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

Inheritance diagram for ome::xml::model::WellSample:

Collaboration diagram for ome::xml::model::WellSample:

Public Member Functions
	WellSample ()
	Default constructor.

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

virtual	~WellSample ()
	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...

const ome::xml::model::primitives::NonNegativeInteger &	getIndex () const
	Get the Index property. More...

void	setIndex (const ome::xml::model::primitives::NonNegativeInteger &index)
	Set the Index property. More...

ome::compat::shared_ptr< double >	getPositionX ()
	Get the PositionX property. More...

const ome::compat::shared_ptr< double >	getPositionX () const
	Get the PositionX property. More...

void	setPositionX (ome::compat::shared_ptr< double > &positionX)
	Set the PositionX property. More...

ome::compat::shared_ptr< double >	getPositionY ()
	Get the PositionY property. More...

const ome::compat::shared_ptr< double >	getPositionY () const
	Get the PositionY property. More...

void	setPositionY (ome::compat::shared_ptr< double > &positionY)
	Set the PositionY 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< ome::xml::model::primitives::Timestamp >	getTimepoint ()
	Get the Timepoint property. More...

const ome::compat::shared_ptr< ome::xml::model::primitives::Timestamp >	getTimepoint () const
	Get the Timepoint property. More...

void	setTimepoint (ome::compat::shared_ptr< ome::xml::model::primitives::Timestamp > &timepoint)
	Set the Timepoint property. More...

ome::compat::weak_ptr< ome::xml::model::Image >	getLinkedImage ()
	Get linked Image. More...

const ome::compat::weak_ptr< ome::xml::model::Image >	getLinkedImage () const
	Get linked Image. More...

void	linkImage (ome::compat::shared_ptr< ome::xml::model::Image > &image)
	Link Image. More...

void	unlinkImage (ome::compat::shared_ptr< ome::xml::model::Image > &image)
	Unlink Image. 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...

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

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

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

const ome::compat::weak_ptr< ome::xml::model::PlateAcquisition > &	setLinkedPlateAcquisition (OMEModelObject::indexed_container< ome::xml::model::PlateAcquisition, ome::compat::weak_ptr >::type::size_type index, const ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > &plateAcquisition_BackReference)
	Set linked PlateAcquisition. More...

bool	linkPlateAcquisition (const ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > &plateAcquisition_BackReference)
	Link PlateAcquisition. More...

bool	unlinkPlateAcquisition (const ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > &plateAcquisition_BackReference)
	Unlink PlateAcquisition. More...

ome::compat::weak_ptr< ome::xml::model::Well >	getWell ()
	Get the Well property. More...

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

void	setWell (ome::compat::weak_ptr< ome::xml::model::Well > &well_BackReference)
	Set the Well property. 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< WellSample >	create (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
	Create a WellSample 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::xml::model::primitives::NonNegativeInteger	index
	Index property.

ome::compat::shared_ptr< double >	positionX
	PositionX property.

ome::compat::shared_ptr< double >	positionY
	PositionY property.

std::string	id
	ID property.

ome::compat::shared_ptr< ome::xml::model::primitives::Timestamp >	timepoint
	Timepoint property.

ome::compat::weak_ptr< ome::xml::model::Image >	image
	ImageRef reference.

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

OMEModelObject::indexed_container< ome::xml::model::PlateAcquisition, ome::compat::weak_ptr >::type	plateAcquisitions
	PlateAcquisition_BackReference back reference (occurs more than once)

ome::compat::weak_ptr< ome::xml::model::Well >	well
	Well_BackReference back reference.

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

Detailed Description

WellSample model object.

Constructor & Destructor Documentation

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

Copy constructor.

Parameters

copy	the WellSample to copy.

Member Function Documentation

common::xml::dom::Element ome::xml::model::WellSample::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::WellSample::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(), id, image, index, positionX, positionY, ome::common::xml::dom::Element::setAttribute(), and timepoint.

Referenced by asXMLElement().

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

static

Create a WellSample 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::Well::update().

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const std::string & ome::xml::model::WellSample::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.

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

Get the ID property.

Returns: the ID property.

References id.

Referenced by update().

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const ome::xml::model::primitives::NonNegativeInteger & ome::xml::model::WellSample::getIndex ( ) const

Get the Index property.

Returns: the Index property.

References index.

const ome::compat::weak_ptr< ome::xml::model::Annotation > & ome::xml::model::WellSample::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::WellSample::getLinkedAnnotationList ( ) const

Get the linked Annotation list.

Returns: a reference to the list.

References annotationLinks.

ome::compat::weak_ptr< ome::xml::model::Image > ome::xml::model::WellSample::getLinkedImage ( )

Get linked Image.

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

References image.

const ome::compat::weak_ptr< ome::xml::model::Image > ome::xml::model::WellSample::getLinkedImage ( ) const

Get linked Image.

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

References image.

const ome::compat::weak_ptr< ome::xml::model::PlateAcquisition > & ome::xml::model::WellSample::getLinkedPlateAcquisition ( OMEModelObject::indexed_container< ome::xml::model::PlateAcquisition, ome::compat::weak_ptr >::type::size_type index ) const

Get linked PlateAcquisition.

Parameters

index the index number of the PlateAcquisition.

Returns: a weak pointer to the PlateAcquisition.

Exceptions

std::out_of_range if the index is invalid.

References plateAcquisitions.

OMEModelObject::indexed_container< ome::xml::model::PlateAcquisition, ome::compat::weak_ptr >::type ome::xml::model::WellSample::getLinkedPlateAcquisitionList ( ) const

Get the linked PlateAcquisition list.

Returns: a reference to the list.

References plateAcquisitions.

ome::compat::shared_ptr< double > ome::xml::model::WellSample::getPositionX ( )

Get the PositionX property.

Returns: the PositionX property.

References positionX.

const ome::compat::shared_ptr< double > ome::xml::model::WellSample::getPositionX ( ) const

Get the PositionX property.

Returns: the PositionX property.

References positionX.

ome::compat::shared_ptr< double > ome::xml::model::WellSample::getPositionY ( )

Get the PositionY property.

Returns: the PositionY property.

References positionY.

const ome::compat::shared_ptr< double > ome::xml::model::WellSample::getPositionY ( ) const

Get the PositionY property.

Returns: the PositionY property.

References positionY.

ome::compat::shared_ptr< ome::xml::model::primitives::Timestamp > ome::xml::model::WellSample::getTimepoint ( )

Get the Timepoint property.

Returns: the Timepoint property.

References timepoint.

const ome::compat::shared_ptr< ome::xml::model::primitives::Timestamp > ome::xml::model::WellSample::getTimepoint ( ) const

Get the Timepoint property.

Returns: the Timepoint property.

References timepoint.

ome::compat::weak_ptr< ome::xml::model::Well > ome::xml::model::WellSample::getWell ( )

Get the Well property.

Returns: the Well property.

References well.

const ome::compat::weak_ptr< ome::xml::model::Well > ome::xml::model::WellSample::getWell ( ) const

Get the Well property.

Returns: the Well property.

References well.

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

virtual

Get the XML namespace for this model object.

Returns: the XML namespace.

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

bool ome::xml::model::WellSample::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 annotationLinks, image, ome::xml::model::detail::OMEModelObject::link(), ome::xml::model::Image::linkWellSample(), ome::xml::model::Annotation::linkWellSample(), and ome::xml::model::detail::OMEModelObject::logger.

bool ome::xml::model::WellSample::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.

void ome::xml::model::WellSample::linkImage ( ome::compat::shared_ptr< ome::xml::model::Image > & image )

Link Image.

Parameters

image the Image to link.

References image.

bool ome::xml::model::WellSample::linkPlateAcquisition ( const ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > & plateAcquisition_BackReference )

Link PlateAcquisition.

Parameters

plateAcquisition_BackReference the PlateAcquisition to link.

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

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

References plateAcquisitions.

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

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

Set the ID property.

Parameters

id	the value to set.

References id.

Referenced by update().

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void ome::xml::model::WellSample::setIndex ( const ome::xml::model::primitives::NonNegativeInteger & index )

Set the Index property.

Parameters

index the value to set.

References index.

Referenced by update().

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const ome::compat::weak_ptr< ome::xml::model::Annotation > & ome::xml::model::WellSample::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::PlateAcquisition > & ome::xml::model::WellSample::setLinkedPlateAcquisition	(	OMEModelObject::indexed_container< ome::xml::model::PlateAcquisition, ome::compat::weak_ptr >::type::size_type	index,
		const ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > &	plateAcquisition_BackReference
	)

Set linked PlateAcquisition.

Note: The index must be valid.

Parameters

index	the index number of the PlateAcquisition.
plateAcquisition_BackReference	the PlateAcquisition to set.

Returns: a weak pointer to the PlateAcquisition.

Exceptions

std::out_of_range if the index is invalid.

References plateAcquisitions.

void ome::xml::model::WellSample::setPositionX ( ome::compat::shared_ptr< double > & positionX )

Set the PositionX property.

Parameters

positionX the value to set.

References positionX.

Referenced by update().

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void ome::xml::model::WellSample::setPositionY ( ome::compat::shared_ptr< double > & positionY )

Set the PositionY property.

Parameters

positionY the value to set.

References positionY.

Referenced by update().

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void ome::xml::model::WellSample::setTimepoint ( ome::compat::shared_ptr< ome::xml::model::primitives::Timestamp > & timepoint )

Set the Timepoint property.

Parameters

timepoint the value to set.

References timepoint.

Referenced by update().

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void ome::xml::model::WellSample::setWell ( ome::compat::weak_ptr< ome::xml::model::Well > & well_BackReference )

Set the Well property.

Parameters

well_BackReference the value to set.

References well.

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

Get size of linked Annotation list.

Returns: the size of the list.

References annotationLinks.

OMEModelObject::indexed_container< ome::xml::model::PlateAcquisition, ome::compat::weak_ptr >::type::size_type ome::xml::model::WellSample::sizeOfLinkedPlateAcquisitionList ( ) const

Get size of linked PlateAcquisition list.

Returns: the size of the list.

References plateAcquisitions.

bool ome::xml::model::WellSample::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.

void ome::xml::model::WellSample::unlinkImage ( ome::compat::shared_ptr< ome::xml::model::Image > & image )

Unlink Image.

Parameters

image the Image 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::WellSample::unlinkPlateAcquisition ( const ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > & plateAcquisition_BackReference )

Unlink PlateAcquisition.

Parameters

plateAcquisition_BackReference the PlateAcquisition to unlink.

Returns: true if the PlateAcquisition was unlinked, otherwise false if the PlateAcquisition 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 plateAcquisitions.

void ome::xml::model::WellSample::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, setID(), setIndex(), setPositionX(), setPositionY(), setTimepoint(), ome::xml::model::detail::OMEModelObject::stripNamespacePrefix(), ome::xml::model::detail::OMEModelObject::update(), and validElementName().