bioformats  5.1.3
Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | List of all members
ome::xml::model::Well Class Reference

Well model object. More...

#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::NonNegativeIntegergetColumn () 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::ColorgetColor ()
 Get the Color property. More...
 
const ome::compat::shared_ptr< ome::xml::model::primitives::ColorgetColor () 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::NonNegativeIntegergetRow () 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::ReagentgetLinkedReagent ()
 Get linked Reagent. More...
 
const ome::compat::weak_ptr< ome::xml::model::ReagentgetLinkedReagent () 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::PlategetPlate ()
 Get the Plate property. More...
 
const ome::compat::weak_ptr< ome::xml::model::PlategetPlate () 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< Wellcreate (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::ElementgetChildrenByTagName (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::Colorcolor
 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::Reagentreagent
 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::Plateplate
 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
copythe Well to copy.

Member Function Documentation

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

Add WellSample.

Parameters
wellSamplethe 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
documentdocument 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
documentXML document for element creation.
elementXML 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
elementroot of the XML DOM tree to from which to construct the model object graph.
modelhandler for the OME model used to track instances and references seen during the update.
Exceptions
EnumerationExceptionif 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
indexthe index number of the Annotation.
Returns
a weak pointer to the Annotation.
Exceptions
std::out_of_rangeif 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
indexthe index number of the WellSample.
Returns
the WellSample.
Exceptions
std::out_of_rangeif 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
indexthe index number of the WellSample.
Returns
the WellSample.
Exceptions
std::out_of_rangeif 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
referencetype 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.
objectModel 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
annotationthe 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
reagentthe Reagent to link.

References reagent.

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

Remove WellSample.

Parameters
wellSamplethe 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
colorthe 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
columnthe 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
externalDescriptionthe 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
externalIdentifierthe 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
idthe 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
indexthe index number of the Annotation.
annotationthe Annotation to set.
Returns
a weak pointer to the Annotation.
Exceptions
std::out_of_rangeif 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_BackReferencethe value to set.

References plate.

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

Set the Row property.

Parameters
rowthe 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
typethe 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
indexthe index number of the WellSample.
wellSamplethe WellSample to set.
Exceptions
std::out_of_rangeif 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
annotationthe 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
reagentthe 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
elementroot of the XML DOM tree to from which to construct the model object graph.
modelhandler for the OME model used to track instances and references seen during the update.
Exceptions
EnumerationExceptionif 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().

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

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

Used for processing nodes when interitance is involved.

Parameters
namethe element name to check.
Returns
true if valid, false if invalid.

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

References ome::xml::model::detail::OMEModelObject::validElementName().

Referenced by update().

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