Package ome.model.screen
Class Well
- java.lang.Object
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- ome.model.screen.Well
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- All Implemented Interfaces:
java.io.Serializable
,IAnnotated
,IMutable
,IObject
,Filterable
@Entity @Indexed(index="FullText") @ClassBridge(name="details", impl=DetailsFieldBridge.class, index=UN_TOKENIZED, store=NO) public class Well extends java.lang.Object implements java.io.Serializable, IObject, IMutable, IAnnotated
These filter definitions are used by the security system to eliminate non-readable objects from queries. The regular user does not need to worry about them, as they will be injected directly into the SQL (not HQL)- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
Well.Details
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Field Summary
Fields Modifier and Type Field Description protected java.util.Map<java.lang.String,java.lang.Object>
_dynamicFields
protected boolean
_loaded
protected java.lang.Integer
alpha
static java.lang.String
ALPHA
protected java.util.Set<WellAnnotationLink>
annotationLinks
static java.lang.String
ANNOTATIONLINKS
static java.lang.String
ANNOTATIONLINKSCOUNTPEROWNER
protected java.lang.Integer
blue
static java.lang.String
BLUE
protected java.lang.Integer
column
static java.lang.String
COLUMN
protected Details
details
static java.lang.String
DETAILS
static java.lang.String
EVENT_FILTER
static java.lang.String
EVENT_FILTER_ANNOTATIONLINKS
static java.lang.String
EVENT_FILTER_REAGENTLINKS
static java.lang.String
EVENT_FILTER_WELLSAMPLES
protected java.lang.String
externalDescription
static java.lang.String
EXTERNALDESCRIPTION
protected java.lang.String
externalIdentifier
static java.lang.String
EXTERNALIDENTIFIER
static java.util.Set<java.lang.String>
FIELDS
protected java.lang.Integer
green
static java.lang.String
GREEN
static java.lang.String
GROUP_FILTER
static java.lang.String
GROUP_FILTER_ANNOTATIONLINKS
static java.lang.String
GROUP_FILTER_REAGENTLINKS
static java.lang.String
GROUP_FILTER_WELLSAMPLES
protected java.lang.Long
id
static java.lang.String
ID
static java.lang.String
OWNER_FILTER
static java.lang.String
OWNER_FILTER_ANNOTATIONLINKS
static java.lang.String
OWNER_FILTER_REAGENTLINKS
static java.lang.String
OWNER_FILTER_WELLSAMPLES
static java.lang.String
PERMS_FILTER
static java.lang.String
PERMS_FILTER_ANNOTATIONLINKS
static java.lang.String
PERMS_FILTER_REAGENTLINKS
static java.lang.String
PERMS_FILTER_WELLSAMPLES
protected Plate
plate
static java.lang.String
PLATE
protected java.util.Set<WellReagentLink>
reagentLinks
static java.lang.String
REAGENTLINKS
static java.lang.String
REAGENTLINKSCOUNTPEROWNER
protected java.lang.Integer
red
static java.lang.String
RED
protected java.lang.Integer
row
static java.lang.String
ROW
protected java.lang.String
status
static java.lang.String
STATUS
protected java.lang.String
type
static java.lang.String
TYPE
protected java.lang.Integer
version
static java.lang.String
VERSION
protected java.util.List<WellSample>
wellSamples
static java.lang.String
WELLSAMPLES
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
acceptFilter(Filter __filter)
void
addWellAnnotationLink(WellAnnotationLink target)
use instead of setAnnotationLinks .void
addWellAnnotationLink(WellAnnotationLink link, boolean bothSides)
Adds a ome.model.annotations.WellAnnotationLink to annotationLinks, allowing for recursion -- whether or not addWellAnnotationLink will be called on the addition if it is loadedvoid
addWellAnnotationLinkSet(java.util.Collection<WellAnnotationLink> targets)
use like addWellAnnotationLink.void
addWellReagentLink(WellReagentLink target)
use instead of setReagentLinks .void
addWellReagentLink(WellReagentLink link, boolean bothSides)
Adds a ome.model.screen.WellReagentLink to reagentLinks, allowing for recursion -- whether or not addWellReagentLink will be called on the addition if it is loadedvoid
addWellReagentLinkSet(java.util.Collection<WellReagentLink> targets)
use like addWellReagentLink.void
addWellSample(WellSample target)
use instead of setWellSamples .void
addWellSampleSet(java.util.Collection<WellSample> targets)
use like addWellSample.void
clearAnnotationLinks()
clears the set.void
clearReagentLinks()
clears the set.void
clearWellSamples()
clears the set.<E> java.util.List<E>
collectAnnotationLinks(CBlock<E> block)
takes a CBlock and calls the block once for each ome.model.annotations.WellAnnotationLink while collecting the results.<E> java.util.List<E>
collectReagentLinks(CBlock<E> block)
takes a CBlock and calls the block once for each ome.model.screen.WellReagentLink while collecting the results.<E> java.util.List<E>
collectWellSamples(CBlock<E> block)
takes a CBlock and calls the block once for each ome.model.screen.WellSample while collecting the results.<E> java.util.List<E>
eachLinkedAnnotation(CBlock<E> block)
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.<E> java.util.List<E>
eachLinkedReagent(CBlock<E> block)
takes a CBlock and calls the block once for each ome.model.screen.Reagent while collecting the results.protected void
errorIfUnloaded()
java.util.Set<java.lang.String>
fields()
returns a Set of field names that belong to this classjava.util.Set<WellAnnotationLink>
findWellAnnotationLink(Annotation target)
find all ome.model.annotations.WellAnnotationLink which have the argument as their child.java.util.Set<WellReagentLink>
findWellReagentLink(Reagent target)
find all ome.model.screen.WellReagentLink which have the argument as their child.java.lang.Integer
getAlpha()
Simple field ome.model.screen.Well.alpha (java.lang.Integer)protected java.util.Set<WellAnnotationLink>
getAnnotationLinks()
returns annotationLinks .java.util.Map<java.lang.Long,java.lang.Long>
getAnnotationLinksCountPerOwner()
If fetched, returns the count(*) of ome.model.annotations.WellAnnotationLink that a user has.java.lang.Integer
getBlue()
Simple field ome.model.screen.Well.blue (java.lang.Integer)java.lang.Integer
getColumn()
Simple field ome.model.screen.Well.column (java.lang.Integer)Details
getDetails()
The details of this object correspond to low-level system information.java.lang.String
getExternalDescription()
Simple field ome.model.screen.Well.externalDescription (java.lang.String)java.lang.String
getExternalIdentifier()
Simple field ome.model.screen.Well.externalIdentifier (java.lang.String)GraphHolder
getGraphHolder()
retrieves theGraphHolder
for this entity.java.lang.Integer
getGreen()
Simple field ome.model.screen.Well.green (java.lang.Integer)java.lang.Long
getId()
The DB unique identifier for this object.Plate
getPlate()
Many-to-one field ome.model.screen.Well.plate (ome.model.screen.Plate)WellSample
getPrimaryWellSample()
Gets the first element of wellSamples which can be interpreted as the primary or default element in some situations.protected java.util.Set<WellReagentLink>
getReagentLinks()
returns reagentLinks .java.util.Map<java.lang.Long,java.lang.Long>
getReagentLinksCountPerOwner()
If fetched, returns the count(*) of ome.model.screen.WellReagentLink that a user has.java.lang.Integer
getRed()
Simple field ome.model.screen.Well.red (java.lang.Integer)java.lang.Integer
getRow()
Simple field ome.model.screen.Well.row (java.lang.Integer)java.lang.String
getStatus()
Simple field ome.model.screen.Well.status (java.lang.String)java.lang.String
getType()
Simple field ome.model.screen.Well.type (java.lang.String)java.lang.Integer
getVersion()
This version number is controlled by the database for optimisitic locking.WellSample
getWellSample(int index)
Gets the ome.model.screen.WellSample at the given index.protected java.util.List<WellSample>
getWellSamples()
returns wellSamples .boolean
isLoaded()
transient field (not stored in the DB) which specifies whether this object has been loaded from the DB or is only a wrapper around the ID.boolean
isValid()
calls the class-specific validator for this instance and returns the value fromValidation.isValid()
java.util.Iterator<WellAnnotationLink>
iterateAnnotationLinks()
should be used rather than accessing the annotationLinks set directly.java.util.Iterator<WellReagentLink>
iterateReagentLinks()
should be used rather than accessing the reagentLinks set directly.java.util.Iterator<WellSample>
iterateWellSamples()
should be used rather than accessing the wellSamples set directly.WellAnnotationLink
linkAnnotation(Annotation addition)
Adds a ome.model.annotations.WellAnnotationLink to annotationLinks .java.util.Iterator<Annotation>
linkedAnnotationIterator()
provides an iterator over the parent values of the annotationLinks.java.util.List<Annotation>
linkedAnnotationList()
produces aList
-copy of the underlying collection.java.util.Iterator<Reagent>
linkedReagentIterator()
provides an iterator over the parent values of the reagentLinks.java.util.List<Reagent>
linkedReagentList()
produces aList
-copy of the underlying collection.WellReagentLink
linkReagent(Reagent addition)
Adds a ome.model.screen.WellReagentLink to reagentLinks .Well
newInstance()
Well
proxy()
void
putAt(java.lang.String field, java.lang.Object value)
stores a value in this instance.void
removeWellAnnotationLink(WellAnnotationLink target)
removes a single element from this set and makes the inverse call on ome.model.annotations.WellAnnotationLinkvoid
removeWellAnnotationLink(WellAnnotationLink link, boolean bothSides)
removes the given WellAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkWell again if loaded.void
removeWellAnnotationLinkSet(java.util.Collection<WellAnnotationLink> targets)
use like removeWellAnnotationLinkvoid
removeWellReagentLink(WellReagentLink target)
removes a single element from this set and makes the inverse call on ome.model.screen.WellReagentLinkvoid
removeWellReagentLink(WellReagentLink link, boolean bothSides)
removes the given WellReagentLink from reagentLinks, allowing for recursion -- whether or not the removal will call unlinkWell again if loaded.void
removeWellReagentLinkSet(java.util.Collection<WellReagentLink> targets)
use like removeWellReagentLinkvoid
removeWellSample(WellSample target)
removes a single element from this set and makes the inverse call on ome.model.screen.WellSamplevoid
removeWellSampleSet(java.util.Collection<WellSample> targets)
use like removeWellSamplejava.lang.Object
retrieve(java.lang.String field)
retrieves a value from this instance.void
setAlpha(java.lang.Integer alpha)
protected void
setAnnotationLinks(java.util.Set<WellAnnotationLink> annotationLinks)
setter for annotationLinks should be avoided.protected void
setAnnotationLinksCountPerOwner(java.util.Map<java.lang.Long,java.lang.Long> map)
void
setBlue(java.lang.Integer blue)
void
setColumn(java.lang.Integer column)
protected void
setDetails(Details details)
void
setExternalDescription(java.lang.String externalDescription)
void
setExternalIdentifier(java.lang.String externalIdentifier)
void
setGreen(java.lang.Integer green)
void
setId(java.lang.Long id)
usually unneeded.void
setPlate(Plate plate)
WellSample
setPrimaryWellSample(WellSample element)
Swaps the first element of wellSamples with the first instance of the given element.protected void
setReagentLinks(java.util.Set<WellReagentLink> reagentLinks)
setter for reagentLinks should be avoided.protected void
setReagentLinksCountPerOwner(java.util.Map<java.lang.Long,java.lang.Long> map)
void
setRed(java.lang.Integer red)
void
setRow(java.lang.Integer row)
void
setStatus(java.lang.String status)
void
setType(java.lang.String type)
void
setVersion(java.lang.Integer version)
use with caution.WellSample
setWellSample(int index, WellSample element)
Sets the ome.model.screen.WellSample at the given index.protected void
setWellSamples(java.util.List<WellSample> wellSamples)
setter for wellSamples should be avoided.int
sizeOfAnnotationLinks()
returns the size of annotationLinks.int
sizeOfReagentLinks()
returns the size of reagentLinks.int
sizeOfWellSamples()
returns the size of wellSamples.protected void
throwNullCollectionException(java.lang.String propertyName)
java.lang.String
toString()
void
unlinkAnnotation(Annotation removal)
unlinks all ome.model.annotations.Annotation instances from this instance.void
unlinkReagent(Reagent removal)
unlinks all ome.model.screen.Reagent instances from this instance.void
unload()
set the loaded field to false, and set all non-ID fields to null.java.util.Collection<WellAnnotationLink>
unmodifiableAnnotationLinks()
Returns an unmodifiable collection-viewjava.util.Collection<WellReagentLink>
unmodifiableReagentLinks()
Returns an unmodifiable collection-viewjava.util.Collection<WellSample>
unmodifiableWellSamples()
Returns an unmodifiable collection-viewValidation
validate()
calls the class-specific validator for this instance and returns theValidation
object.
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Field Detail
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OWNER_FILTER
public static final java.lang.String OWNER_FILTER
- See Also:
- Constant Field Values
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GROUP_FILTER
public static final java.lang.String GROUP_FILTER
- See Also:
- Constant Field Values
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EVENT_FILTER
public static final java.lang.String EVENT_FILTER
- See Also:
- Constant Field Values
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PERMS_FILTER
public static final java.lang.String PERMS_FILTER
- See Also:
- Constant Field Values
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ID
public static final java.lang.String ID
- See Also:
- Constant Field Values
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id
protected java.lang.Long id
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VERSION
public static final java.lang.String VERSION
- See Also:
- Constant Field Values
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version
protected java.lang.Integer version
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status
protected java.lang.String status
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column
protected java.lang.Integer column
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row
protected java.lang.Integer row
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red
protected java.lang.Integer red
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green
protected java.lang.Integer green
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blue
protected java.lang.Integer blue
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alpha
protected java.lang.Integer alpha
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reagentLinks
protected java.util.Set<WellReagentLink> reagentLinks
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OWNER_FILTER_REAGENTLINKS
public static final java.lang.String OWNER_FILTER_REAGENTLINKS
- See Also:
- Constant Field Values
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GROUP_FILTER_REAGENTLINKS
public static final java.lang.String GROUP_FILTER_REAGENTLINKS
- See Also:
- Constant Field Values
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EVENT_FILTER_REAGENTLINKS
public static final java.lang.String EVENT_FILTER_REAGENTLINKS
- See Also:
- Constant Field Values
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PERMS_FILTER_REAGENTLINKS
public static final java.lang.String PERMS_FILTER_REAGENTLINKS
- See Also:
- Constant Field Values
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externalDescription
protected java.lang.String externalDescription
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externalIdentifier
protected java.lang.String externalIdentifier
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type
protected java.lang.String type
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wellSamples
protected java.util.List<WellSample> wellSamples
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OWNER_FILTER_WELLSAMPLES
public static final java.lang.String OWNER_FILTER_WELLSAMPLES
- See Also:
- Constant Field Values
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GROUP_FILTER_WELLSAMPLES
public static final java.lang.String GROUP_FILTER_WELLSAMPLES
- See Also:
- Constant Field Values
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EVENT_FILTER_WELLSAMPLES
public static final java.lang.String EVENT_FILTER_WELLSAMPLES
- See Also:
- Constant Field Values
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PERMS_FILTER_WELLSAMPLES
public static final java.lang.String PERMS_FILTER_WELLSAMPLES
- See Also:
- Constant Field Values
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plate
protected Plate plate
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annotationLinks
protected java.util.Set<WellAnnotationLink> annotationLinks
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OWNER_FILTER_ANNOTATIONLINKS
public static final java.lang.String OWNER_FILTER_ANNOTATIONLINKS
- See Also:
- Constant Field Values
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GROUP_FILTER_ANNOTATIONLINKS
public static final java.lang.String GROUP_FILTER_ANNOTATIONLINKS
- See Also:
- Constant Field Values
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EVENT_FILTER_ANNOTATIONLINKS
public static final java.lang.String EVENT_FILTER_ANNOTATIONLINKS
- See Also:
- Constant Field Values
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PERMS_FILTER_ANNOTATIONLINKS
public static final java.lang.String PERMS_FILTER_ANNOTATIONLINKS
- See Also:
- Constant Field Values
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details
protected Details details
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STATUS
public static final java.lang.String STATUS
- See Also:
- Constant Field Values
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COLUMN
public static final java.lang.String COLUMN
- See Also:
- Constant Field Values
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ROW
public static final java.lang.String ROW
- See Also:
- Constant Field Values
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RED
public static final java.lang.String RED
- See Also:
- Constant Field Values
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GREEN
public static final java.lang.String GREEN
- See Also:
- Constant Field Values
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BLUE
public static final java.lang.String BLUE
- See Also:
- Constant Field Values
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ALPHA
public static final java.lang.String ALPHA
- See Also:
- Constant Field Values
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REAGENTLINKSCOUNTPEROWNER
public static final java.lang.String REAGENTLINKSCOUNTPEROWNER
- See Also:
- Constant Field Values
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REAGENTLINKS
public static final java.lang.String REAGENTLINKS
- See Also:
- Constant Field Values
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EXTERNALDESCRIPTION
public static final java.lang.String EXTERNALDESCRIPTION
- See Also:
- Constant Field Values
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EXTERNALIDENTIFIER
public static final java.lang.String EXTERNALIDENTIFIER
- See Also:
- Constant Field Values
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TYPE
public static final java.lang.String TYPE
- See Also:
- Constant Field Values
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WELLSAMPLES
public static final java.lang.String WELLSAMPLES
- See Also:
- Constant Field Values
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PLATE
public static final java.lang.String PLATE
- See Also:
- Constant Field Values
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ANNOTATIONLINKSCOUNTPEROWNER
public static final java.lang.String ANNOTATIONLINKSCOUNTPEROWNER
- See Also:
- Constant Field Values
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ANNOTATIONLINKS
public static final java.lang.String ANNOTATIONLINKS
- See Also:
- Constant Field Values
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DETAILS
public static final java.lang.String DETAILS
- See Also:
- Constant Field Values
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FIELDS
public static final java.util.Set<java.lang.String> FIELDS
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_dynamicFields
protected java.util.Map<java.lang.String,java.lang.Object> _dynamicFields
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_loaded
protected boolean _loaded
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Constructor Detail
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Well
public Well()
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Well
protected Well(java.lang.Long id)
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Well
public Well(java.lang.Long id, boolean loaded)
Main constructor.
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Well
public Well(Plate _plate)
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Method Detail
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getId
@DocumentId public java.lang.Long getId()
The DB unique identifier for this object. You are not responsible for setting the id; however, it can be useful for creating "unloaded" versions of your objects. Each top-level entity contains an id field of type long. For all objects returned from the server, this value will be non-null, which doesn't necessarily hold for the other fields.
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setId
public void setId(java.lang.Long id)
Description copied from interface:IObject
usually unneeded. Ids are managed by the backend.
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getVersion
public java.lang.Integer getVersion()
This version number is controlled by the database for optimisitic locking.- Specified by:
getVersion
in interfaceIMutable
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setVersion
public void setVersion(java.lang.Integer version)
Description copied from interface:IMutable
use with caution. In general, the version should only be altered by the backend. In the best case, an exception will be thrown for a version not equal to the current DB value. In the worst (though rare) case, the new version could match the database, and override optimistic lock checks that are supposed to prevent data loss.- Specified by:
setVersion
in interfaceIMutable
- Parameters:
version
- Value for this objects version.
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getStatus
@Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields") public java.lang.String getStatus()
Simple field ome.model.screen.Well.status (java.lang.String)
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setStatus
public void setStatus(java.lang.String status)
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getColumn
@Field(index=UN_TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields") public java.lang.Integer getColumn()
Simple field ome.model.screen.Well.column (java.lang.Integer)
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setColumn
public void setColumn(java.lang.Integer column)
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getRow
@Field(index=UN_TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields") public java.lang.Integer getRow()
Simple field ome.model.screen.Well.row (java.lang.Integer)
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setRow
public void setRow(java.lang.Integer row)
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getRed
@Field(index=UN_TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields") public java.lang.Integer getRed()
Simple field ome.model.screen.Well.red (java.lang.Integer)
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setRed
public void setRed(java.lang.Integer red)
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getGreen
@Field(index=UN_TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields") public java.lang.Integer getGreen()
Simple field ome.model.screen.Well.green (java.lang.Integer)
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setGreen
public void setGreen(java.lang.Integer green)
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getBlue
@Field(index=UN_TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields") public java.lang.Integer getBlue()
Simple field ome.model.screen.Well.blue (java.lang.Integer)
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setBlue
public void setBlue(java.lang.Integer blue)
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getAlpha
@Field(index=UN_TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields") public java.lang.Integer getAlpha()
Simple field ome.model.screen.Well.alpha (java.lang.Integer)
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setAlpha
public void setAlpha(java.lang.Integer alpha)
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getReagentLinks
protected java.util.Set<WellReagentLink> getReagentLinks()
returns reagentLinks . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.screen.Well.reagentLinks (ome.model.screen.WellReagentLink)
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setReagentLinks
protected void setReagentLinks(java.util.Set<WellReagentLink> reagentLinks)
setter for reagentLinks should be avoided. Does not fulfill normal semantics.
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sizeOfReagentLinks
public int sizeOfReagentLinks()
returns the size of reagentLinks. If less than zero, the Set was null.
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iterateReagentLinks
public java.util.Iterator<WellReagentLink> iterateReagentLinks()
should be used rather than accessing the reagentLinks set directly. This method will never return null, but rather will return an instance ofEmptyIterator
. To test for a null collection, see ofsizeOfReagentLinks()
is less than zero.
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unmodifiableReagentLinks
public java.util.Collection<WellReagentLink> unmodifiableReagentLinks()
Returns an unmodifiable collection-view
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collectReagentLinks
public <E> java.util.List<E> collectReagentLinks(CBlock<E> block)
takes a CBlock and calls the block once for each ome.model.screen.WellReagentLink while collecting the results. Ifblock == null
, then the iterator values themselves are collected. This method usesiterateReagentLinks()
internally and so will return a value even if the underlying collection is null.
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addWellReagentLink
public void addWellReagentLink(WellReagentLink target)
use instead of setReagentLinks . Makes the necessary call on ome.model.screen.WellReagentLink as well.
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addWellReagentLinkSet
public void addWellReagentLinkSet(java.util.Collection<WellReagentLink> targets)
use like addWellReagentLink.
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removeWellReagentLink
public void removeWellReagentLink(WellReagentLink target)
removes a single element from this set and makes the inverse call on ome.model.screen.WellReagentLink
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removeWellReagentLinkSet
public void removeWellReagentLinkSet(java.util.Collection<WellReagentLink> targets)
use like removeWellReagentLink
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linkReagent
public WellReagentLink linkReagent(Reagent addition)
Adds a ome.model.screen.WellReagentLink to reagentLinks . This entails changing our reagentLinks Set, creating a new ome.model.screen.WellReagentLink and calling linkReagent on the ome.model.screen.Reagent.
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addWellReagentLink
public void addWellReagentLink(WellReagentLink link, boolean bothSides)
Adds a ome.model.screen.WellReagentLink to reagentLinks, allowing for recursion -- whether or not addWellReagentLink will be called on the addition if it is loaded
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linkedReagentIterator
public java.util.Iterator<Reagent> linkedReagentIterator()
provides an iterator over the parent values of the reagentLinks. Like with most Collection iterators, modifications to the underlying collection while iterating will result in anConcurrentModificationException
. UselinkedReagentList()
instead.
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findWellReagentLink
public java.util.Set<WellReagentLink> findWellReagentLink(Reagent target)
find all ome.model.screen.WellReagentLink which have the argument as their child.
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linkedReagentList
public java.util.List<Reagent> linkedReagentList()
produces aList
-copy of the underlying collection. Unlike,linkedReagentIterator()
, while using the returnedList
, modifications can be made to the underlying collection without throwingConcurrentModificationException
.
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eachLinkedReagent
public <E> java.util.List<E> eachLinkedReagent(CBlock<E> block)
takes a CBlock and calls the block once for each ome.model.screen.Reagent while collecting the results. Ifblock == null
, then the iterator values themselves are collected.
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unlinkReagent
public void unlinkReagent(Reagent removal)
unlinks all ome.model.screen.Reagent instances from this instance.
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removeWellReagentLink
public void removeWellReagentLink(WellReagentLink link, boolean bothSides)
removes the given WellReagentLink from reagentLinks, allowing for recursion -- whether or not the removal will call unlinkWell again if loaded.
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clearReagentLinks
public void clearReagentLinks()
clears the set.
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setReagentLinksCountPerOwner
protected void setReagentLinksCountPerOwner(java.util.Map<java.lang.Long,java.lang.Long> map)
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getReagentLinksCountPerOwner
public java.util.Map<java.lang.Long,java.lang.Long> getReagentLinksCountPerOwner()
If fetched, returns the count(*) of ome.model.screen.WellReagentLink that a user has. If unfetched, returns null. No entries in the collection should be null.
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getExternalDescription
@Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields") public java.lang.String getExternalDescription()
Simple field ome.model.screen.Well.externalDescription (java.lang.String)
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setExternalDescription
public void setExternalDescription(java.lang.String externalDescription)
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getExternalIdentifier
@Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields") public java.lang.String getExternalIdentifier()
Simple field ome.model.screen.Well.externalIdentifier (java.lang.String)
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setExternalIdentifier
public void setExternalIdentifier(java.lang.String externalIdentifier)
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getType
@Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields") public java.lang.String getType()
Simple field ome.model.screen.Well.type (java.lang.String)
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setType
public void setType(java.lang.String type)
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getWellSamples
protected java.util.List<WellSample> getWellSamples()
returns wellSamples . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many List ome.model.screen.Well.wellSamples (ome.model.screen.WellSample) Values are indexed by the column "index" on ome.model.screen.WellSample
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setWellSamples
protected void setWellSamples(java.util.List<WellSample> wellSamples)
setter for wellSamples should be avoided. Does not fulfill normal semantics.
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sizeOfWellSamples
public int sizeOfWellSamples()
returns the size of wellSamples. If less than zero, the Set was null.
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iterateWellSamples
public java.util.Iterator<WellSample> iterateWellSamples()
should be used rather than accessing the wellSamples set directly. This method will never return null, but rather will return an instance ofEmptyIterator
. To test for a null collection, see ofsizeOfWellSamples()
is less than zero.
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unmodifiableWellSamples
public java.util.Collection<WellSample> unmodifiableWellSamples()
Returns an unmodifiable collection-view
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collectWellSamples
public <E> java.util.List<E> collectWellSamples(CBlock<E> block)
takes a CBlock and calls the block once for each ome.model.screen.WellSample while collecting the results. Ifblock == null
, then the iterator values themselves are collected. This method usesiterateWellSamples()
internally and so will return a value even if the underlying collection is null.
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addWellSample
public void addWellSample(WellSample target)
use instead of setWellSamples . Makes the necessary call on ome.model.screen.WellSample as well.
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addWellSampleSet
public void addWellSampleSet(java.util.Collection<WellSample> targets)
use like addWellSample.
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removeWellSample
public void removeWellSample(WellSample target)
removes a single element from this set and makes the inverse call on ome.model.screen.WellSample
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removeWellSampleSet
public void removeWellSampleSet(java.util.Collection<WellSample> targets)
use like removeWellSample
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clearWellSamples
public void clearWellSamples()
clears the set.
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getWellSample
public WellSample getWellSample(int index) throws java.lang.IndexOutOfBoundsException
Gets the ome.model.screen.WellSample at the given index.- Throws:
java.lang.IndexOutOfBoundsException
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setWellSample
public WellSample setWellSample(int index, WellSample element) throws java.lang.IndexOutOfBoundsException
Sets the ome.model.screen.WellSample at the given index. Adheres to theList.set(int, Object)
contract. To extend the list, useaddWellSample(WellSample)
.- Throws:
java.lang.IndexOutOfBoundsException
- See Also:
List.set(int, Object)
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getPrimaryWellSample
public WellSample getPrimaryWellSample() throws java.lang.IndexOutOfBoundsException
Gets the first element of wellSamples which can be interpreted as the primary or default element in some situations. If there is not first element, anIndexOutOfBoundsException
is throws. This method will also throw anApiUsageException
if the collection is unloaded. SeesizeOfWellSamples()
for more information.- Throws:
java.lang.IndexOutOfBoundsException
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setPrimaryWellSample
public WellSample setPrimaryWellSample(WellSample element) throws java.lang.IndexOutOfBoundsException
Swaps the first element of wellSamples with the first instance of the given element. If the given element is not in the list, anIndexOutOfBoundsException
will be thrown. Returns the swapped element. This method will also throw anApiUsageException
if the collection is unloaded. SeesizeOfWellSamples()
for more information.- Throws:
java.lang.IndexOutOfBoundsException
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getPlate
public Plate getPlate()
Many-to-one field ome.model.screen.Well.plate (ome.model.screen.Plate)
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setPlate
public void setPlate(Plate plate)
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getAnnotationLinks
protected java.util.Set<WellAnnotationLink> getAnnotationLinks()
returns annotationLinks . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.screen.Well.annotationLinks (ome.model.annotations.WellAnnotationLink)
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setAnnotationLinks
protected void setAnnotationLinks(java.util.Set<WellAnnotationLink> annotationLinks)
setter for annotationLinks should be avoided. Does not fulfill normal semantics.
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sizeOfAnnotationLinks
public int sizeOfAnnotationLinks()
returns the size of annotationLinks. If less than zero, the Set was null.- Specified by:
sizeOfAnnotationLinks
in interfaceIAnnotated
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iterateAnnotationLinks
public java.util.Iterator<WellAnnotationLink> iterateAnnotationLinks()
should be used rather than accessing the annotationLinks set directly. This method will never return null, but rather will return an instance ofEmptyIterator
. To test for a null collection, see ofsizeOfAnnotationLinks()
is less than zero.- Specified by:
iterateAnnotationLinks
in interfaceIAnnotated
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unmodifiableAnnotationLinks
public java.util.Collection<WellAnnotationLink> unmodifiableAnnotationLinks()
Returns an unmodifiable collection-view- Specified by:
unmodifiableAnnotationLinks
in interfaceIAnnotated
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collectAnnotationLinks
public <E> java.util.List<E> collectAnnotationLinks(CBlock<E> block)
takes a CBlock and calls the block once for each ome.model.annotations.WellAnnotationLink while collecting the results. Ifblock == null
, then the iterator values themselves are collected. This method usesiterateAnnotationLinks()
internally and so will return a value even if the underlying collection is null.- Specified by:
collectAnnotationLinks
in interfaceIAnnotated
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addWellAnnotationLink
public void addWellAnnotationLink(WellAnnotationLink target)
use instead of setAnnotationLinks . Makes the necessary call on ome.model.annotations.WellAnnotationLink as well.
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addWellAnnotationLinkSet
public void addWellAnnotationLinkSet(java.util.Collection<WellAnnotationLink> targets)
use like addWellAnnotationLink.
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removeWellAnnotationLink
public void removeWellAnnotationLink(WellAnnotationLink target)
removes a single element from this set and makes the inverse call on ome.model.annotations.WellAnnotationLink
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removeWellAnnotationLinkSet
public void removeWellAnnotationLinkSet(java.util.Collection<WellAnnotationLink> targets)
use like removeWellAnnotationLink
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linkAnnotation
public WellAnnotationLink linkAnnotation(Annotation addition)
Adds a ome.model.annotations.WellAnnotationLink to annotationLinks . This entails changing our annotationLinks Set, creating a new ome.model.annotations.WellAnnotationLink and calling linkAnnotation on the ome.model.annotations.Annotation.- Specified by:
linkAnnotation
in interfaceIAnnotated
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addWellAnnotationLink
public void addWellAnnotationLink(WellAnnotationLink link, boolean bothSides)
Adds a ome.model.annotations.WellAnnotationLink to annotationLinks, allowing for recursion -- whether or not addWellAnnotationLink will be called on the addition if it is loaded
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linkedAnnotationIterator
public java.util.Iterator<Annotation> linkedAnnotationIterator()
provides an iterator over the parent values of the annotationLinks. Like with most Collection iterators, modifications to the underlying collection while iterating will result in anConcurrentModificationException
. UselinkedAnnotationList()
instead.- Specified by:
linkedAnnotationIterator
in interfaceIAnnotated
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findWellAnnotationLink
public java.util.Set<WellAnnotationLink> findWellAnnotationLink(Annotation target)
find all ome.model.annotations.WellAnnotationLink which have the argument as their child.
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linkedAnnotationList
public java.util.List<Annotation> linkedAnnotationList()
produces aList
-copy of the underlying collection. Unlike,linkedAnnotationIterator()
, while using the returnedList
, modifications can be made to the underlying collection without throwingConcurrentModificationException
.- Specified by:
linkedAnnotationList
in interfaceIAnnotated
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eachLinkedAnnotation
public <E> java.util.List<E> eachLinkedAnnotation(CBlock<E> block)
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results. Ifblock == null
, then the iterator values themselves are collected.- Specified by:
eachLinkedAnnotation
in interfaceIAnnotated
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unlinkAnnotation
public void unlinkAnnotation(Annotation removal)
unlinks all ome.model.annotations.Annotation instances from this instance.- Specified by:
unlinkAnnotation
in interfaceIAnnotated
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removeWellAnnotationLink
public void removeWellAnnotationLink(WellAnnotationLink link, boolean bothSides)
removes the given WellAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkWell again if loaded.
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clearAnnotationLinks
public void clearAnnotationLinks()
clears the set.- Specified by:
clearAnnotationLinks
in interfaceIAnnotated
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setAnnotationLinksCountPerOwner
protected void setAnnotationLinksCountPerOwner(java.util.Map<java.lang.Long,java.lang.Long> map)
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getAnnotationLinksCountPerOwner
public java.util.Map<java.lang.Long,java.lang.Long> getAnnotationLinksCountPerOwner()
If fetched, returns the count(*) of ome.model.annotations.WellAnnotationLink that a user has. If unfetched, returns null. No entries in the collection should be null.
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getDetails
public Details getDetails()
The details of this object correspond to low-level system information. Owner, permissions, Details is always guaranteed to be non-null, unless the user actively nulls it. Every entity also contains a Detail reference, which doesn't refer to a separate table but rather to a collection of fields collected into a Hibernate "component" which is embedded in the object. HQL queries which refer to the Details component cannot directly fetch the entity like this: select o from Object join fetch o.details but rather each field of the Details instance must be explicitly joined: select o from Object join fetch o.details.owner It should also be noted that not all types have all the fields which are present on Details. For example, select e from Experimenter e join fetch e.details.owner will fail. Experimenter has no owner, for obvious reasons. Note: subclasses of this class will return a subclass of theDetails
type.- Specified by:
getDetails
in interfaceIObject
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setDetails
protected void setDetails(Details details)
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isValid
public boolean isValid()
Description copied from interface:IObject
calls the class-specific validator for this instance and returns the value fromValidation.isValid()
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validate
public Validation validate()
Description copied from interface:IObject
calls the class-specific validator for this instance and returns theValidation
object.
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newInstance
public Well newInstance()
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proxy
public Well proxy()
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acceptFilter
public boolean acceptFilter(Filter __filter)
- Specified by:
acceptFilter
in interfaceFilterable
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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fields
public java.util.Set<java.lang.String> fields()
Description copied from interface:IObject
returns a Set of field names that belong to this class
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retrieve
public java.lang.Object retrieve(java.lang.String field)
Description copied from interface:IObject
retrieves a value from this instance. Values forfield
which match a field of this instance will be delegated to the accessors. Otherwise, values will be retrieved from a lazy-loaded map filled by calls toIObject.putAt(String, Object)
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putAt
public void putAt(java.lang.String field, java.lang.Object value)
Description copied from interface:IObject
stores a value in this instance. Values forfield
which match a field of this instance will be delegated to the accessors. Otherwise, values will be stored in a lazy-loaded map.
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isLoaded
public boolean isLoaded()
Description copied from interface:IObject
transient field (not stored in the DB) which specifies whether this object has been loaded from the DB or is only a wrapper around the ID.
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errorIfUnloaded
protected void errorIfUnloaded()
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unload
public void unload()
Description copied from interface:IObject
set the loaded field to false, and set all non-ID fields to null. Subsequent calls to all accessors other than getId/setId will throw an ApiUsageException
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getGraphHolder
public final GraphHolder getGraphHolder()
Description copied from interface:IObject
retrieves theGraphHolder
for this entity. If the GraphHolder has not been actively set, a new one will be instatiated.- Specified by:
getGraphHolder
in interfaceIObject
- Returns:
- Non-null GraphHolder
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throwNullCollectionException
protected void throwNullCollectionException(java.lang.String propertyName)
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