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

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

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

Classes
class	Impl
	Private implementation details of Reagent model object. More...

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

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

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

void	setReagentIdentifier (std::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...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

bool	unlinkWell (const std::shared_ptr< ome::xml::model::Well > &well_BackReference)
	Unlink Well. 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 common::xml::dom::Element	asXMLElement (common::xml::dom::Document &document) const
	Transform the object hierarchy rooted at this element to XML. More...

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

virtual bool	link (std::shared_ptr< Reference > &reference, std::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 (std::shared_ptr< Reference > &reference, std::shared_ptr< OMEModelObject > &object)=0
	Link a given OME model object to this model object. More...

Static Public Member Functions
static std::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 void	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. More...

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

template<class C , typename T >
bool	contains (const C &container, const std::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
std::shared_ptr< Impl >	impl
	Private implementation details.

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

◆ Reagent()

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

Copy constructor.

Parameters

copy	the Reagent to copy.

Member Function Documentation

◆ asXMLElementInternal()

void 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.

Concrete model object implementations should override this method.

Parameters

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

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

References ome::common::xml::dom::Node::appendChild(), ome::xml::model::detail::OMEModelObject::asXMLElementInternal(), ome::common::xml::dom::Document::createElementNS(), getXMLNamespace(), impl, and ome::common::xml::dom::Element::setAttribute().

◆ create()

std::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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◆ elementName()

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.

◆ getDescription() [1/2]

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

Get the Description property.

Returns: the Description property.

References impl.

◆ getDescription() [2/2]

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

Get the Description property.

Returns: the Description property.

References impl.

◆ getID()

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

Get the ID property.

Returns: the ID property.

References impl.

Referenced by update().

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◆ getLinkedAnnotation()

const std::weak_ptr< ome::xml::model::Annotation > & ome::xml::model::Reagent::getLinkedAnnotation ( OMEModelObject::indexed_container< ome::xml::model::Annotation, std::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 impl.

◆ getLinkedAnnotationList()

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

Get the linked Annotation list.

Returns: a reference to the list.

References impl.

◆ getLinkedWell()

const std::weak_ptr< ome::xml::model::Well > & ome::xml::model::Reagent::getLinkedWell ( OMEModelObject::indexed_container< ome::xml::model::Well, std::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 impl.

◆ getLinkedWellList()

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

Get the linked Well list.

Returns: a reference to the list.

References impl.

◆ getName() [1/2]

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

Get the Name property.

Returns: the Name property.

References impl.

◆ getName() [2/2]

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

Get the Name property.

Returns: the Name property.

References impl.

◆ getReagentIdentifier() [1/2]

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

Get the ReagentIdentifier property.

Returns: the ReagentIdentifier property.

References impl.

◆ getReagentIdentifier() [2/2]

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

Get the ReagentIdentifier property.

Returns: the ReagentIdentifier property.

References impl.

◆ getScreen() [1/2]

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

Get the Screen property.

Returns: the Screen property.

References impl.

◆ getScreen() [2/2]

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

Get the Screen property.

Returns: the Screen property.

References impl.

◆ getXMLNamespace()

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.

Referenced by asXMLElementInternal().

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◆ link()

bool ome::xml::model::Reagent::link	(	std::shared_ptr< Reference > &	reference,
		std::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 impl, ome::xml::model::detail::OMEModelObject::link(), ome::xml::model::Annotation::linkReagent(), and ome::xml::model::detail::OMEModelObject::logger.

◆ linkAnnotation()

bool ome::xml::model::Reagent::linkAnnotation ( const std::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 impl.

◆ linkWell()

bool ome::xml::model::Reagent::linkWell ( const std::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 impl.

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

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◆ setDescription()

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

Set the Description property.

Parameters

description the value to set.

References impl.

Referenced by update().

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◆ setID()

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

Set the ID property.

Parameters

id	the value to set.

References impl.

Referenced by update().

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◆ setLinkedAnnotation()

const std::weak_ptr< ome::xml::model::Annotation > & ome::xml::model::Reagent::setLinkedAnnotation	(	OMEModelObject::indexed_container< ome::xml::model::Annotation, std::weak_ptr >::type::size_type	index,
		const std::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 impl.

◆ setLinkedWell()

const std::weak_ptr< ome::xml::model::Well > & ome::xml::model::Reagent::setLinkedWell	(	OMEModelObject::indexed_container< ome::xml::model::Well, std::weak_ptr >::type::size_type	index,
		const std::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 impl.

◆ setName()

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

Set the Name property.

Parameters

name	the value to set.

References impl.

Referenced by update().

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◆ setReagentIdentifier()

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

Set the ReagentIdentifier property.

Parameters

reagentIdentifier the value to set.

References impl.

Referenced by update().

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◆ setScreen()

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

Set the Screen property.

Parameters

screen_BackReference the value to set.

References impl.

◆ sizeOfLinkedAnnotationList()

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

Get size of linked Annotation list.

Returns: the size of the list.

References impl.

◆ sizeOfLinkedWellList()

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

Get size of linked Well list.

Returns: the size of the list.

References impl.

◆ unlinkAnnotation()

bool ome::xml::model::Reagent::unlinkAnnotation ( const std::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 impl.

◆ unlinkWell()

bool ome::xml::model::Reagent::unlinkWell ( const std::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 impl.

◆ update()

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::update(), and validElementName().

◆ validElementName()

bool ome::xml::model::Reagent::validElementName ( const std::string & name ) const

virtual

Check if a given element name is valid for processing by this model object.

Used for processing nodes when interitance is involved.

Parameters

name	the element name to check.

Returns: true if valid, false if invalid.

Deprecated:: Always returns true since any element name is now regarded as being valid.

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

Referenced by update().

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

ome/xml/model/Reagent.h
ome/xml/model/Reagent.cpp

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Reagent()

Member Function Documentation

◆ asXMLElementInternal()

◆ create()

◆ elementName()

◆ getDescription() [1/2]

◆ getDescription() [2/2]

◆ getID()

◆ getLinkedAnnotation()

◆ getLinkedAnnotationList()

◆ getLinkedWell()

◆ getLinkedWellList()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getReagentIdentifier() [1/2]

◆ getReagentIdentifier() [2/2]

◆ getScreen() [1/2]

◆ getScreen() [2/2]

◆ getXMLNamespace()

◆ link()

◆ linkAnnotation()

◆ linkWell()

◆ setDescription()

◆ setID()

◆ setLinkedAnnotation()

◆ setLinkedWell()

◆ setName()

◆ setReagentIdentifier()

◆ setScreen()

◆ sizeOfLinkedAnnotationList()

◆ sizeOfLinkedWellList()

◆ unlinkAnnotation()

◆ unlinkWell()

◆ update()

◆ validElementName()