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libsbmlcs.ListOfRules Class Reference
Inheritance diagram for libsbmlcs.ListOfRules:
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Detailed Description

Implementation of SBML's ListOfRules construct.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. All are derived from the abstract class SBase, and inherit the various attributes and subelements of SBase, such as 'metaid' as and 'annotation'. The ListOf___ classes do not add any attributes of their own.

The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 3 and later versions of SBML Level 2 as well):

listof-illustration.jpg
'ListOf___ elements in an SBML Model'

Readers may wonder about the motivations for using the ListOf___ containers. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See Also
ListOfFunctionDefinitions
ListOfUnitDefinitions
ListOfCompartmentTypes
ListOfSpeciesTypes
ListOfCompartments
ListOfSpecies
ListOfParameters
ListOfInitialAssignments
ListOfRules
ListOfConstraints
ListOfReactions
ListOfEvents

Public Member Functions

int addCVTerm (CVTerm term, bool newBag)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
int addCVTerm (CVTerm term)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
int append (SBase item)
 Adds item to the end of this ListOf. More...
 
int appendAndOwn (SBase item)
 Adds item to the end of this ListOf. More...
 
int appendAnnotation (XMLNode annotation)
 Appends the given annotation to the 'annotation' subelement of this object. More...
 
int appendAnnotation (string annotation)
 Appends the given annotation to the 'annotation' subelement of this object. More...
 
int appendFrom (ListOf list)
 Adds a clone of all items in the provided ListOf to this object. More...
 
int appendNotes (XMLNode notes)
 Appends the given notes to the 'notes' subelement of this object. More...
 
int appendNotes (string notes)
 Appends the given notes to the 'notes' subelement of this object. More...
 
int checkCompatibility (SBase arg0)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
string checkMathMLNamespace (XMLToken elem)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
void clear (bool doDelete)
 Removes all items in this ListOf object. More...
 
void clear ()
 Removes all items in this ListOf object. More...
 
new ListOfRules clone ()
 Creates and returns a deep copy of this ListOfRules instance. More...
 
void connectToParent (SBase parent)
 Sets the parent SBML object of this SBML object. More...
 
int disablePackage (string pkgURI, string pkgPrefix)
 Disables the given SBML Level 3 package. More...
 
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...
 
int enablePackage (string pkgURI, string pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package. More...
 
override bool Equals (Object sb)
 
new Rule get (long n)
 Get a Rule from the ListOfRules. More...
 
new Rule get (string sid)
 Get a Rule from the ListOfRules based on its identifier. More...
 
SBase getAncestorOfType (int type, string pkgName)
 Returns the first ancestor object that has the given SBML type code. More...
 
SBase getAncestorOfType (int type)
 Returns the first ancestor object that has the given SBML type code. More...
 
XMLNode getAnnotation ()
 Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More...
 
string getAnnotationString ()
 Returns the content of the 'annotation' subelement of this object as a character string. More...
 
long getColumn ()
 Returns the column number on which this object first appears in the XML representation of the SBML document. More...
 
CVTerm getCVTerm (long n)
 Returns the nth CVTerm in the list of CVTerms of this SBML object. More...
 
CVTermList getCVTerms ()
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
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...
 
SBase getElementFromPluginsByMetaId (string metaid)
 Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found. More...
 
SBase getElementFromPluginsBySId (string id)
 Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found. More...
 
new string getElementName ()
 Returns the XML element name of this object. More...
 
override int GetHashCode ()
 
string getId ()
 Returns the value of the 'metaid' attribute of this object. More...
 
new int getItemTypeCode ()
 Returns the libSBML type code for the objects contained in this ListOf (i.e., Rule objects, if the list is non-empty). More...
 
long getLevel ()
 Returns the SBML Level of the SBMLDocument object containing this 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 ()
 
SBaseList getListOfAllElementsFromPlugins ()
 
string getMetaId ()
 Returns the value of the 'metaid' attribute of this object. More...
 
Model getModel ()
 Returns the Model object in which the current object is located. More...
 
ModelHistory getModelHistory ()
 Returns the ModelHistory object, if any, attached to this object. More...
 
string getName ()
 Returns the value of the 'metaid' attribute of this object. More...
 
XMLNamespaces getNamespaces ()
 Returns a list of the XML Namespaces declared on this SBML document. More...
 
XMLNode getNotes ()
 Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More...
 
string getNotesString ()
 Returns the content of the 'notes' subelement of this object as a string. More...
 
long getNumCVTerms ()
 Returns the number of CVTerm objects in the annotations of this SBML object. More...
 
long getNumPlugins ()
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
string getPackageName ()
 Returns the name of the SBML Level 3 package in which this element is defined. More...
 
long getPackageVersion ()
 Returns the Version of the SBML Level 3 package to which this element belongs to. More...
 
SBase getParentSBMLObject ()
 Returns the parent SBML object containing this object. More...
 
SBasePlugin getPlugin (string package)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
SBasePlugin getPlugin (long n)
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
int getResourceBiologicalQualifier (string resource)
 Returns the MIRIAM biological qualifier associated with the given resource. More...
 
int getResourceModelQualifier (string resource)
 Returns the MIRIAM model qualifier associated with the given resource. More...
 
SBMLDocument getSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
SBMLNamespaces getSBMLNamespaces ()
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
int getSBOTerm ()
 Returns the integer portion of the value of the 'sboTerm' attribute of this object. More...
 
string getSBOTermAsURL ()
 Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object. More...
 
string getSBOTermID ()
 Returns the string representation of the 'sboTerm' attribute of this object. More...
 
new int getTypeCode ()
 Returns the libSBML type code for this SBML object. More...
 
long getVersion ()
 Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...
 
bool hasNonstandardIdentifierBeginningWith (string prefix)
 Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid'). More...
 
bool hasRequiredAttributes ()
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
bool hasRequiredElements ()
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
bool hasValidLevelVersionNamespaceCombination ()
 Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More...
 
int insert (int location, SBase item)
 Inserts the item at the given position of this ListOf. More...
 
int insertAndOwn (int location, SBase item)
 Inserts the item at the given position of this ListOf. More...
 
bool isPackageEnabled (string pkgName)
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPackageURIEnabled (string pkgURI)
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPkgEnabled (string pkgName)
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPkgURIEnabled (string pkgURI)
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isSetAnnotation ()
 Predicate returning true if this object's 'annotation' subelement exists and has content. More...
 
bool isSetId ()
 Predicate returning true if this object's 'metaid' attribute is set. More...
 
bool isSetMetaId ()
 Predicate returning true if this object's 'metaid' attribute is set. More...
 
bool isSetModelHistory ()
 Predicate returning true if this object has a ModelHistory object attached to it. More...
 
bool isSetName ()
 Predicate returning true if this object's 'metaid' attribute is set. More...
 
bool isSetNotes ()
 Predicate returning true if this object's 'notes' subelement exists and has content. More...
 
bool isSetSBOTerm ()
 Predicate returning true if this object's 'sboTerm' attribute is set. More...
 
 ListOfRules (long level, long version)
 Creates a new ListOfRules object. More...
 
 ListOfRules (SBMLNamespaces sbmlns)
 Creates a new ListOfRules object. More...
 
bool matchesRequiredSBMLNamespacesForAddition (SBase sb)
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (SBase sb)
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. 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...
 
new Rule remove (long n)
 Removes the nth item from this ListOfRules items and returns a pointer to it. More...
 
new Rule remove (string sid)
 Removes item in this ListOfRules items with the given identifier. More...
 
int removeFromParentAndDelete ()
 Because ListOf objects typically live as object children of their parent object and not as pointer children, this function clears itself, but does not attempt to do anything else. More...
 
int removeTopLevelAnnotationElement (string elementName, string elementURI)
 Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...
 
int removeTopLevelAnnotationElement (string elementName)
 Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...
 
void renameMetaIdRefs (string oldid, string newid)
 Renames all the MetaIdRef attributes on this element. More...
 
void renameSIdRefs (string oldid, string newid)
 Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists). More...
 
void renameUnitSIdRefs (string oldid, string newid)
 Renames all the UnitSIdRef attributes on this element. More...
 
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 replaceTopLevelAnnotationElement (XMLNode annotation)
 Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More...
 
int replaceTopLevelAnnotationElement (string annotation)
 Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More...
 
int setAnnotation (XMLNode annotation)
 Sets the value of the 'annotation' subelement of this SBML object. More...
 
int setAnnotation (string annotation)
 Sets the value of the 'annotation' subelement of this SBML object. More...
 
int setId (string sid)
 Predicate returning true if this object has a ModelHistory object attached to it. More...
 
int setMetaId (string metaid)
 Sets the value of the 'metaid' attribute of this object. More...
 
int setModelHistory (ModelHistory history)
 Sets the ModelHistory of this object. More...
 
int setName (string name)
 Predicate returning true if this object has a ModelHistory object attached to it. More...
 
int setNamespaces (XMLNamespaces xmlns)
 Sets the namespaces relevant of this SBML object. More...
 
int setNotes (XMLNode notes)
 Sets the value of the 'notes' subelement of this SBML object. More...
 
int setNotes (string notes, bool addXHTMLMarkup)
 Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes. More...
 
int setNotes (string notes)
 Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes. More...
 
void setSBMLNamespacesAndOwn (SBMLNamespaces sbmlns)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
int setSBOTerm (int value)
 Sets the value of the 'sboTerm' attribute. More...
 
int setSBOTerm (string sboid)
 Sets the value of the 'sboTerm' attribute by string. More...
 
long size ()
 Get the size of this ListOf. More...
 
string toSBML ()
 Returns a string consisting of a partial SBML corresponding to just this object. More...
 
int unsetAnnotation ()
 Unsets the value of the 'annotation' subelement of this SBML object. More...
 
int unsetCVTerms ()
 Clears the list of CVTerm objects attached to this SBML object. More...
 
int unsetId ()
 Unsets the value of the 'id' attribute of this SBML object. More...
 
int unsetMetaId ()
 Unsets the value of the 'metaid' attribute of this SBML object. More...
 
int unsetModelHistory ()
 Unsets the ModelHistory object attached to this object. More...
 
int unsetName ()
 Unsets the value of the 'name' attribute of this SBML object. More...
 
int unsetNotes ()
 Unsets the value of the 'notes' subelement of this SBML object. More...
 
int unsetSBOTerm ()
 Unsets the value of the 'sboTerm' attribute of this SBML object. More...
 
void writeExtensionElements (XMLOutputStream stream)
 Writes out contained SBML objects of package extensions (if any) as XML elements. More...
 

Static Public Member Functions

static bool operator!= (SBase lhs, SBase rhs)
 
static bool operator== (SBase lhs, SBase rhs)
 

Protected Attributes

bool swigCMemOwn
 

Constructor & Destructor Documentation

libsbmlcs.ListOfRules.ListOfRules ( long  level,
long  version 
)

Creates a new ListOfRules object.

The object is constructed such that it is valid for the given SBML Level and Version combination.

Parameters
levelthe SBML Level
versionthe Version within the SBML Level
libsbmlcs.ListOfRules.ListOfRules ( SBMLNamespaces  sbmlns)

Creates a new ListOfRules object.

The object is constructed such that it is valid for the SBML Level and Version combination determined by the SBMLNamespaces object in sbmlns.

Parameters
sbmlnsan SBMLNamespaces object that is used to determine the characteristics of the ListOfRules object to be created.

Member Function Documentation

int libsbmlcs.SBase.addCVTerm ( CVTerm  term,
bool  newBag 
)
inherited

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
int libsbmlcs.SBase.addCVTerm ( CVTerm  term)
inherited

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
int libsbmlcs.ListOf.append ( SBase  item)
inherited

Adds item to the end of this ListOf.

This variant of the method makes a clone of the item handed to it. This means that when the ListOf is destroyed, the original items will not be destroyed.

Parameters
itemthe item to be added to the list.
See Also
appendAndOwn(SBase item)
int libsbmlcs.ListOf.appendAndOwn ( SBase  item)
inherited

Adds item to the end of this ListOf.

This variant of the method does not clone the item handed to it; instead, it assumes ownership of it. This means that when the ListOf is destroyed, the item will be destroyed along with it.

Parameters
itemthe item to be added to the list.
See Also
append(SBase item)
int libsbmlcs.SBase.appendAnnotation ( XMLNode  annotation)
inherited

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.SBase.appendAnnotation ( string  annotation)
inherited

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
unsetAnnotation()
int libsbmlcs.ListOf.appendFrom ( ListOf  list)
inherited

Adds a clone of all items in the provided ListOf to this object.

This means that when this ListOf is destroyed, the original items will not be destroyed.

Parameters
listA list of items to be added.
See Also
append(SBase item)
int libsbmlcs.SBase.appendNotes ( XMLNode  notes)
inherited

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML node structure that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.appendNotes ( string  notes)
inherited

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML string that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.checkCompatibility ( SBase  arg0)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

string libsbmlcs.SBase.checkMathMLNamespace ( XMLToken  elem)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

void libsbmlcs.ListOf.clear ( bool  doDelete)
inherited

Removes all items in this ListOf object.

If parameter doDelete is true (default), all items in this ListOf object are deleted and cleared, and thus the caller doesn't have to delete those items. Otherwise, all items are just cleared from this ListOf object and the caller is responsible for deleting all items. (In that case, pointers to all items should be stored elsewhere before calling this function.)

Parameters
doDeleteif true (default), all items are deleted and cleared. Otherwise, all items are just cleared and not deleted.
void libsbmlcs.ListOf.clear ( )
inherited

Removes all items in this ListOf object.

If parameter doDelete is true (default), all items in this ListOf object are deleted and cleared, and thus the caller doesn't have to delete those items. Otherwise, all items are just cleared from this ListOf object and the caller is responsible for deleting all items. (In that case, pointers to all items should be stored elsewhere before calling this function.)

Parameters
doDeleteif true (default), all items are deleted and cleared. Otherwise, all items are just cleared and not deleted.
new ListOfRules libsbmlcs.ListOfRules.clone ( )

Creates and returns a deep copy of this ListOfRules instance.

Returns
a (deep) copy of this ListOfRules.
void libsbmlcs.SBase.connectToParent ( SBase  parent)
inherited

Sets the parent SBML object of this SBML object.

(Creates a child-parent relationship by the child) This function is called when a child element is set/added/created by its parent element (e.g. by setXXX, addXXX, createXXX, and connectToChild functions of the parent element).

Parameters
parentthe SBML object to use
int libsbmlcs.SBase.disablePackage ( string  pkgURI,
string  pkgPrefix 
)
inherited

Disables the given SBML Level 3 package.

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
override void libsbmlcs.ListOfRules.Dispose ( )
virtual

Reimplemented from libsbmlcs.ListOf.

void libsbmlcs.SBase.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.
int libsbmlcs.SBase.enablePackage ( string  pkgURI,
string  pkgPrefix,
bool  flag 
)
inherited

Enables or disables the given SBML Level 3 package.

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
flagwhether to enable (true) or disable (false) the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
override bool libsbmlcs.SBase.Equals ( Object  sb)
inherited
new Rule libsbmlcs.ListOfRules.get ( long  n)

Get a Rule from the ListOfRules.

Parameters
nthe index number of the Rule to get.
Returns
the nth Rule in this ListOfRules.
See Also
size()
new Rule libsbmlcs.ListOfRules.get ( string  sid)

Get a Rule from the ListOfRules based on its identifier.

Parameters
sida string representing the identifier of the Rule to get.
Returns
Rule in this ListOfRules with the given id or null if no such Rule exists.
See Also
get(long n)
size()
SBase libsbmlcs.SBase.getAncestorOfType ( int  type,
string  pkgName 
)
inherited

Returns the first ancestor object that has the given SBML type code.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.
SBase libsbmlcs.SBase.getAncestorOfType ( int  type)
inherited

Returns the first ancestor object that has the given SBML type code.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.
XMLNode libsbmlcs.SBase.getAnnotation ( )
inherited

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
string libsbmlcs.SBase.getAnnotationString ( )
inherited

Returns the content of the 'annotation' subelement of this object as a character string.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form.

Returns
the annotation of this SBML object as a character string.
See Also
getAnnotation()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
long libsbmlcs.SBase.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 this 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()
CVTerm libsbmlcs.SBase.getCVTerm ( long  n)
inherited

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters
nlong the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
CVTermList libsbmlcs.SBase.getCVTerms ( )
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns
the list of CVTerms for this SBML object.
SBase libsbmlcs.ListOf.getElementByMetaId ( string  metaid)
inherited

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.ListOfRules.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.

Note that AssignmentRules and RateRules do not actually have IDs, but the libsbml interface pretends that they do: no assignment rule or rate rule is returned by this function.

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

Returns the first child element it can find with the given metaid from all plug-ins associated with this element, 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.SBase.getElementFromPluginsBySId ( string  id)
inherited

Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, 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.
new string libsbmlcs.ListOfRules.getElementName ( )

Returns the XML element name of this object.

For ListOfRules, the XML element name is 'listOfRules'.

Returns
the name of this element, i.e., 'listOfRules'.
override int libsbmlcs.SBase.GetHashCode ( )
inherited
string libsbmlcs.SBase.getId ( )
inherited

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
the meta-identifier of this SBML object, as a string.
See Also
isSetMetaId()
setMetaId(string metaid)
new int libsbmlcs.ListOfRules.getItemTypeCode ( )

Returns the libSBML type code for the objects contained in this ListOf (i.e., Rule objects, if the list is non-empty).

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml. The names of the type codes all begin with the characters SBML_.

Returns
the SBML type code for the objects contained in this ListOf instance, or SBML_UNKNOWN (default).
See Also
getElementName()
long libsbmlcs.SBase.getLevel ( )
inherited

Returns the SBML Level of the SBMLDocument object containing this object.

Returns
the SBML level of this SBML object.
See Also
getVersion()
getNamespaces()
getPackageVersion()
long libsbmlcs.SBase.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 this 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.SBase.getListOfAllElements ( )
inherited
SBaseList libsbmlcs.SBase.getListOfAllElementsFromPlugins ( )
inherited
string libsbmlcs.SBase.getMetaId ( )
inherited

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
the meta-identifier of this SBML object.
See Also
isSetMetaId()
setMetaId(string metaid)
Model libsbmlcs.SBase.getModel ( )
inherited

Returns the Model object in which the current object is located.

Returns
the parent Model of this SBML object.
See Also
getParentSBMLObject()
getSBMLDocument()
ModelHistory libsbmlcs.SBase.getModelHistory ( )
inherited

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or null if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
string libsbmlcs.SBase.getName ( )
inherited

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
the meta-identifier of this SBML object, as a string.
See Also
isSetMetaId()
setMetaId(string metaid)
XMLNamespaces libsbmlcs.SBase.getNamespaces ( )
inherited

Returns a list of the XML Namespaces declared on this SBML document.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.

Returns
the XML Namespaces associated with this SBML object
See Also
getLevel()
getVersion()
XMLNode libsbmlcs.SBase.getNotes ( )
inherited

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns
the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
string libsbmlcs.SBase.getNotesString ( )
inherited

Returns the content of the 'notes' subelement of this object as a string.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns
the content of the 'notes' subelement of this SBML object as a string.
See Also
getNotes()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
long libsbmlcs.SBase.getNumCVTerms ( )
inherited

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns
the number of CVTerms for this SBML object.
long libsbmlcs.SBase.getNumPlugins ( )
inherited

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
string libsbmlcs.SBase.getPackageName ( )
inherited

Returns the name of the SBML Level 3 package in which this element is defined.

Returns
the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
long libsbmlcs.SBase.getPackageVersion ( )
inherited

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See Also
getLevel()
getVersion()
SBase libsbmlcs.SBase.getParentSBMLObject ( )
inherited

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See Also
getSBMLDocument()
getModel()
SBasePlugin libsbmlcs.SBase.getPlugin ( string  package)
inherited

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
SBasePlugin libsbmlcs.SBase.getPlugin ( long  n)
inherited

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
int libsbmlcs.SBase.getResourceBiologicalQualifier ( string  resource)
inherited

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
int libsbmlcs.SBase.getResourceModelQualifier ( string  resource)
inherited

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
SBMLDocument libsbmlcs.SBase.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 SBML object.
See Also
getParentSBMLObject()
getModel()
SBMLNamespaces libsbmlcs.SBase.getSBMLNamespaces ( )
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

int libsbmlcs.SBase.getSBOTerm ( )
inherited

Returns the integer portion of the value of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.
string libsbmlcs.SBase.getSBOTermAsURL ( )
inherited

Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.

This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.
string libsbmlcs.SBase.getSBOTermID ( )
inherited

Returns the string representation of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.
new int libsbmlcs.ListOfRules.getTypeCode ( )

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml. The names of the type codes all begin with the characters SBML_.

Returns
the SBML type code for this object, or SBML_UNKNOWN (default).
See Also
getElementName()
long libsbmlcs.SBase.getVersion ( )
inherited

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

Returns
the SBML version of this SBML object.
See Also
getLevel()
getNamespaces()
bool libsbmlcs.SBase.hasNonstandardIdentifierBeginningWith ( string  prefix)
inherited

Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid').

bool libsbmlcs.SBase.hasRequiredAttributes ( )
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

bool libsbmlcs.SBase.hasRequiredElements ( )
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

bool libsbmlcs.SBase.hasValidLevelVersionNamespaceCombination ( )
inherited

Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.

The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:

Returns
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
int libsbmlcs.ListOf.insert ( int  location,
SBase  item 
)
inherited

Inserts the item at the given position of this ListOf.

This variant of the method makes a clone of the item handet to it. This means that when the ListOf is destroyed, the original items will not be destroyed.

Parameters
locationthe location where to insert the item
itemthe item to be inserted to the list
See Also
insertAndOwn(int location, SBase item)
int libsbmlcs.ListOf.insertAndOwn ( int  location,
SBase  item 
)
inherited

Inserts the item at the given position of this ListOf.

This variant of the method makes a clone of the item handet to it. This means that when the ListOf is destroyed, the original items will not be destroyed.

Parameters
locationthe location where to insert the item
itemthe item to be inserted to the list
See Also
insert(int location, SBase item)
bool libsbmlcs.SBase.isPackageEnabled ( string  pkgName)
inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPackageURIEnabled()
bool libsbmlcs.SBase.isPackageURIEnabled ( string  pkgURI)
inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPackageEnabled()
bool libsbmlcs.SBase.isPkgEnabled ( string  pkgName)
inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPkgURIEnabled()
bool libsbmlcs.SBase.isPkgURIEnabled ( string  pkgURI)
inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPkgEnabled()
bool libsbmlcs.SBase.isSetAnnotation ( )
inherited

Predicate returning true if this object's 'annotation' subelement exists and has content.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
true if a 'annotation' subelement exists, false otherwise.
See Also
getAnnotation()
getAnnotationString()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
bool libsbmlcs.SBase.isSetId ( )
inherited

Predicate returning true if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
true if the 'metaid' attribute of this SBML object is set, false otherwise.
See Also
getMetaId()
setMetaId(string metaid)
bool libsbmlcs.SBase.isSetMetaId ( )
inherited

Predicate returning true if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
true if the 'metaid' attribute of this SBML object is set, false otherwise.
See Also
getMetaId()
setMetaId(string metaid)
bool libsbmlcs.SBase.isSetModelHistory ( )
inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns
true if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
bool libsbmlcs.SBase.isSetName ( )
inherited

Predicate returning true if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
true if the 'metaid' attribute of this SBML object is set, false otherwise.
See Also
getMetaId()
setMetaId(string metaid)
bool libsbmlcs.SBase.isSetNotes ( )
inherited

Predicate returning true if this object's 'notes' subelement exists and has content.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
true if a 'notes' subelement exists, false otherwise.
See Also
getNotes()
getNotesString()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
bool libsbmlcs.SBase.isSetSBOTerm ( )
inherited

Predicate returning true if this object's 'sboTerm' attribute is set.

Returns
true if the 'sboTerm' attribute of this SBML object is set, false otherwise.
bool libsbmlcs.SBase.matchesRequiredSBMLNamespacesForAddition ( SBase  sb)
inherited

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

Parameters
sban object to compare with respect to namespaces
Returns
bool, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool libsbmlcs.SBase.matchesSBMLNamespaces ( SBase  sb)
inherited

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

Parameters
sban object to compare with respect to namespaces
Returns
bool, true if this object's collection of namespaces is the same as sb's, false otherwise.
void libsbmlcs.SBase.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).

static bool libsbmlcs.SBase.operator!= ( SBase  lhs,
SBase  rhs 
)
staticinherited
static bool libsbmlcs.SBase.operator== ( SBase  lhs,
SBase  rhs 
)
staticinherited
int libsbmlcs.SBase.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.

new Rule libsbmlcs.ListOfRules.remove ( long  n)

Removes the nth item from this ListOfRules items and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it.

Parameters
nthe index of the item to remove
See Also
size()
new Rule libsbmlcs.ListOfRules.remove ( string  sid)

Removes item in this ListOfRules items with the given identifier.

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.

Parameters
sidthe identifier of the item to remove
Returns
the item removed. As mentioned above, the caller owns the returned item.
int libsbmlcs.ListOf.removeFromParentAndDelete ( )
inherited

Because ListOf objects typically live as object children of their parent object and not as pointer children, this function clears itself, but does not attempt to do anything else.

If a particular ListOf subclass does indeed exist as a pointer only, this function will need to be overridden.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string  elementName,
string  elementURI 
)
inherited

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
replaceTopLevelAnnotationElement(XMLNode )
replaceTopLevelAnnotationElement(string)
int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string  elementName)
inherited

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
replaceTopLevelAnnotationElement(XMLNode )
replaceTopLevelAnnotationElement(string)
void libsbmlcs.SBase.renameMetaIdRefs ( string  oldid,
string  newid 
)
inherited

Renames all the MetaIdRef attributes on this element.

This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
void libsbmlcs.SBase.renameSIdRefs ( string  oldid,
string  newid 
)
inherited

Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).

This method works by looking at all attributes and (if appropriate) mathematical formulas, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
void libsbmlcs.SBase.renameUnitSIdRefs ( string  oldid,
string  newid 
)
inherited

Renames all the UnitSIdRef attributes on this element.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
void libsbmlcs.SBase.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.SBase.replaceTopLevelAnnotationElement ( XMLNode  annotation)
inherited

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters
annotationXMLNode representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(string elementName, string elementURI)
replaceTopLevelAnnotationElement(string)
int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( string  annotation)
inherited

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters
annotationstring representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(string elementName, string elementURI)
replaceTopLevelAnnotationElement(XMLNode)
int libsbmlcs.SBase.setAnnotation ( XMLNode  annotation)
inherited

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).

Parameters
annotationan XML structure that is to be used as the new content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.SBase.setAnnotation ( string  annotation)
inherited

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).

Parameters
annotationan XML string that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
int libsbmlcs.SBase.setId ( string  sid)
inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns
true if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
int libsbmlcs.SBase.setMetaId ( string  metaid)
inherited

Sets the value of the 'metaid' attribute of this object.

The string metaid is copied. The value of metaid must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement.

Parameters
metaidthe identifier string to use as the value of the 'metaid' attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getMetaId()
isSetMetaId()
int libsbmlcs.SBase.setModelHistory ( ModelHistory  history)
inherited

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
int libsbmlcs.SBase.setName ( string  name)
inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns
true if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
int libsbmlcs.SBase.setNamespaces ( XMLNamespaces  xmlns)
inherited

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Parameters
xmlnsthe namespaces to set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.setNotes ( XMLNode  notes)
inherited

Sets the value of the 'notes' subelement of this SBML object.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML structure that is to be used as the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.setNotes ( string  notes,
bool  addXHTMLMarkup 
)
inherited

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa bool indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.setNotes ( string  notes)
inherited

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa bool indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
void libsbmlcs.SBase.setSBMLNamespacesAndOwn ( SBMLNamespaces  sbmlns)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

int libsbmlcs.SBase.setSBOTerm ( int  value)
inherited

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
valuethe NNNNNNN integer portion of the SBO identifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm(string sboid)
int libsbmlcs.SBase.setSBOTerm ( string  sboid)
inherited

Sets the value of the 'sboTerm' attribute by string.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
sboidthe SBO identifier string of the form 'SBO:NNNNNNN'
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm(int value)
long libsbmlcs.ListOf.size ( )
inherited

Get the size of this ListOf.

Returns
the number of items in this ListOf items.
string libsbmlcs.SBase.toSBML ( )
inherited

Returns a string consisting of a partial SBML corresponding to just this object.

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
int libsbmlcs.SBase.unsetAnnotation ( )
inherited

Unsets the value of the 'annotation' subelement of this SBML object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
int libsbmlcs.SBase.unsetCVTerms ( )
inherited

Clears the list of CVTerm objects attached to this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetId ( )
inherited

Unsets the value of the 'id' attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always either Sid or UnitSId, depending on the object in question. Both data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The equality of SId and UnitSId type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId and UnitSId.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetMetaId ( )
inherited

Unsets the value of the 'metaid' attribute of this SBML object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetModelHistory ( )
inherited

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
int libsbmlcs.SBase.unsetName ( )
inherited

Unsets the value of the 'name' attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. In contrast to the 'id' attribute, the 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.

The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)

As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetNotes ( )
inherited

Unsets the value of the 'notes' subelement of this SBML object.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.unsetSBOTerm ( )
inherited

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
void libsbmlcs.SBase.writeExtensionElements ( XMLOutputStream  stream)
inherited

Writes out contained SBML objects of package extensions (if any) as XML elements.

Member Data Documentation

bool libsbmlcs.SBase.swigCMemOwn
protectedinherited