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

Inheritance diagram for ome::xml::model::Screen:

Collaboration diagram for ome::xml::model::Screen:

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

Public Member Functions
	Screen ()
	Default constructor.

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

virtual	~Screen ()
	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 >	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 >	getProtocolDescription ()
	Get the ProtocolDescription property. More...

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

void	setProtocolDescription (ome::compat::shared_ptr< std::string > &protocolDescription)
	Set the ProtocolDescription property. More...

ome::compat::shared_ptr< std::string >	getProtocolIdentifier ()
	Get the ProtocolIdentifier property. More...

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

void	setProtocolIdentifier (ome::compat::shared_ptr< std::string > &protocolIdentifier)
	Set the ProtocolIdentifier property. More...

ome::compat::shared_ptr< std::string >	getReagentSetDescription ()
	Get the ReagentSetDescription property. More...

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

void	setReagentSetDescription (ome::compat::shared_ptr< std::string > &reagentSetDescription)
	Set the ReagentSetDescription property. More...

ome::compat::shared_ptr< std::string >	getType ()
	Get the Type property. More...

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

void	setType (ome::compat::shared_ptr< std::string > &type)
	Set the Type 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 >	getReagentSetIdentifier ()
	Get the ReagentSetIdentifier property. More...

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

void	setReagentSetIdentifier (ome::compat::shared_ptr< std::string > &reagentSetIdentifier)
	Set the ReagentSetIdentifier 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...

std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > >::size_type	sizeOfReagentList () const
	Get size of linked Reagent list. More...

std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > > &	getReagentList ()
	Get the Reagent list. More...

const std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > > &	getReagentList () const
	Get the Reagent list. More...

ome::compat::shared_ptr< ome::xml::model::Reagent > &	getReagent (std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > >::size_type index)
	Get Reagent. More...

const ome::compat::shared_ptr< ome::xml::model::Reagent > &	getReagent (std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > >::size_type index) const
	Get Reagent. More...

void	setReagent (std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > >::size_type index, ome::compat::shared_ptr< ome::xml::model::Reagent > &reagent)
	Set Reagent. More...

void	addReagent (ome::compat::shared_ptr< ome::xml::model::Reagent > &reagent)
	Add Reagent. More...

void	removeReagent (ome::compat::shared_ptr< ome::xml::model::Reagent > &reagent)
	Remove Reagent. More...

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

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

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

const ome::compat::weak_ptr< ome::xml::model::Plate > &	setLinkedPlate (OMEModelObject::indexed_container< ome::xml::model::Plate, ome::compat::weak_ptr >::type::size_type index, const ome::compat::shared_ptr< ome::xml::model::Plate > &plate)
	Set linked Plate. More...

bool	linkPlate (const ome::compat::shared_ptr< ome::xml::model::Plate > &plate)
	Link Plate. More...

bool	unlinkPlate (const ome::compat::shared_ptr< ome::xml::model::Plate > &plate)
	Unlink Plate. 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...

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< Screen >	create (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
	Create a Screen 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< 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

Screen model object.

Constructor & Destructor Documentation

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

Copy constructor.

Parameters

copy	the Screen to copy.

Member Function Documentation

void ome::xml::model::Screen::addReagent ( ome::compat::shared_ptr< ome::xml::model::Reagent > & reagent )

Add Reagent.

Parameters

reagent the Reagent to add.

Todo:

Return list position?

Detect and handle duplicates?

References impl.

Referenced by update().

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common::xml::dom::Element ome::xml::model::Screen::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(), ome::common::xml::dom::Document::createElementNS(), and getXMLNamespace().

common::xml::dom::Element ome::xml::model::Screen::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 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().

Referenced by asXMLElement().

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

static

Create a Screen 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::OME::update().

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const std::string & ome::xml::model::Screen::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::Screen::getDescription ( )

Get the Description property.

Returns: the Description property.

References impl.

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

Get the Description property.

Returns: the Description property.

References impl.

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

Get the ID property.

Returns: the ID property.

References impl.

Referenced by update().

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const ome::compat::weak_ptr< ome::xml::model::Annotation > & ome::xml::model::Screen::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 impl.

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

Get the linked Annotation list.

Returns: a reference to the list.

References impl.

const ome::compat::weak_ptr< ome::xml::model::Plate > & ome::xml::model::Screen::getLinkedPlate ( OMEModelObject::indexed_container< ome::xml::model::Plate, ome::compat::weak_ptr >::type::size_type index ) const

Get linked Plate.

Parameters

index the index number of the Plate.

Returns: a weak pointer to the Plate.

Exceptions

std::out_of_range if the index is invalid.

References impl.

OMEModelObject::indexed_container< ome::xml::model::Plate, ome::compat::weak_ptr >::type ome::xml::model::Screen::getLinkedPlateList ( ) const

Get the linked Plate list.

Returns: a reference to the list.

References impl.

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

Get the Name property.

Returns: the Name property.

References impl.

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

Get the Name property.

Returns: the Name property.

References impl.

ome::compat::shared_ptr< std::string > ome::xml::model::Screen::getProtocolDescription ( )

Get the ProtocolDescription property.

Returns: the ProtocolDescription property.

References impl.

const ome::compat::shared_ptr< std::string > ome::xml::model::Screen::getProtocolDescription ( ) const

Get the ProtocolDescription property.

Returns: the ProtocolDescription property.

References impl.

ome::compat::shared_ptr< std::string > ome::xml::model::Screen::getProtocolIdentifier ( )

Get the ProtocolIdentifier property.

Returns: the ProtocolIdentifier property.

References impl.

const ome::compat::shared_ptr< std::string > ome::xml::model::Screen::getProtocolIdentifier ( ) const

Get the ProtocolIdentifier property.

Returns: the ProtocolIdentifier property.

References impl.

ome::compat::shared_ptr< ome::xml::model::Reagent > & ome::xml::model::Screen::getReagent ( std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > >::size_type index )

Get Reagent.

Parameters

index the index number of the Reagent.

Returns: the Reagent.

Exceptions

std::out_of_range if the index is invalid.

References impl.

const ome::compat::shared_ptr< ome::xml::model::Reagent > & ome::xml::model::Screen::getReagent ( std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > >::size_type index ) const

Get Reagent.

Parameters

index the index number of the Reagent.

Returns: the Reagent.

Exceptions

std::out_of_range if the index is invalid.

References impl.

std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > > & ome::xml::model::Screen::getReagentList ( )

Get the Reagent list.

Returns: a reference to the list.

References impl.

const std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > > & ome::xml::model::Screen::getReagentList ( ) const

Get the Reagent list.

Returns: a reference to the list.

References impl.

ome::compat::shared_ptr< std::string > ome::xml::model::Screen::getReagentSetDescription ( )

Get the ReagentSetDescription property.

Returns: the ReagentSetDescription property.

References impl.

const ome::compat::shared_ptr< std::string > ome::xml::model::Screen::getReagentSetDescription ( ) const

Get the ReagentSetDescription property.

Returns: the ReagentSetDescription property.

References impl.

ome::compat::shared_ptr< std::string > ome::xml::model::Screen::getReagentSetIdentifier ( )

Get the ReagentSetIdentifier property.

Returns: the ReagentSetIdentifier property.

References impl.

const ome::compat::shared_ptr< std::string > ome::xml::model::Screen::getReagentSetIdentifier ( ) const

Get the ReagentSetIdentifier property.

Returns: the ReagentSetIdentifier property.

References impl.

ome::compat::shared_ptr< std::string > ome::xml::model::Screen::getType ( )

Get the Type property.

Returns: the Type property.

References impl.

const ome::compat::shared_ptr< std::string > ome::xml::model::Screen::getType ( ) const

Get the Type property.

Returns: the Type property.

References impl.

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

virtual

Get the XML namespace for this model object.

Returns: the XML namespace.

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

Referenced by asXMLElement(), and asXMLElementInternal().

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bool ome::xml::model::Screen::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.

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

References impl, ome::xml::model::detail::OMEModelObject::link(), ome::xml::model::Plate::linkScreen(), ome::xml::model::Annotation::linkScreen(), and ome::xml::model::detail::OMEModelObject::logger.

bool ome::xml::model::Screen::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 impl.

bool ome::xml::model::Screen::linkPlate ( const ome::compat::shared_ptr< ome::xml::model::Plate > & plate )

Link Plate.

Parameters

plate the Plate to link.

Returns: true if the object was added to the internal plateLinks 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.

void ome::xml::model::Screen::removeReagent ( ome::compat::shared_ptr< ome::xml::model::Reagent > & reagent )

Remove Reagent.

Parameters

reagent the Reagent to remove.

Todo:

Doesn't the removal break the indexing?

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

References impl.

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

Set the Description property.

Parameters

description the value to set.

References impl.

Referenced by update().

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

Set the ID property.

Parameters

id	the value to set.

References impl.

Referenced by update().

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const ome::compat::weak_ptr< ome::xml::model::Annotation > & ome::xml::model::Screen::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 impl.

const ome::compat::weak_ptr< ome::xml::model::Plate > & ome::xml::model::Screen::setLinkedPlate	(	OMEModelObject::indexed_container< ome::xml::model::Plate, ome::compat::weak_ptr >::type::size_type	index,
		const ome::compat::shared_ptr< ome::xml::model::Plate > &	plate
	)

Set linked Plate.

Note: The index must be valid.

Parameters

index	the index number of the Plate.
plate	the Plate to set.

Returns: a weak pointer to the Plate.

Exceptions

std::out_of_range if the index is invalid.

References impl.

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

Set the Name property.

Parameters

name	the value to set.

References impl.

Referenced by update().

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void ome::xml::model::Screen::setProtocolDescription ( ome::compat::shared_ptr< std::string > & protocolDescription )

Set the ProtocolDescription property.

Parameters

protocolDescription the value to set.

References impl.

Referenced by update().

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void ome::xml::model::Screen::setProtocolIdentifier ( ome::compat::shared_ptr< std::string > & protocolIdentifier )

Set the ProtocolIdentifier property.

Parameters

protocolIdentifier the value to set.

References impl.

Referenced by update().

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void ome::xml::model::Screen::setReagent	(	std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > >::size_type	index,
		ome::compat::shared_ptr< ome::xml::model::Reagent > &	reagent
	)

Set Reagent.

Parameters

index	the index number of the Reagent.
reagent	the Reagent to set.

Exceptions

std::out_of_range if the index is invalid.

References impl.

void ome::xml::model::Screen::setReagentSetDescription ( ome::compat::shared_ptr< std::string > & reagentSetDescription )

Set the ReagentSetDescription property.

Parameters

reagentSetDescription the value to set.

References impl.

Referenced by update().

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void ome::xml::model::Screen::setReagentSetIdentifier ( ome::compat::shared_ptr< std::string > & reagentSetIdentifier )

Set the ReagentSetIdentifier property.

Parameters

reagentSetIdentifier the value to set.

References impl.

Referenced by update().

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void ome::xml::model::Screen::setType ( ome::compat::shared_ptr< std::string > & type )

Set the Type property.

Parameters

type	the value to set.

References impl.

Referenced by update().

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

Get size of linked Annotation list.

Returns: the size of the list.

References impl.

OMEModelObject::indexed_container< ome::xml::model::Plate, ome::compat::weak_ptr >::type::size_type ome::xml::model::Screen::sizeOfLinkedPlateList ( ) const

Get size of linked Plate list.

Returns: the size of the list.

References impl.

std::vector< ome::compat::shared_ptr< ome::xml::model::Reagent > >::size_type ome::xml::model::Screen::sizeOfReagentList ( ) const

Get size of linked Reagent list.

Returns: the size of the list.

References impl.

bool ome::xml::model::Screen::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 impl.

bool ome::xml::model::Screen::unlinkPlate ( const ome::compat::shared_ptr< ome::xml::model::Plate > & plate )

Unlink Plate.

Parameters

plate the Plate to unlink.

Returns: true if the Plate was unlinked, otherwise false if the Plate 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.

void ome::xml::model::Screen::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(), addReagent(), ome::xml::model::OMEModel::addReference(), ome::xml::model::Reagent::create(), 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(), setProtocolDescription(), setProtocolIdentifier(), setReagentSetDescription(), setReagentSetIdentifier(), setType(), ome::xml::model::detail::OMEModelObject::stripNamespacePrefix(), ome::xml::model::detail::OMEModelObject::update(), and validElementName().