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libSBML Python API
5.18.0
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libSBML Python API
5.18.0
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The Text class represents text to be rendered in the context of a style. The Text class inherits all attributes and methods from its base class GraphicalPrimitive1D.
The text also holds a string for the actual text that is to be rendered for the Text object.
Additional attributes specify how the text is to be rendered, for example which font family is to be used and how the text is to be aligned within the viewport.
Public Member Functions | |
| def | __init__ (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | addCVTerm (self, term, newBag=False) |
| Adds a copy of the given CVTerm object to this SBML object. More... | |
| def | addDash (self, dash) |
| Adds a new length of a dash to the 'stroke-dasharray' attribute. 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 | clearDashes (self) |
| Unsets the value of the 'stroke-dasharray' attribute of this GraphicalPrimitive1D. More... | |
| def | clone (self) |
| Creates and returns a deep copy of this Text object. More... | |
| def | connectToChild (self) |
| def | deleteDisabledPlugins (self, recursive=True) |
| Deletes all information stored in disabled plugins. More... | |
| def | disablePackage (self, pkgURI, pkgPrefix) |
| Disables the given SBML Level 3 package on this object. More... | |
| def | enablePackage (self, pkgURI, pkgPrefix, flag) |
| Enables or disables the given SBML Level 3 package on this object. More... | |
| def | getAncestorOfType (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | getAnnotation (self, args) |
| Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More... | |
| def | getAnnotationString (self, args) |
| Returns the content of the 'annotation' subelement of this object as a character string. More... | |
| def | getColumn (self) |
| Returns the column number where this object first appears in the XML representation of the SBML document. More... | |
| def | getCVTerm (self, n) |
| Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
| def | getCVTerms (self, args) |
| Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
| def | getDashByIndex (self, index) |
| Returns the dash at the given index of the 'stroke-dasharray' attribute. 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, args) |
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, args) |
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 Text object. More... | |
| def | getFontFamily (self) |
| Returns the value of the 'font-family' attribute of this Text. More... | |
| def | getFontSize (self, args) |
| Returns the font size as a reference. More... | |
| def | getFontStyle (self) |
| Returns the value of the 'font-style' attribute of this Text. More... | |
| def | getFontStyleAsString (self) |
| Returns the value of the 'font-style' attribute of this Text. More... | |
| def | getFontWeight (self) |
| Returns the value of the 'font-weight' attribute of this Text. More... | |
| def | getFontWeightAsString (self) |
| Returns the value of the 'font-weight' attribute of this Text. More... | |
| def | getId (self) |
| Returns the value of the 'id' attribute of this GraphicalPrimitive1D. More... | |
| def | getIdAttribute (self) |
| Returns the value of the 'id' attribute of this SBML object. More... | |
| def | getIdentityMatrix () |
| Returns a 3D identity matrix. More... | |
| def | getIdentityMatrix2D () |
| Returns a 2D identity matrix. More... | |
| def | getLevel (self) |
| Returns the SBML Level of the SBMLDocument object containing this object. More... | |
| def | getLine (self) |
| Returns the line number where this object first appears in the XML representation of the SBML document. More... | |
| def | getListOfAllElements (self, filter=None) |
| Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More... | |
| def | getListOfAllElementsFromPlugins (self, filter=None) |
| Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
| def | getMatrix (self) |
| Returns the value of the 'transform' attribute of this Transformation. 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 SBML object. More... | |
| def | getModel (self) |
| Returns the Model object for the SBML Document in which the current object is located. More... | |
| def | getModelHistory (self, args) |
| Returns the ModelHistory object, if any, attached to this object. More... | |
| def | getName (self) |
| Returns the value of the 'name' attribute of this Transformation. 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 in the 'stroke-dasharray' attribute. More... | |
| def | getNumDisabledPlugins (self) |
| Returns the number of disabled plug-in objects (extension 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 | getPackageCoreVersion (self) |
| Returns the SBML Core Version within the SBML Level of the actual object. More... | |
| def | getPackageName (self) |
| Returns the name of the SBML Level 3 package in which this element is defined. More... | |
| def | getPackageVersion (self) |
| Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
| def | getParentSBMLObject (self, args) |
| Returns the parent SBML object containing this object. More... | |
| def | getPlugin (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | getPrefix (self) |
| Returns the XML namespace prefix of this element. More... | |
| def | getResourceBiologicalQualifier (self, resource) |
| Returns the MIRIAM biological qualifier associated with the given resource. More... | |
| def | getResourceModelQualifier (self, resource) |
| Returns the MIRIAM model qualifier associated with the given resource. More... | |
| def | getSBMLDocument (self, args) |
| Returns the SBMLDocument object containing this object instance. More... | |
| def | getSBOTerm (self) |
| Returns the integer portion of the value of the 'sboTerm' attribute of this object. More... | |
| def | getSBOTermAsURL (self) |
| Returns the URL representation of the 'sboTerm' attribute of this object. More... | |
| def | getSBOTermID (self) |
| Returns the string representation of the 'sboTerm' attribute of this object. More... | |
| def | getStroke (self) |
| Returns the value of the 'stroke' attribute of this GraphicalPrimitive1D. More... | |
| def | getStrokeDashArray (self) |
| Returns the value of the 'stroke-dasharray' attribute of this GraphicalPrimitive1D. More... | |
| def | getStrokeWidth (self) |
| Returns the value of the 'stroke-width' attribute of this GraphicalPrimitive1D. More... | |
| def | getText (self) |
| Returns the text for the Text object. More... | |
| def | getTextAnchor (self) |
| Returns the value of the 'text-anchor' attribute of this Text. More... | |
| def | getTextAnchorAsString (self) |
| Returns the value of the 'text-anchor' attribute of this Text. More... | |
| def | getTransform (self, outArray) |
| Returns the value of the 'transform' attribute of this Transformation. More... | |
| def | getTypeCode (self) |
| Returns the libSBML type code for this Text 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 value of the 'vtext-anchor' attribute of this Text. More... | |
| def | getVTextAnchorAsString (self) |
| Returns the value of the 'vtext-anchor' attribute of this Text. 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 | hasRequiredAttributes (self) |
Predicate returning True if all the required attributes for this Text object have been set. More... | |
| def | hasValidLevelVersionNamespaceCombination (self) |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
| def | insertDash (self, index, dash) |
| Inserts the given integer value for the dash length at the given position. More... | |
| def | isEllipse (self) |
| def | isImage (self) |
| def | isLineEnding (self) |
| 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 | isPolygon (self) |
| def | isRectangle (self) |
| def | isRenderCurve (self) |
| def | isRenderGroup (self) |
| def | isSetAnnotation (self) |
Predicate returning True if this object's 'annotation' subelement exists and has content. More... | |
| def | isSetDashArray (self) |
Returns True if the dash array has been set or False otherwise. More... | |
| def | isSetFontFamily (self) |
Predicate returning True if this Text's 'font-family' attribute is set. More... | |
| def | isSetFontSize (self) |
Predicate returning True if this Text's 'font-size' element is set. More... | |
| def | isSetFontStyle (self) |
Predicate returning True if this Text's 'font-style' attribute is set. More... | |
| def | isSetFontWeight (self) |
Predicate returning True if this Text's 'font-weight' attribute is set. More... | |
| def | isSetId (self) |
Predicate returning True if this GraphicalPrimitive1D's 'id' attribute is set. More... | |
| def | isSetIdAttribute (self) |
Predicate returning True if this object's 'id' attribute is 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 | isSetName (self) |
Predicate returning True if this Transformation's 'name' attribute is set. More... | |
| def | isSetNotes (self) |
Predicate returning True if this object's 'notes' subelement exists and has content. More... | |
| def | isSetSBOTerm (self) |
Predicate returning True if this object's 'sboTerm' attribute is set. More... | |
| def | isSetStroke (self) |
Predicate returning True if this GraphicalPrimitive1D's 'stroke' attribute is set. More... | |
| def | isSetStrokeDashArray (self) |
Predicate returning True if this GraphicalPrimitive1D's 'stroke-dasharray' attribute is set. More... | |
| def | isSetStrokeWidth (self) |
Predicate returning True if this GraphicalPrimitive1D's 'stroke-width' attribute is set. More... | |
| def | isSetText (self) |
Returns True if the text is set to something else than the empty string. More... | |
| def | isSetTextAnchor (self) |
Predicate returning True if this Text's 'text-anchor' attribute is set. More... | |
| def | isSetTransform (self) |
Predicate returning True if this Transformation's 'transform' attribute is set. More... | |
| def | isSetUserData (self) |
| Predicate returning true or false depending on whether the user data of this element has been set. More... | |
| def | isSetVTextAnchor (self) |
Predicate returning True if this Text's 'vtext-anchor' attribute is set. More... | |
| def | isSetX (self) |
Predicate returning True if this Text's 'x' element is set. More... | |
| def | isSetY (self) |
Predicate returning True if this Text's 'y' element is set. More... | |
| def | isSetZ (self) |
Predicate returning True if this Text's 'z' element is set. More... | |
| def | isText (self) |
| 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) |
| Removes the dash length at the given index. More... | |
| 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 integer value of the dash at the given position. More... | |
| def | setFontFamily (self, fontFamily) |
| Sets the value of the 'font-family' attribute of this Text. More... | |
| def | setFontSize (self, size) |
| Sets the font size. More... | |
| def | setFontStyle (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setFontWeight (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setId (self, id) |
| Sets the value of the 'id' attribute of this GraphicalPrimitive1D. More... | |
| def | setIdAttribute (self, sid) |
| Sets the value of the 'id' attribute of this SBML object. 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 SBML object. More... | |
| def | setModelHistory (self, history) |
| Sets the ModelHistory of this object. More... | |
| def | setName (self, name) |
| Sets the value of the 'name' attribute of this Transformation. 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) |
| Sets the value of the 'stroke' attribute of this GraphicalPrimitive1D. More... | |
| def | setStrokeDashArray (self, array) |
| Sets the value of the 'stroke-dasharray' attribute of this GraphicalPrimitive1D. More... | |
| def | setStrokeWidth (self, strokeWidth) |
| Sets the value of the 'stroke-width' attribute of this GraphicalPrimitive1D. More... | |
| def | setText (self, text) |
| Sets the text for the text element. More... | |
| def | setTextAnchor (self, args) |
| This method has multiple variants; they differ in the arguments they accept. More... | |
| def | setTransform (self, inArray) |
| Sets the value of the 'transform' attribute of this Transformation. More... | |
| def | setVTextAnchor (self, args) |
| This method has multiple variants; they differ in the arguments they accept. 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 Text object from this Group 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 | unsetFontFamily (self) |
| Unsets the value of the 'font-family' attribute of this Text. More... | |
| def | unsetFontSize (self) |
| Unsets the value of the 'font-size' element of this Text. More... | |
| def | unsetFontStyle (self) |
| Unsets the value of the 'font-style' attribute of this Text. More... | |
| def | unsetFontWeight (self) |
| Unsets the value of the 'font-weight' attribute of this Text. More... | |
| def | unsetId (self) |
| Unsets the value of the 'id' attribute of this GraphicalPrimitive1D. More... | |
| def | unsetIdAttribute (self) |
| Unsets the value of the 'id' attribute of this SBML object. More... | |
| def | unsetMatrix (self) |
| Unsets the value of the 'transform' attribute of this Transformation. 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 Transformation. 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 | unsetStroke (self) |
| Unsets the value of the 'stroke' attribute of this GraphicalPrimitive1D. More... | |
| def | unsetStrokeDashArray (self) |
| Unsets the value of the 'stroke-dasharray' attribute of this GraphicalPrimitive1D. More... | |
| def | unsetStrokeWidth (self) |
| Unsets the value of the 'stroke-width' attribute of this GraphicalPrimitive1D. More... | |
| def | unsetText (self) |
| Unsets the text for the text element. More... | |
| def | unsetTextAnchor (self) |
| Unsets the value of the 'text-anchor' attribute of this Text. More... | |
| def | unsetTransform (self) |
| Unsets the value of the 'transform' attribute of this Transformation. More... | |
| def | unsetUserData (self) |
| Unsets the user data of this element. More... | |
| def | unsetVTextAnchor (self) |
| Unsets the value of the 'vtext-anchor' attribute of this Text. More... | |
| def | unsetX (self) |
| Unsets the value of the 'x' element of this Text. More... | |
| def | unsetY (self) |
| Unsets the value of the 'y' element of this Text. More... | |
| def | unsetZ (self) |
| Unsets the value of the 'z' element of this Text. More... | |
| def libsbml.Text.__init__ | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
__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 __init__(Text orig) Text
Each variant is described separately below.
Text(long level = RenderExtension.getDefaultLevel(), long version = RenderExtension.getDefaultVersion(), long pkgVersion = RenderExtension.getDefaultPackageVersion())
Creates a new Text using the given SBML Level, Version and “render” package version.
| level | a long integer, the SBML Level to assign to this Text. |
| version | a long integer, the SBML Version to assign to this Text. |
| pkgVersion | a long integer, the SBML Render Version to assign to this Text. |
parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.Text(RenderPkgNamespaces renderns, string id,RelAbsVector x(0.0,0.0),RelAbsVector y(0.0,0.0),RelAbsVector z(0.0,0.0))
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.
| renderns | the SBMLNamespaces object for the SBML 'render' package |
| 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 |
Creates a new Text object from the given XMLNode object. The XMLNode object has to contain a valid XML representation of a Text object as defined in the render extension specification. This method is normally called when render information is read from a file and should normally not have to be called explicitly.
| node | the XMLNode object reference that describes the Text object to be instantiated. |
| l2version | an integer indicating the version of SBML Level 2 |
Text(RenderPkgNamespaces renderns)
Creates a new Text using the given RenderPkgNamespaces object.
| renderns | the RenderPkgNamespaces object. |
Text(Text orig)
Copy constructor for Text.
| orig | the Text instance to copy. |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
addCVTerm(CVTerm term, bool newBag) int addCVTerm(CVTerm term) int
| term | the CVTerm to assign. |
| newBag | if True, creates a new RDF bag with the same identifier as a previous bag, and if False, adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
create) for alternatives that do not lead to these issues.parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
|
inherited |
Adds a new length of a dash to the 'stroke-dasharray' attribute.
addDash(long dash)
| dash | the integer length of the dash to add to the end of the 'stroke-dasharray' attribute. |
|
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(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 |
Unsets the value of the 'stroke-dasharray' attribute of this GraphicalPrimitive1D.
clearDashes()
| def libsbml.Text.clone | ( | self | ) |
|
inherited |
connectToChild()
|
inherited |
Deletes all information stored in disabled plugins.
deleteDisabledPlugins(bool recursive) deleteDisabledPlugins()
If the plugin is re-enabled later, it will then not have any previously-stored information.
| recursive | if True, the disabled information will be deleted also from all child elements, otherwise only from this SBase element. |
|
inherited |
Disables the given SBML Level 3 package on this object.
disablePackage(string pkgURI, string pkgPrefix) intThis method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from an other SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
|
inherited |
Enables or disables the given SBML Level 3 package on this object.
enablePackage(string pkgURI, string pkgPrefix, bool flag) intThis method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase.disablePackage().
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
| flag | whether to enable (True) or disable (False) the package. |
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inherited |
This method has multiple variants; they differ in the arguments they accept.
getAncestorOfType(int type, string pkgName) SBase getAncestorOfType(int type) SBase
Each variant is described separately below.
getAncestorOfType(int type, string pkgName = 'core')
Returns the first ancestor object that has the given SBML type code from the given package.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.
| type | the SBML type code of the object sought. |
| pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong. |
None if no ancestor exists.pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.getAncestorOfType(int type, string pkgName = 'core')
Returns the first ancestor object that has the given SBML type code from the given package.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.
| type | the SBML type code of the object sought. |
| pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong. |
None if no ancestor exists.pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
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inherited |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
getAnnotation() XMLNode
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
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inherited |
Returns the content of the 'annotation' subelement of this object as a character string.
getAnnotationString() stringSBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.
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inherited |
Returns the column number where this object first appears in the XML representation of the SBML document.
getColumn() long0.
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inherited |
|
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 of the 'stroke-dasharray' attribute.
getDashByIndex(long index) long| index | the index of the dash length to return from the 'stroke-dasharray' attribute. |
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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
If no such plugin exists, None is returned.
| n | the index of the disabled plug-in to return. |
n is invalid, None is returned.
|
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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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.Text.getElementName | ( | self | ) |
| def libsbml.Text.getFontFamily | ( | self | ) |
| def libsbml.Text.getFontSize | ( | self, | |
| args | |||
| ) |
Returns the font size as a reference.
getFontSize() RelAbsVector
| def libsbml.Text.getFontStyle | ( | self | ) |
Returns the value of the 'font-style' attribute of this Text.
getFontStyle() int'italic', slanted print
'normal', upright print
The possible values returned by this method are:
| def libsbml.Text.getFontStyleAsString | ( | self | ) |
Returns the value of the 'font-style' attribute of this Text.
getFontStyleAsString() string'italic', slanted print
'normal', upright print
'italic' 'normal' '(Unknown FontStyle value)' | def libsbml.Text.getFontWeight | ( | self | ) |
Returns the value of the 'font-weight' attribute of this Text.
getFontWeight() int'bold', darker and/or thicker than normal print.
'normal', the typical print weight; lighter and/or thinner than 'bold'.
The possible values returned by this method are:
| def libsbml.Text.getFontWeightAsString | ( | self | ) |
Returns the value of the 'font-weight' attribute of this Text.
getFontWeightAsString() string'bold', darker and/or thicker than normal print.
'normal', the typical print weight; lighter and/or thinner than 'bold'.
'bold' 'normal' '(Unknown FontWeight value)'
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inherited |
Returns the value of the 'id' attribute of this GraphicalPrimitive1D.
getId() string
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inherited |
Returns the value of the 'id' attribute of this SBML object.
getIdAttribute() stringSId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows: letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*The characters
( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return False for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
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inherited |
Returns a 3D identity matrix.
getIdentityMatrix() float *The matrix contains 12 float values.
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inherited |
Returns a 2D identity matrix.
getIdentityMatrix2D() float *The matrix contains 6 float values.
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inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
getLevel() long
|
inherited |
Returns the line number where this object first appears in the XML representation of the SBML document.
getLine() long0.
|
inherited |
Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.
getListOfAllElements(ElementFilter filter) SBaseList getListOfAllElements() SBaseList
|
inherited |
Returns a List of all child SBase objects contained in SBML package plug-ins.
getListOfAllElementsFromPlugins(ElementFilter filter) SBaseList getListOfAllElementsFromPlugins() SBaseList
This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.
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inherited |
Returns the value of the 'transform' attribute of this Transformation.
getMatrix() float *which is an array of float values of length 12.
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inherited |
Returns the 2D matrix which is an array of float values of length 6.
getMatrix2D() float *
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inherited |
Returns the value of the 'metaid' attribute of this SBML object.
getMetaId() stringID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
getModelHistory() ModelHistory
None if none exist.
|
inherited |
Returns the value of the 'name' attribute of this Transformation.
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.
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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().
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inherited |
Returns the content of the 'notes' subelement of this object as a string.
getNotesString() stringThe format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
getNumCVTerms() long
|
inherited |
Returns the number of defined dashes in the 'stroke-dasharray' attribute.
getNumDashes() long
|
inherited |
Returns the number of disabled plug-in objects (extension 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 SBML Core Version within the SBML Level of the actual object.
getPackageCoreVersion() long
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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.
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inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
getPackageVersion() long0 will be returned if this element belongs to the SBML Level 3 Core package.
|
inherited |
Returns the parent SBML object containing this object.
getParentSBMLObject() SBase
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
getPlugin(string package) SBasePlugin getPlugin(long n) SBasePlugin
Each variant is described separately below.
getPlugin(long n)
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. The returned plug-in will be the appropriate type of plugin requested: calling Model.getPlugin() will return an FbcModelPlugin; calling Parameter.getPlugin() will return CompSBasePlugin, etc.
If no such plugin exists, None is returned.
| n | the index of the plug-in to return. |
n is invalid, None is returned.getPlugin(string package)
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. The returned plug-in will be the appropriate type of plugin requested: calling Model.getPlugin() will return an FbcModelPlugin; calling Parameter.getPlugin() will return CompSBasePlugin, etc.
If no such plugin exists, None is returned.
| package | the name or URI of the package. |
|
inherited |
Returns the XML namespace prefix of this element.
getPrefix() stringThis reports the XML namespace prefix chosen for this class of object in the current SBML document. This may be an empty string if the component has no explicit prefix (for instance, if it is a core SBML object placed in the default SBML namespace of the document). If it is not empty, then it corresponds to the XML namespace prefix used set the object, whatever that may be in a given SBML document.
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inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
getResourceBiologicalQualifier(string resource) longIn MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose name begins with BQB_ from the interface class libsbml.
| resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'. |
BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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inherited |
Returns the MIRIAM model qualifier associated with the given resource.
getResourceModelQualifier(string resource) longIn MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQM_ in the interface class libsbml.
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose name begins with BQM_ from the interface class libsbml.
| resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'. |
BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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inherited |
Returns the SBMLDocument object containing this object instance.
getSBMLDocument() SBMLDocument
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
getSBOTerm() intint, and SBO identifiers are stored simply as integers. -1 if the value is not set.
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inherited |
Returns the URL representation of the 'sboTerm' attribute of this object.
getSBOTermAsURL() stringThis method returns the entire SBO identifier as a text string in the form http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.
|
inherited |
Returns the string representation of the 'sboTerm' attribute of this object.
getSBOTermID() stringint, and SBO identifiers are stored simply as integers.
|
inherited |
Returns the value of the 'stroke' attribute of this GraphicalPrimitive1D.
getStroke() string
|
inherited |
Returns the value of the 'stroke-dasharray' attribute of this GraphicalPrimitive1D.
getStrokeDashArray() std::vector< long > &
|
inherited |
Returns the value of the 'stroke-width' attribute of this GraphicalPrimitive1D.
getStrokeWidth() float| def libsbml.Text.getText | ( | self | ) |
| def libsbml.Text.getTextAnchor | ( | self | ) |
Returns the value of the 'text-anchor' attribute of this Text.
getTextAnchor() int'start', the start of the text is aligned to the horizontal center of the box.
'middle', the horizontal center of the text is aligned to the horizontal center of the box.
'end', the end of the text is aligned to the horizontal center of the box.
| def libsbml.Text.getTextAnchorAsString | ( | self | ) |
Returns the value of the 'text-anchor' attribute of this Text.
getTextAnchorAsString() string'start', the start of the text is aligned to the horizontal center of the box.
'middle', the horizontal center of the text is aligned to the horizontal center of the box.
'end', the end of the text is aligned to the horizontal center of the box.
'start' 'middle' 'end' '(Unknown HTextAnchor value)'
|
inherited |
Returns the value of the 'transform' attribute of this Transformation.
getTransform (float * outArray)
| outArray | float* array that will be used to return the value of the 'transform' attribute of this Transformation. |
| def libsbml.Text.getTypeCode | ( | self | ) |
Returns the libSBML type code for this Text object.
getTypeCode() intSBML_. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the SBase.getPackageName() method on the object.The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.
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inherited |
Gets the namespace URI to which this element belongs to.
getURI() stringFor example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1'.
This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.
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inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
getVersion() long| def libsbml.Text.getVTextAnchor | ( | self | ) |
Returns the value of the 'vtext-anchor' attribute of this Text.
getVTextAnchor() int'top', the top of the text is aligned to the vertical center of the box.
'middle', the vertical center of the text is aligned with the vertical center of the box.
'bottom', the bottom of the text (i.e. the very bottom of any descending letter like 'y' or 'p') is aligned with the vertical center of the box.
'baseline', the baseline of the text (i.e. the bottom of any non-descending letter like 'a' or e') is aligned with the vertical center of the box.
| def libsbml.Text.getVTextAnchorAsString | ( | self | ) |
Returns the value of the 'vtext-anchor' attribute of this Text.
getVTextAnchorAsString() string'top', the top of the text is aligned to the vertical center of the box.
'middle', the vertical center of the text is aligned with the vertical center of the box.
'bottom', the bottom of the text (i.e. the very bottom of any descending letter like 'y' or 'p') is aligned with the vertical center of the box.
'baseline', the baseline of the text (i.e. the bottom of any non-descending letter like 'a' or e') is aligned with the vertical center of the box.
'top' 'middle' 'bottom' 'baseline' '(Unknown VTextAnchor value)' | 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.
| def libsbml.Text.hasRequiredAttributes | ( | self | ) |
|
inherited |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.
hasValidLevelVersionNamespaceCombination() boolThe valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
http://www.sbml.org/sbml/level1 http://www.sbml.org/sbml/level2 http://www.sbml.org/sbml/level2/version2 http://www.sbml.org/sbml/level2/version3 http://www.sbml.org/sbml/level2/version4 http://www.sbml.org/sbml/level3/version1/core true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
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inherited |
Inserts the given integer value for the dash length at the given position.
insertDash(long index, long dash)
| index | the index of the dash length at which the new dash is to be inserted in the 'stroke-dasharray' attribute. The function will fail silently if no such index exists. |
| dash | the integer length to set the inserted dash to. |
|
inherited |
isEllipse() bool Predicate returning True if this abstract GraphicalPrimitive1D is of type Ellipse
True if this abstract GraphicalPrimitive1D is of type Ellipse, False otherwise
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isImage() bool Predicate returning True if this abstract Transformation2D is of type Image
True if this abstract Transformation2D is of type Image, False otherwise
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isLineEnding() bool Predicate returning True if this abstract GraphicalPrimitive1D is of type LineEnding
True if this abstract GraphicalPrimitive1D is of type LineEnding, False otherwise
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Predicate returning True if the given SBML Level 3 package is enabled with this object.
isPackageEnabled(string pkgName) boolThe search ignores the package version.
| pkgName | the name of the package. |
True if the given package is enabled within this object, False otherwise.
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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.
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inherited |
Predicate returning True if the given SBML Level 3 package is enabled with this object.
isPkgEnabled(string pkgName) boolThe search ignores the package version.
| pkgName | the name of the package. |
True if the given package is enabled within this object, False otherwise.
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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.
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isPolygon() bool Predicate returning True if this abstract GraphicalPrimitive1D is of type Polygon
True if this abstract GraphicalPrimitive1D is of type Polygon, False otherwise
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isRectangle() bool Predicate returning True if this abstract GraphicalPrimitive1D is of type Rectangle
True if this abstract GraphicalPrimitive1D is of type Rectangle, False otherwise
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isRenderCurve() bool Predicate returning True if this abstract GraphicalPrimitive1D is of type RenderCurve
True if this abstract GraphicalPrimitive1D is of type Text, False otherwise
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isRenderGroup() bool Predicate returning True if this abstract GraphicalPrimitive1D is of type RenderGroup
True if this abstract GraphicalPrimitive1D is of type RenderGroup, False otherwise
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Predicate returning True if this object's 'annotation' subelement exists and has content.
isSetAnnotation() boolWhereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
True if a 'annotation' subelement exists, False otherwise.
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Returns True if 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.
True if the stroke-dasharray is set, False otherwise. | def libsbml.Text.isSetFontFamily | ( | self | ) |
| def libsbml.Text.isSetFontSize | ( | self | ) |
| def libsbml.Text.isSetFontStyle | ( | self | ) |
Predicate returning True if this Text's 'font-style' attribute is set.
isSetFontStyle() bool'italic', slanted print
'normal', upright print
True if this Text's 'font-style' attribute has been set, otherwise False is returned. | def libsbml.Text.isSetFontWeight | ( | self | ) |
Predicate returning True if this Text's 'font-weight' attribute is set.
isSetFontWeight() bool'bold', darker and/or thicker than normal print.
'normal', the typical print weight; lighter and/or thinner than 'bold'.
True if this Text's 'font-weight' attribute has been set, otherwise False is returned.
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Predicate returning True if this GraphicalPrimitive1D's 'id' attribute is set.
isSetId() boolTrue if this GraphicalPrimitive1D's 'id' attribute has been set, otherwise False is returned.
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Predicate returning True if this object's 'id' attribute is set.
isSetIdAttribute() boolSId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows: letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*The characters
( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return False for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
True if the 'id' attribute of this SBML object is set, False otherwise.
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Returns True if the matrix has been set or False otherwise.
isSetMatrix() boolThe matrix is considered as set if none of the values in the matrix is NaN.
True or False depending on whether a NaN was found.
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Predicate returning True if this object's 'metaid' attribute is set.
isSetMetaId() boolID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.True if the 'metaid' attribute of this SBML object is set, False otherwise.
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Predicate returning True if this object has a ModelHistory object attached to it.
isSetModelHistory() boolTrue if the ModelHistory of this object is set, False otherwise.
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Predicate returning True if this Transformation's 'name' attribute is set.
isSetName() boolTrue if this Transformation's 'name' attribute has been set, otherwise False is returned.
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inherited |
Predicate returning True if this object's 'notes' subelement exists and has content.
isSetNotes() boolThe optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
True if a 'notes' subelement exists, False otherwise.
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Predicate returning True if this object's 'sboTerm' attribute is set.
isSetSBOTerm() boolTrue if the 'sboTerm' attribute of this SBML object is set, False otherwise.
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Predicate returning True if this GraphicalPrimitive1D's 'stroke' attribute is set.
isSetStroke() boolTrue if this GraphicalPrimitive1D's 'stroke' attribute has been set, otherwise False is returned.
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inherited |
Predicate returning True if this GraphicalPrimitive1D's 'stroke-dasharray' attribute is set.
isSetStrokeDashArray() boolTrue if this GraphicalPrimitive1D's 'stroke-dasharray' attribute has been set, otherwise False is returned.
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inherited |
Predicate returning True if this GraphicalPrimitive1D's 'stroke-width' attribute is set.
isSetStrokeWidth() boolTrue if this GraphicalPrimitive1D's 'stroke-width' attribute has been set, otherwise False is returned. | def libsbml.Text.isSetText | ( | self | ) |
Returns True if the text is set to something else than the empty string.
isSetText() boolTrue if the text is not empty. | def libsbml.Text.isSetTextAnchor | ( | self | ) |
Predicate returning True if this Text's 'text-anchor' attribute is set.
isSetTextAnchor() bool'start', the start of the text is aligned to the horizontal center of the box.
'middle', the horizontal center of the text is aligned to the horizontal center of the box.
'end', the end of the text is aligned to the horizontal center of the box.
True if this Text's 'text-anchor' attribute has been set, otherwise False is returned.
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inherited |
Predicate returning True if this Transformation's 'transform' attribute is set.
isSetTransform() boolTrue if this Transformation's 'transform' attribute has been set, otherwise False is returned.
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inherited |
Predicate returning true or false depending on whether the user data of this element has been set.
isSetUserData() boolTrue if this object's user data has been set, False otherwise. | def libsbml.Text.isSetVTextAnchor | ( | self | ) |
Predicate returning True if this Text's 'vtext-anchor' attribute is set.
isSetVTextAnchor() bool'top', the top of the text is aligned to the vertical center of the box.
'middle', the vertical center of the text is aligned with the vertical center of the box.
'bottom', the bottom of the text (i.e. the very bottom of any descending letter like 'y' or 'p') is aligned with the vertical center of the box.
'baseline', the baseline of the text (i.e. the bottom of any non-descending letter like 'a' or e') is aligned with the vertical center of the box.
True if this Text's 'vtext-anchor' attribute has been set, otherwise False is returned. | def libsbml.Text.isSetX | ( | self | ) |
| def libsbml.Text.isSetY | ( | self | ) |
| def libsbml.Text.isSetZ | ( | self | ) |
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inherited |
isText() bool Predicate returning True if this abstract GraphicalPrimitive1D is of type Text
True if this abstract GraphicalPrimitive1D is of type Text, False otherwise
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inherited |
Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces.
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.
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inherited |
Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces.
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.
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inherited |
Removes the dash length at the given index.
removeDash(long index)
| index | the index of the dash length to remove from the 'stroke-dasharray' attribute. The function will fail silently if no such index exists. |
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inherited |
Removes this object from its parent.
removeFromParentAndDelete() intIf the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
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inherited |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
removeTopLevelAnnotationElement(string elementName, string elementURI, bool removeEmpty) int removeTopLevelAnnotationElement(string elementName, string elementURI) int removeTopLevelAnnotationElement(string elementName) int
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
| elementName | a string representing the name of the top level annotation element that is to be removed. |
| elementURI | an optional string that is used to check both the name and URI of the top level element to be removed. |
| removeEmpty | if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default). |
parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
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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. |
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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.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 integer value of the dash at the given position.
setDashByIndex(long index, long dash)
| index | the index of the dash length to replace in the 'stroke-dasharray' attribute. The function will fail silently if no such index exists. |
| dash | the integer length to set the indexed dash to. |
| def libsbml.Text.setFontFamily | ( | self, | |
| fontFamily | |||
| ) |
Sets the value of the 'font-family' attribute of this Text.
setFontFamily(string fontFamily) int| fontFamily | string value of the 'font-family' attribute to be set. Calling this function with fontFamily = None or an empty string is equivalent to calling unsetFontFamily(). |
| def libsbml.Text.setFontSize | ( | self, | |
| size | |||
| ) |
Sets the font size.
setFontSize(RelAbsVector size) int
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, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
setFontStyle(long fontStyle) int setFontStyle(Text::FONT_STYLE style) setFontStyle(string fontStyle) int
Each variant is described separately below.
setFontStyle(string fontStyle)
Sets the value of the 'font-style' attribute of this Text.
'italic', slanted print
'normal', upright print
| fontStyle | the 'font-style' attribute to be set. |
setFontStyle(long fontStyle)
Sets the value of the 'font-style' attribute of this Text.
'italic', slanted print
'normal', upright print
| fontStyle | int value of the 'font-style' attribute to be set. |
| def libsbml.Text.setFontWeight | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
setFontWeight(long fontWeight) int setFontWeight(Text::FONT_WEIGHT weight) setFontWeight(string fontWeight) int
Each variant is described separately below.
setFontWeight(string fontWeight)
Sets the value of the 'font-weight' attribute of this Text.
'bold', darker and/or thicker than normal print.
'normal', the typical print weight; lighter and/or thinner than 'bold'.
| fontWeight | the value of the 'font-weight' attribute to be set. |
setFontWeight(long fontWeight)
Sets the value of the 'font-weight' attribute of this Text.
'bold', darker and/or thicker than normal print.
'normal', the typical print weight; lighter and/or thinner than 'bold'.
| fontWeight | int value of the 'font-weight' attribute to be set. |
|
inherited |
Sets the value of the 'id' attribute of this GraphicalPrimitive1D.
setId(string id) int| id | string value of the 'id' attribute to be set. |
id = None or an empty string is equivalent to calling unsetId().
|
inherited |
Sets the value of the 'id' attribute of this SBML object.
setIdAttribute(string sid) intsid is copied.SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows: letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*The characters
( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return False for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
| sid | the string to use as the identifier of this object. |
|
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. |
|
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. |
|
inherited |
Sets the value of the meta-identifier attribute of this SBML object.
setMetaId(string metaid) intID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.The string metaid is copied.
| metaid | the identifier string to use as the value of the 'metaid' attribute. |
|
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. |
|
inherited |
Sets the value of the 'name' attribute of this Transformation.
setName(string name) int| name | string value of the 'name' attribute to be set. |
name = None or an empty string is equivalent to calling unsetName().
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inherited |
Sets the namespaces relevant of this SBML object.
setNamespaces(XMLNamespaces xmlns) int
The content of xmlns is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
| xmlns | the namespaces to set. |
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
setNotes(XMLNode notes) int setNotes(string notes, bool addXHTMLMarkup) int setNotes(string notes) int
Each variant is described separately below.
setNotes(string notes, bool addXHTMLMarkup = false)
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.
The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.
| notes | an XML string that is to be used as the content of the 'notes' subelement of this object. |
| addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.setNotes(XMLNode notes)
Sets the value of the 'notes' subelement of this SBML object.
The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
| notes | an XML structure that is to be used as the content of the 'notes' subelement of this object. |
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
setSBOTerm(int value) int setSBOTerm(string sboid) int
Each variant is described separately below.
setSBOTerm(int value)
Sets the value of the 'sboTerm' attribute.
int, and SBO identifiers are stored simply as integers. | value | the NNNNNNN integer portion of the SBO identifier. |
setSBOTerm(string sboid)
Sets the value of the 'sboTerm' attribute by string.
int, and SBO identifiers are stored simply as integers.
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inherited |
Sets the value of the 'stroke' attribute of this GraphicalPrimitive1D.
setStroke(string stroke) int| stroke | string value of the 'stroke' attribute to be set. |
stroke = None or an empty string is equivalent to calling unsetStroke().
|
inherited |
Sets the value of the 'stroke-dasharray' attribute of this GraphicalPrimitive1D.
setStrokeDashArray(std::vector< long > & array) int| array | value of the 'stroke-dasharray' attribute to be set. |
|
inherited |
Sets the value of the 'stroke-width' attribute of this GraphicalPrimitive1D.
setStrokeWidth (float strokeWidth) int| strokeWidth | float value of the 'stroke-width' attribute to be set. |
| def libsbml.Text.setText | ( | self, | |
| text | |||
| ) |
Sets the text for the text element.
setText(string text) int| text | The text to be rendered for the Text object. |
| def libsbml.Text.setTextAnchor | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
setTextAnchor(long textAnchor) int setTextAnchor(Text::TEXT_ANCHOR anchor) setTextAnchor(string textAnchor) int
Each variant is described separately below.
setTextAnchor(long textAnchor)
Sets the value of the 'text-anchor' attribute of this Text.
'start', the start of the text is aligned to the horizontal center of the box.
'middle', the horizontal center of the text is aligned to the horizontal center of the box.
'end', the end of the text is aligned to the horizontal center of the box.
| textAnchor | int value of the 'text-anchor' attribute to be set. |
setTextAnchor(string textAnchor)
Sets the value of the 'text-anchor' attribute of this Text.
'start', the start of the text is aligned to the horizontal center of the box.
'middle', the horizontal center of the text is aligned to the horizontal center of the box.
'end', the end of the text is aligned to the horizontal center of the box.
| textAnchor | the value of the 'text-anchor' attribute to be set. |
|
inherited |
Sets the value of the 'transform' attribute of this Transformation.
setTransform (float * inArray) int| inArray | float* array value of the 'transform' attribute to be set. |
| def libsbml.Text.setVTextAnchor | ( | self, | |
| args | |||
| ) |
This method has multiple variants; they differ in the arguments they accept.
setVTextAnchor(long vtextAnchor) int setVTextAnchor(Text::TEXT_ANCHOR anchor) setVTextAnchor(string vtextAnchor) int
Each variant is described separately below.
setVTextAnchor(string vtextAnchor)
Sets the value of the 'vtext-anchor' attribute of this Text.
'top', the top of the text is aligned to the vertical center of the box.
'middle', the vertical center of the text is aligned with the vertical center of the box.
'bottom', the bottom of the text (i.e. the very bottom of any descending letter like 'y' or 'p') is aligned with the vertical center of the box.
'baseline', the baseline of the text (i.e. the bottom of any non-descending letter like 'a' or e') is aligned with the vertical center of the box.
| vtextAnchor | the value of the 'vtext-anchor' attribute to be set. |
setVTextAnchor(long vtextAnchor)
Sets the value of the 'vtext-anchor' attribute of this Text.
'top', the top of the text is aligned to the vertical center of the box.
'middle', the vertical center of the text is aligned with the vertical center of the box.
'bottom', the bottom of the text (i.e. the very bottom of any descending letter like 'y' or 'p') is aligned with the vertical center of the box.
'baseline', the baseline of the text (i.e. the bottom of any non-descending letter like 'a' or e') is aligned with the vertical center of the box.
| vtextAnchor | int value of the 'vtext-anchor' attribute to be set. |
| def libsbml.Text.setX | ( | self, | |
| x | |||
| ) |
Sets the x position of the text within the viewport.
setX(RelAbsVector x) int
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) int
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) int
This is like an offset that is applied after alignment.
| z | z coordinate of the position offset |
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
toSBML() string| def libsbml.Text.toXML | ( | self | ) |
|
inherited |
|
inherited |
Unsets the value of the 'annotation' subelement of this SBML object.
unsetAnnotation() intWhereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
unsetCVTerms() int| def libsbml.Text.unsetFontFamily | ( | self | ) |
Unsets the value of the 'font-family' attribute of this Text.
unsetFontFamily() int| def libsbml.Text.unsetFontSize | ( | self | ) |
Unsets the value of the 'font-size' element of this Text.
unsetFontSize() int| def libsbml.Text.unsetFontStyle | ( | self | ) |
Unsets the value of the 'font-style' attribute of this Text.
unsetFontStyle() int'italic', slanted print
'normal', upright print
| def libsbml.Text.unsetFontWeight | ( | self | ) |
Unsets the value of the 'font-weight' attribute of this Text.
unsetFontWeight() int'bold', darker and/or thicker than normal print.
'normal', the typical print weight; lighter and/or thinner than 'bold'.
|
inherited |
Unsets the value of the 'id' attribute of this GraphicalPrimitive1D.
unsetId() int
|
inherited |
Unsets the value of the 'id' attribute of this SBML object.
unsetIdAttribute() intMost (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier.
|
inherited |
Unsets the value of the 'transform' attribute of this Transformation.
unsetMatrix() int
|
inherited |
Unsets the value of the 'metaid' attribute of this SBML object.
unsetMetaId() intID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
Unsets the ModelHistory object attached to this object.
unsetModelHistory() int
|
inherited |
Unsets the value of the 'name' attribute of this Transformation.
unsetName() int
|
inherited |
Unsets the value of the 'notes' subelement of this SBML object.
unsetNotes() intThe optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
|
inherited |
Unsets the value of the 'sboTerm' attribute of this SBML object.
unsetSBOTerm() int
|
inherited |
Unsets the value of the 'stroke' attribute of this GraphicalPrimitive1D.
unsetStroke() int
|
inherited |
Unsets the value of the 'stroke-dasharray' attribute of this GraphicalPrimitive1D.
unsetStrokeDashArray() int
|
inherited |
Unsets the value of the 'stroke-width' attribute of this GraphicalPrimitive1D.
unsetStrokeWidth() int| def libsbml.Text.unsetText | ( | self | ) |
Unsets the text for the text element.
unsetText() int
| def libsbml.Text.unsetTextAnchor | ( | self | ) |
Unsets the value of the 'text-anchor' attribute of this Text.
unsetTextAnchor() int'start', the start of the text is aligned to the horizontal center of the box.
'middle', the horizontal center of the text is aligned to the horizontal center of the box.
'end', the end of the text is aligned to the horizontal center of the box.
|
inherited |
Unsets the value of the 'transform' attribute of this Transformation.
unsetTransform() int
|
inherited |
Unsets the user data of this element.
unsetUserData() int| def libsbml.Text.unsetVTextAnchor | ( | self | ) |
Unsets the value of the 'vtext-anchor' attribute of this Text.
unsetVTextAnchor() int'top', the top of the text is aligned to the vertical center of the box.
'middle', the vertical center of the text is aligned with the vertical center of the box.
'bottom', the bottom of the text (i.e. the very bottom of any descending letter like 'y' or 'p') is aligned with the vertical center of the box.
'baseline', the baseline of the text (i.e. the bottom of any non-descending letter like 'a' or e') is aligned with the vertical center of the box.
| def libsbml.Text.unsetX | ( | self | ) |
Unsets the value of the 'x' element of this Text.
unsetX() int| def libsbml.Text.unsetY | ( | self | ) |
Unsets the value of the 'y' element of this Text.
unsetY() int| def libsbml.Text.unsetZ | ( | self | ) |
Unsets the value of the 'z' element of this Text.
unsetZ() int