libSBML Perl API  libSBML 5.19.7 Perl API
FbcSpeciesPlugin Class Reference
Inheritance diagram for FbcSpeciesPlugin:
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Detailed Description

@sbmlpackage{fbc}

fbc Extension of Species.

The FbcSpeciesPlugin class codifies an extension of the core SBML Species class defined in the SBML Level 3 Flux Balance Constraints (“fbc”) package. The “fbc” package adds two attributes named "charge" and "chemicalFormula" to Species.

The optional attribute "charge" can contain a signed integer that refers to the Species object's electrical charge (in terms of electrons, not the SI unit of coulombs). Note that this attribute is therefore defined as it is in the SBML Level 2 Version 1 specification. (The charge attribute was removed in higher Versions and Levels of SBML, and is not an attribute of SBML Species in core SBML Level 3. However, it is useful for flux balance constraints models, and thus, the Level 3 “fbc” package adds it.)

The optional attribute "chemicalFormula" can contain a text string that represents the elemental composition of the substance represented by the Species object. The purpose of the "chemicalFormula" attribute is to allow balancing and validating reactions. This is particularly important in constraint-based models. The format of "chemicalFormula" must consist only of atomic names (as given in the Periodic Table of elements) or user-defined compounds, either of which take the form of a single capital letter followed by zero or more lowercase letters. Where there is more than a single atom present, this is indicated with an integer. With regards to order (and to enhance interoperability of models), users are advised to employ the Hill system order. Using this notation, the number of carbon atoms in a molecule is indicated first, followed by the number of hydrogen atoms, and then the number of all other chemical elements in alphabetical order. When the formula contains no carbon, all elements including hydrogen are listed alphabetically.

Here is an example of the XML form of an extended Species definition with these attributes:

<species metaid="meta_M_atp_c" id="M_atp_c" name="ATP" compartment="Cytosol"
boundaryCondition="false" initialConcentration="0" hasOnlySubstanceUnits="false"
fbc:charge="-4" fbc:chemicalFormula="C10H12N5O13P3"/>

Public Member Functions

int addKeyValuePair (const KeyValuePair *kvp)
 Adds a copy of the given KeyValuePair to this FbcSBasePlugin. More...
 
virtual FbcSpeciesPluginclone () const
 Creates and returns a deep copy of this FbcSpeciesPlugin object. More...
 
KeyValuePaircreateKeyValuePair ()
 Creates a new KeyValuePair object, adds it to this FbcSBasePlugin object and returns the KeyValuePair object created. More...
 
 FbcSpeciesPlugin (const FbcSpeciesPlugin &orig)
 Copy constructor for FbcSpeciesPlugin. More...
 
 FbcSpeciesPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns)
 Creates a new FbcSpeciesPlugin. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual int getCharge () const
 doxygenLibsbmlInternal More...
 
virtual double getChargeAsDouble () const
 Returns the value of the "charge" attribute of this FbcSpeciesPlugin. More...
 
virtual const std::string & getChemicalFormula () const
 Returns the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Returns the first child element that has the given metaid, or NULL if no such object is found. More...
 
virtual SBasegetElementBySId (const std::string &id)
 Returns the first child element 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...
 
KeyValuePairgetKeyValuePair (const std::string &sid)
 Get a KeyValuePair from the FbcSBasePlugin based on its identifier. More...
 
const KeyValuePairgetKeyValuePair (const std::string &sid) const
 Get a KeyValuePair from the FbcSBasePlugin based on its identifier. More...
 
KeyValuePairgetKeyValuePair (unsigned int n)
 Get a KeyValuePair from the FbcSBasePlugin. More...
 
const KeyValuePairgetKeyValuePair (unsigned int n) const
 Get a KeyValuePair from the FbcSBasePlugin. More...
 
unsigned int getLevel () const
 Returns the SBML Level of the package extension of this plugin object. More...
 
ListOfKeyValuePairsgetListOfKeyValuePairs ()
 Returns the ListOfKeyValuePairs from this FbcSBasePlugin. More...
 
const ListOfKeyValuePairsgetListOfKeyValuePairs () const
 Returns the ListOfKeyValuePairs from this FbcSBasePlugin. More...
 
unsigned int getNumKeyValuePairs () const
 Get the number of KeyValuePair objects in this FbcSBasePlugin. 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...
 
SBasegetParentSBMLObject ()
 Returns the parent object to which this plugin object is connected. More...
 
const SBasegetParentSBMLObject () 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...
 
SBMLDocumentgetSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
const SBMLDocumentgetSBMLDocument () 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...
 
virtual bool isSetCharge () const
 Predicate returning true or false depending on whether this FbcSpeciesPlugin's "charge" attribute has been set. More...
 
virtual bool isSetChemicalFormula () const
 Predicate returning true or false depending on whether this FbcSpeciesPlugin's "chemicalFormula" attribute has been set. More...
 
virtual bool isValidTypeForList (SBase *item) const
 
FbcSpeciesPluginoperator= (const FbcSpeciesPlugin &rhs)
 Assignment operator for FbcSpeciesPlugin. More...
 
KeyValuePairremoveKeyValuePair (const std::string &sid)
 Removes the KeyValuePair from this FbcSBasePlugin based on its identifier and returns a pointer to it. More...
 
KeyValuePairremoveKeyValuePair (unsigned int n)
 Removes the nth KeyValuePair from this FbcSBasePlugin 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)
 
virtual int setCharge (double charge)
 Sets the value of the "charge" attribute of this FbcSpeciesPlugin. More...
 
virtual int setCharge (int charge)
 Sets the value of the "charge" attribute of this FbcSpeciesPlugin. More...
 
virtual int setChemicalFormula (const std::string &chemicalFormula)
 Sets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. More...
 
int setElementNamespace (const std::string &uri)
 Sets the XML namespace to which this object belongs. More...
 
virtual int unsetCharge ()
 Unsets the value of the "charge" attribute of this FbcSpeciesPlugin. More...
 
virtual int unsetChemicalFormula ()
 Unsets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. More...
 
virtual ~FbcSpeciesPlugin ()
 Destructor for FbcSpeciesPlugin. More...
 

Constructor & Destructor Documentation

◆ FbcSpeciesPlugin() [1/2]

FbcSpeciesPlugin::FbcSpeciesPlugin ( const std::string &  uri,
const std::string &  prefix,
FbcPkgNamespaces fbcns 
)

Creates a new FbcSpeciesPlugin.

◆ FbcSpeciesPlugin() [2/2]

FbcSpeciesPlugin::FbcSpeciesPlugin ( const FbcSpeciesPlugin orig)

Copy constructor for FbcSpeciesPlugin.

Parameters
orig;the FbcSpeciesPlugin instance to copy.

◆ ~FbcSpeciesPlugin()

FbcSpeciesPlugin::~FbcSpeciesPlugin ( )
virtual

Destructor for FbcSpeciesPlugin.

Member Function Documentation

◆ addKeyValuePair()

int FbcSBasePlugin::addKeyValuePair ( const KeyValuePair kvp)
inherited

Adds a copy of the given KeyValuePair to this FbcSBasePlugin.

Parameters
kvpthe KeyValuePair object to add.

◆ clone()

FbcSpeciesPlugin * FbcSpeciesPlugin::clone ( ) const
virtual

Creates and returns a deep copy of this FbcSpeciesPlugin object.

Returns
a (deep) copy of this FbcSpeciesPlugin object.

Reimplemented from FbcSBasePlugin.

◆ createKeyValuePair()

◆ getAllElements()

List * FbcSBasePlugin::getAllElements ( ElementFilter filter = NULL)
virtualinherited

Returns a List of all child SBase objects, including those nested to an arbitrary depth.

Parameters
filteran ElementFilter that may impose restrictions on the objects to be retrieved.
Returns
a List pointer of pointers to all SBase child objects with any restriction imposed.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin, and FbcReactionPlugin.

◆ getCharge()

int FbcSpeciesPlugin::getCharge ( ) const
virtual

doxygenLibsbmlInternal

doxygenLibsbmlInternal doxygenLibsbmlInternal doxygenLibsbmlInternal doxygenLibsbmlInternal

Returns the value of the "charge" attribute of this FbcSpeciesPlugin.

Returns
the value of the "charge" attribute of this FbcSpeciesPlugin as a integer.

◆ getChargeAsDouble()

double FbcSpeciesPlugin::getChargeAsDouble ( ) const
virtual

Returns the value of the "charge" attribute of this FbcSpeciesPlugin.

Returns
the value of the "charge" attribute of this FbcSpeciesPlugin as a double.

◆ getChemicalFormula()

const std::string & FbcSpeciesPlugin::getChemicalFormula ( ) const
virtual

Returns the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.

Returns
the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin as a string.

◆ getElementByMetaId()

SBase * FbcSBasePlugin::getElementByMetaId ( const std::string &  metaid)
virtualinherited

Returns the first child element that has the given metaid, or NULL if no such object is found.

Parameters
metaida string representing the metaid attribute of the object to retrieve.
Returns
a pointer to the SBase element with the given metaid. If no such object is found this method returns NULL.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin.

◆ getElementBySId()

SBase * FbcSBasePlugin::getElementBySId ( const std::string &  id)
virtualinherited

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

Parameters
ida string representing the id attribute of the object to retrieve.
Returns
a pointer to the SBase element with the given id. If no such object is found, this method returns NULL.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin.

◆ getElementNamespace()

const std::string & SBasePlugin::getElementNamespace ( ) const
inherited

Returns the namespace URI of the package to which this plugin object belongs.

Returns
the XML namespace URI of the SBML Level 3 package implemented by this libSBML package extension.

◆ getKeyValuePair() [1/4]

KeyValuePair * FbcSBasePlugin::getKeyValuePair ( const std::string &  sid)
inherited

Get a KeyValuePair from the FbcSBasePlugin based on its identifier.

Parameters
sida string representing the identifier of the KeyValuePair to retrieve.
Returns
the KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin with the given sid or NULL if no such KeyValuePair exists.
See also
addKeyValuePair(const KeyValuePair* object)
createKeyValuePair()
getKeyValuePair(unsigned int n)
getNumKeyValuePairs()
removeKeyValuePair(const std::string& sid)
removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [2/4]

const KeyValuePair * FbcSBasePlugin::getKeyValuePair ( const std::string &  sid) const
inherited

Get a KeyValuePair from the FbcSBasePlugin based on its identifier.

Parameters
sida string representing the identifier of the KeyValuePair to retrieve.
Returns
the KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin with the given sid or NULL if no such KeyValuePair exists.
See also
addKeyValuePair(const KeyValuePair* object)
createKeyValuePair()
getKeyValuePair(unsigned int n)
getNumKeyValuePairs()
removeKeyValuePair(const std::string& sid)
removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [3/4]

KeyValuePair * FbcSBasePlugin::getKeyValuePair ( unsigned int  n)
inherited

◆ getKeyValuePair() [4/4]

const KeyValuePair * FbcSBasePlugin::getKeyValuePair ( unsigned int  n) const
inherited

◆ getLevel()

unsigned int SBasePlugin::getLevel ( ) const
inherited

Returns the SBML Level of the package extension of this plugin object.

Returns
the SBML Level.
See also
getVersion()

◆ getListOfKeyValuePairs() [1/2]

◆ getListOfKeyValuePairs() [2/2]

◆ getNumKeyValuePairs()

◆ getPackageName()

const std::string & SBasePlugin::getPackageName ( ) const
inherited

Returns the short-form name of the package to which this plugin object belongs.

Returns
the short-form package name (or nickname) of the SBML package implemented by this package extension.

◆ getPackageVersion()

unsigned int SBasePlugin::getPackageVersion ( ) const
inherited

Returns the package version of the package extension of this plugin object.

Returns
the package version of the package extension of this plugin object.
See also
getLevel()
getVersion()

◆ getParentSBMLObject() [1/2]

SBase * SBasePlugin::getParentSBMLObject ( )
inherited

Returns the parent object to which this plugin object is connected.

Returns
the parent object of this object.

◆ getParentSBMLObject() [2/2]

const SBase * SBasePlugin::getParentSBMLObject ( ) const
inherited

Returns the parent object to which this plugin object is connected.

Returns
the parent object of this object.

◆ getPrefix()

const std::string & SBasePlugin::getPrefix ( ) const
inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

Returns
the XML namespace prefix of the SBML Level 3 package implemented by this libSBML package extension.

◆ getSBMLDocument() [1/2]

SBMLDocument * SBasePlugin::getSBMLDocument ( )
inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this plugin object.
See also
getParentSBMLObject()

◆ getSBMLDocument() [2/2]

const SBMLDocument * SBasePlugin::getSBMLDocument ( ) const
inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this plugin object.
See also
getParentSBMLObject()

◆ getURI()

std::string SBasePlugin::getURI ( ) const
inherited

Returns the XML namespace URI for the package to which this object belongs.

In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "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().

Returns
a string, the URI of the XML namespace to which this object belongs.
See also
getPackageName()
getElementNamespace()
getSBMLDocument()

◆ getVersion()

unsigned int SBasePlugin::getVersion ( ) const
inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns
the SBML Version.
See also
getLevel()

◆ isSetCharge()

bool FbcSpeciesPlugin::isSetCharge ( ) const
virtual

Predicate returning true or false depending on whether this FbcSpeciesPlugin's "charge" attribute has been set.

Returns
true if this FbcSpeciesPlugin's "charge" attribute has been set, otherwise false is returned.

◆ isSetChemicalFormula()

bool FbcSpeciesPlugin::isSetChemicalFormula ( ) const
virtual

Predicate returning true or false depending on whether this FbcSpeciesPlugin's "chemicalFormula" attribute has been set.

Returns
true if this FbcSpeciesPlugin's "chemicalFormula" attribute has been set, otherwise false is returned.

◆ isValidTypeForList()

virtual bool SBasePlugin::isValidTypeForList ( SBase item) const
virtualinherited

◆ operator=()

FbcSpeciesPlugin & FbcSpeciesPlugin::operator= ( const FbcSpeciesPlugin rhs)

Assignment operator for FbcSpeciesPlugin.

Parameters
rhs;the object whose values are used as the basis of the assignment

◆ removeKeyValuePair() [1/2]

KeyValuePair * FbcSBasePlugin::removeKeyValuePair ( const std::string &  sid)
inherited

Removes the KeyValuePair from this FbcSBasePlugin based on its identifier and returns a pointer to it.

Parameters
sida string representing the identifier of the KeyValuePair to remove.
Returns
the KeyValuePair in this FbcSBasePlugin based on the identifier or NULL if no such KeyValuePair exists.
See also
addKeyValuePair(const KeyValuePair* object)
createKeyValuePair()
getKeyValuePair(const std::string& sid)
getKeyValuePair(unsigned int n)
getNumKeyValuePairs()
removeKeyValuePair(unsigned int n)

◆ removeKeyValuePair() [2/2]

KeyValuePair * FbcSBasePlugin::removeKeyValuePair ( unsigned int  n)
inherited

Removes the nth KeyValuePair from this FbcSBasePlugin and returns a pointer to it.

Parameters
nan unsigned int representing the index of the KeyValuePair to remove.
Returns
a pointer to the nth KeyValuePair in this FbcSBasePlugin.
See also
addKeyValuePair(const KeyValuePair* object)
createKeyValuePair()
getKeyValuePair(const std::string& sid)
getKeyValuePair(unsigned int n)
getNumKeyValuePairs()
removeKeyValuePair(const std::string& sid)

◆ renameMetaIdRefs()

virtual void SBasePlugin::renameMetaIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

◆ renameSIdRefs()

virtual void SBasePlugin::renameSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

Reimplemented in FbcReactionPlugin.

◆ renameUnitSIdRefs()

virtual void SBasePlugin::renameUnitSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

◆ setCharge() [1/2]

int FbcSpeciesPlugin::setCharge ( double  charge)
virtual

Sets the value of the "charge" attribute of this FbcSpeciesPlugin.

Parameters
charge;double value of the "charge" attribute to be set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

◆ setCharge() [2/2]

int FbcSpeciesPlugin::setCharge ( int  charge)
virtual

Sets the value of the "charge" attribute of this FbcSpeciesPlugin.

Parameters
charge;int value of the "charge" attribute to be set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

◆ setChemicalFormula()

int FbcSpeciesPlugin::setChemicalFormula ( const std::string &  chemicalFormula)
virtual

Sets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.

Parameters
chemicalFormula;const std::string& value of the "chemicalFormula" attribute to be set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

◆ setElementNamespace()

int SBasePlugin::setElementNamespace ( const std::string &  uri)
inherited

Sets the XML namespace to which this object belongs.

In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "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/".
Parameters
urithe URI to assign to this object.

◆ unsetCharge()

int FbcSpeciesPlugin::unsetCharge ( )
virtual

Unsets the value of the "charge" attribute of this FbcSpeciesPlugin.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

◆ unsetChemicalFormula()

int FbcSpeciesPlugin::unsetChemicalFormula ( )
virtual

Unsets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are: