libSBML Perl API
libSBML 5.8.0 Perl API
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The Submodel class was introduced by the SBML Level 3 Hierarchical Model Composition package ('comp') as the principle way by which models are structured hierarchically. Submodels are instantiations of models contained within other models. They reference another Model that is to be instantiated within its parent Model, and additionally define how that Model is to be modified before instantiation.
The Submodel object class has a required attribute "modelRef", which must reference another Model or ExternalModelDefinition object present in the SBML Document. This referenced Model is the model to be instantiated.
It also has a required attribute, "id", to give the submodel a unique identifier by which other parts of an SBML model definition can refer to it, and an optional "name" attribute of type string
. Identifiers and names must be used according to the guidelines described in the SBML specification.
The Submodel class also provides constructs that define how the referenced Model object is to be modified before it is instantiated in the enclosing model. If numerical values in the referenced model must be changed in order to fit them into their new context as part of the submodel, the changes can be handled through conversion factors. If one or more structural features in the referenced model are undesirable and should be removed, the changes can be handled through deletions. (For example, an initial assignment or reaction may not be relevant in its new context and should be removed.)
In some cases, the referenced Model may have been written with different units than the containing model. For most model elements, this is not a problem: it is already possible to have Species and Parameter objects with different units in a single model, for example, so in this case the resulting hierarchical model would be treated in exactly the same way as any other model with Species and Parameters with different units.
However, two units in SBML models are fixed and must not vary between SBML elements: time and extent. The units of time are set once per model, and affect the core elements of RateRule, KineticLaw, Delay, and the csymbols 'time' and 'delay'. Even if the model does not explicitly state what the units of time actually are, they are defined to be consistent across the model, and therefore might differ from the units of time across a parent model. To correct this imbalance, the optional attribute "timeConversionFactor" may be used, which, if defined, must reference a constant parameter in the parent model. The value of the time conversion factor should be defined such that a single unit of time in the Submodel multiplied by the time conversion factor should equal a single unit of time in the parent model.
Extent is the unit in SBML that defines how the KineticLaw of a Reaction affects species quantities: kinetic laws are defined to be in units of extent/time. No other SBML core construct is defined in terms of extent. If the effective units of extent in a submodel differ from the effective units of extent in the parent model (regardless of whether either defined what those units actually are), the optional attribute "extentConversionFactor" may be used, which, if defined, must reference a constant parameter in the parent model. The value of the extent conversion factor should be defined such that a single unit of extent in the Submodel multiplied by the extent conversion factor should equal a single unit of extent in the parent model.
If features of the referenced model must be removed, a Deletion should be added to the Submodel object. A Submodel may contain a child ListOfDeletions, which in turn may contain one or more Deletion items. Each Deletion references a single element of the referenced Model that must be removed before instantiating that Model as a submodel of the parent Model.
Public Member Functions | |
virtual bool | accept (SBMLVisitor &v) const |
Accepts the given SBMLVisitor. More... | |
int | addCVTerm (CVTerm *term, bool newBag=false) |
Adds a copy of the given CVTerm object to this SBML object. More... | |
int | addDeletion (const Deletion *deletion) |
Adds a copy of the given Deletion object to the list of deletions. 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 ¬es) |
Appends the given notes to the "notes" subelement of this object. More... | |
virtual void | clearInstantiation () |
Delete the instantiated Model*, if it exists. More... | |
virtual Submodel * | clone () const |
Creates and returns a deep copy of this Submodel object. More... | |
virtual int | convertTimeAndExtent () |
Convert all references to time and extent according to the timeConversionFactor and extentConversionFactor attributes. More... | |
Deletion * | createDeletion () |
Creates a Deletion object, adds it to the end of the deletion objects list and returns a pointer to the newly created object. More... | |
int | disablePackage (const std::string &pkgURI, const std::string &pkgPrefix) |
Disables the given SBML Level 3 package. More... | |
int | enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag) |
Enables or disables the given SBML Level 3 package. More... | |
virtual List * | getAllElements () |
Returns a List of all child SBase objects, including those nested to an arbitrary depth. More... | |
virtual List * | getAllElementsFromPlugins () |
Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
virtual List * | getAllInstantiatedElements () |
Get all instantiated sub-elements, including any elements from instantiated submodels, etc. More... | |
SBase * | getAncestorOfType (int type, const std::string pkgName="core") |
Returns the first ancestor object that has the given SBML type code. More... | |
const SBase * | getAncestorOfType (int type, const std::string pkgName="core") const |
Returns the first ancestor object that has the given SBML type code. More... | |
XMLNode * | getAnnotation () |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
XMLNode * | getAnnotation () 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 on which this object first appears in the XML representation of the SBML document. More... | |
CVTerm * | getCVTerm (unsigned int n) |
Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
List * | getCVTerms () |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
List * | getCVTerms () const |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
Deletion * | getDeletion (unsigned int n) |
Returns the deletion with the given index. More... | |
const Deletion * | getDeletion (unsigned int n) const |
Returns the deletion with the given index. More... | |
Deletion * | getDeletion (std::string id) |
Returns the deletion with the given id . More... | |
const Deletion * | getDeletion (std::string id) const |
Returns the deletion with the given id . More... | |
virtual SBase * | getElementByMetaId (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... | |
virtual SBase * | getElementBySId (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 SBML object. More... | |
virtual const std::string & | getExtentConversionFactor () const |
Returns the value of the "extentConversionFactor" attribute of this Submodel. More... | |
virtual const std::string & | getId () const |
Returns the value of the "id" attribute of this Submodel. More... | |
virtual Model * | getInstantiation () |
Get the instantiated Model this Submodel contains rules to create. More... | |
virtual const Model * | getInstantiation () const |
Get the instantiated Model this Submodel contains rules to create. 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 on which this object first appears in the XML representation of the SBML document. More... | |
const ListOfDeletions * | getListOfDeletions () const |
Returns the ListOf object that holds all deletions. More... | |
ListOfDeletions * | getListOfDeletions () |
Returns the ListOf object that holds all deletions. More... | |
const std::string & | getMetaId () const |
Returns the value of the "metaid" attribute of this object. More... | |
std::string & | getMetaId () |
Returns the value of the "metaid" attribute of this object. More... | |
const Model * | getModel () const |
Returns the Model object in which the current object is located. More... | |
ModelHistory * | getModelHistory () const |
Returns the ModelHistory object, if any, attached to this object. More... | |
ModelHistory * | getModelHistory () |
Returns the ModelHistory object, if any, attached to this object. More... | |
virtual const std::string & | getModelRef () const |
Returns the value of the "modelRef" attribute of this Submodel. More... | |
virtual const std::string & | getName () const |
Returns the value of the "name" attribute of this Submodel. More... | |
virtual XMLNamespaces * | getNamespaces () const |
Returns a list of the XML Namespaces declared on this SBML document. More... | |
XMLNode * | getNotes () |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More... | |
XMLNode * | getNotes () 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 | getNumDeletions () const |
Returns the number of deletions for this Submodel. More... | |
unsigned int | getNumPlugins () const |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
const std::string & | getPackageName () const |
Returns the package name of this plugin object. More... | |
const std::string & | getPackageURI () const |
Returns the XML namespace (URI) of the package extension of this object. More... | |
unsigned int | getPackageVersion () const |
Returns the package version of the package extension of this plugin object. More... | |
SBase * | getParentSBMLObject () |
Returns the parent SBML object containing this object. More... | |
const SBase * | getParentSBMLObject () const |
Returns the parent SBML object containing this object. More... | |
SBasePlugin * | getPlugin (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 SBasePlugin * | getPlugin (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... | |
SBasePlugin * | getPlugin (unsigned int n) |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
const SBasePlugin * | getPlugin (unsigned int n) const |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
const std::string & | getPrefix () const |
Returns the prefix of the package extension of this plugin object. 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 SBMLDocument * | getSBMLDocument () const |
Returns the SBMLDocument object containing this object instance. More... | |
SBMLDocument * | getSBMLDocument () |
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 identifiers.org 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 const std::string & | getSubstanceConversionFactor () const |
Returns the value of the "substanceConversionFactor" attribute of this Submodel. More... | |
virtual const std::string & | getTimeConversionFactor () const |
Returns the value of the "timeConversionFactor" attribute of this Submodel. More... | |
int | getTypeCode () const |
Returns the libSBML type code for this SBML object. 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... | |
virtual bool | hasRequiredAttributes () const |
Returns true if the 'submodel' attribute is set, and if getNumReferents() is exactly 1. More... | |
bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
virtual int | instantiate () |
Follow the rules set out in this object and instantiate a Model object from them. 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 | isSetExtentConversionFactor () const |
Predicate returning true or false depending on whether this Submodel's "extentConversionFactor" attribute has been set. More... | |
virtual bool | isSetId () const |
Predicate returning true or false depending on whether this Submodel's "id" attribute has been set. More... | |
bool | isSetMetaId () const |
Predicate returning true if this object's "metaid" attribute is set. More... | |
bool | isSetModelHistory () |
Predicate returning true if this object has a ModelHistory object attached to it. More... | |
virtual bool | isSetModelRef () const |
Predicate returning true or false depending on whether this Submodel's "modelRef" attribute has been set. More... | |
virtual bool | isSetName () const |
Predicate returning true or false depending on whether this Submodel's "name" attribute has been set. More... | |
bool | isSetNotes () const |
Predicate returning true if this object's "notes" subelement exists and has content. More... | |
bool | isSetSBOTerm () const |
Predicate returning true if this object's "sboTerm" attribute is set. More... | |
virtual bool | isSetSubstanceConversionFactor () const |
Predicate returning true or false depending on whether this Submodel's "substanceConversionFactor" attribute has been set. More... | |
virtual bool | isSetTimeConversionFactor () const |
Predicate returning true or false depending on whether this Submodel's "timeConversionFactor" attribute 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... | |
Submodel & | operator= (const Submodel &source) |
Assignment operator. More... | |
virtual int | performDeletions () |
Delete elements in the instantiated submodel, based on any Deletions from this Submodel's listOfDeletions. More... | |
Deletion * | removeDeletion (unsigned int index) |
Removes the deletion with the given index from the Submodel. More... | |
Deletion * | removeDeletion (const std::string &sid) |
Removes the deletion with the given identifier from the Submodel. More... | |
virtual int | removeFromParentAndDelete () |
Removes itself from its parent. More... | |
int | removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="") |
Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More... | |
virtual void | renameMetaIdRefs (std::string oldid, std::string newid) |
Renames all the MetaIdRef attributes on this element. More... | |
virtual void | renameSIdRefs (std::string oldid, std::string newid) |
Renames the conversion factor attributes on this element if oldid matches. More... | |
virtual void | renameUnitSIdRefs (std::string oldid, std::string newid) |
Renames all the UnitSIdRef attributes on this element. More... | |
virtual int | replaceElement (SBase *toReplace, SBase *replacement) |
Delete the element in question from the stored instantiation object, and replace all references to it with references to the replacement object. 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... | |
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... | |
virtual int | setExtentConversionFactor (const std::string &id) |
Sets the value of the "extentConversionFactor" attribute of this Submodel. More... | |
virtual int | setId (const std::string &id) |
Sets the value of the "id" attribute of this Submodel. More... | |
int | setMetaId (const std::string &metaid) |
Sets the value of the "metaid" attribute of this object. More... | |
int | setModelHistory (ModelHistory *history) |
Sets the ModelHistory of this object. More... | |
virtual int | setModelRef (const std::string &modelRef) |
Sets the value of the "modelRef" attribute of this Submodel. More... | |
virtual int | setName (const std::string &name) |
Sets the value of the "name" attribute of this Submodel. 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 ¬es, bool addXHTMLMarkup=false) |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes . 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... | |
virtual int | setSubstanceConversionFactor (const std::string &id) |
Sets the value of the "substanceConversionFactor" attribute of this Submodel. More... | |
virtual int | setTimeConversionFactor (const std::string &id) |
Sets the value of the "timeConversionFactor" attribute of this Submodel. More... | |
int | setUserData (void *userData) |
Sets the user data of this element. More... | |
Submodel (unsigned int level=CompExtension::getDefaultLevel(), unsigned int version=CompExtension::getDefaultVersion(), unsigned int pkgVersion=CompExtension::getDefaultPackageVersion()) | |
Creates a new Submodel with the given level, version, and package version. More... | |
Submodel (CompPkgNamespaces *compns) | |
Creates a new Submodel with the given CompPkgNamespaces object. More... | |
Submodel (const Submodel &source) | |
Copy constructor. More... | |
char * | toSBML () |
Returns a string consisting of a partial SBML corresponding to just this object. More... | |
int | unsetAnnotation () |
Unsets the value of the "annotation" subelement of this SBML object. More... | |
int | unsetCVTerms () |
Clears the list of CVTerm objects attached to this SBML object. More... | |
virtual int | unsetExtentConversionFactor () |
Unsets the value of the "extentConversionFactor" attribute of this Submodel. More... | |
virtual int | unsetId () |
Unsets the value of the "id" attribute of this Submodel. 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 | unsetModelRef () |
Unsets the value of the "modelRef" attribute of this Submodel. More... | |
virtual int | unsetName () |
Unsets the value of the "name" attribute of this Submodel. 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... | |
virtual int | unsetSubstanceConversionFactor () |
Unsets the value of the "substanceConversionFactor" attribute of this Submodel. More... | |
virtual int | unsetTimeConversionFactor () |
Unsets the value of the "timeConversionFactor" attribute of this Submodel. More... | |
virtual | ~Submodel () |
Destructor. More... | |
Static Public Member Functions | |
static Model * | getParentModel (SBase *child) |
Returns the Model object to which the referenced child object belongs. 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... | |
Static Protected Member Functions | |
static int | removeFromParentAndPorts (SBase *todelete) |
A static function for removing elements–it is illegal to reference an element from a port that has been deleted or replaced, but if it happens, we need to not actually crash. More... | |
Submodel::Submodel | ( | unsigned int | level = CompExtension::getDefaultLevel() , |
unsigned int | version = CompExtension::getDefaultVersion() , |
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unsigned int | pkgVersion = CompExtension::getDefaultPackageVersion() |
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Creates a new Submodel with the given level, version, and package version.
level | the SBML Level |
version | the Version within the SBML Level |
pkgVersion | the version of the package |
Submodel::Submodel | ( | CompPkgNamespaces * | compns | ) |
Creates a new Submodel with the given CompPkgNamespaces object.
compns | the namespace to use |
Submodel::Submodel | ( | const Submodel & | source | ) |
Copy constructor.
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virtual |
Destructor.
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virtual |
Accepts the given SBMLVisitor.
v.visit()
, which indicates whether or not the Visitor would like to visit the SBML object's next sibling object (if available). Implements SBase.
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inherited |
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if 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. |
int Submodel::addDeletion | ( | const Deletion * | deletion | ) |
Adds a copy of the given Deletion object to the list of deletions.
deletion | the Deletion object to be added to the list of deletions. Fails if the added deletion is NULL, does not match the level/version/package of the parent object, or cannot be added to the list of deletions. |
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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.
annotation | an XML structure that is to be copied and appended to the content of the "annotation" subelement of this object |
Reimplemented in Model, and SpeciesReference.
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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.
annotation | an XML string that is to be copied and appended to the content of the "annotation" subelement of this object |
Reimplemented in Model, and SpeciesReference.
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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.
notes | an XML node structure that is to appended to the content of the "notes" subelement of this object |
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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.
notes | an XML string that is to appended to the content of the "notes" subelement of this object |
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Delete the instantiated Model*, if it exists.
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virtual |
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virtual |
Convert all references to time and extent according to the timeConversionFactor and extentConversionFactor attributes.
Deletion * Submodel::createDeletion | ( | ) |
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inherited |
Disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
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inherited |
Enables or disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (true ) or disable (false ) the package |
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virtual |
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virtualinherited |
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Get all instantiated sub-elements, including any elements from instantiated submodels, etc.
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inherited |
Returns the first ancestor object that has the given SBML type code.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
type | the 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 |
NULL
if no ancestor exists.
|
inherited |
Returns the first ancestor object that has the given SBML type code.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
type | the 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 |
NULL
if no ancestor exists.
|
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.
|
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.
|
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.
|
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.
|
inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
Deletion * Submodel::getDeletion | ( | unsigned int | n | ) |
Returns the deletion with the given index.
If the index is invalid, NULL
is returned.
n | the index number of the Deletion to get. |
const Deletion * Submodel::getDeletion | ( | unsigned int | n | ) | const |
Returns the deletion with the given index.
If the index is invalid, NULL
is returned.
n | the index number of the Deletion to get. |
Deletion * Submodel::getDeletion | ( | std::string | id | ) |
Returns the deletion with the given id
.
If the id is invalid, NULL
is returned.
id | the id of the Deletion to get. |
id
. const Deletion * Submodel::getDeletion | ( | std::string | id | ) | const |
Returns the deletion with the given id
.
If the id is invalid, NULL
is returned.
id | the id of the Deletion to get. |
id
.
|
virtual |
|
virtual |
|
virtual |
Returns the XML element name of this SBML object.
Implements SBase.
|
virtual |
|
virtual |
|
virtual |
Get the instantiated Model this Submodel contains rules to create.
Calls instantiate() automatically if this operation has not yet been performed, and/or if the operation failed the last time it was called.
|
virtual |
Get the instantiated Model this Submodel contains rules to create.
Calls instantiate() automatically if this operation has not yet been performed, and/or if the operation failed the last time it was called.
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Returns the line number on which this object first appears in the XML representation of the SBML document.
const ListOfDeletions * Submodel::getListOfDeletions | ( | ) | const |
ListOfDeletions * Submodel::getListOfDeletions | ( | ) |
|
inherited |
Returns the value of the "metaid" attribute of this object.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
|
inherited |
Returns the value of the "metaid" attribute of this object.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL
if none exist.
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL
if none exist.
|
virtual |
|
virtual |
|
virtualinherited |
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.
Reimplemented in SBMLDocument.
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
The "notes" element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
The "notes" element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
|
inherited |
Returns the content of the "notes" subelement of this object as a string.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
|
inherited |
Returns the content of the "notes" subelement of this object as a string.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
unsigned int Submodel::getNumDeletions | ( | ) | const |
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
|
inherited |
Returns the package name of this plugin object.
|
inherited |
Returns the XML namespace (URI) of the package extension of this object.
|
inherited |
Returns the package version of the package extension of this plugin object.
Returns the Model object to which the referenced child object belongs.
|
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.
|
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.
|
inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
|
inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
|
inherited |
Returns the prefix of the package extension of this plugin object.
|
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
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
resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892" . |
|
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
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
resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892" . |
|
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.
|
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.
|
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.
-1
if the value is not set.
|
inherited |
Returns the identifiers.org URL representation of the "sboTerm" attribute of this object.
This method returns the entire SBO identifier as a text string in the form "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN".
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.
|
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.
|
virtual |
|
virtual |
|
virtual |
Returns the libSBML type code for this SBML object.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes.
Reimplemented from SBase.
|
inherited |
Returns the user data that has been previously set via setUserData().
NULL
if no user data has been set.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
|
virtual |
Returns true if the 'submodel' attribute is set, and if getNumReferents() is exactly 1.
|
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:
"http://www.sbml.org/sbml/level1"
"http://www.sbml.org/sbml/level2"
"http://www.sbml.org/sbml/level2/version2"
"http://www.sbml.org/sbml/level2/version3"
"http://www.sbml.org/sbml/level2/version4"
"http://www.sbml.org/sbml/level3/version1/core"
true
if the level, version and namespace values of this SBML object correspond to a valid set of values, false
otherwise.
|
virtual |
Follow the rules set out in this object and instantiate a Model object from them.
Is recursive, in that if the instantiated Model contains any Submodel objects, those Submodels will themselves be instantiated. If an instantiated model previously existed, it is deleted and a new one is created. For this reason, call this function only once, or, better yet, just call 'getInstantiation'
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
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.
true
if a "annotation" subelement exists, false
otherwise.
|
virtual |
|
virtual |
|
inherited |
Predicate returning true
if this object's "metaid" attribute is set.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
true
if the "metaid" attribute of this SBML object is set, false
otherwise.
|
inherited |
Predicate returning true
if this object has a ModelHistory object attached to it.
true
if the ModelHistory of this object is set, false
otherwise.
|
virtual |
|
virtual |
|
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.
true
if a "notes" subelement exists, false
otherwise.
|
inherited |
Predicate returning true
if this object's "sboTerm" attribute is set.
true
if the "sboTerm" attribute of this SBML object is set, false
otherwise.
|
virtual |
|
virtual |
|
inherited |
Returns true
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is a subset of sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is a subset of sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are the same as the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is the same as sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are the same as the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is the same as sb's
, false
otherwise.
|
virtual |
Delete elements in the instantiated submodel, based on any Deletions from this Submodel's listOfDeletions.
Deletion * Submodel::removeDeletion | ( | unsigned int | index | ) |
Removes the deletion with the given index from the Submodel.
A pointer to the deletion that was removed is returned. If no deletion has been removed, NULL
is returned.
index | the index of the Deletion object to remove |
NULL
is returned if the given index is out of range. Deletion * Submodel::removeDeletion | ( | const std::string & | sid | ) |
Removes the deletion with the given identifier from the Submodel.
A pointer to the deletion that was removed is returned. If no deletion has been removed, NULL
is returned.
sid | string representing the identifier of the Deletion object to remove |
NULL
is returned if the given sid
is not found.
|
virtualinherited |
Removes itself from its parent.
If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, 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.
Reimplemented in Model, KineticLaw, SBaseRef, StoichiometryMath, Delay, Trigger, Priority, ListOf, ModelDefinition, and ReplacedBy.
|
staticprotectedinherited |
A static function for removing elements–it is illegal to reference an element from a port that has been deleted or replaced, but if it happens, we need to not actually crash.
This function finds and deletes all such invalid ports before deleting the object.
|
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.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
|
virtualinherited |
Renames all the MetaIdRef
attributes on this element.
This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid
. If any matches are found, the matching identifiers are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier |
newid | the new identifier |
Reimplemented in Port.
|
virtual |
Renames the conversion factor attributes on this element if oldid
matches.
Reimplemented from SBase.
|
virtualinherited |
Renames all the UnitSIdRef
attributes on this element.
This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit identifiers to the value of oldid
. If any matches are found, the matching identifiers are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier |
newid | the new identifier |
Reimplemented in Model, Species, KineticLaw, Compartment, Rule, Parameter, InitialAssignment, EventAssignment, StoichiometryMath, Delay, FunctionDefinition, Trigger, Priority, Constraint, and Port.
Delete the element in question from the stored instantiation object, and replace all references to it with references to the replacement object.
LIBSBML_INVALID_OBJECT means that this Submodel itself or one of the passed-in objects are invalid. LIBSBML_OPERATION_FAILED means that the routine failed for some othe reason.
|
inherited |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name);
with the exception that the placement of the annotation element remains the same.
annotation | XMLNode representing the replacement top level annotation |
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inherited |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name);
with the exception that the placement of the annotation element remains the same.
annotation | string representing the replacement top level annotation |
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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).
annotation | an XML structure that is to be used as the new content of the "annotation" subelement of this object |
Reimplemented in Model, and SpeciesReference.
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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).
annotation | an XML string that is to be used as the content of the "annotation" subelement of this object |
Reimplemented in Model, and SpeciesReference.
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protectedvirtualinherited |
When overridden allows SBase elements to use the text included in between the elements tags.
The default implementation does nothing.
text | the text string found between the element tags. |
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virtual |
Sets the value of the "extentConversionFactor" attribute of this Submodel.
Fails if the id is not a valid syntax for an SIdRef.
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virtual |
Sets the value of the "id" attribute of this Submodel.
Fails if the id is not a valid syntax for an SId.
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inherited |
Sets the value of the "metaid" attribute of this object.
The string metaid
is copied. The value of metaid
must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the "metaid" attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement.
metaid | the identifier string to use as the value of the "metaid" attribute |
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inherited |
Sets the ModelHistory of this object.
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
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virtual |
Sets the value of the "modelRef" attribute of this Submodel.
Fails if the modelRef is not a valid syntax for an SIdRef.
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virtual |
Sets the value of the "name" attribute of this Submodel.
Fails if the name is empty.
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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.
xmlns | the namespaces to set |
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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.
notes | an XML structure that is to be used as the content of the "notes" subelement of this object |
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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.
notes | an XML string that is to be used as the content of the "notes" subelement of this object |
addXHTMLMarkup | a 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. |
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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.
value | the NNNNNNN integer portion of the SBO identifier |
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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 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.
sboid | the SBO identifier string of the form "SBO:NNNNNNN" |
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virtual |
Sets the value of the "substanceConversionFactor" attribute of this Submodel.
Fails if the id is not a valid syntax for an SIdRef.
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virtual |
Sets the value of the "timeConversionFactor" attribute of this Submodel.
Fails if the id is not a valid syntax for an SIdRef.
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inherited |
Sets the user data of this element.
This can be used by the application developer to attach custom information to the node. In case of a deep copy this attribute will passed as it is. The attribute will be never interpreted by this class.
userData | specifies the new user data. |
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inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
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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.
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inherited |
Clears the list of CVTerm objects attached to this SBML object.
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virtual |
Unsets the value of the "extentConversionFactor" attribute of this Submodel.
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virtual |
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inherited |
Unsets the value of the "metaid" attribute of this SBML object.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.
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inherited |
Unsets the ModelHistory object attached to this object.
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virtual |
Unsets the value of the "modelRef" attribute of this Submodel.
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virtual |
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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.
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inherited |
Unsets the value of the "sboTerm" attribute of this SBML object.
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virtual |
Unsets the value of the "substanceConversionFactor" attribute of this Submodel.
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virtual |
Unsets the value of the "timeConversionFactor" attribute of this Submodel.