libSBML Python API
5.11.0
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Instantiates a new Text object with the given id
and position offset.
The position offset coordinates can be omitted and will be set to 0 in that case.
All attributes are set as described for the default constructor of GraphicalPrimitive1D. All the font rendering attributes as well as the text to be rendered are unset.
id | id string for the Text object |
x | x coordinate of the position offset |
y | y coordinate of the position offset |
z | z coordinate of the position offset |
This constructor is deprecated. The new libsbml API only has constructors which take the SBML level and version or one that takes an SBMLNamespaces object.
Public Member Functions | |
def | __init__ (self, args) |
Instantiates a new Text object with the given id and position offset. More... | |
def | addCVTerm |
Adds a copy of the given CVTerm object to this SBML object. More... | |
def | addDash (self, dash) |
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 | clearDashes (self) |
Clears all defined dashes. More... | |
def | clone (self) |
Creates and returns a deep copy of this SBase object. More... | |
def | connectToChild (self) |
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 | 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 | 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 | getDashByIndex (self, index) |
Returns the dash at the given index. More... | |
def | getDisabledPlugin (self, args) |
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
def | getElementByMetaId (self, metaid) |
Returns the first child element 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 object. More... | |
def | getFontFamily (self) |
Returns the font family. More... | |
def | getFontSize (self, args) |
Returns the font size as a reference. More... | |
def | getFontStyle (self) |
Returns the font style. More... | |
def | getFontWeight (self) |
Returns the font weight. More... | |
def | getId (self) |
Returns the value of the 'id' attribute of this GraphicalPrimitive. More... | |
def | getIdentityMatrix () |
implementation of a 3D transformation matrix. More... | |
def | getIdentityMatrix2D () |
implementation of a 2D transformation matrix. 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 | 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 | getMatrix (self) |
Returns the matrix which is an array of float values of length 12. More... | |
def | getMatrix2D (self) |
Returns the 2D matrix which is an array of float values of length 6. 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 | getNamespaces (self) |
Returns a list of the XML Namespaces declared on the SBML document owning this object. More... | |
def | getNotes (self, args) |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More... | |
def | getNotesString (self, args) |
Returns the content of the 'notes' subelement of this object as a string. More... | |
def | getNumCVTerms (self) |
Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
def | getNumDashes (self) |
Returns the number of defined dashes. More... | |
def | getNumDisabledPlugins (self) |
Returns the number of disabled plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
def | getNumPlugins (self) |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. 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 | 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 | getStroke (self) |
Returns the stroke color. More... | |
def | getStrokeWidth (self) |
Returns the stroke width. More... | |
def | getText (self) |
Returns the text for the Text object. More... | |
def | getTextAnchor (self) |
Returns the text anchor. More... | |
def | getTypeCode (self) |
Returns the libSBML type code for this object. More... | |
def | getURI (self) |
Gets the namespace URI to which this element belongs to. More... | |
def | getVersion (self) |
Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
def | getVTextAnchor (self) |
Returns the vertical text anchor. More... | |
def | getX (self, args) |
Returns the x position offset as a reference. More... | |
def | getY (self, args) |
Returns the y position offset as a reference. More... | |
def | getZ (self, args) |
Returns the z position offset as a reference. More... | |
def | hasValidLevelVersionNamespaceCombination (self) |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
def | insertDash (self, index, dash) |
Inserts the dash at the given position. 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 | isSetDashArray (self) |
Returns true is the dash array has been set or false otherwise. More... | |
def | isSetFontFamily (self) |
Returns true if the font family has been set or false otherwise. More... | |
def | isSetFontSize (self) |
Returns true if the font size has been set or false otherwise. More... | |
def | isSetFontStyle (self) |
Returns true if the font style has been set or false otherwise. More... | |
def | isSetFontWeight (self) |
Returns true if the font weight has been set or false otherwise. More... | |
def | isSetId (self) |
Predicate returning True or False depending on whether this GraphicalPrimitive's 'id' attribute has been set. More... | |
def | isSetMatrix (self) |
Returns true if the matrix has been set or false otherwise. 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 | 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 | isSetStroke (self) |
Returns true is the stroke has been set or false otherwise. More... | |
def | isSetStrokeWidth (self) |
Returns true is the stroke width has been set or false otherwise. More... | |
def | isSetText (self) |
Returns true if the text is set to something else than the empty string. More... | |
def | isSetTextAnchor (self) |
Returns true if the horizonal alignment attribute has been set. More... | |
def | isSetVTextAnchor (self) |
Returns true if the vertical alignment attribute has been set. More... | |
def | matchesRequiredSBMLNamespacesForAddition (self, args) |
Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
def | matchesSBMLNamespaces (self, args) |
Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
def | removeDash (self, index) |
def | removeFromParentAndDelete (self) |
Removes this object from its parent. 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 | setCoordinates (self, args) |
Sets the position of the text within the viewport. More... | |
def | setDashByIndex (self, index, dash) |
Sets the dash at the given position. More... | |
def | setFontFamily (self, family) |
Sets the font family. More... | |
def | setFontSize (self, size) |
Sets the font size. More... | |
def | setFontStyle (self, style) |
Sets the font style. More... | |
def | setFontWeight (self, weight) |
Sets the font weight. More... | |
def | setId (self, id) |
Sets the value of the 'id' attribute of this GraphicalPrimitive. More... | |
def | setMatrix (self, m) |
setMatrix (float [12] m) More... | |
def | setMatrix2D (self, m) |
setMatrix2D (float [6] m) 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 | 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 | setStroke (self, stroke) |
base class for all graphical primitives which implements all 1D attributes More... | |
def | setStrokeWidth (self, width) |
Sets the stroke width. More... | |
def | setText (self, text) |
Sets the text for the text element. More... | |
def | setTextAnchor (self, anchor) |
Sets the text anchor. More... | |
def | setVTextAnchor (self, anchor) |
Sets the vertical text anchor. More... | |
def | setX (self, x) |
Sets the x position of the text within the viewport. More... | |
def | setY (self, y) |
Sets the y position of the text within the viewport. More... | |
def | setZ (self, z) |
Sets the z position of the text within the viewport. 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 GraphicalPrimitive1D object. More... | |
def | toXMLNode (self) |
Returns this element as an XMLNode. More... | |
def | unsetAnnotation (self) |
Unsets the value of the 'annotation' subelement of this SBML object. More... | |
def | unsetCVTerms (self) |
Clears the list of CVTerm objects attached to this SBML object. More... | |
def | unsetId (self) |
Unsets the value of the 'id' attribute of this GraphicalPrimitive. 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 SBML object. 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.Text.__init__ | ( | self, | |
args | |||
) |
Instantiates a new Text object with the given id
and position offset.
The position offset coordinates can be omitted and will be set to 0 in that case.
All attributes are set as described for the default constructor of GraphicalPrimitive1D. All the font rendering attributes as well as the text to be rendered are unset.
id | id string for the Text object |
x | x coordinate of the position offset |
y | y coordinate of the position offset |
z | z coordinate of the position offset |
This constructor is deprecated. The new libsbml API only has constructors which take the SBML level and version or one that takes an SBMLNamespaces object.
Instantiates a new Text object with the given id
and position offset.
__init__(long level, long version, long pkgVersion) Text __init__(long level, long version) Text __init__(long level) Text __init__() Text __init__(RenderPkgNamespaces renderns) Text __init__(XMLNode node, long l2version=4) Text __init__(XMLNode node) Text __init__(RenderPkgNamespaces renderns, string id, RelAbsVector x, RelAbsVector y, RelAbsVector z) Text __init__(RenderPkgNamespaces renderns, string id, RelAbsVector x, RelAbsVector y) Text __init__(RenderPkgNamespaces renderns, string id, RelAbsVector x) Text __init__(RenderPkgNamespaces renderns, string id) Text
The position offset coordinates can be omitted and will be set to 0 in that case.
All attributes are set as described for the default constructor of GraphicalPrimitive1D. All the font rendering attributes as well as the text to be rendered are unset.
id | id string for the Text object |
x | x coordinate of the position offset |
y | y coordinate of the position offset |
z | z coordinate of the position offset |
This constructor is deprecated. The new libsbml API only has constructors which take the SBML level and version or one that takes an SBMLNamespaces object.
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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.
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inherited |
addDash(long dash)
Adds a dash at the end of the current list
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inherited |
This method has multiple variants; they differ in the arguments they accept.
appendAnnotation(XMLNode annotation) int appendAnnotation(string annotation) int
Each variant is described separately below.
appendAnnotation(XMLNode annotation)
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object |
appendAnnotation(string annotation)
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object |
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inherited |
This method has multiple variants; they differ in the arguments they accept.
appendNotes(XMLNode notes) int appendNotes(string notes) int
Each variant is described separately below.
appendNotes(string notes)
Appends the given notes
to the 'notes' subelement of this object.
The content of the parameter notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML string that is to appended to the content of the 'notes' subelement of this object |
appendNotes(XMLNode notes)
Appends the given notes
to the 'notes' subelement of this object.
The content of notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML node structure that is to appended to the content of the 'notes' subelement of this object |
|
inherited |
Clears all defined dashes.
clearDashes()
def libsbml.Text.clone | ( | self | ) |
|
inherited |
connectToChild()
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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. |
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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 |
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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 |
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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.
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inherited |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
getAnnotation() XMLNode
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
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inherited |
Returns the content of the 'annotation' subelement of this object as a character string.
getAnnotationString() 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.
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inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
getColumn() long
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inherited |
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inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
getCVTerms() List *
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inherited |
Returns the dash at the given index.
getDashByIndex(long index) long
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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 |
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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. |
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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. |
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inherited |
Returns the XML element name of this object.
getElementName() string
This is overridden by subclasses to return a string appropriate to the SBML component. For example, Model defines it as returning 'model'
, CompartmentType defines it as returning 'compartmentType'
, and so on.
def libsbml.Text.getFontFamily | ( | self | ) |
Returns the font family.
getFontFamily() string
def libsbml.Text.getFontSize | ( | self, | |
args | |||
) |
Returns the font size as a reference.
getFontSize() RelAbsVector
def libsbml.Text.getFontStyle | ( | self | ) |
Returns the font style.
getFontStyle() Text::FONT_STYLE
def libsbml.Text.getFontWeight | ( | self | ) |
Returns the font weight.
getFontWeight() Text::FONT_WEIGHT
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inherited |
Returns the value of the 'id' attribute of this GraphicalPrimitive.
getId() string
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inherited |
implementation of a 3D transformation matrix.
The Transformation class represents a 3D transformation which normally is a 4x4 matrix. Since the last row is always 0 0 0 1 for affine transformations, we leave out those values and store the matrix as an array of 4x3 columns
Returns a 3D identity matrix.
getIdentityMatrix() float *
The matrix contains 12 float values.
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inherited |
implementation of a 2D transformation matrix.
The Transformation2D class represents a 2D transformation. it is derived from Transformation and inherits all the attributes of a 3D transformation. In addition is provides new methods to explicitly get and set 2D transformation properties. A 2D transformation normally consists of a 3x3 matrix, but since the last row is always 0 0 1, this is reduced to a 6 value array.
Using one of the new 2D specific functions to set the matrix always updates the 3D matrix automatically and vice versa, so the 2D data and the 3D data inherited from Transformation should always be consistent.
Returns a 2D identity matrix.
getIdentityMatrix2D() float *
The matrix contains 6 float values.
|
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
|
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.
|
inherited |
Returns the matrix which is an array of float values of length 12.
getMatrix() float *
|
inherited |
Returns the 2D matrix which is an array of float values of length 6.
getMatrix2D() float *
|
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.
|
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.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
getNumCVTerms() long
|
inherited |
Returns the number of defined dashes.
getNumDashes() long
|
inherited |
Returns the number of disabled plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
getNumDisabledPlugins() long
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
getNumPlugins() 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(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 |
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 |
|
inherited |
Returns the namespace prefix of this element.
getPrefix() string
|
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.
|
inherited |
Returns the stroke color.
getStroke() string
|
inherited |
Returns the stroke width.
getStrokeWidth() float
def libsbml.Text.getText | ( | self | ) |
def libsbml.Text.getTextAnchor | ( | self | ) |
Returns the text anchor.
getTextAnchor() Text::TEXT_ANCHOR
def libsbml.Text.getTypeCode | ( | self | ) |
Returns the libSBML type code for this object.
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.long
for the SBML Level 3 Layout extension, long
for the SBML Level 3 Flux Balance Constraints extension, etc.).None
if the value you give it is actually from a package.The following example code illustrates the combined use of SBase.getPackageName() and SBase.getTypeCode():
|
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
def libsbml.Text.getVTextAnchor | ( | self | ) |
Returns the vertical text anchor.
getVTextAnchor() Text::TEXT_ANCHOR
def libsbml.Text.getX | ( | self, | |
args | |||
) |
Returns the x position offset as a reference.
getX() RelAbsVector
This offset is applied after alignment.
def libsbml.Text.getY | ( | self, | |
args | |||
) |
Returns the y position offset as a reference.
getY() RelAbsVector
This offset is applied after alignment.
def libsbml.Text.getZ | ( | self, | |
args | |||
) |
Returns the z position offset as a reference.
getZ() RelAbsVector
This offset is applied after alignment.
|
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.
|
inherited |
Inserts the dash at the given position.
insertDash(long index, long dash)
|
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.
|
inherited |
Returns true is the dash array has been set or false otherwise.
isSetDashArray() bool
The array is considered set if it is not empty and if the first entry is not NaN.
if the dasharray is set.
def libsbml.Text.isSetFontFamily | ( | self | ) |
Returns true if the font family has been set or false otherwise.
isSetFontFamily() bool
def libsbml.Text.isSetFontSize | ( | self | ) |
Returns true if the font size has been set or false otherwise.
isSetFontSize() bool
def libsbml.Text.isSetFontStyle | ( | self | ) |
Returns true if the font style has been set or false otherwise.
isSetFontStyle() bool
def libsbml.Text.isSetFontWeight | ( | self | ) |
Returns true if the font weight has been set or false otherwise.
isSetFontWeight() bool
|
inherited |
Predicate returning True
or False
depending on whether this GraphicalPrimitive's 'id' attribute has been set.
isSetId() bool
|
inherited |
Returns true if the matrix has been set or false otherwise.
isSetMatrix() bool
The matrix is considered as set if none of the values in the matrix is NaN.
|
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.
|
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 is the stroke has been set or false otherwise.
isSetStroke() bool
The stroke color is considered set if the string is not empty.
|
inherited |
Returns true is the stroke width has been set or false otherwise.
isSetStrokeWidth() bool
The stroke width is considered set if it is not NaN.
def libsbml.Text.isSetText | ( | self | ) |
Returns true if the text is set to something else than the empty string.
isSetText() bool
def libsbml.Text.isSetTextAnchor | ( | self | ) |
Returns true if the horizonal alignment attribute has been set.
isSetTextAnchor() bool
def libsbml.Text.isSetVTextAnchor | ( | self | ) |
Returns true if the vertical alignment attribute has been set.
isSetVTextAnchor() bool
|
inherited |
Returns True
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
matchesRequiredSBMLNamespacesForAddition(SBase sb) bool
sb | an object to compare with respect to namespaces |
True
if this object's collection of namespaces is a subset of sb's
, False
otherwise.
|
inherited |
Returns True
if this object's set of XML namespaces are the same as the given object's XML namespaces.
matchesSBMLNamespaces(SBase sb) bool
sb | an object to compare with respect to namespaces |
True
if this object's collection of namespaces is the same as sb's
, False
otherwise.
|
inherited |
removeDash(long index)
Removes the dash at the given index
|
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.
|
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 |
|
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 |
|
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 |
|
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.Text.setCoordinates | ( | self, | |
args | |||
) |
Sets the position of the text within the viewport.
setCoordinates(RelAbsVector x, RelAbsVector y, RelAbsVector z) setCoordinates(RelAbsVector x, RelAbsVector y)
This is like an offset that is applied after alignment. If the z coordinate is omitted, it is set to 0.
x | x coordinate of the position offset |
y | y coordinate of the position offset |
z | z coordinate of the position offset |
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inherited |
Sets the dash at the given position.
setDashByIndex(long index, long dash)
def libsbml.Text.setFontFamily | ( | self, | |
family | |||
) |
Sets the font family.
setFontFamily(string family)
family | The name of the font family, e.g. Helvetica |
def libsbml.Text.setFontSize | ( | self, | |
size | |||
) |
Sets the font size.
setFontSize(RelAbsVector size)
Normally this is an absolute value, e.g. 18 for a 18pt font. It is however allowed the specify the font size in terms of relative values in relation to the current viewport. In most cases the viewport will be the dimensions of a bounding box of a layout object.
size | the new font size. |
def libsbml.Text.setFontStyle | ( | self, | |
style | |||
) |
Sets the font style.
setFontStyle(Text::FONT_STYLE style)
Valid values are Text::STYLE_UNSET, Text::STYLE_NORMAL or Text::STYLE_ITALIC
style | The new font style to be set. |
def libsbml.Text.setFontWeight | ( | self, | |
weight | |||
) |
Sets the font weight.
setFontWeight(Text::FONT_WEIGHT weight)
Valid values are Text::WEIGHT_UNSET, Text::WEIGHT_NORMAL or Text::WEIGHT_BOLD.
weight | The new text weight to be set. |
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inherited |
Sets the value of the 'id' attribute of this GraphicalPrimitive.
setId(string id) int
id | the new id for the GraphicalPrimitive |
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inherited |
setMatrix (float [12] m)
Sets the 2D matrix to the values given in the array. The 2D matrix is updated accordingly.
m | array with new values to be set for this Transformation object. |
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inherited |
setMatrix2D (float [6] m)
Sets the 2D matrix to the values given in the array. The 3D matrix is updated accordingly.
m | array with new values to be set for this Transformation object. |
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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 |
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inherited |
Sets the ModelHistory of this object.
setModelHistory(ModelHistory history) int
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
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inherited |
Sets the namespaces relevant of this SBML object.
setNamespaces(XMLNamespaces xmlns) int
The content of xmlns
is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
xmlns | the namespaces to set |
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inherited |
This method has multiple variants; they differ in the arguments they accept.
setNotes(XMLNode notes) int setNotes(string notes, bool addXHTMLMarkup=False) int setNotes(string notes) int
Each variant is described separately below.
setNotes(string notes, bool addXHTMLMarkup = false)
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.
notes | an XML string that is to be used as the content of the 'notes' subelement of this object |
addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
setNotes(XMLNode notes)
Sets the value of the 'notes' subelement of this SBML object.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML structure that is to be used as the content of the 'notes' subelement of this object |
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inherited |
This method has multiple variants; they differ in the arguments they accept.
setSBOTerm(int value) int setSBOTerm(string sboid) int
Each variant is described separately below.
setSBOTerm(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.
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 |
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inherited |
base class for all graphical primitives which implements all 1D attributes
The GraphicalPrimitive1D class implements attributes and methods necessary for 1D objects like lines. The attributes that are implemented are a stroke color, a stroke width and a stroke dasharray for dashed line drawing.
Additionally this class adds an id attribute with which all graphical primitives can be referenced.
The GraphicalPrimitive1D class is derived from Transformation2D and inherits all its methods and attributes.
Sets the stroke color to the given color definition id or color value string.
setStroke(string stroke)
(
stroke | id of a ColorDefinition object or a valid color value string. |
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inherited |
Sets the stroke width.
setStrokeWidth (float width)
width | New width for strokes. Should be a positive value. |
def libsbml.Text.setText | ( | self, | |
text | |||
) |
Sets the text for the text element.
setText(string text)
text | The text to be rendered for the Text object. |
def libsbml.Text.setTextAnchor | ( | self, | |
anchor | |||
) |
Sets the text anchor.
setTextAnchor(Text::TEXT_ANCHOR anchor)
This is defines the horizontal text position. Valid values are Text::ANCHOR_UNSET, Text::ANCHOR_START, Text::ANCHOR_MIDDLE and Text_ANCHOR_END. Text::ANCHOR_BASELINE is not a valid value for the text-anchor attribute. If you set the text anchor to Text::ANCHOR_BASELINE, it will be set to Text::ANCHOR_UNSET.
anchor | The new horizontal alignment flag. |
def libsbml.Text.setVTextAnchor | ( | self, | |
anchor | |||
) |
Sets the vertical text anchor.
setVTextAnchor(Text::TEXT_ANCHOR anchor)
This is defines the vertical text position. Valid values are Text::ANCHOR_UNSET, Text::ANCHOR_TOP, Text::ANCHOR_MIDDLE and Text_ANCHOR_BOTTOM.
anchor | The new vertical alignment flag. |
def libsbml.Text.setX | ( | self, | |
x | |||
) |
Sets the x position of the text within the viewport.
setX(RelAbsVector x)
This is like an offset that is applied after alignment.
x | x coordinate of the position offset |
def libsbml.Text.setY | ( | self, | |
y | |||
) |
Sets the y position of the text within the viewport.
setY(RelAbsVector y)
This is like an offset that is applied after alignment.
y | y coordinate of the position offset |
def libsbml.Text.setZ | ( | self, | |
z | |||
) |
Sets the z position of the text within the viewport.
setZ(RelAbsVector z)
This is like an offset that is applied after alignment.
z | z coordinate of the position offset |
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inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
toSBML() string
def libsbml.Text.toXML | ( | self | ) |
Creates an XMLNode object from this GraphicalPrimitive1D object.
toXML() XMLNode
This method is purely virtual and has to be implemented by subclasses.
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inherited |
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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.
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inherited |
Clears the list of CVTerm objects attached to this SBML object.
unsetCVTerms() int
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inherited |
Unsets the value of the 'id' attribute of this GraphicalPrimitive.
unsetId() int
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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
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inherited |
Unsets the value of the 'name' attribute of this SBML object.
unsetName() int
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.
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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