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

Parent class for the various NUML list classes e.g. More...

#include <NUMLList.h>

Inheritance diagram for NUMLList:
NMBase Dimension DimensionDescription OntologyTerms ResultComponents AtomicValue CompositeValue Tuple AtomicDescription CompositeDescription TupleDescription

Public Member Functions

 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 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::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

Parent class for the various NUML list classes e.g.

Operations, Result, ResultComponent etc.

Constructor & Destructor Documentation

◆ NUMLList() [1/4]

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

Creates a new NUMLList using the given NUML level and version values.

Parameters
levelan unsigned int, the NUML Level to assign to this NUMLList
versionan unsigned int, the NUML Version to assign to this NUMLList
Note
Once a NUMLList has been added to an NUMLDocument, the level, version for the document override those used to create the NUMLList. 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.

◆ NUMLList() [2/4]

NUMLList::NUMLList ( NUMLNamespaces numlns)

Creates a new DimensionDescription 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.

Parameters
numlnsan NUMLNamespaces object.
Note
Once a DimensionDescription has been added to an NUMLDocument, the level, version and xmlns namespaces for the document override those used to create the DimensionDescription. 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.

◆ NUMLList() [3/4]

NUMLList::NUMLList ( )

◆ ~NUMLList()

NUMLList::~NUMLList ( )
virtual

◆ NUMLList() [4/4]

NUMLList::NUMLList ( const NUMLList orig)

Copy constructor.

Creates a copy of this NUMLList.

Member Function Documentation

◆ accept()

bool NUMLList::accept ( NUMLVisitor v) const
virtual

Accepts the given NUMLVisitor.

Parameters
vthe NUMLVisitor instance to be used.
Returns
the result of calling v.visit(), which indicates whether the Visitor would like to visit the next item in the list.

Implements NMBase.

Reimplemented in AtomicDescription, AtomicValue, CompositeDescription, CompositeValue, Dimension, and DimensionDescription.

◆ append()

void NUMLList::append ( const NMBase item)

Adds item to the end of this NUMLList.

This variant of the method makes a clone of the item handed to it. This means that when the NUMLList is destroyed, the original items will not be destroyed.

Parameters
itemthe item to be added to the list.
See also
appendAndOwn(NMBase* item)

◆ appendAndOwn()

void NUMLList::appendAndOwn ( NMBase item)

Adds item to the end of this NUMLList.

This variant of the method does not clone the item handed to it; instead, it assumes ownership of it. This means that when the NUMLList is destroyed, the item will be destroyed along with it.

Parameters
itemthe item to be added to the list.
See also
append(const NMBase* item)

◆ clear()

void NUMLList::clear ( bool  doDelete = true)

Removes all items in this NUMLList object.

Used by NUMLList::get() to lookup an NMBase based by its id.

If doDelete is true (default), all items in this NUMLList object are deleted and cleared, and thus the caller doesn't have to delete those items. Otherwise, all items are just cleared from this NUMLList object and the caller is responsible for deleting all items (In this case, pointers to all items should be stored elsewhere before calling this function by the caller).

Parameters
doDeleteif true (default), all items are deleted and cleared. Otherwise, all items are just cleared and not deleted.

◆ clone()

NMBase * NUMLList::clone ( ) const
virtual

Creates and returns a deep copy of this NUMLList.

Returns
a (deep) copy of this NUMLList.

Implements NMBase.

Reimplemented in AtomicDescription, AtomicValue, CompositeDescription, CompositeValue, Dimension, DimensionDescription, OntologyTerms, ResultComponents, Tuple, and TupleDescription.

◆ get() [1/2]

NMBase * NUMLList::get ( unsigned int  n)
virtual

Get an item from the list.

Parameters
nthe index number of the item to get.
Returns
the nth item in this NUMLList items.
See also
size()

Reimplemented in CompositeDescription, CompositeValue, Dimension, DimensionDescription, OntologyTerms, and ResultComponents.

◆ get() [2/2]

const NMBase * NUMLList::get ( unsigned int  n) const
virtual

Get an item from the list.

Parameters
nthe index number of the item to get.
Returns
the nth item in this NUMLList items.
See also
size()

Reimplemented in CompositeDescription, CompositeValue, Dimension, DimensionDescription, OntologyTerms, and ResultComponents.

◆ getElementName()

const string & NUMLList::getElementName ( ) const
virtual

Returns the XML element name of this object, which for NUMLList, is always "listOf".

Returns
the XML name of this element.

Implements NMBase.

Reimplemented in AtomicDescription, AtomicValue, CompositeDescription, CompositeValue, Dimension, DimensionDescription, OntologyTerms, ResultComponents, Tuple, and TupleDescription.

◆ getItemTypeCode()

NUMLTypeCode_t NUMLList::getItemTypeCode ( ) const
virtual

Get the type code of the objects contained in this NUMLList.

Returns
the NUML type code for the objects contained in this NUMLList instance, or NUML_UNKNOWN (default).

Reimplemented in CompositeDescription, CompositeValue, Dimension, DimensionDescription, OntologyTerms, ResultComponents, Tuple, and TupleDescription.

◆ getTypeCode()

NUMLTypeCode_t NUMLList::getTypeCode ( ) const
virtual

Get the type code of the objects contained in this SedListOf.

Returns the libnuml type code for this object, namely, @c
NUMLLIST.

@if clike LibNUML attaches an identifying code to every kind of NUML
object.  These are known as <em>NUML type codes</em>.  The set of
possible type codes is defined in the enumeration #SedTypeCode_t.
The names of the type codes all begin with the characters @c
NUML_. @endif@if java LibNUML attaches an identifying code to every
kind of NUML object.  These are known as <em>NUML type codes</em>.  In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libnuml, the type codes are defined as
static integer constants in the interface class {@link
libsbmlConstants}.  The names of the type codes all begin with the
characters @c NUML_. @endif@if python LibNUML attaches an identifying
code to every kind of NUML object.  These are known as <em>NUML type

NUMLLISTem>. In the Python language interface for libnuml, the type codes are defined as static integer constants in the interface class . The names of the type codes all begin with the characters NUML_ 299 304 the NUML type code for this object, or SedTypeCode_t#Sed_UNKNOWN SEDML_UNKNOWN (default).

See also
getElementName()
Returns
the NUML type code for the objects contained in this SedListOf instance, or SEDML_UNKNOWN (default). Returns the libNUML type code for this object, namely, NUMLLIST.
Returns
the NUML type code for this object, or NUML_UNKNOWN (default).
See also
getElementName()

Reimplemented from NMBase.

Reimplemented in AtomicDescription, AtomicValue, CompositeDescription, CompositeValue, Dimension, DimensionDescription, OntologyTerms, ResultComponents, Tuple, and TupleDescription.

◆ operator=()

NUMLList & NUMLList::operator= ( const NUMLList rhs)

Assignment operator for NUMLList.

◆ readAttributes()

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

Subclasses should override this method to read values from the given XMLAttributes set into their specific fields.

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

Reimplemented from NMBase.

Reimplemented in AtomicDescription, AtomicValue, CompositeDescription, CompositeValue, Tuple, and TupleDescription.

◆ remove()

NMBase * NUMLList::remove ( unsigned int  n)
virtual

Removes the nth item from this NUMLList items and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it.

Parameters
nthe index of the item to remove
See also
size()

Reimplemented in CompositeDescription, CompositeValue, Dimension, DimensionDescription, OntologyTerms, and ResultComponents.

◆ setNUMLDocument()

void NUMLList::setNUMLDocument ( NUMLDocument d)
virtual

Sets the parent NUMLDocument of this NUML object.

Parameters
dthe NUMLDocument that should become the parent of this NUMLList.

Reimplemented from NMBase.

◆ setParentNUMLObject()

void NUMLList::setParentNUMLObject ( NMBase sb)
virtual

Sets the parent NUML object of this NUML object.

Parameters
sbthe NUML object to use

Reimplemented from NMBase.

◆ size()

unsigned int NUMLList::size ( ) const

Get the size of this NUMLList.

Returns
the number of items in this NUMLList items.

◆ writeAttributes()

void NUMLList::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 NMBase.

Reimplemented in AtomicDescription, AtomicValue, CompositeDescription, CompositeValue, Tuple, and TupleDescription.

◆ writeElements()

void NUMLList::writeElements ( LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream &  stream) const
virtual

Subclasses should override this method to write out their contained NUML objects as XML elements.

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

Reimplemented from NMBase.

Member Data Documentation

◆ mItems

std::vector<NMBase*> NUMLList::mItems
protected

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