libSBML C++ API
5.11.0
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Public Member Functions | |
int | addFluxBound (const FluxBound *bound) |
Adds a copy of the given FluxBound object to the list of FluxBounds. More... | |
int | addGeneAssociation (const GeneAssociation *association) |
Adds a copy of the given GeneAssociation object to the list of GeneAssociations. More... | |
int | addObjective (const Objective *bound) |
Adds a copy of the given Objective object to the list of Objectives. More... | |
virtual FbcModelPlugin * | clone () const |
Creates and returns a deep copy of this FbcModelPlugin object. More... | |
FluxBound * | createFluxBound () |
Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it. More... | |
GeneAssociation * | createGeneAssociation () |
Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it. More... | |
Objective * | createObjective () |
Creates a new Objective object and adds it to the list of Objective objects and returns it. More... | |
FbcModelPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns) | |
Constructor. More... | |
FbcModelPlugin (const FbcModelPlugin &orig) | |
Copy constructor. More... | |
Objective * | getActiveObjective () |
Returns the current active objective. More... | |
const Objective * | getActiveObjective () const |
Returns the current active objective. More... | |
std::string | getActiveObjectiveId () const |
returns the id of the current active objective. More... | |
virtual List * | getAllElements (ElementFilter *filter=NULL) |
Returns a List of all child SBase* objects, including those nested to an arbitrary depth. More... | |
virtual SBase * | getElementByMetaId (const std::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. More... | |
virtual SBase * | getElementBySId (const std::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. More... | |
const std::string & | getElementNamespace () const |
Returns the namespace URI of the package to which this plugin object belongs. More... | |
const FluxBound * | getFluxBound (unsigned int n) const |
Returns the FluxBound object that belongs to the given index. More... | |
FluxBound * | getFluxBound (unsigned int n) |
Returns the FluxBound object that belongs to the given index. More... | |
FluxBound * | getFluxBound (const std::string &sid) |
Returns the FluxBound object based on its identifier. More... | |
const FluxBound * | getFluxBound (const std::string &sid) const |
Returns the FluxBound object based on its identifier. More... | |
ListOfFluxBounds * | getFluxBoundsForReaction (const std::string &reaction) const |
const GeneAssociation * | getGeneAssociation (unsigned int n) const |
Returns the GeneAssociation object that belongs to the given index. More... | |
GeneAssociation * | getGeneAssociation (unsigned int n) |
Returns the GeneAssociation object that belongs to the given index. More... | |
GeneAssociation * | getGeneAssociation (const std::string &sid) |
Returns the GeneAssociation object based on its identifier. More... | |
const GeneAssociation * | getGeneAssociation (const std::string &sid) const |
Returns the GeneAssociation object based on its identifier. More... | |
unsigned int | getLevel () const |
Returns the SBML Level of the package extension of this plugin object. More... | |
const ListOfFluxBounds * | getListOfFluxBounds () const |
------------------------------------------------------------------ More... | |
ListOfFluxBounds * | getListOfFluxBounds () |
Returns the ListOfFluxBounds in this plugin object. More... | |
const ListOfGeneAssociations * | getListOfGeneAssociations () const |
Returns the ListOfObjectives in this plugin object. More... | |
ListOfGeneAssociations * | getListOfGeneAssociations () |
Returns the ListOfGeneAssociations in this plugin object. More... | |
const ListOfObjectives * | getListOfObjectives () const |
Returns the ListOfObjectives in this plugin object. More... | |
ListOfObjectives * | getListOfObjectives () |
Returns the ListOfObjectives in this plugin object. More... | |
unsigned int | getNumFluxBounds () const |
Returns the number of FluxBound object in this plugin object. More... | |
int | getNumGeneAssociations () const |
Returns the number of GeneAssociation object in this plugin object. More... | |
unsigned int | getNumObjectives () const |
Returns the number of Objective object in this plugin object. More... | |
const Objective * | getObjective (unsigned int n) const |
Returns the Objective object that belongs to the given index. More... | |
Objective * | getObjective (unsigned int n) |
Returns the Objective object that belongs to the given index. More... | |
Objective * | getObjective (const std::string &sid) |
Returns the Objective object based on its identifier. More... | |
const Objective * | getObjective (const std::string &sid) const |
Returns the Objective object based on its identifier. More... | |
const std::string & | getPackageName () const |
Returns the short-form name of the package to which this plugin object belongs. More... | |
unsigned int | getPackageVersion () const |
Returns the package version of the package extension of this plugin object. More... | |
SBase * | getParentSBMLObject () |
Returns the parent object to which this plugin object is connected. More... | |
const SBase * | getParentSBMLObject () const |
Returns the parent object to which this plugin object is connected. More... | |
const std::string & | getPrefix () const |
Returns the XML namespace prefix of the package to which this plugin object belongs. More... | |
SBMLDocument * | getSBMLDocument () |
Returns the SBMLDocument object containing this object instance. More... | |
const SBMLDocument * | getSBMLDocument () const |
Returns the SBMLDocument object containing this object instance. More... | |
std::string | getURI () const |
Returns the XML namespace URI for the package to which this object belongs. More... | |
unsigned int | getVersion () const |
Returns the Version within the SBML Level of the package extension of this plugin object. More... | |
FbcModelPlugin & | operator= (const FbcModelPlugin &orig) |
Assignment operator for FbcModelPlugin . More... | |
FluxBound * | removeFluxBound (unsigned int n) |
Removes the nth FluxBound object from this plugin object and returns a pointer to it. More... | |
FluxBound * | removeFluxBound (const std::string &sid) |
Removes the FluxBound object with the given sid attribute from this plugin object and returns a pointer to it. More... | |
GeneAssociation * | removeGeneAssociation (unsigned int n) |
Removes the nth GeneAssociation object from this plugin object and returns a pointer to it. More... | |
GeneAssociation * | removeGeneAssociation (const std::string &sid) |
Removes the GeneAssociation object with the given sid attribute from this plugin object and returns a pointer to it. More... | |
Objective * | removeObjective (unsigned int n) |
Removes the nth Objective object from this plugin object and returns a pointer to it. More... | |
Objective * | removeObjective (const std::string &sid) |
Removes the Objective object with the given sid attribute from this plugin object and returns a pointer to it. More... | |
int | setActiveObjectiveId (const std::string &objectiveId) |
Sets the id of the active objective. More... | |
int | setElementNamespace (const std::string &uri) |
Sets the XML namespace to which this object belongs. More... | |
void | unsetActiveObjectiveId () |
Unsets the active objective. More... | |
virtual | ~FbcModelPlugin () |
Destroy this object. More... | |
FbcModelPlugin::FbcModelPlugin | ( | const std::string & | uri, |
const std::string & | prefix, | ||
FbcPkgNamespaces * | fbcns | ||
) |
Constructor.
FbcModelPlugin::FbcModelPlugin | ( | const FbcModelPlugin & | orig | ) |
Copy constructor.
Creates a copy of this FbcModelPlugin object.
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virtual |
Destroy this object.
int FbcModelPlugin::addFluxBound | ( | const FluxBound * | bound | ) |
Adds a copy of the given FluxBound object to the list of FluxBounds.
bound | the FluxBound object to be added to the list of FluxBounds. |
int FbcModelPlugin::addGeneAssociation | ( | const GeneAssociation * | association | ) |
Adds a copy of the given GeneAssociation object to the list of GeneAssociations.
association | the GeneAssociation object to be added to the list of GeneAssociations. |
int FbcModelPlugin::addObjective | ( | const Objective * | bound | ) |
Adds a copy of the given Objective object to the list of Objectives.
bound | the Objective object to be added to the list of Objectives. |
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virtual |
Creates and returns a deep copy of this FbcModelPlugin object.
Implements SBasePlugin.
FluxBound * FbcModelPlugin::createFluxBound | ( | ) |
Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it.
GeneAssociation * FbcModelPlugin::createGeneAssociation | ( | ) |
Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it.
Objective * FbcModelPlugin::createObjective | ( | ) |
Creates a new Objective object and adds it to the list of Objective objects and returns it.
Objective * FbcModelPlugin::getActiveObjective | ( | ) |
Returns the current active objective.
const Objective * FbcModelPlugin::getActiveObjective | ( | ) | const |
Returns the current active objective.
std::string FbcModelPlugin::getActiveObjectiveId | ( | ) | const |
returns the id of the current active objective.
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virtual |
Returns a List of all child SBase* objects, including those nested to an arbitrary depth.
Reimplemented from SBasePlugin.
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virtual |
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.
metaid | string representing the metaid of objects to find |
metaid
. Reimplemented from SBasePlugin.
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virtual |
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.
id | string representing the id of objects to find |
id
. Reimplemented from SBasePlugin.
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inherited |
Returns the namespace URI of the package to which this plugin object belongs.
const FluxBound * FbcModelPlugin::getFluxBound | ( | unsigned int | n | ) | const |
Returns the 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 * FbcModelPlugin::getFluxBound | ( | unsigned int | n | ) |
Returns the 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 * FbcModelPlugin::getFluxBound | ( | const std::string & | sid | ) |
Returns the FluxBound object based on its identifier.
sid | a string representing the identifier of the FluxBound to get. |
sid
or NULL if no such FluxBound exists.const FluxBound * FbcModelPlugin::getFluxBound | ( | const std::string & | sid | ) | const |
Returns the FluxBound object based on its identifier.
sid | a string representing the identifier of the FluxBound to get. |
sid
or NULL if no such FluxBound exists.ListOfFluxBounds * FbcModelPlugin::getFluxBoundsForReaction | ( | const std::string & | reaction | ) | const |
const GeneAssociation * FbcModelPlugin::getGeneAssociation | ( | unsigned int | n | ) | const |
Returns the 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 * FbcModelPlugin::getGeneAssociation | ( | unsigned int | n | ) |
Returns the 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 * FbcModelPlugin::getGeneAssociation | ( | const std::string & | sid | ) |
Returns the GeneAssociation object based on its identifier.
sid | a string representing the identifier of the GeneAssociation to get. |
sid
or NULL if no such GeneAssociation exists.const GeneAssociation * FbcModelPlugin::getGeneAssociation | ( | const std::string & | sid | ) | const |
Returns the GeneAssociation object based on its identifier.
sid | a string representing the identifier of the GeneAssociation to get. |
sid
or NULL if no such GeneAssociation exists.
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inherited |
Returns the SBML Level of the package extension of this plugin object.
const ListOfFluxBounds * FbcModelPlugin::getListOfFluxBounds | ( | ) | const |
------------------------------------------------------------------
Additional public functions
------------------------------------------------------------------ Returns the ListOfFluxBounds in this plugin object.
ListOfFluxBounds * FbcModelPlugin::getListOfFluxBounds | ( | ) |
Returns the ListOfFluxBounds in this plugin object.
const ListOfGeneAssociations * FbcModelPlugin::getListOfGeneAssociations | ( | ) | const |
Returns the ListOfObjectives in this plugin object.
ListOfGeneAssociations * FbcModelPlugin::getListOfGeneAssociations | ( | ) |
Returns the ListOfGeneAssociations in this plugin object.
const ListOfObjectives * FbcModelPlugin::getListOfObjectives | ( | ) | const |
Returns the ListOfObjectives in this plugin object.
ListOfObjectives * FbcModelPlugin::getListOfObjectives | ( | ) |
Returns the ListOfObjectives in this plugin object.
unsigned int FbcModelPlugin::getNumFluxBounds | ( | ) | const |
int FbcModelPlugin::getNumGeneAssociations | ( | ) | const |
Returns the number of GeneAssociation object in this plugin object.
unsigned int FbcModelPlugin::getNumObjectives | ( | ) | const |
const Objective * FbcModelPlugin::getObjective | ( | unsigned int | n | ) | const |
Returns the 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 * FbcModelPlugin::getObjective | ( | unsigned int | n | ) |
Returns the 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 * FbcModelPlugin::getObjective | ( | const std::string & | sid | ) |
Returns the Objective object based on its identifier.
sid | a string representing the identifier of the Objective to get. |
id
or NULL if no such Objective exists.const Objective * FbcModelPlugin::getObjective | ( | const std::string & | sid | ) | const |
Returns the Objective object based on its identifier.
sid | a string representing the identifier of the Objective to get. |
sid
or NULL if no such Objective exists.
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inherited |
Returns the short-form name of the package to which this plugin object belongs.
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inherited |
Returns the package version of the package extension of this plugin object.
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inherited |
Returns the parent object to which this plugin object is connected.
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inherited |
Returns the parent object to which this plugin object is connected.
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inherited |
Returns the XML namespace prefix of the package to which this plugin object belongs.
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inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
Returns the XML namespace URI for the package to which this object belongs.
"http://www.sbml.org/sbml/level3/version1/core"
. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/"
.This method first looks into the SBMLNamespaces object possessed by the parent SBMLDocument object of the current object. If this cannot be found, this method returns the result of getElementNamespace().
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inherited |
Returns the Version within the SBML Level of the package extension of this plugin object.
FbcModelPlugin & FbcModelPlugin::operator= | ( | const FbcModelPlugin & | orig | ) |
Assignment operator for FbcModelPlugin .
FluxBound * FbcModelPlugin::removeFluxBound | ( | unsigned int | 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.
n | the index of the FluxBound object to remove |
NULL
is returned if the given index is out of range. FluxBound * FbcModelPlugin::removeFluxBound | ( | const std::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.
sid | the id attribute of the FluxBound object to remove |
NULL
is returned if the given index is out of range. GeneAssociation * FbcModelPlugin::removeGeneAssociation | ( | unsigned int | 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.
n | the index of the GeneAssociation object to remove |
NULL
is returned if the given index is out of range. GeneAssociation * FbcModelPlugin::removeGeneAssociation | ( | const std::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.
sid | the id attribute of the GeneAssociation object to remove |
NULL
is returned if the given index is out of range. Objective * FbcModelPlugin::removeObjective | ( | unsigned int | 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.
n | the index of the Objective object to remove |
NULL
is returned if the given index is out of range. Objective * FbcModelPlugin::removeObjective | ( | const std::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.
sid | the id attribute of the Objective object to remove |
NULL
is returned if the given index is out of range. int FbcModelPlugin::setActiveObjectiveId | ( | const std::string & | objectiveId | ) |
Sets the id of the active objective.
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inherited |
Sets the XML namespace to which this object belongs.
"http://www.sbml.org/sbml/level3/version1/core"
. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/"
.uri | the URI to assign to this object. |
void FbcModelPlugin::unsetActiveObjectiveId | ( | ) |
Unsets the active objective.