ome.formats.model

Interface IObjectContainerStore

All Known Implementing Classes:

OMEROMetadataStoreClient

public interface IObjectContainerStore

An object that handles the storage and manipulation of IObject containers and their references. This interface is generally used in tandem with the Bio-Formats defined MetadataStore.

Author:

Chris Allan

Method Summary

Methods

Modifier and Type	Method and Description
void	addReference(ome.util.LSID source, ome.util.LSID target) Adds a reference to the reference cache.
int	countCachedContainers(Class<? extends omero.model.IObject> klass, int... indexes) Counts the number of containers the MetadataStore has of a given class and at a given index of the hierarchy if specified.
int	countCachedReferences(Class<? extends omero.model.IObject> source, Class<? extends omero.model.IObject> target) Counts the number of references the MetadataStore has between objects of two classes.
Map<Class<? extends omero.model.IObject>,Map<String,omero.metadatastore.IObjectContainer>>	getAuthoritativeContainerCache() Returns the current authoritative LSID container cache.
Map<ome.util.LSID,omero.metadatastore.IObjectContainer>	getContainerCache() Returns the current container cache.
omero.metadatastore.IObjectContainer	getIObjectContainer(Class<? extends omero.model.IObject> klass, LinkedHashMap<Index,Integer> indexes) Retrieves an IObject container for a given class and location within the OME-XML data model.
List<omero.metadatastore.IObjectContainer>	getIObjectContainers(Class<? extends omero.model.IObject> klass) Retrieves all IObject containers of a given class.
loci.formats.IFormatReader	getReader() Returns the current Bio-Formats reader that has been used to populate the container store.
Map<ome.util.LSID,List<ome.util.LSID>>	getReferenceCache() Returns the current reference cache.
Map<String,String[]>	getReferenceStringCache() Returns the current string based reference cache.
omero.model.IObject	getSourceObject(ome.util.LSID LSID) Retrieves an OMERO Blitz source object for a given LSID.
<T extends omero.model.IObject> List<T>	getSourceObjects(Class<T> klass) Retrieves all OMERO Blitz source objects of a given class.
List<omero.model.Annotation>	getUserSpecifiedAnnotations() Returns the user specified annotations.
String	getUserSpecifiedDescription() Returns the user specified image/plate description.
String	getUserSpecifiedName() Returns the user specified image/plate name.
Double[]	getUserSpecifiedPhysicalPixelSizes() Returns the user specified physical pixel sizes.
omero.model.IObject	getUserSpecifiedTarget() Returns the user specified linkage target (usually a Dataset for Images and a Screen for Plates).
boolean	hasReference(ome.util.LSID source, ome.util.LSID target) Checks to see if there is currently an active reference for two LSIDs.
void	removeIObjectContainer(ome.util.LSID lsid) Removes an IObject container from within the OME-XML data model store.
void	setReader(loci.formats.IFormatReader reader) Sets the Bio-Formats reader that will be used to populate the container store.
void	setReferenceStringCache(Map<String,String[]> referenceStringCache) Sets the string based reference cache for this container store.
void	setUserSpecifiedAnnotations(List<omero.model.Annotation> annotations) Sets the user specified image annotations.
void	setUserSpecifiedDescription(String description) Sets the user specified image/plate description.
void	setUserSpecifiedName(String name) Sets the user specified image/plate name.
void	setUserSpecifiedPhysicalPixelSizes(Double physicalSizeX, Double physicalSizeY, Double physicalSizeZ) Sets the user specified physical pixel sizes.
void	setUserSpecifiedTarget(omero.model.IObject target) Sets the user specified linkage target (usually a Dataset for Images and a Screen for Plates).

Method Detail

getReader

loci.formats.IFormatReader getReader()

Returns the current Bio-Formats reader that has been used to populate the container store.

Returns:

See above.

setReader

void setReader(loci.formats.IFormatReader reader)

Sets the Bio-Formats reader that will be used to populate the container store.

Parameters:

reader - Bio-Formats reader.

getUserSpecifiedAnnotations

List<omero.model.Annotation> getUserSpecifiedAnnotations()

Returns the user specified annotations.

Returns:

See above.

setUserSpecifiedAnnotations

void setUserSpecifiedAnnotations(List<omero.model.Annotation> annotations)

Sets the user specified image annotations.

Parameters:

annotations - user specified annotations

getUserSpecifiedName

String getUserSpecifiedName()

Returns the user specified image/plate name.

Returns:

See above.

setUserSpecifiedName

void setUserSpecifiedName(String name)

Sets the user specified image/plate name.

Parameters:

name - user specified image/plate name

getUserSpecifiedDescription

String getUserSpecifiedDescription()

Returns the user specified image/plate description.

Returns:

See above.

setUserSpecifiedDescription

void setUserSpecifiedDescription(String description)

Sets the user specified image/plate description.

Parameters:

name - user specified image/plate description

getUserSpecifiedTarget

omero.model.IObject getUserSpecifiedTarget()

Returns the user specified linkage target (usually a Dataset for Images and a Screen for Plates).

Returns:

See above.

setUserSpecifiedTarget

void setUserSpecifiedTarget(omero.model.IObject target)

Sets the user specified linkage target (usually a Dataset for Images and a Screen for Plates).

Parameters:

name - user specified image description

getUserSpecifiedPhysicalPixelSizes

Double[] getUserSpecifiedPhysicalPixelSizes()

Returns the user specified physical pixel sizes.

Returns:

An array of double[] { physicalSizeX, physicalSizeY, physicalSizeZ } as specified by the user. A value of null for any one index states the user has not made a choice for the size of that particular dimension.

setUserSpecifiedPhysicalPixelSizes

void setUserSpecifiedPhysicalPixelSizes(Double physicalSizeX,
                                      Double physicalSizeY,
                                      Double physicalSizeZ)

Sets the user specified physical pixel sizes. A value of null states the original file physical size for that dimension should be used.

Parameters:

physicalSizeX - Physical pixel size width.

physicalSizeY - Physical pixel height.

physicalSizeZ - Physical pixel depth.

getAuthoritativeContainerCache

Map<Class<? extends omero.model.IObject>,Map<String,omero.metadatastore.IObjectContainer>> getAuthoritativeContainerCache()

Returns the current authoritative LSID container cache. This container cache records the explicitly set LSID to container references.

Returns:

See above.

getContainerCache

Map<ome.util.LSID,omero.metadatastore.IObjectContainer> getContainerCache()

Returns the current container cache.

Returns:

See above.

getReferenceCache

Map<ome.util.LSID,List<ome.util.LSID>> getReferenceCache()

Returns the current reference cache.

Returns:

See above.

addReference

void addReference(ome.util.LSID source,
                ome.util.LSID target)

Adds a reference to the reference cache.

Parameters:

source - Source LSID to add.

target - Target LSID to add.

getReferenceStringCache

Map<String,String[]> getReferenceStringCache()

Returns the current string based reference cache. This is usually populated by a ReferenceProcessor instance.

Returns:

See above.

setReferenceStringCache

void setReferenceStringCache(Map<String,String[]> referenceStringCache)

Sets the string based reference cache for this container store. This is usually called by a ReferenceProcessor instance.

Parameters:

referenceStringCache - String based reference cache to use.

getSourceObject

omero.model.IObject getSourceObject(ome.util.LSID LSID)

Retrieves an OMERO Blitz source object for a given LSID.

Parameters:

LSID - LSID to retrieve a source object for.

Returns:

See above.

getSourceObjects

<T extends omero.model.IObject> List<T> getSourceObjects(Class<T> klass)

Retrieves all OMERO Blitz source objects of a given class.

Parameters:

klass - Class to retrieve source objects for.

Returns:

See above.

getIObjectContainer

omero.metadatastore.IObjectContainer getIObjectContainer(Class<? extends omero.model.IObject> klass,
                                                       LinkedHashMap<Index,Integer> indexes)

Retrieves an IObject container for a given class and location within the OME-XML data model. NOTE: The container will be created if it does not already exist.

Parameters:

klass - Class to retrieve a container for.

indexes - Indexes into the OME-XML data model.

Returns:

See above.

removeIObjectContainer

void removeIObjectContainer(ome.util.LSID lsid)

Removes an IObject container from within the OME-XML data model store.

Parameters:

lsid - LSID of the container to remove.

getIObjectContainers

List<omero.metadatastore.IObjectContainer> getIObjectContainers(Class<? extends omero.model.IObject> klass)

Retrieves all IObject containers of a given class. NOTE: this will only return existing containers.

Parameters:

klass - Class to retrieve containers for.

Returns:

See above.

countCachedContainers

int countCachedContainers(Class<? extends omero.model.IObject> klass,
                        int... indexes)

Counts the number of containers the MetadataStore has of a given class and at a given index of the hierarchy if specified.

Parameters:

klass - Class to count containers of.

indexes - Indexes to use in the container count. For example, if klass is Image and indexes is int[] { 0 }; only containers that have an LSID of type Image and a first index of 0 will be counted.

Returns:

See above.

countCachedReferences

int countCachedReferences(Class<? extends omero.model.IObject> source,
                        Class<? extends omero.model.IObject> target)

Counts the number of references the MetadataStore has between objects of two classes.

Parameters:

source - Class of the source object. If null it is treated as a wild card, all references whose target match target will be counted.

target - Class of the target object. If null it is treated as a wild card, all references whose source match source will be counted.

Returns:

See above.

hasReference

boolean hasReference(ome.util.LSID source,
                   ome.util.LSID target)

Checks to see if there is currently an active reference for two LSIDs.

Parameters:

source - LSID of the source object.

target - LSID of the target object.

Returns:

true if a reference exists, false otherwise.