libSBML Perl API
libSBML 5.12.0 Perl API
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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 annotation object to the list of GeneAssociations. More... | |
int | addGeneProduct (const GeneProduct *gp) |
Adds a copy the given "GeneProduct" to this FbcModelPlugin. More... | |
int | addObjective (const Objective *o) |
Adds a copy the given "Objective" to this FbcModelPlugin. 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 annotation object and adds it to the list of GeneAssociation objects and returns it. More... | |
GeneProduct * | createGeneProduct () |
Creates a new GeneProduct object, adds it to this FbcModelPlugins ListOfGeneProducts and returns the GeneProduct object created. More... | |
Objective * | createObjective () |
Creates a new Objective object, adds it to this FbcModelPlugins ListOfObjectives and returns the Objective object created. More... | |
FbcModelPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns) | |
Creates a new FbcModelPlugin. More... | |
FbcModelPlugin (const FbcModelPlugin &orig) | |
Copy constructor for FbcModelPlugin. 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) |
doxygenLibsbmlInternal More... | |
virtual SBase * | getElementByMetaId (const std::string &metaid) |
Return the first child object found with a given meta identifier. More... | |
virtual SBase * | getElementBySId (const std::string &id) |
Return the first child object found with a given identifier. 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 annotation object that belongs to the given index. More... | |
GeneAssociation * | getGeneAssociation (unsigned int n) |
Returns the GeneAssociation annotation object that belongs to the given index. More... | |
GeneAssociation * | getGeneAssociation (const std::string &sid) |
Returns the GeneAssociation annotation object based on its identifier. More... | |
const GeneAssociation * | getGeneAssociation (const std::string &sid) const |
Returns the GeneAssociation annotation object based on its identifier. More... | |
GeneProduct * | getGeneProduct (unsigned int n) |
Get a GeneProduct from the ListOfGeneProducts. More... | |
const GeneProduct * | getGeneProduct (unsigned int n) const |
Get a GeneProduct from the ListOfGeneProducts. More... | |
GeneProduct * | getGeneProduct (const std::string &sid) |
Get a GeneProduct from the ListOfGeneProducts based on its identifier. More... | |
const GeneProduct * | getGeneProduct (const std::string &sid) const |
Get a GeneProduct from the ListOfGeneProducts based on its identifier. More... | |
GeneProduct * | getGeneProductByLabel (const std::string &label) |
Get a GeneProduct from the ListOfGeneProducts based on its label. More... | |
unsigned int | getLevel () const |
Returns the SBML Level of the package extension of this plugin object. More... | |
const ListOfFluxBounds * | getListOfFluxBounds () const |
Returns the ListOfFluxBounds in this plugin object. More... | |
ListOfFluxBounds * | getListOfFluxBounds () |
Returns the ListOfFluxBounds in this plugin object. More... | |
const ListOfGeneAssociations * | getListOfGeneAssociations () const |
Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object. More... | |
ListOfGeneAssociations * | getListOfGeneAssociations () |
Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object. More... | |
const ListOfGeneProducts * | getListOfGeneProducts () const |
Returns the "ListOfGeneProducts" in this FbcModelPlugin object. More... | |
ListOfGeneProducts * | getListOfGeneProducts () |
Returns the "ListOfGeneProducts" in this FbcModelPlugin object. More... | |
const ListOfObjectives * | getListOfObjectives () const |
Returns the "ListOfObjectives" in this FbcModelPlugin object. More... | |
ListOfObjectives * | getListOfObjectives () |
Returns the "ListOfObjectives" in this FbcModelPlugin 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 annotation object in this plugin object. More... | |
unsigned int | getNumGeneProducts () const |
Get the number of GeneProduct objects in this FbcModelPlugin. More... | |
unsigned int | getNumObjectives () const |
Get the number of Objective objects in this FbcModelPlugin. More... | |
Objective * | getObjective (unsigned int n) |
Get a Objective from the ListOfObjectives. More... | |
const Objective * | getObjective (unsigned int n) const |
Get a Objective from the ListOfObjectives. More... | |
Objective * | getObjective (const std::string &sid) |
Get a Objective from the ListOfObjectives based on its identifier. More... | |
const Objective * | getObjective (const std::string &sid) const |
Get a Objective from the ListOfObjectives 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... | |
virtual bool | getStrict () const |
Returns the value of the "strict" attribute of this FbcModelPlugin. 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... | |
virtual bool | hasRequiredElements () const |
doxygenLibsbmlInternal More... | |
virtual bool | isSetStrict () const |
Predicate returning true if this FbcModelPlugin's "strict" attribute is set. More... | |
virtual bool | isValidTypeForList (SBase *item) const |
FbcModelPlugin & | operator= (const FbcModelPlugin &rhs) |
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 annotation object from this plugin object and returns a pointer to it. More... | |
GeneAssociation * | removeGeneAssociation (const std::string &sid) |
Removes the GeneAssociation annotation object with the given sid attribute from this plugin object and returns a pointer to it. More... | |
GeneProduct * | removeGeneProduct (unsigned int n) |
Removes the nth GeneProduct from the ListOfGeneProducts within this FbcModelPlugin. More... | |
GeneProduct * | removeGeneProduct (const std::string &sid) |
Removes the GeneProduct with the given identifier from the ListOfGeneProducts within this FbcModelPlugin and returns a pointer to it. More... | |
Objective * | removeObjective (unsigned int n) |
Removes the nth Objective from the ListOfObjectives within this FbcModelPlugin. More... | |
Objective * | removeObjective (const std::string &sid) |
Removes the Objective with the given identifier from the ListOfObjectives within this FbcModelPlugin and returns a pointer to it. More... | |
virtual void | renameMetaIdRefs (const std::string &oldid, const std::string &newid) |
virtual void | renameSIdRefs (const std::string &oldid, const std::string &newid) |
virtual void | renameUnitSIdRefs (const std::string &oldid, const std::string &newid) |
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... | |
virtual int | setStrict (bool strict) |
Sets the value of the "strict" attribute of this FbcModelPlugin. More... | |
void | unsetActiveObjectiveId () |
Unsets the active objective. More... | |
virtual int | unsetStrict () |
Unsets the value of the "strict" attribute of this FbcModelPlugin. More... | |
virtual | ~FbcModelPlugin () |
Destructor for FbcModelPlugin. More... | |
FbcModelPlugin::FbcModelPlugin | ( | const std::string & | uri, |
const std::string & | prefix, | ||
FbcPkgNamespaces * | fbcns | ||
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Creates a new FbcModelPlugin.
FbcModelPlugin::FbcModelPlugin | ( | const FbcModelPlugin & | orig | ) |
Copy constructor for FbcModelPlugin.
orig; | the FbcModelPlugin instance to copy. |
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virtual |
Destructor for FbcModelPlugin.
int FbcModelPlugin::addFluxBound | ( | const FluxBound * | bound | ) |
int FbcModelPlugin::addGeneAssociation | ( | const GeneAssociation * | association | ) |
Adds a copy of the given GeneAssociation annotation object to the list of GeneAssociations.
association | the GeneAssociation annotation object to be added to the list of GeneAssociations. |
int FbcModelPlugin::addGeneProduct | ( | const GeneProduct * | gp | ) |
Adds a copy the given "GeneProduct" to this FbcModelPlugin.
gp; | the GeneProduct object to add |
int FbcModelPlugin::addObjective | ( | const Objective * | o | ) |
Adds a copy the given "Objective" to this FbcModelPlugin.
o; | the Objective object to add |
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virtual |
Creates and returns a deep copy of this FbcModelPlugin object.
Reimplemented from SBasePlugin.
FluxBound * FbcModelPlugin::createFluxBound | ( | ) |
GeneAssociation * FbcModelPlugin::createGeneAssociation | ( | ) |
Creates a new GeneAssociation annotation object and adds it to the list of GeneAssociation objects and returns it.
GeneProduct * FbcModelPlugin::createGeneProduct | ( | ) |
Creates a new GeneProduct object, adds it to this FbcModelPlugins ListOfGeneProducts and returns the GeneProduct object created.
Objective * FbcModelPlugin::createObjective | ( | ) |
Creates a new Objective object, adds it to this FbcModelPlugins ListOfObjectives and returns the Objective object created.
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 |
doxygenLibsbmlInternal
doxygenLibsbmlInternal doxygenLibsbmlInternal Returns a List of all child SBase objects, including those nested to an arbitrary depth.
doxygenLibsbmlInternal
Reimplemented from SBasePlugin.
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virtualinherited |
Return the first child object found with a given meta identifier.
This method searches all the subobjects under this one, compares their meta identifiers to metaid
, and returns the first one that machines.
metaid | string, the metaid of the object to find. |
metaid
. Reimplemented in CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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virtualinherited |
Return the first child object found with a given identifier.
This method searches all the subobjects under this one, compares their identifiers to id
, and returns the first one that machines.
Normally, SId
type identifier values are unique across a model in SBML. However, in some circumstances they may not be, such as if a model is invalid because of multiple objects having the same identifier.
id | string representing the identifier of the object to find |
id
. Reimplemented in CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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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 |
reaction | the id of an reaction to find fluxBounds for |
const GeneAssociation * FbcModelPlugin::getGeneAssociation | ( | unsigned int | n | ) | const |
Returns the GeneAssociation annotation object that belongs to the given index.
If the index is invalid, NULL
is returned.
n | the index number of the GeneAssociation annotation to get. |
GeneAssociation * FbcModelPlugin::getGeneAssociation | ( | unsigned int | n | ) |
Returns the GeneAssociation annotation object that belongs to the given index.
If the index is invalid, NULL
is returned.
n | the index number of the GeneAssociation annotation to get. |
GeneAssociation * FbcModelPlugin::getGeneAssociation | ( | const std::string & | sid | ) |
Returns the GeneAssociation annotation object based on its identifier.
sid | a string representing the identifier of the GeneAssociation annotation to get. |
sid
or NULL if no such GeneAssociation annotation exists.const GeneAssociation * FbcModelPlugin::getGeneAssociation | ( | const std::string & | sid | ) | const |
Returns the GeneAssociation annotation object based on its identifier.
sid | a string representing the identifier of the GeneAssociation annotation to get. |
sid
or NULL if no such GeneAssociation annotation exists.GeneProduct * FbcModelPlugin::getGeneProduct | ( | unsigned int | n | ) |
Get a GeneProduct from the ListOfGeneProducts.
n | the index number of the GeneProduct to get. |
const GeneProduct * FbcModelPlugin::getGeneProduct | ( | unsigned int | n | ) | const |
Get a GeneProduct from the ListOfGeneProducts.
n | the index number of the GeneProduct to get. |
GeneProduct * FbcModelPlugin::getGeneProduct | ( | const std::string & | sid | ) |
Get a GeneProduct from the ListOfGeneProducts based on its identifier.
sid | a string representing the identifier of the GeneProduct to get. |
const GeneProduct * FbcModelPlugin::getGeneProduct | ( | const std::string & | sid | ) | const |
Get a GeneProduct from the ListOfGeneProducts based on its identifier.
sid | a string representing the identifier of the GeneProduct to get. |
GeneProduct * FbcModelPlugin::getGeneProductByLabel | ( | const std::string & | label | ) |
Get a GeneProduct from the ListOfGeneProducts based on its label.
label | a string representing the label of the GeneProduct to get. |
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inherited |
Returns the SBML Level of the package extension of this plugin object.
const ListOfFluxBounds * FbcModelPlugin::getListOfFluxBounds | ( | ) | const |
Returns the ListOfFluxBounds in this plugin object.
ListOfFluxBounds * FbcModelPlugin::getListOfFluxBounds | ( | ) |
Returns the ListOfFluxBounds in this plugin object.
const ListOfGeneAssociations * FbcModelPlugin::getListOfGeneAssociations | ( | ) | const |
Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object.
ListOfGeneAssociations * FbcModelPlugin::getListOfGeneAssociations | ( | ) |
Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object.
const ListOfGeneProducts * FbcModelPlugin::getListOfGeneProducts | ( | ) | const |
Returns the "ListOfGeneProducts" in this FbcModelPlugin object.
ListOfGeneProducts * FbcModelPlugin::getListOfGeneProducts | ( | ) |
Returns the "ListOfGeneProducts" in this FbcModelPlugin object.
const ListOfObjectives * FbcModelPlugin::getListOfObjectives | ( | ) | const |
Returns the "ListOfObjectives" in this FbcModelPlugin object.
ListOfObjectives * FbcModelPlugin::getListOfObjectives | ( | ) |
Returns the "ListOfObjectives" in this FbcModelPlugin object.
unsigned int FbcModelPlugin::getNumFluxBounds | ( | ) | const |
int FbcModelPlugin::getNumGeneAssociations | ( | ) | const |
Returns the number of GeneAssociation annotation object in this plugin object.
unsigned int FbcModelPlugin::getNumGeneProducts | ( | ) | const |
Get the number of GeneProduct objects in this FbcModelPlugin.
unsigned int FbcModelPlugin::getNumObjectives | ( | ) | const |
Get the number of Objective objects in this FbcModelPlugin.
Objective * FbcModelPlugin::getObjective | ( | unsigned int | n | ) |
Get a Objective from the ListOfObjectives.
n | the index number of the Objective to get. |
const Objective * FbcModelPlugin::getObjective | ( | unsigned int | n | ) | const |
Get a Objective from the ListOfObjectives.
n | the index number of the Objective to get. |
Objective * FbcModelPlugin::getObjective | ( | const std::string & | sid | ) |
Get a Objective from the ListOfObjectives based on its identifier.
sid | a string representing the identifier of the Objective to get. |
const Objective * FbcModelPlugin::getObjective | ( | const std::string & | sid | ) | const |
Get a Objective from the ListOfObjectives based on its identifier.
sid | a string representing the identifier of the Objective to get. |
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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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Returns the value of the "strict" attribute of this FbcModelPlugin.
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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.
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doxygenLibsbmlInternal
doxygenLibsbmlInternal doxygenLibsbmlInternal Checks if this plugin object has all the required elements.
Subclasses must override this method if they have their specific elements.
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virtual |
Predicate returning true
if this FbcModelPlugin's "strict" attribute is set.
true
if this FbcModelPlugin's "strict" attribute has been set, otherwise false
is returned.
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virtualinherited |
FbcModelPlugin & FbcModelPlugin::operator= | ( | const FbcModelPlugin & | rhs | ) |
Assignment operator for FbcModelPlugin.
rhs; | the object whose values are used as the basis of the assignment |
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 annotation 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 annotation object to remove |
NULL
is returned if the given index is out of range. GeneAssociation * FbcModelPlugin::removeGeneAssociation | ( | const std::string & | sid | ) |
Removes the GeneAssociation annotation 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 annotation object to remove |
NULL
is returned if the given index is out of range. GeneProduct * FbcModelPlugin::removeGeneProduct | ( | unsigned int | n | ) |
Removes the nth GeneProduct from the ListOfGeneProducts within this FbcModelPlugin.
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
n | the index of the GeneProduct to remove. |
GeneProduct * FbcModelPlugin::removeGeneProduct | ( | const std::string & | sid | ) |
Removes the GeneProduct with the given identifier from the ListOfGeneProducts within this FbcModelPlugin and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid
, then NULL
is returned.
sid | the identifier of the GeneProduct to remove. |
Objective * FbcModelPlugin::removeObjective | ( | unsigned int | n | ) |
Removes the nth Objective from the ListOfObjectives within this FbcModelPlugin.
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
n | the index of the Objective to remove. |
Objective * FbcModelPlugin::removeObjective | ( | const std::string & | sid | ) |
Removes the Objective with the given identifier from the ListOfObjectives within this FbcModelPlugin and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid
, then NULL
is returned.
sid | the identifier of the Objective to remove. |
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virtualinherited |
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virtualinherited |
Reimplemented in FbcReactionPlugin.
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virtualinherited |
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. |
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virtual |
Sets the value of the "strict" attribute of this FbcModelPlugin.
strict; | bool value of the "strict" attribute to be set |
void FbcModelPlugin::unsetActiveObjectiveId | ( | ) |
Unsets the active objective.
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virtual |
Unsets the value of the "strict" attribute of this FbcModelPlugin.