|
libSBML Python API
5.5.0
|
|
libSBML Python API
5.5.0
|
LibSBML implementation of SBML's ListOfParameters construct.
The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. All are derived from the abstract class SBase, and inherit the various attributes and subelements of SBase, such as 'metaid' as and 'annotation'. The ListOf___ classes do not add any attributes of their own.
The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):
Readers may wonder about the motivations for using the ListOf___ containers. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.
| def libsbml.ListOf.__len__ | ( | self | ) | [inherited] |
Python method signature(s):
__len__(ListOf self)int
| def libsbml.SBase.addCVTerm | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
addCVTerm(SBase self, CVTerm term, bool newBag=False)
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. |
| def libsbml.ListOf.append | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
append(ListOf self, SBase item)
Adds item to the end of this ListOf.
This variant of the method makes a clone of the item handed to it. This means that when the ListOf is destroyed, the original items will not be destroyed.
| item | the item to be added to the list. |
| def libsbml.ListOf.appendAndOwn | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
appendAndOwn(ListOf self, SBase item)
Adds item to the end of this ListOf.
This variant of the method does not clone the item handed to it; instead, it assumes ownership of it. This means that when the ListOf is destroyed, the item will be destroyed along with it.
| item | the item to be added to the list. |
| def libsbml.SBase.appendAnnotation | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
appendAnnotation(SBase self, XMLNode annotation)
This method has multiple variants that differ in the arguments they accept. Each 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 |
Reimplemented in libsbml.SpeciesReference, and libsbml.Model.
| def libsbml.ListOf.appendFrom | ( | self, | |
| args | |||
| ) | [inherited] |
| def libsbml.SBase.appendNotes | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
appendNotes(SBase self, XMLNode notes)
This method has multiple variants that differ in the arguments they accept. Each 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.ListOf.clear | ( | self, | |
doDelete = True |
|||
| ) | [inherited] |
Python method signature(s):
clear(ListOf self, bool doDelete=True) clear(ListOf self)
Removes all items in this ListOf object.
If doDelete is True (default), all items in this ListOf object are deleted and cleared, and thus the caller doesn't have to delete those items. Otherwise, all items are just cleared from this ListOf object and the caller is responsible for deleting all items. (In that case, pointers to all items should be stored elsewhere before calling this function.)
| doDelete | if True (default), all items are deleted and cleared. Otherwise, all items are just cleared and not deleted. |
| def libsbml.ListOfParameters.clone | ( | self | ) |
LibSBML implementation of SBML's ListOfParameters construct.
The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. All are derived from the abstract class SBase, and inherit the various attributes and subelements of SBase, such as 'metaid' as and 'annotation'. The ListOf___ classes do not add any attributes of their own.
The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):
Readers may wonder about the motivations for using the ListOf___ containers. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.
clone(ListOfParameters self)
Creates and returns a deep copy of this ListOfParameters instance.
Reimplemented from libsbml.ListOf.
Reimplemented in libsbml.ListOfLocalParameters.
| def libsbml.SBase.disablePackage | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
disablePackage(SBase self, string pkgURI, string pkgPrefix)
Disables the given SBML Level 3 package
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
| pkgURI | the URI of the package |
| pkgPrefix | the XML prefix of the package |
| def libsbml.SBase.enablePackage | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
enablePackage(SBase self, string pkgURI, string pkgPrefix, bool flag)
Enables or disables the given SBML Level 3 package
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
| pkgURI | the URI of the package |
| pkgPrefix | the XML prefix of the package |
| flag | whether to enable (True) or disable (False) the package |
| def libsbml.ListOfParameters.get | ( | self, | |
| args | |||
| ) |
Python method signature(s):
get(ListOfParameters self, long n)
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
get(long n)
Returns the Parameter object located at position n within this ListOfParameters instance.
| n | the index number of the Parameter to get. |
n is out of bounds for the length of the list, then None is returned.get(string sid)
Returns the first Parameter object matching the given identifier.
| sid | a string representing the identifier of the Parameter to get. |
sid, then None is returned.Reimplemented from libsbml.ListOf.
Reimplemented in libsbml.ListOfLocalParameters.
| def libsbml.SBase.getAncestorOfType | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
getAncestorOfType(SBase self, int type, string pkgName="core")
Returns the first ancestor object that has the given SBML type code.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the 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. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.
| type | the SBML type code of the object sought |
| pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
None if no ancestor exists.| def libsbml.SBase.getAnnotation | ( | self | ) | [inherited] |
Python method signature(s):
getAnnotation(SBase self)
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
| def libsbml.SBase.getAnnotationString | ( | self | ) | [inherited] |
Python method signature(s):
getAnnotationString(SBase self)
Returns the content of the 'annotation' subelement of this object as a character string.
Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form.
| def libsbml.SBase.getColumn | ( | self | ) | [inherited] |
Python method signature(s):
getColumn(SBase self)
Returns the column number on which this object first appears in the XML representation of the SBML document.
| def libsbml.SBase.getCVTerm | ( | self, | |
| args | |||
| ) | [inherited] |
| def libsbml.SBase.getCVTerms | ( | self | ) | [inherited] |
Python method signature(s):
getCVTerms()
Get the CVTermList of CVTerm objects in this SBase.
Returns the CVTermList for this SBase.
| def libsbml.ListOf.getElementByMetaId | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
getElementByMetaId(ListOf self, string metaid)
Returns the first child element it can find with the given metaid, or None if no such object is found.
| metaid | string representing the metaid of objects to find |
Reimplemented from libsbml.SBase.
| def libsbml.ListOf.getElementBySId | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
getElementBySId(ListOf self, string id)
Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.
| id | string representing the id of objects to find |
Reimplemented from libsbml.SBase.
Reimplemented in libsbml.ListOfEventAssignments, libsbml.ListOfRules, libsbml.ListOfInitialAssignments, libsbml.ListOfLocalParameters, and libsbml.ListOfUnitDefinitions.
| def libsbml.ListOfParameters.getElementName | ( | self | ) |
Python method signature(s):
getElementName(ListOfParameters self)
Returns the XML element name of this object.
For ListOfParameters, the XML element name is 'listOfParameters'.
'listOfParameters'. Reimplemented from libsbml.ListOf.
Reimplemented in libsbml.ListOfLocalParameters.
| def libsbml.ListOfParameters.getItemTypeCode | ( | self | ) |
Python method signature(s):
getItemTypeCode(ListOfParameters self)
Returns the libSBML type code for the objects contained in this ListOf (i.e., Parameter objects, if the list is non-empty).
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the 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_.
Reimplemented from libsbml.ListOf.
Reimplemented in libsbml.ListOfLocalParameters.
| def libsbml.SBase.getLevel | ( | self | ) | [inherited] |
Python method signature(s):
getLevel(SBase self)
Returns the SBML Level of the SBMLDocument object containing this object.
| def libsbml.SBase.getLine | ( | self | ) | [inherited] |
Python method signature(s):
getLine(SBase self)
Returns the line number on which this object first appears in the XML representation of the SBML document.
| def libsbml.SBase.getListOfAllElements | ( | self | ) | [inherited] |
| def libsbml.SBase.getListOfAllElementsFromPlugins | ( | self | ) | [inherited] |
| def libsbml.SBase.getMetaId | ( | self | ) | [inherited] |
Python method signature(s):
getMetaId(SBase self)
Returns the value of the 'metaid' attribute of this object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
| def libsbml.SBase.getModel | ( | self | ) | [inherited] |
Python method signature(s):
getModel(SBase self)
Returns the Model object in which the current object is located.
| def libsbml.SBase.getModelHistory | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
getModelHistory(SBase self)
Returns the ModelHistory object, if any, attached to this object.
None if none exist.| def libsbml.SBase.getNamespaces | ( | self | ) | [inherited] |
Python method signature(s):
getNamespaces(SBase self)
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.
Reimplemented in libsbml.SBMLDocument.
| def libsbml.SBase.getNotes | ( | self | ) | [inherited] |
Python method signature(s):
getNotes(SBase self)
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
| def libsbml.SBase.getNotesString | ( | self | ) | [inherited] |
Python method signature(s):
getNotesString(SBase self)
Returns the content of the 'notes' subelement of this object as a string.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
| def libsbml.SBase.getNumCVTerms | ( | self | ) | [inherited] |
| def libsbml.SBase.getNumPlugins | ( | self | ) | [inherited] |
Python method signature(s):
getNumPlugins(SBase self)
Returns the number of plugin objects (extenstion interfaces) for SBML Level 3 package extensions known.
| def libsbml.SBase.getPackageName | ( | self | ) | [inherited] |
Python method signature(s):
getPackageName(SBase self)
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. | def libsbml.SBase.getPackageVersion | ( | self | ) | [inherited] |
Python method signature(s):
getPackageVersion(SBase self)
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.| def libsbml.SBase.getParentSBMLObject | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
getParentSBMLObject(SBase self)
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.
| def libsbml.SBase.getPlugin | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
getPlugin(SBase self, string package)
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getPlugin(long n)
Returns the nth plugin object (extension interface) for an SBML Level 3 package extension.
| n | the index of the plugin to return |
getPlugin(string package)
Returns a plugin object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
| package | the name or URI of the package |
| def libsbml.SBase.getResourceBiologicalQualifier | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
getResourceBiologicalQualifier(SBase self, string resource)
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose 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. | def libsbml.SBase.getResourceModelQualifier | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
getResourceModelQualifier(SBase self, string resource)
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with 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. | def libsbml.SBase.getSBMLDocument | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
getSBMLDocument(SBase self)
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
| def libsbml.SBase.getSBOTerm | ( | self | ) | [inherited] |
Python method signature(s):
getSBOTerm(SBase self)
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
-1 if the value is not set. | def libsbml.SBase.getSBOTermID | ( | self | ) | [inherited] |
Python method signature(s):
getSBOTermID(SBase self)
Returns the string representation of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
| def libsbml.ListOfParameters.getTypeCode | ( | self | ) |
Python method signature(s):
getTypeCode(ListOfParameters self)
Returns the libSBML type code for this SBML object.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the 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_.
Reimplemented from libsbml.ListOf.
Reimplemented in libsbml.ListOfLocalParameters.
| def libsbml.SBase.getVersion | ( | self | ) | [inherited] |
Python method signature(s):
getVersion(SBase self)
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
| def libsbml.SBase.hasValidLevelVersionNamespaceCombination | ( | self | ) | [inherited] |
Python method signature(s):
hasValidLevelVersionNamespaceCombination(SBase self)
| def libsbml.ListOf.insert | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
insert(ListOf self, int location, SBase item)
Inserts the item at the given position of this ListOf
This variant of the method makes a clone of the item handet to it. This means that when the ListOf is destroyed, the original items will not be destroyed.
| location | the location where to insert the item |
| item | the item to be inserted to the list |
| def libsbml.ListOf.insertAndOwn | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
insertAndOwn(ListOf self, int location, SBase item)
Inserts the item at the given position of this ListOf
This variant of the method makes a clone of the item handet to it. This means that when the ListOf is destroyed, the original items will not be destroyed.
| location | the location where to insert the item |
| item | the item to be inserted to the list |
| def libsbml.SBase.isPackageEnabled | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
isPackageEnabled(SBase self, string pkgName)
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.| def libsbml.SBase.isPackageURIEnabled | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
isPackageURIEnabled(SBase self, string pkgURI)
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.| def libsbml.SBase.isPkgEnabled | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
isPkgEnabled(SBase self, string pkgName)
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.| def libsbml.SBase.isPkgURIEnabled | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
isPkgURIEnabled(SBase self, string pkgURI)
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.| def libsbml.SBase.isSetAnnotation | ( | self | ) | [inherited] |
Python method signature(s):
isSetAnnotation(SBase self)
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.| def libsbml.SBase.isSetMetaId | ( | self | ) | [inherited] |
Python method signature(s):
isSetMetaId(SBase self)
Predicate returning True if this object's 'metaid' attribute is set.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
True if the 'metaid' attribute of this SBML object is set, False otherwise.| def libsbml.SBase.isSetModelHistory | ( | self | ) | [inherited] |
Python method signature(s):
isSetModelHistory(SBase self)
Predicate returning True if this object has a ModelHistory object attached to it.
True if the ModelHistory of this object is set, false otherwise.| def libsbml.SBase.isSetNotes | ( | self | ) | [inherited] |
Python method signature(s):
isSetNotes(SBase self)
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.| def libsbml.SBase.isSetSBOTerm | ( | self | ) | [inherited] |
Python method signature(s):
isSetSBOTerm(SBase self)
Predicate returning True if this object's 'sboTerm' attribute is set.
True if the 'sboTerm' attribute of this SBML object is set, False otherwise. | def libsbml.SBase.matchesRequiredSBMLNamespacesForAddition | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)
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. | def libsbml.SBase.matchesSBMLNamespaces | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
matchesSBMLNamespaces(SBase self, SBase sb)
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. | def libsbml.ListOfParameters.remove | ( | self, | |
| args | |||
| ) |
Python method signature(s):
remove(ListOfParameters self, long n)
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
remove(long n)
Removes the nth item from this ListOfParameters, and returns a pointer to it.
| n | the index of the item to remove |
n is out of bounds for the length of the list, then None is returned.remove(string sid)
Removes the first Parameter object in this ListOfParameters matching the given identifier, and returns a pointer to it.
| sid | the identifier of the item to remove. |
sid, then None is returned. Reimplemented from libsbml.ListOf.
Reimplemented in libsbml.ListOfLocalParameters.
| def libsbml.ListOf.removeFromParentAndDelete | ( | self | ) | [inherited] |
Python method signature(s):
removeFromParentAndDelete(ListOf self)
Because ListOf objects typically live as object children of their parent object and not as pointer children, this function clears itself, but does not attempt to do anything else. If a particular ListOf subclass does indeed exist as a pointer only, this function will need to be overridden.
Reimplemented from libsbml.SBase.
| def libsbml.SBase.removeTopLevelAnnotationElement | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="")
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 |
| def libsbml.SBase.renameMetaIdRefs | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
renameMetaIdRefs(SBase self, string oldid, string newid)
Renames all the MetaIdRef attributes on this element.
This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier |
| newid | the new identifier |
| def libsbml.SBase.renameSIdRefs | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
renameSIdRefs(SBase self, string oldid, string newid)
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate) math formulas, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier |
| newid | the new identifier |
Reimplemented in libsbml.StoichiometryMath, libsbml.Priority, libsbml.Delay, libsbml.Trigger, libsbml.EventAssignment, libsbml.SimpleSpeciesReference, libsbml.KineticLaw, libsbml.Reaction, libsbml.Constraint, libsbml.RateRule, libsbml.AssignmentRule, libsbml.Rule, libsbml.InitialAssignment, libsbml.Species, libsbml.Compartment, and libsbml.Model.
| def libsbml.SBase.renameUnitSIdRefs | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
renameUnitSIdRefs(SBase self, string oldid, string newid)
Renames all the UnitSIdRef attributes on this element.
This method works by looking at all unit identifier attribute values (including, if appropriate, inside math formulas), comparing the unit identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier |
| newid | the new identifier |
Reimplemented in libsbml.StoichiometryMath, libsbml.Priority, libsbml.Delay, libsbml.Trigger, libsbml.EventAssignment, libsbml.KineticLaw, libsbml.Constraint, libsbml.Rule, libsbml.InitialAssignment, libsbml.Parameter, libsbml.Species, libsbml.Compartment, libsbml.FunctionDefinition, and libsbml.Model.
| def libsbml.SBase.replaceTopLevelAnnotationElement | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
replaceTopLevelAnnotationElement(SBase self, XMLNode annotation)
This method has multiple variants that differ in the arguments they accept. Each 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); 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); 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 |
| def libsbml.SBase.setAnnotation | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
setAnnotation(SBase self, XMLNode annotation)
This method has multiple variants that differ in the arguments they accept. Each 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 |
Reimplemented in libsbml.SpeciesReference, and libsbml.Model.
| def libsbml.SBase.setMetaId | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
setMetaId(SBase self, string metaid)
Sets the value of the 'metaid' attribute of this object.
The string metaid is copied. The value of metaid must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement.
| metaid | the identifier string to use as the value of the 'metaid' attribute |
| def libsbml.SBase.setModelHistory | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
setModelHistory(SBase self, ModelHistory history)
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. |
| def libsbml.SBase.setNamespaces | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
setNamespaces(SBase self, XMLNamespaces xmlns)
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 |
| def libsbml.SBase.setNotes | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
setNotes(SBase self, XMLNode notes)
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setNotes(string notes)
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 |
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 |
| def libsbml.SBase.setSBOTerm | ( | self, | |
| args | |||
| ) | [inherited] |
Python method signature(s):
setSBOTerm(SBase self, int value)
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setSBOTerm(int value)
Sets the value of the 'sboTerm' attribute.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
| value | the NNNNNNN integer portion of the SBO identifier |
setSBOTerm(string &sboid)
Sets the value of the 'sboTerm' attribute by string.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
| def libsbml.ListOf.size | ( | self | ) | [inherited] |
| def libsbml.SBase.toSBML | ( | self | ) | [inherited] |
toSBML(SBase self) string *
Returns a string consisting of a partial SBML corresponding to just this object.
| def libsbml.SBase.unsetAnnotation | ( | self | ) | [inherited] |
Python method signature(s):
unsetAnnotation(SBase self)
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.
| def libsbml.SBase.unsetCVTerms | ( | self | ) | [inherited] |
| def libsbml.SBase.unsetId | ( | self | ) | [inherited] |
Python method signature(s):
unsetId(SBase self)
Unsets the value of the 'id' attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always either Sid or UnitSId, depending on the object in question. Both data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The equality of SId and UnitSId type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId and UnitSId.
Reimplemented in libsbml.Event, libsbml.SimpleSpeciesReference, and libsbml.Model.
| def libsbml.SBase.unsetMetaId | ( | self | ) | [inherited] |
Python method signature(s):
unsetMetaId(SBase self)
Unsets the value of the 'metaid' attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
| def libsbml.SBase.unsetModelHistory | ( | self | ) | [inherited] |
Python method signature(s):
unsetModelHistory(SBase self)
Unsets the ModelHistory object attached to this object.
| def libsbml.SBase.unsetName | ( | self | ) | [inherited] |
Python method signature(s):
unsetName(SBase self)
Unsets the value of the 'name' attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. In contrast to the 'id' attribute, the 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Reimplemented in libsbml.Event, libsbml.SimpleSpeciesReference, libsbml.Reaction, libsbml.Parameter, libsbml.Species, libsbml.Compartment, libsbml.SpeciesType, libsbml.CompartmentType, libsbml.UnitDefinition, libsbml.FunctionDefinition, and libsbml.Model.
| def libsbml.SBase.unsetNotes | ( | self | ) | [inherited] |
Python method signature(s):
unsetNotes(SBase self)
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.
| def libsbml.SBase.unsetSBOTerm | ( | self | ) | [inherited] |
Python method signature(s):
unsetSBOTerm(SBase self)
Unsets the value of the 'sboTerm' attribute of this SBML object.