public class FbcModelPlugin extends SBasePlugin
Constructor and Description |
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FbcModelPlugin(FbcModelPlugin orig)
Copy constructor.
|
FbcModelPlugin(java.lang.String uri,
java.lang.String prefix,
FbcPkgNamespaces fbcns)
Constructor
|
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()
|
GeneAssociation |
createGeneAssociation()
Creates a new
GeneAssociation object and adds it to the list of GeneAssociation objects
and returns it. |
Objective |
createObjective()
|
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.
|
getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, setElementNamespace
public FbcModelPlugin(FbcModelPlugin orig)
FbcModelPlugin
object.public FbcModelPlugin(java.lang.String uri, java.lang.String prefix, FbcPkgNamespaces fbcns)
public int addFluxBound(FluxBound bound)
FluxBound
object to the list of FluxBounds.
bound
- the FluxBound
object to be added to the list of FluxBounds.
public int addGeneAssociation(GeneAssociation association)
GeneAssociation
object to the list of GeneAssociations.
association
- the GeneAssociation
object to be added to the list of GeneAssociations.
public int addObjective(Objective bound)
Objective
object to the list of Objectives.
bound
- the Objective
object to be added to the list of Objectives.
public SBasePlugin cloneObject()
FbcModelPlugin
object.
cloneObject
 in class SBasePlugin
FbcModelPlugin
objectpublic FluxBound createFluxBound()
FluxBound
objectpublic GeneAssociation createGeneAssociation()
GeneAssociation
object and adds it to the list of GeneAssociation
objects
and returns it.
GeneAssociation
objectpublic Objective createObjective()
Objective
objectpublic void delete()
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.
delete
 in class SBasePlugin
public Objective getActiveObjective()
public java.lang.String getActiveObjectiveId()
public SBase getElementByMetaId(java.lang.String metaid)
metaid
, or itself if it has the given metaid
, or null
if no such object is found.
getElementByMetaId
 in class SBasePlugin
metaid
- string representing the metaid of objects to find
SBase
element with the given metaid
.public SBase getElementBySId(java.lang.String id)
id
in the model-wide SId namespace, or null
if no such object is found.
getElementBySId
 in class SBasePlugin
id
- string representing the id of objects to find
SBase
element with the given id
.public FluxBound getFluxBound(long n)
FluxBound
object that belongs to the given index. If the
index is invalid, null
is returned.
n
- the index number of the FluxBound
to get.
FluxBound
in the ListOfFluxBounds
.public FluxBound getFluxBound(java.lang.String sid)
FluxBound
object based on its identifier.
sid
- a string representing the identifier
of the FluxBound
to get.
FluxBound
in the ListOfFluxBounds
with the given sid
or null if no such FluxBound
exists.
FbcModelPlugin.getFluxBound(long n)
,
FbcModelPlugin.getListOfFluxBounds()
public ListOfFluxBounds getFluxBoundsForReaction(java.lang.String reaction)
public GeneAssociation getGeneAssociation(long n)
GeneAssociation
object that belongs to the given index. If the
index is invalid, null
is returned.
n
- the index number of the GeneAssociation
to get.
GeneAssociation
in the ListOfGeneAssociations
.public GeneAssociation getGeneAssociation(java.lang.String sid)
GeneAssociation
object based on its identifier.
sid
- a string representing the identifier
of the GeneAssociation
to get.
GeneAssociation
in the ListOfGeneAssociations
with the given sid
or null if no such GeneAssociation
exists.
FbcModelPlugin.getGeneAssociation(long n)
,
FbcModelPlugin.getListOfGeneAssociations()
public ListOfFluxBounds getListOfFluxBounds()
ListOfFluxBounds
in this plugin object.
ListOfFluxBounds
object in this plugin object.public ListOfGeneAssociations getListOfGeneAssociations()
ListOfObjectives
in this plugin object.
ListOfObjectives
object in this plugin object.public ListOfObjectives getListOfObjectives()
ListOfObjectives
in this plugin object.
ListOfObjectives
object in this plugin object.public long getNumFluxBounds()
FluxBound
object in this plugin object.
FluxBound
object in this plugin object.public int getNumGeneAssociations()
GeneAssociation
object in this plugin object.
GeneAssociation
object in this plugin object.public long getNumObjectives()
Objective
object in this plugin object.
Objective
object in this plugin object.public Objective getObjective(long n)
Objective
object that belongs to the given index. If the
index is invalid, null
is returned.
n
- the index number of the Objective
to get.
Objective
in the ListOfObjectives
.public Objective getObjective(java.lang.String sid)
Objective
object based on its identifier.
sid
- a string representing the identifier
of the Objective
to get.
Objective
in the ListOfObjectives
with the given id
or null if no such Objective
exists.
FbcModelPlugin.getObjective(long n)
,
FbcModelPlugin.getListOfObjectives()
public FluxBound removeFluxBound(long n)
FluxBound
object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
public FluxBound removeFluxBound(java.lang.String sid)
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.
public GeneAssociation removeGeneAssociation(long n)
GeneAssociation
object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n
- the index of the GeneAssociation
object to remove
GeneAssociation
object removed. As mentioned above, the
caller owns the returned object. null
is returned if the
given index is out of range.public GeneAssociation removeGeneAssociation(java.lang.String sid)
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.
sid
- the id attribute of the GeneAssociation
object to remove
GeneAssociation
object removed. As mentioned above, the
caller owns the returned object. null
is returned if the
given index is out of range.public Objective removeObjective(long n)
Objective
object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
public Objective removeObjective(java.lang.String sid)
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.
public int setActiveObjectiveId(java.lang.String objectiveId)
public void unsetActiveObjectiveId()