org.sbml.libsbml

Class FbcModelPlugin

java.lang.Object

org.sbml.libsbml.SBasePlugin

org.sbml.libsbml.FbcModelPlugin

public class FbcModelPlugin
extends SBasePlugin

fbc Implementation of the 'fbc' package extention to the Model construct.

Constructor Summary

Constructors

Constructor and Description
FbcModelPlugin(FbcModelPlugin orig) Copy constructor.
FbcModelPlugin(java.lang.String uri, java.lang.String prefix, FbcPkgNamespaces fbcns) Constructor

Method Summary

Methods

Modifier and Type	Method and Description
int	addFluxBound(FluxBound bound) Adds a copy of the given FluxBound object to the list of FluxBounds.
int	addGeneAssociation(GeneAssociation association) Adds a copy of the given GeneAssociation object to the list of GeneAssociations.
int	addObjective(Objective bound) Adds a copy of the given Objective object to the list of Objectives.
SBasePlugin	cloneObject() Creates and returns a deep copy of this FbcModelPlugin object.
FluxBound	createFluxBound() Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it.
GeneAssociation	createGeneAssociation() Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it.
Objective	createObjective() Creates a new Objective object and adds it to the list of Objective objects and returns it.
void	delete() Explicitly deletes the underlying native object.
Objective	getActiveObjective() Returns the current active objective.
java.lang.String	getActiveObjectiveId() returns the id of the current active objective.
SBase	getElementByMetaId(java.lang.String metaid) Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
SBase	getElementBySId(java.lang.String id) Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
FluxBound	getFluxBound(long n) Returns the FluxBound object that belongs to the given index.
FluxBound	getFluxBound(java.lang.String sid) Returns the FluxBound object based on its identifier.
ListOfFluxBounds	getFluxBoundsForReaction(java.lang.String reaction)
GeneAssociation	getGeneAssociation(long n) Returns the GeneAssociation object that belongs to the given index.
GeneAssociation	getGeneAssociation(java.lang.String sid) Returns the GeneAssociation object based on its identifier.
ListOfFluxBounds	getListOfFluxBounds() Returns the ListOfFluxBounds in this plugin object.
ListOfGeneAssociations	getListOfGeneAssociations() Returns the ListOfObjectives in this plugin object.
ListOfObjectives	getListOfObjectives() Returns the ListOfObjectives in this plugin object.
long	getNumFluxBounds() Returns the number of FluxBound object in this plugin object.
int	getNumGeneAssociations() Returns the number of GeneAssociation object in this plugin object.
long	getNumObjectives() Returns the number of Objective object in this plugin object.
Objective	getObjective(long n) Returns the Objective object that belongs to the given index.
Objective	getObjective(java.lang.String sid) Returns the Objective object based on its identifier.
FluxBound	removeFluxBound(long n) Removes the nth FluxBound object from this plugin object and returns a pointer to it.
FluxBound	removeFluxBound(java.lang.String sid) Removes the FluxBound object with the given sid attribute from this plugin object and returns a pointer to it.
GeneAssociation	removeGeneAssociation(long n) Removes the nth GeneAssociation object from this plugin object and returns a pointer to it.
GeneAssociation	removeGeneAssociation(java.lang.String sid) Removes the GeneAssociation object with the given sid attribute from this plugin object and returns a pointer to it.
Objective	removeObjective(long n) Removes the nth Objective object from this plugin object and returns a pointer to it.
Objective	removeObjective(java.lang.String sid) Removes the Objective object with the given sid attribute from this plugin object and returns a pointer to it.
int	setActiveObjectiveId(java.lang.String objectiveId) Sets the id of the active objective.
void	unsetActiveObjectiveId() Unsets the active objective.

Methods inherited from class org.sbml.libsbml.SBasePlugin

getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, setElementNamespace

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FbcModelPlugin

public FbcModelPlugin(FbcModelPlugin orig)

Copy constructor. Creates a copy of this FbcModelPlugin object.

FbcModelPlugin

public FbcModelPlugin(java.lang.String uri,
              java.lang.String prefix,
              FbcPkgNamespaces fbcns)

Constructor

Method Detail

addFluxBound

public int addFluxBound(FluxBound bound)

Adds a copy of the given FluxBound object to the list of FluxBounds.

Parameters:

bound - the FluxBound object to be added to the list of FluxBounds.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS

addGeneAssociation

public int addGeneAssociation(GeneAssociation association)

Adds a copy of the given GeneAssociation object to the list of GeneAssociations.

Parameters:

association - the GeneAssociation object to be added to the list of GeneAssociations.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS

addObjective

public int addObjective(Objective bound)

Adds a copy of the given Objective object to the list of Objectives.

Parameters:

bound - the Objective object to be added to the list of Objectives.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS

cloneObject

public SBasePlugin cloneObject()

Creates and returns a deep copy of this FbcModelPlugin object.

Overrides:

cloneObject in class SBasePlugin

Returns:

a (deep) copy of this FbcModelPlugin object

createFluxBound

public FluxBound createFluxBound()

Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it.

Returns:

a newly created FluxBound object

createGeneAssociation

public GeneAssociation createGeneAssociation()

Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it.

Returns:

a newly created GeneAssociation object

createObjective

public Objective createObjective()

Creates a new Objective object and adds it to the list of Objective objects and returns it.

Returns:

a newly created Objective object

delete

public void delete()

Explicitly deletes the underlying native object.

In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize() methods for the objects. The finalize() methods in turn call the FbcModelPlugin.delete() method on the libSBML object.

This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke FbcModelPlugin.delete() themselves.

Overrides:

delete in class SBasePlugin

getActiveObjective

public Objective getActiveObjective()

Returns the current active objective.

getActiveObjectiveId

public java.lang.String getActiveObjectiveId()

returns the id of the current active objective.

getElementByMetaId

public SBase getElementByMetaId(java.lang.String metaid)

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.

Overrides:

getElementByMetaId in class SBasePlugin

Parameters:

metaid - string representing the metaid of objects to find

Returns:

a pointer to the SBase element with the given metaid.

getElementBySId

public SBase getElementBySId(java.lang.String id)

Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.

Overrides:

getElementBySId in class SBasePlugin

Parameters:

id - string representing the id of objects to find

Returns:

a pointer to the SBase element with the given id.

getFluxBound

public FluxBound getFluxBound(long n)

Returns the FluxBound object that belongs to the given index. If the index is invalid, null is returned.

Parameters:

n - the index number of the FluxBound to get.

Returns:

the nth FluxBound in the ListOfFluxBounds.

getFluxBound

public FluxBound getFluxBound(java.lang.String sid)

Returns the FluxBound object based on its identifier.

Parameters:

sid - a string representing the identifier of the FluxBound to get.

Returns:

FluxBound in the ListOfFluxBounds with the given sid or null if no such FluxBound exists.

See Also:

FbcModelPlugin.getFluxBound(long n), FbcModelPlugin.getListOfFluxBounds()

getFluxBoundsForReaction

public ListOfFluxBounds getFluxBoundsForReaction(java.lang.String reaction)

getGeneAssociation

public GeneAssociation getGeneAssociation(long n)

Returns the GeneAssociation object that belongs to the given index. If the index is invalid, null is returned.

Parameters:

n - the index number of the GeneAssociation to get.

Returns:

the nth GeneAssociation in the ListOfGeneAssociations.

getGeneAssociation

public GeneAssociation getGeneAssociation(java.lang.String sid)

Returns the GeneAssociation object based on its identifier.

Parameters:

sid - a string representing the identifier of the GeneAssociation to get.

Returns:

GeneAssociation in the ListOfGeneAssociations with the given sid or null if no such GeneAssociation exists.

See Also:

FbcModelPlugin.getGeneAssociation(long n), FbcModelPlugin.getListOfGeneAssociations()

getListOfFluxBounds

public ListOfFluxBounds getListOfFluxBounds()

Returns the ListOfFluxBounds in this plugin object.

Returns:

ListOfFluxBounds object in this plugin object.

getListOfGeneAssociations

public ListOfGeneAssociations getListOfGeneAssociations()

Returns the ListOfObjectives in this plugin object.

Returns:

ListOfObjectives object in this plugin object.

getListOfObjectives

public ListOfObjectives getListOfObjectives()

Returns the ListOfObjectives in this plugin object.

Returns:

ListOfObjectives object in this plugin object.

getNumFluxBounds

public long getNumFluxBounds()

Returns the number of FluxBound object in this plugin object.

Returns:

the number of FluxBound object in this plugin object.

getNumGeneAssociations

public int getNumGeneAssociations()

Returns the number of GeneAssociation object in this plugin object.

Returns:

the number of GeneAssociation object in this plugin object.

getNumObjectives

public long getNumObjectives()

Returns the number of Objective object in this plugin object.

Returns:

the number of Objective object in this plugin object.

getObjective

public Objective getObjective(long n)

Returns the Objective object that belongs to the given index. If the index is invalid, null is returned.

Parameters:

n - the index number of the Objective to get.

Returns:

the nth Objective in the ListOfObjectives.

getObjective

public Objective getObjective(java.lang.String sid)

Returns the Objective object based on its identifier.

Parameters:

sid - a string representing the identifier of the Objective to get.

Returns:

Objective in the ListOfObjectives with the given id or null if no such Objective exists.

See Also:

FbcModelPlugin.getObjective(long n), FbcModelPlugin.getListOfObjectives()

removeFluxBound

public FluxBound removeFluxBound(long n)

Removes the nth FluxBound object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n - the index of the FluxBound object to remove

Returns:

the FluxBound object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.

removeFluxBound

public FluxBound removeFluxBound(java.lang.String sid)

Removes the FluxBound object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

sid - the id attribute of the FluxBound object to remove

Returns:

the FluxBound object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.

removeGeneAssociation

public GeneAssociation removeGeneAssociation(long n)

Removes the nth GeneAssociation object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n - the index of the GeneAssociation object to remove

Returns:

the GeneAssociation object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.

removeGeneAssociation

public GeneAssociation removeGeneAssociation(java.lang.String sid)

Removes the GeneAssociation object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

sid - the id attribute of the GeneAssociation object to remove

Returns:

the GeneAssociation object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.

removeObjective

public Objective removeObjective(long n)

Removes the nth Objective object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n - the index of the Objective object to remove

Returns:

the Objective object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.

removeObjective

public Objective removeObjective(java.lang.String sid)

Removes the Objective object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

sid - the id attribute of the Objective object to remove

Returns:

the Objective object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.

setActiveObjectiveId

public int setActiveObjectiveId(java.lang.String objectiveId)

Sets the id of the active objective.

unsetActiveObjectiveId

public void unsetActiveObjectiveId()

Unsets the active objective.