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

Inheritance diagram for ome::xml::model::Experiment:

Collaboration diagram for ome::xml::model::Experiment:

Public Member Functions
	Experiment ()
	Default constructor.

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

virtual	~Experiment ()
	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< ome::xml::model::enums::ExperimentType >	getType ()
	Get the Type property. More...

const ome::compat::shared_ptr< ome::xml::model::enums::ExperimentType >	getType () const
	Get the Type property. More...

void	setType (ome::compat::shared_ptr< ome::xml::model::enums::ExperimentType > &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 >	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...

ome::compat::weak_ptr< ome::xml::model::Experimenter >	getLinkedExperimenter ()
	Get linked Experimenter. More...

const ome::compat::weak_ptr< ome::xml::model::Experimenter >	getLinkedExperimenter () const
	Get linked Experimenter. More...

void	linkExperimenter (ome::compat::shared_ptr< ome::xml::model::Experimenter > &experimenter)
	Link Experimenter. More...

void	unlinkExperimenter (ome::compat::shared_ptr< ome::xml::model::Experimenter > &experimenter)
	Unlink Experimenter. More...

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

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

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

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

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

void	setMicrobeamManipulation (std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > >::size_type index, ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > &microbeamManipulation)
	Set MicrobeamManipulation. More...

void	addMicrobeamManipulation (ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > &microbeamManipulation)
	Add MicrobeamManipulation. More...

void	removeMicrobeamManipulation (ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > &microbeamManipulation)
	Remove MicrobeamManipulation. More...

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

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

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

const ome::compat::weak_ptr< ome::xml::model::Image > &	setLinkedImage (OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type::size_type index, const ome::compat::shared_ptr< ome::xml::model::Image > &image_BackReference)
	Set linked Image. More...

bool	linkImage (const ome::compat::shared_ptr< ome::xml::model::Image > &image_BackReference)
	Link Image. More...

bool	unlinkImage (const ome::compat::shared_ptr< ome::xml::model::Image > &image_BackReference)
	Unlink Image. 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< Experiment >	create (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
	Create a Experiment 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< ome::xml::model::enums::ExperimentType >	type
	Type property.

std::string	id
	ID property.

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

ome::compat::weak_ptr< ome::xml::model::Experimenter >	experimenter
	ExperimenterRef reference.

std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > >	microbeamManipulations
	MicrobeamManipulation property (occurs more than once)

OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type	images
	Image_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

Experiment model object.

Constructor & Destructor Documentation

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

Copy constructor.

Parameters

copy	the Experiment to copy.

Member Function Documentation

void ome::xml::model::Experiment::addMicrobeamManipulation ( ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > & microbeamManipulation )

Add MicrobeamManipulation.

Parameters

microbeamManipulation the MicrobeamManipulation to add.

Todo:

Return list position?

Detect and handle duplicates?

References microbeamManipulations.

Referenced by update().

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common::xml::dom::Element ome::xml::model::Experiment::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::Experiment::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(), description, experimenter, id, microbeamManipulations, ome::common::xml::dom::Element::setAttribute(), and type.

Referenced by asXMLElement().

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

static

Create a Experiment 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::Experiment::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.

References type.

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

Get the Description property.

Returns: the Description property.

References description.

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

Get the Description property.

Returns: the Description property.

References description.

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

Get the ID property.

Returns: the ID property.

References id.

Referenced by update().

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ome::compat::weak_ptr< ome::xml::model::Experimenter > ome::xml::model::Experiment::getLinkedExperimenter ( )

Get linked Experimenter.

Returns: the linked Experimenter. The pointer may be null.

References experimenter.

const ome::compat::weak_ptr< ome::xml::model::Experimenter > ome::xml::model::Experiment::getLinkedExperimenter ( ) const

Get linked Experimenter.

Returns: the linked Experimenter. The pointer may be null.

References experimenter.

const ome::compat::weak_ptr< ome::xml::model::Image > & ome::xml::model::Experiment::getLinkedImage ( OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type::size_type index ) const

Get linked Image.

Parameters

index the index number of the Image.

Returns: a weak pointer to the Image.

Exceptions

std::out_of_range if the index is invalid.

References images.

OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type ome::xml::model::Experiment::getLinkedImageList ( ) const

Get the linked Image list.

Returns: a reference to the list.

References images.

ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > & ome::xml::model::Experiment::getMicrobeamManipulation ( std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > >::size_type index )

Get MicrobeamManipulation.

Parameters

index the index number of the MicrobeamManipulation.

Returns: the MicrobeamManipulation.

Exceptions

std::out_of_range if the index is invalid.

References microbeamManipulations.

const ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > & ome::xml::model::Experiment::getMicrobeamManipulation ( std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > >::size_type index ) const

Get MicrobeamManipulation.

Parameters

index the index number of the MicrobeamManipulation.

Returns: the MicrobeamManipulation.

Exceptions

std::out_of_range if the index is invalid.

References microbeamManipulations.

std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > > & ome::xml::model::Experiment::getMicrobeamManipulationList ( )

Get the MicrobeamManipulation list.

Returns: a reference to the list.

References microbeamManipulations.

const std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > > & ome::xml::model::Experiment::getMicrobeamManipulationList ( ) const

Get the MicrobeamManipulation list.

Returns: a reference to the list.

References microbeamManipulations.

ome::compat::shared_ptr< ome::xml::model::enums::ExperimentType > ome::xml::model::Experiment::getType ( )

Get the Type property.

Returns: the Type property.

References type.

const ome::compat::shared_ptr< ome::xml::model::enums::ExperimentType > ome::xml::model::Experiment::getType ( ) const

Get the Type property.

Returns: the Type property.

References type.

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

virtual

Get the XML namespace for this model object.

Returns: the XML namespace.

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

bool ome::xml::model::Experiment::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 experimenter, ome::xml::model::detail::OMEModelObject::link(), ome::xml::model::Experimenter::linkExperiment(), and ome::xml::model::detail::OMEModelObject::logger.

void ome::xml::model::Experiment::linkExperimenter ( ome::compat::shared_ptr< ome::xml::model::Experimenter > & experimenter )

Link Experimenter.

Parameters

experimenter the Experimenter to link.

References experimenter.

bool ome::xml::model::Experiment::linkImage ( const ome::compat::shared_ptr< ome::xml::model::Image > & image_BackReference )

Link Image.

Parameters

image_BackReference the Image to link.

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

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

References images, and type.

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

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void ome::xml::model::Experiment::removeMicrobeamManipulation ( ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > & microbeamManipulation )

Remove MicrobeamManipulation.

Parameters

microbeamManipulation the MicrobeamManipulation 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 microbeamManipulations.

void ome::xml::model::Experiment::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::Experiment::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::Image > & ome::xml::model::Experiment::setLinkedImage	(	OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type::size_type	index,
		const ome::compat::shared_ptr< ome::xml::model::Image > &	image_BackReference
	)

Set linked Image.

Note: The index must be valid.

Parameters

index	the index number of the Image.
image_BackReference	the Image to set.

Returns: a weak pointer to the Image.

Exceptions

std::out_of_range if the index is invalid.

References images.

void ome::xml::model::Experiment::setMicrobeamManipulation	(	std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > >::size_type	index,
		ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > &	microbeamManipulation
	)

Set MicrobeamManipulation.

Parameters

index	the index number of the MicrobeamManipulation.
microbeamManipulation	the MicrobeamManipulation to set.

Exceptions

std::out_of_range if the index is invalid.

References microbeamManipulations.

void ome::xml::model::Experiment::setType ( ome::compat::shared_ptr< ome::xml::model::enums::ExperimentType > & type )

Set the Type property.

Parameters

type	the value to set.

References type.

Referenced by update().

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OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type::size_type ome::xml::model::Experiment::sizeOfLinkedImageList ( ) const

Get size of linked Image list.

Returns: the size of the list.

References images.

std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > >::size_type ome::xml::model::Experiment::sizeOfMicrobeamManipulationList ( ) const

Get size of linked MicrobeamManipulation list.

Returns: the size of the list.

References microbeamManipulations.

void ome::xml::model::Experiment::unlinkExperimenter ( ome::compat::shared_ptr< ome::xml::model::Experimenter > & experimenter )

Unlink Experimenter.

Parameters

experimenter the Experimenter to unlink.

Todo:: This method is fairly pointless since it's equivalent to linking a null pointer. It could call link(0) internally.

bool ome::xml::model::Experiment::unlinkImage ( const ome::compat::shared_ptr< ome::xml::model::Image > & image_BackReference )

Unlink Image.

Parameters

image_BackReference the Image to unlink.

Returns: true if the Image was unlinked, otherwise false if the Image 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 images.

void ome::xml::model::Experiment::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 addMicrobeamManipulation(), ome::xml::model::OMEModel::addModelObject(), ome::xml::model::OMEModel::addReference(), ome::xml::model::MicrobeamManipulation::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(), setType(), ome::xml::model::detail::OMEModelObject::stripNamespacePrefix(), ome::xml::model::detail::OMEModelObject::update(), and validElementName().