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

Experiment model object. More...

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

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

Public Member Functions

 Experiment ()
 Default constructor.
 
 Experiment (const Experiment &copy)
 Copy constructor. More...
 
virtual ~Experiment ()
 Destructor.
 
const std::string & elementName () const
 Get the element name of this model object. More...
 
bool validElementName (const std::string &name) const
 Check if a given element name is valid for processing by this model object. More...
 
virtual void update (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
 Update the object hierarchy recursively from an XML DOM tree. More...
 
bool link (ome::compat::shared_ptr< Reference > &reference, ome::compat::shared_ptr< ome::xml::model::OMEModelObject > &object)
 Link a given OME model object to this model object. More...
 
ome::compat::shared_ptr< ome::xml::model::enums::ExperimentTypegetType ()
 Get the Type property. More...
 
const ome::compat::shared_ptr< ome::xml::model::enums::ExperimentTypegetType () const
 Get the Type property. More...
 
void setType (ome::compat::shared_ptr< ome::xml::model::enums::ExperimentType > &type)
 Set the Type property. More...
 
const std::string & getID () const
 Get the ID property. More...
 
void setID (const std::string &id)
 Set the ID property. More...
 
ome::compat::shared_ptr< std::string > getDescription ()
 Get the Description property. More...
 
const ome::compat::shared_ptr< std::string > getDescription () const
 Get the Description property. More...
 
void setDescription (ome::compat::shared_ptr< std::string > &description)
 Set the Description property. More...
 
ome::compat::weak_ptr< ome::xml::model::ExperimentergetLinkedExperimenter ()
 Get linked Experimenter. More...
 
const ome::compat::weak_ptr< ome::xml::model::ExperimentergetLinkedExperimenter () const
 Get linked Experimenter. More...
 
void linkExperimenter (ome::compat::shared_ptr< ome::xml::model::Experimenter > &experimenter)
 Link Experimenter. More...
 
void unlinkExperimenter (ome::compat::shared_ptr< ome::xml::model::Experimenter > &experimenter)
 Unlink Experimenter. More...
 
std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > >::size_type sizeOfMicrobeamManipulationList () const
 Get size of linked MicrobeamManipulation list. More...
 
std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > > & getMicrobeamManipulationList ()
 Get the MicrobeamManipulation list. More...
 
const std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > > & getMicrobeamManipulationList () const
 Get the MicrobeamManipulation list. More...
 
ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > & getMicrobeamManipulation (std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > >::size_type index)
 Get MicrobeamManipulation. More...
 
const ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > & getMicrobeamManipulation (std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > >::size_type index) const
 Get MicrobeamManipulation. More...
 
void setMicrobeamManipulation (std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > >::size_type index, ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > &microbeamManipulation)
 Set MicrobeamManipulation. More...
 
void addMicrobeamManipulation (ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > &microbeamManipulation)
 Add MicrobeamManipulation. More...
 
void removeMicrobeamManipulation (ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > &microbeamManipulation)
 Remove MicrobeamManipulation. More...
 
OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type::size_type sizeOfLinkedImageList () const
 Get size of linked Image list. More...
 
OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type getLinkedImageList () const
 Get the linked Image list. More...
 
const ome::compat::weak_ptr< ome::xml::model::Image > & getLinkedImage (OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type::size_type index) const
 Get linked Image. More...
 
const ome::compat::weak_ptr< ome::xml::model::Image > & setLinkedImage (OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type::size_type index, const ome::compat::shared_ptr< ome::xml::model::Image > &image_BackReference)
 Set linked Image. More...
 
bool linkImage (const ome::compat::shared_ptr< ome::xml::model::Image > &image_BackReference)
 Link Image. More...
 
bool unlinkImage (const ome::compat::shared_ptr< ome::xml::model::Image > &image_BackReference)
 Unlink Image. More...
 
virtual common::xml::dom::Element asXMLElement (common::xml::dom::Document &document) const
 Transform the object hierarchy rooted at this element to XML. More...
 
const std::string & getXMLNamespace () const
 Get the XML namespace for this model object. More...
 
- Public Member Functions inherited from ome::xml::model::detail::OMEModelObject
virtual ~OMEModelObject ()
 Destructor.
 
virtual void update (const common::xml::dom::Element &element,::ome::xml::model::OMEModel &model)
 Update the object hierarchy recursively from an XML DOM tree. More...
 
virtual bool link (ome::compat::shared_ptr< Reference > &reference, ome::compat::shared_ptr< ::ome::xml::model::OMEModelObject > &object)
 Link a given OME model object to this model object. More...
 
- Public Member Functions inherited from ome::xml::model::OMEModelObject
virtual bool link (ome::compat::shared_ptr< Reference > &reference, ome::compat::shared_ptr< OMEModelObject > &object)=0
 Link a given OME model object to this model object. More...
 

Static Public Member Functions

static ome::compat::shared_ptr< Experimentcreate (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
 Create a Experiment model object from DOM element. More...
 
- Static Public Member Functions inherited from ome::xml::model::detail::OMEModelObject
static std::vector< common::xml::dom::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< ome::xml::model::enums::ExperimentTypetype
 Type property.
 
std::string id
 ID property.
 
ome::compat::shared_ptr< std::string > description
 Description property.
 
ome::compat::weak_ptr< ome::xml::model::Experimenterexperimenter
 ExperimenterRef reference.
 
std::vector< ome::compat::shared_ptr< ome::xml::model::MicrobeamManipulation > > microbeamManipulations
 MicrobeamManipulation property (occurs more than once)
 
OMEModelObject::indexed_container< ome::xml::model::Image, ome::compat::weak_ptr >::type images
 Image_BackReference back reference (occurs more than once)
 

Additional Inherited Members

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

Detailed Description

Experiment model object.

Constructor & Destructor Documentation

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

Copy constructor.

Parameters
copythe Experiment to copy.

Member Function Documentation

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

Add MicrobeamManipulation.

Parameters
microbeamManipulationthe MicrobeamManipulation to add.
Todo:

Return list position?

Detect and handle duplicates?

References microbeamManipulations.

Referenced by update().

+ Here is the caller graph for this function:

common::xml::dom::Element ome::xml::model::Experiment::asXMLElement ( common::xml::dom::Document document) const
virtual

Transform the object hierarchy rooted at this element to XML.

Parameters
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::Experiment::asXMLElementInternal ( common::xml::dom::Document document,
common::xml::dom::Element element 
) const
protectedvirtual

Transform the object hierarchy rooted at this element to XML.

This internal implementation of asXMLelement also requires an XML element, which must not be null, or may be instantiated and passed from superclasses.

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

Referenced by asXMLElement().

+ Here is the caller graph for this function:

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

Create a Experiment model object from DOM element.

Parameters
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::OME::update().

+ Here is the caller graph for this function:

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

Get the element name of this model object.

This will be the most-derived class name.

Returns
the element type.

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

References type.

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

Get the Description property.

Returns
the Description property.

References description.

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

Get the Description property.

Returns
the Description property.

References description.

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

Get the ID property.

Returns
the ID property.

References id.

Referenced by update().

+ Here is the caller graph for this function:

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

Get linked Experimenter.

Returns
the linked Experimenter. The pointer may be null.

References experimenter.

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

Get linked Experimenter.

Returns
the linked Experimenter. The pointer may be null.

References experimenter.

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

Get linked Image.

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

References images.

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

Get the linked Image list.

Returns
a reference to the list.

References images.

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

Get MicrobeamManipulation.

Parameters
indexthe index number of the MicrobeamManipulation.
Returns
the MicrobeamManipulation.
Exceptions
std::out_of_rangeif the index is invalid.

References microbeamManipulations.

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

Get MicrobeamManipulation.

Parameters
indexthe index number of the MicrobeamManipulation.
Returns
the MicrobeamManipulation.
Exceptions
std::out_of_rangeif the index is invalid.

References microbeamManipulations.

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

Get the MicrobeamManipulation list.

Returns
a reference to the list.

References microbeamManipulations.

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

Get the MicrobeamManipulation list.

Returns
a reference to the list.

References microbeamManipulations.

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

Get the Type property.

Returns
the Type property.

References type.

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

Get the Type property.

Returns
the Type property.

References type.

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

Get the XML namespace for this model object.

Returns
the XML namespace.

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

bool ome::xml::model::Experiment::link ( ome::compat::shared_ptr< Reference > &  reference,
ome::compat::shared_ptr< ome::xml::model::OMEModelObject > &  object 
)

Link a given OME model object to this model object.

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

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

Link Experimenter.

Parameters
experimenterthe Experimenter to link.

References experimenter.

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

Link Image.

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

References images, and type.

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

+ Here is the caller graph for this function:

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

Remove MicrobeamManipulation.

Parameters
microbeamManipulationthe MicrobeamManipulation to remove.
Todo:

Doesn't the removal break the indexing?

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

References microbeamManipulations.

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

Set the Description property.

Parameters
descriptionthe value to set.

References description.

Referenced by update().

+ Here is the caller graph for this function:

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

Set the ID property.

Parameters
idthe value to set.

References id.

Referenced by update().

+ Here is the caller graph for this function:

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

Set linked Image.

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

References images.

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

Set MicrobeamManipulation.

Parameters
indexthe index number of the MicrobeamManipulation.
microbeamManipulationthe MicrobeamManipulation to set.
Exceptions
std::out_of_rangeif the index is invalid.

References microbeamManipulations.

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

Set the Type property.

Parameters
typethe value to set.

References type.

Referenced by update().

+ Here is the caller graph for this function:

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

Get size of linked Image list.

Returns
the size of the list.

References images.

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

Get size of linked MicrobeamManipulation list.

Returns
the size of the list.

References microbeamManipulations.

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

Unlink Experimenter.

Parameters
experimenterthe Experimenter to unlink.
Todo:
This method is fairly pointless since it's equivalent to linking a null pointer. It could call link(0) internally.
bool ome::xml::model::Experiment::unlinkImage ( const ome::compat::shared_ptr< ome::xml::model::Image > &  image_BackReference)

Unlink Image.

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

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

Doesn't the removal break the indexing?

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

References images.

void ome::xml::model::Experiment::update ( const common::xml::dom::Element element,
ome::xml::model::OMEModel model 
)
virtual

Update the object hierarchy recursively from an XML DOM tree.

Note
No properties are removed, only added or updated.
Parameters
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 addMicrobeamManipulation(), ome::xml::model::OMEModel::addModelObject(), ome::xml::model::OMEModel::addReference(), ome::xml::model::MicrobeamManipulation::create(), ome::common::xml::dom::Element::getAttribute(), ome::xml::model::detail::OMEModelObject::getChildrenByTagName(), getID(), ome::common::xml::dom::Element::getTagName(), ome::common::xml::dom::Element::hasAttribute(), ome::xml::model::detail::OMEModelObject::logger, setDescription(), setID(), setType(), ome::xml::model::detail::OMEModelObject::stripNamespacePrefix(), ome::xml::model::detail::OMEModelObject::update(), and validElementName().

bool ome::xml::model::Experiment::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().

+ Here is the caller graph for this function:


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