libSBML C++ API  5.18.0
RenderGroup Class Reference
Inheritance diagram for RenderGroup:
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Detailed Description

render A group of graphical primitives creating a composite.

The RenderGroup concept from the SBML Level 3 Render package is used to to create composite representations from simple primitives. The RenderGroup class is derived from GraphicalPrimitive2D and inherits all its methods and attributes. In addition to those, the class defines attributes to specify text render properties, curve decorations, an id, and a list of child elements which can be any graphical primitive or other group.

The attributes of a group are inherited by all children of the group unless they specify the attribute themselves.

See also
Text
RenderCurve
Examples:
convertLayout.cpp.

Public Member Functions

int addChildElement (const Transformation2D *pChild)
 Adds a copy of the given element to the end of the list of children elements. More...
 
int addCVTerm (CVTerm *term, bool newBag=false)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
void addDash (unsigned int dash)
 Adds a new length of a dash to the 'stroke-dasharray' attribute. More...
 
int addElement (const Transformation2D *td)
 Adds a copy of the given Transformation2D to this RenderGroup. More...
 
virtual int appendAnnotation (const XMLNode *annotation)
 Appends the given annotation to the "annotation" subelement of this object. More...
 
virtual int appendAnnotation (const std::string &annotation)
 Appends the given annotation to the "annotation" subelement of this object. More...
 
int appendNotes (const XMLNode *notes)
 Appends the given notes to the "notes" subelement of this object. More...
 
int appendNotes (const std::string &notes)
 Appends the given notes to the "notes" subelement of this object. More...
 
void clearDashes ()
 Unsets the value of the "stroke-dasharray" attribute of this GraphicalPrimitive1D. More...
 
virtual RenderGroupclone () const
 Creates and returns a deep copy of this RenderGroup object. More...
 
RenderCurvecreateCurve ()
 Creates a new RenderCurve object, adds it to this RenderGroup object and returns the RenderCurve object created. More...
 
EllipsecreateEllipse ()
 Creates a new Ellipse object, adds it to this RenderGroup object and returns the Ellipse object created. More...
 
RenderGroupcreateGroup ()
 Creates a new RenderGroup object, adds it to this RenderGroup object and returns the RenderGroup object created. More...
 
ImagecreateImage ()
 Creates a new Image object, adds it to this RenderGroup object and returns the Image object created. More...
 
LineEndingcreateLineEnding ()
 Creates a new LineEnding object, adds it to this RenderGroup object and returns the LineEnding object created. More...
 
PolygoncreatePolygon ()
 Creates a new Polygon object, adds it to this RenderGroup object and returns the Polygon object created. More...
 
RectanglecreateRectangle ()
 Creates a new Rectangle object, adds it to this RenderGroup object and returns the Rectangle object created. More...
 
TextcreateText ()
 Creates a new Text object, adds it to this RenderGroup object and returns the Text object created. More...
 
void deleteDisabledPlugins (bool recursive=true)
 Deletes all information stored in disabled plugins. More...
 
int disablePackage (const std::string &pkgURI, const std::string &pkgPrefix)
 Disables the given SBML Level 3 package on this object. More...
 
int enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package on this object. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual ListgetAllElementsFromPlugins (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects contained in SBML package plug-ins. More...
 
SBasegetAncestorOfType (int type, const std::string &pkgName="core")
 Returns the first ancestor object that has the given SBML type code from the given package. More...
 
const SBasegetAncestorOfType (int type, const std::string pkgName="core") const
 Returns the first ancestor object that has the given SBML type code from the given package. More...
 
XMLNodegetAnnotation ()
 Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More...
 
XMLNodegetAnnotation () const
 Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More...
 
std::string getAnnotationString ()
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
std::string getAnnotationString () const
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
unsigned int getColumn () const
 Returns the column number where this object first appears in the XML representation of the SBML document. More...
 
CVTermgetCVTerm (unsigned int n)
 Returns the nth CVTerm in the list of CVTerms of this SBML object. More...
 
ListgetCVTerms ()
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
ListgetCVTerms () const
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
const std::vector< unsigned int > & getDashArray () const
 Returns a const reference to the stroke dasharray. More...
 
std::vector< unsigned int > & getDashArray ()
 Returns a reference to the stroke dasharray. More...
 
unsigned int getDashByIndex (unsigned int index) const
 Returns the dash at the given index of the 'stroke-dasharray' attribute. More...
 
SBasePlugingetDisabledPlugin (unsigned int n)
 Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasePlugingetDisabledPlugin (unsigned int n) const
 Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
Transformation2DgetElement (unsigned int n)
 Get a Transformation2D from the RenderGroup. More...
 
const Transformation2DgetElement (unsigned int n) const
 Get a Transformation2D from the RenderGroup. More...
 
Transformation2DgetElement (const std::string &id)
 Returns pointer to the element with the given id. More...
 
const Transformation2DgetElement (const std::string &id) const
 Returns const pointer to the element with given index. More...
 
const SBasegetElementByMetaId (const std::string &metaid) const
 Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Returns the first child element that has the given metaid, or NULL if no such object is found. More...
 
const SBasegetElementBySId (const std::string &id) const
 Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More...
 
virtual SBasegetElementBySId (const std::string &id)
 Returns the first child element that has the given id in the model-wide SId namespace, or NULL if no such object is found. More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this RenderGroup object. More...
 
const std::string & getEndHead () const
 Returns the value of the "endHead" attribute of this RenderGroup. More...
 
const std::string & getFill () const
 Returns the value of the "fill" attribute of this GraphicalPrimitive2D. More...
 
const std::string & getFillColor () const
 Returns the value of the "fill" attribute of this GraphicalPrimitive2D. More...
 
int getFillRule () const
 Returns the value of the "fill-rule" attribute of this GraphicalPrimitive2D. More...
 
std::string getFillRuleAsString () const
 Returns the value of the "fill-rule" attribute of this GraphicalPrimitive2D. More...
 
const std::string & getFontFamily () const
 Returns the value of the "font-family" attribute of this RenderGroup. More...
 
const RelAbsVectorgetFontSize () const
 Returns the value of the "font-size" element of this RenderGroup. More...
 
RelAbsVectorgetFontSize ()
 Returns the value of the "font-size" element of this RenderGroup. More...
 
int getFontStyle () const
 Returns the value of the "font-style" attribute of this RenderGroup. More...
 
std::string getFontStyleAsString () const
 Returns the value of the "font-style" attribute of this RenderGroup. More...
 
int getFontWeight () const
 Returns the value of the "font-weight" attribute of this RenderGroup. More...
 
std::string getFontWeightAsString () const
 Returns the value of the "font-weight" attribute of this RenderGroup. More...
 
virtual const std::string & getId () const
 Returns the value of the "id" attribute of this GraphicalPrimitive1D. More...
 
const std::string & getIdAttribute () const
 Returns the value of the "id" attribute of this SBML object. More...
 
unsigned int getLevel () const
 Returns the SBML Level of the SBMLDocument object containing this object. More...
 
unsigned int getLine () const
 Returns the line number where this object first appears in the XML representation of the SBML document. More...
 
const ListOfDrawablesgetListOfElements () const
 Returns the ListOfDrawables from this RenderGroup. More...
 
ListOfDrawablesgetListOfElements ()
 Returns the ListOfDrawables from this RenderGroup. More...
 
const double * getMatrix () const
 Returns the value of the "transform" attribute of this Transformation. More...
 
const double * getMatrix2D () const
 Returns the 2D matrix which is an array of double values of length 6. More...
 
const std::string & getMetaId () const
 Returns the value of the "metaid" attribute of this SBML object. More...
 
std::string & getMetaId ()
 Returns the value of the "metaid" attribute of this SBML object. More...
 
const ModelgetModel () const
 Returns the Model object for the SBML Document in which the current object is located. More...
 
ModelHistorygetModelHistory () const
 Returns the ModelHistory object, if any, attached to this object. More...
 
ModelHistorygetModelHistory ()
 Returns the ModelHistory object, if any, attached to this object. More...
 
virtual const std::string & getName () const
 Returns the value of the "name" attribute of this Transformation. More...
 
virtual XMLNamespacesgetNamespaces () const
 Returns a list of the XML Namespaces declared on the SBML document owning this object. More...
 
XMLNodegetNotes ()
 Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More...
 
XMLNodegetNotes () const
 Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More...
 
std::string getNotesString ()
 Returns the content of the "notes" subelement of this object as a string. More...
 
std::string getNotesString () const
 Returns the content of the "notes" subelement of this object as a string. More...
 
unsigned int getNumCVTerms ()
 Returns the number of CVTerm objects in the annotations of this SBML object. More...
 
unsigned int getNumDashes () const
 Returns the number of defined dashes in the 'stroke-dasharray' attribute. More...
 
unsigned int getNumDisabledPlugins () const
 Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More...
 
unsigned int getNumElements () const
 Get the number of Transformation2D objects in this RenderGroup. More...
 
unsigned int getNumPlugins () const
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
unsigned int getPackageCoreVersion () const
 Returns the SBML Core Version within the SBML Level of the actual object. More...
 
const std::string & getPackageName () const
 Returns the name of the SBML Level 3 package in which this element is defined. More...
 
unsigned int getPackageVersion () const
 Returns the Version of the SBML Level 3 package to which this element belongs to. More...
 
SBasegetParentSBMLObject ()
 Returns the parent SBML object containing this object. More...
 
const SBasegetParentSBMLObject () const
 Returns the parent SBML object containing this object. More...
 
SBasePlugingetPlugin (const std::string &package)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
const SBasePlugingetPlugin (const std::string &package) const
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
SBasePlugingetPlugin (unsigned int n)
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasePlugingetPlugin (unsigned int n) const
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
std::string getPrefix () const
 Returns the XML namespace prefix of this element. More...
 
BiolQualifierType_t getResourceBiologicalQualifier (std::string resource)
 Returns the MIRIAM biological qualifier associated with the given resource. More...
 
ModelQualifierType_t getResourceModelQualifier (std::string resource)
 Returns the MIRIAM model qualifier associated with the given resource. More...
 
const SBMLDocumentgetSBMLDocument () const
 Returns the SBMLDocument object containing this object instance. More...
 
SBMLDocumentgetSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
int getSBOTerm () const
 Returns the integer portion of the value of the "sboTerm" attribute of this object. More...
 
std::string getSBOTermAsURL () const
 Returns the URL representation of the "sboTerm" attribute of this object. More...
 
std::string getSBOTermID () const
 Returns the string representation of the "sboTerm" attribute of this object. More...
 
const std::string & getStartHead () const
 Returns the value of the "startHead" attribute of this RenderGroup. More...
 
const std::string & getStroke () const
 Returns the value of the "stroke" attribute of this GraphicalPrimitive1D. More...
 
const std::vector< unsigned int > & getStrokeDashArray () const
 Returns the value of the "stroke-dasharray" attribute of this GraphicalPrimitive1D. More...
 
double getStrokeWidth () const
 Returns the value of the "stroke-width" attribute of this GraphicalPrimitive1D. More...
 
int getTextAnchor () const
 Returns the value of the "text-anchor" attribute of this RenderGroup. More...
 
std::string getTextAnchorAsString () const
 Returns the value of the "text-anchor" attribute of this RenderGroup. More...
 
void getTransform (double *outArray) const
 Returns the value of the "transform" attribute of this Transformation. More...
 
virtual int getTypeCode () const
 Returns the libSBML type code for this RenderGroup object. More...
 
std::string getURI () const
 Gets the namespace URI to which this element belongs to. More...
 
void * getUserData () const
 Returns the user data that has been previously set via setUserData(). More...
 
unsigned int getVersion () const
 Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...
 
int getVTextAnchor () const
 Returns the value of the "vtext-anchor" attribute of this RenderGroup. More...
 
std::string getVTextAnchorAsString () const
 Returns the value of the "vtext-anchor" attribute of this RenderGroup. More...
 
virtual bool hasRequiredAttributes () const
 Predicate returning true if all the required attributes for this RenderGroup object have been set. More...
 
virtual bool hasRequiredElements () const
 Predicate returning true if all the required elements for this RenderGroup object have been set. More...
 
bool hasValidLevelVersionNamespaceCombination ()
 Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More...
 
void insertDash (unsigned int index, unsigned int dash)
 Inserts the given integer value for the dash length at the given position. More...
 
virtual bool isEllipse () const
 Predicate returning true if this abstract GraphicalPrimitive2D is of type Ellipse. More...
 
virtual bool isImage () const
 Predicate returning true if this abstract Transformation2D is of type Image. More...
 
virtual bool isLineEnding () const
 Predicate returning true if this abstract GraphicalPrimitive2D is of type LineEnding. More...
 
bool isPackageEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPackageURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPkgEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPkgURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
virtual bool isPolygon () const
 Predicate returning true if this abstract GraphicalPrimitive2D is of type Polygon. More...
 
virtual bool isRectangle () const
 Predicate returning true if this abstract GraphicalPrimitive2D is of type Rectangle. More...
 
virtual bool isRenderCurve () const
 Predicate returning true if this abstract GraphicalPrimitive1D is of type RenderCurve. More...
 
virtual bool isRenderGroup () const
 Predicate returning true if this abstract GraphicalPrimitive2D is of type RenderGroup. More...
 
bool isSetAnnotation () const
 Predicate returning true if this object's "annotation" subelement exists and has content. More...
 
bool isSetDashArray () const
 Returns true if the dash array has been set or false otherwise. More...
 
bool isSetEndHead () const
 Predicate returning true if this RenderGroup's "endHead" attribute is set. More...
 
bool isSetFill () const
 Predicate returning true if this GraphicalPrimitive2D's "fill" attribute is set. More...
 
bool isSetFillColor () const
 Returns true if the fill attribute is set or false otherwise. More...
 
bool isSetFillRule () const
 Predicate returning true if this GraphicalPrimitive2D's "fill-rule" attribute is set. More...
 
bool isSetFontFamily () const
 Predicate returning true if this RenderGroup's "font-family" attribute is set. More...
 
bool isSetFontSize () const
 Predicate returning true if this RenderGroup's "font-size" element is set. More...
 
bool isSetFontStyle () const
 Predicate returning true if this RenderGroup's "font-style" attribute is set. More...
 
bool isSetFontWeight () const
 Predicate returning true if this RenderGroup's "font-weight" attribute is set. More...
 
virtual bool isSetId () const
 Predicate returning true if this GraphicalPrimitive1D's "id" attribute is set. More...
 
bool isSetIdAttribute () const
 Predicate returning true if this object's "id" attribute is set. More...
 
bool isSetMatrix () const
 Returns true if the matrix has been set or false otherwise. More...
 
bool isSetMetaId () const
 Predicate returning true if this object's "metaid" attribute is set. More...
 
bool isSetModelHistory ()
 Predicate returning true if this object has a ModelHistory object attached to it. More...
 
virtual bool isSetName () const
 Predicate returning true if this Transformation's "name" attribute is set. More...
 
bool isSetNotes () const
 Predicate returning true if this object's "notes" subelement exists and has content. More...
 
bool isSetSBOTerm () const
 Predicate returning true if this object's "sboTerm" attribute is set. More...
 
bool isSetStartHead () const
 Predicate returning true if this RenderGroup's "startHead" attribute is set. More...
 
bool isSetStroke () const
 Predicate returning true if this GraphicalPrimitive1D's "stroke" attribute is set. More...
 
bool isSetStrokeDashArray () const
 Predicate returning true if this GraphicalPrimitive1D's "stroke-dasharray" attribute is set. More...
 
bool isSetStrokeWidth () const
 Predicate returning true if this GraphicalPrimitive1D's "stroke-width" attribute is set. More...
 
bool isSetTextAnchor () const
 Predicate returning true if this RenderGroup's "text-anchor" attribute is set. More...
 
bool isSetTransform () const
 Predicate returning true if this Transformation's "transform" attribute is set. More...
 
bool isSetUserData () const
 Predicate returning true or false depending on whether the user data of this element has been set. More...
 
bool isSetVTextAnchor () const
 Predicate returning true if this RenderGroup's "vtext-anchor" attribute is set. More...
 
virtual bool isText () const
 Predicate returning true if this abstract GraphicalPrimitive1D is of type Text. More...
 
bool matchesRequiredSBMLNamespacesForAddition (const SBase *sb)
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (const SBase *sb)
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (const SBase *sb) const
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
RenderGroupoperator= (const RenderGroup &rhs)
 Assignment operator for RenderGroup. More...
 
void read (XMLNode &node, XMLErrorSeverityOverride_t flag=LIBSBML_OVERRIDE_DISABLED)
 Reads (initializes) this SBML object by reading from the given XMLNode. More...
 
void removeDash (unsigned int index)
 Removes the dash length at the given index. More...
 
Transformation2DremoveElement (unsigned int n)
 Removes the nth Transformation2D from this RenderGroup and returns a pointer to it. More...
 
Transformation2DremoveElement (const std::string &sid)
 Removes the Transformation2D with the given id from this RenderGroup and returns a pointer to it. More...
 
virtual int removeFromParentAndDelete ()
 Removes this object from its parent. More...
 
int removeTopLevelAnnotationElement (const std::string &elementName, const std::string elementURI="", bool removeEmpty=true)
 Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More...
 
virtual void renameMetaIdRefs (const std::string &oldid, const std::string &newid)
 Replaces all uses of a given meta identifier attribute value with another value. More...
 
virtual void renameSIdRefs (const std::string &oldid, const std::string &newid)
 Replaces all uses of a given SIdRef type attribute value with another value. More...
 
virtual void renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
 Replaces all uses of a given UnitSIdRef type attribute value with another value. More...
 
 RenderGroup (unsigned int level=RenderExtension::getDefaultLevel(), unsigned int version=RenderExtension::getDefaultVersion(), unsigned int pkgVersion=RenderExtension::getDefaultPackageVersion())
 Creates a new RenderGroup using the given SBML Level, Version and “render” package version. More...
 
 RenderGroup (RenderPkgNamespaces *renderns)
 Creates a new RenderGroup using the given RenderPkgNamespaces object. More...
 
 RenderGroup (const XMLNode &group, unsigned int l2version=4)
 Creates a new RenderGroup object from the given XMLNode object. More...
 
 RenderGroup (RenderPkgNamespaces *renderns, const std::string &id)
 Instantiates a new RenderGroup object. More...
 
 RenderGroup (const RenderGroup &orig)
 Copy constructor for RenderGroup. More...
 
int replaceTopLevelAnnotationElement (const XMLNode *annotation)
 Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More...
 
int replaceTopLevelAnnotationElement (const std::string &annotation)
 Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More...
 
virtual int setAnnotation (const XMLNode *annotation)
 Sets the value of the "annotation" subelement of this SBML object. More...
 
virtual int setAnnotation (const std::string &annotation)
 Sets the value of the "annotation" subelement of this SBML object. More...
 
void setDashArray (const std::vector< unsigned int > &array)
 Sets the 'stroke-dasharray' attribute to have the values in the given array. More...
 
bool setDashArray (const std::string &arrayString)
 Sets the 'stroke-dasharray' attribute from the given string. More...
 
void setDashByIndex (unsigned int index, unsigned int dash)
 Sets the integer value of the dash at the given position. More...
 
int setEndHead (const std::string &endHead)
 Sets the value of the "endHead" attribute of this RenderGroup. More...
 
int setFill (const std::string &fill)
 Sets the value of the "fill" attribute of this GraphicalPrimitive2D. More...
 
void setFillColor (const std::string &color)
 Set fill color to the id of a color definition, the id of a gradient definition or a color value string. More...
 
void setFillRule (FILL_RULE rule)
 Sets the value of the "fill-rule" attribute of this GraphicalPrimitive2D. More...
 
int setFillRule (const FillRule_t fillRule)
 Sets the value of the "fill-rule" attribute of this GraphicalPrimitive2D. More...
 
int setFillRule (const std::string &fillRule)
 Sets the value of the "fill-rule" attribute of this GraphicalPrimitive2D. More...
 
int setFontFamily (const std::string &fontFamily)
 Sets the value of the "font-family" attribute of this RenderGroup. More...
 
int setFontSize (const RelAbsVector &size)
 Sets the font size. More...
 
int setFontStyle (const FontStyle_t fontStyle)
 Sets the value of the "font-style" attribute of this RenderGroup. More...
 
int setFontStyle (const std::string &fontStyle)
 Sets the value of the "font-style" attribute of this RenderGroup. More...
 
int setFontWeight (const FontWeight_t fontWeight)
 Sets the value of the "font-weight" attribute of this RenderGroup. More...
 
int setFontWeight (const std::string &fontWeight)
 Sets the value of the "font-weight" attribute of this RenderGroup. More...
 
virtual int setId (const std::string &id)
 Sets the value of the "id" attribute of this GraphicalPrimitive1D. More...
 
virtual int setIdAttribute (const std::string &sid)
 Sets the value of the "id" attribute of this SBML object. More...
 
void setMatrix (const double m[12])
 Sets the 2D matrix to the values given in the array. More...
 
void setMatrix2D (const double m[6])
 Sets the 2D matrix to the values given in the array. More...
 
int setMetaId (const std::string &metaid)
 Sets the value of the meta-identifier attribute of this SBML object. More...
 
int setModelHistory (ModelHistory *history)
 Sets the ModelHistory of this object. More...
 
virtual int setName (const std::string &name)
 Sets the value of the "name" attribute of this Transformation. More...
 
int setNamespaces (XMLNamespaces *xmlns)
 Sets the namespaces relevant of this SBML object. More...
 
int setNotes (const XMLNode *notes)
 Sets the value of the "notes" subelement of this SBML object. More...
 
int setNotes (const std::string &notes, bool addXHTMLMarkup=false)
 Sets the value of the "notes" subelement of this SBML object to a copy of the string notes. More...
 
virtual int setSBOTerm (int value)
 Sets the value of the "sboTerm" attribute. More...
 
virtual int setSBOTerm (const std::string &sboid)
 Sets the value of the "sboTerm" attribute by string. More...
 
int setStartHead (const std::string &startHead)
 Sets the value of the "startHead" attribute of this RenderGroup. More...
 
int setStroke (const std::string &stroke)
 Sets the value of the "stroke" attribute of this GraphicalPrimitive1D. More...
 
int setStrokeDashArray (const std::vector< unsigned int > &array)
 Sets the value of the "stroke-dasharray" attribute of this GraphicalPrimitive1D. More...
 
int setStrokeWidth (double strokeWidth)
 Sets the value of the "stroke-width" attribute of this GraphicalPrimitive1D. More...
 
int setTextAnchor (const HTextAnchor_t textAnchor)
 Sets the value of the "text-anchor" attribute of this RenderGroup. More...
 
int setTextAnchor (const std::string &textAnchor)
 Sets the value of the "text-anchor" attribute of this RenderGroup. More...
 
int setTransform (double *inArray)
 Sets the value of the "transform" attribute of this Transformation. More...
 
int setUserData (void *userData)
 Sets the user data of this element. More...
 
int setVTextAnchor (Text::TEXT_ANCHOR anchor)
 Sets the value of the "vtext-anchor" attribute of this RenderGroup. More...
 
int setVTextAnchor (const std::string &vtextAnchor)
 Sets the value of the "vtext-anchor" attribute of this RenderGroup. More...
 
int setVTextAnchor (const VTextAnchor_t vtextAnchor)
 Sets the value of the "vtext-anchor" attribute of this RenderGroup. More...
 
char * toSBML ()
 Returns a string consisting of a partial SBML corresponding to just this object. More...
 
XMLNode toXML () const
 Creates an XMLNode object from this RenderGroup object. More...
 
XMLNodetoXMLNode ()
 Returns this element as an XMLNode. More...
 
int unsetAnnotation ()
 Unsets the value of the "annotation" subelement of this SBML object. More...
 
int unsetCVTerms ()
 Clears the list of CVTerm objects attached to this SBML object. More...
 
int unsetEndHead ()
 Unsets the value of the "endHead" attribute of this RenderGroup. More...
 
int unsetFill ()
 Unsets the value of the "fill" attribute of this GraphicalPrimitive2D. More...
 
int unsetFillRule ()
 Unsets the value of the "fill-rule" attribute of this GraphicalPrimitive2D. More...
 
int unsetFontFamily ()
 Unsets the value of the "font-family" attribute of this RenderGroup. More...
 
int unsetFontSize ()
 Unsets the value of the "font-size" element of this RenderGroup. More...
 
int unsetFontStyle ()
 Unsets the value of the "font-style" attribute of this RenderGroup. More...
 
int unsetFontWeight ()
 Unsets the value of the "font-weight" attribute of this RenderGroup. More...
 
virtual int unsetId ()
 Unsets the value of the "id" attribute of this GraphicalPrimitive1D. More...
 
int unsetIdAttribute ()
 Unsets the value of the "id" attribute of this SBML object. More...
 
int unsetMatrix ()
 Unsets the value of the "transform" attribute of this Transformation. More...
 
int unsetMetaId ()
 Unsets the value of the "metaid" attribute of this SBML object. More...
 
int unsetModelHistory ()
 Unsets the ModelHistory object attached to this object. More...
 
virtual int unsetName ()
 Unsets the value of the "name" attribute of this Transformation. More...
 
int unsetNotes ()
 Unsets the value of the "notes" subelement of this SBML object. More...
 
int unsetSBOTerm ()
 Unsets the value of the "sboTerm" attribute of this SBML object. More...
 
int unsetStartHead ()
 Unsets the value of the "startHead" attribute of this RenderGroup. More...
 
int unsetStroke ()
 Unsets the value of the "stroke" attribute of this GraphicalPrimitive1D. More...
 
int unsetStrokeDashArray ()
 Unsets the value of the "stroke-dasharray" attribute of this GraphicalPrimitive1D. More...
 
int unsetStrokeWidth ()
 Unsets the value of the "stroke-width" attribute of this GraphicalPrimitive1D. More...
 
int unsetTextAnchor ()
 Unsets the value of the "text-anchor" attribute of this RenderGroup. More...
 
int unsetTransform ()
 Unsets the value of the "transform" attribute of this Transformation. More...
 
int unsetUserData ()
 Unsets the user data of this element. More...
 
int unsetVTextAnchor ()
 Unsets the value of the "vtext-anchor" attribute of this RenderGroup. More...
 
virtual ~RenderGroup ()
 Destructor for RenderGroup. More...
 

Static Public Member Functions

static const double * getIdentityMatrix ()
 Returns a 3D identity matrix. More...
 
static const double * getIdentityMatrix2D ()
 Returns a 2D identity matrix. More...
 

Protected Member Functions

virtual void setElementText (const std::string &text)
 When overridden allows SBase elements to use the text included in between the elements tags. More...
 

Friends

class Text
 

Constructor & Destructor Documentation

RenderGroup::RenderGroup ( unsigned int  level = RenderExtension::getDefaultLevel(),
unsigned int  version = RenderExtension::getDefaultVersion(),
unsigned int  pkgVersion = RenderExtension::getDefaultPackageVersion() 
)

Creates a new RenderGroup using the given SBML Level, Version and “render” package version.

Parameters
levelan unsigned int, the SBML Level to assign to this RenderGroup.
versionan unsigned int, the SBML Version to assign to this RenderGroup.
pkgVersionan unsigned int, the SBML Render Version to assign to this RenderGroup.
Note
Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
RenderGroup::RenderGroup ( RenderPkgNamespaces renderns)

Creates a new RenderGroup using the given RenderPkgNamespaces object.

The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.
Parameters
rendernsthe RenderPkgNamespaces object.
Note
Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
RenderGroup::RenderGroup ( const XMLNode group,
unsigned int  l2version = 4 
)

Creates a new RenderGroup object from the given XMLNode object.

The XMLNode object has to contain a valid XML representation of a RenderGroup 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.

Parameters
groupthe XMLNode object reference that describes the RenderGroup object to be instantiated.
l2versionthe version of SBML Level 2 to target.
RenderGroup::RenderGroup ( RenderPkgNamespaces renderns,
const std::string &  id 
)

Instantiates a new RenderGroup object.

All attributes are set as described for the default constructor of GraphicalPrimitive2D. All the font rendering attributes and the curve decorations are unset. The id is set to the given string.

Parameters
idthe id for the RenderGroup object.
rendernsthe RenderPkgNamespaces object.
Warning
This constructor is deprecated. The new libSBML API uses constructors that either take the SBML Level and Version, or take an SBMLNamespaces object.
RenderGroup::RenderGroup ( const RenderGroup orig)

Copy constructor for RenderGroup.

Parameters
origthe RenderGroup instance to copy.
RenderGroup::~RenderGroup ( )
virtual

Destructor for RenderGroup.

Member Function Documentation

int RenderGroup::addChildElement ( const Transformation2D pChild)

Adds a copy of the given element to the end of the list of children elements.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this RenderGroup. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the RenderGroup. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see RenderGroup::createXXX() for methods that do not lead to these issues.
See also
createEllipse()
createRectangle()
createPolygon()
createText()
createCurve()
createImage()
int SBase::addCVTerm ( CVTerm term,
bool  newBag = false 
)
inherited

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif 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.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
Since the CV Term uses the "metaid" attribute of the object as a reference, if the object has no "metaid" attribute value set, then the CVTerm will not be added.
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
Examples:
addCVTerms.cpp, addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.
void GraphicalPrimitive1D::addDash ( unsigned int  dash)
inherited

Adds a new length of a dash to the 'stroke-dasharray' attribute.

Parameters
dashthe integer length of the dash to add to the end of the 'stroke-dasharray' attribute.
int RenderGroup::addElement ( const Transformation2D td)

Adds a copy of the given Transformation2D to this RenderGroup.

Parameters
tdthe Transformation2D object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createEllipse()
createRectangle()
createPolygon()
createText()
createCurve()
createImage()
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
int SBase::appendAnnotation ( const XMLNode annotation)
virtualinherited

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(const XMLNode* annotation) or SBase::setAnnotation(const std::string& annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the "annotation" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

Examples:
addingEvidenceCodes_2.cpp, and appendAnnotation.cpp.
int SBase::appendAnnotation ( const std::string &  annotation)
virtualinherited

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(const XMLNode* annotation) or SBase::setAnnotation(const std::string& annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the "annotation" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int SBase::appendNotes ( const XMLNode notes)
inherited

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.

Parameters
notesan XML node structure that is to appended to the content of the "notes" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::appendNotes ( const std::string &  notes)
inherited

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.

Parameters
notesan XML string that is to appended to the content of the "notes" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
void GraphicalPrimitive1D::clearDashes ( )
inherited

Unsets the value of the "stroke-dasharray" attribute of this GraphicalPrimitive1D.

RenderGroup * RenderGroup::clone ( ) const
virtual

Creates and returns a deep copy of this RenderGroup object.

Returns
a (deep) copy of this RenderGroup object.

Reimplemented from GraphicalPrimitive2D.

RenderCurve * RenderGroup::createCurve ( )

Creates a new RenderCurve object, adds it to this RenderGroup object and returns the RenderCurve object created.

Returns
a new RenderCurve object instance.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
Ellipse * RenderGroup::createEllipse ( )

Creates a new Ellipse object, adds it to this RenderGroup object and returns the Ellipse object created.

Returns
a new Ellipse object instance.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
RenderGroup * RenderGroup::createGroup ( )

Creates a new RenderGroup object, adds it to this RenderGroup object and returns the RenderGroup object created.

Returns
a new RenderGroup object instance.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
Image * RenderGroup::createImage ( )

Creates a new Image object, adds it to this RenderGroup object and returns the Image object created.

Returns
a new Image object instance.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
LineEnding * RenderGroup::createLineEnding ( )

Creates a new LineEnding object, adds it to this RenderGroup object and returns the LineEnding object created.

Returns
a new LineEnding object instance.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
Polygon * RenderGroup::createPolygon ( )

Creates a new Polygon object, adds it to this RenderGroup object and returns the Polygon object created.

Returns
a new Polygon object instance.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
Rectangle * RenderGroup::createRectangle ( )

Creates a new Rectangle object, adds it to this RenderGroup object and returns the Rectangle object created.

Returns
a new Rectangle object instance.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
Text * RenderGroup::createText ( )

Creates a new Text object, adds it to this RenderGroup object and returns the Text object created.

Returns
a new Text object instance.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
void SBase::deleteDisabledPlugins ( bool  recursive = true)
inherited

Deletes all information stored in disabled plugins.

If the plugin is re-enabled later, it will then not have any previously-stored information.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
recursiveif true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element.
See also
getNumDisabledPlugins()
int SBase::disablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix 
)
inherited

Disables the given SBML Level 3 package on this object.

This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from an other SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:

// We read in an SBML L3V1 model that uses the 'comp'
// package namespace.
doc = readSBML("sbml-file-with-comp-elements.xml");
// We extract one of the species from the model.
Species* s1 = doc->getModel()->getSpecies(0);
// We construct a new model. This model does not use the
// 'comp' package.
Model * newModel = new Model(3,1);
// The following will fail with an error, because addSpecies()
// will first check that the parent of the given object has
// namespaces declared, and will discover that s1 does but
// newModel does not.
// newModel->addSpecies(s1);
// However, if we disable the 'comp' package on s1, then
// the call to addSpecies will work.
s1->disablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1",
"comp");
newModel->addSpecies(s1);
Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
enablePackage(const std::string& pkgURI, const std::string& pkgPrefix, bool flag)
int SBase::enablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix,
bool  flag 
)
inherited

Enables or disables the given SBML Level 3 package on this object.

This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase::disablePackage(const std::string& pkgURI, const std::string& pkgPrefix).

Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package.
flagwhether to enable (true) or disable (false) the package.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
disablePackage(const std::string& pkgURI, const std::string& pkgPrefix)
Examples:
addLayout.cpp.
List * RenderGroup::getAllElements ( ElementFilter filter = NULL)
virtual

Returns a List of all child SBase objects, including those nested to an arbitrary depth.

Parameters
filteran ElementFilter that may impose restrictions on the objects to be retrieved.
Returns
a List pointer of pointers to all SBase child objects with any restriction imposed.

Reimplemented from SBase.

List * SBase::getAllElementsFromPlugins ( ElementFilter filter = NULL)
virtualinherited

Returns a List of all child SBase objects contained in SBML package plug-ins.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

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.

Parameters
filtera pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.
Returns
a pointer to a List of pointers to all children objects from plug-ins.
SBase * SBase::getAncestorOfType ( int  type,
const std::string &  pkgName = "core" 
)
inherited

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. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. 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.

Parameters
typethe 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.
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBMLTypeCode_t value, or NULL if no ancestor exists.
Warning
The optional argument 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 NULL.
const SBase * SBase::getAncestorOfType ( int  type,
const std::string  pkgName = "core" 
) const
inherited

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. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. 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.

Parameters
typethe 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.
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBMLTypeCode_t value, or NULL if no ancestor exists.
Warning
The optional argument 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 NULL.
XMLNode * SBase::getAnnotation ( )
inherited

Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.

Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
XMLNode * SBase::getAnnotation ( ) const
inherited

Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.

Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
std::string SBase::getAnnotationString ( )
inherited

Returns the content of the "annotation" subelement of this object as a character string.

Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
See also
getAnnotation()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
Examples:
printAnnotation.cpp.
std::string SBase::getAnnotationString ( ) const
inherited

Returns the content of the "annotation" subelement of this object as a character string.

Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
See also
getAnnotation()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
unsigned int SBase::getColumn ( ) const
inherited

Returns the column number where this object first appears in the XML representation of the SBML document.

Returns
the column number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.
Note
The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getLine()
CVTerm * SBase::getCVTerm ( unsigned int  n)
inherited

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters
nunsigned int the index of the CVTerm to retrieve.
Returns
the nth CVTerm in the list of CVTerms for this SBML object. If the index n is invalid, NULL is returned.
List * SBase::getCVTerms ( )
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns
the list of CVTerms for this SBML object.
List * SBase::getCVTerms ( ) const
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns
the list of CVTerms for this SBML object.
const std::vector<unsigned int>& GraphicalPrimitive1D::getDashArray ( ) const
inherited

Returns a const reference to the stroke dasharray.

Returns
const reference to stroke dash array
std::vector<unsigned int>& GraphicalPrimitive1D::getDashArray ( )
inherited

Returns a reference to the stroke dasharray.

Returns
reference to stroke dash array
unsigned int GraphicalPrimitive1D::getDashByIndex ( unsigned int  index) const
inherited

Returns the dash at the given index of the 'stroke-dasharray' attribute.

Parameters
indexthe index of the dash length to return from the 'stroke-dasharray' attribute.
Returns
the value of the dash length from the 'stroke-dasharray' attribute at the given index, or -1 (cast to an unsigned int) if no such index exists.
SBasePlugin * SBase::getDisabledPlugin ( unsigned int  n)
inherited

Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
nthe index of the disabled plug-in to return.
Returns
the nth disabled plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.
See also
getNumDisabledPlugins()
getPlugin(const std::string& package)
const SBasePlugin * SBase::getDisabledPlugin ( unsigned int  n) const
inherited

Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
nthe index of the disabled plug-in to return.
Returns
the nth disabled plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.
See also
getNumDisabledPlugins()
getPlugin(const std::string& package)
Transformation2D * RenderGroup::getElement ( unsigned int  n)

Get a Transformation2D from the RenderGroup.

Parameters
nan unsigned int representing the index of the Transformation2D to retrieve.
Returns
the nth Transformation2D in the ListOfDrawables within this RenderGroup. If the index n is invalid, NULL is returned.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
createEllipse()
createRectangle()
createPolygon()
createText()
createCurve()
createImage()
getElement(const std::string& sid)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
const Transformation2D * RenderGroup::getElement ( unsigned int  n) const

Get a Transformation2D from the RenderGroup.

Parameters
nan unsigned int representing the index of the Transformation2D to retrieve.
Returns
the nth Transformation2D in the ListOfDrawables within this RenderGroup. If the index n is invalid, NULL is returned.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
createEllipse()
createRectangle()
createPolygon()
createText()
createCurve()
createImage()
getElement(const std::string& sid)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
Transformation2D * RenderGroup::getElement ( const std::string &  id)

Returns pointer to the element with the given id.

If there is no such element, NULL is returned. Since the id on all those object is optional, this routine might not be as helpful as similar routines in other classes.

Parameters
idid of element to be returned
Returns
pointer to element with id or NULL if there is no object with that id
const Transformation2D * RenderGroup::getElement ( const std::string &  id) const

Returns const pointer to the element with given index.

If there is no such element, NULL is returned. Since the id on all those object is optional, this routine might not be as helpful as similar routines in other classes.

Parameters
idid of element to be returned
Returns
pointer to element with the given id or NULL if there is no object with that id
const SBase * SBase::getElementByMetaId ( const std::string &  metaid) const
inherited

Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. 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.
Parameters
metaidstring representing the "metaid" attribute value of the object to find.
Returns
pointer to the first element found with the given meta-identifier.
SBase * RenderGroup::getElementByMetaId ( const std::string &  metaid)
virtual

Returns the first child element that has the given metaid, or NULL if no such object is found.

Parameters
metaida string representing the metaid attribute of the object to retrieve.
Returns
a pointer to the SBase element with the given metaid. If no such object is found this method returns NULL.

Reimplemented from SBase.

const SBase * SBase::getElementBySId ( const std::string &  id) const
inherited

Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.

Parameters
idstring representing the "id" attribute value of the object to find.
Returns
pointer to the first element found with the given identifier.
SBase * RenderGroup::getElementBySId ( const std::string &  id)
virtual

Returns the first child element that has the given id in the model-wide SId namespace, or NULL if no such object is found.

Parameters
ida string representing the id attribute of the object to retrieve.
Returns
a pointer to the SBase element with the given id. If no such object is found, this method returns NULL.

Reimplemented from SBase.

const std::string & RenderGroup::getElementName ( ) const
virtual

Returns the XML element name of this RenderGroup object.

For RenderGroup, the XML element name is always "g".

Returns
the name of this element, i.e. "g".

Reimplemented from GraphicalPrimitive2D.

const std::string & RenderGroup::getEndHead ( ) const

Returns the value of the "endHead" attribute of this RenderGroup.

Returns
the value of the "endHead" attribute of this RenderGroup as a string.
const std::string & GraphicalPrimitive2D::getFill ( ) const
inherited

Returns the value of the "fill" attribute of this GraphicalPrimitive2D.

Returns
the value of the "fill" attribute of this GraphicalPrimitive2D as a string.
const std::string & GraphicalPrimitive2D::getFillColor ( ) const
inherited

Returns the value of the "fill" attribute of this GraphicalPrimitive2D.

Returns
the value of the "fill" attribute of this GraphicalPrimitive2D as a string.
int GraphicalPrimitive2D::getFillRule ( ) const
inherited

Returns the value of the "fill-rule" attribute of this GraphicalPrimitive2D.

The attribute "fill-rule" is used to define how polygons should be filled. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "fill-rule":
  • "nonzero": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and then examining the places where a segment of the shape crosses the ray. Starting with a count of zero, add one each time a path segment crosses the ray from left to right and subtract one each time a path segment crosses the ray from right to left. After counting the crossings, if the result is zero then the point is outside the path. Otherwise, it is inside.

  • "evenodd": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and counting the number of path segments from the given shape that the ray crosses. If this number is odd, the point is inside; if even, the point is outside.

  • "inherit": This value declares the "insideness" of a point in the shape by declaring that the property takes the same computed value as the property for the element's parent. The inherited value, which is normally only used as a fallback value, can be clarified by setting 'inherit' explicitly. NOTE: This value is NOT in the Level 3 Version 1 Render specification, but was left out due to an oversight: the value has long been part of the codebase. It is provided here as a convenience. Elements with a fill-rule set to "inherit" actually behave identicaly to elements without a fill-rule attribute at all, since this attribute always takes the value of a parent element if not defined explicitly.

Returns
the value of the "fill-rule" attribute of this GraphicalPrimitive2D as a FillRule_t value. The possible values returned by this method are:
std::string GraphicalPrimitive2D::getFillRuleAsString ( ) const
inherited

Returns the value of the "fill-rule" attribute of this GraphicalPrimitive2D.

The attribute "fill-rule" is used to define how polygons should be filled. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "fill-rule":
  • "nonzero": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and then examining the places where a segment of the shape crosses the ray. Starting with a count of zero, add one each time a path segment crosses the ray from left to right and subtract one each time a path segment crosses the ray from right to left. After counting the crossings, if the result is zero then the point is outside the path. Otherwise, it is inside.

  • "evenodd": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and counting the number of path segments from the given shape that the ray crosses. If this number is odd, the point is inside; if even, the point is outside.

  • "inherit": This value declares the "insideness" of a point in the shape by declaring that the property takes the same computed value as the property for the element's parent. The inherited value, which is normally only used as a fallback value, can be clarified by setting 'inherit' explicitly. NOTE: This value is NOT in the Level 3 Version 1 Render specification, but was left out due to an oversight: the value has long been part of the codebase. It is provided here as a convenience. Elements with a fill-rule set to "inherit" actually behave identicaly to elements without a fill-rule attribute at all, since this attribute always takes the value of a parent element if not defined explicitly.

Returns
the value of the "fill-rule" attribute of this GraphicalPrimitive2D as a string. The possible values returned by this method are:
  • "unset"
  • "nonzero"
  • "evenodd"
  • "inherit"
  • "(Unknown FillRule value)"
const std::string & RenderGroup::getFontFamily ( ) const

Returns the value of the "font-family" attribute of this RenderGroup.

Returns
the value of the "font-family" attribute of this RenderGroup as a string.
const RelAbsVector & RenderGroup::getFontSize ( ) const

Returns the value of the "font-size" element of this RenderGroup.

Returns
the value of the "font-size" element of this RenderGroup as a RelAbsVector.
RelAbsVector & RenderGroup::getFontSize ( )

Returns the value of the "font-size" element of this RenderGroup.

Returns
the value of the "font-size" element of this RenderGroup as a RelAbsVector.
int RenderGroup::getFontStyle ( ) const

Returns the value of the "font-style" attribute of this RenderGroup.

Returns
the value of the "font-style" attribute of this RenderGroup as a FontStyle_t.
The attribute "font-style" is used to specify whether the text is to be "normal" or "italic". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-style":
  • "italic", slanted print

  • "normal", upright print

The value is drawn from the enumeration FontStyle_t. The possible values returned by this method are:
std::string RenderGroup::getFontStyleAsString ( ) const

Returns the value of the "font-style" attribute of this RenderGroup.

Returns
the value of the "font-style" attribute of this RenderGroup as a string.
The attribute "font-style" is used to specify whether the text is to be "normal" or "italic". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-style":
  • "italic", slanted print

  • "normal", upright print

The possible values returned by this method are:
  • "italic"
  • "normal"
  • "(Unknown FontStyle value)"
int RenderGroup::getFontWeight ( ) const

Returns the value of the "font-weight" attribute of this RenderGroup.

Returns
the value of the "font-weight" attribute of this RenderGroup as a FontWeight_t.
The attribute "font-weight" is used to specify whether the text is to be "normal" or "bold". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-weight":
  • "bold", darker and/or thicker than normal print.

  • "normal", the typical print weight; lighter and/or thinner than "bold".

The value is drawn from the enumeration FontWeight_t. The possible values returned by this method are:
std::string RenderGroup::getFontWeightAsString ( ) const

Returns the value of the "font-weight" attribute of this RenderGroup.

Returns
the value of the "font-weight" attribute of this RenderGroup as a string.
The attribute "font-weight" is used to specify whether the text is to be "normal" or "bold". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-weight":
  • "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:
  • "bold"
  • "normal"
  • "(Unknown FontWeight value)"
const std::string & GraphicalPrimitive1D::getId ( ) const
virtualinherited

Returns the value of the "id" attribute of this GraphicalPrimitive1D.

Returns
the value of the "id" attribute of this GraphicalPrimitive1D as a string.

Reimplemented from SBase.

Reimplemented in LineEnding.

const string & SBase::getIdAttribute ( ) const
inherited

Returns the value of the "id" attribute of this SBML object.

The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always 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.

Returns
the id of this SBML object, if set and valid for this level and version of SBML; an empty string otherwise.
Note
Because of the inconsistent behavior of this function with respect to assignments and rules, callers should use getIdAttribute() instead.
See also
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()
const double * Transformation::getIdentityMatrix ( )
staticinherited

Returns a 3D identity matrix.

The matrix contains 12 double values.

const double * Transformation2D::getIdentityMatrix2D ( )
staticinherited

Returns a 2D identity matrix.

The matrix contains 6 double values.

unsigned int SBase::getLevel ( ) const
inherited

Returns the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML level of this SBML object.
See also
getVersion()
getNamespaces()
getPackageVersion()
Examples:
addLayout.cpp, convertSBML.cpp, and printSBML.cpp.
unsigned int SBase::getLine ( ) const
inherited

Returns the line number where this object first appears in the XML representation of the SBML document.

Returns
the line number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.
Note
The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getColumn()
const ListOfDrawables * RenderGroup::getListOfElements ( ) const

Returns the ListOfDrawables from this RenderGroup.

Returns
the ListOfDrawables from this RenderGroup.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
createEllipse()
createRectangle()
createPolygon()
createText()
createCurve()
createImage()
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
Examples:
convertLayout.cpp.
ListOfDrawables * RenderGroup::getListOfElements ( )

Returns the ListOfDrawables from this RenderGroup.

Returns
the ListOfDrawables from this RenderGroup.
Note
The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.
See also
addElement(const Transformation2D* object)
createEllipse()
createRectangle()
createPolygon()
createText()
createCurve()
createImage()
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
removeElement(unsigned int n)
const double * Transformation::getMatrix ( ) const
inherited

Returns the value of the "transform" attribute of this Transformation.

which is an array of double values of length 12.

Returns
a pointer to the array of numbers for the transformation.
const double * Transformation2D::getMatrix2D ( ) const
inherited

Returns the 2D matrix which is an array of double values of length 6.

Returns
a pointer to the array of numbers for the 2D transformation.
const string & SBase::getMetaId ( ) const
inherited

Returns the value of the "metaid" attribute of this SBML object.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. 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.
Returns
the meta-identifier of this SBML object.
See also
isSetMetaId()
setMetaId(const std::string& metaid)
Examples:
addingEvidenceCodes_2.cpp.
string & SBase::getMetaId ( )
inherited

Returns the value of the "metaid" attribute of this SBML object.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. 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.
Returns
the meta-identifier of this SBML object, as a string.
See also
isSetMetaId()
setMetaId(const std::string& metaid)
const Model * SBase::getModel ( ) const
inherited

Returns the Model object for the SBML Document in which the current object is located.

Returns
the Model object for the SBML Document of this SBML object.
See also
getParentSBMLObject()
getSBMLDocument()
ModelHistory * SBase::getModelHistory ( ) const
inherited

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or NULL if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
ModelHistory * SBase::getModelHistory ( )
inherited

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or NULL if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
const std::string & Transformation::getName ( ) const
virtualinherited

Returns the value of the "name" attribute of this Transformation.

Returns
the value of the "name" attribute of this Transformation as a string.

Reimplemented from SBase.

XMLNamespaces * SBase::getNamespaces ( ) const
virtualinherited

Returns a list of the XML Namespaces declared on the SBML document owning this object.

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.

Returns
the XML Namespaces associated with this SBML object, or NULL in certain very usual circumstances where a namespace is not set.
See also
getLevel()
getVersion()

Reimplemented in SBMLDocument.

XMLNode * SBase::getNotes ( )
inherited

Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.

The optional SBML element named "notes", present on every major SBML component type (and in SBML Level 3, the "message" subelement of Constraint), 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 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().

Returns
the content of the "notes" subelement of this SBML object as a tree structure composed of XMLNode objects.
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
XMLNode * SBase::getNotes ( ) const
inherited

Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.

The optional SBML element named "notes", present on every major SBML component type (and in SBML Level 3, the "message" subelement of Constraint), 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 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().

Returns
the content of the "notes" subelement of this SBML object as a tree structure composed of XMLNode objects.
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
std::string SBase::getNotesString ( )
inherited

Returns the content of the "notes" subelement of this object as a string.

The optional SBML element named "notes", present on every major SBML component type (and in SBML Level 3, the "message" subelement of Constraint), 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 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.

Returns
the content of the "notes" subelement of this SBML object as a string.
See also
getNotes()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
printNotes.cpp, and SBMLHttpResolverExample.cpp.
std::string SBase::getNotesString ( ) const
inherited

Returns the content of the "notes" subelement of this object as a string.

The optional SBML element named "notes", present on every major SBML component type (and in SBML Level 3, the "message" subelement of Constraint), 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 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.

Returns
the content of the "notes" subelement of this SBML object as a string.
See also
getNotes()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
unsigned int SBase::getNumCVTerms ( )
inherited

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns
the number of CVTerms for this SBML object.
unsigned int GraphicalPrimitive1D::getNumDashes ( ) const
inherited

Returns the number of defined dashes in the 'stroke-dasharray' attribute.

Returns
the number of dashes in the 'stroke-dasharray' attribute.
unsigned int SBase::getNumDisabledPlugins ( ) const
inherited

Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Returns
the number of disabled plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
unsigned int SBase::getNumPlugins ( ) const
inherited

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
See also
getPlugin(unsigned int n)
unsigned int SBase::getPackageCoreVersion ( ) const
inherited

Returns the SBML Core Version within the SBML Level of the actual object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML core version of this SBML object.
const std::string & SBase::getPackageName ( ) const
inherited

Returns the name of the SBML Level 3 package in which this element is defined.

Returns
the name of the SBML package in which this element is defined. The 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.
unsigned int SBase::getPackageVersion ( ) const
inherited

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See also
getLevel()
getVersion()
SBase * SBase::getParentSBMLObject ( )
inherited

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See also
getSBMLDocument()
getModel()
const SBase * SBase::getParentSBMLObject ( ) const
inherited

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See also
getSBMLDocument()
getModel()
SBasePlugin * SBase::getPlugin ( const std::string &  package)
inherited

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("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
packagethe name or URI of the package.
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
See also
getPlugin(unsigned int n)
Examples:
addLayout.cpp, convertLayout.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, groups_example1.cpp, groups_example2.cpp, qual_example1.cpp, SBMLHttpResolverExample.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.
const SBasePlugin * SBase::getPlugin ( const std::string &  package) const
inherited

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("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
packagethe name or URI of the package.
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
See also
getPlugin(unsigned int n)
SBasePlugin * SBase::getPlugin ( unsigned int  n)
inherited

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("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return.
Returns
the nth plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.
See also
getNumPlugins()
getPlugin(const std::string& package)
const SBasePlugin * SBase::getPlugin ( unsigned int  n) const
inherited

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("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return.
Returns
the nth plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.
See also
getNumPlugins()
getPlugin(const std::string& package)
std::string SBase::getPrefix ( ) const
inherited

Returns the XML namespace prefix of this element.

This 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.

Returns
a text string representing the XML namespace prefix.
BiolQualifierType_t SBase::getResourceBiologicalQualifier ( std::string  resource)
inherited

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include "is" and "has part", but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using values from the enumeration type BiolQualifierType_t.

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 value from the enumeration type BiolQualifierType_t.

Parameters
resourcestring representing the resource; e.g., "http://www.geneontology.org/#GO:0005892".
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values in the enumeration BiolQualifierType_t are up to date with MIRIAM at the time of a given libSBML release. The set of values may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
ModelQualifierType_t SBase::getResourceModelQualifier ( std::string  resource)
inherited

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is "isDerivedFrom", to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using values from the enumeration type ModelQualifierType_t.

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 value from the enumeration type ModelQualifierType_t.

Parameters
resourcestring representing the resource; e.g., "http://www.geneontology.org/#GO:0005892".
Returns
the ModelQualifierType_t value associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values in the enumeration ModelQualifierType_t are up to date with MIRIAM at the time of a given libSBML release. The set of values may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
const SBMLDocument * SBase::getSBMLDocument ( ) const
inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See also
getParentSBMLObject()
getModel()
SBMLDocument * SBase::getSBMLDocument ( )
inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See also
getParentSBMLObject()
getModel()
int SBase::getSBOTerm ( ) const
inherited

Returns the integer portion of the value of the "sboTerm" attribute of this object.

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". More details can be found in SBML specifications for Level 2 Version 2 and above.
Returns
the value of the "sboTerm" attribute as an integer, or -1 if the value is not set.
Examples:
printSBML.cpp.
std::string SBase::getSBOTermAsURL ( ) const
inherited

Returns the URL representation of the "sboTerm" attribute of this object.

This method returns the entire SBO identifier as a text string in the form http://identifiers.org/biomodels.sbo/SBO:NNNNNNN".

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". More details can be found in SBML specifications for Level 2 Version 2 and above.
Returns
the value of the "sboTerm" attribute as an identifiers.org URL, or an empty string if the value is not set.
std::string SBase::getSBOTermID ( ) const
inherited

Returns the string representation of the "sboTerm" attribute of this object.

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". More details can be found in SBML specifications for Level 2 Version 2 and above.
Returns
the value of the "sboTerm" attribute as a string (its value will be of the form "SBO:NNNNNNN"), or an empty string if the value is not set.
const std::string & RenderGroup::getStartHead ( ) const

Returns the value of the "startHead" attribute of this RenderGroup.

Returns
the value of the "startHead" attribute of this RenderGroup as a string.
const std::string & GraphicalPrimitive1D::getStroke ( ) const
inherited

Returns the value of the "stroke" attribute of this GraphicalPrimitive1D.

Returns
the value of the "stroke" attribute of this GraphicalPrimitive1D as a string.
const std::vector< unsigned int > & GraphicalPrimitive1D::getStrokeDashArray ( ) const
inherited

Returns the value of the "stroke-dasharray" attribute of this GraphicalPrimitive1D.

Note
the value of the "stroke-dasharray" attribute of this GraphicalPrimitive1D is returned in the argument array.
double GraphicalPrimitive1D::getStrokeWidth ( ) const
inherited

Returns the value of the "stroke-width" attribute of this GraphicalPrimitive1D.

Returns
the value of the "stroke-width" attribute of this GraphicalPrimitive1D as a double.
int RenderGroup::getTextAnchor ( ) const

Returns the value of the "text-anchor" attribute of this RenderGroup.

Returns
the value of the "text-anchor" attribute of this RenderGroup as a HTextAnchor_t.
The attribute "text-anchor" is used to specify the horizontal alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "text-anchor":
  • "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.

The value is drawn from the enumeration HTextAnchor_t.

The possible values returned by this method are:

std::string RenderGroup::getTextAnchorAsString ( ) const

Returns the value of the "text-anchor" attribute of this RenderGroup.

Returns
the value of the "text-anchor" attribute of this RenderGroup as a string.
The attribute "text-anchor" is used to specify the horizontal alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "text-anchor":
  • "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.

The possible values returned by this method are:
  • "start"
  • "middle"
  • "end"
  • "(Unknown HTextAnchor value)"
void Transformation::getTransform ( double *  outArray) const
inherited

Returns the value of the "transform" attribute of this Transformation.

Parameters
outArraydouble* array that will be used to return the value of the "transform" attribute of this Transformation.
Note
the value of the "transform" attribute of this Transformation is returned in the argument array.
int RenderGroup::getTypeCode ( ) const
virtual

Returns the libSBML type code for this RenderGroup object.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. The set of possible type codes for core elements is defined in the enumeration SBMLTypeCode_t, and in addition, libSBML plug-ins for SBML Level 3 packages define their own extra enumerations of type codes (e.g., SBMLLayoutTypeCode_t for the Level 3 Layout package). 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.

Returns
the SBML type code for this object: SBML_RENDER_GROUP.
Warning
The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getPackageName() and getTypeCode() (or ListOf::getItemTypeCode()).
See also
getElementName()
getPackageName()

Reimplemented from GraphicalPrimitive2D.

std::string SBase::getURI ( ) const
inherited

Gets the namespace URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/layout/version1".

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.

Returns
the URI of this element, as a text string.
See also
getSBMLDocument()
getPackageName()
void * SBase::getUserData ( ) const
inherited

Returns the user data that has been previously set via setUserData().

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
the user data of this node, or NULL if no user data has been set.
See also
ASTNode::setUserData(void *userData)
unsigned int SBase::getVersion ( ) const
inherited

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML version of this SBML object.
See also
getLevel()
getNamespaces()
Examples:
addLayout.cpp, convertSBML.cpp, and printSBML.cpp.
int RenderGroup::getVTextAnchor ( ) const

Returns the value of the "vtext-anchor" attribute of this RenderGroup.

Returns
the value of the "vtext-anchor" attribute of this RenderGroup as a VTextAnchor_t.
The attribute "vtext-anchor" is used to specify the vertical alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "vtext-anchor":
  • "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.

The value is drawn from the enumeration VTextAnchor_t.

The possible values returned by this method are:

std::string RenderGroup::getVTextAnchorAsString ( ) const

Returns the value of the "vtext-anchor" attribute of this RenderGroup.

Returns
the value of the "vtext-anchor" attribute of this RenderGroup as a string.
The attribute "vtext-anchor" is used to specify the vertical alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "vtext-anchor":
  • "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.

The possible values returned by this method are:
  • "top"
  • "middle"
  • "bottom"
  • "baseline"
  • "(Unknown VTextAnchor value)"
bool RenderGroup::hasRequiredAttributes ( ) const
virtual

Predicate returning true if all the required attributes for this RenderGroup object have been set.

Returns
true to indicate that all the required attributes of this RenderGroup have been set, otherwise false is returned.

Reimplemented from GraphicalPrimitive2D.

bool RenderGroup::hasRequiredElements ( ) const
virtual

Predicate returning true if all the required elements for this RenderGroup object have been set.

Returns
true to indicate that all the required elements of this RenderGroup have been set, otherwise false is returned.
Note
The required elements for the RenderGroup object are:
bool SBase::hasValidLevelVersionNamespaceCombination ( )
inherited

Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.

The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:

  • Level 1 Version 2: "http://www.sbml.org/sbml/level1"
  • Level 2 Version 1: "http://www.sbml.org/sbml/level2"
  • Level 2 Version 2: "http://www.sbml.org/sbml/level2/version2"
  • Level 2 Version 3: "http://www.sbml.org/sbml/level2/version3"
  • Level 2 Version 4: "http://www.sbml.org/sbml/level2/version4"
  • Level 2 Version 5: "http://www.sbml.org/sbml/level2/version5"
  • Level 3 Version 1 Core: "http://www.sbml.org/sbml/level3/version1/core"
  • Level 3 Version 2 Core: "http://www.sbml.org/sbml/level3/version2/core"
Returns
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
void GraphicalPrimitive1D::insertDash ( unsigned int  index,
unsigned int  dash 
)
inherited

Inserts the given integer value for the dash length at the given position.

Parameters
indexthe 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.
dashthe integer length to set the inserted dash to.
bool GraphicalPrimitive2D::isEllipse ( ) const
virtualinherited

Predicate returning true if this abstract GraphicalPrimitive2D is of type Ellipse.

Returns
true if this abstract GraphicalPrimitive2D is of type Ellipse, false otherwise

Reimplemented from GraphicalPrimitive1D.

bool Transformation2D::isImage ( ) const
virtualinherited

Predicate returning true if this abstract Transformation2D is of type Image.

Returns
true if this abstract Transformation2D is of type Image, false otherwise

Reimplemented from Transformation.

bool GraphicalPrimitive2D::isLineEnding ( ) const
virtualinherited

Predicate returning true if this abstract GraphicalPrimitive2D is of type LineEnding.

Returns
true if this abstract GraphicalPrimitive2D is of type LineEnding, false otherwise

Reimplemented from GraphicalPrimitive1D.

bool SBase::isPackageEnabled ( const std::string &  pkgName) const
inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package.
Returns
true if the given package is enabled within this object, false otherwise.
See also
isPackageURIEnabled()
bool SBase::isPackageURIEnabled ( const std::string &  pkgURI) const
inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package.
Returns
true if the given package is enabled within this object, false otherwise.
See also
isPackageEnabled()
bool SBase::isPkgEnabled ( const std::string &  pkgName) const
inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package.
Returns
true if the given package is enabled within this object, false otherwise.
See also
isPkgURIEnabled()
bool SBase::isPkgURIEnabled ( const std::string &  pkgURI) const
inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package.
Returns
true if the given package is enabled within this object, false otherwise.
See also
isPkgEnabled()
bool GraphicalPrimitive2D::isPolygon ( ) const
virtualinherited

Predicate returning true if this abstract GraphicalPrimitive2D is of type Polygon.

Returns
true if this abstract GraphicalPrimitive2D is of type Polygon, false otherwise

Reimplemented from GraphicalPrimitive1D.

bool GraphicalPrimitive2D::isRectangle ( ) const
virtualinherited

Predicate returning true if this abstract GraphicalPrimitive2D is of type Rectangle.

Returns
true if this abstract GraphicalPrimitive2D is of type Rectangle, false otherwise

Reimplemented from GraphicalPrimitive1D.

bool GraphicalPrimitive1D::isRenderCurve ( ) const
virtualinherited

Predicate returning true if this abstract GraphicalPrimitive1D is of type RenderCurve.

Returns
true if this abstract GraphicalPrimitive1D is of type Text, false otherwise

Reimplemented from Transformation2D.

bool GraphicalPrimitive2D::isRenderGroup ( ) const
virtualinherited

Predicate returning true if this abstract GraphicalPrimitive2D is of type RenderGroup.

Returns
true if this abstract GraphicalPrimitive2D is of type RenderGroup, false otherwise

Reimplemented from GraphicalPrimitive1D.

bool SBase::isSetAnnotation ( ) const
inherited

Predicate returning true if this object's "annotation" subelement exists and has content.

Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
true if a "annotation" subelement exists, false otherwise.
See also
getAnnotation()
getAnnotationString()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
Examples:
printAnnotation.cpp.
bool GraphicalPrimitive1D::isSetDashArray ( ) const
inherited

Returns true if the dash array has been set or false otherwise.

The array is considered set if it is not empty and if the first entry is not NaN.

Returns
true if the stroke-dasharray is set, false otherwise.
bool RenderGroup::isSetEndHead ( ) const

Predicate returning true if this RenderGroup's "endHead" attribute is set.

Returns
true if this RenderGroup's "endHead" attribute has been set, otherwise false is returned.
bool GraphicalPrimitive2D::isSetFill ( ) const
inherited

Predicate returning true if this GraphicalPrimitive2D's "fill" attribute is set.

Returns
true if this GraphicalPrimitive2D's "fill" attribute has been set, otherwise false is returned.
bool GraphicalPrimitive2D::isSetFillColor ( ) const
inherited

Returns true if the fill attribute is set or false otherwise.

The fill attribute is considered set if the string is not empty.

Returns
true if the fill color is set.
bool GraphicalPrimitive2D::isSetFillRule ( ) const
inherited

Predicate returning true if this GraphicalPrimitive2D's "fill-rule" attribute is set.

The attribute "fill-rule" is used to define how polygons should be filled. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "fill-rule":
  • "nonzero": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and then examining the places where a segment of the shape crosses the ray. Starting with a count of zero, add one each time a path segment crosses the ray from left to right and subtract one each time a path segment crosses the ray from right to left. After counting the crossings, if the result is zero then the point is outside the path. Otherwise, it is inside.

  • "evenodd": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and counting the number of path segments from the given shape that the ray crosses. If this number is odd, the point is inside; if even, the point is outside.

  • "inherit": This value declares the "insideness" of a point in the shape by declaring that the property takes the same computed value as the property for the element's parent. The inherited value, which is normally only used as a fallback value, can be clarified by setting 'inherit' explicitly. NOTE: This value is NOT in the Level 3 Version 1 Render specification, but was left out due to an oversight: the value has long been part of the codebase. It is provided here as a convenience. Elements with a fill-rule set to "inherit" actually behave identicaly to elements without a fill-rule attribute at all, since this attribute always takes the value of a parent element if not defined explicitly.

Returns
true if this GraphicalPrimitive2D's "fill-rule" attribute has been set, otherwise false is returned.
bool RenderGroup::isSetFontFamily ( ) const

Predicate returning true if this RenderGroup's "font-family" attribute is set.

Returns
true if this RenderGroup's "font-family" attribute has been set, otherwise false is returned.
bool RenderGroup::isSetFontSize ( ) const

Predicate returning true if this RenderGroup's "font-size" element is set.

Returns
true if this RenderGroup's "font-size" element has been set, otherwise false is returned.
bool RenderGroup::isSetFontStyle ( ) const

Predicate returning true if this RenderGroup's "font-style" attribute is set.

Returns
true if this RenderGroup's "font-style" attribute has been set, otherwise false is returned.
The attribute "font-style" is used to specify whether the text is to be "normal" or "italic". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-style":
  • "italic", slanted print

  • "normal", upright print

bool RenderGroup::isSetFontWeight ( ) const

Predicate returning true if this RenderGroup's "font-weight" attribute is set.

Returns
true if this RenderGroup's "font-weight" attribute has been set, otherwise false is returned.
The attribute "font-weight" is used to specify whether the text is to be "normal" or "bold". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-weight":
  • "bold", darker and/or thicker than normal print.

  • "normal", the typical print weight; lighter and/or thinner than "bold".

bool GraphicalPrimitive1D::isSetId ( ) const
virtualinherited

Predicate returning true if this GraphicalPrimitive1D's "id" attribute is set.

Returns
true if this GraphicalPrimitive1D's "id" attribute has been set, otherwise false is returned.

Reimplemented from SBase.

Reimplemented in LineEnding.

bool SBase::isSetIdAttribute ( ) const
inherited

Predicate returning true if this object's "id" attribute is set.

The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always 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.

Returns
true if the "id" attribute of this SBML object is set, false otherwise.
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
unsetIdAttribute()
bool Transformation::isSetMatrix ( ) const
inherited

Returns true if the matrix has been set or false otherwise.

The matrix is considered as set if none of the values in the matrix is NaN.

Returns
true or false depending on whether a NaN was found.
bool SBase::isSetMetaId ( ) const
inherited

Predicate returning true if this object's "metaid" attribute is set.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. 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.
Returns
true if the "metaid" attribute of this SBML object is set, false otherwise.
See also
getMetaId()
setMetaId(const std::string& metaid)
Examples:
addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.
bool SBase::isSetModelHistory ( )
inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns
true if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
bool Transformation::isSetName ( ) const
virtualinherited

Predicate returning true if this Transformation's "name" attribute is set.

Returns
true if this Transformation's "name" attribute has been set, otherwise false is returned.

Reimplemented from SBase.

bool SBase::isSetNotes ( ) const
inherited

Predicate returning true if this object's "notes" subelement exists and has content.

The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

Returns
true if a "notes" subelement exists, false otherwise.
See also
getNotes()
getNotesString()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
getAllElementsWithNotes.cpp, printNotes.cpp, and SBMLHttpResolverExample.cpp.
bool SBase::isSetSBOTerm ( ) const
inherited

Predicate returning true if this object's "sboTerm" attribute is set.

Returns
true if the "sboTerm" attribute of this SBML object is set, false otherwise.
Examples:
printSBML.cpp.
bool RenderGroup::isSetStartHead ( ) const

Predicate returning true if this RenderGroup's "startHead" attribute is set.

Returns
true if this RenderGroup's "startHead" attribute has been set, otherwise false is returned.
bool GraphicalPrimitive1D::isSetStroke ( ) const
inherited

Predicate returning true if this GraphicalPrimitive1D's "stroke" attribute is set.

Returns
true if this GraphicalPrimitive1D's "stroke" attribute has been set, otherwise false is returned.
bool GraphicalPrimitive1D::isSetStrokeDashArray ( ) const
inherited

Predicate returning true if this GraphicalPrimitive1D's "stroke-dasharray" attribute is set.

Returns
true if this GraphicalPrimitive1D's "stroke-dasharray" attribute has been set, otherwise false is returned.
bool GraphicalPrimitive1D::isSetStrokeWidth ( ) const
inherited

Predicate returning true if this GraphicalPrimitive1D's "stroke-width" attribute is set.

Returns
true if this GraphicalPrimitive1D's "stroke-width" attribute has been set, otherwise false is returned.
bool RenderGroup::isSetTextAnchor ( ) const

Predicate returning true if this RenderGroup's "text-anchor" attribute is set.

Returns
true if this RenderGroup's "text-anchor" attribute has been set, otherwise false is returned.
The attribute "text-anchor" is used to specify the horizontal alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "text-anchor":
  • "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.

bool Transformation::isSetTransform ( ) const
inherited

Predicate returning true if this Transformation's "transform" attribute is set.

Returns
true if this Transformation's "transform" attribute has been set, otherwise false is returned.
bool SBase::isSetUserData ( ) const
inherited

Predicate returning true or false depending on whether the user data of this element has been set.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
boolean, true if this object's user data has been set, false otherwise.
bool RenderGroup::isSetVTextAnchor ( ) const

Predicate returning true if this RenderGroup's "vtext-anchor" attribute is set.

Returns
true if this RenderGroup's "vtext-anchor" attribute has been set, otherwise false is returned.
The attribute "vtext-anchor" is used to specify the vertical alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "vtext-anchor":
  • "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.

bool GraphicalPrimitive1D::isText ( ) const
virtualinherited

Predicate returning true if this abstract GraphicalPrimitive1D is of type Text.

Returns
true if this abstract GraphicalPrimitive1D is of type Text, false otherwise

Reimplemented from Transformation2D.

bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase sb)
inherited

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase sb) const
inherited

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool SBase::matchesSBMLNamespaces ( const SBase sb)
inherited

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is the same as sb's, false otherwise.
bool SBase::matchesSBMLNamespaces ( const SBase sb) const
inherited

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is the same as sb's, false otherwise.
RenderGroup & RenderGroup::operator= ( const RenderGroup rhs)

Assignment operator for RenderGroup.

Parameters
rhsthe RenderGroup object whose values are to be used as the basis of the assignment.
void SBase::read ( XMLNode node,
XMLErrorSeverityOverride_t  flag = LIBSBML_OVERRIDE_DISABLED 
)
inherited

Reads (initializes) this SBML object by reading from the given XMLNode.

Parameters
nodethe XMLNode to read from.
flagan optional flag that determines how how errors are logged during the reading process.
Warning
This method is computationally expensive, because the given node has to be serialized to a string first. Attempting to serialize a large tree structure (e.g., a large Model) may consume significant computer memory and time.
void GraphicalPrimitive1D::removeDash ( unsigned int  index)
inherited

Removes the dash length at the given index.

Parameters
indexthe index of the dash length to remove from the 'stroke-dasharray' attribute. The function will fail silently if no such index exists.
Transformation2D * RenderGroup::removeElement ( unsigned int  n)

Removes the nth Transformation2D from this RenderGroup and returns a pointer to it.

Parameters
nan unsigned int representing the index of the Transformation2D to remove.
Returns
a pointer to the nth Transformation2D in this RenderGroup.
Warning
The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf::appendAndOwn() or ListOf::insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.
See also
addElement(const Transformation2D* object)
createEllipse()
createRectangle()
createPolygon()
createText()
createCurve()
createImage()
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(const std::string& sid)
Transformation2D * RenderGroup::removeElement ( const std::string &  sid)

Removes the Transformation2D with the given id from this RenderGroup and returns a pointer to it.

Parameters
sidthe ID of the Transformation2D to remove.
Returns
a pointer to the removed Transformation2D in this RenderGroup, or NULL if no such Transformation2D exists.
Warning
The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf::appendAndOwn() or ListOf::insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.
See also
addElement(const Transformation2D* object)
createEllipse()
createRectangle()
createPolygon()
createText()
createCurve()
createImage()
getElement(const std::string& sid)
getElement(unsigned int n)
getNumElements()
removeElement(unsigned int n)
int SBase::removeFromParentAndDelete ( )
virtualinherited

Removes this object from its parent.

If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented in Model, KineticLaw, SBaseRef, StoichiometryMath, Trigger, Delay, ListOf, Priority, ModelDefinition, and ReplacedBy.

int SBase::removeTopLevelAnnotationElement ( const std::string &  elementName,
const std::string  elementURI = "",
bool  removeEmpty = true 
)
inherited

Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed.
elementURIan optional string that is used to check both the name and URI of the top level element to be removed.
removeEmptyif after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
replaceTopLevelAnnotationElement(const XMLNode *)
replaceTopLevelAnnotationElement(const std::string&)
void SBase::renameMetaIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

Replaces all uses of a given meta identifier attribute value with another value.

In SBML, object "meta" identifiers are of the XML data type 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.

Parameters
oldidthe old identifier.
newidthe new identifier.

Reimplemented in Port, and GraphicalObject.

void RenderGroup::renameSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtual

Replaces all uses of a given SIdRef type attribute value with another value.

In SBML, object identifiers are of a data type called 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.

Parameters
oldidthe old identifier.
newidthe new identifier.

Reimplemented from SBase.

void SBase::renameUnitSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

Replaces all uses of a given UnitSIdRef type attribute value with another value.

In SBML, unit definitions have identifiers of type 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.

Parameters
oldidthe old identifier.
newidthe new identifier.

Reimplemented in Model, Species, Compartment, KineticLaw, Rule, Parameter, EventAssignment, InitialAssignment, StoichiometryMath, Delay, FunctionDefinition, Trigger, Priority, Constraint, and Port.

int SBase::replaceTopLevelAnnotationElement ( const XMLNode annotation)
inherited

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.

Parameters
annotationXMLNode representing the replacement top level annotation.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI, bool removeEmpty)
replaceTopLevelAnnotationElement(const std::string&)
int SBase::replaceTopLevelAnnotationElement ( const std::string &  annotation)
inherited

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.

Parameters
annotationstring representing the replacement top level annotation.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI)
replaceTopLevelAnnotationElement(const XMLNode*)
int SBase::setAnnotation ( const XMLNode annotation)
virtualinherited

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(const XMLNode* annotation) or SBase::appendAnnotation(const std::string& annotation).

Parameters
annotationan XML structure that is to be used as the new content of the "annotation" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

int SBase::setAnnotation ( const std::string &  annotation)
virtualinherited

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(const XMLNode* annotation) or SBase::appendAnnotation(const std::string& annotation).

Parameters
annotationan XML string that is to be used as the content of the "annotation" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()

Reimplemented in Model, and SpeciesReference.

void GraphicalPrimitive1D::setDashArray ( const std::vector< unsigned int > &  array)
inherited

Sets the 'stroke-dasharray' attribute to have the values in the given array.

Parameters
arrayArray of alternating stroke and gap length values.
bool GraphicalPrimitive1D::setDashArray ( const std::string &  arrayString)
inherited

Sets the 'stroke-dasharray' attribute from the given string.

If the string is not a valid dasharray string, false is returned and the dasharray remains in the state is was before the call.

The individual numerical values in the string have to be separated by commas.

Parameters
arrayStringa string with number representing a dash array.
Returns
true if setting 'stroke-dasharray' from the string succeeds or false otherwise.
void GraphicalPrimitive1D::setDashByIndex ( unsigned int  index,
unsigned int  dash 
)
inherited

Sets the integer value of the dash at the given position.

Parameters
indexthe index of the dash length to replace in the 'stroke-dasharray' attribute. The function will fail silently if no such index exists.
dashthe integer length to set the indexed dash to.
void SBase::setElementText ( const std::string &  text)
protectedvirtualinherited

When overridden allows SBase elements to use the text included in between the elements tags.

The default implementation does nothing.

Parameters
textthe text string found between the element tags.
int RenderGroup::setEndHead ( const std::string &  endHead)

Sets the value of the "endHead" attribute of this RenderGroup.

Parameters
endHeadstd::string& value of the "endHead" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int GraphicalPrimitive2D::setFill ( const std::string &  fill)
inherited

Sets the value of the "fill" attribute of this GraphicalPrimitive2D.

Parameters
fillstd::string& value of the "fill" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value: Calling this function with fill = NULL or an empty string is equivalent to calling unsetFill().
void GraphicalPrimitive2D::setFillColor ( const std::string &  color)
inherited

Set fill color to the id of a color definition, the id of a gradient definition or a color value string.

Parameters
colorthe id of a color deifnition or a gradient or a color value string.
void GraphicalPrimitive2D::setFillRule ( FILL_RULE  rule)
inherited

Sets the value of the "fill-rule" attribute of this GraphicalPrimitive2D.

The attribute "fill-rule" is used to define how polygons should be filled. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "fill-rule":
  • "nonzero": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and then examining the places where a segment of the shape crosses the ray. Starting with a count of zero, add one each time a path segment crosses the ray from left to right and subtract one each time a path segment crosses the ray from right to left. After counting the crossings, if the result is zero then the point is outside the path. Otherwise, it is inside.

  • "evenodd": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and counting the number of path segments from the given shape that the ray crosses. If this number is odd, the point is inside; if even, the point is outside.

  • "inherit": This value declares the "insideness" of a point in the shape by declaring that the property takes the same computed value as the property for the element's parent. The inherited value, which is normally only used as a fallback value, can be clarified by setting 'inherit' explicitly. NOTE: This value is NOT in the Level 3 Version 1 Render specification, but was left out due to an oversight: the value has long been part of the codebase. It is provided here as a convenience. Elements with a fill-rule set to "inherit" actually behave identicaly to elements without a fill-rule attribute at all, since this attribute always takes the value of a parent element if not defined explicitly.

Parameters
ruleFillRule_t value of the "fill-rule" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int GraphicalPrimitive2D::setFillRule ( const FillRule_t  fillRule)
inherited

Sets the value of the "fill-rule" attribute of this GraphicalPrimitive2D.

The attribute "fill-rule" is used to define how polygons should be filled. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "fill-rule":
  • "nonzero": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and then examining the places where a segment of the shape crosses the ray. Starting with a count of zero, add one each time a path segment crosses the ray from left to right and subtract one each time a path segment crosses the ray from right to left. After counting the crossings, if the result is zero then the point is outside the path. Otherwise, it is inside.

  • "evenodd": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and counting the number of path segments from the given shape that the ray crosses. If this number is odd, the point is inside; if even, the point is outside.

  • "inherit": This value declares the "insideness" of a point in the shape by declaring that the property takes the same computed value as the property for the element's parent. The inherited value, which is normally only used as a fallback value, can be clarified by setting 'inherit' explicitly. NOTE: This value is NOT in the Level 3 Version 1 Render specification, but was left out due to an oversight: the value has long been part of the codebase. It is provided here as a convenience. Elements with a fill-rule set to "inherit" actually behave identicaly to elements without a fill-rule attribute at all, since this attribute always takes the value of a parent element if not defined explicitly.

Parameters
fillRuleFillRule_t value of the "fill-rule" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int GraphicalPrimitive2D::setFillRule ( const std::string &  fillRule)
inherited

Sets the value of the "fill-rule" attribute of this GraphicalPrimitive2D.

The attribute "fill-rule" is used to define how polygons should be filled. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "fill-rule":
  • "nonzero": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and then examining the places where a segment of the shape crosses the ray. Starting with a count of zero, add one each time a path segment crosses the ray from left to right and subtract one each time a path segment crosses the ray from right to left. After counting the crossings, if the result is zero then the point is outside the path. Otherwise, it is inside.

  • "evenodd": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and counting the number of path segments from the given shape that the ray crosses. If this number is odd, the point is inside; if even, the point is outside.

  • "inherit": This value declares the "insideness" of a point in the shape by declaring that the property takes the same computed value as the property for the element's parent. The inherited value, which is normally only used as a fallback value, can be clarified by setting 'inherit' explicitly. NOTE: This value is NOT in the Level 3 Version 1 Render specification, but was left out due to an oversight: the value has long been part of the codebase. It is provided here as a convenience. Elements with a fill-rule set to "inherit" actually behave identicaly to elements without a fill-rule attribute at all, since this attribute always takes the value of a parent element if not defined explicitly.

Parameters
fillRulestd::string& of the "fill-rule" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int RenderGroup::setFontFamily ( const std::string &  fontFamily)

Sets the value of the "font-family" attribute of this RenderGroup.

Parameters
fontFamilystd::string& value of the "font-family" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value: Calling this function with fontFamily = NULL or an empty string is equivalent to calling unsetFontFamily().
int RenderGroup::setFontSize ( const RelAbsVector size)

Sets the font size.

Normally this is an absolute value, e.g. 18 for a 18pt font. It is however allowed the specify the font size in terms of relative values in relation to the current viewport. In most cases the viewport will be the dimensions of a bounding box of a layout object.

Parameters
sizethe new font size.
int RenderGroup::setFontStyle ( const FontStyle_t  fontStyle)

Sets the value of the "font-style" attribute of this RenderGroup.

Parameters
fontStyleFontStyle_t value of the "font-style" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
The attribute "font-style" is used to specify whether the text is to be "normal" or "italic". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-style":
  • "italic", slanted print

  • "normal", upright print

int RenderGroup::setFontStyle ( const std::string &  fontStyle)

Sets the value of the "font-style" attribute of this RenderGroup.

Parameters
fontStylestd::string& of the "font-style" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
The attribute "font-style" is used to specify whether the text is to be "normal" or "italic". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-style":
  • "italic", slanted print

  • "normal", upright print

int RenderGroup::setFontWeight ( const FontWeight_t  fontWeight)

Sets the value of the "font-weight" attribute of this RenderGroup.

Parameters
fontWeightFontWeight_t value of the "font-weight" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
The attribute "font-weight" is used to specify whether the text is to be "normal" or "bold". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-weight":
  • "bold", darker and/or thicker than normal print.

  • "normal", the typical print weight; lighter and/or thinner than "bold".

int RenderGroup::setFontWeight ( const std::string &  fontWeight)

Sets the value of the "font-weight" attribute of this RenderGroup.

Parameters
fontWeightstd::string& of the "font-weight" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
The attribute "font-weight" is used to specify whether the text is to be "normal" or "bold". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-weight":
  • "bold", darker and/or thicker than normal print.

  • "normal", the typical print weight; lighter and/or thinner than "bold".

int GraphicalPrimitive1D::setId ( const std::string &  id)
virtualinherited

Sets the value of the "id" attribute of this GraphicalPrimitive1D.

Parameters
idstd::string& value of the "id" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are: Calling this function with id = NULL or an empty string is equivalent to calling unsetId().

Reimplemented from SBase.

Reimplemented in LineEnding.

int SBase::setIdAttribute ( const std::string &  sid)
virtualinherited

Sets the value of the "id" attribute of this SBML object.

The string sid is copied.
The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always 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.

Parameters
sidthe string to use as the identifier of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()
void Transformation2D::setMatrix ( const double  m[12])
inherited

Sets the 2D matrix to the values given in the array.

The 2D matrix is updated accordingly.

Parameters
marray with new values to be set for this Transformation object.
void Transformation2D::setMatrix2D ( const double  m[6])
inherited

Sets the 2D matrix to the values given in the array.

The 3D matrix is updated accordingly.

Parameters
marray with new values to be set for this Transformation object.
int SBase::setMetaId ( const std::string &  metaid)
inherited

Sets the value of the meta-identifier attribute of this SBML object.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. 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.

Parameters
metaidthe identifier string to use as the value of the "metaid" attribute.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getMetaId()
isSetMetaId()
Examples:
addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.
int SBase::setModelHistory ( ModelHistory history)
inherited

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
Examples:
addModelHistory.cpp.
int Transformation::setName ( const std::string &  name)
virtualinherited

Sets the value of the "name" attribute of this Transformation.

Parameters
namestd::string& value of the "name" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value: Calling this function with name = NULL or an empty string is equivalent to calling unsetName().

Reimplemented from SBase.

int SBase::setNamespaces ( XMLNamespaces xmlns)
inherited

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Parameters
xmlnsthe namespaces to set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::setNotes ( const XMLNode notes)
inherited

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.

Parameters
notesan XML structure that is to be used as the content of the "notes" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
createExampleSBML.cpp.
int SBase::setNotes ( const std::string &  notes,
bool  addXHTMLMarkup = false 
)
inherited

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.

SBMLDocument* s = new SBMLDocument(3, 1);
s->setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></body>");
Parameters
notesan XML string that is to be used as the content of the "notes" subelement of this object.
addXHTMLMarkupa 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.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::setSBOTerm ( int  value)
virtualinherited

Sets the value of the "sboTerm" attribute.

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". More details can be found in SBML specifications for Level 2 Version 2 and above.
Parameters
valuethe NNNNNNN integer portion of the SBO identifier.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
setSBOTerm(const std::string &sboid)
Examples:
groups_example1.cpp, and qual_example1.cpp.
int SBase::setSBOTerm ( const std::string &  sboid)
virtualinherited

Sets the value of the "sboTerm" attribute by string.

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". More details can be found in SBML specifications for Level 2 Version 2 and above.
Parameters
sboidthe SBO identifier string of the form "SBO:NNNNNNN".
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
setSBOTerm(int value)
int RenderGroup::setStartHead ( const std::string &  startHead)

Sets the value of the "startHead" attribute of this RenderGroup.

Parameters
startHeadstd::string& value of the "startHead" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int GraphicalPrimitive1D::setStroke ( const std::string &  stroke)
inherited

Sets the value of the "stroke" attribute of this GraphicalPrimitive1D.

Parameters
strokestd::string& value of the "stroke" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value: Calling this function with stroke = NULL or an empty string is equivalent to calling unsetStroke().
int GraphicalPrimitive1D::setStrokeDashArray ( const std::vector< unsigned int > &  array)
inherited

Sets the value of the "stroke-dasharray" attribute of this GraphicalPrimitive1D.

Parameters
arrayvalue of the "stroke-dasharray" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int GraphicalPrimitive1D::setStrokeWidth ( double  strokeWidth)
inherited

Sets the value of the "stroke-width" attribute of this GraphicalPrimitive1D.

Parameters
strokeWidthdouble value of the "stroke-width" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int RenderGroup::setTextAnchor ( const HTextAnchor_t  textAnchor)

Sets the value of the "text-anchor" attribute of this RenderGroup.

Parameters
textAnchorHTextAnchor_t value of the "text-anchor" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
The attribute "text-anchor" is used to specify the horizontal alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "text-anchor":
  • "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.

int RenderGroup::setTextAnchor ( const std::string &  textAnchor)

Sets the value of the "text-anchor" attribute of this RenderGroup.

Parameters
textAnchorstd::string& of the "text-anchor" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
The attribute "text-anchor" is used to specify the horizontal alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "text-anchor":
  • "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.

int Transformation::setTransform ( double *  inArray)
inherited

Sets the value of the "transform" attribute of this Transformation.

Parameters
inArraydouble* array value of the "transform" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::setUserData ( void *  userData)
inherited

Sets the user data of this element.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Parameters
userDataspecifies the new user data.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int RenderGroup::setVTextAnchor ( Text::TEXT_ANCHOR  anchor)

Sets the value of the "vtext-anchor" attribute of this RenderGroup.

Parameters
anchorVTextAnchor_t value of the "vtext-anchor" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
The attribute "vtext-anchor" is used to specify the vertical alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "vtext-anchor":
  • "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.

int RenderGroup::setVTextAnchor ( const std::string &  vtextAnchor)

Sets the value of the "vtext-anchor" attribute of this RenderGroup.

Parameters
vtextAnchorstd::string& of the "vtext-anchor" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
The attribute "vtext-anchor" is used to specify the vertical alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "vtext-anchor":
  • "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.

int RenderGroup::setVTextAnchor ( const VTextAnchor_t  vtextAnchor)

Sets the value of the "vtext-anchor" attribute of this RenderGroup.

Parameters
vtextAnchorstd::string& of the "vtext-anchor" attribute to be set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
The attribute "vtext-anchor" is used to specify the vertical alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "vtext-anchor":
  • "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.

char * SBase::toSBML ( )
inherited

Returns a string consisting of a partial SBML corresponding to just this object.

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
XMLNode RenderGroup::toXML ( ) const
virtual

Creates an XMLNode object from this RenderGroup object.

Returns
the XMLNode with the XML representation for the RenderGroup object.

Implements GraphicalPrimitive1D.

XMLNode* SBase::toXMLNode ( )
inherited

Returns this element as an XMLNode.

Returns
this element as an XMLNode.
Warning
This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.
int SBase::unsetAnnotation ( )
inherited

Unsets the value of the "annotation" subelement of this SBML object.

Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
See also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
Examples:
unsetAnnotation.cpp.
int SBase::unsetCVTerms ( )
inherited

Clears the list of CVTerm objects attached to this SBML object.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int RenderGroup::unsetEndHead ( )

Unsets the value of the "endHead" attribute of this RenderGroup.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int GraphicalPrimitive2D::unsetFill ( )
inherited

Unsets the value of the "fill" attribute of this GraphicalPrimitive2D.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int GraphicalPrimitive2D::unsetFillRule ( )
inherited

Unsets the value of the "fill-rule" attribute of this GraphicalPrimitive2D.

The attribute "fill-rule" is used to define how polygons should be filled. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "fill-rule":
  • "nonzero": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and then examining the places where a segment of the shape crosses the ray. Starting with a count of zero, add one each time a path segment crosses the ray from left to right and subtract one each time a path segment crosses the ray from right to left. After counting the crossings, if the result is zero then the point is outside the path. Otherwise, it is inside.

  • "evenodd": This value determines the "insideness" of a point in the shape by drawing a ray from that point to infinity in any direction and counting the number of path segments from the given shape that the ray crosses. If this number is odd, the point is inside; if even, the point is outside.

  • "inherit": This value declares the "insideness" of a point in the shape by declaring that the property takes the same computed value as the property for the element's parent. The inherited value, which is normally only used as a fallback value, can be clarified by setting 'inherit' explicitly. NOTE: This value is NOT in the Level 3 Version 1 Render specification, but was left out due to an oversight: the value has long been part of the codebase. It is provided here as a convenience. Elements with a fill-rule set to "inherit" actually behave identicaly to elements without a fill-rule attribute at all, since this attribute always takes the value of a parent element if not defined explicitly.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
int RenderGroup::unsetFontFamily ( )

Unsets the value of the "font-family" attribute of this RenderGroup.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int RenderGroup::unsetFontSize ( )

Unsets the value of the "font-size" element of this RenderGroup.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int RenderGroup::unsetFontStyle ( )

Unsets the value of the "font-style" attribute of this RenderGroup.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
The attribute "font-style" is used to specify whether the text is to be "normal" or "italic". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-style":
  • "italic", slanted print

  • "normal", upright print

int RenderGroup::unsetFontWeight ( )

Unsets the value of the "font-weight" attribute of this RenderGroup.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
The attribute "font-weight" is used to specify whether the text is to be "normal" or "bold". If omitted, the text may be rendered in either way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "font-weight":
  • "bold", darker and/or thicker than normal print.

  • "normal", the typical print weight; lighter and/or thinner than "bold".

int GraphicalPrimitive1D::unsetId ( )
virtualinherited

Unsets the value of the "id" attribute of this GraphicalPrimitive1D.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented from SBase.

Reimplemented in LineEnding.

int SBase::unsetIdAttribute ( )
inherited

Unsets the value of the "id" attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: "id" and "name". The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
int Transformation::unsetMatrix ( )
inherited

Unsets the value of the "transform" attribute of this Transformation.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::unsetMetaId ( )
inherited

Unsets the value of the "metaid" attribute of this SBML object.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. 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.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::unsetModelHistory ( )
inherited

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
int Transformation::unsetName ( )
virtualinherited

Unsets the value of the "name" attribute of this Transformation.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented from SBase.

int SBase::unsetNotes ( )
inherited

Unsets the value of the "notes" subelement of this SBML object.

The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
unsetNotes.cpp.
int SBase::unsetSBOTerm ( )
inherited

Unsets the value of the "sboTerm" attribute of this SBML object.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int RenderGroup::unsetStartHead ( )

Unsets the value of the "startHead" attribute of this RenderGroup.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int GraphicalPrimitive1D::unsetStroke ( )
inherited

Unsets the value of the "stroke" attribute of this GraphicalPrimitive1D.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int GraphicalPrimitive1D::unsetStrokeDashArray ( )
inherited

Unsets the value of the "stroke-dasharray" attribute of this GraphicalPrimitive1D.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int GraphicalPrimitive1D::unsetStrokeWidth ( )
inherited

Unsets the value of the "stroke-width" attribute of this GraphicalPrimitive1D.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int RenderGroup::unsetTextAnchor ( )

Unsets the value of the "text-anchor" attribute of this RenderGroup.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
The attribute "text-anchor" is used to specify the horizontal alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "text-anchor":
  • "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.

int Transformation::unsetTransform ( )
inherited

Unsets the value of the "transform" attribute of this Transformation.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::unsetUserData ( )
inherited

Unsets the user data of this element.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int RenderGroup::unsetVTextAnchor ( )

Unsets the value of the "vtext-anchor" attribute of this RenderGroup.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
The attribute "vtext-anchor" is used to specify the vertical alignment of the text. If omitted, the text may be aligned in any way. In the SBML Level 3 Version 1 Render specification, the following are the allowable values for "vtext-anchor":
  • "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.

Friends And Related Function Documentation

friend class Text
friend