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libSBML Python API
5.18.0
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libSBML Python API
5.18.0
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The Group class is the first and most central class in the SBML Level 3 Groups package. This class represents a group of entities: a simple mechanism for indicating that particular components of an SBML model are related in some way. The nature of the relationship is left up to the modeler, and can be clarified by means of annotations on model components. Groups may contain either the same or different types of SBML objects, and groups may be nested if desired. There are no predefined modeling or mathematical semantics associated with groups.
The Groups class has one required attribute, 'kind'; two optional attributes, 'id' and 'name'; and a single child element, ListOfMembers. The membership of a group is determined by the contents of the list of members stored in Member objects within the ListOfMembers child of a Group object. Since the Group class of objects is derived from SBase, and SBase provides the ability to attach SBO terms as well as MIRIAM annotations, the semantics of a given group in a model can be made more precise using references to external controlled vocabularies and ontologies.
The attribute 'kind' on Group is used to indicate the nature of the group defined by a Group instance. The 'kind' attribute must always have one of the following three possible values:
'classification': The group represents a class, and its members have an is-a relationship to the group. For example, the group could represent a type of molecule such as ATP, and the members could be species located in different compartments, thereby establishing that the species are pools of the same molecule in different locations.'partonomy': The group represents a collection of parts, and its members have a part-of relationship to the group. For example, the group could represent a cellular structure, and individual compartments could be made members of the group to indicate they represent subparts of that cellular structure.'collection': The grouping is merely a collection for convenience, without an implied relationship between the members. For example, the group could be used to collect together multiple disparate components of a model—species, reactions, events—involved in a particular phenotype, and apply a common annotation rather than having to copy the same annotation to each component individually.In the libSBML API for Groups, these possible values for the 'kind' attribute are programmatically represented as constants so that callers will not normally need to deal with text string values. The following are the constants defined for the three values of 'kind' (plus an additional constant to represent unrecognized values):
If an SBML element is referenced by a Group's child Member (directly or indirectly), it is considered to be a member of that Group. If the same element is referenced by multiple Member objects, this is equivalent to including it just once. (It is considered best practice to avoid this, but does not make for an invalid SBML document.)
Children of referenced elements are not considered to be members of the Group: a KineticLaw of a referenced Reaction is not itself a Group member. Even the membership of so-called SBML container classes (e.g., ListOfSpecies, ListOfCompartments, etc.) does not imply inclusion of children as members of the Group. The sole exception to this rule is the handling of ListOfMembers class, described below.
The implication of this is that any rule that applies to members of a group (such the meaning of the 'kind' attribute, or the restrictions on the application of 'sboTerm' attributes on a ListOfMembers) applies to the child group when referenced by the Group 'id', and to the members of the child group when referenced by the ListOfMembers 'id'. In an example situation where a parent group includes two Species plus a Group which itself contains three other Species, if the parent group's ListOfMembers is given an 'sboTerm' attribute value, that SBO term applies to the two species and the group, not to the three child species members of the second group. (Note also that in such a case, the parent group's 'kind' attribute value would almost certainly be 'collection' or 'partonomy', and not 'classification', as two species and a group are very unlikely to be classified as the same thing.) In contrast, in the situation where a parent group includes two Species plus a ListOfMembers which contains three other Species, the parent group's ListOfMembers 'sboTerm' would apply to the five Species, and could be more reasonably marked as a 'classification'.
In a future version of this SBML Level 3 Groups specification, it may be possible to perform set operations on groups, but for now, this type of union is the only set operation that is possible.
Groups are not permitted to be circular: no Member may reference itself, its parent ListOfMembers, nor its parent Group. If a Member references a Group, the same restrictions apply to that subgroup's children: they may not reference the Member, its parent ListOfMembers, nor its parent Group, and if any of those children reference a Group, the same restrictions apply to them, etc.
If a Member has a 'idRef' or 'metaIdRef' attribute which references an object from a namespace that is not understood by the interpreter of the SBML model, that Member must be ignored. The referenced object will not be understood by the interpreter, and therefore has no need to become a member of the group. If an interpreter cannot tell whether a referenced object does not exist or if exists in an unparsed namespace, it may choose to produce a warning.
Public Member Functions | |
| def | __init__ (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | addCVTerm (self, term, newBag=False) |
| Adds a copy of the given CVTerm object to this SBML object. More... | |
| def | addMember (self, m) |
| Adds a copy of the given Member to this Group. More... | |
| def | appendAnnotation (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | appendNotes (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | clone (self) |
| Creates and returns a deep copy of this Group object. More... | |
| def | connectToChild (self) |
| def | createMember (self) |
| Creates a new Member object, adds it to this Group object and returns the Member object created. More... | |
| def | deleteDisabledPlugins (self, recursive=True) |
| Deletes all information stored in disabled plugins. More... | |
| def | disablePackage (self, pkgURI, pkgPrefix) |
| Disables the given SBML Level 3 package on this object. More... | |
| def | enablePackage (self, pkgURI, pkgPrefix, flag) |
| Enables or disables the given SBML Level 3 package on this object. More... | |
| def | getAncestorOfType (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | getAnnotation (self, args) |
| Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More... | |
| def | getAnnotationString (self, args) |
| Returns the content of the 'annotation' subelement of this object as a character string. More... | |
| def | getColumn (self) |
| Returns the column number where this object first appears in the XML representation of the SBML document. More... | |
| def | getCVTerm (self, n) |
| Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
| def | getCVTerms (self, args) |
| Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
| def | getDisabledPlugin (self, args) |
| Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| def | getElementByMetaId (self, metaid) |
Returns the first child element that has the given metaid, or None if no such object is found. More... | |
| def | getElementBySId (self, id) |
Returns the first child element that has the given id in the model-wide SId namespace, or None if no such object is found. More... | |
| def | getElementName (self) |
| Returns the XML element name of this Group object. More... | |
| def | getId (self) |
| Returns the value of the 'id' attribute of this Group. More... | |
| def | getIdAttribute (self) |
| Returns the value of the 'id' attribute of this SBML object. More... | |
| def | getKind (self) |
| Returns the value of the 'kind' attribute of this Group. More... | |
| def | getKindAsString (self) |
| Returns the value of the 'kind' attribute of this Group. More... | |
| def | getLevel (self) |
| Returns the SBML Level of the SBMLDocument object containing this object. More... | |
| def | getLine (self) |
| Returns the line number where this object first appears in the XML representation of the SBML document. More... | |
| def | getListOfAllElements (self, filter=None) |
| Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More... | |
| def | getListOfAllElementsFromPlugins (self, filter=None) |
| Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
| def | getListOfMembers (self, args) |
| Returns the ListOfMembers from this Group. More... | |
| def | getMember (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | getMemberByIdRef (self, args) |
| Get a Member from the Group based on the element to which it refers. More... | |
| def | getMetaId (self) |
| Returns the value of the 'metaid' attribute of this SBML object. More... | |
| def | getModel (self) |
| Returns the Model object for the SBML Document in which the current object is located. More... | |
| def | getModelHistory (self, args) |
| Returns the ModelHistory object, if any, attached to this object. More... | |
| def | getName (self) |
| Returns the value of the 'name' attribute of this Group. More... | |
| def | getNamespaces (self) |
| Returns a list of the XML Namespaces declared on the SBML document owning this object. More... | |
| def | getNotes (self, args) |
| Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More... | |
| def | getNotesString (self, args) |
| Returns the content of the 'notes' subelement of this object as a string. More... | |
| def | getNumCVTerms (self) |
| Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
| def | getNumDisabledPlugins (self) |
| Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More... | |
| def | getNumMembers (self) |
| Get the number of Member objects in this Group. More... | |
| def | getNumPlugins (self) |
| Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
| def | getPackageCoreVersion (self) |
| Returns the SBML Core Version within the SBML Level of the actual object. More... | |
| def | getPackageName (self) |
| Returns the name of the SBML Level 3 package in which this element is defined. More... | |
| def | getPackageVersion (self) |
| Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
| def | getParentSBMLObject (self, args) |
| Returns the parent SBML object containing this object. More... | |
| def | getPlugin (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | getPrefix (self) |
| Returns the XML namespace prefix of this element. More... | |
| def | getResourceBiologicalQualifier (self, resource) |
| Returns the MIRIAM biological qualifier associated with the given resource. More... | |
| def | getResourceModelQualifier (self, resource) |
| Returns the MIRIAM model qualifier associated with the given resource. More... | |
| def | getSBMLDocument (self, args) |
| Returns the SBMLDocument object containing this object instance. More... | |
| def | getSBOTerm (self) |
| Returns the integer portion of the value of the 'sboTerm' attribute of this object. More... | |
| def | getSBOTermAsURL (self) |
| Returns the URL representation of the 'sboTerm' attribute of this object. More... | |
| def | getSBOTermID (self) |
| Returns the string representation of the 'sboTerm' attribute of this object. More... | |
| def | getTypeCode (self) |
| Returns the libSBML type code for this Group object. More... | |
| def | getURI (self) |
| Gets the namespace URI to which this element belongs to. More... | |
| def | getVersion (self) |
| Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
| def | hasRequiredAttributes (self) |
Predicate returning True if all the required attributes for this Group object have been set. More... | |
| def | hasValidLevelVersionNamespaceCombination (self) |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
| def | isPackageEnabled (self, pkgName) |
Predicate returning True if the given SBML Level 3 package is enabled with this object. More... | |
| def | isPackageURIEnabled (self, pkgURI) |
Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| def | isPkgEnabled (self, pkgName) |
Predicate returning True if the given SBML Level 3 package is enabled with this object. More... | |
| def | isPkgURIEnabled (self, pkgURI) |
Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| def | isSetAnnotation (self) |
Predicate returning True if this object's 'annotation' subelement exists and has content. More... | |
| def | isSetId (self) |
Predicate returning True if this Group's 'id' attribute is set. More... | |
| def | isSetIdAttribute (self) |
Predicate returning True if this object's 'id' attribute is set. More... | |
| def | isSetKind (self) |
Predicate returning True if this Group's 'kind' attribute is set. More... | |
| def | isSetMetaId (self) |
Predicate returning True if this object's 'metaid' attribute is set. More... | |
| def | isSetModelHistory (self) |
Predicate returning True if this object has a ModelHistory object attached to it. More... | |
| def | isSetName (self) |
Predicate returning True if this Group's 'name' attribute is set. More... | |
| def | isSetNotes (self) |
Predicate returning True if this object's 'notes' subelement exists and has content. More... | |
| def | isSetSBOTerm (self) |
Predicate returning True if this object's 'sboTerm' attribute is set. More... | |
| def | isSetUserData (self) |
| Predicate returning true or false depending on whether the user data of this element has been set. More... | |
| def | matchesRequiredSBMLNamespacesForAddition (self, args) |
Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
| def | matchesSBMLNamespaces (self, args) |
Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
| def | removeFromParentAndDelete (self) |
| Removes this object from its parent. More... | |
| def | removeMember (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | removeTopLevelAnnotationElement (self, args) |
| Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
| def | renameMetaIdRefs (self, oldid, newid) |
| Replaces all uses of a given meta identifier attribute value with another value. More... | |
| def | renameSIdRefs (self, oldid, newid) |
Replaces all uses of a given SIdRef type attribute value with another value. More... | |
| def | renameUnitSIdRefs (self, oldid, newid) |
Replaces all uses of a given UnitSIdRef type attribute value with another value. More... | |
| def | replaceTopLevelAnnotationElement (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setAnnotation (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setId (self, id) |
| Sets the value of the 'id' attribute of this Group. More... | |
| def | setIdAttribute (self, sid) |
| Sets the value of the 'id' attribute of this SBML object. More... | |
| def | setKind (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setMetaId (self, metaid) |
| Sets the value of the meta-identifier attribute of this SBML object. More... | |
| def | setModelHistory (self, history) |
| Sets the ModelHistory of this object. More... | |
| def | setName (self, name) |
| Sets the value of the 'name' attribute of this Group. More... | |
| def | setNamespaces (self, xmlns) |
| Sets the namespaces relevant of this SBML object. More... | |
| def | setNotes (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setSBOTerm (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | toSBML (self) |
| Returns a string consisting of a partial SBML corresponding to just this object. More... | |
| def | toXMLNode (self) |
| Returns this element as an XMLNode. More... | |
| def | unsetAnnotation (self) |
| Unsets the value of the 'annotation' subelement of this SBML object. More... | |
| def | unsetCVTerms (self) |
| Clears the list of CVTerm objects attached to this SBML object. More... | |
| def | unsetId (self) |
| Unsets the value of the 'id' attribute of this Group. More... | |
| def | unsetIdAttribute (self) |
| Unsets the value of the 'id' attribute of this SBML object. More... | |
| def | unsetKind (self) |
| Unsets the value of the 'kind' attribute of this Group. More... | |
| def | unsetMetaId (self) |
| Unsets the value of the 'metaid' attribute of this SBML object. More... | |
| def | unsetModelHistory (self) |
| Unsets the ModelHistory object attached to this object. More... | |
| def | unsetName (self) |
| Unsets the value of the 'name' attribute of this Group. More... | |
| def | unsetNotes (self) |
| Unsets the value of the 'notes' subelement of this SBML object. More... | |
| def | unsetSBOTerm (self) |
| Unsets the value of the 'sboTerm' attribute of this SBML object. More... | |
| def | unsetUserData (self) |
| Unsets the user data of this element. More... | |
| def libsbml.Group.__init__ | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
__init__(long level, long version, long pkgVersion) Group __init__(long level, long version) Group __init__(long level) Group __init__() Group __init__(GroupsPkgNamespaces groupsns) Group __init__(Group orig) Group
Each variant is described separately below.
Group(Group orig)
Copy constructor for Group.
| orig | the Group instance to copy. |
Group(long level = GroupsExtension.getDefaultLevel(), long version = GroupsExtension.getDefaultVersion(), long pkgVersion = GroupsExtension.getDefaultPackageVersion())
Creates a new Group using the given SBML Level, Version and “groups” package version.
| level | a long integer, the SBML Level to assign to this Group. |
| version | a long integer, the SBML Version to assign to this Group. |
| pkgVersion | a long integer, the SBML Groups Version to assign to this Group. |
parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.Group(GroupsPkgNamespaces groupsns)
Creates a new Group using the given GroupsPkgNamespaces object.
| groupsns | the GroupsPkgNamespaces object. |
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inherited |
Adds a copy of the given CVTerm object to this SBML object.
addCVTerm(CVTerm term, bool newBag) int addCVTerm(CVTerm term) int
| 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.parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense. | def libsbml.Group.addMember | ( | self, | |
| m | |||
| ) |
Adds a copy of the given Member to this Group.
addMember(Member m) int
| m | the Member object to add. |
create) for alternatives that do not lead to these issues.
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inherited |
This method has multiple variants; they differ in the arguments they accept.
appendAnnotation(XMLNode annotation) int appendAnnotation(string annotation) int
Each variant is described separately below.
appendAnnotation(XMLNode annotation)
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() or SBase.setAnnotation(), 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. |
appendAnnotation(string annotation)
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() or SBase.setAnnotation(), 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. |
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inherited |
This method has multiple variants; they differ in the arguments they accept.
appendNotes(XMLNode notes) int appendNotes(string notes) int
Each variant is described separately below.
appendNotes(string notes)
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. |
appendNotes(XMLNode notes)
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. |
| def libsbml.Group.clone | ( | self | ) |
|
inherited |
connectToChild()
| def libsbml.Group.createMember | ( | self | ) |
Creates a new Member object, adds it to this Group object and returns the Member object created.
createMember() Member
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inherited |
Deletes all information stored in disabled plugins.
deleteDisabledPlugins(bool recursive) deleteDisabledPlugins()
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. |
|
inherited |
Disables the given SBML Level 3 package on this object.
disablePackage(string pkgURI, string pkgPrefix) intThis 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. |
|
inherited |
Enables or disables the given SBML Level 3 package on this object.
enablePackage(string pkgURI, string pkgPrefix, bool flag) intThis 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().
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
| flag | whether to enable (True) or disable (False) the package. |
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
getAncestorOfType(int type, string pkgName) SBase getAncestorOfType(int type) SBase
Each variant is described separately below.
getAncestorOfType(int type, string pkgName = 'core')
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. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code 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. |
None 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 None.parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.getAncestorOfType(int type, string pkgName = 'core')
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. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code 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. |
None 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 None.parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
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inherited |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
getAnnotation() XMLNode
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.
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inherited |
Returns the content of the 'annotation' subelement of this object as a character string.
getAnnotationString() stringSBML 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.
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inherited |
Returns the column number where this object first appears in the XML representation of the SBML document.
getColumn() long0.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
getCVTerms() List *
|
inherited |
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.
getDisabledPlugin(long n) SBasePlugin
If no such plugin exists, None is returned.
| n | the index of the disabled plug-in to return. |
n is invalid, None is returned.| def libsbml.Group.getElementByMetaId | ( | self, | |
| metaid | |||
| ) |
Returns the first child element that has the given metaid, or None if no such object is found.
getElementByMetaId(string metaid) SBase
| metaid | a string representing the metaid attribute of the object to retrieve. |
metaid. If no such object is found this method returns None. | def libsbml.Group.getElementBySId | ( | self, | |
| id | |||
| ) |
Returns the first child element that has the given id in the model-wide SId namespace, or None if no such object is found.
getElementBySId(string id) SBase
| id | a string representing the id attribute of the object to retrieve. |
id. If no such object is found, this method returns None. | def libsbml.Group.getElementName | ( | self | ) |
| def libsbml.Group.getId | ( | self | ) |
|
inherited |
Returns the value of the 'id' attribute of this SBML object.
getIdAttribute() stringSId 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.
| def libsbml.Group.getKind | ( | self | ) |
Returns the value of the 'kind' attribute of this Group.
getKind() long'classification', to indicate that the group represents a class, and its members have an is-a relationship to the group.
'partonomy', to indicate that the group represents a collection of parts, and its members have a part-of relationship to the group.
'collection', to indicate that the grouping is merely a collection for convenience, without an implied relationship between the members. The possible values returned by this method are:
| def libsbml.Group.getKindAsString | ( | self | ) |
Returns the value of the 'kind' attribute of this Group.
getKindAsString() string'classification', to indicate that the group represents a class, and its members have an is-a relationship to the group.
'partonomy', to indicate that the group represents a collection of parts, and its members have a part-of relationship to the group.
'collection', to indicate that the grouping is merely a collection for convenience, without an implied relationship between the members. 'classification' 'partonomy' 'collection' 'unknown'
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
getLevel() long
|
inherited |
Returns the line number where this object first appears in the XML representation of the SBML document.
getLine() long0.
|
inherited |
Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.
getListOfAllElements(ElementFilter filter) SBaseList getListOfAllElements() SBaseList
|
inherited |
Returns a List of all child SBase objects contained in SBML package plug-ins.
getListOfAllElementsFromPlugins(ElementFilter filter) SBaseList getListOfAllElementsFromPlugins() SBaseList
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.
| def libsbml.Group.getListOfMembers | ( | self, | |
| args | |||
| ) |
Returns the ListOfMembers from this Group.
getListOfMembers() ListOfMembers
Using the SBML Level 3 Groups package, the membership of a group is determined by the contents of the list of members stored in Member objects within the ListOfMembers child of a Group object.
| def libsbml.Group.getMember | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
getMember(long n) Member getMember(string sid) Member
Each variant is described separately below.
getMember(long n)
| n | a long integer representing the index of the Member to retrieve. |
None if no such object exists..getMember(string sid)
Get a Member from the Group based on its identifier.
| sid | a string representing the identifier of the Member to retrieve. |
sid or None if no such Member exists.| def libsbml.Group.getMemberByIdRef | ( | self, | |
| args | |||
| ) |
Get a Member from the Group based on the element to which it refers.
getMemberByIdRef(string sid) Member
| sid | a string representing the 'idRef' attribute of the Member object to retrieve. |
|
inherited |
Returns the value of the 'metaid' attribute of this SBML object.
getMetaId() stringID, 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.
getModelHistory() ModelHistory
None if none exist.| def libsbml.Group.getName | ( | self | ) |
|
inherited |
Returns a list of the XML Namespaces declared on the SBML document owning this object.
getNamespaces() XMLNamespaces
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.
None in certain very usual circumstances where a namespace is not set.
|
inherited |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
getNotes() XMLNode
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.
getNotesString() stringThe 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.
getNumCVTerms() long
|
inherited |
Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.
getNumDisabledPlugins() long| def libsbml.Group.getNumMembers | ( | self | ) |
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
getNumPlugins() long
|
inherited |
Returns the SBML Core Version within the SBML Level of the actual object.
getPackageCoreVersion() long
|
inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
getPackageName() string"core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
|
inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
getPackageVersion() long0 will be returned if this element belongs to the SBML Level 3 Core package.
|
inherited |
Returns the parent SBML object containing this object.
getParentSBMLObject() SBase
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
getPlugin(string package) SBasePlugin getPlugin(long n) SBasePlugin
Each variant is described separately below.
getPlugin(long n)
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() will return an FbcModelPlugin; calling Parameter.getPlugin() will return CompSBasePlugin, etc.
If no such plugin exists, None is returned.
| n | the index of the plug-in to return. |
n is invalid, None is returned.getPlugin(string package)
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() will return an FbcModelPlugin; calling Parameter.getPlugin() will return CompSBasePlugin, etc.
If no such plugin exists, None is returned.
| package | the name or URI of the package. |
|
inherited |
Returns the XML namespace prefix of this element.
getPrefix() stringThis 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.
|
inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
getResourceBiologicalQualifier(string resource) longIn MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose name begins with BQB_ from the interface class libsbml.
| resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'. |
BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
|
inherited |
Returns the MIRIAM model qualifier associated with the given resource.
getResourceModelQualifier(string resource) longIn MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQM_ in the interface class libsbml.
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose name begins with BQM_ from the interface class libsbml.
| resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'. |
BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
|
inherited |
Returns the SBMLDocument object containing this object instance.
getSBMLDocument() SBMLDocument
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.
getSBOTerm() intint, 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.
getSBOTermAsURL() stringThis 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.
getSBOTermID() stringint, and SBO identifiers are stored simply as integers. | def libsbml.Group.getTypeCode | ( | self | ) |
Returns the libSBML type code for this Group object.
getTypeCode() intSBML_. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. 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.
|
inherited |
Gets the namespace URI to which this element belongs to.
getURI() stringFor 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.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
getVersion() long| def libsbml.Group.hasRequiredAttributes | ( | self | ) |
|
inherited |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.
hasValidLevelVersionNamespaceCombination() boolThe valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
http://www.sbml.org/sbml/level1 http://www.sbml.org/sbml/level2 http://www.sbml.org/sbml/level2/version2 http://www.sbml.org/sbml/level2/version3 http://www.sbml.org/sbml/level2/version4 http://www.sbml.org/sbml/level3/version1/core true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
|
inherited |
Predicate returning True if the given SBML Level 3 package is enabled with this object.
isPackageEnabled(string pkgName) boolThe search ignores the package version.
| pkgName | the name of the package. |
True if the given package is enabled within this object, False otherwise.
|
inherited |
Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.
isPackageURIEnabled(string pkgURI) bool| pkgURI | the URI of the package. |
True if the given package is enabled within this object, False otherwise.
|
inherited |
Predicate returning True if the given SBML Level 3 package is enabled with this object.
isPkgEnabled(string pkgName) boolThe search ignores the package version.
| pkgName | the name of the package. |
True if the given package is enabled within this object, False otherwise.
|
inherited |
Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.
isPkgURIEnabled(string pkgURI) bool| pkgURI | the URI of the package. |
True if the given package is enabled within this object, False otherwise.
|
inherited |
Predicate returning True if this object's 'annotation' subelement exists and has content.
isSetAnnotation() boolWhereas 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.| def libsbml.Group.isSetId | ( | self | ) |
|
inherited |
Predicate returning True if this object's 'id' attribute is set.
isSetIdAttribute() boolSId 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.| def libsbml.Group.isSetKind | ( | self | ) |
Predicate returning True if this Group's 'kind' attribute is set.
isSetKind() boolTrue if this Group's 'kind' attribute has been set, otherwise False is returned.'classification', to indicate that the group represents a class, and its members have an is-a relationship to the group.
'partonomy', to indicate that the group represents a collection of parts, and its members have a part-of relationship to the group.
'collection', to indicate that the grouping is merely a collection for convenience, without an implied relationship between the members.
|
inherited |
Predicate returning True if this object's 'metaid' attribute is set.
isSetMetaId() boolID, 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.
|
inherited |
Predicate returning True if this object has a ModelHistory object attached to it.
isSetModelHistory() boolTrue if the ModelHistory of this object is set, False otherwise.| def libsbml.Group.isSetName | ( | self | ) |
|
inherited |
Predicate returning True if this object's 'notes' subelement exists and has content.
isSetNotes() boolThe optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
True if a 'notes' subelement exists, False otherwise.
|
inherited |
Predicate returning True if this object's 'sboTerm' attribute is set.
isSetSBOTerm() boolTrue if the 'sboTerm' attribute of this SBML object is set, False otherwise.
|
inherited |
Predicate returning true or false depending on whether the user data of this element has been set.
isSetUserData() boolTrue if this object's user data has been set, False otherwise.
|
inherited |
Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces.
matchesRequiredSBMLNamespacesForAddition(SBase sb) bool
| sb | an object to compare with respect to namespaces. |
True if this object's collection of namespaces is a subset of sb's, False otherwise.
|
inherited |
Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces.
matchesSBMLNamespaces(SBase sb) bool
| sb | an object to compare with respect to namespaces. |
True if this object's collection of namespaces is the same as sb's, False otherwise.
|
inherited |
Removes this object from its parent.
removeFromParentAndDelete() intIf the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
| def libsbml.Group.removeMember | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
removeMember(long n) Member removeMember(string sid) Member
Each variant is described separately below.
removeMember(long n)
Removes the nth Member from this Group and returns a pointer to it.
| n | a long integer representing the index of the Member to remove. |
removeMember(string sid)
Removes the Member from this Group based on its identifier and returns a pointer to it.
| sid | a string representing the identifier of the Member to remove. |
|
inherited |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
removeTopLevelAnnotationElement(string elementName, string elementURI, bool removeEmpty) int removeTopLevelAnnotationElement(string elementName, string elementURI) int removeTopLevelAnnotationElement(string elementName) int
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). |
parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
|
inherited |
Replaces all uses of a given meta identifier attribute value with another value.
renameMetaIdRefs(string oldid, string newid)
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. |
|
inherited |
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(string oldid, string newid)
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. |
|
inherited |
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(string oldid, string newid)
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. |
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inherited |
This method has multiple variants; they differ in the arguments they accept.
replaceTopLevelAnnotationElement(XMLNode annotation) int replaceTopLevelAnnotationElement(string annotation) int
Each variant is described separately below.
replaceTopLevelAnnotationElement(XMLNode annotation)
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. |
replaceTopLevelAnnotationElement(string annotation)
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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inherited |
This method has multiple variants; they differ in the arguments they accept.
setAnnotation(XMLNode annotation) int setAnnotation(string annotation) int
Each variant is described separately below.
setAnnotation(XMLNode annotation)
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() or SBase.appendAnnotation().
| annotation | an XML structure that is to be used as the new content of the 'annotation' subelement of this object. |
setAnnotation(string annotation)
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() or SBase.appendAnnotation().
| annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object. |
| def libsbml.Group.setId | ( | self, | |
| id | |||
| ) |
Sets the value of the 'id' attribute of this Group.
setId(string id) int| id | string value of the 'id' attribute to be set. |
id = None or an empty string is equivalent to calling unsetId().
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inherited |
Sets the value of the 'id' attribute of this SBML object.
setIdAttribute(string sid) intsid 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. |
| def libsbml.Group.setKind | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
setKind(long kind) int setKind(string kind) int
Each variant is described separately below.
setKind(long kind)
Sets the value of the 'kind' attribute of this Group.
| kind | int value of the 'kind' attribute to be set. The value must be one of the predefined constants that represent valid SBML Level 3 Version 1 Group 'kind' names, which means it must be one of the following values: |
'classification', to indicate that the group represents a class, and its members have an is-a relationship to the group.
'partonomy', to indicate that the group represents a collection of parts, and its members have a part-of relationship to the group.
'collection', to indicate that the grouping is merely a collection for convenience, without an implied relationship between the members. setKind(string kind)
Sets the value of the 'kind' attribute of this Group.
| kind | string of the 'kind' attribute to be set. The value must be one of the following possible strings:
|
'classification', to indicate that the group represents a class, and its members have an is-a relationship to the group.
'partonomy', to indicate that the group represents a collection of parts, and its members have a part-of relationship to the group.
'collection', to indicate that the grouping is merely a collection for convenience, without an implied relationship between the members.
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inherited |
Sets the value of the meta-identifier attribute of this SBML object.
setMetaId(string metaid) intID, 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.
setModelHistory(ModelHistory history) int
The content of history is copied, and this object's existing model history content is deleted.
| history | ModelHistory of this object. |
| def libsbml.Group.setName | ( | self, | |
| name | |||
| ) |
Sets the value of the 'name' attribute of this Group.
setName(string name) int| name | string value of the 'name' attribute to be set. |
name = None or an empty string is equivalent to calling unsetName().
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inherited |
Sets the namespaces relevant of this SBML object.
setNamespaces(XMLNamespaces xmlns) int
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 |
This method has multiple variants; they differ in the arguments they accept.
setNotes(XMLNode notes) int setNotes(string notes, bool addXHTMLMarkup) int setNotes(string notes) int
Each variant is described separately below.
setNotes(string notes, bool addXHTMLMarkup = false)
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. |
parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.setNotes(XMLNode notes)
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 |
This method has multiple variants; they differ in the arguments they accept.
setSBOTerm(int value) int setSBOTerm(string sboid) int
Each variant is described separately below.
setSBOTerm(int value)
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. |
setSBOTerm(string sboid)
Sets the value of the 'sboTerm' attribute by string.
int, and SBO identifiers are stored simply as integers.
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inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
toSBML() string
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inherited |
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inherited |
Unsets the value of the 'annotation' subelement of this SBML object.
unsetAnnotation() intWhereas 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.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
unsetCVTerms() int| def libsbml.Group.unsetId | ( | self | ) |
Unsets the value of the 'id' attribute of this Group.
unsetId() int
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inherited |
Unsets the value of the 'id' attribute of this SBML object.
unsetIdAttribute() intMost (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.
| def libsbml.Group.unsetKind | ( | self | ) |
Unsets the value of the 'kind' attribute of this Group.
unsetKind() int'classification', to indicate that the group represents a class, and its members have an is-a relationship to the group.
'partonomy', to indicate that the group represents a collection of parts, and its members have a part-of relationship to the group.
'collection', to indicate that the grouping is merely a collection for convenience, without an implied relationship between the members.
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inherited |
Unsets the value of the 'metaid' attribute of this SBML object.
unsetMetaId() intID, 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.
unsetModelHistory() int| def libsbml.Group.unsetName | ( | self | ) |
Unsets the value of the 'name' attribute of this Group.
unsetName() int
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inherited |
Unsets the value of the 'notes' subelement of this SBML object.
unsetNotes() intThe 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.
unsetSBOTerm() int
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inherited |
Unsets the user data of this element.
unsetUserData() int