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libsbmlcs.CompModelPlugin Class Reference
Inheritance diagram for libsbmlcs.CompModelPlugin:
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Public Member Functions

override bool acceptComp (SWIGTYPE_p_CompVisitor v)
 
int addPort (Port port)
 
int addReplacedElement (ReplacedElement replacedElement)
 
int addSubmodel (Submodel submodel)
 
virtual void clearReplacedElements ()
 
SBasePlugin clone ()
 Creates and returns a deep copy of this SBasePlugin object. More...
 
 CompModelPlugin (string uri, string prefix, CompPkgNamespaces compns)
 
 CompModelPlugin (CompModelPlugin orig)
 
override void connectToChild ()
 
void connectToParent (SBase parent)
 Sets the parent SBML object of this plugin object to this object and child elements (if any). More...
 
override SBase createObject (XMLInputStream stream)
 
Port createPort ()
 
ReplacedBy createReplacedBy ()
 
ReplacedElement createReplacedElement ()
 
Submodel createSubmodel ()
 
override void Dispose ()
 
void divideAssignmentsToSIdByFunction (string id, ASTNode function)
 If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More...
 
void enablePackageInternal (string pkgURI, string pkgPrefix, bool flag)
 Enables/Disables the given package with child elements in this plugin object (if any). More...
 
long getColumn ()
 Returns the column number on which this object first appears in the XML representation of the SBML document. More...
 
string getDivider ()
 
SBase getElementByMetaId (string metaid)
 Returns the first child element it can find with the given metaid, or null if no such object is found. More...
 
SBase getElementBySId (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...
 
string getElementNamespace ()
 Returns the XML namespace (URI) of the package extension of this plugin object. More...
 
long getLevel ()
 Returns the SBML level of the package extension of this plugin object. More...
 
long getLine ()
 Returns the line number on which this object first appears in the XML representation of the SBML document. More...
 
SBaseList getListOfAllElements ()
 
ListOfPorts getListOfPorts ()
 
ListOfReplacedElements getListOfReplacedElements ()
 
ListOfSubmodels getListOfSubmodels ()
 
long getNumPorts ()
 
long getNumReplacedElements ()
 
long getNumSubmodels ()
 
string getPackageName ()
 Returns the package name of this plugin object. More...
 
long getPackageVersion ()
 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...
 
Port getPort (long n)
 
Port getPort (string id)
 
string getPrefix ()
 Returns the prefix of the package extension of this plugin object. More...
 
ReplacedBy getReplacedBy ()
 
ReplacedElement getReplacedElement (long n)
 
SBMLDocument getSBMLDocument ()
 Returns the parent SBMLDocument of this plugin object. More...
 
SBMLNamespaces getSBMLNamespaces ()
 Returns the column number on which this object first appears in the XML representation of the SBML document. More...
 
Submodel getSubmodel (long n)
 
Submodel getSubmodel (string id)
 
string getURI ()
 Gets the URI to which this element belongs to. More...
 
long getVersion ()
 Returns the SBML version of the package extension of this plugin object. More...
 
bool hasIdentifierBeginningWith (string prefix)
 Check to see if the given prefix is used by any of the IDs defined by extension elements. More...
 
bool isSetReplacedBy ()
 
virtual void logInvalidId (string attribute, string wrongattribute)
 
void logUnknownElement (string element, long sbmlLevel, long sbmlVersion, long pkgVersion)
 Helper to log a common type of error for elements. More...
 
void multiplyAssignmentsToSIdByFunction (string id, ASTNode function)
 If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More...
 
int prependStringToAllIdentifiers (string prefix)
 Add the given string to all identifiers in the object. More...
 
Port removePort (long index)
 
ReplacedElement removeReplacedElement (long index)
 
Submodel removeSubmodel (long index)
 
void replaceSIDWithFunction (string id, ASTNode function)
 If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More...
 
int setDivider (string divider)
 
int setElementNamespace (string uri)
 Sets the XML namespace to which this element belongs to. More...
 
int setReplacedBy (ReplacedBy replacedBy)
 
bool stripPackage (string pkgPrefix, bool flag)
 Enables/Disables the given package with child elements in this plugin object (if any). More...
 
virtual int unsetReplacedBy ()
 

Protected Attributes

bool swigCMemOwn
 

Constructor & Destructor Documentation

libsbmlcs.CompModelPlugin.CompModelPlugin ( string  uri,
string  prefix,
CompPkgNamespaces  compns 
)
libsbmlcs.CompModelPlugin.CompModelPlugin ( CompModelPlugin  orig)

Member Function Documentation

override bool libsbmlcs.CompModelPlugin.acceptComp ( SWIGTYPE_p_CompVisitor  v)
virtual

Reimplemented from libsbmlcs.CompSBasePlugin.

int libsbmlcs.CompModelPlugin.addPort ( Port  port)
int libsbmlcs.CompSBasePlugin.addReplacedElement ( ReplacedElement  replacedElement)
inherited
int libsbmlcs.CompModelPlugin.addSubmodel ( Submodel  submodel)
virtual void libsbmlcs.CompSBasePlugin.clearReplacedElements ( )
virtualinherited
SBasePlugin libsbmlcs.CompModelPlugin.clone ( )

Creates and returns a deep copy of this SBasePlugin object.

Returns
a (deep) copy of this SBase object
override void libsbmlcs.CompModelPlugin.connectToChild ( )
virtual

Reimplemented from libsbmlcs.CompSBasePlugin.

void libsbmlcs.CompModelPlugin.connectToParent ( SBase  parent)

Sets the parent SBML object of this plugin object to this object and child elements (if any).

(Creates a child-parent relationship by this plugin object)

This function is called when this object is created by the parent element. Subclasses must override this this function if they have one or more child elements. Also, SBasePlugin::connectToParent() must be called in the overridden function.

Parameters
sbasethe SBase object to use
See Also
setSBMLDocument
enablePackageInternal
override SBase libsbmlcs.CompModelPlugin.createObject ( XMLInputStream  stream)
virtual

Reimplemented from libsbmlcs.CompSBasePlugin.

Port libsbmlcs.CompModelPlugin.createPort ( )
ReplacedBy libsbmlcs.CompSBasePlugin.createReplacedBy ( )
inherited
ReplacedElement libsbmlcs.CompSBasePlugin.createReplacedElement ( )
inherited
Submodel libsbmlcs.CompModelPlugin.createSubmodel ( )
override void libsbmlcs.CompModelPlugin.Dispose ( )
virtual

Reimplemented from libsbmlcs.SBasePlugin.

void libsbmlcs.SBasePlugin.divideAssignmentsToSIdByFunction ( string  id,
ASTNode  function 
)
inherited

If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).

Note
This function does nothing itself–subclasses with ASTNode subelements must override this function.
void libsbmlcs.CompModelPlugin.enablePackageInternal ( string  pkgURI,
string  pkgPrefix,
bool  flag 
)

Enables/Disables the given package with child elements in this plugin object (if any).

(This is an internal implementation invoked from SBase::enablePackageInternal() function)

Subclasses which contain one or more SBase derived elements should override this function if elements defined in them can be extended by some other package extension.

See Also
setSBMLDocument
connectToParent
long libsbmlcs.SBasePlugin.getColumn ( )
inherited

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns
the column number of the underlying SBML object.
Note
The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See Also
getLine()
string libsbmlcs.CompModelPlugin.getDivider ( )
SBase libsbmlcs.CompModelPlugin.getElementByMetaId ( string  metaid)

Returns the first child element it can find with the given metaid, or null if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
SBase libsbmlcs.CompModelPlugin.getElementBySId ( 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.

Parameters
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.
string libsbmlcs.SBasePlugin.getElementNamespace ( )
inherited

Returns the XML namespace (URI) of the package extension of this plugin object.

Returns
the URI of the package extension of this plugin object.
long libsbmlcs.SBasePlugin.getLevel ( )
inherited

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

Returns
the SBML level of the package extension of this plugin object.
long libsbmlcs.SBasePlugin.getLine ( )
inherited

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns
the line number of the underlying SBML object.
Note
The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See Also
getColumn()
SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( )
inherited
ListOfPorts libsbmlcs.CompModelPlugin.getListOfPorts ( )
ListOfReplacedElements libsbmlcs.CompSBasePlugin.getListOfReplacedElements ( )
inherited
ListOfSubmodels libsbmlcs.CompModelPlugin.getListOfSubmodels ( )
long libsbmlcs.CompModelPlugin.getNumPorts ( )
long libsbmlcs.CompSBasePlugin.getNumReplacedElements ( )
inherited
long libsbmlcs.CompModelPlugin.getNumSubmodels ( )
string libsbmlcs.SBasePlugin.getPackageName ( )
inherited

Returns the package name of this plugin object.

Returns
the package name of this plugin object.
long libsbmlcs.SBasePlugin.getPackageVersion ( )
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.
SBase libsbmlcs.SBasePlugin.getParentSBMLObject ( )
inherited

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

Returns
the parent SBase object to which this plugin object connected.
Port libsbmlcs.CompModelPlugin.getPort ( long  n)
Port libsbmlcs.CompModelPlugin.getPort ( string  id)
string libsbmlcs.SBasePlugin.getPrefix ( )
inherited

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

Returns
the prefix of the package extension of this plugin object.
ReplacedBy libsbmlcs.CompSBasePlugin.getReplacedBy ( )
inherited
ReplacedElement libsbmlcs.CompSBasePlugin.getReplacedElement ( long  n)
inherited
SBMLDocument libsbmlcs.SBasePlugin.getSBMLDocument ( )
inherited

Returns the parent SBMLDocument of this plugin object.

Returns
the parent SBMLDocument object of this plugin object.
SBMLNamespaces libsbmlcs.SBasePlugin.getSBMLNamespaces ( )
inherited

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns
the column number of the underlying SBML object.
Note
The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See Also
getLine()
Submodel libsbmlcs.CompModelPlugin.getSubmodel ( long  n)
Submodel libsbmlcs.CompModelPlugin.getSubmodel ( string  id)
string libsbmlcs.SBasePlugin.getURI ( )
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

Returns
the URI this elements
See Also
getPackageName
getElementNamespace
SBMLDocument::getSBMLNamespaces
getSBMLDocument
long libsbmlcs.SBasePlugin.getVersion ( )
inherited

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

Returns
the SBML version of the package extension of this plugin object.
bool libsbmlcs.SBasePlugin.hasIdentifierBeginningWith ( string  prefix)
inherited

Check to see if the given prefix is used by any of the IDs defined by extension elements.

A package that defines its own 'id' attribute for a core element would check that attribute here.

bool libsbmlcs.CompSBasePlugin.isSetReplacedBy ( )
inherited
virtual void libsbmlcs.CompSBasePlugin.logInvalidId ( string  attribute,
string  wrongattribute 
)
virtualinherited
void libsbmlcs.SBasePlugin.logUnknownElement ( string  element,
long  sbmlLevel,
long  sbmlVersion,
long  pkgVersion 
)
inherited

Helper to log a common type of error for elements.

void libsbmlcs.SBasePlugin.multiplyAssignmentsToSIdByFunction ( string  id,
ASTNode  function 
)
inherited

If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).

int libsbmlcs.SBasePlugin.prependStringToAllIdentifiers ( string  prefix)
inherited

Add the given string to all identifiers in the object.

If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.

Port libsbmlcs.CompModelPlugin.removePort ( long  index)
ReplacedElement libsbmlcs.CompSBasePlugin.removeReplacedElement ( long  index)
inherited
Submodel libsbmlcs.CompModelPlugin.removeSubmodel ( long  index)
void libsbmlcs.SBasePlugin.replaceSIDWithFunction ( string  id,
ASTNode  function 
)
inherited

If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.

Note
This function does nothing itself–subclasses with ASTNode subelements must override this function.
int libsbmlcs.CompModelPlugin.setDivider ( string  divider)
int libsbmlcs.SBasePlugin.setElementNamespace ( string  uri)
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/'

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.CompSBasePlugin.setReplacedBy ( ReplacedBy  replacedBy)
inherited
bool libsbmlcs.SBasePlugin.stripPackage ( string  pkgPrefix,
bool  flag 
)
inherited

Enables/Disables the given package with child elements in this plugin object (if any).

(This is an internal implementation invoked from SBase::enablePackageInternal() function)

Subclasses which contain one or more SBase derived elements should override this function if elements defined in them can be extended by some other package extension.

See Also
setSBMLDocument
connectToParent
virtual int libsbmlcs.CompSBasePlugin.unsetReplacedBy ( )
virtualinherited

Member Data Documentation

bool libsbmlcs.SBasePlugin.swigCMemOwn
protectedinherited