ome.xml.model

Class Reagent

java.lang.Object

ome.xml.model.AbstractOMEModelObject

ome.xml.model.Reagent

All Implemented Interfaces:

OMEModelObject

public class Reagent
extends AbstractOMEModelObject

Field Summary

Fields

Modifier and Type	Field and Description
private List<Annotation>	annotationLinks
private String	description
private String	id
private static org.slf4j.Logger	LOGGER Logger for this class.
private String	name
static String	NAMESPACE
private String	reagentIdentifier
private Screen	screen
private List<Well>	wells

Constructor Summary

Constructors

Constructor and Description
Reagent() Default constructor.
Reagent(Element element, OMEModel model) Constructs Reagent recursively from an XML DOM tree.
Reagent(Reagent orig) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
Element	asXMLElement(Document document) Takes the entire object hierarchy and produces an XML DOM tree.
protected Element	asXMLElement(Document document, Element Reagent_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
List<Annotation>	copyLinkedAnnotationList()
List<Well>	copyLinkedWellList()
String	getDescription()
String	getID()
Annotation	getLinkedAnnotation(int index)
Well	getLinkedWell(int index)
String	getName()
String	getReagentIdentifier()
Screen	getScreen()
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
boolean	linkAnnotation(Annotation o)
boolean	linkWell(Well o)
void	setDescription(String description)
void	setID(String id)
Annotation	setLinkedAnnotation(int index, Annotation o)
Well	setLinkedWell(int index, Well o)
void	setName(String name)
void	setReagentIdentifier(String reagentIdentifier)
void	setScreen(Screen screen_BackReference)
int	sizeOfLinkedAnnotationList()
int	sizeOfLinkedWellList()
boolean	unlinkAnnotation(Annotation o)
boolean	unlinkWell(Well o)
void	update(Element element, OMEModel model) Updates Reagent recursively from an XML DOM tree.

Methods inherited from class ome.xml.model.AbstractOMEModelObject

getChildrenByTagName, stripNamespacePrefix

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NAMESPACE

public static final String NAMESPACE

See Also:

Constant Field Values

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

reagentIdentifier

private String reagentIdentifier

id

private String id

name

private String name

description

private String description

annotationLinks

private List<Annotation> annotationLinks

screen

private Screen screen

wells

private List<Well> wells

Constructor Detail

Reagent

public Reagent()

Default constructor.

Reagent

public Reagent(Element element,
       OMEModel model)
        throws EnumerationException

Constructs Reagent recursively from an XML DOM tree.

Parameters:

element - Root of the XML DOM tree to construct a model object graph from.

model - Handler for the OME model which keeps track of instances and references seen during object population.

Throws:

EnumerationException - If there is an error instantiating an enumeration during model object creation.

Reagent

public Reagent(Reagent orig)

Copy constructor.

Method Detail

update

public void update(Element element,
          OMEModel model)
            throws EnumerationException

Updates Reagent recursively from an XML DOM tree. NOTE: No properties are removed, only added or updated.

Specified by:

update in interface OMEModelObject

Overrides:

update in class AbstractOMEModelObject

Parameters:

element - Root of the XML DOM tree to construct a model object graph from.

model - Handler for the OME model which keeps track of instances and references seen during object population.

Throws:

EnumerationException - If there is an error instantiating an enumeration during model object creation.

link

public boolean link(Reference reference,
           OMEModelObject o)

Description copied from interface: OMEModelObject

Link a given OME model object to this model object.

Specified by:

link in interface OMEModelObject

Overrides:

link in class AbstractOMEModelObject

Parameters:

reference - The type qualifier for the reference. This should be the corresponding reference type for o. If, for example, o is of type Image, reference MUST be of type ImageRef.

o - Model object to link to.

Returns:

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

getReagentIdentifier

public String getReagentIdentifier()

setReagentIdentifier

public void setReagentIdentifier(String reagentIdentifier)

getID

public String getID()

setID

public void setID(String id)

getName

public String getName()

setName

public void setName(String name)

getDescription

public String getDescription()

setDescription

public void setDescription(String description)

sizeOfLinkedAnnotationList

public int sizeOfLinkedAnnotationList()

copyLinkedAnnotationList

public List<Annotation> copyLinkedAnnotationList()

getLinkedAnnotation

public Annotation getLinkedAnnotation(int index)

setLinkedAnnotation

public Annotation setLinkedAnnotation(int index,
                             Annotation o)

linkAnnotation

public boolean linkAnnotation(Annotation o)

unlinkAnnotation

public boolean unlinkAnnotation(Annotation o)

getScreen

public Screen getScreen()

setScreen

public void setScreen(Screen screen_BackReference)

sizeOfLinkedWellList

public int sizeOfLinkedWellList()

copyLinkedWellList

public List<Well> copyLinkedWellList()

getLinkedWell

public Well getLinkedWell(int index)

setLinkedWell

public Well setLinkedWell(int index,
                 Well o)

linkWell

public boolean linkWell(Well o)

unlinkWell

public boolean unlinkWell(Well o)

asXMLElement

public Element asXMLElement(Document document)

Description copied from interface: OMEModelObject

Takes the entire object hierarchy and produces an XML DOM tree.

Specified by:

asXMLElement in interface OMEModelObject

Specified by:

asXMLElement in class AbstractOMEModelObject

Parameters:

document - Destination document for element creation, etc.

Returns:

XML DOM tree root element for this model object.

asXMLElement

protected Element asXMLElement(Document document,
                   Element Reagent_element)

Description copied from class: AbstractOMEModelObject

Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.

Overrides:

asXMLElement in class AbstractOMEModelObject

Parameters:

document - Destination document for element creation, etc.

Reagent_element - Element from the subclass. If null a new element will be created of this class.

Returns:

element populated with properties from this class.