libNuML 1.1.1
Library for reading / writing NuML documents
AtomicDescription Class Reference

This class stores the atomic description. More...

#include <AtomicDescription.h>

Inheritance diagram for AtomicDescription:
DimensionDescription NUMLList NMBase

Public Member Functions

 AtomicDescription (unsigned int level, unsigned int version)
 Creates an new AtomicDescription using the given NUML level and version values. More...
 
 AtomicDescription (NUMLNamespaces *numlns)
 Creates a new AtomicDescription using the given NUMLNamespaces object numlns. More...
 
virtual bool accept (NUMLVisitor &v) const
 Accepts the given NUMLVisitor for this instance of AtomicDescription. More...
 
virtual NUMLTypeCode_t getTypeCode () const
 Returns the libNUML type code for this NUML object. More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this object, which for AtomicDescription, is always "atomicValue". More...
 
const std::string & getValueType () const
 Returns the value of the "valueType" attribute of this AtomicDescription. More...
 
const std::string & getOntologyTerm () const
 Returns the value of the "ontologyTerm" attribute of this AtomicDescription. More...
 
virtual const std::string & getName () const
 Returns the character name in this object. More...
 
int setOntologyTerm (const std::string &ontologyTerm)
 Sets the ontologyTerm of the "ontologyTerm" attribute of this NUML object. More...
 
int setValueType (const std::string &valueType)
 Sets the valueType of the "valueType" attribute of this NUML object. More...
 
int setName (const std::string &name)
 Sets the name of the "name" attribute of this NUML object. More...
 
virtual const std::string & getId () const
 
virtual int setId (const std::string &id)
 set the id of this element More...
 
virtual AtomicDescriptionclone () const
 Creates and returns a deep copy of this AtomicDescription. More...
 
 AtomicDescription ()
 
virtual ~AtomicDescription ()
 
- Public Member Functions inherited from DimensionDescription
 DimensionDescription ()
 
 DimensionDescription (unsigned int level, unsigned int version)
 Creates a new DimensionDescription using the given NUML level and version values. More...
 
 DimensionDescription (NUMLNamespaces *numlns)
 Creates a new DimensionDescription using the given NUMLNamespaces object numlns. More...
 
virtual bool accept (NUMLVisitor &v) const
 Accepts the given NUMLVisitor for this instance of NMBase. More...
 
virtual DimensionDescriptionclone () const
 Creates and returns a deep copy of this NMBase object. More...
 
CompositeDescriptioncreateCompositeDescription ()
 Returns a list of the XML Namespaces declared on this NUML document. More...
 
TupleDescriptioncreateTupleDescription ()
 creates a new tupledescription and adds it to the dimensiondescription More...
 
AtomicDescriptioncreateAtomicDescription ()
 creates a new atomic description and adds it to the dimensiondescription More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this object, which for DimensionDescription, is always "model". More...
 
virtual NUMLTypeCode_t getTypeCode () const
 Returns the libNUML type code for this NUML object. More...
 
virtual NUMLTypeCode_t getItemTypeCode () const
 Returns the libNUML type code for the objects contained in this NUMLList (i.e., CompositeDescription objects, if the list is non-empty). More...
 
virtual DimensionDescriptionget (unsigned int n)
 Returns the XML element name of this object. More...
 
virtual const DimensionDescriptionget (unsigned int n) const
 Get a CompositeDescription from the DimensionDescription. More...
 
virtual DimensionDescriptionget (const std::string &sid)
 Get a CompositeDescription from the DimensionDescription based on its identifier. More...
 
virtual const DimensionDescriptionget (const std::string &sid) const
 Get a CompositeDescription from the DimensionDescription based on its identifier. More...
 
virtual const std::string & getId () const
 
virtual int setId (const std::string &id)
 
virtual const std::string & getName () const
 
virtual int setName (const std::string &name)
 
virtual DimensionDescriptionremove (unsigned int n)
 Removes the nth item from this DimensionDescription items and returns a pointer to it. More...
 
virtual DimensionDescriptionremove (const std::string &sid)
 Removes item in this DimensionDescription items with the given identifier. More...
 
virtual int getElementPosition () const
 Get the ordinal position of this element in the containing object (which in this case is the Model object). More...
 
virtual ~DimensionDescription ()
 
- Public Member Functions inherited from NUMLList
 NUMLList (unsigned int level, unsigned int version)
 Creates a new NUMLList using the given NUML level and version values. More...
 
 NUMLList (NUMLNamespaces *numlns)
 Creates a new DimensionDescription using the given NUMLNamespaces object numlns. More...
 
 NUMLList ()
 
virtual ~NUMLList ()
 
 NUMLList (const NUMLList &orig)
 Copy constructor. More...
 
NUMLListoperator= (const NUMLList &rhs)
 Assignment operator for NUMLList. More...
 
virtual bool accept (NUMLVisitor &v) const
 Accepts the given NUMLVisitor. More...
 
virtual NMBaseclone () const
 Creates and returns a deep copy of this NUMLList. More...
 
void append (const NMBase *item)
 Adds item to the end of this NUMLList. More...
 
void appendAndOwn (NMBase *item)
 Adds item to the end of this NUMLList. More...
 
virtual const NMBaseget (unsigned int n) const
 Get an item from the list. More...
 
virtual NMBaseget (unsigned int n)
 Get an item from the list. More...
 
void clear (bool doDelete=true)
 Removes all items in this NUMLList object. More...
 
virtual NMBaseremove (unsigned int n)
 Removes the nth item from this NUMLList items and returns a pointer to it. More...
 
unsigned int size () const
 Get the size of this NUMLList. More...
 
virtual void setNUMLDocument (NUMLDocument *d)
 Sets the parent NUMLDocument of this NUML object. More...
 
virtual void setParentNUMLObject (NMBase *sb)
 Sets the parent NUML object of this NUML object. More...
 
virtual NUMLTypeCode_t getTypeCode () const
 Get the type code of the objects contained in this SedListOf. More...
 
virtual NUMLTypeCode_t getItemTypeCode () const
 Get the type code of the objects contained in this NUMLList. More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this object, which for NUMLList, is always "listOf". More...
 
virtual void writeElements (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const
 Subclasses should override this method to write out their contained NUML objects as XML elements. More...
 
- Public Member Functions inherited from NMBase
virtual ~NMBase ()
 Destroy this object. More...
 
NMBaseoperator= (const NMBase &orig)
 Assignment operator for NMBase. More...
 
virtual bool accept (NUMLVisitor &v) const =0
 Accepts the given NUMLVisitor for this instance of NMBase. More...
 
virtual NMBaseclone () const =0
 Creates and returns a deep copy of this NMBase object. More...
 
const std::string & getMetaId () const
 Returns the value of the "metaid" attribute of this object. More...
 
std::string & getMetaId ()
 Returns the value of the "metaid" attribute of this object. More...
 
virtual const std::string & getId () const
 
virtual const std::string & getName () const
 
virtual LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces * getNamespaces () const
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
const NUMLDocumentgetNUMLDocument () const
 Returns the parent NUMLDocument object. More...
 
NUMLDocumentgetNUMLDocument ()
 Returns the parent NUMLDocument object. More...
 
NMBasegetParentNUMLObject ()
 Returns the parent NUML object. More...
 
NMBasegetAncestorOfType (NUMLTypeCode_t type)
 Returns the ancestor NUML object that corresponds to the given NUMLTypeCode_t. More...
 
unsigned int getLine () const
 Returns the line number on which this object first appears in the XML representation of the NUML document. More...
 
unsigned int getColumn () const
 Returns the column number on which this object first appears in the XML representation of the NUML document. More...
 
bool isSetMetaId () const
 Predicate returning true or false depending on whether this object's "metaid" attribute has been set. More...
 
bool isSetName () const
 
int setMetaId (const std::string &metaid)
 Sets the value of the "metaid" attribute of this object. More...
 
virtual int setId (const std::string &sid)
 
virtual void setNUMLDocument (NUMLDocument *d)
 Sets the parent NUMLDocument of this NUML object. More...
 
virtual void setParentNUMLObject (NMBase *sb)
 Sets the parent NUML object of this NUML object. More...
 
int setNamespaces (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces *xmlns)
 Sets the namespaces relevant of this NUML object. More...
 
int unsetMetaId ()
 Unsets the value of the "metaid" attribute of this NUML object. More...
 
unsigned int getLevel () const
 Returns the NUML Level of the overall NUML document. More...
 
unsigned int getVersion () const
 Returns the Version within the NUML Level of the overall NUML document. More...
 
virtual NUMLTypeCode_t getTypeCode () const
 Returns the libnuml type code for this object. More...
 
bool hasValidLevelVersionNamespaceCombination ()
 Predicate returning true or false depending on whether this object's level/version and namespace values correspond to a valid NUML specification. More...
 
virtual const std::string & getElementName () const =0
 Returns the XML element name of this object. More...
 
char * toNUML ()
 Returns a string that consists of the partial NUML describing this object. More...
 
void read (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream)
 Reads (initializes) this NUML object by reading from XMLInputStream. More...
 
void write (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const
 Writes (serializes) this NUML object by writing it to XMLOutputStream. More...
 
virtual void writeElements (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const
 Subclasses should override this method to write out their contained NUML objects as XML elements. More...
 
virtual bool hasRequiredAttributes () const
 
virtual bool hasRequiredElements () const
 
void setNUMLNamespaces (NUMLNamespaces *numlns)
 
NUMLNamespacesgetNUMLNamespaces () const
 
void syncAnnotation ()
 
bool isSetNotes () const
 
bool isSetAnnotation () const
 
virtual int setAnnotation (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *annotation)
 
virtual int setAnnotation (const std::string &annotation)
 
virtual int appendAnnotation (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *annotation)
 
virtual int appendAnnotation (const std::string &annotation)
 
int removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="")
 
int replaceTopLevelAnnotationElement (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *annotation)
 
int replaceTopLevelAnnotationElement (const std::string &annotation)
 
int setNotes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *notes)
 
int setNotes (const std::string &notes, bool addXHTMLMarkup=false)
 
int appendNotes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *notes)
 
int appendNotes (const std::string &notes)
 
int unsetNotes ()
 
int unsetAnnotation ()
 
LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * getNotes () const
 
std::string getNotesString () const
 
LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * getAnnotation () const
 
std::string getAnnotationString () const
 

Protected Member Functions

virtual void readAttributes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLAttributes &attributes)
 Subclasses should override this method to create, store, and then return an NUML object corresponding to the next XMLToken in the XMLInputStream. More...
 
virtual void writeAttributes (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const
 Subclasses should override this method to write their XML attributes to the XMLOutputStream. More...
 
- Protected Member Functions inherited from DimensionDescription
virtual NMBasecreateObject (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream)
 
virtual void writeXMLNS (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const
 Subclasses should override this method to write their xmlns attriubutes (if any) to the XMLOutputStream. More...
 
virtual void readAttributes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLAttributes &attributes)
 Subclasses should override this method to read values from the given XMLAttributes set into their specific fields. More...
 
virtual void writeAttributes (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const
 Subclasses should override this method to write their XML attributes to the XMLOutputStream. More...
 
- Protected Member Functions inherited from NMBase
virtual void writeXMLNS (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const
 Subclasses should override this method to write their xmlns attriubutes (if any) to the XMLOutputStream. More...
 
 NMBase (const std::string &id="", const std::string &name="")
 Only subclasses may create NMBase objects. More...
 
 NMBase (unsigned int level, unsigned int version)
 Creates a new NMBase object with the given sboTerm. More...
 
 NMBase (NUMLNamespaces *numlns)
 Creates a new NMBase object with the given NUMLNamespaces. More...
 
 NMBase (const NMBase &orig)
 Copy constructor. More...
 
virtual NMBasecreateObject (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream)
 Subclasses should override this method to create, store, and then return an NUML object corresponding to the next XMLToken in the XMLInputStream. More...
 
virtual bool readOtherXML (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream &stream)
 Subclasses should override this method to read (and store) XHTML, MathML, etc. More...
 
virtual int getElementPosition () const
 The NUML XML Schema is written such that the order of child elements is significant. More...
 
NUMLErrorLoggetErrorLog ()
 
void logError (unsigned int id, const unsigned int level=2, const unsigned int version=3, const std::string &details="")
 Convenience method for easily logging problems from within method implementations. More...
 
void logUnknownAttribute (std::string attribute, const unsigned int level, const unsigned int version, const std::string element)
 Helper to log a common type of error. More...
 
void logUnknownElement (const std::string element, const unsigned int level, const unsigned int version)
 Helper to log a common type of error. More...
 
void logEmptyString (std::string attribute, const unsigned int level, const unsigned int version, std::string element)
 Helper to log a common type of error. More...
 
virtual void readAttributes (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLAttributes &attributes)
 Subclasses should override this method to read values from the given XMLAttributes set into their specific fields. More...
 
virtual void writeAttributes (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &stream) const
 Subclasses should override this method to write their XML attributes to the XMLOutputStream. More...
 
void checkOrderAndLogError (NMBase *object, int expected)
 Checks that NUML element has been read in the proper order. More...
 
void checkNUMLListPopulated (NMBase *object)
 Checks that an NUML NUMLList element has been populated. More...
 
void checkDefaultNamespace (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces *xmlns, const std::string &elementName)
 Checks that the given default namespace in the given element is valid. More...
 
void checkXHTML (const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode *)
 Checks that the XHTML is valid. More...
 
void checkAnnotation ()
 Checks the annotation does not declare an numl namespace. More...
 

Protected Attributes

std::string mId
 
std::string mName
 
std::string mOntologyTerm
 
std::string mValueType
 
- Protected Attributes inherited from DimensionDescription
std::string mId
 
std::string mName
 
- Protected Attributes inherited from NUMLList
std::vector< NMBase * > mItems
 
- Protected Attributes inherited from NMBase
std::string mMetaId
 
std::string mId
 
std::string mName
 
NUMLDocumentmNUML
 
LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * mNotes
 
LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNode * mAnnotation
 
NUMLNamespacesmNUMLNamespaces
 
unsigned int mLine
 
unsigned int mColumn
 
int mDept
 
NMBasemParentNUMLObject
 
bool mHasBeenDeleted
 
std::string mEmptyString
 

Detailed Description

This class stores the atomic description.

Constructor & Destructor Documentation

◆ AtomicDescription() [1/3]

LIBNUML_CPP_NAMESPACE_BEGIN AtomicDescription::AtomicDescription ( unsigned int  level,
unsigned int  version 
)

Creates an new AtomicDescription using the given NUML level and version values.

Parameters
levelan unsigned int, the NUML Level to assign to this AtomicDescription
versionan unsigned int, the NUML Version to assign to this AtomicDescription
Note
Once an AtomicDescription has been added to an NUMLDocument, the level, version for the document override those used to create the AtomicDescription. Despite this, the ability to supply the values at creation time is an important aid to creating valid NUML. Knowledge of the intented NUML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing NUMLDocument.

◆ AtomicDescription() [2/3]

AtomicDescription::AtomicDescription ( NUMLNamespaces numlns)

Creates a new AtomicDescription using the given NUMLNamespaces object numlns.

The NUMLNamespaces object encapsulates NUML Level/Version/namespaces information. It is used to communicate the NUML Level, Version, and (in Level 3) packages used in addition to NUML Level  Core. A common approach to using this class constructor is to create an NUMLNamespaces object somewhere in a program, once, then pass it to object constructors such as this one when needed.

It is worth emphasizing that although this constructor does not take an identifier argument, in NUML Level 2 and beyond, the "id" (identifier) attribute of an AtomicDescription is required to have a value. Thus, callers are cautioned to assign a value after calling this constructor. Setting the identifier can be accomplished using the method

Parameters
numlnsan NUMLNamespaces object.
Note
Once an AtomicDescription has been added to an NUMLDocument, the level, version and xmlns namespaces for the document override those used to create the AtomicDescription. Despite this, the ability to supply the values at creation time is an important aid to creating valid NUML. Knowledge of the intented NUML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing NUMLDocument.

◆ AtomicDescription() [3/3]

AtomicDescription::AtomicDescription ( )

◆ ~AtomicDescription()

AtomicDescription::~AtomicDescription ( )
virtual

Member Function Documentation

◆ accept()

bool AtomicDescription::accept ( NUMLVisitor v) const
virtual

Accepts the given NUMLVisitor for this instance of AtomicDescription.

Parameters
vthe NUMLVisitor instance to be used.
Returns
the result of calling v.visit().

Reimplemented from DimensionDescription.

◆ clone()

AtomicDescription * AtomicDescription::clone ( ) const
virtual

Creates and returns a deep copy of this AtomicDescription.

Returns
a (deep) copy of this AtomicDescription.

Reimplemented from DimensionDescription.

◆ getElementName()

const string & AtomicDescription::getElementName ( ) const
virtual

Returns the XML element name of this object, which for AtomicDescription, is always "atomicValue".

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

Reimplemented from DimensionDescription.

◆ getId()

const std::string & AtomicDescription::getId ( ) const
virtual
Returns
the id of this element

Reimplemented from DimensionDescription.

◆ getName()

const string & AtomicDescription::getName ( ) const
virtual

Returns the character name in this object.

Returns
the string name".

Reimplemented from DimensionDescription.

◆ getOntologyTerm()

const string & AtomicDescription::getOntologyTerm ( ) const

Returns the value of the "ontologyTerm" attribute of this AtomicDescription.

Returns
the ontologyTerm of this AtomicDescription.

◆ getTypeCode()

NUMLTypeCode_t AtomicDescription::getTypeCode ( ) const
virtual

Returns the libNUML type code for this NUML object.

Returns
the NUML type code for this object, or NUML_UNKNOWN (default).
See also
getElementName()

Reimplemented from DimensionDescription.

◆ getValueType()

const string & AtomicDescription::getValueType ( ) const

Returns the value of the "valueType" attribute of this AtomicDescription.

Returns
the valueType of this AtomicDescription.

◆ readAttributes()

void AtomicDescription::readAttributes ( const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLAttributes &  attributes)
protectedvirtual

Subclasses should override this method to create, store, and then return an NUML object corresponding to the next XMLToken in the XMLInputStream.

Returns
the NUML object corresponding to next XMLToken in the XMLInputStream or NULL if the token was not recognized.

Reimplemented from NUMLList.

◆ setId()

int AtomicDescription::setId ( const std::string &  id)
virtual

set the id of this element

Parameters
idthe id to set
Returns
success code

Reimplemented from DimensionDescription.

◆ setName()

int AtomicDescription::setName ( const std::string &  name)
virtual

Sets the name of the "name" attribute of this NUML object.

The string in name is copied.

Parameters
namethe new name for the object
Returns
integer value indicating success/failure of the function.

Reimplemented from DimensionDescription.

◆ setOntologyTerm()

int AtomicDescription::setOntologyTerm ( const std::string &  ontologyTerm)

Sets the ontologyTerm of the "ontologyTerm" attribute of this NUML object.

The string in ontologyTerm is copied.

Parameters
ontologyTermthe new ontologyTerm for the object
Returns
integer value indicating success/failure of the function.

◆ setValueType()

int AtomicDescription::setValueType ( const std::string &  valueType)

Sets the valueType of the "valueType" attribute of this NUML object.

The string in valueType is copied.

Parameters
valueTypethe new valueType for the object
Returns
integer value indicating success/failure of the function.

◆ writeAttributes()

void AtomicDescription::writeAttributes ( LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &  stream) const
protectedvirtual

Subclasses should override this method to write their XML attributes to the XMLOutputStream.

Be sure to call your parents implementation of this method as well. For example:

NMBase::writeAttributes(stream); stream.writeAttribute( "id" , mId ); stream.writeAttribute( "name", mName ); ...

Reimplemented from NUMLList.

Member Data Documentation

◆ mId

std::string AtomicDescription::mId
protected

◆ mName

std::string AtomicDescription::mName
protected

◆ mOntologyTerm

std::string AtomicDescription::mOntologyTerm
protected

◆ mValueType

std::string AtomicDescription::mValueType
protected

The documentation for this class was generated from the following files: