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
 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 getUserSpecifiedImageDescription()
          Returns the user specified image description.
 String getUserSpecifiedImageName()
          Returns the user specified image name.
 Double[] getUserSpecifiedPhysicalPixelSizes()
          Returns the user specified physical pixel sizes.
 String getUserSpecifiedPlateDescription()
          Returns the user specified plate description.
 String getUserSpecifiedPlateName()
          Returns the user specified plate name.
 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 setUserSpecifiedImageDescription(String description)
          Sets the user specified image description.
 void setUserSpecifiedImageName(String name)
          Sets the user specified image name.
 void setUserSpecifiedPhysicalPixelSizes(Double physicalSizeX, Double physicalSizeY, Double physicalSizeZ)
          Sets the user specified physical pixel sizes.
 void setUserSpecifiedPlateDescription(String description)
          Sets the user specified plate description.
 void setUserSpecifiedPlateName(String name)
          Sets the user specified plate name.
 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

getUserSpecifiedImageName

String getUserSpecifiedImageName()
Returns the user specified image name.

Returns:
See above.

setUserSpecifiedImageName

void setUserSpecifiedImageName(String name)
Sets the user specified image name.

Parameters:
name - user specified image name

getUserSpecifiedImageDescription

String getUserSpecifiedImageDescription()
Returns the user specified image description.

Returns:
See above.

setUserSpecifiedImageDescription

void setUserSpecifiedImageDescription(String description)
Sets the user specified image description.

Parameters:
name - user specified image description

getUserSpecifiedPlateName

String getUserSpecifiedPlateName()
Returns the user specified plate name.

Returns:
See above.

setUserSpecifiedPlateName

void setUserSpecifiedPlateName(String name)
Sets the user specified plate name.

Parameters:
name - user specified plate name

getUserSpecifiedPlateDescription

String getUserSpecifiedPlateDescription()
Returns the user specified plate description.

Returns:
See above.

setUserSpecifiedPlateDescription

void setUserSpecifiedPlateDescription(String description)
Sets the user specified plate description.

Parameters:
name - user specified 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.


OmeroJava Api

Version: 4.3.3-00d1137e-b2894

Copyright © 2009 The University of Dundee. All Rights Reserved.