ome-xml  5.2.0
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ome::xml::model::Reagent Class Reference

Reagent model object. More...

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

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Classes

class  Impl
 Private implementation details of Reagent model object. More...
 

Public Member Functions

 Reagent ()
 Default constructor.
 
 Reagent (const Reagent &copy)
 Copy constructor. More...
 
virtual ~Reagent ()
 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 > getReagentIdentifier ()
 Get the ReagentIdentifier property. More...
 
const ome::compat::shared_ptr< std::string > getReagentIdentifier () const
 Get the ReagentIdentifier property. More...
 
void setReagentIdentifier (ome::compat::shared_ptr< std::string > &reagentIdentifier)
 Set the ReagentIdentifier 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 > getName ()
 Get the Name property. More...
 
const ome::compat::shared_ptr< std::string > getName () const
 Get the Name property. More...
 
void setName (ome::compat::shared_ptr< std::string > &name)
 Set the Name property. More...
 
ome::compat::shared_ptr< std::string > 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...
 
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::ScreengetScreen ()
 Get the Screen property. More...
 
const ome::compat::weak_ptr< ome::xml::model::ScreengetScreen () const
 Get the Screen property. More...
 
void setScreen (ome::compat::weak_ptr< ome::xml::model::Screen > &screen_BackReference)
 Set the Screen property. More...
 
OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type sizeOfLinkedWellList () const
 Get size of linked Well list. More...
 
OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type getLinkedWellList () const
 Get the linked Well list. More...
 
const ome::compat::weak_ptr< ome::xml::model::Well > & getLinkedWell (OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type index) const
 Get linked Well. More...
 
const ome::compat::weak_ptr< ome::xml::model::Well > & setLinkedWell (OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type index, const ome::compat::shared_ptr< ome::xml::model::Well > &well_BackReference)
 Set linked Well. More...
 
bool linkWell (const ome::compat::shared_ptr< ome::xml::model::Well > &well_BackReference)
 Link Well. More...
 
bool unlinkWell (const ome::compat::shared_ptr< ome::xml::model::Well > &well_BackReference)
 Unlink Well. 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< Reagentcreate (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
 Create a Reagent 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< Implimpl
 Private implementation details.
 

Additional Inherited Members

- Protected Attributes inherited from ome::xml::model::detail::OMEModelObject
ome::common::Logger logger
 Message logger.
 

Detailed Description

Reagent model object.

Constructor & Destructor Documentation

ome::xml::model::Reagent::Reagent ( const Reagent copy)

Copy constructor.

Parameters
copythe Reagent to copy.

Member Function Documentation

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

common::xml::dom::Element ome::xml::model::Reagent::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 ome::common::xml::dom::Node::appendChild(), ome::xml::model::detail::OMEModelObject::asXMLElementInternal(), ome::common::xml::dom::Document::createElementNS(), getXMLNamespace(), impl, and ome::common::xml::dom::Element::setAttribute().

Referenced by asXMLElement().

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

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

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const std::string & ome::xml::model::Reagent::elementName ( ) const
virtual

Get the element name of this model object.

This will be the most-derived class name.

Returns
the element type.

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

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

Get the Description property.

Returns
the Description property.

References impl.

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

Get the Description property.

Returns
the Description property.

References impl.

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

Get the ID property.

Returns
the ID property.

References impl.

Referenced by update().

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

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

Get the linked Annotation list.

Returns
a reference to the list.

References impl.

const ome::compat::weak_ptr< ome::xml::model::Well > & ome::xml::model::Reagent::getLinkedWell ( OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type  index) const

Get linked Well.

Parameters
indexthe index number of the Well.
Returns
a weak pointer to the Well.
Exceptions
std::out_of_rangeif the index is invalid.

References impl.

OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type ome::xml::model::Reagent::getLinkedWellList ( ) const

Get the linked Well list.

Returns
a reference to the list.

References impl.

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

Get the Name property.

Returns
the Name property.

References impl.

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

Get the Name property.

Returns
the Name property.

References impl.

ome::compat::shared_ptr< std::string > ome::xml::model::Reagent::getReagentIdentifier ( )

Get the ReagentIdentifier property.

Returns
the ReagentIdentifier property.

References impl.

const ome::compat::shared_ptr< std::string > ome::xml::model::Reagent::getReagentIdentifier ( ) const

Get the ReagentIdentifier property.

Returns
the ReagentIdentifier property.

References impl.

ome::compat::weak_ptr< ome::xml::model::Screen > ome::xml::model::Reagent::getScreen ( )

Get the Screen property.

Returns
the Screen property.

References impl.

const ome::compat::weak_ptr< ome::xml::model::Screen > ome::xml::model::Reagent::getScreen ( ) const

Get the Screen property.

Returns
the Screen property.

References impl.

const std::string & ome::xml::model::Reagent::getXMLNamespace ( ) const
virtual

Get the XML namespace for this model object.

Returns
the XML namespace.

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

Referenced by asXMLElement(), and asXMLElementInternal().

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bool ome::xml::model::Reagent::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.

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

bool ome::xml::model::Reagent::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 impl.

bool ome::xml::model::Reagent::linkWell ( const ome::compat::shared_ptr< ome::xml::model::Well > &  well_BackReference)

Link Well.

Parameters
well_BackReferencethe Well to link.
Returns
true if the object was added to the internal wells list, otherwise false.
Todo:
Why have a return value here; what is it used for? Is this an artifact of the Java API?

References impl.

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

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

Set the Description property.

Parameters
descriptionthe value to set.

References impl.

Referenced by update().

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

Set the ID property.

Parameters
idthe value to set.

References impl.

Referenced by update().

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

const ome::compat::weak_ptr< ome::xml::model::Well > & ome::xml::model::Reagent::setLinkedWell ( OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type  index,
const ome::compat::shared_ptr< ome::xml::model::Well > &  well_BackReference 
)

Set linked Well.

Note
The index must be valid.
Parameters
indexthe index number of the Well.
well_BackReferencethe Well to set.
Returns
a weak pointer to the Well.
Exceptions
std::out_of_rangeif the index is invalid.

References impl.

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

Set the Name property.

Parameters
namethe value to set.

References impl.

Referenced by update().

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void ome::xml::model::Reagent::setReagentIdentifier ( ome::compat::shared_ptr< std::string > &  reagentIdentifier)

Set the ReagentIdentifier property.

Parameters
reagentIdentifierthe value to set.

References impl.

Referenced by update().

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void ome::xml::model::Reagent::setScreen ( ome::compat::weak_ptr< ome::xml::model::Screen > &  screen_BackReference)

Set the Screen property.

Parameters
screen_BackReferencethe value to set.

References impl.

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

Get size of linked Annotation list.

Returns
the size of the list.

References impl.

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

Get size of linked Well list.

Returns
the size of the list.

References impl.

bool ome::xml::model::Reagent::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 impl.

bool ome::xml::model::Reagent::unlinkWell ( const ome::compat::shared_ptr< ome::xml::model::Well > &  well_BackReference)

Unlink Well.

Parameters
well_BackReferencethe Well to unlink.
Returns
true if the Well was unlinked, otherwise false if the Well was not linked and could hence not be unlinked.
Todo:

Does the return value serve any useful purpose? Is this also inherited Java API?

Doesn't the removal break the indexing?

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

References impl.

void ome::xml::model::Reagent::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(), ome::common::xml::dom::Element::getAttribute(), ome::xml::model::detail::OMEModelObject::getChildrenByTagName(), getID(), ome::common::xml::dom::Element::getTagName(), ome::common::xml::dom::Element::hasAttribute(), ome::xml::model::detail::OMEModelObject::logger, setDescription(), setID(), setName(), setReagentIdentifier(), ome::xml::model::detail::OMEModelObject::stripNamespacePrefix(), ome::xml::model::detail::OMEModelObject::update(), and validElementName().

bool ome::xml::model::Reagent::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: