libSBML Perl API
libSBML 5.10.0 Perl API
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{fbc} Implementation of the 'fbc' package extention to the Model construct.
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 XML namespace (URI) of the package extension of this plugin object. 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 package name of this plugin object. More... | |
unsigned int | getPackageVersion () const |
Returns the package version of the package extension of this plugin object. More... | |
SBase * | getParentSBMLObject () |
Returns the parent SBase object to which this plugin object connected. More... | |
const SBase * | getParentSBMLObject () const |
Returns the parent SBase object to which this plugin object connected. More... | |
const std::string & | getPrefix () const |
Returns the prefix of the package extension of this plugin object. More... | |
SBMLDocument * | getSBMLDocument () |
Returns the parent SBMLDocument of this plugin object. More... | |
const SBMLDocument * | getSBMLDocument () const |
Returns the parent SBMLDocument of this plugin object. More... | |
std::string | getURI () const |
Gets the URI to which this element belongs to. More... | |
unsigned int | getVersion () const |
Returns the SBML version 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 element belongs to. 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 | ) |
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 | ) |
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virtual |
Creates and returns a deep copy of this FbcModelPlugin object.
Implements SBasePlugin.
FluxBound * FbcModelPlugin::createFluxBound | ( | ) |
GeneAssociation * FbcModelPlugin::createGeneAssociation | ( | ) |
Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it.
Objective * FbcModelPlugin::createObjective | ( | ) |
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 XML namespace (URI) of the package extension of this plugin object.
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 package name of this plugin object.
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inherited |
Returns the package version of the package extension of this plugin object.
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inherited |
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inherited |
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inherited |
Returns the prefix of the package extension of this plugin object.
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inherited |
Returns the parent SBMLDocument of this plugin object.
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inherited |
Returns the parent SBMLDocument of this plugin object.
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inherited |
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
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inherited |
Returns the SBML version 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 element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to "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 set the namespace to "http://www.sbml.org/sbml/level3/version1/layout/version1/"
void FbcModelPlugin::unsetActiveObjectiveId | ( | ) |
Unsets the active objective.