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Reagent.h
1 /*
2 * #%L
3 * OME-XML C++ library for working with OME-XML metadata structures.
4 * %%
5 * Copyright © 2006 - 2016 Open Microscopy Environment:
6 * - Massachusetts Institute of Technology
7 * - National Institutes of Health
8 * - University of Dundee
9 * - Board of Regents of the University of Wisconsin-Madison
10 * - Glencoe Software, Inc.
11 * %%
12 * Redistribution and use in source and binary forms, with or without
13 * modification, are permitted provided that the following conditions are met:
14 *
15 * 1. Redistributions of source code must retain the above copyright notice,
16 * this list of conditions and the following disclaimer.
17 * 2. Redistributions in binary form must reproduce the above copyright notice,
18 * this list of conditions and the following disclaimer in the documentation
19 * and/or other materials provided with the distribution.
20 *
21 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
22 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
23 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
24 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
25 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
26 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
27 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
28 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
29 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
30 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
31 * POSSIBILITY OF SUCH DAMAGE.
32 *
33 * The views and conclusions contained in the software and documentation are
34 * those of the authors and should not be interpreted as representing official
35 * policies, either expressed or implied, of any organization.
36 * #L%
37 */
38
39 /*─────────────────────────────────────────────────────────────────────────────
40 *
41 * THIS IS AUTOMATICALLY GENERATED CODE. DO NOT MODIFY.
42 *
43 *─────────────────────────────────────────────────────────────────────────────
44 */
45
46 #ifndef OME_XML_MODEL_REAGENT_H
47 #define OME_XML_MODEL_REAGENT_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/Screen.h>
63 #include <ome/xml/model/detail/OMEModelObject.h>
64
65 namespace ome
66 {
67 namespace xml
68 {
69 namespace model
70 {
71
72 // Forward declarations.
73 class Annotation;
74 class OMEModel;
75 class Well;
76
80 class Reagent : public detail::OMEModelObject
81 {
82 private:
83 class Impl;
85 ome::compat::shared_ptr<Impl> impl;
86
87 public:
89 Reagent();
90
96 Reagent (const Reagent& copy);
97
99 virtual
100 ~Reagent ();
101
116 static ome::compat::shared_ptr< Reagent>
117 create(const common::xml::dom::Element& element,
118 ome::xml::model::OMEModel& model);
119
120 // Documented in superclass.
121 const std::string&
122 elementName() const;
123
124 // Documented in superclass.
125 bool
126 validElementName(const std::string& name) const;
127
128
129 // -- OMEModelObject API methods --
130
132 virtual void
133 update(const common::xml::dom::Element& element,
134 ome::xml::model::OMEModel& model);
135
136 public:
137 // -- Reagent API methods --
138
140 bool
141 link (ome::compat::shared_ptr<Reference>& reference,
142 ome::compat::shared_ptr< ome::xml::model::OMEModelObject>& object);
143
149 ome::compat::shared_ptr<std::string>
150 getReagentIdentifier ();
151
157 const ome::compat::shared_ptr<std::string>
158 getReagentIdentifier () const;
159
165 void
166 setReagentIdentifier (ome::compat::shared_ptr<std::string>& reagentIdentifier);
167
173 const std::string&
174 getID () const;
175
181 void
182 setID (const std::string& id);
183
189 ome::compat::shared_ptr<std::string>
190 getName ();
191
197 const ome::compat::shared_ptr<std::string>
198 getName () const;
199
205 void
206 setName (ome::compat::shared_ptr<std::string>& name);
207
213 ome::compat::shared_ptr<std::string>
214 getDescription ();
215
221 const ome::compat::shared_ptr<std::string>
222 getDescription () const;
223
229 void
230 setDescription (ome::compat::shared_ptr<std::string>& description);
231
237 OMEModelObject::indexed_container<ome::xml::model::Annotation, ome::compat::weak_ptr>::type::size_type
238 sizeOfLinkedAnnotationList () const;
239
245 OMEModelObject::indexed_container<ome::xml::model::Annotation, ome::compat::weak_ptr>::type
246 getLinkedAnnotationList () const;
247
255 const ome::compat::weak_ptr<ome::xml::model::Annotation>&
256 getLinkedAnnotation (OMEModelObject::indexed_container<ome::xml::model::Annotation, ome::compat::weak_ptr>::type::size_type index) const;
257
268 const ome::compat::weak_ptr<ome::xml::model::Annotation>&
269 setLinkedAnnotation (OMEModelObject::indexed_container<ome::xml::model::Annotation, ome::compat::weak_ptr>::type::size_type index,
270 const ome::compat::shared_ptr<ome::xml::model::Annotation>& annotation);
271
282 bool
283 linkAnnotation (const ome::compat::shared_ptr<ome::xml::model::Annotation>& annotation);
284
300 bool
301 unlinkAnnotation (const ome::compat::shared_ptr<ome::xml::model::Annotation>& annotation);
302
308 ome::compat::weak_ptr<ome::xml::model::Screen>
309 getScreen ();
310
316 const ome::compat::weak_ptr<ome::xml::model::Screen>
317 getScreen () const;
318
324 void
325 setScreen (ome::compat::weak_ptr<ome::xml::model::Screen>& screen_BackReference);
326
332 OMEModelObject::indexed_container<ome::xml::model::Well, ome::compat::weak_ptr>::type::size_type
333 sizeOfLinkedWellList () const;
334
340 OMEModelObject::indexed_container<ome::xml::model::Well, ome::compat::weak_ptr>::type
341 getLinkedWellList () const;
342
350 const ome::compat::weak_ptr<ome::xml::model::Well>&
351 getLinkedWell (OMEModelObject::indexed_container<ome::xml::model::Well, ome::compat::weak_ptr>::type::size_type index) const;
352
363 const ome::compat::weak_ptr<ome::xml::model::Well>&
364 setLinkedWell (OMEModelObject::indexed_container<ome::xml::model::Well, ome::compat::weak_ptr>::type::size_type index,
365 const ome::compat::shared_ptr<ome::xml::model::Well>& well_BackReference);
366
377 bool
378 linkWell (const ome::compat::shared_ptr<ome::xml::model::Well>& well_BackReference);
379
395 bool
396 unlinkWell (const ome::compat::shared_ptr<ome::xml::model::Well>& well_BackReference);
397
398
400 virtual common::xml::dom::Element
401 asXMLElement (common::xml::dom::Document& document) const;
402
403
404 protected:
405 // Documented in base class.
406 virtual common::xml::dom::Element
407 asXMLElementInternal (common::xml::dom::Document& document,
408 common::xml::dom::Element& element) const;
409
410 public:
411 // Documented in superclass.
412 const std::string&
413 getXMLNamespace() const;
414 };
415
416 }
417 }
418 }
419
420 #endif // OME_XML_MODEL_REAGENT_H
421
422 /*
423 * Local Variables:
424 * mode:C++
425 * End:
426 */
ome::xml::model::OMEModel
OME model interface (abstract top-level container)
Definition: OMEModel.h:62
ome::xml::model::Reagent::linkWell
bool linkWell(const ome::compat::shared_ptr< ome::xml::model::Well > &well_BackReference)
Link Well.
Definition: Reagent.cpp:494
ome::xml::model::Reagent::sizeOfLinkedWellList
OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type::size_type sizeOfLinkedWellList() const
Get size of linked Well list.
Definition: Reagent.cpp:466
ome::xml::model::Reagent::asXMLElementInternal
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: Reagent.cpp:531
ome::xml::model::Reagent::getLinkedWellList
OMEModelObject::indexed_container< ome::xml::model::Well, ome::compat::weak_ptr >::type getLinkedWellList() const
Get the linked Well list.
Definition: Reagent.cpp:472
ome::xml::model::Reagent::setName
void setName(ome::compat::shared_ptr< std::string > &name)
Set the Name property.
Definition: Reagent.cpp:357
ome::xml::model::Reagent::getLinkedAnnotation
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: Reagent.cpp:397
ome::xml::model::Reagent::getReagentIdentifier
ome::compat::shared_ptr< std::string > getReagentIdentifier()
Get the ReagentIdentifier property.
Definition: Reagent.cpp:308
ome::xml::model::Reagent::getDescription
ome::compat::shared_ptr< std::string > getDescription()
Get the Description property.
Definition: Reagent.cpp:364
ome::xml::model::Reagent::unlinkAnnotation
bool unlinkAnnotation(const ome::compat::shared_ptr< ome::xml::model::Annotation > &annotation)
Unlink Annotation.
Definition: Reagent.cpp:427
ome::xml::model::Reagent::setLinkedAnnotation
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: Reagent.cpp:403
ome::common::xml::dom::Document
ome::xml::model::Reagent::getScreen
ome::compat::weak_ptr< ome::xml::model::Screen > getScreen()
Get the Screen property.
Definition: Reagent.cpp:445
ome::common::xml::dom::Element
ome::xml::model::Reagent::getLinkedWell
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.
Definition: Reagent.cpp:478
ome::xml::model::detail::OMEModelObject
OME model object (concrete implementation).
Definition: OMEModelObject.h:64
ome::xml::model::OMEModelObject::indexed_container::type
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
ome::xml::model::Reagent::unlinkWell
bool unlinkWell(const ome::compat::shared_ptr< ome::xml::model::Well > &well_BackReference)
Unlink Well.
Definition: Reagent.cpp:507
ome::xml::model::Reagent::setLinkedWell
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.
Definition: Reagent.cpp:484
ome::xml::model::Reagent::sizeOfLinkedAnnotationList
OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type::size_type sizeOfLinkedAnnotationList() const
Get size of linked Annotation list.
Definition: Reagent.cpp:385
ome::xml::model::Reagent::setReagentIdentifier
void setReagentIdentifier(ome::compat::shared_ptr< std::string > &reagentIdentifier)
Set the ReagentIdentifier property.
Definition: Reagent.cpp:322
ome::xml::model::Reagent::setID
void setID(const std::string &id)
Set the ID property.
Definition: Reagent.cpp:336
ome::xml::model::Reagent::setScreen
void setScreen(ome::compat::weak_ptr< ome::xml::model::Screen > &screen_BackReference)
Set the Screen property.
Definition: Reagent.cpp:459
ome::xml::model::OMEModelObject::indexed_container
Multi-index container for efficient ordered insertion and deletion of model object references...
Definition: OMEModelObject.h:85
ome::xml::model::Reagent
Reagent model object.
Definition: Reagent.h:80
ome
Open Microscopy Environment C++ implementation.
ome::xml::model::Reagent::elementName
const std::string & elementName() const
Get the element name of this model object.
Definition: Reagent.cpp:189
ome::xml::model::Reagent::setDescription
void setDescription(ome::compat::shared_ptr< std::string > &description)
Set the Description property.
Definition: Reagent.cpp:378
ome::xml::model::Reagent::linkAnnotation
bool linkAnnotation(const ome::compat::shared_ptr< ome::xml::model::Annotation > &annotation)
Link Annotation.
Definition: Reagent.cpp:413
ome::xml::model::Reagent::getID
const std::string & getID() const
Get the ID property.
Definition: Reagent.cpp:329
ome::xml::model::Reagent::~Reagent
virtual ~Reagent()
Destructor.
Definition: Reagent.cpp:175
ome::xml::model::Reagent::update
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: Reagent.cpp:205
ome::xml::model::Reagent::asXMLElement
virtual common::xml::dom::Element asXMLElement(common::xml::dom::Document &document) const
Transform the object hierarchy rooted at this element to XML.
Definition: Reagent.cpp:524
ome::xml::model::Reagent::link
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: Reagent.cpp:277
ome::xml::model::Reagent::create
static ome::compat::shared_ptr< Reagent > create(const common::xml::dom::Element &element, ome::xml::model::OMEModel &model)
Create a Reagent model object from DOM element.
Definition: Reagent.cpp:180
ome::xml::model::Reagent::getXMLNamespace
const std::string & getXMLNamespace() const
Get the XML namespace for this model object.
Definition: Reagent.cpp:620
ome::xml::model::Reagent::impl
ome::compat::shared_ptr< Impl > impl
Private implementation details.
Definition: Reagent.h:83
ome::xml::model::Reagent::getLinkedAnnotationList
OMEModelObject::indexed_container< ome::xml::model::Annotation, ome::compat::weak_ptr >::type getLinkedAnnotationList() const
Get the linked Annotation list.
Definition: Reagent.cpp:391
log.h
ome::xml::model::Reagent::validElementName
bool validElementName(const std::string &name) const
Check if a given element name is valid for processing by this model object.
Definition: Reagent.cpp:196
ome::xml::model::Reagent::Impl
Private implementation details of Reagent model object.
Definition: Reagent.cpp:74
ome::xml::model::Reagent::Reagent
Reagent()
Default constructor.
Definition: Reagent.cpp:156
ome::xml::model::Reagent::getName
ome::compat::shared_ptr< std::string > getName()
Get the Name property.
Definition: Reagent.cpp:343