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libSBML C++ API
5.18.0
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libSBML C++ API
5.18.0
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This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
The ListOfGeneAssociations is a container for GeneAssociation elements; both constructs are part of a proposed approach to annotating models in Version 1 of the SBML Level 3 Flux Balance Constraints (“fbc”) package. They are not part of the official “fbc” specification, and are not defined in Version 2 of the “fbc” package specification.
The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):
SBML Level 3 Version 1 has essentially the same structure as Level 2 Version 4, depicted above, but SBML Level 3 Version 2 allows containers to contain zero or more of the relevant object, instead of requiring at least one. As such, libsbml will write out an otherwise-empty ListOf___ element that has any optional attribute set (such as 'id' or 'metaid'), that has an optional child (such as a 'notes' or 'annotation'), or that has attributes or children set from any SBML Level 3 package, whether or not the ListOf___ has any other children.
Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's "annotation".
Public Member Functions | |
| int | addCVTerm (CVTerm *term, bool newBag=false) |
| Adds a copy of the given CVTerm object to this SBML object. More... | |
| int | append (const SBase *item) |
| Adds an item to the end of this ListOf's list of items. More... | |
| int | appendAndOwn (SBase *disownedItem) |
| Adds an item to the end of this ListOf's list of items. 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... | |
| virtual int | appendFrom (const ListOf *list) |
| Adds a clone of a list of items to this ListOf's list. 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... | |
| void | clear (bool doDelete=true) |
| Removes all items in this ListOf object. More... | |
| virtual ListOfGeneAssociations * | clone () const |
| Creates and returns a deep copy of this ListOfGeneAssociations. 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 | enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag) |
| Enables or disables the given SBML Level 3 package on this object. More... | |
| virtual GeneAssociation * | get (unsigned int n) |
| Get a GeneAssociation from the ListOfGeneAssociations. More... | |
| virtual const GeneAssociation * | get (unsigned int n) const |
| Get a GeneAssociation from the ListOfGeneAssociations. More... | |
| virtual GeneAssociation * | get (const std::string &sid) |
| Get a GeneAssociation from the ListOfGeneAssociations based on its identifier. More... | |
| virtual const GeneAssociation * | get (const std::string &sid) const |
| Get a GeneAssociation from the ListOfGeneAssociations based on its identifier. More... | |
| virtual List * | getAllElements (ElementFilter *filter=NULL) |
| Returns a List of all child SBase objects. More... | |
| virtual List * | getAllElementsFromPlugins (ElementFilter *filter=NULL) |
| Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
| SBase * | getAncestorOfType (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 SBase * | getAncestorOfType (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... | |
| 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 where 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... | |
| SBasePlugin * | getDisabledPlugin (unsigned int n) |
| Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| const SBasePlugin * | getDisabledPlugin (unsigned int n) const |
| Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| const SBase * | getElementByMetaId (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 SBase * | getElementByMetaId (const std::string &metaid) |
| Returns the first child element found with the given meta-identifier. More... | |
| const SBase * | getElementBySId (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 SBase * | getElementBySId (const std::string &id) |
| Returns the first child element found that has the given identifier. More... | |
| virtual const std::string & | getElementName () const |
| Returns the XML element name of this object. 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... | |
| virtual int | getItemTypeCode () const |
| Returns the libSBML type code for the SBML objects contained in this ListOf 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... | |
| 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 Model * | getModel () const |
| Returns the Model object for the SBML Document 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 & | getName () const |
| Returns the value of the "name" attribute of this SBML object. More... | |
| virtual XMLNamespaces * | getNamespaces () const |
| Returns a list of the XML Namespaces declared on the SBML document owning this object. 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 | getNumDisabledPlugins () const |
| Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More... | |
| unsigned int | getNumPlugins () const |
| Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
| unsigned int | getPackageCoreVersion () const |
| Returns the SBML Core 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... | |
| unsigned int | getPackageVersion () const |
| Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
| SBase * | getParentSBMLObject () |
| Returns the parent SBML object containing this object. More... | |
| 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... | |
| 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 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 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 object, namely, SBML_LIST_OF. 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... | |
| int | insert (int location, const SBase *item) |
| Inserts an item at a given position in this ListOf's list of items. More... | |
| int | insertAndOwn (int location, SBase *disownedItem) |
| Inserts an item at a given position in this ListOf's list of items. 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 | 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 | 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... | |
| ListOfGeneAssociations (unsigned int level=FbcExtension::getDefaultLevel(), unsigned int version=FbcExtension::getDefaultVersion(), unsigned int pkgVersion=FbcExtension::getDefaultPackageVersion()) | |
| Creates a new ListOfGeneAssociations with the given level, version, and package version. More... | |
| ListOfGeneAssociations (FbcPkgNamespaces *fbcns) | |
| Creates a new ListOfGeneAssociations with the given FbcPkgNamespaces object. 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... | |
| void | read (XMLNode &node, XMLErrorSeverityOverride_t flag=LIBSBML_OVERRIDE_DISABLED) |
| Reads (initializes) this SBML object by reading from the given XMLNode. More... | |
| virtual GeneAssociation * | remove (unsigned int n) |
| Removes the nth item from this ListOfGeneAssociations items and returns a pointer to it. More... | |
| virtual GeneAssociation * | remove (const std::string &sid) |
| Removes item in this ListOfGeneAssociations items with the given identifier. More... | |
| virtual int | removeFromParentAndDelete () |
| Removes all items in this ListOf object and deletes its properties too. 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... | |
| 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 | 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... | |
| int | setMetaId (const std::string &metaid) |
| Sets the value of the meta-identifier attribute of this SBML object. 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 ¬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... | |
| int | setUserData (void *userData) |
| Sets the user data of this element. More... | |
| unsigned int | size () const |
| Returns number of items in this ListOf list. More... | |
| char * | toSBML () |
| Returns a string consisting of a partial SBML corresponding to just this object. More... | |
| XMLNode * | toXMLNode () |
| 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... | |
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... | |
| ListOfGeneAssociations::ListOfGeneAssociations | ( | unsigned int | level = FbcExtension::getDefaultLevel(), |
| unsigned int | version = FbcExtension::getDefaultVersion(), |
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| unsigned int | pkgVersion = FbcExtension::getDefaultPackageVersion() |
||
| ) |
Creates a new ListOfGeneAssociations 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. |
| ListOfGeneAssociations::ListOfGeneAssociations | ( | FbcPkgNamespaces * | fbcns | ) |
Creates a new ListOfGeneAssociations with the given FbcPkgNamespaces object.
| fbcns | the FbcPkgNamespaces object. |
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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. |
create) for alternatives that do not lead to these issues.
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inherited |
Adds an item to the end of this ListOf's list of items.
This method makes a clone of the item handed to it. This means that when the ListOf object is destroyed, the original items will not be destroyed. For a method with an alternative ownership behavior, see the ListOf::appendAndOwn() method.
| item | the item to be added to the list. |
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inherited |
Adds an item to the end of this ListOf's list of items.
This method does not clone the disownedItem handed to it; instead, it assumes ownership of it. This means that when the ListOf is destroyed, the item will be destroyed along with it. For a method with an alternative ownership behavior, see the ListOf::append(SBase* item) method.
| disownedItem | the item to be added to the list. Will become a child of the parent list. |
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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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virtualinherited |
Adds a clone of a list of items to this ListOf's list.
Note that because this clones the objects handed to it, the original items will not be destroyed when this ListOf object is destroyed.
| list | a list of items to be added. |
Reimplemented in ListOfObjectives.
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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. |
|
inherited |
Removes all items in this ListOf object.
Used by ListOf::get() to lookup an SBase based by its id.
If parameter doDelete is true (default), all items in this ListOf object are deleted and cleared, and thus the caller doesn't have to delete those items. Otherwise, all items are cleared only from this ListOf object; the caller is still responsible for deleting the actual items. (In the latter case, callers are advised to store pointers to all items elsewhere before calling this function.)
| doDelete | if true (default), all items are deleted and cleared. Otherwise, all items are just cleared and not deleted. |
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virtual |
Creates and returns a deep copy of this ListOfGeneAssociations.
Reimplemented from ListOf.
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inherited |
Deletes all information stored in disabled plugins.
If the plugin is re-enabled later, it will then not have any previously-stored information.
| recursive | if true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element. |
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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:
| 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 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).
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
| flag | whether to enable (true) or disable (false) the package. |
|
virtual |
Get a GeneAssociation from the ListOfGeneAssociations.
| n | the index number of the GeneAssociation to get. |
n is invalid, NULL is returned.Reimplemented from ListOf.
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virtual |
Get a GeneAssociation from the ListOfGeneAssociations.
| n | the index number of the GeneAssociation to get. |
n is invalid, NULL is returned.Reimplemented from ListOf.
|
virtual |
Get a GeneAssociation from the ListOfGeneAssociations based on its identifier.
| sid | a string representing the identifier of the GeneAssociation to get. |
sid or NULL if no such GeneAssociation exists.
|
virtual |
Get a GeneAssociation from the ListOfGeneAssociations based on its identifier.
| sid | a string representing the identifier of the GeneAssociation to get. |
sid or NULL if no such GeneAssociation exists.
|
virtualinherited |
Returns a List of all child SBase objects.
The values returned include all children of the objects in this ListOf list, nested to an arbitrary depth.
| filter | a 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. |
Reimplemented from SBase.
Reimplemented in ListOfFunctionTerms, ListOfGlobalRenderInformation, and ListOfLocalRenderInformation.
|
virtualinherited |
Returns a List of all child SBase objects contained in SBML package plug-ins.
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.
| filter | a 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. |
|
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.
| 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.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.
|
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.
| 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.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.
|
inherited |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.
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.
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.
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.
|
inherited |
Returns the content of the "annotation" subelement of this object as a character string.
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.
|
inherited |
Returns the column number where this object first appears in the XML representation of the SBML document.
0.
|
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.
|
inherited |
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.
If no such plugin exists, NULL is returned.
| n | the index of the disabled plug-in to return. |
n is invalid, NULL is returned.
|
inherited |
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.
If no such plugin exists, NULL is returned.
| n | the index of the disabled plug-in to return. |
n is invalid, NULL is returned.
|
inherited |
Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found.
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.| metaid | string representing the "metaid" attribute value of the object to find. |
|
virtualinherited |
Returns the first child element found with the given meta-identifier.
| metaid | string representing the "metaid" attribute of the object to find. |
metaid, or NULL if no such object is found. Reimplemented from SBase.
Reimplemented in ListOfGlobalRenderInformation, and ListOfLocalRenderInformation.
|
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.
| id | string representing the "id" attribute value of the object to find. |
|
virtualinherited |
Returns the first child element found that has the given identifier.
This method searches this ListOf's list of items for SBML objects based on their "id" attribute value in the model-wide SId identifier namespace.
| id | string representing the id of the object to find. |
id, or NULL if no such object is found. Reimplemented from SBase.
Reimplemented in ListOfUnitDefinitions, ListOfRules, ListOfEventAssignments, ListOfInitialAssignments, ListOfLocalParameters, ListOfGlobalRenderInformation, ListOfLocalRenderInformation, and ListOfPorts.
|
virtual |
Returns the XML element name of this object.
For ListOfGeneAssociations, the XML element name is always "listOfGeneAssociations".
"listOfGeneAssociations". Reimplemented from ListOf.
|
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.
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.Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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.
Reimplemented in Rule, Layout, Model, EventAssignment, Compartment, InitialAssignment, Species, Event, UnitDefinition, Reaction, Parameter, Submodel, Group, ColorDefinition, Dimensions, FunctionDefinition, Objective, GraphicalObject, GradientBase, ExternalModelDefinition, Point, OutwardBindingSite, FluxBound, CompartmentType, Transition, RenderInformationBase, SpeciesType, Input, GeneProductAssociation, LineEnding, Deletion, GraphicalPrimitive1D, Image, FluxObjective, Style, Output, ListOfMembers, SubListOfSpeciesFeatures, GeneProduct, QualitativeSpecies, BoundingBox, GeneProductRef, SpeciesFeature, MultiSpeciesType, Port, SimpleSpeciesReference, SpeciesFeatureType, SpeciesTypeInstance, Member, GeneAssociation, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, InSpeciesTypeBond, PossibleSpeciesFeatureValue, and CompartmentReference.
|
inherited |
Returns the value of the "id" attribute of this SBML object.
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.Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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.
|
virtual |
Returns the libSBML type code for the SBML objects contained in this ListOf object.
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 SBase::getPackageName() method on the object.The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.
Reimplemented from ListOf.
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Returns the line number where this object first appears in the XML representation of the SBML document.
0.
|
inherited |
Returns the value of the "metaid" attribute of this SBML object.
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.
|
inherited |
Returns the value of the "metaid" attribute of this SBML object.
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.
|
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.
|
virtualinherited |
Returns the value of the "name" attribute of this SBML object.
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.
Reimplemented in Layout, Model, Compartment, Species, Event, UnitDefinition, Reaction, Parameter, Submodel, ColorDefinition, Group, OutwardBindingSite, ExternalModelDefinition, FunctionDefinition, FluxBound, Objective, GradientBase, Deletion, SubListOfSpeciesFeatures, Input, CompartmentType, RenderInformationBase, SpeciesType, Output, Transition, MultiSpeciesType, SpeciesFeature, QualitativeSpecies, GeneProductAssociation, Port, FluxObjective, SpeciesFeatureType, SpeciesTypeComponentMapInProduct, SpeciesTypeInstance, Style, SpeciesTypeComponentIndex, ListOfMembers, GeneProduct, GeneProductRef, InSpeciesTypeBond, PossibleSpeciesFeatureValue, CompartmentReference, Transformation, SimpleSpeciesReference, and Member.
|
virtualinherited |
Returns a list of the XML Namespaces declared on the SBML document owning this object.
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.
NULL in certain very usual circumstances where a namespace is not set.Reimplemented in SBMLDocument.
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
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().
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
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().
|
inherited |
Returns the content of the "notes" subelement of this object as a string.
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.
|
inherited |
Returns the content of the "notes" subelement of this object as a string.
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.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
|
inherited |
Returns the SBML Core Version within the SBML Level of the actual object.
|
inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
"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.
|
inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
0 will be returned if this element belongs to the SBML Level 3 Core package.
|
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.
The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.
If no such plugin exists, NULL is returned.
| 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.
The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.
If no such plugin exists, NULL is returned.
| package | the name or URI of the package. |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.
If no such plugin exists, NULL is returned.
| n | the index of the plug-in to return. |
n is invalid, NULL is returned.
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.
If no such plugin exists, NULL is returned.
| n | the index of the plug-in to return. |
n is invalid, NULL is returned.
|
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.
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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.
| 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 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.
| resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892". |
|
inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the SBMLDocument object containing this object instance.
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.
int, and SBO identifiers are stored simply as integers. -1 if the value is not set.
|
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".
|
inherited |
Returns the string representation of the "sboTerm" attribute of this object.
int, and SBO identifiers are stored simply as integers.
|
virtualinherited |
Returns the libSBML type code for this object, namely, SBML_LIST_OF.
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 SBase::getPackageName() method on the object.The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.
Reimplemented from SBase.
Reimplemented in ListOfObjectives, ListOfMultiSpeciesTypes, ListOfSpeciesFeatures, ListOfFluxObjectives, ListOfGeneProducts, ListOfFbcAssociations, ListOfSpeciesFeatureTypes, ListOfOutwardBindingSites, ListOfSpeciesTypeComponentMapInProducts, ListOfLocalRenderInformation, ListOfGlobalRenderInformation, ListOfInSpeciesTypeBonds, ListOfSpeciesTypeComponentIndexes, ListOfSpeciesTypeInstances, ListOfDrawables, ListOfCompartmentReferences, ListOfPossibleSpeciesFeatureValues, ListOfMembers, SubListOfSpeciesFeatures, ListOfSpeciesFeatureValues, ListOfGradientDefinitions, ListOfCurveElements, ListOfGradientStops, ListOfLineEndings, ListOfColorDefinitions, ListOfLocalStyles, ListOfGlobalStyles, and ListOfGroups.
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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.
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inherited |
Returns the user data that has been previously set via setUserData().
NULL if no user data has been set.
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inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
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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/level2/version5" http://www.sbml.org/sbml/level3/version1/core" http://www.sbml.org/sbml/level3/version2/core" true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
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inherited |
Inserts an item at a given position in this ListOf's list of items.
This variant of the method makes a clone of the item handed to it. This means that when the ListOf is destroyed, the original item will not be destroyed.
| location | the location in the list where to insert the item. |
| item | the item to be inserted to the list. |
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inherited |
Inserts an item at a given position in this ListOf's list of items.
This variant of the method does not make a clone of the disownedItem handed to it. This means that when the ListOf is destroyed, the original item will be destroyed.
| location | the location where to insert the item. |
| disownedItem | the item to be inserted to the list. Will become a child of the parent list. |
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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.
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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.
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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.
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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.
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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.
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virtualinherited |
Predicate returning true if a call to getId() returns a non-empty string.
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.
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.Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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.
true if the "id" attribute of this SBML object is set, false otherwise.Reimplemented in Layout, Compartment, Model, Species, Event, Reaction, UnitDefinition, Parameter, ColorDefinition, Group, GradientBase, RenderInformationBase, Submodel, FunctionDefinition, Objective, Dimensions, GeneProductAssociation, Input, GraphicalPrimitive1D, GraphicalObject, QualitativeSpecies, Output, FluxObjective, CompartmentType, ExternalModelDefinition, OutwardBindingSite, Point, LineEnding, SpeciesType, FluxBound, Transition, GeneProduct, Image, Style, Deletion, ListOfMembers, GeneProductRef, SubListOfSpeciesFeatures, Member, SimpleSpeciesReference, BoundingBox, MultiSpeciesType, SpeciesFeature, Port, SpeciesFeatureType, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, GeneAssociation, SpeciesTypeComponentIndex, InSpeciesTypeBond, PossibleSpeciesFeatureValue, and CompartmentReference.
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inherited |
Predicate returning true if this object's "id" attribute is set.
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.Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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.
true if the "id" attribute of this SBML object is set, false otherwise.
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inherited |
Predicate returning true if this object's "metaid" attribute is set.
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.true if the "metaid" attribute of this SBML object is set, false otherwise.
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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.
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virtualinherited |
Predicate returning true if this object's "name" attribute is set.
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.
true if the "name" attribute of this SBML object is set, false otherwise.Reimplemented in Layout, Compartment, Model, Species, Event, Reaction, UnitDefinition, Parameter, ColorDefinition, Submodel, GradientBase, Group, RenderInformationBase, Input, FunctionDefinition, Objective, OutwardBindingSite, QualitativeSpecies, Output, ExternalModelDefinition, GeneProductAssociation, FluxBound, SubListOfSpeciesFeatures, Deletion, FluxObjective, CompartmentType, SpeciesType, Transition, GeneProduct, Transformation, GeneProductRef, MultiSpeciesType, SpeciesFeature, Style, ListOfMembers, SpeciesFeatureType, SpeciesTypeComponentMapInProduct, Port, SpeciesTypeInstance, SpeciesTypeComponentIndex, InSpeciesTypeBond, PossibleSpeciesFeatureValue, Member, SimpleSpeciesReference, and CompartmentReference.
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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.
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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.
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inherited |
Predicate returning true or false depending on whether the user data of this element has been set.
true if this object's user data has been set, false otherwise.
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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.
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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.
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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.
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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.
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inherited |
Reads (initializes) this SBML object by reading from the given XMLNode.
| node | the XMLNode to read from. |
| flag | an optional flag that determines how how errors are logged during the reading process. |
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virtual |
Removes the nth item from this ListOfGeneAssociations items and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
| n | the index of the item to remove. |
Reimplemented from ListOf.
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virtual |
Removes item in this ListOfGeneAssociations items with the given identifier.
The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then NULL is returned.
| sid | the identifier of the item to remove. |
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virtualinherited |
Removes all items in this ListOf object and deletes its properties too.
This performs a call to clear() with an argument of true (thus removing all the child objects in the list), followed by calls to various libSBML unsetFoo methods to delete everything else: CVTerm objects, model history objects, etc.
Implementations of subclasses of ListOf may need to override this method if different handling of child objects is needed.
Reimplemented from SBase.
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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. |
| removeEmpty | if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default). |
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virtualinherited |
Replaces all uses of a given meta identifier attribute value with another value.
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.
| oldid | the old identifier. |
| newid | the new identifier. |
Reimplemented in Port, and GraphicalObject.
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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.
| oldid | the old identifier. |
| newid | the new identifier. |
Reimplemented in Model, DefaultValues, Species, RenderInformationBase, ListOfObjectives, RenderGroup, Compartment, KineticLaw, Rule, MultiSpeciesType, Submodel, EventAssignment, InitialAssignment, StoichiometryMath, SpeciesFeature, Delay, SBaseRef, RenderCurve, Trigger, Input, FluxBound, QualitativeSpecies, OutwardBindingSite, ReactionGlyph, Priority, SpeciesTypeComponentMapInProduct, Output, GeneralGlyph, FluxObjective, Constraint, GeneProduct, SpeciesTypeComponentIndex, Reaction, SpeciesTypeInstance, InSpeciesTypeBond, ReplacedElement, Member, Port, PossibleSpeciesFeatureValue, SimpleSpeciesReference, GeneProductRef, CompartmentReference, AssignmentRule, RateRule, FunctionTerm, SpeciesReferenceGlyph, CompartmentGlyph, SpeciesFeatureValue, Replacing, ReferenceGlyph, TextGlyph, and SpeciesGlyph.
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virtualinherited |
Replaces all uses of a given UnitSIdRef type attribute value with another value.
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.
| oldid | the old identifier. |
| newid | the new identifier. |
Reimplemented in Model, Species, Compartment, KineticLaw, Rule, Parameter, EventAssignment, InitialAssignment, StoichiometryMath, Delay, FunctionDefinition, Trigger, Priority, Constraint, and Port.
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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) followed by calling 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) followed by calling 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.
|
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. |
|
virtualinherited |
Sets the value of the "id" attribute of this SBML object.
sid is copied.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.Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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.
| sid | the string to use as the identifier of this object. |
Reimplemented in Layout, Compartment, Species, Model, Event, Reaction, Parameter, UnitDefinition, RenderInformationBase, ColorDefinition, GradientBase, Group, Input, GraphicalPrimitive1D, FunctionDefinition, Submodel, Objective, QualitativeSpecies, Output, GeneProductAssociation, FluxObjective, Dimensions, GeneProduct, Image, LineEnding, GraphicalObject, CompartmentType, SpeciesType, Transition, OutwardBindingSite, Member, Point, Style, SimpleSpeciesReference, FluxBound, ListOfMembers, GeneProductRef, SubListOfSpeciesFeatures, ExternalModelDefinition, BoundingBox, MultiSpeciesType, SpeciesFeature, Port, SpeciesFeatureType, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, Deletion, GeneAssociation, InSpeciesTypeBond, PossibleSpeciesFeatureValue, and CompartmentReference.
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virtualinherited |
Sets the value of the "id" attribute of this SBML object.
sid is copied.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.Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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.
| sid | the string to use as the identifier of this object. |
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inherited |
Sets the value of the meta-identifier attribute of this SBML object.
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.
| 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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virtualinherited |
Sets the value of the "name" attribute of this SBML object.
The string in name is copied.
| name | the new name for the SBML object. |
Reimplemented in Layout, Compartment, Species, Model, Event, Reaction, Parameter, UnitDefinition, RenderInformationBase, ColorDefinition, GradientBase, Group, Input, Submodel, QualitativeSpecies, Output, FunctionDefinition, Objective, GeneProductAssociation, OutwardBindingSite, FluxObjective, GeneProduct, FluxBound, Transformation, CompartmentType, SubListOfSpeciesFeatures, GeneProductRef, SpeciesType, Member, Transition, Style, ListOfMembers, ExternalModelDefinition, SimpleSpeciesReference, MultiSpeciesType, SpeciesFeature, SpeciesTypeComponentMapInProduct, SpeciesFeatureType, SpeciesTypeInstance, Deletion, SpeciesTypeComponentIndex, Port, InSpeciesTypeBond, PossibleSpeciesFeatureValue, and CompartmentReference.
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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.
int, and SBO identifiers are stored simply as integers. | value | the NNNNNNN integer portion of the SBO identifier. |
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virtualinherited |
Sets the value of the "sboTerm" attribute by string.
int, and SBO identifiers are stored simply as integers. | sboid | the SBO identifier string of the form "SBO:NNNNNNN". |
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inherited |
Sets the user data of this element.
| userData | specifies the new user data. |
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inherited |
Returns number of items in this ListOf list.
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inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
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inherited |
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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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virtualinherited |
Unsets the value of the "id" attribute of this SBML object.
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.Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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.
Reimplemented in Model, Layout, Event, RenderInformationBase, ColorDefinition, GraphicalPrimitive1D, GradientBase, Group, Input, QualitativeSpecies, Objective, GeneProductAssociation, Output, FluxObjective, GeneProduct, Submodel, Image, Member, LineEnding, Dimensions, GeneProductRef, Style, GraphicalObject, Transition, ListOfMembers, SimpleSpeciesReference, OutwardBindingSite, Point, FluxBound, ExternalModelDefinition, SubListOfSpeciesFeatures, Deletion, BoundingBox, MultiSpeciesType, SpeciesFeature, Port, SpeciesFeatureType, SpeciesTypeInstance, SpeciesTypeComponentMapInProduct, SpeciesTypeComponentIndex, InSpeciesTypeBond, PossibleSpeciesFeatureValue, GeneAssociation, and CompartmentReference.
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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.
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inherited |
Unsets the value of the "metaid" attribute of this SBML object.
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.
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inherited |
Unsets the ModelHistory object attached to this object.
|
virtualinherited |
Unsets the value of the "name" attribute of this SBML object.
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.
Reimplemented in Compartment, Species, Model, Layout, Event, Reaction, Parameter, RenderInformationBase, ColorDefinition, UnitDefinition, GradientBase, Group, Input, QualitativeSpecies, Output, Objective, GeneProductAssociation, Submodel, FunctionDefinition, FluxObjective, GeneProduct, Member, OutwardBindingSite, Transformation, GeneProductRef, FluxBound, ExternalModelDefinition, Style, ListOfMembers, Transition, SubListOfSpeciesFeatures, CompartmentType, SimpleSpeciesReference, SpeciesType, Deletion, MultiSpeciesType, SpeciesFeature, SpeciesTypeComponentMapInProduct, SpeciesFeatureType, SpeciesTypeInstance, SpeciesTypeComponentIndex, Port, PossibleSpeciesFeatureValue, InSpeciesTypeBond, and CompartmentReference.
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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.
|
inherited |
Unsets the user data of this element.