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

Inheritance diagram for ome::xml::model::Well:

Collaboration diagram for ome::xml::model::Well:

Public Member Functions
	Well ()
	Default constructor.

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

virtual	~Well ()
	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 >	getExternalIdentifier ()
	Get the ExternalIdentifier property. More...

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

void	setExternalIdentifier (ome::compat::shared_ptr< std::string > &externalIdentifier)
	Set the ExternalIdentifier property. More...

const ome::xml::model::primitives::NonNegativeInteger &	getColumn () const
	Get the Column property. More...

void	setColumn (const ome::xml::model::primitives::NonNegativeInteger &column)
	Set the Column property. More...

ome::compat::shared_ptr< std::string >	getExternalDescription ()
	Get the ExternalDescription property. More...

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

void	setExternalDescription (ome::compat::shared_ptr< std::string > &externalDescription)
	Set the ExternalDescription property. More...

ome::compat::shared_ptr< ome::xml::model::primitives::Color >	getColor ()
	Get the Color property. More...

const ome::compat::shared_ptr< ome::xml::model::primitives::Color >	getColor () const
	Get the Color property. More...

void	setColor (ome::compat::shared_ptr< ome::xml::model::primitives::Color > &color)
	Set the Color 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...

const ome::xml::model::primitives::NonNegativeInteger &	getRow () const
	Get the Row property. More...

void	setRow (const ome::xml::model::primitives::NonNegativeInteger &row)
	Set the Row property. More...

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

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

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

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

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

void	setWellSample (std::vector< ome::compat::shared_ptr< ome::xml::model::WellSample > >::size_type index, ome::compat::shared_ptr< ome::xml::model::WellSample > &wellSample)
	Set WellSample. More...

void	addWellSample (ome::compat::shared_ptr< ome::xml::model::WellSample > &wellSample)
	Add WellSample. More...

void	removeWellSample (ome::compat::shared_ptr< ome::xml::model::WellSample > &wellSample)
	Remove WellSample. More...

ome::compat::weak_ptr< ome::xml::model::Reagent >	getLinkedReagent ()
	Get linked Reagent. More...

const ome::compat::weak_ptr< ome::xml::model::Reagent >	getLinkedReagent () const
	Get linked Reagent. More...

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

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

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

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

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

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

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

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

ome::compat::weak_ptr< ome::xml::model::Plate >	getPlate ()
	Get the Plate property. More...

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

void	setPlate (ome::compat::weak_ptr< ome::xml::model::Plate > &plate_BackReference)
	Set the Plate 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< Well >	create (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
	Create a Well model object from DOM element. More...

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

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

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

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

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

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

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

Private Attributes
ome::compat::shared_ptr< std::string >	externalIdentifier
	ExternalIdentifier property.

ome::xml::model::primitives::NonNegativeInteger	column
	Column property.

ome::compat::shared_ptr< std::string >	externalDescription
	ExternalDescription property.

ome::compat::shared_ptr< ome::xml::model::primitives::Color >	color
	Color property.

ome::compat::shared_ptr< std::string >	type
	Type property.

std::string	id
	ID property.

ome::xml::model::primitives::NonNegativeInteger	row
	Row property.

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

ome::compat::weak_ptr< ome::xml::model::Reagent >	reagent
	ReagentRef reference.

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

ome::compat::weak_ptr< ome::xml::model::Plate >	plate
	Plate_BackReference back reference.

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

Detailed Description

Well model object.

Constructor & Destructor Documentation

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

Copy constructor.

Parameters

copy	the Well to copy.

Member Function Documentation

void ome::xml::model::Well::addWellSample ( ome::compat::shared_ptr< ome::xml::model::WellSample > & wellSample )

Add WellSample.

Parameters

wellSample the WellSample to add.

Todo:

Return list position?

Detect and handle duplicates?

References wellSamples.

Referenced by update().

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common::xml::dom::Element ome::xml::model::Well::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::Well::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(), color, column, ome::common::xml::dom::Document::createElementNS(), externalDescription, externalIdentifier, id, reagent, row, ome::common::xml::dom::Element::setAttribute(), type, and wellSamples.

Referenced by asXMLElement().

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

static

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

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const std::string & ome::xml::model::Well::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< ome::xml::model::primitives::Color > ome::xml::model::Well::getColor ( )

Get the Color property.

Returns: the Color property.

References color.

const ome::compat::shared_ptr< ome::xml::model::primitives::Color > ome::xml::model::Well::getColor ( ) const

Get the Color property.

Returns: the Color property.

References color.

const ome::xml::model::primitives::NonNegativeInteger & ome::xml::model::Well::getColumn ( ) const

Get the Column property.

Returns: the Column property.

References column.

ome::compat::shared_ptr< std::string > ome::xml::model::Well::getExternalDescription ( )

Get the ExternalDescription property.

Returns: the ExternalDescription property.

References externalDescription.

const ome::compat::shared_ptr< std::string > ome::xml::model::Well::getExternalDescription ( ) const

Get the ExternalDescription property.

Returns: the ExternalDescription property.

References externalDescription.

ome::compat::shared_ptr< std::string > ome::xml::model::Well::getExternalIdentifier ( )

Get the ExternalIdentifier property.

Returns: the ExternalIdentifier property.

References externalIdentifier.

const ome::compat::shared_ptr< std::string > ome::xml::model::Well::getExternalIdentifier ( ) const

Get the ExternalIdentifier property.

Returns: the ExternalIdentifier property.

References externalIdentifier.

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

Get the ID property.

Returns: the ID property.

References id.

Referenced by update().

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

Get the linked Annotation list.

Returns: a reference to the list.

References annotationLinks.

ome::compat::weak_ptr< ome::xml::model::Reagent > ome::xml::model::Well::getLinkedReagent ( )

Get linked Reagent.

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

References reagent.

const ome::compat::weak_ptr< ome::xml::model::Reagent > ome::xml::model::Well::getLinkedReagent ( ) const

Get linked Reagent.

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

References reagent.

ome::compat::weak_ptr< ome::xml::model::Plate > ome::xml::model::Well::getPlate ( )

Get the Plate property.

Returns: the Plate property.

References plate.

const ome::compat::weak_ptr< ome::xml::model::Plate > ome::xml::model::Well::getPlate ( ) const

Get the Plate property.

Returns: the Plate property.

References plate.

const ome::xml::model::primitives::NonNegativeInteger & ome::xml::model::Well::getRow ( ) const

Get the Row property.

Returns: the Row property.

References row.

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

Get the Type property.

Returns: the Type property.

References type.

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

Get the Type property.

Returns: the Type property.

References type.

ome::compat::shared_ptr< ome::xml::model::WellSample > & ome::xml::model::Well::getWellSample ( std::vector< ome::compat::shared_ptr< ome::xml::model::WellSample > >::size_type index )

Get WellSample.

Parameters

index the index number of the WellSample.

Returns: the WellSample.

Exceptions

std::out_of_range if the index is invalid.

References wellSamples.

const ome::compat::shared_ptr< ome::xml::model::WellSample > & ome::xml::model::Well::getWellSample ( std::vector< ome::compat::shared_ptr< ome::xml::model::WellSample > >::size_type index ) const

Get WellSample.

Parameters

index the index number of the WellSample.

Returns: the WellSample.

Exceptions

std::out_of_range if the index is invalid.

References wellSamples.

std::vector< ome::compat::shared_ptr< ome::xml::model::WellSample > > & ome::xml::model::Well::getWellSampleList ( )

Get the WellSample list.

Returns: a reference to the list.

References wellSamples.

const std::vector< ome::compat::shared_ptr< ome::xml::model::WellSample > > & ome::xml::model::Well::getWellSampleList ( ) const

Get the WellSample list.

Returns: a reference to the list.

References wellSamples.

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

virtual

Get the XML namespace for this model object.

Returns: the XML namespace.

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

bool ome::xml::model::Well::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, ome::xml::model::detail::OMEModelObject::link(), ome::xml::model::Reagent::linkWell(), ome::xml::model::Annotation::linkWell(), ome::xml::model::detail::OMEModelObject::logger, reagent, and type.

bool ome::xml::model::Well::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, and type.

void ome::xml::model::Well::linkReagent ( ome::compat::shared_ptr< ome::xml::model::Reagent > & reagent )

Link Reagent.

Parameters

reagent the Reagent to link.

References reagent.

void ome::xml::model::Well::removeWellSample ( ome::compat::shared_ptr< ome::xml::model::WellSample > & wellSample )

Remove WellSample.

Parameters

wellSample the WellSample 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 wellSamples.

void ome::xml::model::Well::setColor ( ome::compat::shared_ptr< ome::xml::model::primitives::Color > & color )

Set the Color property.

Parameters

color the value to set.

References color.

Referenced by update().

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void ome::xml::model::Well::setColumn ( const ome::xml::model::primitives::NonNegativeInteger & column )

Set the Column property.

Parameters

column the value to set.

References column.

Referenced by update().

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void ome::xml::model::Well::setExternalDescription ( ome::compat::shared_ptr< std::string > & externalDescription )

Set the ExternalDescription property.

Parameters

externalDescription the value to set.

References externalDescription.

Referenced by update().

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void ome::xml::model::Well::setExternalIdentifier ( ome::compat::shared_ptr< std::string > & externalIdentifier )

Set the ExternalIdentifier property.

Parameters

externalIdentifier the value to set.

References externalIdentifier.

Referenced by update().

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

Set the ID property.

Parameters

id	the value to set.

References id.

Referenced by update().

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

void ome::xml::model::Well::setPlate ( ome::compat::weak_ptr< ome::xml::model::Plate > & plate_BackReference )

Set the Plate property.

Parameters

plate_BackReference the value to set.

References plate.

void ome::xml::model::Well::setRow ( const ome::xml::model::primitives::NonNegativeInteger & row )

Set the Row property.

Parameters

row	the value to set.

References row.

Referenced by update().

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

Set the Type property.

Parameters

type	the value to set.

References type.

Referenced by update().

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void ome::xml::model::Well::setWellSample	(	std::vector< ome::compat::shared_ptr< ome::xml::model::WellSample > >::size_type	index,
		ome::compat::shared_ptr< ome::xml::model::WellSample > &	wellSample
	)

Set WellSample.

Parameters

index	the index number of the WellSample.
wellSample	the WellSample to set.

Exceptions

std::out_of_range if the index is invalid.

References wellSamples.

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

Get size of linked Annotation list.

Returns: the size of the list.

References annotationLinks.

std::vector< ome::compat::shared_ptr< ome::xml::model::WellSample > >::size_type ome::xml::model::Well::sizeOfWellSampleList ( ) const

Get size of linked WellSample list.

Returns: the size of the list.

References wellSamples.

bool ome::xml::model::Well::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::Well::unlinkReagent ( ome::compat::shared_ptr< ome::xml::model::Reagent > & reagent )

Unlink Reagent.

Parameters

reagent the Reagent to unlink.

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

void ome::xml::model::Well::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(), addWellSample(), ome::xml::model::WellSample::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, setColor(), setColumn(), setExternalDescription(), setExternalIdentifier(), setID(), setRow(), setType(), ome::xml::model::detail::OMEModelObject::stripNamespacePrefix(), ome::xml::model::detail::OMEModelObject::update(), and validElementName().