libSBML C++ API  5.15.0
SBMLDocument Class Reference
Inheritance diagram for SBMLDocument:
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Detailed Description

Overall SBML container object.

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). The two primary means of reading an SBML model, SBMLReader::readSBML() and SBMLReader::readSBMLFromString(), both return a pointer to an SBMLDocument object. From there, callers can inquire about any errors encountered (e.g., using SBMLDocument::getNumErrors()), access the Model object, and perform other actions such as consistency-checking and model translation.

When creating fresh models programmatically, the starting point is typically the creation of an SBMLDocument object instance. The SBMLDocument constructor accepts arguments for the SBML Level and Version of the model to be created. After creating the SBMLDocument object, calling programs then typically call SBMLDocument::createModel() almost immediately, and then proceed to call the methods on the Model object to fill out the model's contents.

SBMLDocument corresponds roughly to the class Sbml defined in the SBML Level 2 specification and SBML in the Level 3 specification. It does not have a direct correspondence in SBML Level 1. (However, to make matters simpler for applications, libSBML creates an SBMLDocument no matter whether the model is Level 1, Level 2 or Level 3.) In its barest form, when written out in XML format for (e.g.) SBML Level 2 Version 4, the corresponding structure is the following:

<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
  ...
</sbml>

SBMLDocument is derived from SBase, and therefore contains the usual SBase attributes (in SBML Level 2 and Level 3) of "metaid" and "sboTerm", as well as the subelements "notes" and "annotation". It also contains the attributes "level" and "version" indicating the Level and Version of the SBML data structure. These can be accessed using the methods defined by the SBase class for that purpose.

Checking consistency and adherence to SBML specifications

One of the most important features of libSBML is its ability to perform SBML validation to ensure that a model adheres to the SBML specification for whatever Level+Version combination the model uses. SBMLDocument provides the methods for running consistency-checking and validation rules on the SBML content.

First, a brief explanation of the rationale is in order. In libSBML versions up to and including the version 3.3.x series, the individual methods for creating and setting attributes and other components were quite lenient, and allowed a caller to compose SBML entities that might not, in the end, represent valid SBML. This allowed applications the freedom to do things such as save incomplete models (which is useful when models are being developed over long periods of time). In the version 4.x series, libSBML is somewhat stricter, but still permits structures to be created independently and the results to be combined in a separate step. In all these cases, it means that a separate validation step is necessary when a calling program finally wants to finish a complete SBML document.

The primary interface to this validation facility is SBMLDocument's SBMLDocument::checkInternalConsistency() and SBMLDocument::checkConsistency(). The former verifies the basic internal consistency and syntax of an SBML document, and the latter implements more elaborate validation rules (both those defined by the SBML specifications, as well as additional rules offered by libSBML).

The checks performed by SBMLDocument::checkInternalConsistency() are hardwired and cannot be changed by calling programs, but the validation performed by SBMLDocument::checkConsistency() is under program control using the method SBMLDocument::setConsistencyChecks(). Applications can selectively disable specific kinds of checks that they may not be interested in, by calling SBMLDocument::setConsistencyChecks() with appropriate parameters.

These methods have slightly different relevance depending on whether a model is created programmaticaly from scratch, or whether it is read in from a file or data stream. The following list summarizes the possible scenarios.

Scenario 1: Creating a model from scratch. Before writing out the model,

Scenario 2: Reading a model from a file or data stream. After reading the model,

  • Basic consistency checks will have been performed automatically by libSBML upon reading the content, so you only need to inquire about the results by using SBMLDocument::getNumErrors()

An example of using the consistency-checking and validation facilities is provided in this manual in the section Tutorial: creating a complete model.

It should be noted that as of SBML Level 3 Version 2, the Model became an optional child of SBMLDocument, instead of being required. This means that one can no longer use SBMLDocument::getModel() as a cheap method of checking if an SBML document was read in properly: the more robust getError methods detailed above must be used instead.

Converting documents between Levels and Versions of SBML

LibSBML provides facilities for limited translation of SBML between Levels and Versions of the SBML specifications. The method for doing is is setLevelAndVersion() . In general, models can be converted upward without difficulty (e.g., from SBML Level 1 to Level 2, or from an earlier Version of Level 2 to the latest Version of Level 2). Sometimes models can be translated downward as well, if they do not use constructs specific to more advanced Levels of SBML.

Calling SBMLDocument::setLevelAndVersion() will not necessarily lead to a successful conversion. The method will return a boolean value to indicate success or failure. Callers must check the error log (see next section) attached to the SBMLDocument object after calling SBMLDocument::setLevelAndVersion() in order to assess whether any problems arose.

If an application is interested in translating to a lower Level and/or Version of SBML within a Level, the following methods allow for prior assessment of whether there is sufficient compatibility to make a translation possible:

Some changes between Versions of SBML Level 2 may lead to unexpected behaviors when attempting conversions in either direction. For example, SBML Level 2 Version 4 relaxed the requirement for consistency in units of measurement between expressions annd quantities in a model. As a result, a model written in Version 4, if converted to Version 3 with no other changes, may fail validation as a Version 3 model because Version 3 imposed stricter requirements on unit consistency.

Other changes between SBML Level 2 and Level 3 make downward conversions challenging. In some cases, it means that a model converted to Level 2 from Level 3 will contain attributes that were not explicitly given in the Level 3 model, because in Level 2 these attributes may have been optional or have default values.

Error handling

Upon reading a model, SBMLDocument logs any problems encountered while reading the model from the file or data stream. The log contains objects that record diagnostic information about any notable issues that arose. Whether the problems are warnings or errors, they are both reported through a single common interface involving the object class SBMLError.

The methods SBMLDocument::getNumErrors(), SBMLDocument::getError() and SBMLDocument::printErrors() allow callers to interact with the warnings or errors logged. Alternatively, callers may retrieve the entire log as an SBMLErrorLog object using the method SBMLDocument::getErrorLog(). The SBMLErrorLog object provides some alternative methods for interacting with the set of errors and warnings. In either case, applications typically should first call SBMLDocument::getNumErrors() to find out if any issues have been logged after specific libSBML operations such as the ones discussed in the sections above. If they have, then an application will should proceed to inspect the individual reports using either the direct interfaces on SBMLDocument or using the methods on the SBMLErrorLog object.

An example of using the error facility is provided in this manual in the section Tutorial: creating a complete model.

Examples:
addCustomValidator.cpp, addCVTerms.cpp, addingEvidenceCodes_1.cpp, addingEvidenceCodes_2.cpp, addLayout.cpp, addModelHistory.cpp, appendAnnotation.cpp, callExternalValidator.cpp, convertCobraToFbc.cpp, convertFbcToCobra.cpp, convertLayout.cpp, convertSBML.cpp, createExampleSBML.cpp, echoSBML.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, flattenModel.cpp, getAllElementsWithNotes.cpp, groups_example1.cpp, groups_example2.cpp, inlineFunctionDefintions.cpp, printAnnotation.cpp, printMath.cpp, printNotes.cpp, printSBML.cpp, printUnits.cpp, promoteParameters.cpp, qual_example1.cpp, readSBML.cpp, renameSId.cpp, rngvalidator.cpp, SBMLHttpResolverExample.cpp, setIdFromNames.cpp, setNamesFromIds.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, spec_example4.cpp, stripPackage.cpp, translateL3Math.cpp, unsetAnnotation.cpp, unsetNotes.cpp, and validateSBML.cpp.

Public Member Functions

int addCVTerm (CVTerm *term, bool newBag=false)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
virtual int appendAnnotation (const XMLNode *annotation)
 Appends the given annotation to the "annotation" subelement of this object. More...
 
virtual int appendAnnotation (const std::string &annotation)
 Appends the given annotation to the "annotation" subelement of this object. More...
 
int appendNotes (const XMLNode *notes)
 Appends the given notes to the "notes" subelement of this object. More...
 
int appendNotes (const std::string &notes)
 Appends the given notes to the "notes" subelement of this object. More...
 
unsigned int checkConsistency ()
 Performs consistency checking and validation on this SBML document. More...
 
unsigned int checkConsistencyWithStrictUnits ()
 Performs consistency checking and validation on this SBML document using the ultra strict units validator that assumes that there are no hidden numerical conversion factors. More...
 
unsigned int checkInternalConsistency ()
 Performs consistency checking on libSBML's internal representation of an SBML Model. More...
 
unsigned int checkL1Compatibility (bool inConversion=false)
 Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 1 and can be converted to Level 1. More...
 
unsigned int checkL2v1Compatibility (bool inConversion=false)
 Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 1 and can be converted to Level 2 Version 1. More...
 
unsigned int checkL2v2Compatibility (bool inConversion=false)
 Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 2 and can be converted to Level 2 Version 2. More...
 
unsigned int checkL2v3Compatibility (bool inConversion=false)
 Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 3 and can be converted to Level 2 Version 3. More...
 
unsigned int checkL2v4Compatibility ()
 Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 4 and can be converted to Level 2 Version 4. More...
 
unsigned int checkL2v5Compatibility ()
 Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 5 and can be converted to Level 2 Version 5. More...
 
unsigned int checkL3v1Compatibility ()
 Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 3 Version 1 and can be converted to Level 3 Version 1. More...
 
unsigned int checkL3v2Compatibility ()
 Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 3 Version 2 and can be converted to Level 3 Version 2. More...
 
virtual SBMLDocumentclone () const
 Creates and returns a deep copy of this SBMLDocument object. More...
 
virtual int convert (const ConversionProperties &props)
 Converts this document using the converter that best matches the given conversion properties. More...
 
ModelcreateModel (const std::string &sid="")
 Creates a new Model inside this SBMLDocument, and returns a pointer to it. More...
 
void deleteDisabledPlugins (bool recursive=true)
 Deletes all information stored in disabled plugins. More...
 
int disablePackage (const std::string &pkgURI, const std::string &pkgPrefix)
 Disables the given SBML Level 3 package on this object. More...
 
int enableDefaultNS (const std::string &package, bool flag)
 Set/unset default namespace to each top-level element defined in the given package extension. More...
 
int enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package on this object. More...
 
bool expandFunctionDefinitions ()
 Removes FunctionDefinition constructs from the document and expands any instances of their use within <math> elements. More...
 
bool expandInitialAssignments ()
 Removes InitialAssignment constructs from the document and replaces them with appropriate values. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual ListgetAllElementsFromPlugins (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects contained in SBML package plug-ins. More...
 
SBasegetAncestorOfType (int type, const std::string pkgName="core")
 Returns the first ancestor object that has the given SBML type code from the given package. More...
 
const SBasegetAncestorOfType (int type, const std::string pkgName="core") const
 Returns the first ancestor object that has the given SBML type code from the given package. More...
 
XMLNodegetAnnotation ()
 Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More...
 
XMLNodegetAnnotation () const
 Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More...
 
std::string getAnnotationString ()
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
std::string getAnnotationString () const
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
unsigned int getColumn () const
 Returns the column number where this object first appears in the XML representation of the SBML document. More...
 
CVTermgetCVTerm (unsigned int n)
 Returns the nth CVTerm in the list of CVTerms of this SBML object. More...
 
ListgetCVTerms ()
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
ListgetCVTerms () const
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
SBasePlugingetDisabledPlugin (unsigned int n)
 Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasePlugingetDisabledPlugin (unsigned int n) const
 Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasegetElementByMetaId (const std::string &metaid) const
 Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or NULL if no such object is found. More...
 
const SBasegetElementBySId (const std::string &id) const
 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...
 
virtual SBasegetElementBySId (const std::string &id)
 Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this object, which for SBMLDocument, is always "sbml". More...
 
const SBMLErrorgetError (unsigned int n) const
 Returns the nth error or warning encountered during parsing, consistency checking, or attempted translation of this model. More...
 
SBMLErrorLoggetErrorLog ()
 Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model. More...
 
const SBMLErrorLoggetErrorLog () const
 Returns a constant pointer to the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model. More...
 
const SBMLErrorgetErrorWithSeverity (unsigned int n, unsigned int severity) const
 Returns the nth error or warning with the given severity encountered during parsing, consistency checking, or attempted translation of this model. More...
 
virtual const std::string & getId () const
 Returns the value of the "id" attribute of this SBML object, if it has one, or the "variable" attribute of a Rule, or the "symbol" attribute of an InitialAssignment. More...
 
const std::string & getIdAttribute () const
 Returns the value of the "id" attribute of this SBML object. More...
 
unsigned int getLevel () const
 Returns the SBML Level of the SBMLDocument object containing this object. More...
 
unsigned int getLine () const
 Returns the line number where this object first appears in the XML representation of the SBML document. More...
 
std::string getLocationURI () const
 Get the location of this SBMLDocument. More...
 
std::string getLocationURI ()
 Get the location of this SBMLDocument. More...
 
const std::string & getMetaId () const
 Returns the value of the "metaid" attribute of this SBML object. More...
 
std::string & getMetaId ()
 Returns the value of the "metaid" attribute of this SBML object. More...
 
const ModelgetModel () const
 Returns the Model object stored in this SBMLDocument. More...
 
ModelgetModel ()
 Returns the Model object stored in this SBMLDocument. More...
 
ModelHistorygetModelHistory () const
 Returns the ModelHistory object, if any, attached to this object. More...
 
ModelHistorygetModelHistory ()
 Returns the ModelHistory object, if any, attached to this object. More...
 
virtual const std::string & getName () const
 Returns the value of the "name" attribute of this SBML object. More...
 
virtual XMLNamespacesgetNamespaces () const
 Returns a list of XML Namespaces associated with the XML content of this SBML document. More...
 
XMLNodegetNotes ()
 Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More...
 
XMLNodegetNotes () const
 Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More...
 
std::string getNotesString ()
 Returns the content of the "notes" subelement of this object as a string. More...
 
std::string getNotesString () const
 Returns the content of the "notes" subelement of this object as a string. More...
 
unsigned int getNumCVTerms ()
 Returns the number of CVTerm objects in the annotations of this SBML object. More...
 
unsigned int getNumDisabledPlugins () const
 Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More...
 
unsigned int getNumErrors () const
 Returns the number of errors or warnings encountered during parsing, consistency checking, or attempted translation of this model. More...
 
unsigned int getNumErrors (unsigned int severity) const
 Returns the number of errors or warnings encountered with the given severity during parsing, consistency checking, or attempted translation of this model. More...
 
unsigned int getNumPlugins () const
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
unsigned int getObjectVersion () const
 Returns the Version within the SBML Level of the actual object. More...
 
const std::string & getPackageName () const
 Returns the name of the SBML Level 3 package in which this element is defined. More...
 
bool getPackageRequired (const std::string &package)
 Returns the required attribute of the given package extension. More...
 
unsigned int getPackageVersion () const
 Returns the Version of the SBML Level 3 package to which this element belongs to. More...
 
SBasegetParentSBMLObject ()
 Returns the parent SBML object containing this object. More...
 
const SBasegetParentSBMLObject () const
 Returns the parent SBML object containing this object. More...
 
bool getPkgRequired (const std::string &package)
 Returns the required attribute of the given package extension. More...
 
SBasePlugingetPlugin (const std::string &package)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
const SBasePlugingetPlugin (const std::string &package) const
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
SBasePlugingetPlugin (unsigned int n)
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasePlugingetPlugin (unsigned int n) const
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
std::string getPrefix () const
 Returns the XML namespace prefix of this element. More...
 
BiolQualifierType_t getResourceBiologicalQualifier (std::string resource)
 Returns the MIRIAM biological qualifier associated with the given resource. More...
 
ModelQualifierType_t getResourceModelQualifier (std::string resource)
 Returns the MIRIAM model qualifier associated with the given resource. More...
 
const SBMLDocumentgetSBMLDocument () const
 Returns the SBMLDocument object containing this object instance. More...
 
SBMLDocumentgetSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
int getSBOTerm () const
 Returns the integer portion of the value of the "sboTerm" attribute of this object. More...
 
std::string getSBOTermAsURL () const
 Returns the URL representation of the "sboTerm" attribute of this object. More...
 
std::string getSBOTermID () const
 Returns the string representation of the "sboTerm" attribute of this object. More...
 
virtual int getTypeCode () const
 Returns the libSBML type code for this SBML object. More...
 
std::string getURI () const
 Gets the namespace URI to which this element belongs to. More...
 
void * getUserData () const
 Returns the user data that has been previously set via setUserData(). More...
 
unsigned int getVersion () const
 Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...
 
bool hasValidLevelVersionNamespaceCombination ()
 Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More...
 
bool isDisabledIgnoredPackage (const std::string &pkgURI)
 Returns true if the given package extension is one of an ignored packages that has been disabled, otherwise returns false. More...
 
bool isEnabledDefaultNS (const std::string &package)
 Returns true if a default namespace is added to each top-level element defined in the given package extension, otherwise returns false. More...
 
bool isIgnoredPackage (const std::string &pkgURI)
 Returns true if the given package extension is one of an ignored packages, otherwise returns false. More...
 
bool isIgnoredPkg (const std::string &pkgURI)
 Returns true if the given package extension is one of ignored packages, otherwise returns false. More...
 
bool isPackageEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPackageURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPkgEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPkgURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isSetAnnotation () const
 Predicate returning true if this object's "annotation" subelement exists and has content. More...
 
virtual bool isSetId () const
 Predicate returning true if a call to getId() returns a non-empty string. More...
 
bool isSetIdAttribute () const
 Predicate returning true if this object's "id" attribute is set. More...
 
bool isSetMetaId () const
 Predicate returning true if this object's "metaid" attribute is set. More...
 
bool isSetModel () const
 Returns true if the Model object has been set, otherwise returns false. More...
 
bool isSetModelHistory ()
 Predicate returning true if this object has a ModelHistory object attached to it. More...
 
virtual bool isSetName () const
 Predicate returning true if this object's "name" attribute is set. More...
 
bool isSetNotes () const
 Predicate returning true if this object's "notes" subelement exists and has content. More...
 
bool isSetPackageRequired (const std::string &package)
 Returns true if the required attribute of the given package extension is defined, otherwise returns false. More...
 
bool isSetPkgRequired (const std::string &package)
 Returns true if the required attribute of the given package extension is defined, otherwise returns false. More...
 
bool isSetSBOTerm () const
 Predicate returning true if this object's "sboTerm" attribute is set. More...
 
bool isSetUserData () const
 Predicate returning true or false depending on whether the user data of this element has been set. More...
 
bool matchesRequiredSBMLNamespacesForAddition (const SBase *sb)
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (const SBase *sb)
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (const SBase *sb) const
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
SBMLDocumentoperator= (const SBMLDocument &rhs)
 Assignment operator for SBMLDocument. More...
 
void printErrors (std::ostream &stream=std::cerr) const
 Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document. More...
 
void printErrors (std::ostream &stream, unsigned int severity) const
 Prints all the errors or warnings with the given severity encountered trying to parse, check, or translate this SBML document. More...
 
void read (XMLNode &node, XMLErrorSeverityOverride_t flag=LIBSBML_OVERRIDE_DISABLED)
 Reads (initializes) this SBML object by reading from the given XMLNode. More...
 
virtual int removeFromParentAndDelete ()
 Removes this object from its parent. More...
 
int removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="", bool removeEmpty=true)
 Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More...
 
virtual void renameMetaIdRefs (const std::string &oldid, const std::string &newid)
 Replaces all uses of a given meta identifier attribute value with another value. More...
 
virtual void renameSIdRefs (const std::string &oldid, const std::string &newid)
 Replaces all uses of a given SIdRef type attribute value with another value. More...
 
virtual void renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
 Replaces all uses of a given UnitSIdRef type attribute value with another value. More...
 
int replaceTopLevelAnnotationElement (const 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 (const std::string &annotation)
 Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More...
 
 SBMLDocument (unsigned int level=0, unsigned int version=0)
 Creates a new SBMLDocument, optionally with given values for the SBML Level and Version. More...
 
 SBMLDocument (SBMLNamespaces *sbmlns)
 Creates a new SBMLDocument using the given SBMLNamespaces object sbmlns. More...
 
 SBMLDocument (const SBMLDocument &orig)
 Copy constructor; creates a copy of this SBMLDocument. More...
 
virtual int setAnnotation (const XMLNode *annotation)
 Sets the value of the "annotation" subelement of this SBML object. More...
 
virtual int setAnnotation (const std::string &annotation)
 Sets the value of the "annotation" subelement of this SBML object. More...
 
void setConsistencyChecks (SBMLErrorCategory_t category, bool apply)
 Controls the consistency checks that are performed when SBMLDocument::checkConsistency() is called. More...
 
void setConsistencyChecksForConversion (SBMLErrorCategory_t category, bool apply)
 Controls the consistency checks that are performed when SBMLDocument::setLevelAndVersion() is called. More...
 
virtual int setId (const std::string &sid)
 Sets the value of the "id" attribute of this SBML object. More...
 
virtual int setIdAttribute (const std::string &sid)
 Sets the value of the "id" attribute of this SBML object. More...
 
bool setLevelAndVersion (unsigned int level, unsigned int version, bool strict=true, bool ignorePackages=false)
 Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed. More...
 
void setLocationURI (const std::string &uri)
 Sets the location of this SBMLDocument. More...
 
int setMetaId (const std::string &metaid)
 Sets the value of the meta-identifier attribute of this SBML object. More...
 
int setModel (const Model *m)
 Sets the Model for this SBMLDocument to a copy of the given Model. More...
 
int setModelHistory (ModelHistory *history)
 Sets the ModelHistory of this object. More...
 
virtual int setName (const std::string &name)
 Sets the value of the "name" attribute of this SBML object. More...
 
int setNamespaces (XMLNamespaces *xmlns)
 Sets the namespaces relevant of this SBML object. More...
 
int setNotes (const XMLNode *notes)
 Sets the value of the "notes" subelement of this SBML object. More...
 
int setNotes (const std::string &notes, bool addXHTMLMarkup=false)
 Sets the value of the "notes" subelement of this SBML object to a copy of the string notes. More...
 
int setPackageRequired (const std::string &package, bool flag)
 Sets the required attribute value of the given package extension. More...
 
int setPkgRequired (const std::string &package, bool flag)
 Sets the value of the required attribute for the given package. More...
 
virtual int setSBOTerm (int value)
 Sets the value of the "sboTerm" attribute. More...
 
virtual int setSBOTerm (const std::string &sboid)
 Sets the value of the "sboTerm" attribute by string. More...
 
int setUserData (void *userData)
 Sets the user data of this element. More...
 
char * toSBML ()
 Returns a string consisting of a partial SBML corresponding to just this object. More...
 
XMLNodetoXMLNode ()
 Returns this element as an XMLNode. 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...
 
virtual int unsetId ()
 Unsets the value of the "id" attribute of this SBML object. More...
 
int unsetIdAttribute ()
 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...
 
virtual 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...
 
int unsetUserData ()
 Unsets the user data of this element. More...
 
unsigned int validateSBML ()
 Performs consistency checking and validation on this SBML document. More...
 
virtual ~SBMLDocument ()
 Destroys this SBMLDocument. More...
 

Static Public Member Functions

static unsigned int getDefaultLevel ()
 The default SBML Level of new SBMLDocument objects. More...
 
static unsigned int getDefaultVersion ()
 The default Version of new SBMLDocument objects. More...
 

Protected Member Functions

virtual void setElementText (const std::string &text)
 When overridden allows SBase elements to use the text included in between the elements tags. More...
 

Constructor & Destructor Documentation

SBMLDocument::SBMLDocument ( unsigned int  level = 0,
unsigned int  version = 0 
)

Creates a new SBMLDocument, optionally with given values for the SBML Level and Version.

If both the SBML Level and Version attributes are not specified, the SBML document is treated as having the latest Level and Version of SBML as determined by SBMLDocument::getDefaultLevel() and SBMLDocument::getDefaultVersion(); however, the SBMLDocument object is otherwise left blank. In particular, the blank SBMLDocument object has no associated XML attributes, including (but not limited to) an XML namespace declaration. The XML namespace declaration is not added until the model is written out, or the method SBMLDocument::setLevelAndVersion() is called. This may be important to keep in mind if an application needs to add additional XML namespace declarations on the <sbml> element. Application writers should either provide values for level and version on the call to this constructor, or else call SBMLDocument::setLevelAndVersion() shortly after creating the SBMLDocument object.

Parameters
levelan integer for the SBML Level.
versionan integer for the Version within the SBML Level.
Exceptions
SBMLConstructorExceptionThrown if the given level and version combination are invalid or if this object is incompatible with the given level and version.
See also
SBMLDocument::setLevelAndVersion()
getDefaultLevel()
getDefaultVersion()
SBMLDocument::SBMLDocument ( SBMLNamespaces sbmlns)

Creates a new SBMLDocument using the given SBMLNamespaces object sbmlns.

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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sbmlnsan SBMLNamespaces object.
Exceptions
SBMLConstructorExceptionThrown if the given sbmlns is inconsistent or incompatible with this object.
SBMLDocument::~SBMLDocument ( )
virtual

Destroys this SBMLDocument.

SBMLDocument::SBMLDocument ( const SBMLDocument orig)

Copy constructor; creates a copy of this SBMLDocument.

Parameters
origthe object to copy.

Member Function Documentation

int SBase::addCVTerm ( CVTerm term,
bool  newBag = false 
)
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 value is drawn from the enumeration OperationReturnValues_t. 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.
This method should be used with some caution. 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. 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. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
Examples:
addCVTerms.cpp, addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.
int SBase::appendAnnotation ( const XMLNode annotation)
virtualinherited

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(const XMLNode* annotation) or SBase::setAnnotation(const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

Examples:
addingEvidenceCodes_2.cpp, and appendAnnotation.cpp.
int SBase::appendAnnotation ( const std::string &  annotation)
virtualinherited

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(const XMLNode* annotation) or SBase::setAnnotation(const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int SBase::appendNotes ( const 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::appendNotes ( const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
unsigned int SBMLDocument::checkConsistency ( )

Performs consistency checking and validation on this SBML document.

If this method returns a nonzero value (meaning, one or more consistency checks have failed for SBML document), the failures may be due to warnings or errors. Callers should inspect the severity flag in the individual SBMLError objects returned by SBMLDocument::getError() to determine the nature of the failures.

Returns
the number of failed checks (errors) encountered.
See also
SBMLDocument::checkInternalConsistency()
Examples:
addCustomValidator.cpp, callExternalValidator.cpp, createExampleSBML.cpp, rngvalidator.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, spec_example4.cpp, and validateSBML.cpp.
unsigned int SBMLDocument::checkConsistencyWithStrictUnits ( )

Performs consistency checking and validation on this SBML document using the ultra strict units validator that assumes that there are no hidden numerical conversion factors.

If this method returns a nonzero value (meaning, one or more consistency checks have failed for SBML document), the failures may be due to warnings or errors. Callers should inspect the severity flag in the individual SBMLError objects returned by SBMLDocument::getError() to determine the nature of the failures.

Returns
the number of failed checks (errors) encountered.
See also
SBMLDocument::checkInternalConsistency()
unsigned int SBMLDocument::checkInternalConsistency ( )

Performs consistency checking on libSBML's internal representation of an SBML Model.

Callers should query the results of the consistency check by calling SBMLDocument::getError().

Returns
the number of failed checks (errors) encountered.

The distinction between this method and SBMLDocument::checkConsistency() is that this method reports on fundamental syntactic and structural errors that violate the XML Schema for SBML; by contrast, SBMLDocument::checkConsistency() performs more elaborate model verifications and also validation according to the validation rules written in the appendices of the SBML Level 2 Versions 2–4 specification documents.

See also
SBMLDocument::checkConsistency()
Examples:
createExampleSBML.cpp.
unsigned int SBMLDocument::checkL1Compatibility ( bool  inConversion = false)

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 1 and can be converted to Level 1.

Callers should query the results of the consistency check by calling SBMLDocument::getError().

Returns
the number of failed checks (errors) encountered.
unsigned int SBMLDocument::checkL2v1Compatibility ( bool  inConversion = false)

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 1 and can be converted to Level 2 Version 1.

Callers should query the results of the consistency check by calling SBMLDocument::getError().

Returns
the number of failed checks (errors) encountered.
unsigned int SBMLDocument::checkL2v2Compatibility ( bool  inConversion = false)

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 2 and can be converted to Level 2 Version 2.

Callers should query the results of the consistency check by calling SBMLDocument::getError().

Returns
the number of failed checks (errors) encountered.
unsigned int SBMLDocument::checkL2v3Compatibility ( bool  inConversion = false)

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 3 and can be converted to Level 2 Version 3.

Callers should query the results of the consistency check by calling SBMLDocument::getError().

Returns
the number of failed checks (errors) encountered.
unsigned int SBMLDocument::checkL2v4Compatibility ( )

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 4 and can be converted to Level 2 Version 4.

Callers should query the results of the consistency check by calling SBMLDocument::getError().

Returns
the number of failed checks (errors) encountered.
unsigned int SBMLDocument::checkL2v5Compatibility ( )

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 5 and can be converted to Level 2 Version 5.

Callers should query the results of the consistency check by calling SBMLDocument::getError().

Returns
the number of failed checks (errors) encountered.
unsigned int SBMLDocument::checkL3v1Compatibility ( )

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 3 Version 1 and can be converted to Level 3 Version 1.

Callers should query the results of the consistency check by calling SBMLDocument::getError().

Returns
the number of failed checks (errors) encountered.
unsigned int SBMLDocument::checkL3v2Compatibility ( )

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 3 Version 2 and can be converted to Level 3 Version 2.

Callers should query the results of the consistency check by calling SBMLDocument::getError().

Returns
the number of failed checks (errors) encountered.
SBMLDocument * SBMLDocument::clone ( ) const
virtual

Creates and returns a deep copy of this SBMLDocument object.

Returns
the (deep) copy of this SBMLDocument object.

Implements SBase.

virtual int SBMLDocument::convert ( const ConversionProperties props)
virtual

Converts this document using the converter that best matches the given conversion properties.

Parameters
propsthe conversion properties to use.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Examples:
convertCobraToFbc.cpp, convertFbcToCobra.cpp, inlineFunctionDefintions.cpp, promoteParameters.cpp, and stripPackage.cpp.
Model * SBMLDocument::createModel ( const std::string &  sid = "")

Creates a new Model inside this SBMLDocument, and returns a pointer to it.

In SBML Level 2, the use of an identifier on a Model object is optional. This method takes an optional argument, sid, for setting the identifier. If not supplied, the identifier attribute on the Model instance is not set.

Parameters
sidthe identifier of the new Model to create.
See also
getModel()
SBMLDocument::setModel()
Examples:
createExampleSBML.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, groups_example1.cpp, groups_example2.cpp, qual_example1.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.
void SBase::deleteDisabledPlugins ( bool  recursive = true)
inherited

Deletes all information stored in disabled plugins.

If the plugin is re-enabled later, it will then not have any previously-stored information.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
recursiveif true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element.
See also
getNumDisabledPlugins()
int SBase::disablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix 
)
inherited

Disables the given SBML Level 3 package on this object.

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

An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from an other SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:

// We read in an SBML L3V1 model that uses the 'comp'
// package namespace.
doc = readSBML("sbml-file-with-comp-elements.xml");
// We extract one of the species from the model.
Species* s1 = doc->getModel()->getSpecies(0);
// We construct a new model. This model does not use the
// 'comp' package.
Model * newModel = new Model(3,1);
// The following will fail with an error, because addSpecies()
// will first check that the parent of the given object has
// namespaces declared, and will discover that s1 does but
// newModel does not.
// newModel->addSpecies(s1);
// However, if we disable the 'comp' package on s1, then
// the call to addSpecies will work.
s1->disablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1",
"comp");
newModel->addSpecies(s1);
Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
enablePackage(const std::string& pkgURI, const std::string& pkgPrefix, bool flag)
int SBMLDocument::enableDefaultNS ( const std::string &  package,
bool  flag 
)

Set/unset default namespace to each top-level element defined in the given package extension.

This works by adding a xmlns="..." attribute. No prefix will be written when writing elements defined in the given package extension if true is given as second argument.

Parameters
packagethe name or URI of the package extension.
flagboolean value to indicate whether to write a namespace prefix.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Examples:
example2-L3.cpp.
int SBase::enablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix,
bool  flag 
)
inherited

Enables or disables the given SBML Level 3 package on this object.

This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase::disablePackage(const std::string& pkgURI, const std::string& pkgPrefix).

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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
disablePackage(const std::string& pkgURI, const std::string& pkgPrefix)
Examples:
addLayout.cpp.
bool SBMLDocument::expandFunctionDefinitions ( )

Removes FunctionDefinition constructs from the document and expands any instances of their use within <math> elements.

For example, suppose a Model contains a FunctionDefinition with identifier "f" representing the math expression: f(x, y) = x * y. Suppose further that there is a reaction in which the <math> element of the KineticLaw object contains f(s, p), where s and p are other identifiers defined in the model. The outcome of invoking this method is that the <math> of the KineticLaw now represents the expression s * p and the model no longer contains any FunctionDefinition objects.

Returns
bool true if the transformation was successful, false, otherwise.
Note
This function will check the consistency of a model before attemptimg the transformation. If the model is not valid SBML, the transformation will not be performed and the function will return false.
bool SBMLDocument::expandInitialAssignments ( )

Removes InitialAssignment constructs from the document and replaces them with appropriate values.

For example, suppose a Model contains a InitialAssignment to a symbol "k" where "k" is the identifier of a Parameter. The outcome of invoking this method is that the "value" attribute of the Parameter definition is set to the result calculated using the InitialAssignment object's <math> formula, and the corresponding InitialAssignment is then removed from the Model.

Returns
bool true if the transformation was successful, false, otherwise.
Note
This function will check the consistency of a model before attemptimg the transformation. If the model is not valid SBML, the transformation will not be performed and the function will return false. As part of that process, this method will check that it has values for any components referred to by the <math> elements of InitialAssignment objects. In cases where not all of the values have been declared (e.g., if the mathematical expression refers to model entities that have no declared values), the InitialAssignment in question will not be removed and this method will return false.
List * SBMLDocument::getAllElements ( ElementFilter filter = NULL)
virtual

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

Parameters
filtera pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.
Returns
a List of pointers to all children objects.

Reimplemented from SBase.

Examples:
getAllElementsWithNotes.cpp, renameSId.cpp, setIdFromNames.cpp, and setNamesFromIds.cpp.
List * SBase::getAllElementsFromPlugins ( ElementFilter filter = NULL)
virtualinherited

Returns a List of all child SBase objects contained in SBML package plug-ins.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.

Parameters
filtera pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.
Returns
a pointer to a List of pointers to all children objects from plug-ins.
SBase * SBase::getAncestorOfType ( int  type,
const std::string  pkgName = "core" 
)
inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. 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 from the given pkgName.

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 SBMLTypeCode_t value, or NULL if no ancestor exists.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the "core" namespace alone, not find any corresponding elements, and return NULL.
const SBase * SBase::getAncestorOfType ( int  type,
const std::string  pkgName = "core" 
) const
inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. 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 from the given pkgName.

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 SBMLTypeCode_t value, or NULL if no ancestor exists.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the "core" namespace alone, not find any corresponding elements, and return NULL.
XMLNode * 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(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
XMLNode * SBase::getAnnotation ( ) const
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(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
std::string 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. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
See also
getAnnotation()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
Examples:
printAnnotation.cpp.
std::string SBase::getAnnotationString ( ) const
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. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
See also
getAnnotation()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
unsigned int SBase::getColumn ( ) const
inherited

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

Returns
the column number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.
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 * SBase::getCVTerm ( unsigned int  n)
inherited

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

Parameters
nunsigned int the index of the CVTerm to retrieve.
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
List * 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.
List * SBase::getCVTerms ( ) const
inherited

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

Returns
the list of CVTerms for this SBML object.
unsigned int SBMLDocument::getDefaultLevel ( )
static

The default SBML Level of new SBMLDocument objects.

This "default Level" corresponds to the most recent SBML specification Level available at the time libSBML version 5.15.3 was released. The default Level is used by SBMLDocument if no Level is explicitly specified at the time of the construction of an SBMLDocument instance.
Returns
an integer indicating the most recent SBML specification Level.
See also
getDefaultVersion()
Examples:
convertSBML.cpp.
unsigned int SBMLDocument::getDefaultVersion ( )
static

The default Version of new SBMLDocument objects.

This "default Version" corresponds to the most recent Version within the most recent Level of SBML available at the time libSBML version 5.15.3 was released. The default Version is used by SBMLDocument if no Version is explicitly specified at the time of the construction of an SBMLDocument instance.
Returns
an integer indicating the most recent SBML specification Version.
See also
getDefaultLevel()
Examples:
convertSBML.cpp.
SBasePlugin * SBase::getDisabledPlugin ( unsigned int  n)
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
nthe index of the disabled plug-in to return.
Returns
the nth disabled plug-in object (the libSBML extension interface) of a package extension.
See also
getNumDisabledPlugins()
getPlugin(const std::string& package)
const SBasePlugin * SBase::getDisabledPlugin ( unsigned int  n) const
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
nthe index of the disabled plug-in to return.
Returns
the nth disabled plug-in object (the libSBML extension interface) of a package extension.
See also
getNumDisabledPlugins()
getPlugin(const std::string& package)
const SBase * SBase::getElementByMetaId ( const std::string &  metaid) const
inherited

Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found.

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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Parameters
metaidstring representing the "metaid" attribute value of the object to find.
Returns
pointer to the first element found with the given meta-identifier.
SBase * SBMLDocument::getElementByMetaId ( const std::string &  metaid)
virtual

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

Parameters
metaidstring representing the metaid of the object to find.
Returns
pointer to the first element found with the given metaid.

Reimplemented from SBase.

const SBase * SBase::getElementBySId ( const std::string &  id) const
inherited

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

Parameters
idstring representing the "id" attribute value of the object to find.
Returns
pointer to the first element found with the given identifier.
SBase * SBMLDocument::getElementBySId ( const std::string &  id)
virtual

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

Parameters
idstring representing the id of the object to find.
Returns
pointer to the first element found with the given id.

Reimplemented from SBase.

Examples:
renameSId.cpp.
const string & SBMLDocument::getElementName ( ) const
virtual

Returns the XML element name of this object, which for SBMLDocument, is always "sbml".

Returns
the name of this element, i.e., "sbml".

Reimplemented from SBase.

const SBMLError * SBMLDocument::getError ( unsigned int  n) const

Returns the nth error or warning encountered during parsing, consistency checking, or attempted translation of this model.

Callers can use method XMLError::getSeverity() on the result to assess the severity of the problem. The possible severity levels range from informational messages to fatal errors.

Returns
the error or warning indexed by integer n, or return NULL if n > (getNumErrors() - 1).
Parameters
nthe integer index of the error sought.
See also
SBMLDocument::getNumErrors()
Examples:
createExampleSBML.cpp, and validateSBML.cpp.
SBMLErrorLog * SBMLDocument::getErrorLog ( )

Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model.

Returns
the SBMLErrorLog used for this SBMLDocument.
See also
SBMLDocument::getNumErrors()
Examples:
echoSBML.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.
const SBMLErrorLog * SBMLDocument::getErrorLog ( ) const

Returns a constant pointer to the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model.

Returns
the SBMLErrorLog used for this SBMLDocument.
See also
SBMLDocument::getNumErrors()
const SBMLError * SBMLDocument::getErrorWithSeverity ( unsigned int  n,
unsigned int  severity 
) const

Returns the nth error or warning with the given severity encountered during parsing, consistency checking, or attempted translation of this model.

Returns
the error or warning indexed by integer n, or return NULL if n > (getNumErrors(severity) - 1).
Parameters
nthe integer index of the error sought.
severitythe severity of the error sought.
See also
SBMLDocument::getNumErrors()
const string & SBase::getId ( ) const
virtualinherited

Returns the value of the "id" attribute of this SBML object, if it has one, or the "variable" attribute of a Rule, or the "symbol" attribute of an InitialAssignment.

Note
Because of the inconsistent behavior of this function with respect to assignments and rules, it is now recommended to use the getIdAttribute() function instead.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the "variable" attribute (for the rules and event assignments) or the "symbol" attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a "variable" nor a "symbol" attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual "id" attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns
the id of this SBML object, or the "variable" if the object is a Rule, or the "symbol" if the object is an InitialAssignment.
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()

Reimplemented in Rule, Layout, EventAssignment, Model, Compartment, InitialAssignment, Species, Event, UnitDefinition, Reaction, Parameter, Submodel, Group, Dimensions, FunctionDefinition, Member, GraphicalObject, ExternalModelDefinition, Point, FluxBound, CompartmentType, SpeciesType, Objective, Transition, GeneProductAssociation, Deletion, FluxObjective, OutwardBindingSite, Input, ListOfMembers, BoundingBox, Output, QualitativeSpecies, SpeciesFeature, MultiSpeciesType, GeneProductRef, GeneProduct, Port, SimpleSpeciesReference, SpeciesFeatureType, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, GeneAssociation, InSpeciesTypeBond, SubListOfSpeciesFeatures, PossibleSpeciesFeatureValue, and CompartmentReference.

Examples:
getAllElementsWithNotes.cpp, printAnnotation.cpp, printNotes.cpp, setIdFromNames.cpp, and setNamesFromIds.cpp.
const string & SBase::getIdAttribute ( ) const
inherited

Returns the value of the "id" attribute of this SBML object.

Note
Because of the inconsistent behavior of the old SBase::getId() function with respect to assignments and rules, it is now recommended to use this getIdAttribute() function instead.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the "variable" attribute (for the rules and event assignments) or the "symbol" attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a "variable" nor a "symbol" attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual "id" attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns
the id of this SBML object, if set and valid for this level and version of SBML; an empty string otherwise.
See also
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()
unsigned int SBase::getLevel ( ) const
inherited

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

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.)
Returns
the SBML level of this SBML object.
See also
getVersion()
getNamespaces()
getPackageVersion()
Examples:
addLayout.cpp, convertSBML.cpp, and printSBML.cpp.
unsigned int SBase::getLine ( ) const
inherited

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

Returns
the line number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.
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()
std::string SBMLDocument::getLocationURI ( ) const

Get the location of this SBMLDocument.

If this document was read from a file or had its location set manually, that filename or set location will be returned, otherwise, an empty string is returned.

std::string SBMLDocument::getLocationURI ( )

Get the location of this SBMLDocument.

If this document was read from a file or had its location set manually, that filename or set location will be returned, otherwise, an empty string is returned.

const string & SBase::getMetaId ( ) const
inherited

Returns 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object.
See also
isSetMetaId()
setMetaId(const std::string& metaid)
Examples:
addingEvidenceCodes_2.cpp.
string & SBase::getMetaId ( )
inherited

Returns 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object, as a string.
See also
isSetMetaId()
setMetaId(const std::string& metaid)
const Model * SBMLDocument::getModel ( ) const

Returns the Model object stored in this SBMLDocument.

It is important to note that this method does not create a Model instance. The model in the SBMLDocument must have been created at some prior time, for example using SBMLDocument::createModel() or SBMLDocument::setModel(). This method returns NULL if a model does not yet exist.

Returns
the Model contained in this SBMLDocument, or NULL if no such model exists.
See also
createModel()
Examples:
addCVTerms.cpp, addingEvidenceCodes_1.cpp, addingEvidenceCodes_2.cpp, addLayout.cpp, addModelHistory.cpp, appendAnnotation.cpp, createExampleSBML.cpp, printAnnotation.cpp, printMath.cpp, printNotes.cpp, printSBML.cpp, printUnits.cpp, SBMLHttpResolverExample.cpp, setIdFromNames.cpp, setNamesFromIds.cpp, translateL3Math.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
Model * SBMLDocument::getModel ( )

Returns the Model object stored in this SBMLDocument.

It is important to note that this method does not create a Model instance. The model in the SBMLDocument must have been created at some prior time, for example using SBMLDocument::createModel() or SBMLDocument::setModel(). This method returns NULL if a model does not yet exist.

Returns
the Model contained in this SBMLDocument.
See also
createModel()
ModelHistory * SBase::getModelHistory ( ) const
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.
ModelHistory * 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.
const string & SBase::getName ( ) const
virtualinherited

Returns the value of the "name" attribute of this SBML object.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

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.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a "name" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write "name" attributes for those objects.

Returns
the name of this SBML object, or the empty string if not set or unsettable.
See also
getIdAttribute()
isSetName()
setName(const std::string& sid)
unsetName()

Reimplemented in Layout, Model, Compartment, Species, Event, UnitDefinition, Reaction, Parameter, Submodel, Group, ExternalModelDefinition, FunctionDefinition, FluxBound, Member, OutwardBindingSite, Deletion, CompartmentType, SpeciesType, Input, Objective, MultiSpeciesType, SpeciesFeature, GeneProductAssociation, Transition, SpeciesFeatureType, SpeciesTypeComponentMapInProduct, Output, SpeciesTypeInstance, SpeciesTypeComponentIndex, Port, FluxObjective, SubListOfSpeciesFeatures, QualitativeSpecies, ListOfMembers, InSpeciesTypeBond, PossibleSpeciesFeatureValue, GeneProductRef, CompartmentReference, GeneProduct, and SimpleSpeciesReference.

Examples:
setIdFromNames.cpp, and setNamesFromIds.cpp.
XMLNamespaces * SBMLDocument::getNamespaces ( ) const
virtual

Returns a list of XML Namespaces associated with the XML content of this SBML document.

Returns
the XML Namespaces associated with this SBML object.

Reimplemented from SBase.

Examples:
createExampleSBML.cpp.
XMLNode * 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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
XMLNode * SBase::getNotes ( ) const
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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
std::string 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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
printNotes.cpp, and SBMLHttpResolverExample.cpp.
std::string SBase::getNotesString ( ) const
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 (and in SBML Level 3, the "message" subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
unsigned int 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.
unsigned int SBase::getNumDisabledPlugins ( ) const
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Returns
the number of disabled plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
unsigned int SBMLDocument::getNumErrors ( ) const
unsigned int SBMLDocument::getNumErrors ( unsigned int  severity) const

Returns the number of errors or warnings encountered with the given severity during parsing, consistency checking, or attempted translation of this model.

Parameters
severitythe severity of the error sought.
Returns
the number of errors or warnings encountered.
See also
SBMLDocument::getError(unsigned int n)
unsigned int SBase::getNumPlugins ( ) const
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
See also
getPlugin(unsigned int n)
unsigned int SBase::getObjectVersion ( ) const
inherited

Returns the Version within the SBML Level of the actual object.

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.)
Returns
the SBML version of this SBML object.
const std::string & SBase::getPackageName ( ) const
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.
bool SBMLDocument::getPackageRequired ( const std::string &  package)

Returns the required attribute of the given package extension.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
Returns
Boolean flag indicating whether the package is flagged as being required.
unsigned int SBase::getPackageVersion ( ) const
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 * 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()
const SBase * SBase::getParentSBMLObject ( ) const
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()
bool SBMLDocument::getPkgRequired ( const std::string &  package)

Returns the required attribute of the given package extension.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
Returns
a Boolean value indicating whether the package is flagged as being required in this SBML document.
SBasePlugin * SBase::getPlugin ( const std::string &  package)
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
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.
See also
getPlugin(unsigned int n)
Examples:
addLayout.cpp, convertLayout.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, groups_example1.cpp, groups_example2.cpp, qual_example1.cpp, SBMLHttpResolverExample.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.
const SBasePlugin * SBase::getPlugin ( const std::string &  package) const
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
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.
See also
getPlugin(unsigned int n)
SBasePlugin * SBase::getPlugin ( unsigned int  n)
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return.
Returns
the nth plug-in object (the libSBML extension interface) of a package extension.
See also
getNumPlugins()
getPlugin(const std::string& package)
const SBasePlugin * SBase::getPlugin ( unsigned int  n) const
inherited

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

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return.
Returns
the nth plug-in object (the libSBML extension interface) of a package extension.
See also
getNumPlugins()
getPlugin(const std::string& package)
std::string SBase::getPrefix ( ) const
inherited

Returns the XML namespace prefix of this element.

This reports the XML namespace prefix chosen for this class of object in the current SBML document. This may be an empty string if the component has no explicit prefix (for instance, if it is a core SBML object placed in the default SBML namespace of the document). If it is not empty, then it corresponds to the XML namespace prefix used set the object, whatever that may be in a given SBML document.

Returns
a text string representing the XML namespace prefix.
BiolQualifierType_t SBase::getResourceBiologicalQualifier ( std::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 values from the enumeration type BiolQualifierType_t.

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 value from the enumeration type BiolQualifierType_t.

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 in the enumeration BiolQualifierType_t are up to date with MIRIAM at the time of a given libSBML release. The set of values may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
ModelQualifierType_t SBase::getResourceModelQualifier ( std::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 values from the enumeration type ModelQualifierType_t.

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 value from the enumeration type ModelQualifierType_t.

Parameters
resourcestring representing the resource; e.g., "http://www.geneontology.org/#GO:0005892".
Returns
the ModelQualifierType_t value associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values in the enumeration ModelQualifierType_t are up to date with MIRIAM at the time of a given libSBML release. The set of values may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
const SBMLDocument * SBase::getSBMLDocument ( ) const
inherited

Returns the SBMLDocument object containing this object instance.

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

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

Returns
the parent SBMLDocument object of this SBML object.
See also
getParentSBMLObject()
getModel()
SBMLDocument * 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()
int SBase::getSBOTerm ( ) const
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.
Examples:
printSBML.cpp.
std::string SBase::getSBOTermAsURL ( ) const
inherited

Returns the 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, or an empty string if the value is not set.
std::string SBase::getSBOTermID ( ) const
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.
int SBMLDocument::getTypeCode ( ) const
virtual

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. The set of possible type codes for core elements is defined in the enumeration SBMLTypeCode_t, and in addition, libSBML plug-ins for SBML Level 3 packages define their own extra enumerations of type codes (e.g., SBMLLayoutTypeCode_t for the Level 3 Layout package). Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName() method on the object.
Returns
the SBML type code for this object: SBML_DOCUMENT (default).
Warning
The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
See also
SBMLDocument::getElementName()
getPackageName()

Reimplemented from SBase.

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

Gets the namespace URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/layout/version1".

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.

Returns
the URI of this element, as a text string.
See also
getSBMLDocument()
getPackageName()
void * SBase::getUserData ( ) const
inherited

Returns the user data that has been previously set via setUserData().

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
the user data of this node, or NULL if no user data has been set.
See also
ASTNode::setUserData(void *userData)
unsigned int SBase::getVersion ( ) const
inherited

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

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.)
Returns
the SBML version of this SBML object.
See also
getLevel()
getNamespaces()
Examples:
addLayout.cpp, convertSBML.cpp, and printSBML.cpp.
bool 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:

  • Level 1 Version 2: "http://www.sbml.org/sbml/level1"
  • Level 2 Version 1: "http://www.sbml.org/sbml/level2"
  • Level 2 Version 2: "http://www.sbml.org/sbml/level2/version2"
  • Level 2 Version 3: "http://www.sbml.org/sbml/level2/version3"
  • Level 2 Version 4: "http://www.sbml.org/sbml/level2/version4"
  • Level 2 Version 5: "http://www.sbml.org/sbml/level2/version5"
  • Level 3 Version 1 Core: "http://www.sbml.org/sbml/level3/version1/core"
  • Level 3 Version 2 Core: "http://www.sbml.org/sbml/level3/version2/core"
Returns
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
bool SBMLDocument::isDisabledIgnoredPackage ( const std::string &  pkgURI)

Returns true if the given package extension is one of an ignored packages that has been disabled, otherwise returns false.

An ignored package is one that is defined to be used in this SBML document, but the package is not enabled in this copy of libSBML. It may have been disabled to avoid reproducing the package information when writing out the file.

Parameters
pkgURIthe URI of the package extension.
Returns
a Boolean, true if the package is being ignored and false otherwise.
bool SBMLDocument::isEnabledDefaultNS ( const std::string &  package)

Returns true if a default namespace is added to each top-level element defined in the given package extension, otherwise returns false.

This basically checks if the attribute xmlns="..." is present.

Parameters
packagethe name or URI of the package extension.
Returns
a boolean indicating whether the given package's default namespace is enabled.
bool SBMLDocument::isIgnoredPackage ( const std::string &  pkgURI)

Returns true if the given package extension is one of an ignored packages, otherwise returns false.

An ignored package is one that is defined to be used in this SBML document, but the package is not enabled in this copy of libSBML.

Parameters
pkgURIthe URI of the package extension.
Returns
a Boolean, true if the package is being ignored and false otherwise.
bool SBMLDocument::isIgnoredPkg ( const std::string &  pkgURI)

Returns true if the given package extension is one of ignored packages, otherwise returns false.

An ignored package is one that is defined to be used in this SBML document, but the package is not enabled in this copy of libSBML.

Parameters
pkgURIthe URI of the package extension.
Returns
a boolean indicating whether the given package is being ignored.
bool SBase::isPackageEnabled ( const std::string &  pkgName) const
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 SBase::isPackageURIEnabled ( const std::string &  pkgURI) const
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 SBase::isPkgEnabled ( const std::string &  pkgName) const
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 SBase::isPkgURIEnabled ( const std::string &  pkgURI) const
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 SBase::isSetAnnotation ( ) const
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(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
Examples:
printAnnotation.cpp.
bool SBase::isSetId ( ) const
virtualinherited

Predicate returning true if a call to getId() returns a non-empty string.

This means that for most objects, this function will return true if its "id" attribute is set, and false if it is not, or if the object has no "id" attribute at all. However, for an EventAssignment or a Rule, isSetId() checks whether the "variable" attribute is set, and for an InitialAssignment, it checks whether the "symbol" attribute is set. Because those elements will also have an "id" attribute in SBML Level 3 Version 2 which isSetId() will not check, the function itself is deprecated, and it is recommended to use isSetIdAttribute() in all cases where one needs to know whether the "id" attribute is set, and to use EventAssignment::isSetVariable(), Rule::isSetVariable() and InitialAssignment::isSetSymbol() when the status of the "variable" or "symbol" attributes need to be checked.

Note
Because of the inconsistent behavior of this function with respect to assignments and rules, it is now recommended to use the isSetIdAttribute() function instead.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the "variable" attribute (for the rules and event assignments) or the "symbol" attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a "variable" nor a "symbol" attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual "id" attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns
true if the "id" attribute of this SBML object is set, false otherwise.
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
unsetIdAttribute()
isSetIdAttribute()

Reimplemented in Layout, Compartment, Model, Species, Event, Reaction, UnitDefinition, Parameter, Group, Submodel, Member, FunctionDefinition, Dimensions, GeneProductAssociation, GraphicalObject, Input, Objective, FluxObjective, CompartmentType, ExternalModelDefinition, Point, SpeciesType, QualitativeSpecies, FluxBound, Output, Transition, ListOfMembers, Deletion, GeneProduct, GeneProductRef, OutwardBindingSite, SimpleSpeciesReference, BoundingBox, MultiSpeciesType, SpeciesFeature, Port, SpeciesFeatureType, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, SubListOfSpeciesFeatures, GeneAssociation, InSpeciesTypeBond, PossibleSpeciesFeatureValue, and CompartmentReference.

Examples:
getAllElementsWithNotes.cpp, printAnnotation.cpp, printNotes.cpp, setIdFromNames.cpp, and setNamesFromIds.cpp.
bool SBase::isSetIdAttribute ( ) const
inherited

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

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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the "variable" attribute (for the rules and event assignments) or the "symbol" attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a "variable" nor a "symbol" attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual "id" attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns
true if the "id" attribute of this SBML object is set, false otherwise.
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
unsetIdAttribute()
bool SBase::isSetMetaId ( ) const
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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
true if the "metaid" attribute of this SBML object is set, false otherwise.
See also
getMetaId()
setMetaId(const std::string& metaid)
Examples:
addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.
bool SBMLDocument::isSetModel ( ) const

Returns true if the Model object has been set, otherwise returns false.

Returns
true if the Model object has been set
bool 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 SBase::isSetName ( ) const
virtualinherited

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

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

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.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a "name" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write "name" attributes for those objects.

Returns
true if the "name" attribute of this SBML object is set, false otherwise.
See also
getName()
setName(const std::string& sid)
unsetName()

Reimplemented in Layout, Compartment, Model, Species, Event, Reaction, UnitDefinition, Parameter, Submodel, Group, Member, FunctionDefinition, Input, ExternalModelDefinition, GeneProductAssociation, FluxBound, QualitativeSpecies, Output, Objective, OutwardBindingSite, Deletion, FluxObjective, CompartmentType, SpeciesType, MultiSpeciesType, Transition, GeneProductRef, SpeciesFeature, ListOfMembers, SpeciesFeatureType, SpeciesTypeComponentMapInProduct, GeneProduct, SpeciesTypeInstance, SpeciesTypeComponentIndex, Port, SubListOfSpeciesFeatures, InSpeciesTypeBond, PossibleSpeciesFeatureValue, CompartmentReference, and SimpleSpeciesReference.

Examples:
setIdFromNames.cpp.
bool SBase::isSetNotes ( ) const
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(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
getAllElementsWithNotes.cpp, printNotes.cpp, and SBMLHttpResolverExample.cpp.
bool SBMLDocument::isSetPackageRequired ( const std::string &  package)

Returns true if the required attribute of the given package extension is defined, otherwise returns false.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
Returns
a Boolean indicating whether the package's 'required' flag is set.
bool SBMLDocument::isSetPkgRequired ( const std::string &  package)

Returns true if the required attribute of the given package extension is defined, otherwise returns false.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
Returns
a Boolean value.
bool SBase::isSetSBOTerm ( ) const
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.
Examples:
printSBML.cpp.
bool SBase::isSetUserData ( ) const
inherited

Predicate returning true or false depending on whether the user data of this element has been set.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
boolean, true if this object's user data has been set, false otherwise.
bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase sb)
inherited

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

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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase sb) const
inherited

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

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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool SBase::matchesSBMLNamespaces ( const SBase sb)
inherited

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

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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is the same as sb's, false otherwise.
bool SBase::matchesSBMLNamespaces ( const SBase sb) const
inherited

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

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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is the same as sb's, false otherwise.
SBMLDocument & SBMLDocument::operator= ( const SBMLDocument rhs)

Assignment operator for SBMLDocument.

Parameters
rhsthe object whose values are used as the basis of the assignment.
void SBMLDocument::printErrors ( std::ostream &  stream = std::cerr) const

Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document.

It prints the text to the stream given by the optional parameter stream. If no parameter is given, it prints the output to the standard error stream.

If no errors have occurred, i.e., getNumErrors() == 0, no output will be sent to the stream.

The format of the output is:

  N error(s):
    line NNN: (id) message
Parameters
streamthe ostream or ostringstream object indicating where the output should be printed.
See also
getNumErrors()
getErrorLog()
SBMLDocument::getError(unsigned int n)
Examples:
addCustomValidator.cpp, addCVTerms.cpp, addingEvidenceCodes_1.cpp, addingEvidenceCodes_2.cpp, addLayout.cpp, addModelHistory.cpp, appendAnnotation.cpp, callExternalValidator.cpp, convertCobraToFbc.cpp, convertFbcToCobra.cpp, convertSBML.cpp, createExampleSBML.cpp, echoSBML.cpp, flattenModel.cpp, getAllElementsWithNotes.cpp, inlineFunctionDefintions.cpp, printAnnotation.cpp, printMath.cpp, printNotes.cpp, printSBML.cpp, printUnits.cpp, promoteParameters.cpp, readSBML.cpp, renameSId.cpp, rngvalidator.cpp, setIdFromNames.cpp, setNamesFromIds.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, spec_example4.cpp, stripPackage.cpp, unsetAnnotation.cpp, unsetNotes.cpp, and validateSBML.cpp.
void SBMLDocument::printErrors ( std::ostream &  stream,
unsigned int  severity 
) const

Prints all the errors or warnings with the given severity encountered trying to parse, check, or translate this SBML document.

It prints the text to the stream given by the parameter stream.

If no errors have occurred, i.e., getNumErrors(severity) == 0, no output will be sent to the stream.

The format of the output is:

    N error(s):
      line NNN: (id) message
Parameters
streamthe ostream or ostringstream object indicating where the output should be printed.
severityof the errors sought.
See also
getNumErrors(unsigned int severity)
getErrorLog()
SBMLDocument::getErrorWithSeverity(unsigned int n, unsigned int severity)
void SBase::read ( XMLNode node,
XMLErrorSeverityOverride_t  flag = LIBSBML_OVERRIDE_DISABLED 
)
inherited

Reads (initializes) this SBML object by reading from the given XMLNode.

Parameters
nodethe XMLNode to read from.
flagan optional flag that determines how how errors are logged during the reading process.
Warning
This method is computationally expensive, because the given node has to be serialized to a string first. Attempting to serialize a large tree structure (e.g., a large Model) may consume significant computer memory and time.
int SBase::removeFromParentAndDelete ( )
virtualinherited

Removes this object from its parent.

If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented in Model, KineticLaw, SBaseRef, StoichiometryMath, Trigger, Delay, ListOf, Priority, ModelDefinition, and ReplacedBy.

int SBase::removeTopLevelAnnotationElement ( const std::string  elementName,
const std::string  elementURI = "",
bool  removeEmpty = true 
)
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.
removeEmptyif after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
replaceTopLevelAnnotationElement(const XMLNode *)
replaceTopLevelAnnotationElement(const std::string&)
void SBase::renameMetaIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

Replaces all uses of a given meta identifier attribute value with another value.

In SBML, object "meta" identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as "metaid refs", in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier 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.

Reimplemented in Port, and GraphicalObject.

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

Replaces all uses of a given SIdRef type attribute value with another value.

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to an identifier", but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

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

Parameters
oldidthe old identifier.
newidthe new identifier.

Reimplemented in Model, Species, ListOfObjectives, Compartment, Rule, KineticLaw, MultiSpeciesType, Submodel, EventAssignment, InitialAssignment, StoichiometryMath, SpeciesFeature, Delay, SBaseRef, Trigger, Input, FluxBound, Member, ReactionGlyph, Priority, QualitativeSpecies, SpeciesTypeComponentMapInProduct, OutwardBindingSite, Output, GeneralGlyph, FluxObjective, SpeciesTypeComponentIndex, SpeciesTypeInstance, Constraint, Reaction, InSpeciesTypeBond, ReplacedElement, GeneProduct, Port, PossibleSpeciesFeatureValue, CompartmentReference, SimpleSpeciesReference, GeneProductRef, AssignmentRule, RateRule, FunctionTerm, SpeciesReferenceGlyph, CompartmentGlyph, SpeciesFeatureValue, Replacing, ReferenceGlyph, TextGlyph, and SpeciesGlyph.

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

Replaces all uses of a given UnitSIdRef type attribute value with another value.

In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to a unit identifier", but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

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

Parameters
oldidthe old identifier.
newidthe new identifier.

Reimplemented in Model, Species, Compartment, Rule, KineticLaw, Parameter, EventAssignment, InitialAssignment, StoichiometryMath, Delay, FunctionDefinition, Trigger, Priority, Constraint, and Port.

int SBase::replaceTopLevelAnnotationElement ( const 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) followed by calling 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI, bool removeEmpty)
replaceTopLevelAnnotationElement(const std::string&)
int SBase::replaceTopLevelAnnotationElement ( const std::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) followed by calling 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI)
replaceTopLevelAnnotationElement(const XMLNode*)
int SBase::setAnnotation ( const XMLNode annotation)
virtualinherited

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(const XMLNode* annotation) or SBase::appendAnnotation(const std::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 value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int SBase::setAnnotation ( const std::string &  annotation)
virtualinherited

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(const XMLNode* annotation) or SBase::appendAnnotation(const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

void SBMLDocument::setConsistencyChecks ( SBMLErrorCategory_t  category,
bool  apply 
)

Controls the consistency checks that are performed when SBMLDocument::checkConsistency() is called.

This method works by adding or subtracting consistency checks from the set of all possible checks that SBMLDocument::checkConsistency() knows how to perform. This method may need to be called multiple times in order to achieve the desired combination of checks. The first argument (category) in a call to this method indicates the category of consistency/error checks that are to be turned on or off, and the second argument (apply, a boolean) indicates whether to turn it on (value of true) or off (value of false).

The possible categories (values to the argument category) are the set of values from the enumeration SBMLErrorCategory_t. The following are the possible choices:

  • LIBSBML_CAT_GENERAL_CONSISTENCY: Correctness and consistency of specific SBML language constructs. Performing this set of checks is highly recommended. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Correctness and consistency of identifiers used for model entities. An example of inconsistency would be using a species identifier in a reaction rate formula without first having declared the species. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of measurement units associated with quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_MATHML_CONSISTENCY: Syntax of MathML constructs. With respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_SBO_CONSISTENCY: Consistency and validity of SBO identifiers (if any) used in the model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_OVERDETERMINED_MODEL: Static analysis of whether the system of equations implied by a model is mathematically overdetermined. With respect to the SBML specification, this is validation rule #10601 in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_MODELING_PRACTICE: Additional checks for recommended good modeling practice. (These are tests performed by libSBML and do not have equivalent SBML validation rules.)

By default, all validation checks are applied to the model in an SBMLDocument object unless SBMLDocument::setConsistencyChecks() is called to indicate that only a subset should be applied. Further, this default (i.e., performing all checks) applies separately to each new SBMLDocument object created. In other words, each time a model is read using SBMLReader::readSBML(), SBMLReader::readSBMLFromString(), or the global functions readSBML() and readSBMLFromString(), a new SBMLDocument is created and for that document, a call to SBMLDocument::checkConsistency() will default to applying all possible checks. Calling programs must invoke SBMLDocument::setConsistencyChecks() for each such new model if they wish to change the consistency checks applied.

Parameters
categorya value drawn from SBMLErrorCategory_t indicating the consistency checking/validation to be turned on or off.
applya boolean indicating whether the checks indicated by category should be applied or not.
See also
SBMLDocument::checkConsistency()
Examples:
spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, spec_example4.cpp, and validateSBML.cpp.
void SBMLDocument::setConsistencyChecksForConversion ( SBMLErrorCategory_t  category,
bool  apply 
)

Controls the consistency checks that are performed when SBMLDocument::setLevelAndVersion() is called.

This method works by adding or subtracting consistency checks from the set of all possible checks that may be performed to avoid conversion to or from an invalid document. This method may need to be called multiple times in order to achieve the desired combination of checks. The first argument (category) in a call to this method indicates the category of consistency/error checks that are to be turned on or off, and the second argument (apply, a boolean) indicates whether to turn it on (value of true) or off (value of false).

The possible categories (values to the argument category) are the set of values from the enumeration SBMLErrorCategory_t. The following are the possible choices:

  • LIBSBML_CAT_GENERAL_CONSISTENCY: Correctness and consistency of specific SBML language constructs. Performing this set of checks is highly recommended. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Correctness and consistency of identifiers used for model entities. An example of inconsistency would be using a species identifier in a reaction rate formula without first having declared the species. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_UNITS_CONSISTENCY:

    Consistency of measurement units associated with quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_MATHML_CONSISTENCY: Syntax of MathML constructs. With respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_SBO_CONSISTENCY: Consistency and validity of SBO identifiers (if any) used in the model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_OVERDETERMINED_MODEL: Static analysis of whether the system of equations implied by a model is mathematically overdetermined. With respect to the SBML specification, this is validation rule #10601 in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications.

  • LIBSBML_CAT_MODELING_PRACTICE: Additional checks for recommended good modeling practice. (These are tests performed by libSBML and do not have equivalent SBML validation rules.)

By default, all validation checks are applied to the model in an SBMLDocument object unless SBMLDocument::setConsistencyChecks() is called to indicate that only a subset should be applied. Further, this default (i.e., performing all checks) applies separately to each new SBMLDocument object created. In other words, each time a model is read using SBMLReader::readSBML(), SBMLReader::readSBMLFromString(), or the global functions readSBML() and readSBMLFromString(), a new SBMLDocument is created and for that document, a call to SBMLDocument::checkConsistency() will default to applying all possible checks. Calling programs must invoke SBMLDocument::setConsistencyChecks() for each such new model if they wish to change the consistency checks applied.

Parameters
categorya value drawn from SBMLErrorCategory_t indicating the consistency checking/validation to be turned on or off.
applya boolean indicating whether the checks indicated by category should be applied or not.
See also
SBMLDocument::setLevelAndVersion()
void SBase::setElementText ( const std::string &  text)
protectedvirtualinherited

When overridden allows SBase elements to use the text included in between the elements tags.

The default implementation does nothing.

Parameters
textthe text string found between the element tags.
int SBase::setId ( const std::string &  sid)
virtualinherited

Sets the value of the "id" attribute of this SBML object.

The string sid is copied.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the "variable" attribute (for the rules and event assignments) or the "symbol" attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a "variable" nor a "symbol" attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual "id" attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Parameters
sidthe string to use as the identifier of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()

Reimplemented in Compartment, Layout, Species, Model, Event, Reaction, Parameter, UnitDefinition, Group, Member, Input, FunctionDefinition, Submodel, QualitativeSpecies, GeneProductAssociation, Output, FluxObjective, Objective, Dimensions, GraphicalObject, CompartmentType, GeneProduct, SpeciesType, Point, SimpleSpeciesReference, Transition, FluxBound, GeneProductRef, ListOfMembers, OutwardBindingSite, ExternalModelDefinition, BoundingBox, MultiSpeciesType, SpeciesFeature, SpeciesFeatureType, SpeciesTypeInstance, Port, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, SubListOfSpeciesFeatures, InSpeciesTypeBond, Deletion, PossibleSpeciesFeatureValue, CompartmentReference, and GeneAssociation.

Examples:
renameSId.cpp, and setIdFromNames.cpp.
int SBase::setIdAttribute ( const std::string &  sid)
virtualinherited

Sets the value of the "id" attribute of this SBML object.

The string sid is copied.
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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the "variable" attribute (for the rules and event assignments) or the "symbol" attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a "variable" nor a "symbol" attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual "id" attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Parameters
sidthe string to use as the identifier of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()
bool SBMLDocument::setLevelAndVersion ( unsigned int  level,
unsigned int  version,
bool  strict = true,
bool  ignorePackages = false 
)

Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.

This method is the principal way in libSBML to convert models between Levels and Versions of SBML. Generally, models can be converted upward without difficulty (e.g., from SBML Level 1 to Level 2, or from an earlier Version of Level 2 to the latest Version of Level 2). Sometimes models can be translated downward as well, if they do not use constructs specific to more advanced Levels of SBML.

Before calling this method, callers may check compatibility directly using the methods SBMLDocument::checkL1Compatibility(), SBMLDocument::checkL2v1Compatibility(), SBMLDocument::checkL2v2Compatibility(), SBMLDocument::checkL2v3Compatibility(), SBMLDocument::checkL2v4Compatibility(), SBMLDocument::checkL2v5Compatibility(), and SBMLDocument::checkL3v1Compatibility().

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

  • Level 1 Version 2
  • Level 2 Version 1
  • Level 2 Version 2
  • Level 2 Version 3
  • Level 2 Version 4
  • Level 2 Version 5
  • Level 3 Version 1
  • Level 3 Version 2

Strict conversion applies the additional criteria that both the source and the target model must be consistent SBML. Users can control the consistency checks that are applied using the SBMLDocument::setConsistencyChecksForConversion() method. If either the source or the potential target model have validation errors, the conversion is not performed. When a strict conversion is successful, the underlying SBML object model is altered to reflect the new level and version. Thus, information that cannot be converted (e.g. sboTerms) will be lost.

Parameters
levelthe desired SBML Level.
versionthe desired Version within the SBML Level.
strictboolean indicating whether to check consistency of both the source and target model when performing conversion (defaults to true ).
ignorePackagesboolean indicating whether the presence of packages should be ignored by the conversion routine (defaults to false ).
Returns
true if the level and version of the document were successfully set to the requested values (which may have required conversion of the model), false otherwise.
Note
Calling this method will not necessarily lead to a successful conversion. If the conversion fails, it will be logged in the error list associated with this SBMLDocument. Callers should consult getNumErrors() to find out if the conversion succeeded without problems. For conversions from Level 2 to Level 1, callers can also check the Level of the model after calling this method to find out whether it is Level 1. (If the conversion to Level 1 failed, the Level of this model will be left unchanged.)
See also
checkL1Compatibility()
checkL2v1Compatibility()
checkL2v2Compatibility()
checkL2v3Compatibility()
checkL2v4Compatibility()
checkL2v5Compatibility()
checkL3v1Compatibility()
Examples:
convertSBML.cpp.
void SBMLDocument::setLocationURI ( const std::string &  uri)

Sets the location of this SBMLDocument.

Called automatically when readSBMLFromFile is used, but may be set manually as well.

int SBase::setMetaId ( const std::string &  metaid)
inherited

Sets the value of the meta-identifier 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

The string metaid is copied.

Parameters
metaidthe identifier string to use as the value of the "metaid" attribute.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getMetaId()
isSetMetaId()
Examples:
addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.
int SBMLDocument::setModel ( const Model m)

Sets the Model for this SBMLDocument to a copy of the given Model.

Parameters
mthe new Model to use.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
createModel()
getModel()
Examples:
example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, and groups_example2.cpp.
int 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 value is drawn from the enumeration OperationReturnValues_t. 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.
Examples:
addModelHistory.cpp.
int SBase::setName ( const std::string &  name)
virtualinherited
int 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::setNotes ( const 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
createExampleSBML.cpp.
int SBase::setNotes ( const std::string &  notes,
bool  addXHTMLMarkup = false 
)
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'><p>here is my note</p></body>");
Parameters
notesan XML string that is to be used as the content of the "notes" subelement of this object.
addXHTMLMarkupa boolean 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBMLDocument::setPackageRequired ( const std::string &  package,
bool  flag 
)

Sets the required attribute value of the given package extension.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
flagBoolean value indicating whether the package is required.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Examples:
fbc_example1.cpp, groups_example1.cpp, groups_example2.cpp, and qual_example1.cpp.
int SBMLDocument::setPkgRequired ( const std::string &  package,
bool  flag 
)

Sets the value of the required attribute for the given package.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
flaga Boolean value.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Examples:
example1-L3.cpp.
int SBase::setSBOTerm ( int  value)
virtualinherited

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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
setSBOTerm(const std::string &sboid)
Examples:
groups_example1.cpp, and qual_example1.cpp.
int SBase::setSBOTerm ( const std::string &  sboid)
virtualinherited

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 SBase::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
setSBOTerm(int value)
int SBase::setUserData ( void *  userData)
inherited

Sets the user data of this element.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Parameters
userDataspecifies the new user data.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
char * 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.
XMLNode* SBase::toXMLNode ( )
inherited

Returns this element as an XMLNode.

Returns
this element as an XMLNode.
Warning
This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.
int 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 value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
See also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
Examples:
unsetAnnotation.cpp.
int SBase::unsetCVTerms ( )
inherited

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

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::unsetId ( )
virtualinherited

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

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 SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the "variable" attribute (for the rules and event assignments) or the "symbol" attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a "variable" nor a "symbol" attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual "id" attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()

Reimplemented in Model, Layout, Event, Group, Member, Input, QualitativeSpecies, GeneProductAssociation, Output, FluxObjective, Objective, Submodel, GeneProduct, Dimensions, GeneProductRef, GraphicalObject, ListOfMembers, SimpleSpeciesReference, Transition, Point, FluxBound, ExternalModelDefinition, OutwardBindingSite, Deletion, BoundingBox, MultiSpeciesType, SpeciesFeature, SpeciesFeatureType, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, Port, SpeciesTypeComponentIndex, SubListOfSpeciesFeatures, InSpeciesTypeBond, PossibleSpeciesFeatureValue, CompartmentReference, and GeneAssociation.

int SBase::unsetIdAttribute ( )
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.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
int 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. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, 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 the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::unsetModelHistory ( )
inherited

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. 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 SBase::unsetName ( )
virtualinherited

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

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

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.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a "name" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write "name" attributes for those objects.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getName()
setName(const std::string& sid)
isSetName()

Reimplemented in Compartment, Species, Model, Layout, Event, Reaction, Parameter, UnitDefinition, Group, Input, Member, QualitativeSpecies, Output, GeneProductAssociation, Submodel, FunctionDefinition, FluxObjective, Objective, GeneProduct, GeneProductRef, FluxBound, ExternalModelDefinition, OutwardBindingSite, ListOfMembers, CompartmentType, SimpleSpeciesReference, SpeciesType, Transition, Deletion, MultiSpeciesType, SpeciesFeature, SpeciesTypeComponentMapInProduct, SpeciesFeatureType, SpeciesTypeInstance, SpeciesTypeComponentIndex, SubListOfSpeciesFeatures, PossibleSpeciesFeatureValue, InSpeciesTypeBond, Port, and CompartmentReference.

int 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 value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
unsetNotes.cpp.
int SBase::unsetSBOTerm ( )
inherited

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

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::unsetUserData ( )
inherited

Unsets the user data of this element.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
unsigned int SBMLDocument::validateSBML ( )

Performs consistency checking and validation on this SBML document.

If this method returns a nonzero value (meaning, one or more consistency checks have failed for SBML document), the failures may be due to warnings or errors. Callers should inspect the severity flag in the individual SBMLError objects returned by SBMLDocument::getError() to determine the nature of the failures.

Note
unlike checkConsistency this method will write the document in order to determine all errors for the document. This will also clear the error log.
Returns
the number of failed checks (errors) encountered.
See also
SBMLDocument::checkConsistency()