Index (omero-common 5.7.0 API)

A B C D E F G H I J L M N O P Q R S T U V W X Z
All Classes All Packages

A

AbstractChecksumProvider - Class in ome.util.checksum: Abstract skeleton class implementing ChecksumProvider and providing implementations of the interface methods using a universal checksum class object.
AbstractChecksumProvider(HashFunction) - Constructor for class ome.util.checksum.AbstractChecksumProvider: Protected constructor.
activate() - Method in interface ome.api.StatefulServiceInterface: Completely restore this service for active use from whatever passivation it has implemented.
activate(long) - Method in interface ome.api.IShare: Deprecated.

Turns on the access control lists attached to the given share for the current session.
activeQueries() - Method in interface ome.api.Search: Returns the number of active queries.
addCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine: Deprecated.
addCodomainMapToChannel(CodomainMapContext, int) - Method in interface omeis.providers.re.RenderingEngine: Adds the context to the mapping chain.
addComment(long, String) - Method in interface ome.api.IShare: Deprecated.

Creates comment for share.
addGroupOwners(ExperimenterGroup, Experimenter...) - Method in interface ome.api.IAdmin: adds the given users to the owner list for this group.
addGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.api.IAdmin: adds a user to the given groups.
addGuest(long, String) - Method in interface ome.api.IShare: Deprecated.

Add guest email address to the share.
addGuests(long, String...) - Method in interface ome.api.IShare: Deprecated.

Adds guest email addresses to the share.
addObject(long, T) - Method in interface ome.api.IShare: Deprecated.

Adds new item to share.
addObjects(long, T...) - Method in interface ome.api.IShare: Deprecated.

Adds new items to share.
addOrderByAsc(String) - Method in interface ome.api.Search: A path from the target entity which will be added to the current stack of order statements applied to the query.
addOrderByDesc(String) - Method in interface ome.api.Search: A path from the target entity which will be added to the current stack of order statements applied to the query.
addReply(long, String, CommentAnnotation) - Method in interface ome.api.IShare: Deprecated.

Creates comment which replies to an existing comment.
addUser(long, Experimenter) - Method in interface ome.api.IShare: Deprecated.

Adds experimenter to share
addUsers(long, Experimenter...) - Method in interface ome.api.IShare: Deprecated.

Adds experimenters to share
ADLER32 - ome.util.checksum.ChecksumType
Adler32ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using Adler32 as the message digest algorithm.
Adler32ChecksumProviderImpl() - Constructor for class ome.util.checksum.Adler32ChecksumProviderImpl
admin - ome.system.Preference.Visibility
adminPrivileges - Variable in class ome.system.SimpleEventContext
afterPropertiesSet() - Method in class ome.system.metrics.DefaultMetrics
all - ome.system.Preference.Visibility
allEnumerations(Class<T>) - Method in interface ome.api.ITypes
ALLOW_LEADING_WILDCARD - Static variable in interface ome.api.Search: Default leading-wildcard setting
allTypes() - Method in interface ome.api.Search: Permits all types to be returned.
and() - Method in interface ome.api.Search: Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the intersection of the two calls.
AnnotationUtils - Class in ome.annotations: Checks metadata constraints on API calls.
AnnotationUtils() - Constructor for class ome.annotations.AnnotationUtils
ApiConstraintChecker - Class in ome.annotations: Checks metadata constraints on API calls.
ApiConstraintChecker() - Constructor for class ome.annotations.ApiConstraintChecker
append(ILoggingEvent) - Method in class ome.util.logback.SiftingWhileRejectingDefaultAppender
applyBeanPropertyValues(Object, Class<? extends ServiceInterface>) - Method in class ome.system.OmeroContext: Uses the methods of this context's BeanFactory to autowire any Object based on the service class.
applyBeanPropertyValues(Object, String) - Method in class ome.system.OmeroContext: Uses the methods of this context's BeanFactory to autowire any Object based on the given beanName.
applySettingsToDataset(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to all images in a given Dataset.
applySettingsToImage(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to a given Image.
applySettingsToImages(long, List<Long>) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to a given Image.
applySettingsToPixels(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to a given Pixels.
applySettingsToProject(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to all images in all Datasets of a given Project.
applySettingsToSet(long, Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to one or many containers.
asProperties() - Method in class ome.system.Login: produces a copy of the internal fields as a Properties instance.
asProperties() - Method in class ome.system.Server: produces a copy of the internal fields as a Properties instance.
attach(long) - Method in interface ome.api.JobHandle

B

B_BAND - Static variable in class omeis.providers.re.RGBBuffer: Index of the blue band in the image's data buffer.
BIT_EIGHT - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 8 i.e.
BIT_FIVE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 5 i.e.
BIT_FOUR - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 4 i.e.
BIT_ONE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 1 i.e.
BIT_SEVEN - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 7 i.e.
BIT_SIX - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 6 i.e.
BIT_THREE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 3 i.e.
BIT_TWO - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 2 i.e.
BIT_ZERO - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 0 i.e.
blues - Variable in class omeis.providers.re.lut.LutReader: Holds the blues values.
buildLuceneQuery(List<String>, String) - Static method in class ome.util.search.LuceneQueryBuilder: Builds a query with the provided input terms over the given fields
buildLuceneQuery(List<String>, Date, Date, String, String) - Static method in class ome.util.search.LuceneQueryBuilder: Builds a query with the provided input terms over the given fields
byAnnotatedWith(Annotation...) - Method in interface ome.api.Search: Finds entities annotated with an Annotation similar to the example.
byFullText(String) - Method in interface ome.api.Search: Passes the query as is to the Lucene backend.
byGroupForTags(String) - Method in interface ome.api.Search: Returns transient (without ID) TagAnnotation instances which represent all the tags in the given group.
byHqlQuery(String, Parameters) - Method in interface ome.api.Search: Delegates to IQuery.findAllByQuery(String, Parameters) method to take advantage of the Search.and(), Search.or(), and Search.not() methods, or queue-semantics.
byLuceneQueryBuilder(String, String, String, String, String) - Method in interface ome.api.Search: Builds a Lucene query and passes it to the Lucene backend.
bySimilarTerms(String...) - Method in interface ome.api.Search: Returns transient (without ID) TextAnnotation instances which represent terms which are similar to the given terms.
bySomeMustNone(String[], String[], String[]) - Method in interface ome.api.Search: Builds a Lucene query and passes it to Search.byFullText(String).
byTagForGroups(String) - Method in interface ome.api.Search: Creates a query which will return transient (without ID) TagAnnotation instances which represent all the tag groups which the given tag belongs to.

C

calculateMessageDigest() - Method in interface ome.api.RawPixelsStore
cancelJob() - Method in interface ome.api.JobHandle: Marks a job for cancellation.
CANCELLED - Static variable in interface ome.api.JobHandle
canRead(EventContext, String) - Method in class ome.system.PreferenceContext
canUpdate(IObject) - Method in interface ome.api.IAdmin: Returns true if the currently logged in user can modify the given IObject.
ceId - Variable in class ome.system.SimpleEventContext
ceType - Variable in class ome.system.SimpleEventContext
cgId - Variable in class ome.system.SimpleEventContext
cgName - Variable in class ome.system.SimpleEventContext
changeExpiredCredentials(String, String, String) - Method in interface ome.api.IAdmin: Used after an ExpiredCredentialException instance is thrown.
changeGroup(IObject, String) - Method in interface ome.api.IAdmin: call details.setGroup() on this instance.
changeOwner(IObject, String) - Method in interface ome.api.IAdmin: call details.setOwner() on this instance.
changePassword(String) - Method in interface ome.api.IAdmin: change the password for the current user.
changePasswordWithOldPassword(String, String) - Method in interface ome.api.IAdmin: change the password for the current user by passing the old password.
changePermissions(IObject, Permissions) - Method in interface ome.api.IAdmin: call defaults.setPermissions() on this instance.
changeUserPassword(String, String) - Method in interface ome.api.IAdmin: change the password for the a given user.
checkDatabase(String) - Method in class ome.system.PreferenceContext
checkImageDelete(long, boolean) - Method in interface ome.api.IDelete: Returns all entities which would prevent the given Image id from being deleted.
checksumAsBytes() - Method in class ome.util.checksum.AbstractChecksumProvider
checksumAsBytes() - Method in interface ome.util.checksum.ChecksumProvider: Returns a byte array representation of the calculated checksum.
checksumAsBytes() - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
checksumAsString() - Method in class ome.util.checksum.AbstractChecksumProvider
checksumAsString() - Method in interface ome.util.checksum.ChecksumProvider: Returns a String representing the checksum in hex form.
checksumAsString() - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
ChecksumProvider - Interface in ome.util.checksum: An interface producing checksums or message digests (depending on the implementing class) of a given type of input.
ChecksumProviderFactory - Interface in ome.util.checksum: A factory producing throw-away objects of the ChecksumProvider type.
ChecksumProviderFactoryImpl - Class in ome.util.checksum: An implementation of the ChecksumProviderFactory interface.
ChecksumProviderFactoryImpl() - Constructor for class ome.util.checksum.ChecksumProviderFactoryImpl
ChecksumType - Enum in ome.util.checksum: Enumeration defining the possible algorithms used for calculating checksums.
clearQueries() - Method in interface ome.api.Search: Removes all active queries (leaving settings alone), such that Search.activeQueries() will return 0.
CLIENT_CONTEXT - Static variable in class ome.system.OmeroContext: identifier for an OmeroContext configured in classpath*:beanRefContext.xml for use by remote (via JNDI/RMI) clients.
close() - Method in interface ome.api.StatefulServiceInterface: signals the end of the service lifecycle.
closeAll() - Method in class ome.system.OmeroContext: closes all the nested OmeroContexts within this instance.
closeSession() - Method in class ome.system.ServiceFactory
closeSession(Session) - Method in interface ome.api.ISession: Closes session and releases all resources.
closeShare(long) - Method in interface ome.api.IShare: Deprecated.

Closes share.
CodomainMap - Interface in omeis.providers.re.codomain: Declares the interface common to all codomain maps.
CodomainMapContext - Class in omeis.providers.re.codomain: Each concrete subclass defines transformation parameters for a CodomainMap implementation.
CodomainMapContext() - Constructor for class omeis.providers.re.codomain.CodomainMapContext
containedExperimenters(long) - Method in interface ome.api.IAdmin: fetch all users contained in this group.
containedGroups(long) - Method in interface ome.api.IAdmin: fetch all groups of which the given user is a member.
Context(Timer.Context) - Constructor for class ome.system.metrics.DefaultTimer.Context
ContrastStretchingContext - Class in omeis.providers.re.codomain: Two points pStart and pEnd define the context of this transformation.
ContrastStretchingContext() - Constructor for class omeis.providers.re.codomain.ContrastStretchingContext
copy() - Method in class omeis.providers.re.codomain.CodomainMapContext: Returns a deep copy of this object.
copy() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Implemented as specified by superclass.
copy() - Method in class omeis.providers.re.codomain.IdentityMapContext: Implemented as specified by superclass.
copy() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Implemented as specified by superclass.
copy() - Method in class omeis.providers.re.codomain.ReverseIntensityContext: Deprecated.

Implemented as specified by superclass.
copy(EventContext) - Method in class ome.system.SimpleEventContext: Copies all values directly from the given instance into this instance.
copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in interface ome.api.IPixels: Copies the metadata, and only the metadata linked to a Image object into a new Image object of equal or differing size across one or many of its three physical dimensions or temporal dimension.
copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in interface ome.api.IPixels: Copies the metadata, and only the metadata linked to a Pixels object into a new Pixels object of equal or differing size across one or many of its three physical dimensions or temporal dimension.
countAnnotationsUsedNotOwned(Class, long) - Method in interface ome.api.IMetadata: Counts the number of annotation of a given type used by the specified user but not owned by the user.
counter(Object, String) - Method in class ome.system.metrics.DefaultMetrics
counter(Object, String) - Method in interface ome.system.metrics.Metrics
counter(Object, String) - Method in class ome.system.metrics.NullMetrics
Counter - Interface in ome.system.metrics: Thin wrapper around Counter
countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata: Counts the number of annotation of a given type.
CRC32 - ome.util.checksum.ChecksumType
CRC32ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using CRC32 as the message digest algorithm.
CRC32ChecksumProviderImpl() - Constructor for class ome.util.checksum.CRC32ChecksumProviderImpl
createDataObject(T, Parameters) - Method in interface ome.api.IContainer: Creates the specified data object.
createDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer: convenience method to save network calls.
createEnumeration(T) - Method in interface ome.api.ITypes
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin: create and return a new user in the given groups.
createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin: create and return a new user in the given groups with password.
createGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin: create and return a new group.
createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in interface ome.api.IPixels: Creates the metadata, and only the metadata linked to an Image object.
createJobHandle() - Method in class ome.system.ServiceFactory: create a new JobHandle proxy.
createNewRenderingDef(Pixels) - Method in interface ome.api.IRenderingSettings: Creates a new rendering definition object along with its sub-objects.
createPrincipal() - Method in class ome.system.SessionInitializer
createRawFileStore() - Method in class ome.system.ServiceFactory: create a new RawFileStore proxy.
createRawPixelsStore() - Method in class ome.system.ServiceFactory: create a new RawPixelsStore proxy.
createRenderingEngine() - Method in class ome.system.ServiceFactory: create a new RenderingEngine proxy.
createRestrictedSystemUser(Experimenter, List<AdminPrivilege>) - Method in interface ome.api.IAdmin: Create and return a new system user.
createRestrictedSystemUserWithPassword(Experimenter, List<AdminPrivilege>, String) - Method in interface ome.api.IAdmin: Create and return a new system user.
createSearchService() - Method in class ome.system.ServiceFactory: create a new Search proxy.
createSession(Principal, String) - Method in interface ome.api.ISession: Creates a new session and returns it to the user.
createSessionWithTimeout(Principal, long) - Method in interface ome.api.ISession: Allows an admin to create a Session for the give Principal
createSessionWithTimeouts(Principal, long, long) - Method in interface ome.api.ISession: Allows an admin to create a Session for the give Principal
createShare(String, Timestamp, List<T>, List<Experimenter>, List<String>, boolean) - Method in interface ome.api.IShare: Deprecated.

Creates share with all related: items, members, and guests.
createSystemUser(Experimenter) - Method in interface ome.api.IAdmin: create and return a new system user.
createThumbnail(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Creates a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) in the on-disk cache.
createThumbnails() - Method in interface ome.api.ThumbnailStore: Creates thumbnails for a pixels set using a given set of rendering settings (RenderingDef) in the on-disk cache for every sizeX/sizeY combination already cached.
createThumbnailsByLongestSideSet(Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore: Creates thumbnails for a number of pixels sets using a given set of rendering settings (RenderingDef) in the on-disk cache.
createThumbnailService() - Method in class ome.system.ServiceFactory: create a new ThumbnailStore proxy.
createUser(String) - Method in interface ome.api.ILdap: Creates an Experimenter entry in the OMERO DB based on the supplied LDAP username.
createUser(Experimenter, String) - Method in interface ome.api.IAdmin: create and return a new user.
createUserSession(long, long, String) - Method in interface ome.api.ISession: Allows a user to open up another session for him/herself with the given defaults without needing to re-enter password.
credentials - Variable in class ome.system.SessionInitializer
csId - Variable in class ome.system.SimpleEventContext
csName - Variable in class ome.system.SimpleEventContext
csuId - Variable in class ome.system.SimpleEventContext
csuName - Variable in class ome.system.SimpleEventContext
ctx - Variable in class ome.system.ServiceFactory: the context instance which this ServiceFactory uses to look up all of its state.
cuId - Variable in class ome.system.SimpleEventContext
cuName - Variable in class ome.system.SimpleEventContext
currentMetadata() - Method in interface ome.api.Search: Provides access to the extra query information (for example Lucene score and boost values) for a single call to Search.next().
currentMetadataList() - Method in interface ome.api.Search: Provides access to the extra query information (for example Lucene score and boost values) for a single call to Search.results().

D

DATE_ACQUISITION - Static variable in class ome.util.search.LuceneQueryBuilder
DATE_IMPORT - Static variable in class ome.util.search.LuceneQueryBuilder
DATE_TYPE_ACQUISITION - Static variable in interface ome.api.Search: Treat date range as acquisition date
DATE_TYPE_IMPORT - Static variable in interface ome.api.Search: Treat date range as import date
deactivate() - Method in interface ome.api.IShare: Deprecated.

Turns off the access control lists with the current share.
dec() - Method in interface ome.system.metrics.Counter
dec() - Method in class ome.system.metrics.DefaultCounter
DEFAULT_BATCH_SIZE - Static variable in interface ome.api.Search: Default batch size
DEFAULT_CASE_SENSITIVTY - Static variable in interface ome.api.Search: Default case sensitivity
DEFAULT_MERGED_BATCHES - Static variable in interface ome.api.Search: Default merged-batches
DEFAULT_PORT - Static variable in class ome.system.Server
DEFAULT_RETURN_UNLOADED - Static variable in interface ome.api.Search: Default return-unloaded
DEFAULT_TIMEOUT - Static variable in class ome.system.UpgradeCheck: Default timeout is 10 seconds.
DEFAULT_USE_PROJECTIONS - Static variable in interface ome.api.Search: Default use-projections
DefaultCounter - Class in ome.system.metrics: Thin wrapper around Counter
DefaultCounter(Counter) - Constructor for class ome.system.metrics.DefaultCounter
DefaultHistogram - Class in ome.system.metrics: Thin wrapper around Histogram
DefaultHistogram(Histogram) - Constructor for class ome.system.metrics.DefaultHistogram
DefaultMetrics - Class in ome.system.metrics: Spring bean for configuring metrics in this JVM.
DefaultMetrics() - Constructor for class ome.system.metrics.DefaultMetrics
DefaultSnapshot - Class in ome.system.metrics: Thin wrapper around Snapshot
DefaultSnapshot(Snapshot) - Constructor for class ome.system.metrics.DefaultSnapshot
DefaultTimer - Class in ome.system.metrics: Thin wrapper around Timer
DefaultTimer(Timer) - Constructor for class ome.system.metrics.DefaultTimer
DefaultTimer.Context - Class in ome.system.metrics
deleteComment(Annotation) - Method in interface ome.api.IShare: Deprecated.

Deletes comment from the database.
deleteEnumeration(T) - Method in interface ome.api.ITypes: deletes enumeration value specified by object
deleteExperimenter(Experimenter) - Method in interface ome.api.IAdmin: removes a user by removing the password information for that user as well as all GroupExperimenterMap instances.
deleteGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin: removes a group by first removing all users in the group, and then deleting the actual ExperimenterGroup instance.
deleteImage(long, boolean) - Method in interface ome.api.IDelete: Deletes an Image and all related (subordinate) metadata as defined below.
deleteImages(Set<Long>, boolean) - Method in interface ome.api.IDelete: Deletes several Image instances within a single transaction via the IDelete.deleteImage(long, boolean) method.
deleteImagesByDataset(long, boolean) - Method in interface ome.api.IDelete: Deletes the user-visible Image instances of the given Dataset within a single transaction via the IDelete.deleteImage(long, boolean).
deleteObject(IObject) - Method in interface ome.api.IUpdate: Deletes a single entity.
deletePlate(long) - Method in interface ome.api.IDelete: Deletes all the images contained in a plate as if deleted by: deleteImage(id, true) so that all Dataset and Annotation links are broken, with WellSamples removed first.
deleteSettings(long) - Method in interface ome.api.IDelete: Deletes all rendering settings for the given Pixel id.
discover() - Method in interface ome.api.ILdap: Discovers and lists Experimenters who are present in the remote LDAP server and in the local DB but have the ldap property set to false.
discoverGroups() - Method in interface ome.api.ILdap: Discovers and lists ExperimenterGroups which are present in the remote LDAP server and in the local DB but have the ldap property set to false.

E

equals(Object) - Method in class omeis.providers.re.codomain.CodomainMapContext: This method is overridden so that objects of the same class are considered the same.
equals(Object) - Method in class omeis.providers.re.data.PlaneDef: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
ERROR - Static variable in interface ome.api.JobHandle
errorOnViolation(Class, Method, Object[]) - Static method in class ome.annotations.ApiConstraintChecker
EventContext - Interface in ome.system: manages authenticated principals and other context for a given event.
exists() - Method in interface ome.api.RawFileStore: Checks to see if a raw file exists with the file ID that the service was initialized with.

F

fetchAlso(String...) - Method in interface ome.api.Search: Adds a fetch clause for loading non-annotation fields of returned entities.
fetchAnnotations(Class...) - Method in interface ome.api.Search: Queries the database for all annotations of the given types for all returned instances.
file - Variable in class omeis.providers.re.lut.LutReader: The file to read.
FILE_SIZE - ome.util.checksum.ChecksumType
FileSizeChecksumProviderImpl - Class in ome.util.checksum: Trivial checksum provider whose hash is simply the number of bytes that were put into the calculation.
FileSizeChecksumProviderImpl() - Constructor for class ome.util.checksum.FileSizeChecksumProviderImpl
find(Class<T>, long) - Method in interface ome.api.IQuery: lookup an entity by class and id.
findAll(Class<T>, Filter) - Method in interface ome.api.IQuery: lookup all entities that belong to this class and match filter.
findAllByExample(T, Filter) - Method in interface ome.api.IQuery: search based on provided example entity.
findAllByFullText(Class<T>, String, Parameters) - Method in interface ome.api.IQuery: executes a full text search based on Lucene.
findAllByQuery(String, Parameters) - Method in interface ome.api.IQuery: executes the stored query with the given name.
findAllByString(Class<T>, String, String, boolean, Filter) - Method in interface ome.api.IQuery: search a given field matching against a String.
findByExample(T) - Method in interface ome.api.IQuery: search based on provided example entity.
findByQuery(String, Parameters) - Method in interface ome.api.IQuery: executes the stored query with the given name.
findByString(Class<T>, String, String) - Method in interface ome.api.IQuery: search a given field matching against a String.
findContainerHierarchies(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer: Retrieves hierarchy trees in various hierarchies that contain the specified Images.
findDN(String) - Method in interface ome.api.ILdap: Searches unique Distinguished Name - String in LDAP for Common Name equals username.
findExperimenter(String) - Method in interface ome.api.ILdap: Searches Experimenter by unique Distinguished Name - String in LDAP for Common Name equals username.
findGroup(String) - Method in interface ome.api.ILdap: Looks up a specific ExperimenterGroup in LDAP using the provided group name.
findGroupDN(String) - Method in interface ome.api.ILdap: Looks up the DN for a group.
findMethodAnnotations(Class, Method) - Static method in class ome.annotations.AnnotationUtils: finds all parameter annotations for the given class including on all implemented interfaces.
findMinMax(int[]) - Method in interface ome.api.RawPixelsStore
findParameterAnnotations(Class, Method) - Static method in class ome.annotations.AnnotationUtils: finds all parameter annotations for the given class including on all implemented interfaces.
FINISHED - Static variable in interface ome.api.JobHandle

G

G_BAND - Static variable in class omeis.providers.re.RGBBuffer: Index of the green band in the image's data buffer.
get(Class<T>, long) - Method in interface ome.api.IQuery: lookup an entity by class and id.
get75thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
get75thPercentile() - Method in interface ome.system.metrics.Snapshot
get95thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
get95thPercentile() - Method in interface ome.system.metrics.Snapshot
get98thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
get98thPercentile() - Method in interface ome.system.metrics.Snapshot
get999thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
get999thPercentile() - Method in interface ome.system.metrics.Snapshot
get99thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
get99thPercentile() - Method in interface ome.system.metrics.Snapshot
getA0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the slope of the first line.
getA1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the slope of the second line.
getA2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the slope of the third line.
getActiveConnections(long) - Method in interface ome.api.IShare: Deprecated.

Gets actual active connections to share.
getAdminPrivileges(Experimenter) - Method in interface ome.api.IAdmin: Gets the light administrator privileges for the given user.
getAdminService() - Method in class ome.system.ServiceFactory
getAdminsWithPrivileges(List<AdminPrivilege>) - Method in interface ome.api.IAdmin: Gets the administrators who have all the given privileges.
getAllDatasets() - Method in interface ome.api.IAnalysis
getAllEnumerations(Class<T>) - Method in interface ome.api.IPixels: Retrieves the exhaustive list of enumerations for a given enumeration class.
getAllForImage(long) - Method in interface ome.api.IAnalysis
getAllGuests(long) - Method in interface ome.api.IShare: Deprecated.

Get the email addresses for all share guests.
getAllMembers(long) - Method in interface ome.api.IShare: Deprecated.

Get all users who are a member of the share.
getAllUsers(long) - Method in interface ome.api.IShare: Deprecated.

Get a single set containing the login names of the users as well email addresses for guests.
getAnalysisService() - Method in class ome.system.ServiceFactory
getAnnotationTypes() - Method in interface ome.api.ITypes: Returns a list of classes which implement IAnnotated.
getAvailableFamilies() - Method in interface omeis.providers.re.RenderingEngine: Returns the list of mapping families supported by the Rendering engine.
getAvailableModels() - Method in interface omeis.providers.re.RenderingEngine: Returns the list of color models supported by the Rendering engine.
getAvailableTypes() - Method in interface ome.util.checksum.ChecksumProviderFactory
getAvailableTypes() - Method in class ome.util.checksum.ChecksumProviderFactoryImpl
getB0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-intercept of the first line.
getB1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-intercept of the second line.
getB2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-intercept of the third line.
getBatchSize() - Method in interface ome.api.Search: Returns the current batch size.
getBitDepth(PixelsType) - Method in interface ome.api.IPixels: Bit depth for a given pixel type.
getBlue(int) - Method in class omeis.providers.re.lut.LutReader: Returns the blue value.
getBlueBand() - Method in class omeis.providers.re.RGBBuffer: Returns the data buffer for the blue band.
getBlueValue(int) - Method in class omeis.providers.re.RGBAIntBuffer: Retrieves the Blue value for a particular pixel index.
getBlueValue(int) - Method in class omeis.providers.re.RGBBuffer: Retrieves the Blue value for a particular pixel index.
getBlueValue(int) - Method in class omeis.providers.re.RGBIntBuffer: Retrieves the Blue value for a particular pixel index.
getByteWidth() - Method in interface ome.api.RawPixelsStore
getChannelCurveCoefficient(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the coefficient identifying a map in the family.
getChannelFamily(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the family associated to the specified channel.
getChannelLookupTable(int) - Method in interface omeis.providers.re.RenderingEngine
getChannelNoiseReduction(int) - Method in interface omeis.providers.re.RenderingEngine: Returns true if the noise reduction algorithm used to map the pixels intensity values is turned on, false if the algorithm is turned off.
getChannelStats(int) - Method in interface omeis.providers.re.RenderingEngine
getChannelWindowEnd(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the upper bound of the pixels intensity interval.
getChannelWindowStart(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the lower bound of the pixels intensity interval.
getClientConfigDefaults() - Method in interface ome.api.IConfig: reads the etc/omero.properties file and returns all the key/value pairs that are found there which match the prefix "omero.client".
getClientConfigValues() - Method in interface ome.api.IConfig: retrieves configuration values like IConfig.getConfigValues(String) but only those with the prefix "omero.client".
getClientContext() - Static method in class ome.system.OmeroContext: create (if necessary) and return the single default client OmeroContext.
getClientContext(Properties) - Static method in class ome.system.OmeroContext: initialize a new client OmeroContext (named OmeroContext.CLIENT_CONTEXT), using the OmeroContext.getContext(Properties, String) method.
getCodomainMapContext(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the list of codomain contexts associated to the specified channel.
getCol(int, int, int, int) - Method in interface ome.api.RawPixelsStore
getCollectionCount(String, String, Set<Long>, Parameters) - Method in interface ome.api.IContainer: Counts the number of members in a collection for a given object.
getCommentCount(Set<Long>) - Method in interface ome.api.IShare: Deprecated.

Returns a map from share id to comment count.
getComments(long) - Method in interface ome.api.IShare: Deprecated.

Looks up all comments which belong to the share.
getCompressionLevel() - Method in interface omeis.providers.re.RenderingEngine: Returns the current compression level for the service.
getConfigDefaults() - Method in interface ome.api.IConfig: reads the etc/omero.properties file and returns all the key/value pairs that are found there.
getConfigService() - Method in class ome.system.ServiceFactory
getConfigValue(String) - Method in interface ome.api.IConfig: retrieve a configuration value from the backend store.
getConfigValues(String) - Method in interface ome.api.IConfig: retrieves configuration values from the backend store which match the given regex.
getContainerService() - Method in class ome.system.ServiceFactory
getContentMap(long) - Method in interface ome.api.IShare: Deprecated.

Returns the contents of the share keyed by type.
getContents(long) - Method in interface ome.api.IShare: Deprecated.

Looks up all items belong to the share.
getContentSize(long) - Method in interface ome.api.IShare: Deprecated.

Returns the number of items in the share.
getContentSubList(long, int, int) - Method in interface ome.api.IShare: Deprecated.

Returns a range of items from the share.
getContext(Properties, String) - Static method in class ome.system.OmeroContext: initialize a new client OmeroContext using the Properties provided as values for property (e.g.
getCount() - Method in interface ome.system.metrics.Counter
getCount() - Method in class ome.system.metrics.DefaultCounter
getCount() - Method in class ome.system.metrics.DefaultTimer
getCount() - Method in interface ome.system.metrics.Timer
getCurrentAdminPrivileges() - Method in interface ome.api.IAdmin: Gets the light administrator privileges for the current user.
getCurrentAdminPrivileges() - Method in interface ome.system.EventContext
getCurrentAdminPrivileges() - Method in class ome.system.SimpleEventContext
getCurrentEventContext() - Method in interface ome.api.StatefulServiceInterface: Returns the current EventContext for this instance.
getCurrentEventId() - Method in interface ome.system.EventContext
getCurrentEventId() - Method in class ome.system.SimpleEventContext
getCurrentEventType() - Method in interface ome.system.EventContext
getCurrentEventType() - Method in class ome.system.SimpleEventContext
getCurrentGroupId() - Method in interface ome.system.EventContext
getCurrentGroupId() - Method in class ome.system.SimpleEventContext
getCurrentGroupName() - Method in interface ome.system.EventContext
getCurrentGroupName() - Method in class ome.system.SimpleEventContext
getCurrentGroupPermissions() - Method in interface ome.system.EventContext
getCurrentGroupPermissions() - Method in class ome.system.SimpleEventContext
getCurrentSessionId() - Method in interface ome.system.EventContext
getCurrentSessionId() - Method in class ome.system.SimpleEventContext
getCurrentSessionUuid() - Method in interface ome.system.EventContext
getCurrentSessionUuid() - Method in class ome.system.SimpleEventContext
getCurrentShareId() - Method in interface ome.system.EventContext
getCurrentShareId() - Method in class ome.system.SimpleEventContext
getCurrentSudoerId() - Method in interface ome.system.EventContext
getCurrentSudoerId() - Method in class ome.system.SimpleEventContext
getCurrentSudoerName() - Method in interface ome.system.EventContext
getCurrentSudoerName() - Method in class ome.system.SimpleEventContext
getCurrentUmask() - Method in class ome.system.SimpleEventContext
getCurrentUserId() - Method in interface ome.system.EventContext
getCurrentUserId() - Method in class ome.system.SimpleEventContext
getCurrentUserName() - Method in interface ome.system.EventContext
getCurrentUserName() - Method in class ome.system.SimpleEventContext
getDatabaseTime() - Method in interface ome.api.IConfig: checks the database for its time using a SELECT statement.
getDatabaseUuid() - Method in interface ome.api.IConfig: Provides the UUID for this OMERO (database) instance.
getDataBuffer() - Method in class omeis.providers.re.RGBAIntBuffer: Retrieves the data buffer that contains the pixel values.
getDataBuffer() - Method in class omeis.providers.re.RGBIntBuffer: Retrieves the data buffer that contains the pixel values.
getDatasetsForProject(long) - Method in interface ome.api.IAnalysis
getDefaultContext() - Method in class ome.system.ServiceFactory: used when no context name is provided to the constructor.
getDefaultGroup(long) - Method in interface ome.api.IAdmin: retrieve the default group for the given user id.
getDefaultT() - Method in interface omeis.providers.re.RenderingEngine: Returns the default timepoint index.
getDefaultZ() - Method in interface omeis.providers.re.RenderingEngine: Returns the index of the default focal section.
getDeleteService() - Method in class ome.system.ServiceFactory
getEnumeration(Class<T>, String) - Method in interface ome.api.IPixels: Retrieves a particular enumeration for a given enumeration class.
getEnumeration(Class<T>, String) - Method in interface ome.api.ITypes: lookup an enumeration value.
getEnumerationsWithEntries() - Method in interface ome.api.ITypes: Gets all metadata classes which are IEnum type with contained objects.
getEnumerationTypes() - Method in interface ome.api.ITypes: Gets all metadata classes which are IEnum type.
getEvent() - Method in class ome.system.Login: simple getter for the event type passed into the constructor
getEventContext() - Method in interface ome.api.IAdmin: returns an implementation of EventContext loaded with the security for the current user and thread.
getEvents(long, Experimenter, Timestamp, Timestamp) - Method in interface ome.api.IShare: Deprecated.

Gets events for share per experimenter for period of time.
getEventType() - Method in class ome.system.Principal
getException() - Method in exception ome.util.messages.MessageException: Get the exception which this instance wraps.
getExceptionThrown() - Method in class ome.system.UpgradeCheck
getExperimenter(long) - Method in interface ome.api.IAdmin: fetch an Experimenter and all related groups.
getFileId() - Method in interface ome.api.RawFileStore: Returns the current file id or null if none has been set.
getFreeSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo: This method returns the free or available space on this file system including nested subdirectories.
getGreen(int) - Method in class omeis.providers.re.lut.LutReader: Returns the green value.
getGreenBand() - Method in class omeis.providers.re.RGBBuffer: Returns the data buffer for the green band.
getGreenValue(int) - Method in class omeis.providers.re.RGBAIntBuffer: Retrieves the Green value for a particular pixel index.
getGreenValue(int) - Method in class omeis.providers.re.RGBBuffer: Retrieves the Green value for a particular pixel index.
getGreenValue(int) - Method in class omeis.providers.re.RGBIntBuffer: Retrieves the Green value for a particular pixel index.
getGroup() - Method in class ome.system.Login: simple getter for the group name passed into the constructor
getGroup() - Method in class ome.system.Principal
getGroup(long) - Method in interface ome.api.IAdmin: fetch an ExperimenterGroup and all contained users.
getGuestGroupId() - Method in class ome.system.Roles
getGuestGroupName() - Method in class ome.system.Roles
getGuestId() - Method in class ome.system.Roles
getGuestName() - Method in class ome.system.Roles
getHeight() - Method in class omeis.providers.re.data.RegionDef: Returns the height of the region.
getHistogram(int[], int, boolean, PlaneDef) - Method in interface ome.api.RawPixelsStore
getHost() - Method in class ome.system.Server: simple getter for the server host passed into the constructor
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.api.RawPixelsStore
getImages(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer: Retrieve a user's (or all users') images within any given container.
getImagesByOptions(Parameters) - Method in interface ome.api.IContainer: Retrieve images by options.
getImagesBySplitFilesets(Map<Class<? extends IObject>, List<Long>>, Parameters) - Method in interface ome.api.IContainer: Given a list of IDs of certain entity types, calculates which filesets are split such that a non-empty proper subset of their images are referenced, directly or indirectly, as being included.
getImagesForDataset(long) - Method in interface ome.api.IAnalysis
getInput(String, String) - Method in interface ome.api.ISession: Retrieves an entry from the given session's input environment.
getInputKeys(String) - Method in interface ome.api.ISession: Retrieves all keys in the session's input environment.
getInputs(String) - Method in interface ome.api.ISession: Retrieves all inputs from the given session's input environment.
getInstance(String) - Static method in class ome.system.OmeroContext: create (if necessary) and return the single default OmeroContext named by the beanFactoryName parameter.
getJob() - Method in interface ome.api.JobHandle
getKeySet() - Method in class ome.system.PreferenceContext
getLdapService() - Method in class ome.system.ServiceFactory
getLeaderOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin: Finds the ids for all groups for which the given Experimenter is owner/leader.
getLeaderOfGroupsList() - Method in interface ome.system.EventContext
getLeaderOfGroupsList() - Method in class ome.system.SimpleEventContext
getLowerLimit() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the constant level for bit-planes < planeSelected w.r.t the higher-order bits.
getLutReaders(ChannelBinding[]) - Method in interface omeis.providers.re.lut.LutProvider: Returns the list of lookup table readers that can be used by a set of channel bindings.
getManagedServerContext() - Static method in class ome.system.OmeroContext: create (if necessary) and return the single default managed OmeroContext.
getMax() - Method in class ome.system.metrics.DefaultSnapshot
getMax() - Method in interface ome.system.metrics.Snapshot
getMean() - Method in class ome.system.metrics.DefaultSnapshot
getMean() - Method in interface ome.system.metrics.Snapshot
getMedian() - Method in class ome.system.metrics.DefaultSnapshot
getMedian() - Method in interface ome.system.metrics.Snapshot
getMemberCount(Set<Long>) - Method in interface ome.api.IShare: Deprecated.

Returns a map from share id to the count of total members (including the owner).
getMemberOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin: Finds the ids for all groups for which the given Experimenter is a member.
getMemberOfGroupsList() - Method in interface ome.system.EventContext
getMemberOfGroupsList() - Method in class ome.system.SimpleEventContext
getMemberShares(boolean) - Method in interface ome.api.IShare: Deprecated.

Gets all shares where current Experimenter is a member.
getMemberSharesFor(Experimenter, boolean) - Method in interface ome.api.IShare: Deprecated.

Gets all shares where given Experimenter is a member.
getMetadataService() - Method in class ome.system.ServiceFactory
getMin() - Method in class ome.system.metrics.DefaultSnapshot
getMin() - Method in interface ome.system.metrics.Snapshot
getModel() - Method in interface omeis.providers.re.RenderingEngine: Returns the model that dictates how transformed raw data has to be mapped onto a color space.
getMyOpenAgentSessions(String) - Method in interface ome.api.ISession: Like ISession.getMyOpenSessions() but returns only those sessions with the given agent string.
getMyOpenClientSessions() - Method in interface ome.api.ISession: Like ISession.getMyOpenSessions() but returns only those sessions started by official OMERO clients.
getMyOpenSessions() - Method in interface ome.api.ISession: Returns a list of open sessions for the current user.
getMyUserPhotos() - Method in interface ome.api.IAdmin: Retrieve the OriginalFile object attached to this user as specified by IAdmin.uploadMyUserPhoto(String, String, byte[]).
getName() - Method in class ome.system.Login: simple getter for the user name passed into the constructor
getName() - Method in class ome.system.Preference
getName() - Method in class ome.system.Principal
getOriginalEnumerations() - Method in interface ome.api.ITypes: Gets all original values.
getOutput(String, String) - Method in interface ome.api.ISession: Retrieves an entry from the session's output environment.
getOutputKeys(String) - Method in interface ome.api.ISession: Retrieves all keys in the sesson's output environment.
getOutputs(String) - Method in interface ome.api.ISession: Retrieves all outputs from the given session's input environment.
getOwnShares(boolean) - Method in interface ome.api.IShare: Deprecated.

Gets all owned shares for the current Experimenter
getPassword() - Method in class ome.system.Login: simple getter for the password passed into the constructor
getPastConnections(long) - Method in interface ome.api.IShare: Deprecated.

Gets previous connections to share.
getPixels() - Method in interface omeis.providers.re.RenderingEngine: Returns the Pixels set the Rendering engine is for.
getPixelsId() - Method in interface ome.api.RawPixelsStore: Returns the current Pixels set identifier.
getPixelsPath() - Method in interface ome.api.RawPixelsStore: Returns the current Pixels path.
getPixelsService() - Method in class ome.system.ServiceFactory
getPixelsTypeLowerBound(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeUpperBound(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPlane(int, int, int) - Method in interface ome.api.RawPixelsStore
getPlaneOffset(int, int, int) - Method in interface ome.api.RawPixelsStore
getPlanePrevious() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the value corresponding to the index of the bit-plane ranged just before the one selected.
getPlaneRegion(int, int, int, int, int) - Method in interface ome.api.RawPixelsStore
getPlaneSelected() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the value corresponding to the index of the selected bit-plane.
getPlaneSize() - Method in interface ome.api.RawPixelsStore: Returns the plane size
getPort() - Method in class ome.system.Server: simple getter for the port passed into the constructor or the default port if none.
getPrefix() - Method in class ome.system.ServiceFactory: used by ServiceFactory.getServiceByClass(Class) to find the correct service proxy in the ServiceFactory.ctx
getProjectionService() - Method in class ome.system.ServiceFactory
getProjectsForDataset(long) - Method in interface ome.api.IAnalysis
getProjectsForUser(long) - Method in interface ome.api.IAnalysis
getProperty(String) - Method in class ome.system.OmeroContext
getProperty(String) - Method in class ome.system.PreferenceContext: Lookup method for getting access to the merged properties for this instance.
getProvider(ChecksumType) - Method in interface ome.util.checksum.ChecksumProviderFactory: Returns an implementation of ChecksumProvider depending on the specified ChecksumType.
getProvider(ChecksumType) - Method in class ome.util.checksum.ChecksumProviderFactoryImpl
getQuantumDef() - Method in interface omeis.providers.re.RenderingEngine: Returns the quantization object.
getQueryService() - Method in class ome.system.ServiceFactory
getRed(int) - Method in class omeis.providers.re.lut.LutReader: Returns the red value.
getRedBand() - Method in class omeis.providers.re.RGBBuffer: Returns the data buffer for the red band.
getRedValue(int) - Method in class omeis.providers.re.RGBAIntBuffer: Retrieves the Red value for a particular pixel index.
getRedValue(int) - Method in class omeis.providers.re.RGBBuffer: Retrieves the Red value for a particular pixel index.
getRedValue(int) - Method in class omeis.providers.re.RGBIntBuffer: Retrieves the Red value for a particular pixel index.
getReferenceCount(String) - Method in interface ome.api.ISession: Retrieves the current reference count for the given uuid.
getRegion() - Method in class omeis.providers.re.data.PlaneDef: Returns the region to render.
getRegion(int, long) - Method in interface ome.api.RawPixelsStore
getRenderingDefId() - Method in interface ome.api.ThumbnailStore: Return the id of the RenderingDef loaded in this instance.
getRenderingDefId() - Method in interface omeis.providers.re.RenderingEngine: Returns the id of the RenderingDef loaded by either RenderingEngine.lookupRenderingDef(long) or RenderingEngine.loadRenderingDef(long).
getRenderingSettings(long) - Method in interface ome.api.IRenderingSettings: Returns the default rendering settings for a given pixels for the current user.
getRenderingSettingsService() - Method in class ome.system.ServiceFactory
getRenderShapes() - Method in class omeis.providers.re.data.PlaneDef: Returns whether or not the shapes (masks) will be rendered.
getRepositoryInfoService() - Method in class ome.system.ServiceFactory
getResolutionDescriptions() - Method in interface ome.api.RawPixelsStore
getResolutionDescriptions() - Method in interface omeis.providers.re.RenderingEngine
getResolutionLevel() - Method in interface ome.api.RawPixelsStore: Retrieves the active resolution level.
getResolutionLevel() - Method in interface omeis.providers.re.RenderingEngine
getResolutionLevels() - Method in interface ome.api.RawPixelsStore: Retrieves the number of resolution levels that the backing pixels pyramid contains.
getResolutionLevels() - Method in interface omeis.providers.re.RenderingEngine
getRGBA(int) - Method in interface omeis.providers.re.RenderingEngine: Returns a 4D-array representing the color associated to the specified channel.
getRootId() - Method in class ome.system.Roles
getRootName() - Method in class ome.system.Roles
getRow(int, int, int, int) - Method in interface ome.api.RawPixelsStore
getRowOffset(int, int, int, int) - Method in interface ome.api.RawPixelsStore
getRowSize() - Method in interface ome.api.RawPixelsStore
getSecurityRoles() - Method in interface ome.api.IAdmin: returns the active Roles in use by the server.
getServerTime() - Method in interface ome.api.IConfig: checks the current server for its time.
getServiceByClass(Class<T>) - Method in class ome.system.ServiceFactory: looks up services based on the current prefix and the class name of the service type.
getServiceInterface() - Method in interface ome.system.SelfConfigurableService
getSession() - Method in class ome.system.ServiceFactory
getSession() - Method in class ome.system.SessionInitializer
getSession(String) - Method in interface ome.api.ISession: Retrieves the session associated with this uuid, updating the last access time as well.
getSessionInitializer() - Method in class ome.system.ServiceFactory
getSessionService() - Method in class ome.system.ServiceFactory
getSetting() - Method in interface ome.api.ILdap: Gets config value from properties.
getShapeIds() - Method in class omeis.providers.re.data.PlaneDef: Returns whether or not the shapes (masks) will be rendered.
getShare(long) - Method in interface ome.api.IShare: Deprecated.

Gets a share as a Session with all related: comments, members, fully loaded.
getShareService() - Method in class ome.system.ServiceFactory
getSharesOwnedBy(Experimenter, boolean) - Method in interface ome.api.IShare: Deprecated.

Gets all shares owned by the given Experimenter.
getSizeX1() - Method in class omeis.providers.re.RGBBuffer: Returns the number of pixels on the X1-axis.
getSizeX2() - Method in class omeis.providers.re.RGBBuffer: Returns the number of pixels on the X2-axis.
getSlice() - Method in class omeis.providers.re.data.PlaneDef: Returns an identifier to tell which kind of plane this object identifies.
getSnapshot() - Method in class ome.system.metrics.DefaultHistogram
getSnapshot() - Method in interface ome.system.metrics.Histogram
getStack(int, int) - Method in interface ome.api.RawPixelsStore
getStackOffset(int, int) - Method in interface ome.api.RawPixelsStore
getStackSize() - Method in interface ome.api.RawPixelsStore
getStdDev() - Method in class ome.system.metrics.DefaultSnapshot
getStdDev() - Method in interface ome.system.metrics.Snapshot
getStride() - Method in class omeis.providers.re.data.PlaneDef: Returns the stride.
getSystemGroupId() - Method in class ome.system.Roles
getSystemGroupName() - Method in class ome.system.Roles
getT() - Method in class omeis.providers.re.data.PlaneDef: Returns the timepoint.
getTaggedObjectsCount(Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Returns a map whose key is a tag's id and the value the number of Projects, Datasets, and Images linked to that tag.
getThumbnail(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailByLongestSide(Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailByLongestSideDirect(Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore: Retrieves a number of thumbnails for pixels sets using given sets of rendering settings (RenderingDef).
getThumbnailDirect(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) for a particular section.
getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) for a particular section.
getThumbnailSet(Integer, Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore: Retrieves a number of thumbnails for pixels sets using given sets of rendering settings (RenderingDef).
getThumbnailWithoutDefault(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getTile(int, int, int, int, int, int, int) - Method in interface ome.api.RawPixelsStore
getTileSize() - Method in interface ome.api.RawPixelsStore
getTileSize() - Method in interface omeis.providers.re.RenderingEngine
getTimepoint(int) - Method in interface ome.api.RawPixelsStore
getTimepointOffset(int) - Method in interface ome.api.RawPixelsStore
getTimepointSize() - Method in interface ome.api.RawPixelsStore
getTotalSize() - Method in interface ome.api.RawPixelsStore
getTypesService() - Method in class ome.system.ServiceFactory
getUpdateService() - Method in class ome.system.ServiceFactory
getUpgradeUrl() - Method in class ome.system.UpgradeCheck
getUpperLimit() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the constant level for bit-planes > planeSelected w.r.t the higher-order bits.
getUsageFraction() - Method in interface ome.api.IRepositoryInfo: This method returns a double of the used space divided by the free space.
getUsedSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo: This method returns the total space in bytes for this file system including nested subdirectories.
getUserGroupId() - Method in class ome.system.Roles
getUserGroupName() - Method in class ome.system.Roles
getUserImages(Parameters) - Method in interface ome.api.IContainer: Retrieve a user's images.
getValue(double) - Method in class ome.system.metrics.DefaultSnapshot
getValue(double) - Method in interface ome.system.metrics.Snapshot
getValues() - Method in class ome.system.metrics.DefaultSnapshot
getValues() - Method in interface ome.system.metrics.Snapshot
getVersion() - Method in interface ome.api.IConfig: Provides the release version.
getVisibility() - Method in class ome.system.Preference
getWidth() - Method in class omeis.providers.re.data.RegionDef: Returns the width of the region.
getX() - Method in class omeis.providers.re.data.PlaneDef: Returns the index of the plane in the set identified by this object.
getX() - Method in class omeis.providers.re.data.RegionDef: Returns the x-coordinate of the top-left corner.
getXEnd() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the x-coordinate of the pEnd point.
getXStart() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the x-coordinate of the pStart point.
getY() - Method in class omeis.providers.re.data.PlaneDef: Returns the index of the plane in the set identified by this object.
getY() - Method in class omeis.providers.re.data.RegionDef: Returns the y-coordinate of the top-left corner.
getYEnd() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-coordinate of the pEnd point.
getYStart() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-coordinate of the pStart point.
getZ() - Method in class omeis.providers.re.data.PlaneDef: Returns the index of the plane in the set identified by this object.
greens - Variable in class omeis.providers.re.lut.LutReader: Holds the green values.
group - Variable in class ome.system.Principal
GUEST - Static variable in class ome.system.Login: Login constant which has username and password values set to null and other values set to their default.

H

hasAlias(String) - Method in class ome.system.Preference
hashCode() - Method in class omeis.providers.re.data.PlaneDef: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hasNext() - Method in interface ome.api.Search: Returns true if another call to Search.next() is valid.
hasSession() - Method in class ome.system.SessionInitializer
hidden - ome.system.Preference.Visibility
Hidden - Annotation Type in ome.annotations: annotation which specifies that a method parameter (e.g.
histogram(Object, String) - Method in class ome.system.metrics.DefaultMetrics
histogram(Object, String) - Method in interface ome.system.metrics.Metrics
histogram(Object, String) - Method in class ome.system.metrics.NullMetrics
Histogram - Interface in ome.system.metrics: Thin wrapper around Histogram

I

IAdmin - Interface in ome.api: Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.
IAnalysis - Interface in ome.api: Provides access to the model objects involved in analysis.
IConfig - Interface in ome.api: Access to server configuration.
IContainer - Interface in ome.api: Provides methods for dealing with the core "Pojos" of OME.
IDelete - Interface in ome.api: Provides simplifed methods for deleting instances from the database.
IdentityMapContext - Class in omeis.providers.re.codomain: An empty context for the identity map.
IdentityMapContext() - Constructor for class omeis.providers.re.codomain.IdentityMapContext
ILdap - Interface in ome.api: Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.
IMetadata - Interface in ome.api: Provides method to interact with acquisition metadata and annotations.
inc() - Method in interface ome.system.metrics.Counter
inc() - Method in class ome.system.metrics.DefaultCounter
indexObject(IObject) - Method in interface ome.api.IUpdate: Initiates full-text indexing for the given object.
InternalMessage - Class in ome.util.messages: Message which can be published via OmeroContext.publishEvent(ApplicationEvent) or OmeroContext.publishMessage(InternalMessage).
InternalMessage(Object) - Constructor for class ome.util.messages.InternalMessage: Sole constructor which takes the "source" of this EventObject.
intervalEnd - Variable in class omeis.providers.re.codomain.CodomainMapContext: The upper bound of the codomain interval.
intervalStart - Variable in class omeis.providers.re.codomain.CodomainMapContext: The lower bound of the codomain interval.
invalidateConnection(long, Experimenter) - Method in interface ome.api.IShare: Deprecated.

Makes the connection invalid for share for specifiec user.
InvalidQueryException - Exception in ome.util.search: Exception to indicate that the query string was invalid
InvalidQueryException() - Constructor for exception ome.util.search.InvalidQueryException
InvalidQueryException(String) - Constructor for exception ome.util.search.InvalidQueryException
InvalidQueryException(String, Throwable) - Constructor for exception ome.util.search.InvalidQueryException
InvalidQueryException(Throwable) - Constructor for exception ome.util.search.InvalidQueryException
IPixels - Interface in ome.api: Metadata gateway for the RenderingEngine and clients.
IProjection - Interface in ome.api: Provides methods for performing projections of Pixels sets.
IQuery - Interface in ome.api: Provides methods for directly querying object graphs.
IRenderingSettings - Interface in ome.api: Provides method to apply rendering settings to a collection of images.
IRepositoryInfo - Interface in ome.api: Provides methods for obtaining information for server repository disk space allocation.
isActive(int) - Method in interface omeis.providers.re.RenderingEngine: Returns true if the channel is mapped, false otherwise.
isAdmin - Variable in class ome.system.SimpleEventContext
isAllowLeadingWildcard() - Method in interface ome.api.Search: Returns the current leading-wildcard setting.
IScale - Interface in ome.api: Provides methods for performing scaling (change of the image size through interpolation or other means) on BufferedImages.
isCaseSensitive() - Method in interface ome.api.Search: Returns the current case sensitivity setting.
IsConstant() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the type of bit-planes mapping.
isCurrentUserAdmin() - Method in interface ome.system.EventContext
isCurrentUserAdmin() - Method in class ome.system.SimpleEventContext
isDb() - Method in class ome.system.Preference
ISession - Interface in ome.api: Start here: Session creation service for OMERO.
isExceptionThrown() - Method in class ome.system.UpgradeCheck
isFloat() - Method in interface ome.api.RawPixelsStore
IShare - Interface in ome.api: Deprecated.
isInProgress() - Method in interface ome.api.ThumbnailStore: This returns the last available in progress state for a thumbnail.
isMergedBatches() - Method in interface ome.api.Search: Returns the current merged-batches setting.
isPixelsTypeSigned() - Method in interface omeis.providers.re.RenderingEngine: Returns true if the pixels type is signed, false otherwise.
isPrefs() - Method in class ome.system.Preference
isReadOnly - Variable in class ome.system.SimpleEventContext
isReadOnly() - Method in interface ome.system.EventContext
isReadOnly() - Method in class ome.system.SimpleEventContext
isReturnUnloaded() - Method in interface ome.api.Search: Returns the current return-unloaded setting.
isRootUser(Experimenter) - Method in class ome.system.Roles
isSigned() - Method in interface ome.api.RawPixelsStore
isSystemGroup(ExperimenterGroup) - Method in class ome.system.Roles
isThreadSafe() - Method in class ome.util.messages.InternalMessage: Returns true if this message can safely be passed to another Thread.
isUpgradeNeeded() - Method in class ome.system.UpgradeCheck
isUseProjections() - Method in interface ome.api.Search: Returns the current use-projection setting.
isUserGroup(ExperimenterGroup) - Method in class ome.system.Roles
ITypes - Interface in ome.api: Access to reflective type information.
IUpdate - Interface in ome.api: Provides methods for directly updating object graphs.

J

jobError() - Method in interface ome.api.JobHandle: Returns true if the Job has thrown an error.
jobFinished() - Method in interface ome.api.JobHandle
JobHandle - Interface in ome.api: Allows submission of asynchronous jobs.
jobMessage() - Method in interface ome.api.JobHandle
jobRunning() - Method in interface ome.api.JobHandle: Returns true if the Job is running, i.e.
jobStatus() - Method in interface ome.api.JobHandle

L

leaderOfGroups - Variable in class ome.system.SimpleEventContext
link(ILink[], Parameters) - Method in interface ome.api.IContainer: Convenience method for creating links.
load() - Method in interface omeis.providers.re.RenderingEngine: Creates a instance of the rendering engine.
loadAnnotation(Set<Long>) - Method in interface ome.api.IMetadata: Loads the specified annotations.
loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Loads all the annotations of given types, that have been attached to the specified rootNodes for the specified annotatorIds.
loadAnnotationsUsedNotOwned(Class, long) - Method in interface ome.api.IMetadata: Loads the annotations of a given type used by the specified user but not owned by the user.
loadChannelAcquisitionData(Set<Long>) - Method in interface ome.api.IMetadata: Loads the logical channels and the acquisition metadata related to them.
loadContainerHierarchy(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer: Retrieves hierarchy trees rooted by a given node (unless orphan is specified -- See below)
loadInstrument(long) - Method in interface ome.api.IMetadata: Loads the instrument and its components i.e.
loadLogFiles(Class<? extends IObject>, Set<Long>) - Method in interface ome.api.IMetadata: Find the original file IDs for the import logs corresponding to the given Image or Fileset IDs.
loadRenderingDef(long) - Method in interface omeis.providers.re.RenderingEngine: Loads a specific set of rendering settings that does not necessarily have to be linked to the given Pixels set.
loadRndSettings(long) - Method in interface ome.api.IPixels: Loads a specific set of rendering settings with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata: Loads all the annotations of a given type.
loadSpecifiedAnnotationsLinkedTo(Class, Set<String>, Set<String>, Class, Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Loads the annotations of a given type linked to the specified objects.
loadTagContent(Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Loads the Tag Set if the id is specified otherwise loads all the Tag Set.
loadTagSets(Parameters) - Method in interface ome.api.IMetadata: Loads all the tag Sets.
Locator() - Constructor for class ome.system.OmeroContext.Locator
Login - Class in ome.system: Provides simplified handling of login properties when creating a ServiceFactory.
Login(String, String) - Constructor for class ome.system.Login: standard constructor which leaves OMERO_GROUP and OMERO_EVENT null.
Login(String, String, String, String) - Constructor for class ome.system.Login: extended constructor.
lookup(String, ApplicationContext) - Method in class ome.system.OmeroContext.Locator: uses ContextSingletonBeanFactoryLocator.createDefinition(java.lang.String, java.lang.String) and ContextSingletonBeanFactoryLocator.initializeDefinition(org.springframework.beans.factory.BeanFactory) to create a new context from a given definition.
lookupExperimenter(String) - Method in interface ome.api.IAdmin: look up an Experimenter and all related groups by name.
lookupExperimenters() - Method in interface ome.api.IAdmin: Looks up all experimenters present and all related groups.
lookupGroup(String) - Method in interface ome.api.IAdmin: look up an ExperimenterGroup and all contained users by name.
lookupGroups() - Method in interface ome.api.IAdmin: Looks up all groups present and all related experimenters.
lookupLdapAuthExperimenter(long) - Method in interface ome.api.IAdmin: Looks up experimenters who uses LDAP authentication (has set dn on password table).
lookupLdapAuthExperimenters() - Method in interface ome.api.IAdmin: Looks up all id of experimenters who uses LDAP authentication (has set dn on password table).
lookupPixels(long) - Method in interface omeis.providers.re.RenderingEngine: Loads the Pixels set this Rendering Engine is for.
lookupRenderingDef(long) - Method in interface omeis.providers.re.RenderingEngine: Loads the rendering settings associated to the specified pixels set.
LuceneQueryBuilder - Class in ome.util.search: Utility class for building lucene queries

Example:
Fields to search for: 'name', 'description'
Input query: a b AND c AND d f

will be transformed to this lucene expression:
name:a description:a name:f description:f ((name:b description:b) AND (name:c description:c) AND (name:d description:d))
LuceneQueryBuilder() - Constructor for class ome.util.search.LuceneQueryBuilder
LutProvider - Interface in omeis.providers.re.lut: Interface for lookup table providers.
LutReader - Class in omeis.providers.re.lut: Class to be extended by LUT reader.
LutReaderFactory - Class in omeis.providers.re.lut: Initializes the reader corresponding to the specified lookup table.
LutReaderFactory() - Constructor for class omeis.providers.re.lut.LutReaderFactory

M

MANAGED_CONTEXT - Static variable in class ome.system.OmeroContext: identifier for an OmeroContext configured in classpath*:beanRefContext.xml for use by server-side processes.
MAXIMUM_INTENSITY - Static variable in interface ome.api.IProjection: Maximum intensity projection (MIP)
MD5 - ome.util.checksum.ChecksumType
MD5ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using MD5 as the message digest algorithm.
MD5ChecksumProviderImpl() - Constructor for class ome.util.checksum.MD5ChecksumProviderImpl
MEAN_INTENSITY - Static variable in interface ome.api.IProjection: Mean intensity projection
memberOfGroups - Variable in class ome.system.SimpleEventContext
MessageException - Exception in ome.util.messages: Message which wraps a Throwable instance since OmeroContext.publishEvent(org.springframework.context.ApplicationEvent) cannot throw a checked exception.
MessageException(String, Throwable) - Constructor for exception ome.util.messages.MessageException: Create an instance.
METHODOLOGY_STRINGS - Static variable in interface ome.api.IProjection: Methodology strings
Metrics - Interface in ome.system.metrics: Thin-interface around MetricSet.
moveToCommonSpace(IObject...) - Method in interface ome.api.IAdmin: Moves the given objects into the "user" group to make them visible and linkable from all security contexts.
MOVIE_MPEG_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is an MPEG file.
MOVIE_QT_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is an QT file.
MOVIE_WMV_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is an WMV file.
MURMUR128 - ome.util.checksum.ChecksumType
Murmur128ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using Murmur3_128 as the hash algorithm.
Murmur128ChecksumProviderImpl() - Constructor for class ome.util.checksum.Murmur128ChecksumProviderImpl
MURMUR32 - ome.util.checksum.ChecksumType
Murmur32ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using Murmur3_32 as the hash algorithm.
Murmur32ChecksumProviderImpl() - Constructor for class ome.util.checksum.Murmur32ChecksumProviderImpl
mutex - Variable in class ome.system.SessionInitializer

N

name - Variable in class ome.system.Principal
next() - Method in interface ome.api.Search: Returns the next entity from the current query.
not() - Method in interface ome.api.Search: Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the intersection of the two calls.
notAnnotatedBy(Details) - Method in interface ome.api.Search: Restricts entities by who has not annotated them with an Annotation matching the other filters.
notifyMembersOfShare(long, String, String, boolean) - Method in interface ome.api.IShare: Deprecated.

Notify via email selected members of share.
NotNull - Annotation Type in ome.annotations: annotation used for determining the types of a Set
notOwnedBy(Details) - Method in interface ome.api.Search: Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.
NS_IMPORTER_ARCHIVED - Static variable in interface ome.api.IMetadata: The name space indicating that the Boolean annotation indicated if an archived image is imported with the image.
NS_INSIGHT_RATING - Static variable in interface ome.api.IMetadata: The name space indicating that the Long annotation is a rating annotation i.e.
NS_INSIGHT_TAG_SET - Static variable in interface ome.api.IMetadata: The name space indicating that the tag is used a tag set.
NullMetrics - Class in ome.system.metrics: No-op version of Metrics
NullMetrics() - Constructor for class ome.system.metrics.NullMetrics

O

ome.annotations - package ome.annotations
ome.api - package ome.api
ome.system - package ome.system
ome.system.metrics - package ome.system.metrics: General metrics registry for use by all server-side components.
ome.util.checksum - package ome.util.checksum
ome.util.logback - package ome.util.logback
ome.util.messages - package ome.util.messages
ome.util.search - package ome.util.search
omeis.providers.re - package omeis.providers.re
omeis.providers.re.codomain - package omeis.providers.re.codomain
omeis.providers.re.data - package omeis.providers.re.data
omeis.providers.re.lut - package omeis.providers.re.lut
OMERO_EVENT - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
OMERO_GROUP - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
OMERO_HOST - Static variable in class ome.system.Server: Java property name for use in configuration of the client connection.
OMERO_PASS - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
OMERO_PORT - Static variable in class ome.system.Server: Java property name for use in configuration of the client connection.
OMERO_USER - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
OmeroContext - Class in ome.system: Provides static access for the creation of singleton and non-singleton application contexts.
OmeroContext(String) - Constructor for class ome.system.OmeroContext
OmeroContext(String[]) - Constructor for class ome.system.OmeroContext
OmeroContext(String[], boolean) - Constructor for class ome.system.OmeroContext
OmeroContext(String[], boolean, ApplicationContext) - Constructor for class ome.system.OmeroContext
OmeroContext(String[], ApplicationContext) - Constructor for class ome.system.OmeroContext
OmeroContext.Locator - Class in ome.system: provides access to the protected methods of ContextSingletonBeanFactoryLocator which cannot be used externally.
onlyAnnotatedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search: Restricts entities by the time in which any annotation (which matches the other filters) was added them.
onlyAnnotatedBy(Details) - Method in interface ome.api.Search: Restricts entities by who has annotated them with an Annotation matching the other filters.
onlyAnnotatedWith(Class...) - Method in interface ome.api.Search: Restricts entities to having an Annotation of all the given types.
onlyCreatedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search: Restricts the time between which an entity may have been created.
onlyIds(Long...) - Method in interface ome.api.Search: Restricts the set of ids which will be checked.
onlyModifiedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search: Restricts the time between which an entity may have last been modified.
onlyOwnedBy(Details) - Method in interface ome.api.Search: Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.
onlyType(Class<T>) - Method in interface ome.api.Search: Restricts the search to a single type.
onlyTypes(Class<T>...) - Method in interface ome.api.Search: Restricts searches to a set of types.
onRefresh() - Method in class ome.system.OmeroContext
or() - Method in interface ome.api.Search: Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the union of the two calls.

P

passivate() - Method in interface ome.api.StatefulServiceInterface: Perform whatever passivation is possible or throw an exception.
PermitAll - Annotation Type in ome.annotations: Security annotation which allows a method to be called by all users regardless of their status.
PlaneDef - Class in omeis.providers.re.data: Identifies a 2D-plane in the XYZ moving frame of the 3D stack.
PlaneDef(int, int) - Constructor for class omeis.providers.re.data.PlaneDef: Creates a new instance.
PlaneSlicingContext - Class in omeis.providers.re.codomain: We consider that the image is composed of eight 1-bit planes ranging from bit-plane 0 for the least significant bit to bit-plane 7 for the most significant bit.
PlaneSlicingContext(int, int, boolean) - Constructor for class omeis.providers.re.codomain.PlaneSlicingContext: Creates a new instance.
postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ome.system.PreferenceContext
Preference - Class in ome.system: Definition of a server configuration variable ("preference") along with its mutability, visibility, aliases and other important information.
Preference() - Constructor for class ome.system.Preference: By default, configures this instance for PropertyPlaceholderConfigurer.SYSTEM_PROPERTIES_MODE_OVERRIDE as well as ignoring unfound resources.
Preference(String, boolean, Preference.Visibility, String[]) - Constructor for class ome.system.Preference
Preference.Visibility - Enum in ome.system
PreferenceContext - Class in ome.system: Central configuration for OMERO properties from (in order): Any injected Properties instances Java System.getProperties() Any configured property files As of OMERO 4.2, server configurations are not stored in Java's Preferences API but in an IceGrid xml file under etc/grid of the server installation.
PreferenceContext() - Constructor for class ome.system.PreferenceContext: By default, configures this instance for PropertyPlaceholderConfigurer.SYSTEM_PROPERTIES_MODE_OVERRIDE as well as ignoring unfound resources.
prepare(Set<Long>) - Method in interface ome.api.RawPixelsStore: Prepares the stateful service with a cache of loaded Pixels objects.
previewImageDelete(long, boolean) - Method in interface ome.api.IDelete: Returns all entities which would be deleted by a call to IDelete.deleteImage(long, boolean).
principal - Variable in class ome.system.SessionInitializer: Principal given by the user
Principal - Class in ome.system: implementation of Principal.
Principal(String) - Constructor for class ome.system.Principal: Creates a Principal with null group and event type.
Principal(String, String, String) - Constructor for class ome.system.Principal
projection(String, Parameters) - Method in interface ome.api.IQuery: Return a list of Java Object instances (not IObject instances).
projectPixels(long, PixelsType, int, int, int, List<Integer>, int, int, int, String) - Method in interface ome.api.IProjection: Performs a projection through selected optical sections and optical sections for a given set of time points of a Pixels set.
projectStack(long, PixelsType, int, int, int, int, int, int) - Method in interface ome.api.IProjection: Performs a projection through the optical sections of a particular wavelength at a given time point of a Pixels set.
publishEvent(ApplicationEvent) - Method in class ome.system.OmeroContext
publishMessage(InternalMessage) - Method in class ome.system.OmeroContext: Convenience method around OmeroContext.publishEvent(org.springframework.context.ApplicationEvent) which catches all MessageException and unwraps the contained Throwable instance and rethrows.
putBytes(byte[]) - Method in class ome.util.checksum.AbstractChecksumProvider
putBytes(byte[]) - Method in interface ome.util.checksum.ChecksumProvider: Updates the internal checksum value with data from a byte array.
putBytes(byte[]) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
putBytes(byte[], int, int) - Method in class ome.util.checksum.AbstractChecksumProvider
putBytes(byte[], int, int) - Method in interface ome.util.checksum.ChecksumProvider: Updates the internal checksum value with data from a chunk of a byte array.
putBytes(byte[], int, int) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
putBytes(ByteBuffer) - Method in class ome.util.checksum.AbstractChecksumProvider
putBytes(ByteBuffer) - Method in interface ome.util.checksum.ChecksumProvider: Updates the internal checksum value with data from a byte buffer.
putBytes(ByteBuffer) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
putFile(String) - Method in class ome.util.checksum.AbstractChecksumProvider
putFile(String) - Method in interface ome.util.checksum.ChecksumProvider: Updates the internal checksum value with data from a file identified by a path.
putFile(String) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl

Q

QUEUED - Static variable in interface ome.api.JobHandle

R

R_BAND - Static variable in class omeis.providers.re.RGBBuffer: Index of the red band in the image's data buffer.
raw - Variable in class omeis.providers.re.lut.LutReader: Flag indicating to read 32 byte NIH Image LUT header.
RawFileStore - Interface in ome.api: Raw file gateway which provides access to the OMERO file repository.
RawPixelsStore - Interface in ome.api: Binary data provider.
read(long, int) - Method in interface ome.api.RawFileStore: Reads length bytes of data at the position from the raw file into an array of bytes
read(File) - Static method in class omeis.providers.re.lut.LutReaderFactory: Reads the specified file.
read(String, String) - Static method in class omeis.providers.re.lut.LutReaderFactory: Reads the specified file.
reds - Variable in class omeis.providers.re.lut.LutReader: Holds the red values.
refresh(T) - Method in interface ome.api.IQuery: refreshes an entire IObject graph, recursive loading all data for the managed instances in the graph from the database.
refreshAll() - Method in class ome.system.OmeroContext: refreshes all the nested OmeroContexts within this instance.
refreshAllIfNecessary() - Method in class ome.system.OmeroContext: Calls OmeroContext.refreshAll() if AbstractApplicationContext.isRunning() throws an IllegalStateException.
RegionDef - Class in omeis.providers.re.data: Identifies a rectangular region.
RegionDef() - Constructor for class omeis.providers.re.data.RegionDef: Creates a default instance.
RegionDef(int, int, int, int) - Constructor for class omeis.providers.re.data.RegionDef: Creates a rectangular region.
remove() - Method in interface ome.api.Search: Unsupported operation.
removeCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine: Deprecated.
removeCodomainMapFromChannel(CodomainMapContext, int) - Method in interface omeis.providers.re.RenderingEngine: Removes the specified context from the chain.
removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in interface ome.api.IAdmin: removes the given users from the owner list for this group.
removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.api.IAdmin: Removes an experimenter from the given groups.
removeGuest(long, String) - Method in interface ome.api.IShare: Deprecated.

Removes guest email address from share.
removeGuests(long, String...) - Method in interface ome.api.IShare: Deprecated.

Removes guest email addresses from the share.
removeObject(long, T) - Method in interface ome.api.IShare: Deprecated.

Removes existing object from the share.
removeObjects(long, T...) - Method in interface ome.api.IShare: Deprecated.

Remove existing items from the share.
removeUnusedFiles() - Method in interface ome.api.IRepositoryInfo: Removes all files from the server that do not have an OriginalFile complement in the database, all the Pixels that do not have a complement in the database and all the Thumbnail's that do not have a complement in the database.
removeUser(long, Experimenter) - Method in interface ome.api.IShare: Deprecated.

Removes experimenter from share
removeUsers(long, List<Experimenter>) - Method in interface ome.api.IShare: Deprecated.

Removes experimenters from share
render(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine: Renders the data selected by pd according to the current rendering settings.
renderAsPackedInt(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine: Renders the data selected by pd according to the current rendering settings.
renderCompressed(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine: Renders the data selected by pd according to the current rendering settings and compresses the resulting RGBA composite image.
RenderingEngine - Interface in omeis.providers.re: Defines a service to render a given pixels set.
renderProjectedAsPackedInt(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine: Performs a projection through selected optical sections of a particular timepoint with the currently active channels and renders the data for display.
renderProjectedCompressed(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine: Performs a projection through selected optical sections of a particular timepoint with the currently active channels, renders the data for display and compresses the resulting RGBA composite image.
reportForgottenPassword(String, String) - Method in interface ome.api.IAdmin: Deprecated.
REQUEUED - Static variable in interface ome.api.JobHandle
requiresPixelsPyramid() - Method in interface ome.api.RawPixelsStore
requiresPixelsPyramid() - Method in interface omeis.providers.re.RenderingEngine
resetDefaults() - Method in interface ome.api.Search: Resets all settings (non-query state) to the original default values, as if the instance had just be created.
resetDefaults() - Method in interface ome.api.ThumbnailStore: Resets the rendering definition for the active pixels set to its default settings.
resetDefaults(RenderingDef, Pixels) - Method in interface ome.api.IRenderingSettings: Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.
resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets the rendering settings of a given group of containers based on the owner's (essentially a copy).
resetDefaultSettings(boolean) - Method in interface omeis.providers.re.RenderingEngine: Resets the default settings i.e.
resetDefaultsForPixels(long) - Method in interface ome.api.IRenderingSettings: Resets a Pixels' default rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInDataset(long) - Method in interface ome.api.IRenderingSettings: Resets a dataset's rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInImage(long) - Method in interface ome.api.IRenderingSettings: Resets an image's default rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets a rendering settings back to one or many containers that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsNoSave(RenderingDef, Pixels) - Method in interface ome.api.IRenderingSettings: Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.
resetEnumerations(Class<T>) - Method in interface ome.api.ITypes
resetMinMaxInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets a the channel windows for one or many containers back to their global minimum and global maximum for the channel.
resolveAlias(String) - Method in class ome.system.PreferenceContext
RESUBMITTED - Static variable in interface ome.api.JobHandle
results() - Method in interface ome.api.Search: Returns up to batch size number of results along with the related query metadata.
retrieveAllRndSettings(long, long) - Method in interface ome.api.IPixels: Retrieves all the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
retrieveCollection(IObject, String, Parameters) - Method in interface ome.api.IContainer: Retrieves a collection with all members initialized ("loaded").
retrievePixDescription(long) - Method in interface ome.api.IPixels: Retrieves the pixels metadata with the following objects pre-linked: pixels.pixelsType pixels.pixelsDimensions pixels.channels pixels.channnels.statsInfo pixels.channnels.colorComponent pixels.channnels.logicalChannel pixels.channnels.logicalChannel.photometricInterpretation
retrieveRndSettings(long) - Method in interface ome.api.IPixels: Retrieves the rendering settings for a given pixels set and the currently logged in user.
retrieveRndSettingsFor(long, long) - Method in interface ome.api.IPixels: Retrieves the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
ReverseIntensityContext - Class in omeis.providers.re.codomain: Deprecated.
This class will be renamed to InverseIntensityContext (or similar) in future versions
ReverseIntensityContext() - Constructor for class omeis.providers.re.codomain.ReverseIntensityContext: Deprecated.
RGBAIntBuffer - Class in omeis.providers.re: Holds the data of an RGBA image.
RGBAIntBuffer(int, int) - Constructor for class omeis.providers.re.RGBAIntBuffer: Creates a new 4-band packed integer buffer.
RGBBuffer - Class in omeis.providers.re: Holds the data of an RGB image.
RGBBuffer() - Constructor for class omeis.providers.re.RGBBuffer: Simple constructor to avoid memory allocations.
RGBBuffer(int, int) - Constructor for class omeis.providers.re.RGBBuffer: Creates a new 3-band buffer.
RGBIntBuffer - Class in omeis.providers.re: Holds the data of an RGB image.
RGBIntBuffer(int, int) - Constructor for class omeis.providers.re.RGBIntBuffer: Creates a new 3-band packed integer buffer.
Roles - Class in ome.system: encapsulates the naming scheme for critical system groups and accounts.
Roles() - Constructor for class ome.system.Roles: default constructor which assigns hard-coded values to all roles
Roles(long, String, long, String, long, String, long, String, long, String) - Constructor for class ome.system.Roles: constructor which allows full specification of all roles
RolesAllowed - Annotation Type in ome.annotations: Security annotation which specifies a list of user roles which will be permitted to execute this method.
run() - Method in class ome.system.UpgradeCheck: If the url has been set to null or the empty string, then no upgrade check will be performed (silently).
RUNNING - Static variable in interface ome.api.JobHandle

S

sanityCheckPixels(Pixels, Pixels) - Method in interface ome.api.IRenderingSettings: Checks if the specified sets of pixels are compatible.
sanityCheckRepository() - Method in interface ome.api.IRepositoryInfo: Checks that image data repository has not exceeded 95% disk space use level.
save() - Method in interface ome.api.RawFileStore: Saves the OriginalFile associated with the service if it has been modified.
save() - Method in interface ome.api.RawPixelsStore
saveAndReturnArray(IObject[]) - Method in interface ome.api.IUpdate
saveAndReturnIds(IObject[]) - Method in interface ome.api.IUpdate: Logic differs from other methods.
saveAndReturnObject(T) - Method in interface ome.api.IUpdate
saveArray(IObject[]) - Method in interface ome.api.IUpdate
saveAsNewSettings() - Method in interface omeis.providers.re.RenderingEngine: Saves the current rendering settings in the database as a new RenderingDef and loads the object into the current RenderingEngine.
saveCollection(Collection<IObject>) - Method in interface ome.api.IUpdate
saveCurrentSettings() - Method in interface omeis.providers.re.RenderingEngine: Saves the current rendering settings in the database.
saveObject(IObject) - Method in interface ome.api.IUpdate
saveRndSettings(RenderingDef) - Method in interface ome.api.IPixels: Saves the specified rendering settings.
scaleBufferedImage(BufferedImage, float, float) - Method in interface ome.api.IScale: Scales a buffered image using defined X and Y axis scale factors.
SCORE - Static variable in interface ome.api.Search: String constant used to look up the score value of Lucene queries returned by this interface.
Search - Interface in ome.api: Central search interface, allowing Web2.0 style queries.
searchAll() - Method in interface ome.api.ILdap: Searches all Experimenter list on LDAP for attribute objectClass = person.
searchByAttribute(String, String, String) - Method in interface ome.api.ILdap: Searches all Experimenter in LDAP for specified attribute
searchByAttributes(String, String[], String[]) - Method in interface ome.api.ILdap: Searches all Experimenter in LDAP for specified attributes.
searchByDN(String) - Method in interface ome.api.ILdap: Searches one Experimenter in LDAP for specified Distinguished Name - String
searchDnInGroups(String, String) - Method in interface ome.api.ILdap: Searches Distinguished Name - String in groups
SelfConfigurableService - Interface in ome.system
selfConfigure() - Method in interface ome.system.SelfConfigurableService
Server - Class in ome.system: Provides simplified handling of server properties when creating a ServiceFactory.
Server(String) - Constructor for class ome.system.Server: standard constructor which users Server.DEFAULT_PORT.
Server(String, int) - Constructor for class ome.system.Server: extended constructor.
ServiceFactory - Class in ome.system: Entry point for all client calls.
ServiceFactory() - Constructor for class ome.system.ServiceFactory: default constructor which obtains the global static client context from OmeroContext.
ServiceFactory(String) - Constructor for class ome.system.ServiceFactory: constructor which finds the global static OmeroContext with the given name.
ServiceFactory(Properties) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new client context, passing in the provided properties for configuration.
ServiceFactory(Login) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new (non-static) client context, passing in the Properties representation of the Login for configuration.
ServiceFactory(OmeroContext) - Constructor for class ome.system.ServiceFactory: constructor which uses the provided OmeroContext for all loookups.
ServiceFactory(Server) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new (non-static) client context, passing in the Properties representation of the Server for configuration.
ServiceFactory(Server, Login) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new (non-static) client context, passing in the Properties representation of both the Server and the Login for configuration.
ServiceInterface - Interface in ome.api: Marker interface representing an OMERO API Interface.
session - Variable in class ome.system.SessionInitializer
SessionInitializer - Class in ome.system: Manages the creation of a single Session created via the injected ISession service.
SessionInitializer() - Constructor for class ome.system.SessionInitializer
sessions - Variable in class ome.system.SessionInitializer
setActive(int, boolean) - Method in interface omeis.providers.re.RenderingEngine: Maps the specified channel if true, unmaps the channel otherwise.
setActive(long, boolean) - Method in interface ome.api.IShare: Deprecated.
setAdminPrivileges(Experimenter, List<AdminPrivilege>) - Method in interface ome.api.IAdmin: Sets the set of light administrator privileges for the given user.
setAliases(String[]) - Method in class ome.system.Preference: Setter injector
setAllowLeadingWildcard(boolean) - Method in interface ome.api.Search: Permits full-text queries with a leading query if true.
setBatchSize(int) - Method in interface ome.api.Search: Sets the maximum number of results that will be returned by one call to Search.results().
setBeanName(String) - Method in class ome.system.Preference: Setter injector
setBeginsWith(Collection<String>) - Method in class ome.system.metrics.DefaultMetrics
setBlueValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer: Sets the Blue value for a particular pixel index.
setBlueValue(int, int) - Method in class omeis.providers.re.RGBBuffer: Sets the Blue value for a particular pixel index.
setBlueValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer: Sets the Blue value for a particular pixel index.
setCaseSensitive(boolean) - Method in interface ome.api.Search: Sets the case sensitivity on all queries where case-sensitivity is supported.
setCaseSentivice(boolean) - Method in interface ome.api.Search: Deprecated.
use Search.setCaseSensitive(boolean)
setChannelGlobalMinMax(long, int, double, double) - Method in interface ome.api.IPixels: Sets the channel global (all 2D optical sections corresponding to a particular channel) minimum and maximum for a Pixels set.
setChannelLookupTable(int, String) - Method in interface omeis.providers.re.RenderingEngine
setChannelWindow(int, double, double) - Method in interface omeis.providers.re.RenderingEngine: Returns the pixels intensity interval.
setCodomain(int, int) - Method in class omeis.providers.re.codomain.CodomainMapContext: Sets the codomain interval.
setCodomainInterval(int, int) - Method in interface omeis.providers.re.RenderingEngine: Sets the sub-interval of the device space i.e.
setCompressionLevel(float) - Method in interface omeis.providers.re.RenderingEngine: Sets the current compression level for the service.
setConfigValue(String, String) - Method in interface ome.api.IConfig: set a configuration value in the backend store.
setConfigValueIfEquals(String, String, String) - Method in interface ome.api.IConfig: Calls IConfig.setConfigValue(String, String) if and only if the configuration property is currently equal to the test argument.
setConstant(boolean) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Sets the type of mapping.
setContext(CodomainMapContext) - Method in interface omeis.providers.re.codomain.CodomainMap: Sets the parameters used to write the equation of the specified codomain transformation.
setCoordinates(int, int, int, int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Sets the coordinates of the points used to determine the equations of the lines.
setCredentials(String) - Method in class ome.system.SessionInitializer
setDb(boolean) - Method in class ome.system.Preference: Setter injector
setDefaultGroup(Experimenter, ExperimenterGroup) - Method in interface ome.api.IAdmin: sets the default group for a given user.
setDefaultT(int) - Method in interface omeis.providers.re.RenderingEngine: Sets the default timepoint index.
setDefaultZ(int) - Method in interface omeis.providers.re.RenderingEngine: Sets the index of the default focal section.
setDescription(long, String) - Method in interface ome.api.IShare: Deprecated.
setDN(Long, String) - Method in interface ome.api.ILdap: Deprecated.
As of release 5.1, relevant model objects have the "ldap" property added to their state.
setExpiration(long, Timestamp) - Method in interface ome.api.IShare: Deprecated.
setFileId(long) - Method in interface ome.api.RawFileStore: This method manages the state of the service.
setGraphiteAddress(String) - Method in class ome.system.metrics.DefaultMetrics
setGreenValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer: Sets the Green value for a particular pixel index.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBBuffer: Sets the Green value for a particular pixel index.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer: Sets the Green value for a particular pixel index.
setGroupOwner(ExperimenterGroup, Experimenter) - Method in interface ome.api.IAdmin: adds the user to the owner list for this group.
setGroupPermissions(Permissions) - Method in class ome.system.SimpleEventContext
setHeight(int) - Method in class omeis.providers.re.data.RegionDef: Sets the height of the region.
setInput(String, String, Object) - Method in interface ome.api.ISession: Places an entry in the given session's input environment.
setLimits(int, int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Set the limits.
setLowerLimit(int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Sets the value (in [intervalStart, intervalEnd]) used to set the level of the bit-plane < bit-plane selected.
setMergedBatches(boolean) - Method in interface ome.api.Search: Set whether or not results from two separate queries can be returned in the same call to Search.results().
setMessage(String) - Method in interface ome.api.JobHandle: Sets the job's message string, and returns the previous value.
setModel(RenderingModel) - Method in interface omeis.providers.re.RenderingEngine: Specifies the model that dictates how transformed raw data has to be mapped onto a color space.
setMutable(boolean) - Method in class ome.system.Preference: Setter injector
setOriginalSettingsForPixels(long) - Method in interface ome.api.IRenderingSettings: Resets an Pixels' default rendering settings back to channel global minimum and maximum.
setOriginalSettingsInDataset(long) - Method in interface ome.api.IRenderingSettings: Resets a dataset's rendering settings back to channel global minimum and maximum.
setOriginalSettingsInImage(long) - Method in interface ome.api.IRenderingSettings: Resets an image's default rendering settings back to channel global minimum and maximum.
setOriginalSettingsInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets a rendering settings back to channel global minimum and maximum for the specified containers.
setOutput(String, String, Object) - Method in interface ome.api.ISession: Places an entry in the given session's output environment.
setOverlays(Map<byte[], Integer>) - Method in interface omeis.providers.re.RenderingEngine: Informs the rendering engine that it should render a set of overlays on each rendered frame.
setPixelsId(long) - Method in interface ome.api.ThumbnailStore: This method manages the state of the service; it must be invoked before using any other methods.
setPixelsId(long, boolean) - Method in interface ome.api.RawPixelsStore: Initializes the stateful service for a given Pixels set.
setPlane(byte[], int, int, int) - Method in interface ome.api.RawPixelsStore
setPlanes(int, int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Sets the value of the selected planes i.e.
setPreferences(List<Preference>) - Method in class ome.system.PreferenceContext
setPrefs(boolean) - Method in class ome.system.Preference
setPrincipal(Principal) - Method in class ome.system.SessionInitializer
setProperty(String, String) - Method in class ome.system.PreferenceContext: With ticket:2214, preferences are no longer mutable.
setQuantizationMap(int, Family, double, boolean) - Method in interface omeis.providers.re.RenderingEngine: Sets the quantization map, one per channel.
setQuantumStrategy(int) - Method in interface omeis.providers.re.RenderingEngine: Sets the quantization strategy.
setRedValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer: Sets the Red value for a particular pixel index.
setRedValue(int, int) - Method in class omeis.providers.re.RGBBuffer: Sets the Red value for a particular pixel index.
setRedValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer: Sets the Red value for a particular pixel index.
setRegion(int, long, byte[]) - Method in interface ome.api.RawPixelsStore
setRegion(RegionDef) - Method in class omeis.providers.re.data.PlaneDef: Sets the region to render.
setRenderingDefId(long) - Method in interface ome.api.ThumbnailStore: This method manages the state of the service; it should be invoked directly after ThumbnailStore.setPixelsId(long).
setRenderShapes(boolean) - Method in class omeis.providers.re.data.PlaneDef: Sets whether or not to render the shapes (masks).
setResolutionLevel(int) - Method in interface ome.api.RawPixelsStore: Sets the active resolution level.
setResolutionLevel(int) - Method in interface omeis.providers.re.RenderingEngine
setReturnUnloaded(boolean) - Method in interface ome.api.Search: Determines if all results should be returned as unloaded objects.
setRGBA(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine: Sets the four components composing the color associated to the specified channel.
setRow(byte[], int, int, int, int) - Method in interface ome.api.RawPixelsStore
setSession(Session) - Method in class ome.system.ServiceFactory
setSession(Session) - Method in class ome.system.SessionInitializer
setSessionService(ISession) - Method in class ome.system.SessionInitializer
setShapeIds(List<Long>) - Method in class omeis.providers.re.data.PlaneDef: Sets whether or not to render the shapes (masks).
setSlf4jMinutes(int) - Method in class ome.system.metrics.DefaultMetrics
setStack(byte[], int, int, int) - Method in interface ome.api.RawPixelsStore
setStatus(String) - Method in interface ome.api.JobHandle: Updates the JobStatus for the current job.
setStatusAndMessage(String, String) - Method in interface ome.api.JobHandle: Like JobHandle.setStatus(String) but also sets the message.
setStride(int) - Method in class omeis.providers.re.data.PlaneDef: Returns the stride.
setTile(byte[], int, int, int, int, int, int, int) - Method in interface ome.api.RawPixelsStore
setTimepoint(byte[], int) - Method in interface ome.api.RawPixelsStore
setUpperLimit(int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Sets the value (in [intervalStart, intervalEnd]) used to set the level of the bit-plane > bit-plane selected.
setUseProjections(boolean) - Method in interface ome.api.Search: Determines if Lucene queries should not hit the database.
setVisibility(Preference.Visibility) - Method in class ome.system.Preference: Setter injector
setWidth(int) - Method in class omeis.providers.re.data.RegionDef: Sets the width of the region.
setX(int) - Method in class omeis.providers.re.data.PlaneDef: Selects a plane in the set identified by this object.
setX(int) - Method in class omeis.providers.re.data.RegionDef: Sets the x-coordinate of the top-left corner.
setXEnd(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Sets the x-coodinate of the pEnd point.
setXStart(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Sets the x-coodinate of the pStart point.
setY(int) - Method in class omeis.providers.re.data.PlaneDef: Selects a plane in the set identified by this object.
setY(int) - Method in class omeis.providers.re.data.RegionDef: Sets the y-coordinate of the top-left corner.
setYEnd(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Sets the y-coodinate of the pEnd point.
setYStart(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Sets the y-coodinate of the pStart point.
setZ(int) - Method in class omeis.providers.re.data.PlaneDef: Selects a plane in the set identified by this object.
SHA1 - ome.util.checksum.ChecksumType
SHA1ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using SHA1 as the secure hash algorithm.
SHA1ChecksumProviderImpl() - Constructor for class ome.util.checksum.SHA1ChecksumProviderImpl
shareId - Variable in class ome.system.SimpleEventContext
ShutdownMessage - Class in ome.util.messages: Published when the server is shutting down.
ShutdownMessage(Object) - Constructor for class ome.util.messages.ShutdownMessage
SiftingWhileRejectingDefaultAppender - Class in ome.util.logback
SiftingWhileRejectingDefaultAppender() - Constructor for class ome.util.logback.SiftingWhileRejectingDefaultAppender
signal - Variable in class ome.util.messages.UserSignalMessage
SimpleEventContext - Class in ome.system: simple, non-thread-safe, serializable EventContext
SimpleEventContext() - Constructor for class ome.system.SimpleEventContext: Constructor for subclasses
SimpleEventContext(EventContext) - Constructor for class ome.system.SimpleEventContext: copy constructor.
size() - Method in interface ome.api.RawFileStore: Returns the size of the file on disk (not as stored in the database since that value will only be updated on RawFileStore.save().
size() - Method in class ome.system.metrics.DefaultSnapshot
size() - Method in interface ome.system.metrics.Snapshot
Snapshot - Interface in ome.system.metrics: Thin wrapper around Snapshot
StatefulServiceInterface - Interface in ome.api: OMERO API Interface with stateful semantics.
stop() - Method in class ome.system.metrics.DefaultTimer.Context
stop() - Method in interface ome.system.metrics.Timer.Context
submit(Job) - Method in interface ome.api.JobHandle: Submits a Job and returns its database id.
SUBMITTED - Static variable in interface ome.api.JobHandle
SUM_INTENSITY - Static variable in interface ome.api.IProjection: Sum intensity projection
synchronizeLoginCache() - Method in interface ome.api.IAdmin: uses JMX to refresh the login cache if supported.

T

t - Variable in exception ome.util.messages.MessageException
threadSafe - Variable in class ome.util.messages.InternalMessage
thumbnailExists(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Checks if a thumbnail of a particular size exists for a pixels set.
ThumbnailStore - Interface in ome.api: Provides methods for dealing with thumbnails.
time() - Method in class ome.system.metrics.DefaultTimer
time() - Method in interface ome.system.metrics.Timer
timer(Object, String) - Method in class ome.system.metrics.DefaultMetrics
timer(Object, String) - Method in interface ome.system.metrics.Metrics
timer(Object, String) - Method in class ome.system.metrics.NullMetrics
Timer - Interface in ome.system.metrics: Thin wrapper around Timer
Timer.Context - Interface in ome.system.metrics
toString() - Method in class ome.system.Principal: returns only the name of the instance because that is the expected behavior of Principal implementations
toString() - Method in class omeis.providers.re.data.PlaneDef: Overrides generic toString method to provide a specific string representation of this object.
toString() - Method in class omeis.providers.re.data.RegionDef: Overridden to return the region as a string.
transform(int) - Method in interface omeis.providers.re.codomain.CodomainMap: Performs the transformation.
truncate(long) - Method in interface ome.api.RawFileStore: Limits the size of a file to the given length.
type - Variable in class ome.system.Principal

U

umask - Variable in class ome.system.SimpleEventContext
unlink(ILink[], Parameters) - Method in interface ome.api.IContainer: Removes links between OmeroDataObjects e.g Project-Dataset, Dataset-Image Note that the objects themselves aren't deleted, only the Link objects.
unordered() - Method in interface ome.api.Search: Removes the current stack of order statements.
unsetGroupOwner(ExperimenterGroup, Experimenter) - Method in interface ome.api.IAdmin: removes the user from the owner list for this group.
update(int) - Method in class ome.system.metrics.DefaultHistogram
update(int) - Method in interface ome.system.metrics.Histogram
updateCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine: Deprecated.
updateDataObject(T, Parameters) - Method in interface ome.api.IContainer: Updates a data object.
updateDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer: convenience method to save network calls.
updateEnumeration(T) - Method in interface ome.api.ITypes: updates enumeration value specified by object
updateEnumerations(List<T>) - Method in interface ome.api.ITypes: updates enumeration value specified by object
updateExperimenter(Experimenter) - Method in interface ome.api.IAdmin: Updates an experimenter if admin or owner of group.
updateExperimenterWithPassword(Experimenter, String) - Method in interface ome.api.IAdmin: Updates an experimenter if admin or owner of group.
updateGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin: Updates an experimenter group if admin or owner of group.
updateSelf(Experimenter) - Method in interface ome.api.IAdmin: Allows a user to update his/her own information.
updateSettings(RenderingDef) - Method in interface omeis.providers.re.RenderingEngine: Updates the current rendering settings based on a provided rendering definition and associated sub-objects.
UpgradeCheck - Class in ome.system: Contacts a given URL which should be an OME server which will return either an empty String or a URL which points to a needed upgrade.
UpgradeCheck(String, String, String) - Constructor for class ome.system.UpgradeCheck: Calls UpgradeCheck(String, String, String, int) using DEFAULT_TIMEOUT
UpgradeCheck(String, String, String, int) - Constructor for class ome.system.UpgradeCheck: Main constructor.
uploadMyUserPhoto(String, String, byte[]) - Method in interface ome.api.IAdmin: Uploads a photo for the user which will be displayed on his/her profile.
user - ome.system.Preference.Visibility
UserSignalMessage - Class in ome.util.messages: Published if the Posix USR1 or USR2 signal is received.
UserSignalMessage(Object, int) - Constructor for class ome.util.messages.UserSignalMessage

V

Validate - Annotation Type in ome.annotations: annotation used for determining the types of a Set
value() - Method in annotation type ome.annotations.RolesAllowed
value() - Method in annotation type ome.annotations.Validate
valueOf(String) - Static method in enum ome.system.Preference.Visibility: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.util.checksum.ChecksumType: Returns the enum constant of this type with the specified name.
values() - Static method in enum ome.system.Preference.Visibility: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.util.checksum.ChecksumType: Returns an array containing the constants of this enum type, in the order they are declared.
VERSION_REGEX - Static variable in interface ome.api.IConfig: Defines how the omero.version Preference will be parsed into the form: Major.minor.patch for IConfig.getVersion()

W

WAITING - Static variable in interface ome.api.JobHandle
write(byte[], long, int) - Method in interface ome.api.RawFileStore: Writes length bytes of data from the specified buf byte array starting at at position to the raw file

X

XY - Static variable in class omeis.providers.re.data.PlaneDef: Flag to identify an XY-plane.
XZ - Static variable in class omeis.providers.re.data.PlaneDef: Flag to identify an XZ-plane.

Z

zero() - Method in class omeis.providers.re.RGBAIntBuffer
zero() - Method in class omeis.providers.re.RGBBuffer: Zeros out (sets every pixel offset to zero) each band.
zero() - Method in class omeis.providers.re.RGBIntBuffer
ZY - Static variable in class omeis.providers.re.data.PlaneDef: Flag to identify an YZ-plane.

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