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ome::xml::model::WellSample Class Reference

WellSample model object. More...

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

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## Classes
class | Impl
| Private implementation details of WellSample model object. More...

## Public Member Functions
| WellSample ()
| Default constructor.
| WellSample (const WellSample &copy)
| Copy constructor. More...
virtual | ~WellSample ()
| Destructor.
const std::string & | elementName () const
| Get the element name of this model object. More...
bool | validElementName (const std::string &name) const
| Check if a given element name is valid for processing by this model object. More...
virtual void | update (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
| Update the object hierarchy recursively from an XML DOM tree. More...
bool | link (ome::compat::shared_ptr< Reference > &reference, ome::compat::shared_ptr< ome::xml::model::OMEModelObject > &object)
| Link a given OME model object to this model object. More...
const ome::xml::model::primitives::NonNegativeInteger & | getIndex () const
| Get the Index property. More...
void | setIndex (const ome::xml::model::primitives::NonNegativeInteger &index)
| Set the Index property. More...
ome::compat::shared_ptr< double > | getPositionX ()
| Get the PositionX property. More...
const ome::compat::shared_ptr< double > | getPositionX () const
| Get the PositionX property. More...
void | setPositionX (ome::compat::shared_ptr< double > &positionX)
| Set the PositionX property. More...
ome::compat::shared_ptr< double > | getPositionY ()
| Get the PositionY property. More...
const ome::compat::shared_ptr< double > | getPositionY () const
| Get the PositionY property. More...
void | setPositionY (ome::compat::shared_ptr< double > &positionY)
| Set the PositionY property. More...
const std::string & | getID () const
| Get the ID property. More...
void | setID (const std::string &id)
| Set the ID property. More...
ome::compat::shared_ptr< ome::xml::model::primitives::Timestamp > | getTimepoint ()
| Get the Timepoint property. More...
const ome::compat::shared_ptr< ome::xml::model::primitives::Timestamp > | getTimepoint () const
| Get the Timepoint property. More...
void | setTimepoint (ome::compat::shared_ptr< ome::xml::model::primitives::Timestamp > &timepoint)
| Set the Timepoint property. More...
ome::compat::weak_ptr< ome::xml::model::Image > | getLinkedImage ()
| Get linked Image. More...
const ome::compat::weak_ptr< ome::xml::model::Image > | getLinkedImage () const
| Get linked Image. More...
void | linkImage (ome::compat::shared_ptr< ome::xml::model::Image > &image)
| Link Image. More...
void | unlinkImage (ome::compat::shared_ptr< ome::xml::model::Image > &image)
| Unlink Image. More...
OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type | sizeOfLinkedAnnotationList () const
| Get size of linked Annotation list. More...
OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type | getLinkedAnnotationList () const
| Get the linked Annotation list. More...
const ome::compat::weak_ptr< ome::xml::model::Annotation > & | getLinkedAnnotation (OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type index) const
| Get linked Annotation. More...
const ome::compat::weak_ptr< ome::xml::model::Annotation > & | setLinkedAnnotation (OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type index, const ome::compat::shared_ptr< ome::xml::model::Annotation > &annotation)
| Set linked Annotation. More...
bool | linkAnnotation (const ome::compat::shared_ptr< ome::xml::model::Annotation > &annotation)
| Link Annotation. More...
bool | unlinkAnnotation (const ome::compat::shared_ptr< ome::xml::model::Annotation > &annotation)
| Unlink Annotation. More...
OMEModelObject::indexed_container< ome::xml::model::PlateAcquisition, ome::compat::weak_ptr >::type::size_type | sizeOfLinkedPlateAcquisitionList () const
| Get size of linked PlateAcquisition list. More...
OMEModelObject::indexed_container< ome::xml::model::PlateAcquisition, ome::compat::weak_ptr >::type | getLinkedPlateAcquisitionList () const
| Get the linked PlateAcquisition list. More...
const ome::compat::weak_ptr< ome::xml::model::PlateAcquisition > & | getLinkedPlateAcquisition (OMEModelObject::indexed_container< ome::xml::model::PlateAcquisition, ome::compat::weak_ptr >::type::size_type index) const
| Get linked PlateAcquisition. More...
const ome::compat::weak_ptr< ome::xml::model::PlateAcquisition > & | setLinkedPlateAcquisition (OMEModelObject::indexed_container< ome::xml::model::PlateAcquisition, ome::compat::weak_ptr >::type::size_type index, const ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > &plateAcquisition_BackReference)
| Set linked PlateAcquisition. More...
bool | linkPlateAcquisition (const ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > &plateAcquisition_BackReference)
| Link PlateAcquisition. More...
bool | unlinkPlateAcquisition (const ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > &plateAcquisition_BackReference)
| Unlink PlateAcquisition. More...
ome::compat::weak_ptr< ome::xml::model::Well > | getWell ()
| Get the Well property. More...
const ome::compat::weak_ptr< ome::xml::model::Well > | getWell () const
| Get the Well property. More...
void | setWell (ome::compat::weak_ptr< ome::xml::model::Well > &well_BackReference)
| Set the Well property. More...
virtual common::xml::dom::Element | asXMLElement (common::xml::dom::Document &document) const
| Transform the object hierarchy rooted at this element to XML. More...
const std::string & | getXMLNamespace () const
| Get the XML namespace for this model object. More...
Public Member Functions inherited from ome::xml::model::detail::OMEModelObject
virtual | ~OMEModelObject ()
| Destructor.
virtual void | update (const common::xml::dom::Element &element,::ome::xml::model::OMEModel &model)
| Update the object hierarchy recursively from an XML DOM tree. More...
virtual bool | link (ome::compat::shared_ptr< Reference > &reference, ome::compat::shared_ptr< ::ome::xml::model::OMEModelObject > &object)
| Link a given OME model object to this model object. More...
Public Member Functions inherited from ome::xml::model::OMEModelObject
virtual bool | link (ome::compat::shared_ptr< Reference > &reference, ome::compat::shared_ptr< OMEModelObject > &object)=0
| Link a given OME model object to this model object. More...

## Static Public Member Functions
static ome::compat::shared_ptr< WellSample > | create (const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
| Create a WellSample model object from DOM element. More...
Static Public Member Functions inherited from ome::xml::model::detail::OMEModelObject
static std::vector< common::xml::dom::Element > | getChildrenByTagName (const common::xml::dom::Element &parent, const std::string &name)
| Retrieve all the children of an element that have a given tag name. More...
static std::string | stripNamespacePrefix (const std::string &value)
| Strip the namespace prefix from a tag name. More...

## Protected Member Functions
virtual common::xml::dom::Element | asXMLElementInternal (common::xml::dom::Document &document, common::xml::dom::Element &element) const
| Transform the object hierarchy rooted at this element to XML. More...
Protected Member Functions inherited from ome::xml::model::detail::OMEModelObject
| OMEModelObject (const std::string &objectType="OMEModelObject")
| Constructor.
| OMEModelObject (const OMEModelObject &copy)
| Copy constructor. More...
template<class C , typename T >
bool | contains (const C &container, const ome::compat::shared_ptr< T > &element)
| Check if a container contains a particular element. More...
Protected Member Functions inherited from ome::xml::model::OMEModelObject
| OMEModelObject ()
| Constructor.

## Private Attributes
ome::compat::shared_ptr< Impl > | impl
| Private implementation details.

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

## Detailed Description

WellSample model object.

## Constructor & Destructor Documentation

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

Copy constructor.

Parameters

  copy | the WellSample to copy.

## Member Function Documentation

common::xml::dom::Element ome::xml::model::WellSample::asXMLElement | ( | common::xml::dom::Document & | document | ) | const
| virtual

Transform the object hierarchy rooted at this element to XML.

Parameters

  document | document for element creation

Returns
  an XML DOM tree root element for this model object.

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

References asXMLElementInternal(), ome::common::xml::dom::Document::createElementNS(), and getXMLNamespace().

common::xml::dom::Element ome::xml::model::WellSample::asXMLElementInternal | ( | common::xml::dom::Document & | document,
|  | common::xml::dom::Element & | element
| ) |  | const
| protected virtual

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

Create a WellSample model object from DOM element.

Parameters

  element | root of the XML DOM tree to from which to construct the model object graph.
  model | handler for the OME model used to track instances and references seen during the update.

Exceptions

  EnumerationException | if there is an error instantiating an enumeration during model object creation, or ModelException if there are any consistency or validity errors found during processing.

Returns
  a new model object.

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

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

Get the element name of this model object.

This will be the most-derived class name.

Returns
  the element type.

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

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

Get the ID property.

Returns
  the ID property.

References impl.

Referenced by update().

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

Get the Index property.

Returns
  the Index property.

References impl.

const ome::compat::weak_ptr< ome::xml::model::Annotation > & ome::xml::model::WellSample::getLinkedAnnotation | ( | OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type | index | ) | const

Get linked Annotation.

Parameters

  index | the index number of the Annotation.

Returns
  a weak pointer to the Annotation.

Exceptions

  std::out_of_range | if the index is invalid.

References impl.

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

Get the linked Annotation list.

Returns
  a reference to the list.

References impl.

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

Get linked Image.

Returns
  the linked Image. The pointer may be null.

References impl.

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

Get linked Image.

Returns
  the linked Image. The pointer may be null.

References impl.

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

Get linked PlateAcquisition.

Parameters

  index | the index number of the PlateAcquisition.

Returns
  a weak pointer to the PlateAcquisition.

Exceptions

  std::out_of_range | if the index is invalid.

References impl.

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

Get the linked PlateAcquisition list.

Returns
  a reference to the list.

References impl.

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

Get the PositionX property.

Returns
  the PositionX property.

References impl.

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

Get the PositionX property.

Returns
  the PositionX property.

References impl.

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

Get the PositionY property.

Returns
  the PositionY property.

References impl.

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

Get the PositionY property.

Returns
  the PositionY property.

References impl.

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

Get the Timepoint property.

Returns
  the Timepoint property.

References impl.

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

Get the Timepoint property.

Returns
  the Timepoint property.

References impl.

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

Get the Well property.

Returns
  the Well property.

References impl.

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

Get the Well property.

Returns
  the Well property.

References impl.

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

Get the XML namespace for this model object.

Returns
  the XML namespace.

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

Referenced by asXMLElement(), and asXMLElementInternal().

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

Link a given OME model object to this model object.

Parameters

  reference | type qualifier for the reference. This should be the corresponding reference type for object. If, for example, object is of type Image, reference must be of type ImageRef.
  object | Model object to link to.

Returns
  `true` if this model object was able to handle the reference, otherwise `false`.

Todo:
  the use of reference to provide type information for the type of object is unconventional and quite possibly unnecessary–a simple string or type_info would suffice for what it's being used for, if it's needed at all. Is this true for all cases? The implementation also needs to do strict checking of the object type; it's not currently failing if it's of the wrong type. This applies to all generated model objects implementing this interface.

Todo:
  This bit is silly; why do we have two dynamic_casts here.

Todo:
  This bit is silly; why do we have two dynamic_casts here.

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

bool ome::xml::model::WellSample::linkAnnotation | ( | const ome::compat::shared_ptr< ome::xml::model::Annotation > & | annotation | ) |

Link Annotation.

Parameters

  annotation | the Annotation to link.

Returns
  `true` if the object was added to the internal annotationLinks list, otherwise `false`.

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

References impl.

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

Link Image.

Parameters

  image | the Image to link.

References impl.

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

Link PlateAcquisition.

Parameters

  plateAcquisition_BackReference | the PlateAcquisition to link.

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

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

References impl.

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

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

Set the ID property.

Parameters

  id | the value to set.

References impl.

Referenced by update().

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

Set the Index property.

Parameters

  index | the value to set.

References impl.

Referenced by update().

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const ome::compat::weak_ptr< ome::xml::model::Annotation > & ome::xml::model::WellSample::setLinkedAnnotation | ( | OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type | index,
|  | const ome::compat::shared_ptr< ome::xml::model::Annotation > & | annotation
| ) |  |

Set linked Annotation.

Note
  The index must be valid.

Parameters

  index | the index number of the Annotation.
  annotation | the Annotation to set.

Returns
  a weak pointer to the Annotation.

Exceptions

  std::out_of_range | if the index is invalid.

References impl.

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

Set linked PlateAcquisition.

Note
  The index must be valid.

Parameters

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

Returns
  a weak pointer to the PlateAcquisition.

Exceptions

  std::out_of_range | if the index is invalid.

References impl.

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

Set the PositionX property.

Parameters

  positionX | the value to set.

References impl.

Referenced by update().

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

Set the PositionY property.

Parameters

  positionY | the value to set.

References impl.

Referenced by update().

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

Set the Timepoint property.

Parameters

  timepoint | the value to set.

References impl.

Referenced by update().

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

Set the Well property.

Parameters

  well_BackReference | the value to set.

References impl.

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

Get size of linked Annotation list.

Returns
  the size of the list.

References impl.

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

Get size of linked PlateAcquisition list.

Returns
  the size of the list.

References impl.

bool ome::xml::model::WellSample::unlinkAnnotation | ( | const ome::compat::shared_ptr< ome::xml::model::Annotation > & | annotation | ) |

Unlink Annotation.

Parameters

  annotation | the Annotation to unlink.

Returns
  `true` if the Annotation was unlinked, otherwise `false` if the Annotation was not linked and could hence not be unlinked.

Todo:

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

  Doesn't the removal break the indexing?

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

References impl.

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

Unlink Image.

Parameters

  image | the Image to unlink.

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

References impl.

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

Unlink PlateAcquisition.

Parameters

  plateAcquisition_BackReference | the PlateAcquisition to unlink.

Returns
  `true` if the PlateAcquisition was unlinked, otherwise `false` if the PlateAcquisition was not linked and could hence not be unlinked.

Todo:

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

  Doesn't the removal break the indexing?

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

References impl.

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

Update the object hierarchy recursively from an XML DOM tree.

Note
  No properties are removed, only added or updated.

Parameters

  element | root of the XML DOM tree to from which to construct the model object graph.
  model | handler for the OME model used to track instances and references seen during the update.

Exceptions

  EnumerationException | if there is an error instantiating an enumeration during model object creation, or ModelException if there are any consistency or validity errors found during processing.

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

References ome::xml::model::OMEModel::addModelObject(), ome::xml::model::OMEModel::addReference(), ome::common::xml::dom::Element::getAttribute(), ome::xml::model::detail::OMEModelObject::getChildrenByTagName(), getID(), ome::common::xml::dom::Element::getTagName(), ome::common::xml::dom::Element::hasAttribute(), ome::xml::model::detail::OMEModelObject::logger, setID(), setIndex(), setPositionX(), setPositionY(), setTimepoint(), ome::xml::model::detail::OMEModelObject::stripNamespacePrefix(), ome::xml::model::detail::OMEModelObject::update(), and validElementName().

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

  name | the 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:

- ome/xml/model/WellSample.h
- ome/xml/model/WellSample.cpp