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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.
Method Summary | ||
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void |
addReference(ome.util.LSID source,
ome.util.LSID target)
Adds a reference to the reference cache. |
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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. |
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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. |
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Map<Class<? extends omero.model.IObject>,Map<String,omero.metadatastore.IObjectContainer>> |
getAuthoritativeContainerCache()
Returns the current authoritative LSID container cache. |
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Map<ome.util.LSID,omero.metadatastore.IObjectContainer> |
getContainerCache()
Returns the current container cache. |
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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. |
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List<omero.metadatastore.IObjectContainer> |
getIObjectContainers(Class<? extends omero.model.IObject> klass)
Retrieves all IObject containers of a given class. |
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loci.formats.IFormatReader |
getReader()
Returns the current Bio-Formats reader that has been used to populate the container store. |
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Map<ome.util.LSID,List<ome.util.LSID>> |
getReferenceCache()
Returns the current reference cache. |
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Map<String,String[]> |
getReferenceStringCache()
Returns the current string based reference cache. |
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omero.model.IObject |
getSourceObject(ome.util.LSID LSID)
Retrieves an OMERO Blitz source object for a given LSID. |
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getSourceObjects(Class<T> klass)
Retrieves all OMERO Blitz source objects of a given class. |
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List<omero.model.Annotation> |
getUserSpecifiedAnnotations()
Returns the user specified annotations. |
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String |
getUserSpecifiedImageDescription()
Returns the user specified image description. |
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String |
getUserSpecifiedImageName()
Returns the user specified image name. |
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Double[] |
getUserSpecifiedPhysicalPixelSizes()
Returns the user specified physical pixel sizes. |
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String |
getUserSpecifiedPlateDescription()
Returns the user specified plate description. |
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String |
getUserSpecifiedPlateName()
Returns the user specified plate name. |
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omero.model.IObject |
getUserSpecifiedTarget()
Returns the user specified linkage target (usually a Dataset for Images and a Screen for Plates). |
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boolean |
hasReference(ome.util.LSID source,
ome.util.LSID target)
Checks to see if there is currently an active reference for two LSIDs. |
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void |
removeIObjectContainer(ome.util.LSID lsid)
Removes an IObject container from within the OME-XML data model store. |
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void |
setReader(loci.formats.IFormatReader reader)
Sets the Bio-Formats reader that will be used to populate the container store. |
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void |
setReferenceStringCache(Map<String,String[]> referenceStringCache)
Sets the string based reference cache for this container store. |
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void |
setUserSpecifiedAnnotations(List<omero.model.Annotation> annotations)
Sets the user specified image annotations. |
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void |
setUserSpecifiedImageDescription(String description)
Sets the user specified image description. |
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void |
setUserSpecifiedImageName(String name)
Sets the user specified image name. |
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void |
setUserSpecifiedPhysicalPixelSizes(Double physicalSizeX,
Double physicalSizeY,
Double physicalSizeZ)
Sets the user specified physical pixel sizes. |
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void |
setUserSpecifiedPlateDescription(String description)
Sets the user specified plate description. |
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void |
setUserSpecifiedPlateName(String name)
Sets the user specified plate name. |
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void |
setUserSpecifiedTarget(omero.model.IObject target)
Sets the user specified linkage target (usually a Dataset for Images and a Screen for Plates). |
Method Detail |
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loci.formats.IFormatReader getReader()
void setReader(loci.formats.IFormatReader reader)
reader
- Bio-Formats reader.List<omero.model.Annotation> getUserSpecifiedAnnotations()
void setUserSpecifiedAnnotations(List<omero.model.Annotation> annotations)
annotations
- user specified annotationsString getUserSpecifiedImageName()
void setUserSpecifiedImageName(String name)
name
- user specified image nameString getUserSpecifiedImageDescription()
void setUserSpecifiedImageDescription(String description)
name
- user specified image descriptionString getUserSpecifiedPlateName()
void setUserSpecifiedPlateName(String name)
name
- user specified plate nameString getUserSpecifiedPlateDescription()
void setUserSpecifiedPlateDescription(String description)
name
- user specified plate descriptionomero.model.IObject getUserSpecifiedTarget()
void setUserSpecifiedTarget(omero.model.IObject target)
name
- user specified image descriptionDouble[] getUserSpecifiedPhysicalPixelSizes()
null
for any one index states the user has not made a choice for the size
of that particular dimension.void setUserSpecifiedPhysicalPixelSizes(Double physicalSizeX, Double physicalSizeY, Double physicalSizeZ)
null
states the original file physical size for that
dimension should be used.
physicalSizeX
- Physical pixel size width.physicalSizeY
- Physical pixel height.physicalSizeZ
- Physical pixel depth.Map<Class<? extends omero.model.IObject>,Map<String,omero.metadatastore.IObjectContainer>> getAuthoritativeContainerCache()
Map<ome.util.LSID,omero.metadatastore.IObjectContainer> getContainerCache()
Map<ome.util.LSID,List<ome.util.LSID>> getReferenceCache()
void addReference(ome.util.LSID source, ome.util.LSID target)
source
- Source LSID to add.target
- Target LSID to add.Map<String,String[]> getReferenceStringCache()
void setReferenceStringCache(Map<String,String[]> referenceStringCache)
referenceStringCache
- String based reference cache to use.omero.model.IObject getSourceObject(ome.util.LSID LSID)
LSID
- LSID to retrieve a source object for.
<T extends omero.model.IObject> List<T> getSourceObjects(Class<T> klass)
klass
- Class to retrieve source objects for.
omero.metadatastore.IObjectContainer getIObjectContainer(Class<? extends omero.model.IObject> klass, LinkedHashMap<Index,Integer> indexes)
klass
- Class to retrieve a container for.indexes
- Indexes into the OME-XML data model.
void removeIObjectContainer(ome.util.LSID lsid)
lsid
- LSID of the container to remove.List<omero.metadatastore.IObjectContainer> getIObjectContainers(Class<? extends omero.model.IObject> klass)
klass
- Class to retrieve containers for.
int countCachedContainers(Class<? extends omero.model.IObject> klass, int... indexes)
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.
int countCachedReferences(Class<? extends omero.model.IObject> source, Class<? extends omero.model.IObject> target)
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.
boolean hasReference(ome.util.LSID source, ome.util.LSID target)
source
- LSID of the source object.target
- LSID of the target object.
true
if a reference exists, false
otherwise.
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Version: 4.3.4-dbcbce5a-b4
Copyright © 2009 The University of Dundee. All Rights Reserved.