bioformats  5.1.0
Plate.h
1 /*
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3  * OME-XML C++ library for working with OME-XML metadata structures.
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38 
39 /*─────────────────────────────────────────────────────────────────────────────
40  *
41  * THIS IS AUTOMATICALLY GENERATED CODE. DO NOT MODIFY.
42  *
43  *─────────────────────────────────────────────────────────────────────────────
44  */
45 
46 #ifndef OME_XML_MODEL_PLATE_H
47 #define OME_XML_MODEL_PLATE_H
48 
49 #include <algorithm>
50 #include <list>
51 #include <stdexcept>
52 #include <string>
53 #include <vector>
54 
55 #include <ome/common/log.h>
56 
57 #include <ome/common/xml/dom/Document.h>
58 #include <ome/common/xml/dom/Element.h>
59 #include <ome/common/xml/dom/Node.h>
60 #include <ome/common/xml/dom/NodeList.h>
61 
62 #include <ome/xml/model/detail/OMEModelObject.h>
63 #include <ome/xml/model/enums/NamingConvention.h>
64 #include <ome/xml/model/primitives/NonNegativeInteger.h>
65 #include <ome/xml/model/primitives/PositiveInteger.h>
66 
67 namespace ome
68 {
69  namespace xml
70  {
71  namespace model
72  {
73 
74  // Forward declarations.
75  class Annotation;
76  class OMEModel;
77  class PlateAcquisition;
78  class Screen;
79  class Well;
80 
85  {
86  private:
88  ome::compat::shared_ptr<std::string> status;
90  ome::compat::shared_ptr<ome::xml::model::primitives::PositiveInteger> rows;
92  ome::compat::shared_ptr<std::string> externalIdentifier;
94  ome::compat::shared_ptr<ome::xml::model::enums::NamingConvention> rowNamingConvention;
96  ome::compat::shared_ptr<ome::xml::model::enums::NamingConvention> columnNamingConvention;
98  ome::compat::shared_ptr<ome::xml::model::primitives::NonNegativeInteger> fieldIndex;
100  ome::compat::shared_ptr<double> wellOriginY;
102  ome::compat::shared_ptr<double> wellOriginX;
104  std::string id;
106  ome::compat::shared_ptr<ome::xml::model::primitives::PositiveInteger> columns;
108  ome::compat::shared_ptr<std::string> name;
110  ome::compat::shared_ptr<std::string> description;
112  std::vector<ome::compat::shared_ptr<ome::xml::model::Well> > wells;
116  std::vector<ome::compat::shared_ptr<ome::xml::model::PlateAcquisition> > plateAcquisitions;
119 
120  public:
122  Plate ();
123 
129  Plate (const Plate& copy);
130 
132  virtual
133  ~Plate ();
134 
135 
136 
151  static ome::compat::shared_ptr< Plate>
152  create(const common::xml::dom::Element& element,
154 
155  // Documented in superclass.
156  const std::string&
157  elementName() const;
158 
159  // Documented in superclass.
160  bool
161  validElementName(const std::string& name) const;
162 
163 
164  // -- OMEModelObject API methods --
165 
167  virtual void
168  update(const common::xml::dom::Element& element,
170 
171  public:
172  // -- Plate API methods --
173 
175  bool
176  link (ome::compat::shared_ptr<Reference>& reference,
177  ome::compat::shared_ptr< ome::xml::model::OMEModelObject>& object);
178 
184  ome::compat::shared_ptr<std::string>
185  getStatus ();
186 
192  const ome::compat::shared_ptr<std::string>
193  getStatus () const;
194 
200  void
201  setStatus (ome::compat::shared_ptr<std::string>& status);
202 
208  ome::compat::shared_ptr<ome::xml::model::primitives::PositiveInteger>
209  getRows ();
210 
216  const ome::compat::shared_ptr<ome::xml::model::primitives::PositiveInteger>
217  getRows () const;
218 
224  void
225  setRows (ome::compat::shared_ptr<ome::xml::model::primitives::PositiveInteger>& rows);
226 
232  ome::compat::shared_ptr<std::string>
234 
240  const ome::compat::shared_ptr<std::string>
241  getExternalIdentifier () const;
242 
248  void
249  setExternalIdentifier (ome::compat::shared_ptr<std::string>& externalIdentifier);
250 
256  ome::compat::shared_ptr<ome::xml::model::enums::NamingConvention>
258 
264  const ome::compat::shared_ptr<ome::xml::model::enums::NamingConvention>
265  getRowNamingConvention () const;
266 
272  void
273  setRowNamingConvention (ome::compat::shared_ptr<ome::xml::model::enums::NamingConvention>& rowNamingConvention);
274 
280  ome::compat::shared_ptr<ome::xml::model::enums::NamingConvention>
282 
288  const ome::compat::shared_ptr<ome::xml::model::enums::NamingConvention>
289  getColumnNamingConvention () const;
290 
296  void
297  setColumnNamingConvention (ome::compat::shared_ptr<ome::xml::model::enums::NamingConvention>& columnNamingConvention);
298 
304  ome::compat::shared_ptr<ome::xml::model::primitives::NonNegativeInteger>
305  getFieldIndex ();
306 
312  const ome::compat::shared_ptr<ome::xml::model::primitives::NonNegativeInteger>
313  getFieldIndex () const;
314 
320  void
321  setFieldIndex (ome::compat::shared_ptr<ome::xml::model::primitives::NonNegativeInteger>& fieldIndex);
322 
328  ome::compat::shared_ptr<double>
329  getWellOriginY ();
330 
336  const ome::compat::shared_ptr<double>
337  getWellOriginY () const;
338 
344  void
345  setWellOriginY (ome::compat::shared_ptr<double>& wellOriginY);
346 
352  ome::compat::shared_ptr<double>
353  getWellOriginX ();
354 
360  const ome::compat::shared_ptr<double>
361  getWellOriginX () const;
362 
368  void
369  setWellOriginX (ome::compat::shared_ptr<double>& wellOriginX);
370 
376  const std::string&
377  getID () const;
378 
384  void
385  setID (const std::string& id);
386 
392  ome::compat::shared_ptr<ome::xml::model::primitives::PositiveInteger>
393  getColumns ();
394 
400  const ome::compat::shared_ptr<ome::xml::model::primitives::PositiveInteger>
401  getColumns () const;
402 
408  void
409  setColumns (ome::compat::shared_ptr<ome::xml::model::primitives::PositiveInteger>& columns);
410 
416  ome::compat::shared_ptr<std::string>
417  getName ();
418 
424  const ome::compat::shared_ptr<std::string>
425  getName () const;
426 
432  void
433  setName (ome::compat::shared_ptr<std::string>& name);
434 
440  ome::compat::shared_ptr<std::string>
441  getDescription ();
442 
448  const ome::compat::shared_ptr<std::string>
449  getDescription () const;
450 
456  void
457  setDescription (ome::compat::shared_ptr<std::string>& description);
458 
464  std::vector<ome::compat::shared_ptr<ome::xml::model::Well> >::size_type
465  sizeOfWellList () const;
466 
473  std::vector<ome::compat::shared_ptr<ome::xml::model::Well> >&
474  getWellList ();
475 
482  const std::vector<ome::compat::shared_ptr<ome::xml::model::Well> >&
483  getWellList () const;
484 
492  ome::compat::shared_ptr<ome::xml::model::Well>&
493  getWell (std::vector<ome::compat::shared_ptr<ome::xml::model::Well> >::size_type index);
494 
502  const ome::compat::shared_ptr<ome::xml::model::Well>&
503  getWell (std::vector<ome::compat::shared_ptr<ome::xml::model::Well> >::size_type index) const;
504 
512  void
513  setWell (std::vector<ome::compat::shared_ptr<ome::xml::model::Well> >::size_type index,
514  ome::compat::shared_ptr<ome::xml::model::Well>& well);
515 
524  void
525  addWell (ome::compat::shared_ptr<ome::xml::model::Well>& well);
526 
536  void
537  removeWell (ome::compat::shared_ptr<ome::xml::model::Well>& well);
538 
546 
553  getLinkedAnnotationList () const;
554 
562  const ome::compat::weak_ptr<ome::xml::model::Annotation>&
564 
575  const ome::compat::weak_ptr<ome::xml::model::Annotation>&
577  const ome::compat::shared_ptr<ome::xml::model::Annotation>& annotation);
578 
589  bool
590  linkAnnotation (const ome::compat::shared_ptr<ome::xml::model::Annotation>& annotation);
591 
607  bool
608  unlinkAnnotation (const ome::compat::shared_ptr<ome::xml::model::Annotation>& annotation);
609 
615  std::vector<ome::compat::shared_ptr<ome::xml::model::PlateAcquisition> >::size_type
617 
624  std::vector<ome::compat::shared_ptr<ome::xml::model::PlateAcquisition> >&
626 
633  const std::vector<ome::compat::shared_ptr<ome::xml::model::PlateAcquisition> >&
634  getPlateAcquisitionList () const;
635 
643  ome::compat::shared_ptr<ome::xml::model::PlateAcquisition>&
644  getPlateAcquisition (std::vector<ome::compat::shared_ptr<ome::xml::model::PlateAcquisition> >::size_type index);
645 
653  const ome::compat::shared_ptr<ome::xml::model::PlateAcquisition>&
654  getPlateAcquisition (std::vector<ome::compat::shared_ptr<ome::xml::model::PlateAcquisition> >::size_type index) const;
655 
663  void
664  setPlateAcquisition (std::vector<ome::compat::shared_ptr<ome::xml::model::PlateAcquisition> >::size_type index,
665  ome::compat::shared_ptr<ome::xml::model::PlateAcquisition>& plateAcquisition);
666 
675  void
676  addPlateAcquisition (ome::compat::shared_ptr<ome::xml::model::PlateAcquisition>& plateAcquisition);
677 
687  void
688  removePlateAcquisition (ome::compat::shared_ptr<ome::xml::model::PlateAcquisition>& plateAcquisition);
689 
696  sizeOfLinkedScreenList () const;
697 
704  getLinkedScreenList () const;
705 
713  const ome::compat::weak_ptr<ome::xml::model::Screen>&
715 
726  const ome::compat::weak_ptr<ome::xml::model::Screen>&
728  const ome::compat::shared_ptr<ome::xml::model::Screen>& screen_BackReference);
729 
740  bool
741  linkScreen (const ome::compat::shared_ptr<ome::xml::model::Screen>& screen_BackReference);
742 
758  bool
759  unlinkScreen (const ome::compat::shared_ptr<ome::xml::model::Screen>& screen_BackReference);
760 
761 
764  asXMLElement (common::xml::dom::Document& document) const;
765 
766 
767  protected:
768  // Documented in base class.
771  common::xml::dom::Element& element) const;
772 
773  public:
774  // Documented in superclass.
775  const std::string&
776  getXMLNamespace() const;
777  };
778 
779  }
780  }
781 }
782 
783 #endif // OME_XML_MODEL_PLATE_H
784 
785 /*
786  * Local Variables:
787  * mode:C++
788  * End:
789  */
OME model interface (abstract top-level container)
Definition: OMEModel.h:62
void setWell(std::vector< ome::compat::shared_ptr< ome::xml::model::Well > >::size_type index, ome::compat::shared_ptr< ome::xml::model::Well > &well)
Set Well.
Definition: Plate.cpp:701
bool linkScreen(const ome::compat::shared_ptr< ome::xml::model::Screen > &screen_BackReference)
Link Screen.
Definition: Plate.cpp:875
std::vector< ome::compat::shared_ptr< ome::xml::model::Well > >::size_type sizeOfWellList() const
Get size of linked Well list.
Definition: Plate.cpp:671
virtual ~Plate()
Destructor.
Definition: Plate.cpp:201
OMEModelObject::indexed_container< ome::xml::model::Screen, ome::compat::weak_ptr >::type screenLinks
Screen_BackReference back reference (occurs more than once)
Definition: Plate.h:118
ome::compat::shared_ptr< double > wellOriginX
WellOriginX property.
Definition: Plate.h:102
Plate model object.
Definition: Plate.h:84
std::vector< ome::compat::shared_ptr< ome::xml::model::Well > > wells
Well property (occurs more than once)
Definition: Plate.h:112
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.
Definition: Plate.cpp:912
bool unlinkAnnotation(const ome::compat::shared_ptr< ome::xml::model::Annotation > &annotation)
Unlink Annotation.
Definition: Plate.cpp:771
const std::string & getID() const
Get the ID property.
Definition: Plate.cpp:594
virtual void update(const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
Update the object hierarchy recursively from an XML DOM tree.
Definition: Plate.cpp:231
const std::string & elementName() const
Get the element name of this model object.
Definition: Plate.cpp:215
void removeWell(ome::compat::shared_ptr< ome::xml::model::Well > &well)
Remove Well.
Definition: Plate.cpp:718
void setID(const std::string &id)
Set the ID property.
Definition: Plate.cpp:601
OMEModelObject::indexed_container< ome::xml::model::Screen, ome::compat::weak_ptr >::type getLinkedScreenList() const
Get the linked Screen list.
Definition: Plate.cpp:853
virtual common::xml::dom::Element asXMLElement(common::xml::dom::Document &document) const
Transform the object hierarchy rooted at this element to XML.
Definition: Plate.cpp:905
const ome::compat::weak_ptr< ome::xml::model::Screen > & getLinkedScreen(OMEModelObject::indexed_container< ome::xml::model::Screen, ome::compat::weak_ptr >::type::size_type index) const
Get linked Screen.
Definition: Plate.cpp:859
OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type annotationLinks
AnnotationRef reference (occurs more than once)
Definition: Plate.h:114
std::vector< ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > >::size_type sizeOfPlateAcquisitionList() const
Get size of linked PlateAcquisition list.
Definition: Plate.cpp:789
ome::compat::shared_ptr< ome::xml::model::primitives::PositiveInteger > rows
Rows property.
Definition: Plate.h:90
DOM Document wrapper.
Definition: Document.h:80
DOM Element wrapper.
Definition: Element.h:66
OME model object (concrete implementation).
Definition: OMEModelObject.h:64
boost::multi_index_container< Ptr< T >, boost::multi_index::indexed_by< boost::multi_index::random_access<>, boost::multi_index::ordered_unique< boost::multi_index::identity< Ptr< T > >, ome::compat::owner_less< Ptr< T > > > > > type
Multi-index container type.
Definition: OMEModelObject.h:94
const ome::compat::weak_ptr< ome::xml::model::Screen > & setLinkedScreen(OMEModelObject::indexed_container< ome::xml::model::Screen, ome::compat::weak_ptr >::type::size_type index, const ome::compat::shared_ptr< ome::xml::model::Screen > &screen_BackReference)
Set linked Screen.
Definition: Plate.cpp:865
OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type getLinkedAnnotationList() const
Get the linked Annotation list.
Definition: Plate.cpp:735
ome::compat::shared_ptr< std::string > description
Description property.
Definition: Plate.h:110
void addPlateAcquisition(ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > &plateAcquisition)
Add PlateAcquisition.
Definition: Plate.cpp:828
ome::compat::shared_ptr< ome::xml::model::primitives::NonNegativeInteger > fieldIndex
FieldIndex property.
Definition: Plate.h:98
bool linkAnnotation(const ome::compat::shared_ptr< ome::xml::model::Annotation > &annotation)
Link Annotation.
Definition: Plate.cpp:757
ome::compat::shared_ptr< ome::xml::model::primitives::PositiveInteger > getColumns()
Get the Columns property.
Definition: Plate.cpp:608
void setRowNamingConvention(ome::compat::shared_ptr< ome::xml::model::enums::NamingConvention > &rowNamingConvention)
Set the RowNamingConvention property.
Definition: Plate.cpp:503
void setRows(ome::compat::shared_ptr< ome::xml::model::primitives::PositiveInteger > &rows)
Set the Rows property.
Definition: Plate.cpp:461
ome::compat::shared_ptr< ome::xml::model::enums::NamingConvention > getRowNamingConvention()
Get the RowNamingConvention property.
Definition: Plate.cpp:489
Plate()
Default constructor.
Definition: Plate.cpp:152
void setWellOriginY(ome::compat::shared_ptr< double > &wellOriginY)
Set the WellOriginY property.
Definition: Plate.cpp:566
ome::compat::shared_ptr< std::string > getDescription()
Get the Description property.
Definition: Plate.cpp:650
void setDescription(ome::compat::shared_ptr< std::string > &description)
Set the Description property.
Definition: Plate.cpp:664
void setExternalIdentifier(ome::compat::shared_ptr< std::string > &externalIdentifier)
Set the ExternalIdentifier property.
Definition: Plate.cpp:482
std::vector< ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > > plateAcquisitions
PlateAcquisition property (occurs more than once)
Definition: Plate.h:116
void setStatus(ome::compat::shared_ptr< std::string > &status)
Set the Status property.
Definition: Plate.cpp:440
ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > & getPlateAcquisition(std::vector< ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > >::size_type index)
Get PlateAcquisition.
Definition: Plate.cpp:807
OMEModelObject::indexed_container< ome::xml::model::Screen, ome::compat::weak_ptr >::type::size_type sizeOfLinkedScreenList() const
Get size of linked Screen list.
Definition: Plate.cpp:847
Multi-index container for efficient ordered insertion and deletion of model object references...
Definition: OMEModelObject.h:85
ome::compat::shared_ptr< double > getWellOriginY()
Get the WellOriginY property.
Definition: Plate.cpp:552
std::vector< ome::compat::shared_ptr< ome::xml::model::Well > > & getWellList()
Get the Well list.
Definition: Plate.cpp:677
ome::compat::shared_ptr< ome::xml::model::primitives::PositiveInteger > columns
Columns property.
Definition: Plate.h:106
Open Microscopy Environment C++ implementation.
Definition: CoreMetadata.cpp:40
ome::compat::shared_ptr< std::string > status
Status property.
Definition: Plate.h:88
ome::compat::shared_ptr< std::string > getName()
Get the Name property.
Definition: Plate.cpp:629
void addWell(ome::compat::shared_ptr< ome::xml::model::Well > &well)
Add Well.
Definition: Plate.cpp:710
ome::compat::shared_ptr< ome::xml::model::primitives::PositiveInteger > getRows()
Get the Rows property.
Definition: Plate.cpp:447
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.
Definition: Plate.cpp:395
std::string id
ID property.
Definition: Plate.h:104
void setColumns(ome::compat::shared_ptr< ome::xml::model::primitives::PositiveInteger > &columns)
Set the Columns property.
Definition: Plate.cpp:622
void setColumnNamingConvention(ome::compat::shared_ptr< ome::xml::model::enums::NamingConvention > &columnNamingConvention)
Set the ColumnNamingConvention property.
Definition: Plate.cpp:524
void setFieldIndex(ome::compat::shared_ptr< ome::xml::model::primitives::NonNegativeInteger > &fieldIndex)
Set the FieldIndex property.
Definition: Plate.cpp:545
ome::compat::shared_ptr< ome::xml::model::enums::NamingConvention > rowNamingConvention
RowNamingConvention property.
Definition: Plate.h:94
ome::compat::shared_ptr< std::string > getStatus()
Get the Status property.
Definition: Plate.cpp:426
ome::compat::shared_ptr< std::string > getExternalIdentifier()
Get the ExternalIdentifier property.
Definition: Plate.cpp:468
ome::compat::shared_ptr< ome::xml::model::enums::NamingConvention > columnNamingConvention
ColumnNamingConvention property.
Definition: Plate.h:96
void removePlateAcquisition(ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > &plateAcquisition)
Remove PlateAcquisition.
Definition: Plate.cpp:836
ome::compat::shared_ptr< ome::xml::model::enums::NamingConvention > getColumnNamingConvention()
Get the ColumnNamingConvention property.
Definition: Plate.cpp:510
ome::compat::shared_ptr< ome::xml::model::primitives::NonNegativeInteger > getFieldIndex()
Get the FieldIndex property.
Definition: Plate.cpp:531
ome::compat::shared_ptr< double > getWellOriginX()
Get the WellOriginX property.
Definition: Plate.cpp:573
void setWellOriginX(ome::compat::shared_ptr< double > &wellOriginX)
Set the WellOriginX property.
Definition: Plate.cpp:587
bool validElementName(const std::string &name) const
Check if a given element name is valid for processing by this model object.
Definition: Plate.cpp:222
ome::compat::shared_ptr< std::string > name
Name property.
Definition: Plate.h:108
void setName(ome::compat::shared_ptr< std::string > &name)
Set the Name property.
Definition: Plate.cpp:643
bool unlinkScreen(const ome::compat::shared_ptr< ome::xml::model::Screen > &screen_BackReference)
Unlink Screen.
Definition: Plate.cpp:888
void setPlateAcquisition(std::vector< ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > >::size_type index, ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > &plateAcquisition)
Set PlateAcquisition.
Definition: Plate.cpp:819
std::vector< ome::compat::shared_ptr< ome::xml::model::PlateAcquisition > > & getPlateAcquisitionList()
Get the PlateAcquisition list.
Definition: Plate.cpp:795
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.
Definition: Plate.cpp:747
const std::string & getXMLNamespace() const
Get the XML namespace for this model object.
Definition: Plate.cpp:1127
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.
Definition: Plate.cpp:741
Boost.Log compatibility.
ome::compat::shared_ptr< double > wellOriginY
WellOriginY property.
Definition: Plate.h:100
ome::compat::shared_ptr< std::string > externalIdentifier
ExternalIdentifier property.
Definition: Plate.h:92
OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type sizeOfLinkedAnnotationList() const
Get size of linked Annotation list.
Definition: Plate.cpp:729
Xerces-C modern C++ wrapper.
Definition: Base.h:53
ome::compat::shared_ptr< ome::xml::model::Well > & getWell(std::vector< ome::compat::shared_ptr< ome::xml::model::Well > >::size_type index)
Get Well.
Definition: Plate.cpp:689
static ome::compat::shared_ptr< Plate > create(const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
Create a Plate model object from DOM element.
Definition: Plate.cpp:206