libSBML Python API
5.11.0
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The Layout class stores layout information for some or all elements of the SBML model as well as additional objects that need not be connected to the model. The Layout has two attributes: id and name. Additionally, a Dimensions element specifies the size of the layout. The actual layout elements are contained in several lists, namely: a ListOfCompartmentGlyphs, a ListOfSpeciesGlyphs, a ListOfReactionGlyphs, a ListOfTextGlyphs, and a ListOfAdditionalGraphicalObjects. Each of these lists can only occur once, and, if present, are not allowed to be empty.
Public Member Functions | |
def | __init__ (self, args) |
layout
The layout of a diagram of an SBML model. More... | |
def | addAdditionalGraphicalObject (self, glyph) |
Adds a new additional graphical object glyph. More... | |
def | addCompartmentGlyph (self, glyph) |
Adds a new compartment glyph. More... | |
def | addCVTerm |
Adds a copy of the given CVTerm object to this SBML object. More... | |
def | addGeneralGlyph (self, glyph) |
Adds a new general glyph. More... | |
def | addReactionGlyph (self, glyph) |
Adds a new reaction glyph. More... | |
def | addSpeciesGlyph (self, glyph) |
Adds a new species glyph. More... | |
def | addTextGlyph (self, glyph) |
Adds a new text glyph. 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 Layout. More... | |
def | connectToChild (self) |
def | createAdditionalGraphicalObject (self) |
Creates a GraphicalObject object, adds it to the end of the additional graphical objects list and returns a pointer to the newly created object. More... | |
def | createCompartmentGlyph (self) |
Creates a CompartmentGlyph object, adds it to the end of the compartment glyph objects list and returns a pointer to the newly created object. More... | |
def | createCubicBezier (self) |
Creates a new CubicBezier for the Curve object of the last ReactionGlyph or the last SpeciesReferenceGlyph in the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects. More... | |
def | createGeneralGlyph (self) |
Creates a GeneralGlyph object, adds it to the end of the additional objects list and returns a reference to the newly created object. More... | |
def | createLineSegment (self) |
Creates a new LineSegment for the Curve object of the last ReactionGlyph or the last SpeciesReferenceGlyph in the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects. More... | |
def | createReactionGlyph (self) |
Creates a ReactionGlyph object, adds it to the end of the reaction glyph objects list and returns a pointer to the newly created object. More... | |
def | createSpeciesGlyph (self) |
Creates a SpeciesGlyph object, adds it to the end of the species glyph objects list and returns a pointer to the newly created object. More... | |
def | createSpeciesReferenceGlyph (self) |
Creates a new SpeciesReferenceGlyph for the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects. More... | |
def | createTextGlyph (self) |
Creates a TextGlyph object, adds it to the end of the text glyph objects list and returns a pointer to the newly created object. More... | |
def | deleteDisabledPlugins |
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 | getAdditionalGraphicalObject (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | getAncestorOfType (self, args) |
Returns the first ancestor object that has the given SBML type code from the given package. 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 on which this object first appears in the XML representation of the SBML document. More... | |
def | getCompartmentGlyph (self, args) |
This method has multiple variants; they differ in the arguments they accept. 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 | getDimensions (self) |
Returns the dimensions of the layout. More... | |
def | getDimensionsExplicitlySet (self) |
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 it can find with a specific 'metaid' attribute value, or None if no such object is found. More... | |
def | getElementBySId (self, 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. More... | |
def | getElementName (self) |
Returns the XML element name of this SBML object. More... | |
def | getGeneralGlyph (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | getId (self) |
Returns the value of the 'id' attribute of this Layout. More... | |
def | getLevel (self) |
Returns the SBML Level of the SBMLDocument object containing this object. More... | |
def | getLine (self) |
Returns the line number on which this object first appears in the XML representation of the SBML document. More... | |
def | getListOfAdditionalGraphicalObjects (self) |
Returns the ListOf object that holds all additonal graphical objects. More... | |
def | getListOfAllElements |
Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More... | |
def | getListOfAllElementsFromPlugins |
Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
def | getListOfCompartmentGlyphs (self) |
Returns the ListOf object that holds all compartment glyphs. More... | |
def | getListOfReactionGlyphs (self) |
Returns the ListOf object that holds all reaction glyphs. More... | |
def | getListOfSpeciesGlyphs (self) |
Returns the ListOf object that holds all species glyphs. More... | |
def | getListOfTextGlyphs (self) |
Returns the ListOf object that holds all text glyphs. More... | |
def | getMetaId (self) |
Returns the value of the 'metaid' attribute of this 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 Layout. 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 | getNumAdditionalGraphicalObjects (self) |
Returns the number of additional graphical objects for the layout. More... | |
def | getNumCompartmentGlyphs (self) |
Returns the number of compartment glyphs for the layout. 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 (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
def | getNumGeneralGlyphs (self) |
Returns the number of general glyphs for the layout. More... | |
def | getNumPlugins (self) |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
def | getNumReactionGlyphs (self) |
Returns the number of reaction glyphs for the layout. More... | |
def | getNumSpeciesGlyphs (self) |
Returns the number of species glyphs for the layout. More... | |
def | getNumTextGlyphs (self) |
Returns the number of text glyphs for the layout. 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 namespace prefix of this element. More... | |
def | getReactionGlyph (self, args) |
This method has multiple variants; they differ in the arguments they accept. 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 | getSpeciesGlyph (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | getTextGlyph (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | getTypeCode (self) |
Returns the libSBML type code of this object instance. 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 | hasValidLevelVersionNamespaceCombination (self) |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
def | initDefaults (self) |
Does nothing since no defaults are defined for Layout. 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 or False depending on whether this Layout's 'id' attribute has been 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 or False depending on whether this Layout's 'name' attribute has been 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 | 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 | removeAdditionalGraphicalObject (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | removeCompartmentGlyph (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | removeFromParentAndDelete (self) |
Removes this object from its parent. More... | |
def | removeReactionGlyph (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | removeSpeciesGlyph (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | removeSpeciesReferenceGlyph (self, id) |
Remove the species reference glyph with the given id . More... | |
def | removeTextGlyph (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 | setDimensions (self, dimensions) |
Sets the dimensions of the layout. More... | |
def | setId (self, id) |
Sets the value of the 'id' attribute of this Layout. More... | |
def | setMetaId (self, metaid) |
Sets the value of the meta-identifier attribute of this 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 Layout. 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 | toXML (self) |
Creates an XMLNode object from this. 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 Layout. 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 Layout. 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 libsbml.Layout.addAdditionalGraphicalObject | ( | self, | |
glyph | |||
) |
Adds a new additional graphical object glyph.
addAdditionalGraphicalObject(GraphicalObject glyph)
def libsbml.Layout.addCompartmentGlyph | ( | self, | |
glyph | |||
) |
Adds a new compartment glyph.
addCompartmentGlyph(CompartmentGlyph glyph)
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
addCVTerm(CVTerm term, bool newBag=False) 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. def libsbml.Layout.addGeneralGlyph | ( | self, | |
glyph | |||
) |
Adds a new general glyph.
addGeneralGlyph(GeneralGlyph glyph)
def libsbml.Layout.addReactionGlyph | ( | self, | |
glyph | |||
) |
Adds a new reaction glyph.
addReactionGlyph(ReactionGlyph glyph)
def libsbml.Layout.addSpeciesGlyph | ( | self, | |
glyph | |||
) |
Adds a new species glyph.
addSpeciesGlyph(SpeciesGlyph glyph)
def libsbml.Layout.addTextGlyph | ( | self, | |
glyph | |||
) |
Adds a new text glyph.
addTextGlyph(TextGlyph glyph)
|
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 |
|
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(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 |
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 |
def libsbml.Layout.clone | ( | self | ) |
def libsbml.Layout.connectToChild | ( | self | ) |
connectToChild()
def libsbml.Layout.createAdditionalGraphicalObject | ( | self | ) |
Creates a GraphicalObject object, adds it to the end of the additional graphical objects list and returns a pointer to the newly created object.
createAdditionalGraphicalObject() GraphicalObject
def libsbml.Layout.createCompartmentGlyph | ( | self | ) |
Creates a CompartmentGlyph object, adds it to the end of the compartment glyph objects list and returns a pointer to the newly created object.
createCompartmentGlyph() CompartmentGlyph
def libsbml.Layout.createCubicBezier | ( | self | ) |
Creates a new CubicBezier for the Curve object of the last ReactionGlyph or the last SpeciesReferenceGlyph in the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects.
createCubicBezier() CubicBezier
A pointer to the newly created object is returned.
def libsbml.Layout.createGeneralGlyph | ( | self | ) |
Creates a GeneralGlyph object, adds it to the end of the additional objects list and returns a reference to the newly created object.
createGeneralGlyph() GeneralGlyph
def libsbml.Layout.createLineSegment | ( | self | ) |
Creates a new LineSegment for the Curve object of the last ReactionGlyph or the last SpeciesReferenceGlyph in the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects.
createLineSegment() LineSegment
A pointer to the newly created object is returned.
def libsbml.Layout.createReactionGlyph | ( | self | ) |
Creates a ReactionGlyph object, adds it to the end of the reaction glyph objects list and returns a pointer to the newly created object.
createReactionGlyph() ReactionGlyph
def libsbml.Layout.createSpeciesGlyph | ( | self | ) |
Creates a SpeciesGlyph object, adds it to the end of the species glyph objects list and returns a pointer to the newly created object.
createSpeciesGlyph() SpeciesGlyph
def libsbml.Layout.createSpeciesReferenceGlyph | ( | self | ) |
Creates a new SpeciesReferenceGlyph for the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects.
createSpeciesReferenceGlyph() SpeciesReferenceGlyph
A pointer to the newly created object is returned.
def libsbml.Layout.createTextGlyph | ( | self | ) |
|
inherited |
Deletes all information stored in disabled plugins.
deleteDisabledPlugins(bool recursive=True) deleteDisabledPlugins()
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) int
This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from an other SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
|
inherited |
Enables or disables the given SBML Level 3 package on this object.
enablePackage(string pkgURI, string pkgPrefix, bool flag) int
This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase.disablePackage().
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.Layout.getAdditionalGraphicalObject | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getAdditionalGraphicalObject(long index) GraphicalObject getAdditionalGraphicalObject(string id) GraphicalObject
Each variant is described separately below.
getAdditionalGraphicalObject(long index)
Returns the additional graphical object with the given index. If the index is invalid, None
is returned.
getAdditionalGraphicalObject(string id)
Returns the additional graphical object that has the given id
, or None
if no graphical object has the id.
|
inherited |
Returns the first ancestor object that has the given SBML type code from the given package.
getAncestorOfType(int type, string pkgName) SBase getAncestorOfType(int type) SBase
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.
|
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.
|
inherited |
Returns the content of the 'annotation' subelement of this object as a character string.
getAnnotationString() string
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.
|
inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
getColumn() long
def libsbml.Layout.getCompartmentGlyph | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getCompartmentGlyph(long index) CompartmentGlyph getCompartmentGlyph(string id) CompartmentGlyph
Each variant is described separately below.
getCompartmentGlyph(long index)
Returns the compartment glyph with the given index. If the index is invalid, None
is returned.
getCompartmentGlyph(string id)
Returns the compartment glyph that has the given id
, or None
if no compartment glyph has the id.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
getCVTerms() List *
def libsbml.Layout.getDimensions | ( | self | ) |
Returns the dimensions of the layout.
getDimensions() Dimensions
def libsbml.Layout.getDimensionsExplicitlySet | ( | self | ) |
getDimensionsExplicitlySet() bool
Predicate returning true if the dimensions has been set
|
inherited |
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.
getDisabledPlugin(long n) SBasePlugin
n | the index of the disabled plug-in to return |
|
inherited |
Returns the first child element it can find with a specific 'metaid' attribute value, or None
if no such object is found.
getElementByMetaId(string metaid) SBase
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.metaid | string representing the 'metaid' attribute value of the object to find. |
|
inherited |
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.
getElementBySId(string id) SBase
id | string representing the 'id' attribute value of the object to find. |
def libsbml.Layout.getElementName | ( | self | ) |
Returns the XML element name of this SBML object.
getElementName() string
def libsbml.Layout.getGeneralGlyph | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getGeneralGlyph(long index) GeneralGlyph getGeneralGlyph(string id) GeneralGlyph
Each variant is described separately below.
getGeneralGlyph(long index)
Returns the general glyph with the given index. If the index is invalid, None
is returned.
getGeneralGlyph(string id)
Returns the general glyph that has the given id
, or None
if no graphical object has the id.
def libsbml.Layout.getId | ( | self | ) |
Returns the value of the 'id' attribute of this Layout.
getId() string
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
getLevel() long
|
inherited |
Returns the line number on which this object first appears in the XML representation of the SBML document.
getLine() long
def libsbml.Layout.getListOfAdditionalGraphicalObjects | ( | self | ) |
Returns the ListOf object that holds all additonal graphical objects.
getListOfAdditionalGraphicalObjects() ListOfGraphicalObjects
|
inherited |
Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.
getListOfAllElements(ElementFilter filter=None) SBaseList getListOfAllElements() SBaseList
|
inherited |
Returns a List of all child SBase objects contained in SBML package plug-ins.
getListOfAllElementsFromPlugins(ElementFilter filter=None) 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.Layout.getListOfCompartmentGlyphs | ( | self | ) |
Returns the ListOf object that holds all compartment glyphs.
getListOfCompartmentGlyphs() ListOfCompartmentGlyphs
def libsbml.Layout.getListOfReactionGlyphs | ( | self | ) |
Returns the ListOf object that holds all reaction glyphs.
getListOfReactionGlyphs() ListOfReactionGlyphs
def libsbml.Layout.getListOfSpeciesGlyphs | ( | self | ) |
Returns the ListOf object that holds all species glyphs.
getListOfSpeciesGlyphs() ListOfSpeciesGlyphs
def libsbml.Layout.getListOfTextGlyphs | ( | self | ) |
Returns the ListOf object that holds all text glyphs.
getListOfTextGlyphs() ListOfTextGlyphs
|
inherited |
Returns the value of the 'metaid' attribute of this object.
getMetaId() string
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
getModelHistory() ModelHistory
None
if none exist.def libsbml.Layout.getName | ( | self | ) |
Returns the value of the 'name' attribute of this Layout.
getName() string
|
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() string
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
def libsbml.Layout.getNumAdditionalGraphicalObjects | ( | self | ) |
Returns the number of additional graphical objects for the layout.
getNumAdditionalGraphicalObjects() long
def libsbml.Layout.getNumCompartmentGlyphs | ( | self | ) |
Returns the number of compartment glyphs for the layout.
getNumCompartmentGlyphs() long
|
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 (extenstion interfaces) for SBML Level 3 package extensions known.
getNumDisabledPlugins() long
def libsbml.Layout.getNumGeneralGlyphs | ( | self | ) |
Returns the number of general glyphs for the layout.
getNumGeneralGlyphs() long
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
getNumPlugins() long
def libsbml.Layout.getNumReactionGlyphs | ( | self | ) |
Returns the number of reaction glyphs for the layout.
getNumReactionGlyphs() long
def libsbml.Layout.getNumSpeciesGlyphs | ( | self | ) |
Returns the number of species glyphs for the layout.
getNumSpeciesGlyphs() long
def libsbml.Layout.getNumTextGlyphs | ( | self | ) |
Returns the number of text glyphs for the layout.
getNumTextGlyphs() 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() long
0
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.
n | the index of the plug-in to return |
getPlugin(string package)
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
|
inherited |
Returns the namespace prefix of this element.
getPrefix() string
def libsbml.Layout.getReactionGlyph | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getReactionGlyph(long index) ReactionGlyph getReactionGlyph(string id) ReactionGlyph
Each variant is described separately below.
getReactionGlyph(long index)
Returns the reaction glyph with the given index. If the index is invalid, None
is returned.
getReactionGlyph(string id)
Returns the reaction glyph that has the given id
, or None
if no reaction glyph has the id.
|
inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
getResourceBiologicalQualifier(string resource) long
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.
|
inherited |
Returns the MIRIAM model qualifier associated with the given resource.
getResourceModelQualifier(string resource) long
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.
|
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() int
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
-1
if the value is not set.
|
inherited |
Returns the URL representation of the 'sboTerm' attribute of this object.
getSBOTermAsURL() string
This method returns the entire SBO identifier as a text string in the form http
://identifiers.org/biomodels.sbo/SBO:NNNNNNN'
.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
|
inherited |
Returns the string representation of the 'sboTerm' attribute of this object.
getSBOTermID() 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 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.Layout.getSpeciesGlyph | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getSpeciesGlyph(long index) SpeciesGlyph getSpeciesGlyph(string id) SpeciesGlyph
Each variant is described separately below.
getSpeciesGlyph(long index)
Returns the species glyph with the given index. If the index is invalid, None
is returned.
getSpeciesGlyph(string id)
Returns the species glyph that has the given id
, or None
if no species glyph has the id.
def libsbml.Layout.getTextGlyph | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getTextGlyph(long index) TextGlyph getTextGlyph(string id) TextGlyph
Each variant is described separately below.
getTextGlyph(long index)
Returns the text glyph with the given index. If the index is invalid, None
is returned.
getTextGlyph(string id)
Returns the text glyph that has the given id
, or None
if no text glyph has the id.
def libsbml.Layout.getTypeCode | ( | self | ) |
Returns the libSBML type code of this object instance.
getTypeCode() int
SBML_
. 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 getPackageName()
method on the object.
|
inherited |
Gets the namespace URI to which this element belongs to.
getURI() string
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'
; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1'
.
This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it willreturn the XML namespace to which this element belongs.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
getVersion() long
|
inherited |
Predicate returning true
if this object's level/version and namespace values correspond to a valid SBML specification.
hasValidLevelVersionNamespaceCombination() bool
The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
http
://www.sbml.org/sbml/level1
http
://www.sbml.org/sbml/level2
http
://www.sbml.org/sbml/level2/version2
http
://www.sbml.org/sbml/level2/version3
http
://www.sbml.org/sbml/level2/version4
http
://www.sbml.org/sbml/level3/version1/core
true
if the level, version and namespace values of this SBML object correspond to a valid set of values, false
otherwise. def libsbml.Layout.initDefaults | ( | self | ) |
Does nothing since no defaults are defined for Layout.
initDefaults()
|
inherited |
Predicate returning True
if the given SBML Level 3 package is enabled with this object.
isPackageEnabled(string pkgName) bool
The search ignores the package version.
pkgName | the name of the package |
True
if the given package is enabled within this object, False
otherwise.
|
inherited |
Predicate returning True
if an SBML Level 3 package with the given URI is enabled with this object.
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) bool
The search ignores the package version.
pkgName | the name of the package |
True
if the given package is enabled within this object, False
otherwise.
|
inherited |
Predicate returning True
if an SBML Level 3 package with the given URI is enabled with this object.
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() bool
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.Layout.isSetId | ( | self | ) |
Predicate returning True
or False
depending on whether this Layout's 'id' attribute has been set.
isSetId() bool
|
inherited |
Predicate returning True
if this object's 'metaid' attribute is set.
isSetMetaId() bool
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.True
if the 'metaid' attribute of this SBML object is set, False
otherwise.
|
inherited |
Predicate returning True
if this object has a ModelHistory object attached to it.
isSetModelHistory() bool
True
if the ModelHistory of this object is set, False
otherwise.def libsbml.Layout.isSetName | ( | self | ) |
Predicate returning True
or False
depending on whether this Layout's 'name' attribute has been set.
isSetName() bool
|
inherited |
Predicate returning True
if this object's 'notes' subelement exists and has content.
isSetNotes() bool
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
True
if a 'notes' subelement exists, False
otherwise.
|
inherited |
Predicate returning True
if this object's 'sboTerm' attribute is set.
isSetSBOTerm() bool
True
if the 'sboTerm' attribute of this SBML object is 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. def libsbml.Layout.removeAdditionalGraphicalObject | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeAdditionalGraphicalObject(long index) GraphicalObject removeAdditionalGraphicalObject(string id) GraphicalObject
Each variant is described separately below.
removeAdditionalGraphicalObject(long index)
Removes the graphical object with the given index from the layout. A pointer to the graphical object that was removed is returned. If no graphical object has been removed, None
is returned.
removeAdditionalGraphicalObject(string id)
Remove the graphical object with the given id
. A pointer to the removed graphical object is returned. If no graphical object has been removed, None
is returned.
def libsbml.Layout.removeCompartmentGlyph | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeCompartmentGlyph(long index) CompartmentGlyph removeCompartmentGlyph(string id) CompartmentGlyph
Each variant is described separately below.
removeCompartmentGlyph(long index)
Removes the compartment glyph with the given index from the layout. A pointer to the compartment glyph that was removed is returned. If no compartment glyph has been removed, None
is returned.
removeCompartmentGlyph(string id)
Remove the compartment glyph with the given id
. A pointer to the removed compartment glyph is returned. If no compartment glyph has been removed, None
is returned.
|
inherited |
Removes this object from its parent.
removeFromParentAndDelete() int
If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
def libsbml.Layout.removeReactionGlyph | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeReactionGlyph(long index) ReactionGlyph removeReactionGlyph(string id) ReactionGlyph
Each variant is described separately below.
removeReactionGlyph(long index)
Removes the reaction glyph with the given index from the layout. A pointer to the reaction glyph that was removed is returned. If no reaction glyph has been removed, None
is returned.
removeReactionGlyph(string id)
Remove the reaction glyph with the given id
. A pointer to the removed reaction glyph is returned. If no reaction glyph has been removed, None
is returned.
def libsbml.Layout.removeSpeciesGlyph | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeSpeciesGlyph(long index) SpeciesGlyph removeSpeciesGlyph(string id) SpeciesGlyph
Each variant is described separately below.
removeSpeciesGlyph(long index)
Removes the species glyph with the given index from the layout. A pointer to the species glyph that was removed is returned. If no species glyph has been removed, None
is returned.
removeSpeciesGlyph(string id)
Remove the species glyph with the given id
. A pointer to the removed species glyph is returned. If no species glyph has been removed, None
is returned.
def libsbml.Layout.removeSpeciesReferenceGlyph | ( | self, | |
id | |||
) |
Remove the species reference glyph with the given id
.
removeSpeciesReferenceGlyph(string id) SpeciesReferenceGlyph
A pointer to the removed species reference glyph is returned. If no species reference glyph has been removed, None
is returned.
def libsbml.Layout.removeTextGlyph | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeTextGlyph(long index) TextGlyph removeTextGlyph(string id) TextGlyph
Each variant is described separately below.
removeTextGlyph(long index)
Removes the text glyph with the given index from the layout. A pointer to the text glyph that was removed is returned. If no text glyph has been removed, None
is returned.
removeTextGlyph(string id)
Remove the text glyph with the given id
. A pointer to the removed text glyph is returned. If no text glyph has been removed, None
is returned.
|
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=True) 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). |
|
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 |
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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.Layout.setDimensions | ( | self, | |
dimensions | |||
) |
Sets the dimensions of the layout.
setDimensions(Dimensions dimensions)
def libsbml.Layout.setId | ( | self, | |
id | |||
) |
Sets the value of the 'id' attribute of this Layout.
setId(string id) int
|
inherited |
Sets the value of the meta-identifier attribute of this object.
setMetaId(string metaid) int
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.The string metaid
is copied.
metaid | the identifier string to use as the value of the 'metaid' attribute |
|
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.Layout.setName | ( | self, | |
name | |||
) |
Sets the value of the 'name' attribute of this Layout.
setName(string name) int
|
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 |
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
setNotes(XMLNode notes) int setNotes(string notes, bool addXHTMLMarkup=False) int setNotes(string notes) int
Each variant is described separately below.
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 |
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. |
|
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.
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(stringsboid)
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.
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
toSBML() string
|
inherited |
|
inherited |
Unsets the value of the 'annotation' subelement of this SBML object.
unsetAnnotation() int
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.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
unsetCVTerms() int
def libsbml.Layout.unsetId | ( | self | ) |
Unsets the value of the 'id' attribute of this Layout.
unsetId() int
|
inherited |
Unsets the value of the 'metaid' attribute of this SBML object.
unsetMetaId() int
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
Unsets the ModelHistory object attached to this object.
unsetModelHistory() int
def libsbml.Layout.unsetName | ( | self | ) |
Unsets the value of the 'name' attribute of this Layout.
unsetName() int
|
inherited |
Unsets the value of the 'notes' subelement of this SBML object.
unsetNotes() int
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.
|
inherited |
Unsets the value of the 'sboTerm' attribute of this SBML object.
unsetSBOTerm() int