#include <ome/xml/model/Reagent.h>

Inheritance diagram for ome::xml::model::Reagent:

Collaboration diagram for ome::xml::model::Reagent:

Public Member Functions
	Reagent ()
	Default constructor.

	Reagent (const Reagent &copy)
	Copy constructor. More...

virtual	~Reagent ()
	Destructor.

const std::string &	elementName () const
	Get the element name of this model object. More...

bool	validElementName (const std::string &name) const
	Check if a given element name is valid for processing by this model object. More...

virtual void	update (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
	Update the object hierarchy recursively from an XML DOM tree. More...

bool	link (ome::compat::shared_ptr< Reference > &reference, ome::compat::shared_ptr< ome::xml::model::OMEModelObject > &object)
	Link a given OME model object to this model object. More...

ome::compat::shared_ptr< std::string >	getReagentIdentifier ()
	Get the ReagentIdentifier property. More...

const ome::compat::shared_ptr< std::string >	getReagentIdentifier () const
	Get the ReagentIdentifier property. More...

void	setReagentIdentifier (ome::compat::shared_ptr< std::string > &reagentIdentifier)
	Set the ReagentIdentifier property. More...

const std::string &	getID () const
	Get the ID property. More...

void	setID (const std::string &id)
	Set the ID property. More...

ome::compat::shared_ptr< std::string >	getName ()
	Get the Name property. More...

const ome::compat::shared_ptr< std::string >	getName () const
	Get the Name property. More...

void	setName (ome::compat::shared_ptr< std::string > &name)
	Set the Name property. More...

ome::compat::shared_ptr< std::string >	getDescription ()
	Get the Description property. More...

const ome::compat::shared_ptr< std::string >	getDescription () const
	Get the Description property. More...

void	setDescription (ome::compat::shared_ptr< std::string > &description)
	Set the Description property. More...

OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type	sizeOfLinkedAnnotationList () const
	Get size of linked Annotation list. More...

OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type	getLinkedAnnotationList () const
	Get the linked Annotation list. More...

const ome::compat::weak_ptr< ome::xml::model::Annotation > &	getLinkedAnnotation (OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type index) const
	Get linked Annotation. More...

const ome::compat::weak_ptr< ome::xml::model::Annotation > &	setLinkedAnnotation (OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type index, const ome::compat::shared_ptr< ome::xml::model::Annotation > &annotation)
	Set linked Annotation. More...

bool	linkAnnotation (const ome::compat::shared_ptr< ome::xml::model::Annotation > &annotation)
	Link Annotation. More...

bool	unlinkAnnotation (const ome::compat::shared_ptr< ome::xml::model::Annotation > &annotation)
	Unlink Annotation. More...

ome::compat::weak_ptr< ome::xml::model::Screen >	getScreen ()
	Get the Screen property. More...

const ome::compat::weak_ptr< ome::xml::model::Screen >	getScreen () const
	Get the Screen property. More...

void	setScreen (ome::compat::weak_ptr< ome::xml::model::Screen > &screen_BackReference)
	Set the Screen property. More...

OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type	sizeOfLinkedWellList () const
	Get size of linked Well list. More...

OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type	getLinkedWellList () const
	Get the linked Well list. More...

const ome::compat::weak_ptr< ome::xml::model::Well > &	getLinkedWell (OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type index) const
	Get linked Well. More...

const ome::compat::weak_ptr< ome::xml::model::Well > &	setLinkedWell (OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type index, const ome::compat::shared_ptr< ome::xml::model::Well > &well_BackReference)
	Set linked Well. More...

bool	linkWell (const ome::compat::shared_ptr< ome::xml::model::Well > &well_BackReference)
	Link Well. More...

bool	unlinkWell (const ome::compat::shared_ptr< ome::xml::model::Well > &well_BackReference)
	Unlink Well. More...

virtual common::xml::dom::Element	asXMLElement (common::xml::dom::Document &document) const
	Transform the object hierarchy rooted at this element to XML. More...

const std::string &	getXMLNamespace () const
	Get the XML namespace for this model object. More...

Public Member Functions inherited from ome::xml::model::detail::OMEModelObject
virtual	~OMEModelObject ()
	Destructor.

virtual void	update (const common::xml::dom::Element &element,::ome::xml::model::OMEModel &model)
	Update the object hierarchy recursively from an XML DOM tree. More...

virtual bool	link (ome::compat::shared_ptr< Reference > &reference, ome::compat::shared_ptr< ::ome::xml::model::OMEModelObject > &object)
	Link a given OME model object to this model object. More...

Public Member Functions inherited from ome::xml::model::OMEModelObject
virtual bool	link (ome::compat::shared_ptr< Reference > &reference, ome::compat::shared_ptr< OMEModelObject > &object)=0
	Link a given OME model object to this model object. More...

Static Public Member Functions
static ome::compat::shared_ptr< Reagent >	create (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
	Create a Reagent model object from DOM element. More...

Static Public Member Functions inherited from ome::xml::model::detail::OMEModelObject
static std::vector< common::xml::dom::Element >	getChildrenByTagName (const common::xml::dom::Element &parent, const std::string &name)
	Retrieve all the children of an element that have a given tag name. More...

static std::string	stripNamespacePrefix (const std::string &value)
	Strip the namespace prefix from a tag name. More...

Protected Member Functions
virtual common::xml::dom::Element	asXMLElementInternal (common::xml::dom::Document &document, common::xml::dom::Element &element) const
	Transform the object hierarchy rooted at this element to XML. More...

Protected Member Functions inherited from ome::xml::model::detail::OMEModelObject
	OMEModelObject (const std::string &objectType="OMEModelObject")
	Constructor.

	OMEModelObject (const OMEModelObject &copy)
	Copy constructor. More...

template<class C , typename T >
bool	contains (const C &container, const ome::compat::shared_ptr< T > &element)
	Check if a container contains a particular element. More...

Protected Member Functions inherited from ome::xml::model::OMEModelObject
	OMEModelObject ()
	Constructor.

Private Attributes
ome::compat::shared_ptr< std::string >	reagentIdentifier
	ReagentIdentifier property.

std::string	id
	ID property.

ome::compat::shared_ptr< std::string >	name
	Name property.

ome::compat::shared_ptr< std::string >	description
	Description property.

OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type	annotationLinks
	AnnotationRef reference (occurs more than once)

ome::compat::weak_ptr< ome::xml::model::Screen >	screen
	Screen_BackReference back reference.

OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type	wells
	Well_BackReference back reference (occurs more than once)

Additional Inherited Members
Protected Attributes inherited from ome::xml::model::detail::OMEModelObject
ome::common::Logger	logger
	Message logger.

Detailed Description

Reagent model object.

Constructor & Destructor Documentation

ome::xml::model::Reagent::Reagent ( const Reagent & copy )

Copy constructor.

Parameters

copy	the Reagent to copy.

Member Function Documentation

common::xml::dom::Element ome::xml::model::Reagent::asXMLElement ( common::xml::dom::Document & document ) const

virtual

Transform the object hierarchy rooted at this element to XML.

Parameters

document document for element creation

Returns: an XML DOM tree root element for this model object.

Implements ome::xml::model::OMEModelObject.

References asXMLElementInternal(), and ome::common::xml::dom::Document::createElementNS().

common::xml::dom::Element ome::xml::model::Reagent::asXMLElementInternal	(	common::xml::dom::Document &	document,
		common::xml::dom::Element &	element
	)		const

protectedvirtual

Transform the object hierarchy rooted at this element to XML.

This internal implementation of asXMLelement also requires an XML element, which must not be null, or may be instantiated and passed from superclasses.

Parameters

document	XML document for element creation.
element	XML element for setting model data.

Returns: an XML DOM tree root element for this model object.

Implements ome::xml::model::detail::OMEModelObject.

References annotationLinks, ome::common::xml::dom::Node::appendChild(), ome::xml::model::detail::OMEModelObject::asXMLElementInternal(), ome::common::xml::dom::Document::createElementNS(), description, id, name, reagentIdentifier, and ome::common::xml::dom::Element::setAttribute().

Referenced by asXMLElement().

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ome::compat::shared_ptr< Reagent > ome::xml::model::Reagent::create	(	const common::xml::dom::Element &	element,
		ome::xml::model::OMEModel &	model
	)

static

Create a Reagent model object from DOM element.

Parameters

element	root of the XML DOM tree to from which to construct the model object graph.
model	handler for the OME model used to track instances and references seen during the update.

Exceptions

EnumerationException if there is an error instantiating an enumeration during model object creation, or ModelException if there are any consistency or validity errors found during processing.

Returns: a new model object.

Referenced by ome::xml::model::Screen::update().

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const std::string & ome::xml::model::Reagent::elementName ( ) const

virtual

Get the element name of this model object.

This will be the most-derived class name.

Returns: the element type.

Implements ome::xml::model::OMEModelObject.

ome::compat::shared_ptr< std::string > ome::xml::model::Reagent::getDescription ( )

Get the Description property.

Returns: the Description property.

References description.

const ome::compat::shared_ptr< std::string > ome::xml::model::Reagent::getDescription ( ) const

Get the Description property.

Returns: the Description property.

References description.

const std::string & ome::xml::model::Reagent::getID ( ) const

Get the ID property.

Returns: the ID property.

References id.

Referenced by update().

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const ome::compat::weak_ptr< ome::xml::model::Annotation > & ome::xml::model::Reagent::getLinkedAnnotation ( OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type index ) const

Get linked Annotation.

Parameters

index the index number of the Annotation.

Returns: a weak pointer to the Annotation.

Exceptions

std::out_of_range if the index is invalid.

References annotationLinks.

OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type ome::xml::model::Reagent::getLinkedAnnotationList ( ) const

Get the linked Annotation list.

Returns: a reference to the list.

References annotationLinks.

const ome::compat::weak_ptr< ome::xml::model::Well > & ome::xml::model::Reagent::getLinkedWell ( OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type index ) const

Get linked Well.

Parameters

index the index number of the Well.

Returns: a weak pointer to the Well.

Exceptions

std::out_of_range if the index is invalid.

References wells.

OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type ome::xml::model::Reagent::getLinkedWellList ( ) const

Get the linked Well list.

Returns: a reference to the list.

References wells.

ome::compat::shared_ptr< std::string > ome::xml::model::Reagent::getName ( )

Get the Name property.

Returns: the Name property.

References name.

const ome::compat::shared_ptr< std::string > ome::xml::model::Reagent::getName ( ) const

Get the Name property.

Returns: the Name property.

References name.

ome::compat::shared_ptr< std::string > ome::xml::model::Reagent::getReagentIdentifier ( )

Get the ReagentIdentifier property.

Returns: the ReagentIdentifier property.

References reagentIdentifier.

const ome::compat::shared_ptr< std::string > ome::xml::model::Reagent::getReagentIdentifier ( ) const

Get the ReagentIdentifier property.

Returns: the ReagentIdentifier property.

References reagentIdentifier.

ome::compat::weak_ptr< ome::xml::model::Screen > ome::xml::model::Reagent::getScreen ( )

Get the Screen property.

Returns: the Screen property.

References screen.

const ome::compat::weak_ptr< ome::xml::model::Screen > ome::xml::model::Reagent::getScreen ( ) const

Get the Screen property.

Returns: the Screen property.

References screen.

const std::string & ome::xml::model::Reagent::getXMLNamespace ( ) const

virtual

Get the XML namespace for this model object.

Returns: the XML namespace.

Implements ome::xml::model::OMEModelObject.

bool ome::xml::model::Reagent::link	(	ome::compat::shared_ptr< Reference > &	reference,
		ome::compat::shared_ptr< ome::xml::model::OMEModelObject > &	object
	)

Link a given OME model object to this model object.

Parameters

reference	type qualifier for the reference. This should be the corresponding reference type for object. If, for example, object is of type Image, reference must be of type ImageRef.
object	Model object to link to.

Returns: true if this model object was able to handle the reference, otherwise false.

Todo:: the use of reference to provide type information for the type of object is unconventional and quite possibly unnecessary–a simple string or type_info would suffice for what it's being used for, if it's needed at all. Is this true for all cases? The implementation also needs to do strict checking of the object type; it's not currently failing if it's of the wrong type. This applies to all generated model objects implementing this interface.

Todo:: This bit is silly; why do we have two dynamic_casts here.

References annotationLinks, ome::xml::model::detail::OMEModelObject::link(), ome::xml::model::Annotation::linkReagent(), ome::xml::model::detail::OMEModelObject::logger, and name.

bool ome::xml::model::Reagent::linkAnnotation ( const ome::compat::shared_ptr< ome::xml::model::Annotation > & annotation )

Link Annotation.

Parameters

annotation the Annotation to link.

Returns: true if the object was added to the internal annotationLinks list, otherwise false.

Todo:: Why have a return value here; what is it used for? Is this an artifact of the Java API?

References annotationLinks.

bool ome::xml::model::Reagent::linkWell ( const ome::compat::shared_ptr< ome::xml::model::Well > & well_BackReference )

Link Well.

Parameters

well_BackReference the Well to link.

Returns: true if the object was added to the internal wells list, otherwise false.

Todo:: Why have a return value here; what is it used for? Is this an artifact of the Java API?

References wells.

Referenced by ome::xml::model::Well::link().

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void ome::xml::model::Reagent::setDescription ( ome::compat::shared_ptr< std::string > & description )

Set the Description property.

Parameters

description the value to set.

References description.

Referenced by update().

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void ome::xml::model::Reagent::setID ( const std::string & id )

Set the ID property.

Parameters

id	the value to set.

References id.

Referenced by update().

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const ome::compat::weak_ptr< ome::xml::model::Annotation > & ome::xml::model::Reagent::setLinkedAnnotation	(	OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type	index,
		const ome::compat::shared_ptr< ome::xml::model::Annotation > &	annotation
	)

Set linked Annotation.

Note: The index must be valid.

Parameters

index	the index number of the Annotation.
annotation	the Annotation to set.

Returns: a weak pointer to the Annotation.

Exceptions

std::out_of_range if the index is invalid.

References annotationLinks.

const ome::compat::weak_ptr< ome::xml::model::Well > & ome::xml::model::Reagent::setLinkedWell	(	OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type	index,
		const ome::compat::shared_ptr< ome::xml::model::Well > &	well_BackReference
	)

Set linked Well.

Note: The index must be valid.

Parameters

index	the index number of the Well.
well_BackReference	the Well to set.

Returns: a weak pointer to the Well.

Exceptions

std::out_of_range if the index is invalid.

References wells.

void ome::xml::model::Reagent::setName ( ome::compat::shared_ptr< std::string > & name )

Set the Name property.

Parameters

name	the value to set.

References name.

Referenced by update().

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void ome::xml::model::Reagent::setReagentIdentifier ( ome::compat::shared_ptr< std::string > & reagentIdentifier )

Set the ReagentIdentifier property.

Parameters

reagentIdentifier the value to set.

References reagentIdentifier.

Referenced by update().

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void ome::xml::model::Reagent::setScreen ( ome::compat::weak_ptr< ome::xml::model::Screen > & screen_BackReference )

Set the Screen property.

Parameters

screen_BackReference the value to set.

References screen.

OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type ome::xml::model::Reagent::sizeOfLinkedAnnotationList ( ) const

Get size of linked Annotation list.

Returns: the size of the list.

References annotationLinks.

OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type ome::xml::model::Reagent::sizeOfLinkedWellList ( ) const

Get size of linked Well list.

Returns: the size of the list.

References wells.

bool ome::xml::model::Reagent::unlinkAnnotation ( const ome::compat::shared_ptr< ome::xml::model::Annotation > & annotation )

Unlink Annotation.

Parameters

annotation the Annotation to unlink.

Returns: true if the Annotation was unlinked, otherwise false if the Annotation was not linked and could hence not be unlinked.

Todo:

Does the return value serve any useful purpose? Is this also inherited Java API?

Doesn't the removal break the indexing?

Does the removal deal with multiple instances; we aren't preventing duplicates on insertion.

References annotationLinks.

bool ome::xml::model::Reagent::unlinkWell ( const ome::compat::shared_ptr< ome::xml::model::Well > & well_BackReference )

Unlink Well.

Parameters

well_BackReference the Well to unlink.

Returns: true if the Well was unlinked, otherwise false if the Well was not linked and could hence not be unlinked.

Todo:

Does the return value serve any useful purpose? Is this also inherited Java API?

Doesn't the removal break the indexing?

Does the removal deal with multiple instances; we aren't preventing duplicates on insertion.

References wells.

void ome::xml::model::Reagent::update	(	const common::xml::dom::Element &	element,
		ome::xml::model::OMEModel &	model
	)

virtual

Update the object hierarchy recursively from an XML DOM tree.

Note: No properties are removed, only added or updated.

Parameters

element	root of the XML DOM tree to from which to construct the model object graph.
model	handler for the OME model used to track instances and references seen during the update.

Exceptions

EnumerationException if there is an error instantiating an enumeration during model object creation, or ModelException if there are any consistency or validity errors found during processing.

Implements ome::xml::model::OMEModelObject.

References ome::xml::model::OMEModel::addModelObject(), ome::xml::model::OMEModel::addReference(), ome::common::xml::dom::Element::getAttribute(), ome::xml::model::detail::OMEModelObject::getChildrenByTagName(), getID(), ome::common::xml::dom::Element::getTagName(), ome::common::xml::dom::Element::hasAttribute(), ome::xml::model::detail::OMEModelObject::logger, setDescription(), setID(), setName(), setReagentIdentifier(), ome::xml::model::detail::OMEModelObject::stripNamespacePrefix(), ome::xml::model::detail::OMEModelObject::update(), and validElementName().