- c2c() - Method in class omero.util.IceMapper
-
- cache - Variable in class ome.services.sessions.SessionManagerImpl
-
- CacheFactory - Class in ome.services.sessions.state
-
- CacheFactory() - Constructor for class ome.services.sessions.state.CacheFactory
-
- CacheListener - Class in ome.services.sessions.state
-
Basic CacheEventListener
which does nothing.
- CacheListener() - Constructor for class ome.services.sessions.state.CacheListener
-
- calculate(Pixels) - Method in class ome.io.nio.SimpleBackOff
-
- calculate() - Method in class ome.io.nio.SimpleBackOff
-
- calculateBackOff(int) - Method in class ome.services.db.SelfCorrectingDataSource
-
- calculateMessageDigest() - Method in interface ome.api.RawPixelsStore
-
- calculateMessageDigest() - Method in class ome.io.bioformats.BfPixelBuffer
-
- calculateMessageDigest() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- calculateMessageDigest() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- calculateMessageDigest() - Method in interface ome.io.nio.PixelBuffer
-
Calculates a SHA-1 message digest for the entire pixel buffer.
- calculateMessageDigest() - Method in class ome.io.nio.RomioPixelBuffer
-
- calculateMessageDigest() - Method in class ome.services.RawPixelsBean
-
- calculateMessageDigest_async(AMD_RawPixelsStore_calculateMessageDigest, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- calculateMessageDigest_async(AMD_RawPixelsStore_calculateMessageDigest, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- calculateXYWidths(Pixels, int) - Method in class ome.services.ThumbnailCtx
-
Calculates the ratio of the two sides of a Pixel set and returns the
X and Y widths based on the longest side maintaining aspect ratio.
- call(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource
-
- call(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.Action
-
- call(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
-
- call() - Method in interface omeis.providers.re.RenderingTask
-
Renders wavelength.
- Callback - Class in ome.services.throttling
-
Manages AMD-based method dispatches from blitz.
- Callback(Boolean, Boolean, ServiceInterface, IceMethodInvoker, Object, IceMapper, Current, Object...) - Constructor for class ome.services.throttling.Callback
-
- Callback(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Constructor for class ome.services.throttling.Callback
-
- callback - Variable in class omero.cmd.SessionI
-
- Callback2<R> - Class in ome.services.throttling
-
Callable
-based callback which guarantees that ice_response or
ice_exception is called.
- Callback2(Current, Object, boolean, Callable<R>) - Constructor for class ome.services.throttling.Callback2
-
- CallContext - Class in omero.cmd
-
Interceptor which takes any context provided by the
client and calls setContext on CurrentDetails.
- CallContext(OmeroContext) - Constructor for class omero.cmd.CallContext
-
- CallContext(CurrentDetails) - Constructor for class omero.cmd.CallContext
-
- callContextWrapper(Object) - Method in class omero.cmd.SessionI
-
- callInvokerOnMappedArgs(IceMapper, Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant
-
- callInvokerOnRawArgs(Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant
-
- callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor
-
- callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy
-
- callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy
-
- callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor
-
Passes the given arguments to
IceMethodInvoker
with the
assumption that all conversion from omero.* to ome.* has taken place.
- callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy
-
- callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy
-
- callWithRetries(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource
-
- canAnnotate(Current) - Method in class omero.model.PermissionsI
-
- canAnnotate() - Method in class pojos.DataObject
-
Returns true
if the object can be annotated
false
otherwise, depending on permissions level.
- cancel() - Method in class ome.formats.importer.ImportCandidates.SCANNING
-
Can be called to cancel the current action.
- cancel - Variable in class ome.formats.importer.util.ErrorFilePart
-
- cancel() - Method in class ome.formats.importer.util.FileUploader
-
cancel's upload
- cancel(Current) - Method in class ome.services.blitz.impl.DeleteHandleI
-
- cancel(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
-
- cancel() - Method in interface ome.services.procs.Process
-
- cancel() - Method in class ome.services.procs.ProcessSkeleton
-
- cancel(String) - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
-
- cancel(Current) - Method in class omero.cmd.HandleI
-
- cancel(ERR, Throwable, String, String...) - Method in class omero.cmd.Helper
-
- cancel(ERR, Throwable, String, Map<String, String>) - Method in class omero.cmd.Helper
-
- cancelJob() - Method in interface ome.api.JobHandle
-
Marks a job for cancellation.
- cancelJob() - Method in class ome.services.JobBean
-
- cancelJob_async(AMD_JobHandle_cancelJob, Current) - Method in class ome.services.blitz.impl.JobHandleI
-
- CANCELLED - Static variable in interface ome.api.JobHandle
-
- cancelUploads - Variable in class ome.formats.importer.util.ErrorHandler
-
- canDelete(Current) - Method in class omero.model.PermissionsI
-
- canDelete() - Method in class pojos.DataObject
-
Returns true
if the object can be deleted by the user
currently logged in,
false
otherwise, depending on permissions level.
- canEdit(Current) - Method in class omero.model.PermissionsI
-
- canEdit() - Method in class pojos.DataObject
-
Returns true
if the object can be edited by the user
currently logged in false
otherwise,
depending on permissions level.
- canLink(Current) - Method in class omero.model.PermissionsI
-
- canLink() - Method in class pojos.DataObject
-
Returns true
if the object can be linked e.g. image
add to dataset, by the user currently logged in,
false
otherwise, depending on
permissions level.
- canLogin() - Method in class ome.formats.importer.ImportConfig
-
Confirm all information for login is supplied
- canMapReturnValue() - Method in class omero.util.IceMapper
-
- canRead(EventContext, String) - Method in class ome.system.PreferenceContext
-
- canRunScript_async(AMD_IScript_canRunScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI
-
- canUpdate(IObject) - Method in interface ome.api.IAdmin
-
Returns true if the currently logged in user can modify the given
IObject
.
- canUpdate(IObject) - Method in class ome.logic.AdminImpl
-
- canUpdate_async(AMD_IAdmin_canUpdate, IObject, Current) - Method in class ome.services.blitz.impl.AdminI
-
- caseSensitive - Variable in class ome.services.search.SearchValues
-
- cause(Throwable) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities
-
- cb - Variable in class ome.services.throttling.Task
-
- cd - Variable in class ome.security.basic.BasicSecuritySystem
-
- cd - Variable in class ome.security.basic.EventLogListener
-
- cd - Variable in class ome.security.SecurityFilterHolder
-
- 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
-
- chainedList - Variable in class ome.services.search.SearchAction
-
List of IObject
instances which have currently been found.
- chainedSearch(List<IObject>) - Method in class ome.services.search.SearchAction
-
Set the current list of found ids from previous searches, which should be
chained in this search.
- changeDistinguisedName(String, String) - Method in class ome.security.auth.PasswordProviders
-
- changeExpiredCredentials(String, String, String) - Method in interface ome.api.IAdmin
-
Used after an ExpiredCredentialsException
instance is thrown.
- changeExpiredCredentials(String, String, String) - Method in class ome.logic.AdminImpl
-
- changeExpiredCredentials_async(AMD_IAdmin_changeExpiredCredentials, String, String, String, Current) - Method in class ome.services.blitz.impl.AdminI
-
- changeGroup(IObject, String) - Method in interface ome.api.IAdmin
-
call
details.setGroup()
on this instance.
- changeGroup(IObject, String) - Method in class ome.logic.AdminImpl
-
- changeGroup_async(AMD_IAdmin_changeGroup, IObject, String, Current) - Method in class ome.services.blitz.impl.AdminI
-
- changeOwner(IObject, String) - Method in interface ome.api.IAdmin
-
call
details.setOwner()
on this instance.
- changeOwner(IObject, String) - Method in class ome.logic.AdminImpl
-
- changeOwner_async(AMD_IAdmin_changeOwner, IObject, String, Current) - Method in class ome.services.blitz.impl.AdminI
-
- changePassword(String) - Method in interface ome.api.IAdmin
-
change the password for the current user.
- changePassword(String) - Method in class ome.logic.AdminImpl
-
- changePassword(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
Throws by default.
- changePassword(String, String) - Method in class ome.security.auth.JdbcHashedPasswordProvider
-
- changePassword(String, String) - Method in class ome.security.auth.JdbcPasswordProvider
-
- changePassword(String, String, PasswordUtil.METHOD) - Method in class ome.security.auth.JdbcPasswordProvider
-
Actually perform the password change in the database and log the event against the user.
- changePassword(String, String) - Method in interface ome.security.auth.PasswordProvider
-
Attempts to change the password for the given user.
- changePassword(String, String) - Method in class ome.security.auth.PasswordProviders
-
- changePassword_async(AMD_IAdmin_changePassword, RString, Current) - Method in class ome.services.blitz.impl.AdminI
-
- changePasswordWithOldPassword(String, String) - Method in interface ome.api.IAdmin
-
change the password for the current user by passing the old password.
- changePasswordWithOldPassword(String, String) - Method in class ome.logic.AdminImpl
-
- changePasswordWithOldPassword_async(AMD_IAdmin_changePasswordWithOldPassword, RString, RString, Current) - Method in class ome.services.blitz.impl.AdminI
-
- changePermissions(IObject, Permissions) - Method in interface ome.api.IAdmin
-
call
defaults.setPermissions()
on this instance.
- changePermissions(IObject, Permissions) - Method in class ome.logic.AdminImpl
-
the implementation of this method is somewhat tricky in that
Permissions
changes must be allowed even when other updates are
not.
- changePermissions_async(AMD_IAdmin_changePermissions, IObject, Permissions, Current) - Method in class ome.services.blitz.impl.AdminI
-
- ChangeSecurityContextEvent - Class in ome.services.sessions.events
-
InteralMessage
published by the
SessionManager
when
setSecurityContext() is called.
- ChangeSecurityContextEvent(Object, String, IObject, IObject) - Constructor for class ome.services.sessions.events.ChangeSecurityContextEvent
-
- changeUserPassword(String, String) - Method in interface ome.api.IAdmin
-
change the password for the a given user.
- changeUserPassword(String, String) - Method in class ome.logic.AdminImpl
-
- changeUserPassword_async(AMD_IAdmin_changeUserPassword, String, RString, Current) - Method in class ome.services.blitz.impl.AdminI
-
- changeUserPasswordById(Long, String) - Method in class ome.security.auth.PasswordUtil
-
Calls {@link #changeUserPasswordById(Long, String, boolean) with
"false" as the value of the salt argument in order to provide backwards
compatibility.
- changeUserPasswordById(Long, String, PasswordUtil.METHOD) - Method in class ome.security.auth.PasswordUtil
-
- ChannelAcquisitionData - Class in pojos
-
Object hosting the acquisition related to a logical channel.
- ChannelAcquisitionData(LogicalChannel) - Constructor for class pojos.ChannelAcquisitionData
-
Creates a new instance.
- ChannelData - Class in ome.formats.model
-
Represents all the metadata required to make accurate decisions about
channel colour and name.
- ChannelData() - Constructor for class ome.formats.model.ChannelData
-
- ChannelData - Class in pojos
-
The data that makes up an OME Channel along with links to its logical
channel.
- ChannelData(int) - Constructor for class pojos.ChannelData
-
Creates a new instance.
- ChannelData(int, Channel) - Constructor for class pojos.ChannelData
-
Creates a new instance.
- CHANNELID_QUERY - Static variable in class ome.services.delete.DeleteBean
-
- ChannelProcessor - Class in ome.formats.model
-
Processes the pixels sets of an IObjectContainerStore and ensures
that LogicalChannel containers are present in the container cache, and
populating channel name and colour where appropriate.
- ChannelProcessor() - Constructor for class ome.formats.model.ChannelProcessor
-
- check(IObject, Object) - Method in class ome.security.basic.GroupChmodStrategy
-
Here we used the checks returned from
ExtendedMetadata
to iterate
through every non-system table and check that it has no FKs which point
to back to its rows and violate the read permissions which are being
reduced.
- check(IObject, Object) - Method in interface ome.security.ChmodStrategy
-
- check(String) - Method in class ome.services.query.Query
-
- check() - Method in interface omero.util.Resources.Entry
-
Called during each cycle.
- CheckAllJobs - Class in ome.services.blitz.util
-
- CheckAllJobs(Executor, ObjectAdapter, TopicManager) - Constructor for class ome.services.blitz.util.CheckAllJobs
-
- CheckAllJobs(Executor, ObjectAdapter, TopicManager, long) - Constructor for class ome.services.blitz.util.CheckAllJobs
-
- checkAndRegister() - Method in class ome.services.JobBean
-
- checkArgs(Object...) - Method in class ome.services.graphs.GraphEntry
-
- checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
-
Checks to ensure that no one particular axis has an offset out of bounds.
- checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- checkCluster() - Method in class ome.services.blitz.fire.Ring
-
Method called during initialization to get all the active uuids within
the cluster, and remove any dead nodes.
- checkDatabase(String) - Method in class ome.system.PreferenceContext
-
- checkDelayedCallContext(BasicEventContext) - Method in class ome.security.basic.CurrentDetails
-
- checkImageDelete(long, boolean) - Method in interface ome.api.IDelete
-
Returns all entities which would prevent the given Image
id from
being deleted.
- checkImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean
-
- checkImageDelete_async(AMD_IDelete_checkImageDelete, long, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI
-
- checkIndex(int) - Method in class ome.util.mem.ReadOnlyByteArray
-
Makes sure that i
is in [0, length)
.
- checkManagedDetails(IObject, Details) - Method in class ome.security.basic.BasicSecuritySystem
-
- checkManagedDetails(IObject, Details) - Method in class ome.security.basic.OmeroInterceptor
-
- checkManagedDetails(IObject, Details, Details) - Method in class ome.security.basic.OmeroInterceptor
-
- checkManagedDetails(IObject, Details) - Method in interface ome.security.SecuritySystem
-
checks that a non-privileged user has not attempted to edit the entity's
security details
.
- checkManagedDetails(IObject, Details) - Method in class ome.security.SecuritySystemHolder
-
- checkManagedDetails(IObject, Details) - Method in class ome.security.sharing.SharingSecuritySystem
-
- checkMethod(Object, Method, Principal, boolean) - Method in class ome.security.basic.BasicMethodSecurity
-
See MethodSecurity#checkMethod(Object, Method, Principal)
- checkMethod(Object, Method, Principal, boolean) - Method in interface ome.security.MethodSecurity
-
Throws a
SecurityViolation
exception if the given
Principal
does not have the proper permissions to execute the
given method.
- checkNonNull(List<Point>) - Static method in class omero.model.SmartShape.Util
-
Used from assert statements of the form:
assert Util.checkNonNull(points) : "Null points in " + this;
in all the implementations of
SmartShape.asPoints()
.
- checkParameters() - Method in class ome.services.query.Query
-
check the
Parameters
instance against the
Definitions
instance for this Query.
- checkPassword(String, String, boolean) - Method in interface ome.api.local.LocalAdmin
-
Checks password for given user.
- checkPassword(String, String, boolean) - Method in class ome.logic.AdminImpl
-
If ldap plugin turned, creates Ldap accounts and authentication by LDAP
available.
- checkPassword(String, String, boolean) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
- checkPassword(String, String, boolean) - Method in class ome.security.auth.FilePasswordProvider
-
- checkPassword(String, String, boolean) - Method in class ome.security.auth.JdbcPasswordProvider
-
- checkPassword(String, String, boolean) - Method in class ome.security.auth.LdapPasswordProvider
-
- checkPassword(String, String, boolean) - Method in interface ome.security.auth.PasswordProvider
-
Authenticates the give user given the password token.
- checkPassword(String, String, boolean) - Method in class ome.security.auth.PasswordProviders
-
- checkPassword(String, String, boolean) - Method in class ome.security.auth.providers.LdapPasswordProvider431
-
- checkPassword(String) - Method in class ome.services.blitz.fire.Ring
-
Currently only returns false since if the regular password check
performed by
SessionManager
cannot find the
session, then the cluster has no extra information.
- checkPermissions(String, String, StringHolder, Current) - Method in class ome.services.blitz.fire.PermissionsVerifierI
-
- checkProperty(String, String) - Method in interface ome.api.local.LocalQuery
-
Checks if a property is defined on a mapped Hibernate type.
- checkProperty(String, String) - Method in class ome.logic.PojosImpl
-
- checkProperty(String, String) - Method in class ome.logic.QueryImpl
-
- checkReady(String) - Method in class ome.security.basic.BasicSecuritySystem
-
- checkState() - Method in class ome.services.procs.ProcessSkeleton
-
- 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.
- 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.
- 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
-
- ChecksumProviderFactoryImpl - Class in ome.util.checksum
-
- ChecksumProviderFactoryImpl() - Constructor for class ome.util.checksum.ChecksumProviderFactoryImpl
-
- ChecksumType - Enum in ome.util.checksum
-
Enumeration defining the possible algorithms used for calculating checksums.
- checkType(String) - Method in interface ome.api.local.LocalQuery
-
Checks if a type has been mapped in Hibernate.
- checkType(String) - Method in class ome.logic.PojosImpl
-
- checkType(String) - Method in class ome.logic.QueryImpl
-
- checkWriteOperationAllowed(Session) - Method in class ome.tools.spring.ManualFlushHibernateTemplate
-
- ChgrpI - Class in omero.cmd.graphs
-
- ChgrpI(ChgrpStepFactory, ApplicationContext) - Constructor for class omero.cmd.graphs.ChgrpI
-
- chgrpQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.BaseGraphSpec
-
- chgrpQuery(EventContext, String, GraphOpts) - Method in interface ome.services.graphs.GraphSpec
-
- chgrpQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.LightSourceGraphSpec
-
- ChgrpStep - Class in ome.services.chgrp
-
- ChgrpStep(OmeroContext, ExtendedMetadata, Roles, int, List<GraphStep>, GraphSpec, GraphEntry, long[], long) - Constructor for class ome.services.chgrp.ChgrpStep
-
- ChgrpStepFactory - Class in ome.services.chgrp
-
- ChgrpStepFactory(OmeroContext, ExtendedMetadata, Roles) - Constructor for class ome.services.chgrp.ChgrpStepFactory
-
- ChgrpValidation - Class in ome.services.chgrp
-
- ChgrpValidation(OmeroContext, ExtendedMetadata, Roles, int, List<GraphStep>, GraphSpec, GraphEntry, long[], long) - Constructor for class ome.services.chgrp.ChgrpValidation
-
- chmod - Variable in class ome.logic.AdminImpl
-
- chmod(IObject, String) - Method in class ome.security.basic.GroupChmodStrategy
-
- chmod(IObject, String) - Method in interface ome.security.ChmodStrategy
-
Change the permissions for the given object.
- ChmodI - Class in omero.cmd.graphs
-
- ChmodI(ChmodStrategy) - Constructor for class omero.cmd.graphs.ChmodI
-
- chmodQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.BaseGraphSpec
-
- chmodQuery(EventContext, String, GraphOpts) - Method in interface ome.services.graphs.GraphSpec
-
- ChmodStrategy - Interface in ome.security
-
Strategy for changing the permissions of objects in the database
as well as verifying that the permissions for the modified objects
are sensible after the change.
- choose() - Method in class ome.security.CompositeACLVoter
-
- choose() - Method in class ome.security.SecurityFilterHolder
-
- choose() - Method in class ome.security.SecuritySystemHolder
-
- chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.ConfigRedirector
-
- chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.NullRedirector
-
Does nothing.
- chooseNextRedirect(Redirector.Context, Set<String>) - Method in interface ome.services.blitz.redirect.Redirector
-
Gives the
Redirector
a chance to configure the next appropriate
redirect based on the
Set
of current
Node
uuids.
- chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.ScaleRedirector
-
- ChownI - Class in omero.cmd.graphs
-
- ChownI(ChownStepFactory, ApplicationContext) - Constructor for class omero.cmd.graphs.ChownI
-
- ChownStep - Class in ome.services.chown
-
- ChownStep(OmeroContext, ExtendedMetadata, Roles, int, List<GraphStep>, GraphSpec, GraphEntry, long[], long) - Constructor for class ome.services.chown.ChownStep
-
- ChownStepFactory - Class in ome.services.chown
-
- ChownStepFactory(OmeroContext, ExtendedMetadata, Roles) - Constructor for class ome.services.chown.ChownStepFactory
-
- ChownValidation - Class in ome.services.chown
-
- ChownValidation(OmeroContext, ExtendedMetadata, Roles, int, List<GraphStep>, GraphSpec, GraphEntry, long[], long) - Constructor for class ome.services.chown.ChownValidation
-
- classes - Variable in class ome.services.fulltext.FullTextBridge
-
- ClassQuerySource - Class in ome.services.query
-
creates a query based on the id string by interpreting it as a Class.
- ClassQuerySource() - Constructor for class ome.services.query.ClassQuerySource
-
- clean() - Method in class ome.services.RawFileBean
-
- clean() - Method in class ome.services.RawPixelsBean
-
- cleanServants(boolean) - Method in class omero.cmd.SessionI
-
- cleanServants(boolean, String, ServantHolder, ObjectAdapter) - Static method in class omero.cmd.SessionI
-
Clean all servants that are in the current holder and remove them from
the adapter.
- cleanTempDir() - Method in class omero.util.TempFileManager
-
- cleanThread() - Method in class ome.tools.hibernate.SessionHandler
-
- cleanup() - Method in class ome.services.util.ServiceHandler
-
- cleanup() - Method in class omero.util.Resources
-
- cleanup() - Method in interface omero.util.Resources.Entry
-
Gives an
Resources.Entry
a chance to cleanup resources before it is
removed from checking.
- cleanup() - Method in class omero.util.TempFileManager
-
- cleanupSelf() - Method in class omero.cmd.SessionI
-
Called if this isn't a kill-everything event.
- cleanUserDir() - Method in class omero.util.TempFileManager
-
Attempts to delete all directories under self.userdir other than the one
owned by this process.
- clear() - Method in interface ome.api.local.LocalQuery
-
- clear() - Method in class ome.formats.importer.ImportLibrary
-
- clear() - Method in class ome.logic.QueryImpl
-
- clear() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
reset all statistics
- clearDisabled() - Method in class ome.security.basic.CurrentDetails
-
- clearErrors(int) - Method in class ome.formats.importer.util.ErrorHandler
-
- clearFiles() - Method in class ome.formats.importer.util.ErrorContainer
-
Clear the list of files to upload.
- clearLogs() - Method in class ome.security.basic.BasicSecuritySystem
-
- clearLogs() - Method in class ome.security.basic.CurrentDetails
-
- clearQueries() - Method in interface ome.api.Search
-
- clearQueries() - Method in class ome.services.SearchBean
-
- clearQueries_async(AMD_Search_clearQueries, Current) - Method in class ome.services.blitz.impl.SearchI
-
- clearToken(GraphHolder) - Method in class ome.security.basic.TokenHolder
-
- client - Class in omero
-
Central client-side blitz entry point.
- client() - Constructor for class omero.client
-
- client(InitializationData) - Constructor for class omero.client
-
Creates an Communicator
from a InitializationData
instance.
- client(String) - Constructor for class omero.client
-
Creates an Communicator
pointing at the given server using
the #DEFAULT_PORT
.
- client(String, int) - Constructor for class omero.client
-
Creates an Communicator
pointing at the given server with the
non-standard port.
- client(String[]) - Constructor for class omero.client
-
- client(String[], InitializationData) - Constructor for class omero.client
-
Creates an Communicator
from command-line arguments.
- client(File...) - Constructor for class omero.client
-
Creates an Communicator
from multiple files.
- client(Map) - Constructor for class omero.client
-
Creates an
Communicator
from a
Map
instance.
- client - Variable in class omero.model.DetailsI
-
- 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.
- ClientError - Exception in omero
-
abstract superclass of all Omero exceptions.
- ClientError(String) - Constructor for exception omero.ClientError
-
- clientId - Variable in class omero.cmd.SessionI
-
- clientId(Current) - Static method in class omero.cmd.SessionI
-
Helpers method to extract the CLIENTUUID
out of the given
Ice.Current.
- clientIds - Variable in class omero.util.ServantHolder
-
An internal mapping to all client ids from
SessionI
for a given
DB session since there is no method on
ObjectAdapter
to retrieve
all servants.
- ClientKeepAlive - Class in ome.formats.importer.util
-
A
Runnable
which keeps a
Connector
's server side resources
from timing out.
- ClientKeepAlive() - Constructor for class ome.formats.importer.util.ClientKeepAlive
-
- clone() - Method in class ome.services.sessions.state.CacheListener
-
- cloneWithPrefix(String) - Method in class ome.services.blitz.util.CommonsLoggingAdapter
-
- close() - Method in interface ome.api.StatefulServiceInterface
-
signals the end of the service lifecycle.
- close() - Method in class ome.formats.importer.OMEROWrapper
-
- close() - Method in class ome.io.bioformats.BfPixelBuffer
-
- close() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- close() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- close() - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
-
- close() - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter
-
- close() - Method in class ome.io.nio.FileBuffer
-
Closes the buffer, cleaning up file state.
- close() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- close() - Method in interface ome.io.nio.PixelBuffer
-
Closes the buffer, cleaning up file state.
- close() - Method in class ome.io.nio.RomioPixelBuffer
-
Closes the buffer, cleaning up file state.
- close(Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
-
- close(boolean, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
-
- close(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
Deprecated.
- close() - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- close() - Method in class ome.services.blitz.repo.FileMaker
-
- close() - Method in class ome.services.formats.OmeroReader
-
- close() - Method in class ome.services.JobBean
-
- close() - Method in class ome.services.messages.RegisterServiceCleanupMessage
-
Used to close the passed in resource.
- close() - Method in class ome.services.RawFileBean
-
- close() - Method in class ome.services.RawPixelsBean
-
- close() - Method in class ome.services.RenderingBean
-
- close() - Method in class ome.services.SearchBean
-
- close() - Method in interface ome.services.sessions.SessionCallback
-
- close(String) - Method in interface ome.services.sessions.SessionManager
-
If reference count for the session is less than 1, close the session.
- close(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- close() - Method in class ome.services.sharing.ShareStore
-
- close() - Method in class ome.services.ThumbnailBean
-
- close() - Method in class omeis.providers.re.Renderer
-
Closes the buffer, cleaning up file state.
- close(boolean) - Method in class omero.cmd.CmdCallbackI
-
First removes self from the adapter so as to no longer receive
notifications, and the calls close on the remote handle if requested.
- close(Current) - Method in class omero.cmd.HandleI
-
- close() - Method in class omero.grid.DeleteCallbackI
-
- close(Current) - Method in class omero.grid.InteractiveProcessorI
-
- close() - Method in class omero.grid.ProcessCallbackI
-
- close(Current) - Method in interface omero.util.CloseableServant
-
- close() - Method in class omero.util.RPSTileData
-
- close() - Method in interface omero.util.TileData
-
- close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
-
SessionHandler
also
specially catches close() calls, but cannot remove the servant
from the
ObjectAdapter
and thereby prevent any
further communication.
- close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- CloseableServant - Interface in omero.util
-
- closeAll() - Method in interface ome.services.sessions.SessionManager
-
Close all sessions with checking for the necessary reference counts.
- closeAll() - Method in class ome.services.sessions.SessionManagerImpl
-
- closeAll() - Method in class ome.system.OmeroContext
-
closes all the nested OmeroContexts within this instance.
- closeOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- closeRaf() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- closeService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
- closeService() - Method in interface ome.services.blitz.gateway.services.GatewayService
-
Close the service and all it's surrogate services.
- closeServices() - Method in class ome.formats.OMEROMetadataStoreClient
-
Closes all stateful services.
- closeSession(Session) - Method in interface ome.api.ISession
-
Closes session and releases all resources.
- closeSession(Session) - Method in class ome.services.sessions.SessionBean
-
- closeSession() - Method in class ome.system.ServiceFactory
-
- closeSession() - Method in class omero.client
-
Closes the session and nulls out the communicator.
- closeSession() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- closeSession_async(AMD_ISession_closeSession, Session, Current) - Method in class ome.services.blitz.impl.SessionI
-
- closeShare(long) - Method in interface ome.api.IShare
-
Closes share
.
- closeShare(long) - Method in class ome.services.sharing.ShareBean
-
- closeShare_async(AMD_IShare_closeShare, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- closeStatement() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- closeWriter() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
This method should never exit without releasing the lock.
- CmdCallbackI - Class in omero.cmd
-
Callback servant used to wait until a HandlePrx would
return non-null on getReponse.
- CmdCallbackI(client, HandlePrx) - Constructor for class omero.cmd.CmdCallbackI
-
- CmdCallbackI(ObjectAdapter, String, HandlePrx) - Constructor for class omero.cmd.CmdCallbackI
-
- CodomainChain - Class in omeis.providers.re.codomain
-
Queues the contexts that define the spatial domain transformations that have
to be applied to the image.
- CodomainChain(int, int) - Constructor for class omeis.providers.re.codomain.CodomainChain
-
Creates a new chain.
- CodomainChain(int, int, List) - Constructor for class omeis.providers.re.codomain.CodomainChain
-
Creates a new chain.
- 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
-
- collapse(boolean) - Method in class ome.services.graphs.GraphState
-
- collapse(boolean) - Method in interface ome.services.graphs.GraphStep.Callback
-
- collect(UnloadedCollector, Image) - Method in class ome.services.delete.DeleteBean
-
Walks the Image
graph collecting unloaded instances of all
entities for later delete.
- collectionCast(Class<T>, List<IObject>) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities
-
Helper method for the conversion of base types in containers(normally
of type IObject) to a concrete type.
- CollectionCountQueryDefinition - Class in ome.services.query
-
counts the number of members in a collection.
- CollectionCountQueryDefinition(Parameters) - Constructor for class ome.services.query.CollectionCountQueryDefinition
-
- CollectionQueryParameterDef - Class in ome.services.query
-
- CollectionQueryParameterDef(String, boolean, Class) - Constructor for class ome.services.query.CollectionQueryParameterDef
-
- ColorsFactory - Class in ome.formats.model
-
Utility class to determine the color usually associated to a specified
channel depending on its emission wavelength.
- ColorsFactory() - Constructor for class ome.formats.model.ColorsFactory
-
- ColorsFactory - Class in omeis.providers.re
-
Utility class to determine the color usually associated to a specified
channel depending on its emission wavelength.
- ColorsFactory() - Constructor for class omeis.providers.re.ColorsFactory
-
- columnSets(GraphEntry, long[]) - Method in class ome.services.graphs.GraphTables
-
Returns all column sets where the first LENGTH - 1 members of "match"
coincide with the values of the columns in the set.
- COMBINED - Static variable in class ome.services.fulltext.BridgeHelper
-
Name of the Field
which contains the union of all fields.
- commands(Current) - Method in class ome.services.blitz.impl.DeleteHandleI
-
- CommonsLoggingAdapter - Class in ome.services.blitz.util
-
A simple Adapter to have the ICE runtime log to our log file.
- CommonsLoggingAdapter(Log) - Constructor for class ome.services.blitz.util.CommonsLoggingAdapter
-
- COMPANION_FILE_NS - Static variable in class pojos.FileAnnotationData
-
The name space used to indicate that the FileAnnotation
is a companion file.
- companionFile - Variable in class ome.formats.importer.ImportConfig
-
- compare(LSID, LSID) - Method in class ome.formats.OMEXMLModelComparator
-
- compare(Dataset, Dataset) - Method in class ome.formats.SortDatasetsByName
-
- compare(Project, Project) - Method in class ome.formats.SortProjectsByName
-
- compare(Object, Object) - Method in class pojos.ROICoordinate
-
- comparePasswords(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
Compares the password provided by the user (unhashed) against the given
trusted password.
- comparePasswords(Long, String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
Compares the password provided by the user (unhashed) against the given
trusted password.
- comparePasswords(Long, String, String, PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
- comparePasswords(String, String) - Method in interface ome.security.auth.PasswordUtility
-
- Complement - Class in ome.services.search
-
Complement
SearchAction
which combines two other search actions into
one logical unit, e.g.
- Complement(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Complement
-
- complete() - Method in class ome.formats.OverlayMetadataStore
-
Completes overlay population, flushing in memory ROI.
- COMPLEX_TYPE - Static variable in class pojos.PixelsData
-
Identifies the type used to store pixel values.
- CompositeACLVoter - Class in ome.security
-
- CompositeACLVoter(CurrentDetails, BasicACLVoter, SharingACLVoter) - Constructor for class ome.security.CompositeACLVoter
-
- CompressImpl - Class in ome.logic
-
- CompressImpl() - Constructor for class ome.logic.CompressImpl
-
- compressToStream(BufferedImage, OutputStream) - Method in interface ome.api.local.LocalCompress
-
Compresses a buffered image to an output stream.
- compressToStream(BufferedImage, OutputStream) - Method in class ome.logic.CompressImpl
-
- computeLocationStats(Pixels, PixelBuffer, PlaneDef, int) - Method in class omeis.providers.re.metadata.StatsFactory
-
Helper object to determine the location of the pixels' values, the
inputWindow i.e.
- ConcurrentStatisticsImpl - Class in org.hibernate.stat
-
Implementation of
Statistics
, as well as
StatisticsImplementor
, based on the
java.util.concurrent
package introduced in Java 5.
- ConcurrentStatisticsImpl() - Constructor for class org.hibernate.stat.ConcurrentStatisticsImpl
-
- ConcurrentStatisticsImpl(SessionFactoryImplementor) - Constructor for class org.hibernate.stat.ConcurrentStatisticsImpl
-
- config - Variable in class ome.formats.importer.util.ErrorHandler
-
- configGroup(EventContext, List<Long>) - Method in class ome.security.basic.AllGroupsSecurityFilter
-
- ConfigI - Class in ome.services.blitz.impl
-
Implementation of the IConfig service.
- ConfigI(IConfig, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ConfigI
-
- ConfigImpl - Class in ome.logic
-
implementation of the IConfig service interface.
- ConfigImpl() - Constructor for class ome.logic.ConfigImpl
-
- ConfigRedirector - Class in ome.services.blitz.redirect
-
Redirector
implementation which uses the
REDIRECT
config key
via
LocalConfig
to know which
Node
is currently active.
- ConfigRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ConfigRedirector
-
- ConfigurablePasswordProvider - Class in ome.security.auth
-
Base class for most
PasswordProvider
implementations, providing
configuration for default behaviors.
- ConfigurablePasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
-
- ConfigurablePasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
-
- ConfigurablePasswordProvider(PasswordUtil, boolean, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
-
- configure(List<HardWiredInterceptor>, OmeroContext) - Static method in class ome.logic.HardWiredInterceptor
-
- configure(SelfConfigurableService) - Method in class ome.services.util.BeanHelper
-
- configure(Type, Properties, Dialect) - Method in class ome.tools.hibernate.MySeqGenerator
-
If the parameters do not contain a SequenceGenerator.SEQUENCE
name, we assign one based on the table name.
- configureDebug(Level) - Method in class ome.formats.importer.ImportConfig
-
Modifies the Log4j logging level of everything under the
ome.format
and loci
package hierarchically.
- ConfiguredTileSizes - Class in ome.io.nio
-
Implementation which has all values injected during configuration.
- ConfiguredTileSizes() - Constructor for class ome.io.nio.ConfiguredTileSizes
-
- ConfiguredTileSizes(int, int, int, int) - Constructor for class ome.io.nio.ConfiguredTileSizes
-
- configureLogging() - Static method in class ome.services.blitz.Entry
-
Most ome/omero classes use the Log
and LogFactory
classes for logging.
- connect() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- containedExperimenters(long) - Method in interface ome.api.IAdmin
-
fetch all users
contained in this group.
- containedExperimenters(long) - Method in class ome.logic.AdminImpl
-
- containedExperimenters_async(AMD_IAdmin_containedExperimenters, long, Current) - Method in class ome.services.blitz.impl.AdminI
-
- containedGroups(long) - Method in interface ome.api.IAdmin
-
fetch all groups
of which the given user is a
member.
- containedGroups(long) - Method in class ome.logic.AdminImpl
-
- containedGroups_async(AMD_IAdmin_containedGroups, long, Current) - Method in class ome.services.blitz.impl.AdminI
-
- ContainerI - Class in ome.services.blitz.impl
-
Implementation of the IContainer service.
- ContainerI(IContainer, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ContainerI
-
- contains(Object) - Method in interface ome.api.local.LocalQuery
-
Tests if an object is currently contained in the session.
- contains(Object) - Method in class ome.logic.QueryImpl
-
- contains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
-
- contains(double, double) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- contains(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- contains(Point2D) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- contains(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- contains(double, double) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- contains(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- contains(Point2D) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- contains(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- contains(String) - Method in class pojos.WorkflowData
-
Returns true
if the keyword exist in the workflow,
false
otherwise.
- containsKey(Object) - Method in class ome.services.query.Definitions
-
- contentLength - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
-
- context - Variable in class ome.logic.AdminImpl
-
- context - Variable in class ome.services.blitz.fire.SessionManagerI
-
- context - Variable in class ome.services.fulltext.FileParser
-
- context - Variable in class ome.services.messages.ContextMessage
-
- context - Variable in class ome.services.sessions.SessionManagerImpl
-
- context - Variable in class ome.services.util.Executor.Impl
-
- context - Variable in class omero.cmd.SessionI
-
- ContextMessage - Class in ome.services.messages
-
- ContextMessage(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage
-
- ContextMessage.Pop - Class in ome.services.messages
-
Published when an internal service is finished with
the context previously signaled through publishing
a
ContextMessage.Push
.
- ContextMessage.Pop(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage.Pop
-
- ContextMessage.Push - Class in ome.services.messages
-
Published when an internal service would like to
modify the current
EventContext
.
- ContextMessage.Push(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage.Push
-
- contOnError - Variable in class ome.formats.importer.ImportConfig
-
- 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
-
- control - Variable in class omero.cmd.SessionI
-
- convert(IceMapper) - Method in interface omero.rtypes.Conversion
-
Convert the "val" field on the given RType instance to an ome.model.*
representation.
- convert(EventContext) - Static method in class omero.util.IceMapper
-
- convert(RGBBuffer) - Static method in class omero.util.IceMapper
-
- convert(PlaneDef) - Static method in class omero.util.IceMapper
-
Converts the passed Ice Object and returns the converted object.
- convert(Principal) - Static method in class omero.util.IceMapper
-
- convert(Roles) - Static method in class omero.util.IceMapper
-
- convert(Date) - Static method in class omero.util.IceMapper
-
- convert(RTime) - Static method in class omero.util.IceMapper
-
- convert(Parameters) - Method in class omero.util.IceMapper
-
- convert(String, Object) - Method in class omero.util.IceMapper
-
- convert(Options) - Static method in class omero.util.IceMapper
-
- convert(Filter) - Static method in class omero.util.IceMapper
-
- convert(Permissions) - Static method in class omero.util.IceMapper
-
- convert(Permissions) - Static method in class omero.util.IceMapper
-
- convertPojos(ContainerClass) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities
-
Converts the specified POJO into the corresponding model.
- ConvertToBlitzExceptionMessage - Class in ome.services.blitz.util
-
Internal event which gives third party services a chance to map their
exceptions to a blitz exception.
- ConvertToBlitzExceptionMessage(Object, Throwable) - Constructor for class ome.services.blitz.util.ConvertToBlitzExceptionMessage
-
- convertXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI
-
- Copiable - Interface in ome.util.mem
-
Requires an implementing class to provide deep copies of its
instances.
- CopiableArray - Class in ome.util.mem
-
This abstract class provides an implementation of the
Copiable
interface.
- CopiableArray(int) - Constructor for class ome.util.mem.CopiableArray
-
Creates a new instance.
- copy(SearchValues) - Method in class ome.services.search.SearchValues
-
- copy(Parameters) - Method in class ome.services.search.SearchValues
-
Copies all known values from Parameters
- copy(Session) - Method in class ome.services.sessions.SessionManagerImpl
-
- copy(EventContext) - Method in class ome.system.SimpleEventContext
-
Copies all values directly from the given instance into this instance.
- copy(Map) - Static method in class ome.tools.hibernate.HibernateUtils
-
- copy(Collection) - Static method in class ome.tools.hibernate.HibernateUtils
-
- copy() - Method in interface ome.util.mem.Copiable
-
Makes a copy of this object.
- copy(int, int) - Method in class ome.util.mem.CopiableArray
-
Copies the
Copiable
from the specified position
from
into the specified position
to
.
- copy() - Method in class ome.util.mem.CopiableArray
-
Implements the method as specified by
Copiable
.
- copy() - Method in class ome.util.mem.Handle
-
Returns a deep copy of this object.
- 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
-
Implemented as specified by superclass.
- 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.
- copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
-
- copyAndResizeImage_async(AMD_IPixels_copyAndResizeImage, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI
-
- 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.
- copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
-
- copyAndResizePixels_async(AMD_IPixels_copyAndResizePixels, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI
-
- copyClassListToArray(List<Class>) - Static method in class ome.services.search.SearchValues
-
- copyDetails(Details) - Static method in class ome.services.search.SearchValues
-
- copyGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
-
- copyImage(long, int, int, int, int, List<Integer>, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- copyImage(long, int, int, int, int, List<Integer>, String) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Copy the image and pixels from image.
- copyImage(long, int, int, int, int, List<Integer>, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- copyList(List<T>) - Static method in class ome.services.search.SearchValues
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.DetailsI
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.PermissionsI
-
- copyOfValues() - Method in class ome.services.search.SearchAction
-
- copyPixels(long, List<Integer>, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- copyPixels(long, int, int, int, int, List<Integer>, String) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Copy the pixels set from pixels to a new set.
- copyPixels(long, List<Integer>, String) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Copy the pixels set from pixels to a new set.
- copyPixels(long, int, int, int, int, List<Integer>, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- copyPixels(long, List<Integer>, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- copyPixelsXYTZ(long, int, int, int, int, List<Integer>, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- copyTimestamp(Timestamp) - Static method in class ome.services.search.SearchValues
-
- copyToken(IObject, IObject) - Method in class ome.security.basic.BasicSecuritySystem
-
See {@link TokenHolder#copyToken(IObject, IObject)
- copyToken(IObject, IObject) - Method in class ome.security.basic.TokenHolder
-
copy a token from one IObject
to another.
- copyUser(Experimenter) - Method in class ome.security.auth.SimpleRoleProvider
-
- copyValues(EntityPersister, Object, Object, SessionImplementor, Map) - Method in class ome.security.basic.MergeEventListener
-
- copyValues(EntityPersister, Object, Object, SessionImplementor, Map, ForeignKeyDirection) - Method in class ome.security.basic.MergeEventListener
-
- count - Variable in class ome.io.nio.SimpleBackOff
-
- count() - Method in interface ome.services.sessions.SessionContext
-
- count() - Method in class ome.services.sessions.SessionContextImpl
-
- count - Variable in class ome.services.sessions.stats.LongCounter
-
- 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.
- countAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl
-
Implemented as specified by the
IMetadata
I/F
- countAnnotationsUsedNotOwned_async(AMD_IMetadata_countAnnotationsUsedNotOwned, String, long, Current) - Method in class ome.services.blitz.impl.MetadataI
-
- countByPeriod_async(AMD_ITimeline_countByPeriod, List<String>, RTime, RTime, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
-
- countCachedContainers(Class<? extends IObject>, int...) - Method in interface ome.formats.model.IObjectContainerStore
-
Counts the number of containers the MetadataStore has of a given class
and at a given index of the hierarchy if specified.
- countCachedContainers(Class<? extends IObject>, int...) - Method in class ome.formats.OMEROMetadataStoreClient
-
- countCachedReferences(Class<? extends IObject>, Class<? extends IObject>) - Method in interface ome.formats.model.IObjectContainerStore
-
Counts the number of references the MetadataStore has between objects
of two classes.
- countCachedReferences(Class<? extends IObject>, Class<? extends IObject>) - Method in class ome.formats.OMEROMetadataStoreClient
-
- CounterFactory - Class in ome.services.sessions.stats
-
Factory for creating counter objects.
- CounterFactory() - Constructor for class ome.services.sessions.stats.CounterFactory
-
- countInDb() - Method in class ome.services.scripts.ScriptRepoHelper
-
- countInDb(SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper
-
- countLocks(Session, Long, String[][], String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
- countLocks(Session, Long, String[][], String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- countOnDisk() - Method in class ome.services.scripts.ScriptRepoHelper
-
- countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata
-
Counts the number of annotation of a given type.
- countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl
-
Implemented as specified by the
IMetadata
I/F
- countSpecifiedAnnotations_async(AMD_IMetadata_countSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
-
- countTiles(Pixels) - Method in class ome.io.nio.SimpleBackOff
-
- cpf - Variable in class ome.logic.AdminImpl
-
- cpf - Variable in class ome.services.blitz.impl.ScriptI
-
- create(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.SessionManagerI
-
- create(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Create a file in the repository if one doesn't already exist.
- create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.chgrp.ChgrpStepFactory
-
- create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.chown.ChownStepFactory
-
- create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.delete.DeleteStepFactory
-
- create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.export.ExporterStepFactory
-
- create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in interface ome.services.graphs.GraphStepFactory
-
- create(String) - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
-
- create(File) - Method in class omero.util.TempFileManager
-
If the given directory doesn't exist, creates it and returns true.
- create_path() - Static method in class omero.util.TempFileManager
-
- create_path(String) - Static method in class omero.util.TempFileManager
-
- create_path(String, String) - Static method in class omero.util.TempFileManager
-
- create_path(String, String, boolean) - Static method in class omero.util.TempFileManager
-
- createAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration
-
Creates an adapter with the name "BlitzAdapter", which must be properly
configured via --Ice.Config or ICE_CONFIG or similar.
- createAndPrepareMissingRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx
-
Resets a given set of Pixels rendering settings to the default
effectively creating any which do not exist.
- createAndRegisterManager(SessionManager, SecuritySystem, Executor) - Method in class ome.services.blitz.util.BlitzConfiguration
-
- createAndRegisterVerifier(SessionManager, Executor) - Method in class ome.services.blitz.util.BlitzConfiguration
-
- createBfPixelBuffer(String, int) - Method in class ome.io.nio.PixelsService
-
Helper method to properly log any exceptions raised by Bio-Formats.
- createBufferedImage() - Method in class ome.services.SVGRasterizer
-
Returns the image that represents the SVG document.
- createByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- createCache(CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
-
- createCache(String, boolean, int) - Method in class ome.services.sessions.state.SessionCache
-
- createClient(boolean) - Method in class omero.client
-
- createCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration
-
- createCommunicator(String, String[]) - Method in class ome.services.blitz.util.BlitzConfiguration
-
- createData() - Method in class omero.util.RPSTileLoop
-
- createData() - Method in class omero.util.TileLoop
-
Subclasses must provide a fresh instance of
TileData
.
- createDataObject(T, Parameters) - Method in interface ome.api.IContainer
-
Creates the specified data object.
- createDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl
-
- createDataObject_async(AMD_IContainer_createDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
-
- createDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer
-
convenience method to save network calls.
- createDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl
-
- createDataObjects_async(AMD_IContainer_createDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
-
- createDetails() - Method in class ome.security.basic.CurrentDetails
-
Creates a Details
object for the current security context.
- createDirectories() - Method in class ome.services.util.ServerDirectoryCheck
-
- createdOrModified(Class, Criteria) - Method in class ome.services.search.SearchAction
-
- createdOrModified(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction
-
- createdStart - Variable in class ome.services.search.SearchValues
-
- createdStop - Variable in class ome.services.search.SearchValues
-
- createEnumeration(T) - Method in interface ome.api.ITypes
-
- createEnumeration(T) - Method in class ome.logic.TypesImpl
-
- createEnumeration_async(AMD_ITypes_createEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
-
- createException(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
-
- createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin
-
create and return a new user in the given groups.
- createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
-
- createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
-
- createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
-
- createExperimenter_async(AMD_IAdmin_createExperimenter, Experimenter, ExperimenterGroup, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
-
- createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin
-
create and return a new user in the given groups with password.
- createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
-
- createExperimenterWithPassword_async(AMD_IAdmin_createExperimenterWithPassword, Experimenter, RString, ExperimenterGroup, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
-
- createExporter(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- createFactories() - Method in class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
-
- createFactories() - Method in class ome.services.roi.RoiTypes.RoiTypesObjectFactoryRegistry
-
- createFactories() - Method in class omero.cmd.RequestObjectFactoryRegistry
-
- createFactories() - Method in class omero.rtypes.RTypeObjectFactoryRegistry
-
- createFactories() - Method in class omero.util.ObjectFactoryRegistry
-
- createFullTextThread(EventLogLoader) - Static method in class ome.services.fulltext.Main
-
- createGateway(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- createGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin
-
create and return a new group.
- createGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
-
- createGroup(ExperimenterGroup) - Method in interface ome.security.auth.RoleProvider
-
- createGroup(String, Permissions, boolean) - Method in interface ome.security.auth.RoleProvider
-
- createGroup(String, Permissions, boolean) - Method in class ome.security.auth.SimpleRoleProvider
-
- createGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
-
- createGroup_async(AMD_IAdmin_createGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
-
- createHandle(Request) - Method in class omero.cmd.HandleFactory
-
- 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.
- createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in class ome.logic.PixelsImpl
-
- createImage(int, int, int, int, List<Integer>, PixelsType, String, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Create a new image of specified X,Y, Z, T and channels plus pixelsType
with name and description
- createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- createImage(int, int) - Method in class ome.services.SVGRasterizer.Rasterizer
-
- createImage_async(AMD_IPixels_createImage, int, int, int, int, List<Integer>, PixelsType, String, String, Current) - Method in class ome.services.blitz.impl.PixelsI
-
- createInstance() - Method in class ome.security.basic.EventListenersFactoryBean
-
First, adds all default listeners.
- createInstance() - Method in class ome.services.delete.Deletion.Builder
-
- createJob(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder
-
Returns a fresh (unsaved) ScriptJob
which can be passed to
acquireProcessor for background processing.
- createJobHandle(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- createJobHandle() - Method in class ome.system.ServiceFactory
-
- createJPEG(OutputStream) - Method in class ome.services.SVGRasterizer
-
Returns the image that represents the SVG document as a JPEG.
- createMinMaxBfPixelBuffer(String, int, IMinMaxStore) - Method in class ome.io.nio.PixelsService
-
Helper method to properly log any exceptions raised by Bio-Formats and
add a min/max calculator wrapper to the reader stack.
- createNewRenderingDef(Pixels) - Method in interface ome.api.IRenderingSettings
-
Creates a new rendering definition object along with its sub-objects.
- createNewRenderingDef(Pixels) - Method in class ome.logic.RenderingSettingsImpl
-
- createNewRenderingDef_async(AMD_IRenderingSettings_createNewRenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
-
- createPath(String, String, boolean) - Method in class omero.util.TempFileManager
-
- createPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService
-
Creates a PixelBuffer for a given pixels set.
- createPlane(PlaneDef, int, Pixels, PixelBuffer) - Static method in class omeis.providers.re.data.PlaneFactory
-
Factory method to fetch plane data and create an object to access it.
- createPrincipal() - Method in class ome.system.SessionInitializer
-
- createPyramidPixelBuffer(Pixels, String, boolean) - Method in class ome.io.nio.PixelsService
-
Helper method to properly log any exceptions raised by Bio-Formats.
- createRawFileStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- createRawFileStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- createRawFileStore() - Method in class ome.system.ServiceFactory
-
- createRawPixelsStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- createRawPixelsStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- createRawPixelsStore() - Method in class ome.system.ServiceFactory
-
- createRenderingEngine(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- createRenderingEngine(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- createRenderingEngine() - Method in class ome.system.ServiceFactory
-
- createRomioPixelBuffer(String, Pixels, boolean) - Method in class ome.io.nio.PixelsService
-
Helper method to properlty create a RomioPixelBuffer.
- createRoot() - Method in class ome.formats.OMEROMetadataStore
-
- createRoot() - Method in class ome.formats.OMEROMetadataStoreClient
-
- createRoot_async(AMD_MetadataStore_createRoot, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
-
- createSafeInputStream(Communicator, byte[]) - Static method in class ome.services.util.IceUtil
-
Creates an InputStream
with the appropriate encoding.
- createSafeOutputStream(Communicator) - Static method in class ome.services.util.IceUtil
-
Creates an OutputStream
with the appropriate encoding.
- createSearchService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- createSearchService() - Method in class ome.system.ServiceFactory
-
- createServantDelegate(String) - Method in class omero.cmd.SessionI
-
Creates a proxy according to the ServantDefinition
for the given
name.
- createSession(Principal, String) - Method in interface ome.api.ISession
-
Creates a new session and returns it to the user.
- createSession(Principal, String) - Method in class ome.services.sessions.SessionBean
-
- createSession() - Method in class omero.client
-
- createSession(String, String) - Method in class omero.client
-
Performs the actual logic of logging in, which is done via the
#getRouter()
.
- createSession_async(AMD_ISession_createSession, Principal, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- createSessionContext(List<?>, SessionContext) - Method in class ome.services.sessions.SessionManagerImpl
-
Takes a snapshot as from
#executeSessionContextLookup(ServiceFactory, Principal)
and turns
it into a
SessionContext
instance.
- CreateSessionMessage - Class in ome.services.messages
-
Published after a successful session creation.
- CreateSessionMessage(Object, String) - Constructor for class ome.services.messages.CreateSessionMessage
-
- createSessionWithTimeout(Principal, long) - Method in interface ome.api.ISession
-
Allows an admin to create a
Session
for the give
Principal
- createSessionWithTimeout(Principal, long) - Method in class ome.services.sessions.SessionBean
-
- createSessionWithTimeout_async(AMD_ISession_createSessionWithTimeout, Principal, long, Current) - Method in class ome.services.blitz.impl.SessionI
-
- createSessionWithTimeouts(Principal, long, long) - Method in interface ome.api.ISession
-
Allows an admin to create a
Session
for the give
Principal
- createSessionWithTimeouts(Principal, long, long) - Method in class ome.services.sessions.SessionBean
-
- createSessionWithTimeouts_async(AMD_ISession_createSessionWithTimeouts, Principal, long, long, Current) - Method in class ome.services.blitz.impl.SessionI
-
- createShare(String, Timestamp, List<T>, List<Experimenter>, List<String>, boolean) - Method in interface ome.api.IShare
-
Creates share
with all related:
items
, members
, and guests.
- createShare(Principal, boolean, long, String, String, long) - Method in interface ome.services.sessions.SessionManager
-
- createShare(Principal, boolean, long, String, String, long) - Method in class ome.services.sessions.SessionManagerImpl
-
- createShare(String, Timestamp, List<T>, List<Experimenter>, List<String>, boolean) - Method in class ome.services.sharing.ShareBean
-
- createShare_async(AMD_IShare_createShare, String, RTime, List<IObject>, List<Experimenter>, List<String>, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
-
- createStats() - Method in class ome.services.sessions.stats.CounterFactory
-
- createStore() - Method in class ome.formats.importer.ImportConfig
-
Create and return a new OMEROMetadataStoreClient
- createSubpath(String) - Method in class ome.io.nio.AbstractFileSystemService
-
Makes sure that for a given path, it's subpath exists.
- createSystemUser(Experimenter) - Method in interface ome.api.IAdmin
-
create and return a new system user.
- createSystemUser(Experimenter) - Method in class ome.logic.AdminImpl
-
- createSystemUser_async(AMD_IAdmin_createSystemUser, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
-
- createTempFile(String, String) - Static method in class omero.util.TempFileManager
-
- 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.
- createThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService
-
Creates thumbnail on disk using byte array
- createThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
-
- createThumbnail_async(AMD_ThumbnailStore_createThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- createThumbnailMetadata(Pixels, Dimension) - Method in class ome.services.ThumbnailCtx
-
Creates metadata for a thumbnail of a given set of pixels set and X-Y
dimensions.
- 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.
- createThumbnails() - Method in class ome.services.ThumbnailBean
-
- createThumbnails_async(AMD_ThumbnailStore_createThumbnails, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- 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.
- createThumbnailsByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
-
- createThumbnailsByLongestSideSet_async(AMD_ThumbnailStore_createThumbnailsByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- createThumbnailService() - Method in class ome.system.ServiceFactory
-
- createThumbnailStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- createThumbnailStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- createUser(Experimenter, String) - Method in interface ome.api.IAdmin
-
create and return a new user.
- createUser(Experimenter, String) - Method in class ome.logic.AdminImpl
-
- createUser_async(AMD_IAdmin_createUser, Experimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI
-
- createUserDirectories(Set<String>) - Method in class ome.services.util.DropBoxDirectoryCheck
-
- createUserFromLdap(String, String) - Method in class ome.logic.LdapImpl
-
Gets user from LDAP for checking him by requirements and setting his
details on DB
- 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.
- createUserSession(long, long, String) - Method in class ome.services.sessions.SessionBean
-
- createUserSession_async(AMD_ISession_createUserSession, long, long, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- createWithAgent(Principal, String, String) - Method in interface ome.services.sessions.SessionManager
-
- createWithAgent(Principal, String) - Method in interface ome.services.sessions.SessionManager
-
- createWithAgent(Principal, String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- createWithAgent(Principal, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- credentials - Variable in class ome.system.SessionInitializer
-
- CRITICAL_USAGE - Static variable in class ome.logic.RepositoryInfoImpl
-
- csId - Variable in class ome.system.SimpleEventContext
-
- csName - Variable in class ome.system.SimpleEventContext
-
- CSV - Static variable in class pojos.FileAnnotationData
-
Identifies the CSV
file formats.
- ctx - Variable in class ome.security.auth.ConfigurablePasswordProvider
-
- ctx - Variable in class ome.security.basic.BasicSecuritySystem
-
- ctx - Variable in class ome.services.blitz.impl.AbstractAmdServant
-
- ctx - Variable in class ome.services.delete.Deletion.Builder
-
- ctx - Variable in class ome.services.sharing.BlobShareStore
-
- ctx - Variable in class ome.services.throttling.AbstractThrottlingStrategy
-
- ctx - Variable in class ome.system.ServiceFactory
-
- cuId - Variable in class ome.system.SimpleEventContext
-
- cuName - Variable in class ome.system.SimpleEventContext
-
- current - Variable in class ome.security.SecurityFilterHolder
-
- current - Variable in class ome.security.SecuritySystemHolder
-
- current - Variable in class ome.services.throttling.Task
-
- current_group - Static variable in class ome.security.basic.OneGroupSecurityFilter
-
- current_user - Static variable in interface ome.security.SecurityFilter
-
- CurrentDetails - Class in ome.security.basic
-
Stores information related to the security context of the current thread.
- CurrentDetails() - Constructor for class ome.security.basic.CurrentDetails
-
Default constructor.
- CurrentDetails(SessionCache) - Constructor for class ome.security.basic.CurrentDetails
-
- CurrentDetails(SessionCache, Roles) - Constructor for class ome.security.basic.CurrentDetails
-
- 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()
.
- currentMetadata() - Method in class ome.services.SearchBean
-
- currentMetadata_async(AMD_Search_currentMetadata, Current) - Method in class ome.services.blitz.impl.SearchI
-
- 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()
.
- currentMetadataList() - Method in class ome.services.SearchBean
-
- currentMetadataList_async(AMD_Search_currentMetadataList, Current) - Method in class ome.services.blitz.impl.SearchI
-
- CurrentSessionContext - Class in ome.tools.hibernate
-
Implementation of Hibernate's current_session_context_class extension point.
- CurrentSessionContext(SessionFactoryImplementor) - Constructor for class ome.tools.hibernate.CurrentSessionContext
-
- CurrentSessionStats - Class in ome.services.sessions.stats
-
Wrapper which delegates to a
SessionStats
instance acquired during
construction.
- CurrentSessionStats(CurrentDetails, SessionManager) - Constructor for class ome.services.sessions.stats.CurrentSessionStats
-
- currentUser - Variable in class ome.security.basic.BasicACLVoter
-
- G_BAND - Static variable in class omeis.providers.re.RGBBuffer
-
Index of the green band in the image's data buffer.
- GatewayFactory - Class in ome.services.blitz.gateway.services
-
- GatewayFactory(ServiceFactoryPrx) - Constructor for class ome.services.blitz.gateway.services.GatewayFactory
-
Create services from the serviceFactory.
- GatewayService - Interface in ome.services.blitz.gateway.services
-
- generateRandomPasswd() - Method in class ome.security.auth.PasswordUtil
-
- generateRepoUuid() - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
Called when this repository is creating a new OriginalFile
repository object.
- generateRepoUuid() - Method in class ome.services.blitz.repo.ScriptRepositoryI
-
- generateTiff_async(AMD_Exporter_generateTiff, Current) - Method in class ome.services.blitz.impl.ExporterI
-
- generateXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI
-
- generateXml_async(AMD_Exporter_generateXml, Current) - Method in class ome.services.blitz.impl.ExporterI
-
Generate XML and return the length
- geomTool - Variable in class ome.services.blitz.impl.RoiI
-
- GeomTool - Class in ome.services.roi
-
Strategy for handling the conversion between shapes
and
database-specific geometries.
- GeomTool(PixelData, SqlAction, SessionFactory) - Constructor for class ome.services.roi.GeomTool
-
- GeomTool(PixelData, SqlAction, SessionFactory, Executor, String) - Constructor for class ome.services.roi.GeomTool
-
- get(Class<T>, long) - Method in interface ome.api.IQuery
-
lookup an entity by class and id.
- get() - Method in class ome.formats.importer.ImportConfig.FileValue
-
- get() - Method in class ome.formats.importer.ImportConfig.Value
-
Returns the generic type contained by this holder.
- get(Class, long) - Method in class ome.logic.QueryImpl
-
- get(String, DirContextAdapter) - Method in class ome.security.auth.PersonContextMapper
-
- get() - Method in class ome.services.blitz.util.ResultHolder
-
- get(Session, Class, long) - Method in class ome.services.fulltext.FullTextIndexer
-
- get(Object) - Method in class ome.services.query.Definitions
-
- get(String) - Method in class ome.services.query.Query
-
get the QueryParameter
for this name argument.
- get(PixelBuffer, int, int, int, int, int) - Method in class ome.services.roi.PixelData
-
- get() - Method in class ome.services.sessions.SessionContext.Count
-
Return the current number of references which this session is aware of.
- get(long) - Method in class ome.services.sharing.BlobShareStore
-
- get(long) - Method in class ome.services.sharing.ShareStore
-
- get(Future<T>) - Method in interface ome.services.util.Executor
-
Helper method to perform
Future.get()
and properly unwrap the
exceptions.
- get(Future<T>) - Method in class ome.services.util.Executor.Impl
-
- get(int) - Method in class ome.util.mem.CopiableArray
-
Return the
Copiable
at the specified position.
- get(int) - Method in class ome.util.mem.ReadOnlyByteArray
-
Reads the element at the index
position within this slice.
- get(Identity) - Method in class omero.util.ServantHolder
-
- get(String[]) - Static method in class prefs
-
Returns either the given key=value pairs (or all if no argument is
given).
- get_async(AMD_IQuery_get, String, long, Current) - Method in class ome.services.blitz.impl.QueryI
-
- 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.
- getAbsolutePath() - Method in class ome.formats.importer.util.ErrorContainer
-
get path for file
- getAbsolutePath() - Method in class pojos.FileData
-
Returns the absolute path.
- getAcquisitionData() - Method in class omero.sys.ParametersI
-
- getAcquisitionDate() - Method in class pojos.ImageData
-
Returns the acquisition date.
- getActiveConnections(long) - Method in interface ome.api.IShare
-
Gets actual active connections to share
.
- getActiveConnections(long) - Method in class ome.services.sharing.ShareBean
-
- getActiveConnections_async(AMD_IShare_getActiveConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getActualDeletes() - Method in class ome.services.delete.Deletion
-
- getAdapter() - Method in class omero.client
-
- getAdapter() - Method in class omero.cmd.SessionI
-
- getAdminService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Return the admin service.
- getAdminService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getAdminService() - Method in class ome.system.ServiceFactory
-
- getAdminSession() - Method in interface ome.services.blitz.fire.Registry
-
Create a new AdminSessionPrx
with the
RegistryPrx
.
- getAdminSession() - Method in class ome.services.blitz.fire.Registry.Impl
-
- getAgent(Current) - Method in class ome.services.blitz.fire.SessionManagerI
-
- getAirPressure() - Method in class pojos.ImageAcquisitionData
-
Returns the air pressure in bar
- getAll(String) - Method in class ome.security.auth.AttributeSet
-
- 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.
- getAllEnumerations(Class<T>) - Method in class ome.logic.PixelsImpl
-
- getAllEnumerations_async(AMD_IPixels_getAllEnumerations, String, Current) - Method in class ome.services.blitz.impl.PixelsI
-
- getAllForImage(long) - Method in interface ome.api.IAnalysis
-
- getAllGuests(long) - Method in interface ome.api.IShare
-
Get the email addresses for all share guests.
- getAllGuests(long) - Method in class ome.services.sharing.ShareBean
-
- getAllGuests_async(AMD_IShare_getAllGuests, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getAllMembers(long) - Method in interface ome.api.IShare
-
Get all users
who are a member of the share.
- getAllMembers(long) - Method in class ome.services.sharing.ShareBean
-
- getAllMembers_async(AMD_IShare_getAllMembers, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getAllPixels() - Method in class pojos.ImageData
-
Returns all the sets of pixels related to this image.
- getAllUsers(long) - Method in interface ome.api.IShare
-
Get a single set containing the login names
of the Experimenters
as well email addresses for guests.
- getAllUsers(long) - Method in class ome.services.sharing.ShareBean
-
- getAllUsers_async(AMD_IShare_getAllUsers, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getAlpha() - Method in class pojos.WellData
-
Returns the alpha component of the color associated to the well,
or -1
.
- getAmplificationGain() - Method in class pojos.DetectorData
-
Returns the amplification gain of the detector.
- getAnalysisService() - Method in class ome.system.ServiceFactory
-
- getAndLogException(Throwable) - Method in class ome.services.util.ServiceHandler
-
- getAnnotatableTypes() - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Returns all the classes which implement IAnnotated
- getAnnotatableTypes() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getAnnotations() - Method in class pojos.DatasetData
-
Returns the annotations related to this dataset.
- getAnnotations() - Method in class pojos.ImageData
-
Returns the annotations
- getAnnotationsCounts() - Method in class pojos.DatasetData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class pojos.ImageData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class pojos.PlateAcquisitionData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class pojos.PlateData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class pojos.ProjectData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class pojos.ScreenData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class pojos.WellData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationTypes() - Method in interface ome.api.ITypes
-
Returns a list of classes which implement IAnnotated
.
- getAnnotationTypes() - Method in class ome.logic.TypesImpl
-
- getAnnotationTypes() - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Returns all the classes which subclass Annotation
- getAnnotationTypes() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getAnnotationTypes_async(AMD_ITypes_getAnnotationTypes, Current) - Method in class ome.services.blitz.impl.TypesI
-
- getAppTitle() - Method in class ome.formats.importer.ImportConfig
-
- getAppTitle() - Method in class ome.formats.importer.util.IniFileLoader
-
- getAppVersion() - Method in class ome.formats.importer.util.ErrorContainer
-
- getArchive() - Method in class ome.formats.importer.ImportContainer
-
- getArray() - Method in class ome.tools.hibernate.SqlArray
-
- getArray(long, int) - Method in class ome.tools.hibernate.SqlArray
-
- getArray(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
-
- getArray(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
-
- getAttachedFile() - Method in class pojos.FileAnnotationData
-
Returns the file to upload to the server.
- getAttribute(Experimenter) - Method in class ome.security.auth.PersonContextMapper
-
- getAttributeSet(Experimenter) - Method in class ome.security.auth.PersonContextMapper
-
- getAuthoritativeContainerCache() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the current authoritative LSID container cache.
- getAuthoritativeContainerCache() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getAuthority() - Method in class ome.services.db.DatabaseIdentity
-
- getAvailableFamilies() - Method in class ome.services.RenderingBean
-
- getAvailableFamilies() - Method in interface omeis.providers.re.RenderingEngine
-
Returns the list of mapping families supported by the Rendering engine.
- getAvailableFamilies_async(AMD_RenderingEngine_getAvailableFamilies, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getAvailableFamilies_async(AMD_RenderingEngine_getAvailableFamilies, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getAvailableModels() - Method in class ome.services.RenderingBean
-
- getAvailableModels() - Method in interface omeis.providers.re.RenderingEngine
-
Returns the list of color models supported by the Rendering engine.
- getAvailableModels_async(AMD_RenderingEngine_getAvailableModels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getAvailableModels_async(AMD_RenderingEngine_getAvailableModels, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- 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.
- getBaseType() - Method in class ome.tools.hibernate.SqlArray
-
- getBaseTypeName() - Method in class ome.tools.hibernate.SqlArray
-
- getBatchSize() - Method in interface ome.api.Search
-
Returns the current batch size.
- getBatchSize() - Method in class ome.services.eventlogs.EventLogLoader
-
- getBatchSize() - Method in class ome.services.SearchBean
-
- getBatchSize_async(AMD_Search_getBatchSize, Current) - Method in class ome.services.blitz.impl.SearchI
-
- getBeanHelper() - Method in class ome.logic.AbstractLevel1Service
-
- getBeanHelper() - Method in class ome.logic.AbstractLevel2Service
-
- getBeanHelper() - Method in class ome.services.AbstractStatefulBean
-
- getBfImageCount() - Method in class ome.formats.importer.ImportContainer
-
- getBfImageNames() - Method in class ome.formats.importer.ImportContainer
-
- getBfPixels() - Method in class ome.formats.importer.ImportContainer
-
- getBit(byte[], int) - Method in class pojos.MaskData
-
Sets the bit value in a byte array at position bit to be the value
value.
- getBitDepth(PixelsType) - Method in interface ome.api.IPixels
-
Bit depth for a given pixel type.
- getBitDepth(PixelsType) - Method in class ome.logic.PixelsImpl
-
- getBitDepth_async(AMD_IPixels_getBitDepth, PixelsType, Current) - Method in class ome.services.blitz.impl.PixelsI
-
- getBlitzAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration
-
- getBlitzManager() - Method in class ome.services.blitz.util.BlitzConfiguration
-
- getBlitzVerifier() - Method in class ome.services.blitz.util.BlitzConfiguration
-
- getBlue() - Method in class pojos.WellData
-
Returns the blue component of the color associated to the well,
or -1
.
- 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.
- getBody() - Method in class ome.util.mem.Handle
-
Returns a reference to the Body object that is currently paired
up with this handle.
- getBooleanAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getBooleanAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getBooleanAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getBooleanAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getBooleanAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getBoost() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
- getBounds() - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- getBounds() - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- getBounds2D() - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- getBounds2D() - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- getBuffer(long) - Method in class ome.services.roi.PixelData
-
- getBugTrackerURL() - Method in class ome.formats.importer.util.IniFileLoader
-
- getByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getByPeriod_async(AMD_ITimeline_getByPeriod, List<String>, RTime, RTime, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI
-
- getByteOrder() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
Returns the current pixel byte order.
- getByteWidth() - Method in interface ome.api.RawPixelsStore
-
- getByteWidth() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getByteWidth() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getByteWidth() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getByteWidth() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getByteWidth() - Method in interface ome.io.nio.PixelBuffer
-
Returns the byte width for the pixel buffer.
- getByteWidth() - Method in class ome.io.nio.RomioPixelBuffer
-
- getByteWidth(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
-
- getByteWidth(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService
-
Get the bytewidth of the image
- getByteWidth() - Method in class ome.services.RawPixelsBean
-
- getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getC() - Method in class pojos.ShapeData
-
Returns the channel.
- getCalibratedMagnification() - Method in class pojos.ObjectiveData
-
Returns the objective's calibrated magnification factor.
- getCallbackObject(String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getCallContext() - Method in class ome.security.basic.BasicEventContext
-
- getCallContext() - Method in class ome.services.blitz.impl.commands.SaveI
-
- getCallContext() - Method in class omero.cmd.basic.DoAllI
-
- getCallContext() - Method in class omero.cmd.basic.ListRequestsI
-
- getCallContext() - Method in class omero.cmd.basic.TimingI
-
- getCallContext() - Method in class omero.cmd.graphs.ChgrpI
-
- getCallContext() - Method in class omero.cmd.graphs.ChmodI
-
- getCallContext() - Method in class omero.cmd.graphs.ChownI
-
- getCallContext() - Method in class omero.cmd.graphs.DeleteI
-
- getCallContext() - Method in class omero.cmd.graphs.GraphSpecListI
-
- getCallContext() - Method in interface omero.cmd.IRequest
-
Returns the desired call context for this request.
- getCallContext() - Method in class omero.model.DetailsI
-
- getCategory() - Method in class omero.client
-
Returns the category which should be used for all callbacks
passed to the server.
- getChannel() - Method in class ome.formats.model.ChannelData
-
Returns the channel this channel data is for.
- getChannel(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getChannelAcquisitionMode(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelBindings() - Method in class omeis.providers.re.Renderer
-
Returns an array containing the channel bindings.
- getChannelBindingsAsList() - Method in class omeis.providers.re.Renderer
-
Returns a list containing the channel bindings.
- getChannelColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelContrastMethod(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelCurveCoefficient(int) - Method in class ome.services.RenderingBean
-
- getChannelCurveCoefficient(int) - Method in interface omeis.providers.re.RenderingEngine
-
Returns the coefficient identifying a map in the family.
- getChannelCurveCoefficient_async(AMD_RenderingEngine_getChannelCurveCoefficient, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getChannelCurveCoefficient_async(AMD_RenderingEngine_getChannelCurveCoefficient, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getChannelEmissionWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelExcitationWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelFamily(int) - Method in class ome.services.RenderingBean
-
- getChannelFamily(int) - Method in interface omeis.providers.re.RenderingEngine
-
Returns the family associated to the specified channel.
- getChannelFamily_async(AMD_RenderingEngine_getChannelFamily, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getChannelFamily_async(AMD_RenderingEngine_getChannelFamily, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getChannelFluor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelIlluminationType(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelIndex() - Method in class ome.formats.model.ChannelData
-
Returns the index of the channel this channel data is for.
- getChannelLabeling() - Method in class pojos.ChannelData
-
Returns the label of the channel.
- getChannelName(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelNDFilter(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelNoiseReduction(int) - Method in class ome.services.RenderingBean
-
- 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.
- getChannelNoiseReduction_async(AMD_RenderingEngine_getChannelNoiseReduction, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getChannelNoiseReduction_async(AMD_RenderingEngine_getChannelNoiseReduction, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getChannelPinholeSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelPockelCellSetting(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelSamplesPerPixel(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getChannelStats(int) - Method in class ome.services.RenderingBean
-
- getChannelStats(int) - Method in interface omeis.providers.re.RenderingEngine
-
- getChannelStats_async(AMD_RenderingEngine_getChannelStats, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getChannelStats_async(AMD_RenderingEngine_getChannelStats, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getChannelWindowEnd(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
- getChannelWindowEnd(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService
-
Get the channel max.
- getChannelWindowEnd(int) - Method in class ome.services.RenderingBean
-
- getChannelWindowEnd(int) - Method in interface omeis.providers.re.RenderingEngine
-
Returns the upper bound of the pixels intensity interval.
- getChannelWindowEnd_async(AMD_RenderingEngine_getChannelWindowEnd, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getChannelWindowEnd_async(AMD_RenderingEngine_getChannelWindowEnd, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getChannelWindowStart(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
- getChannelWindowStart(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService
-
Get the channel min.
- getChannelWindowStart(int) - Method in class ome.services.RenderingBean
-
- getChannelWindowStart(int) - Method in interface omeis.providers.re.RenderingEngine
-
Returns the lower bound of the pixels intensity interval.
- getChannelWindowStart_async(AMD_RenderingEngine_getChannelWindowStart, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getChannelWindowStart_async(AMD_RenderingEngine_getChannelWindowStart, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getChecks(IObject, String) - Method in class ome.security.basic.GroupChmodStrategy
-
- getChecks(IObject, String) - Method in interface ome.security.ChmodStrategy
-
Return all the checks necessary to validate the
given object if it were to have its permissions.
- getChildTransformer(Class) - Static method in class ome.services.query.Hierarchy
-
- getClass(String) - Method in class ome.services.graphs.GraphState
-
- getClass(String) - Method in interface ome.services.graphs.GraphStep.Callback
-
- getClasses() - Method in interface ome.tools.hibernate.ExtendedMetadata
-
- getClasses() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getClassName(Class) - Static method in class ome.tools.StringUtils
-
- getClient() - Method in class ome.formats.importer.util.ClientKeepAlive
-
- getClient() - Method in class omero.model.DetailsI
-
- 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
-
- getClientIds() - Method in class omero.util.ServantHolder
-
- getCloseStatementCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getCo2Percent() - Method in class pojos.ImageAcquisitionData
-
Returns the Co2 level, this is a percent value in the interval [0, 1].
- getCodomainChain() - Method in class omeis.providers.re.Renderer
-
Returns the object that defines the sequence of spatial transformations
to be applied to quantized data.
- getCol(int, int, int, int) - Method in interface ome.api.RawPixelsStore
-
- getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getCol(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getCol(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a particular column from this pixel buffer.
- getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getCol(int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- getCol_async(AMD_RawPixelsStore_getCol, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getCol_async(AMD_RawPixelsStore_getCol, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a particular column from this pixel buffer.
- getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
-
- getCollectionCount(String, String, Set<Long>, Parameters) - Method in interface ome.api.IContainer
-
Counts the number of members in a collection for a given object.
- getCollectionCount(String, String, Set, Parameters) - Method in class ome.logic.PojosImpl
-
- getCollectionCount_async(AMD_IContainer_getCollectionCount, String, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
-
- getCollectionFetchCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getCollectionLoadCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getCollectionRecreateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getCollectionRemoveCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getCollectionRoleNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
Get the names of all collection roles
- getCollectionStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
Get collection statistics per role
- getCollectionUpdateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getColor(ChannelData) - Static method in class ome.formats.model.ColorsFactory
-
Determines the color usually associated to the specified
wavelength or explicitly defined for a particular channel.
- getColor(int, Channel) - Static method in class omeis.providers.re.ColorsFactory
-
Determines the color usually associated to the specified wavelength.
- getColor(int, Channel, LogicalChannel) - Static method in class omeis.providers.re.ColorsFactory
-
Determines the color usually associated to the specified wavelength.
- getColorArray(ChannelBinding) - Static method in class omeis.providers.re.Renderer
-
Returns an array whose ascending indices represent the color
components Red, Green and Blue.
- getColSize() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getColSize() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getColSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getColSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getColSize() - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the in memory size of a column of pixels in this pixel buffer.
- getColSize() - Method in class ome.io.nio.RomioPixelBuffer
-
- getColumn() - Method in class pojos.WellData
-
Returns the column used to indicate the location of the well on the grid.
- getColumnSequenceIndex() - Method in class pojos.PlateData
-
Returns the index indicating how to label a column.
- getComment() - Method in class ome.formats.importer.util.ErrorContainer
-
- getCommentAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getCommentAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getCommentAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getCommentAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getCommentAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getCommentCount(Set<Long>) - Method in interface ome.api.IShare
-
Returns a map from share id to comment count.
- getCommentCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
-
- getCommentCount_async(AMD_IShare_getCommentCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getComments(long) - Method in interface ome.api.IShare
-
Looks up all comments
which
belong to the share
.
- getComments(long) - Method in class ome.services.sharing.ShareBean
-
- getComments_async(AMD_IShare_getComments, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getCommentType() - Method in class ome.formats.importer.util.ErrorContainer
-
- getCommunicator() - Method in class ome.services.blitz.fire.Ring
-
- getCommunicator() - Method in interface ome.services.blitz.redirect.Redirector.Context
-
Active communicator for use by the
Redirector
instance.
- getCommunicator() - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- getCommunicator() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
-
- getCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration
-
- getCommunicator() - Method in class omero.client
-
Returns the Communicator
for this instance or throws an
exception if null.
- getComponents() - Method in class pojos.MultiImageData
-
Returns the collection of images composing the file.
- getCompressionLevel() - Method in interface ome.api.local.LocalCompress
-
Returns the current compression level for the service.
- getCompressionLevel() - Method in class ome.logic.CompressImpl
-
- getCompressionLevel() - Method in class ome.services.RenderingBean
-
- getCompressionLevel() - Method in interface omeis.providers.re.RenderingEngine
-
Returns the current compression level for the service.
- getCompressionLevel_async(AMD_RenderingEngine_getCompressionLevel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getCompressionLevel_async(AMD_RenderingEngine_getCompressionLevel, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getConfig() - Method in class ome.formats.importer.OMEROWrapper
-
- getConfigService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getConfigService() - Method in class ome.system.ServiceFactory
-
- getConfigValue(String) - Method in interface ome.api.IConfig
-
retrieve a configuration value from the backend store.
- getConfigValue(String) - Method in class ome.formats.OMEROMetadataStoreClient
-
Retrieves a configuration value from the IConfig
service.
- getConfigValue(String) - Method in class ome.logic.ConfigImpl
-
- getConfigValue_async(AMD_IConfig_getConfigValue, String, Current) - Method in class ome.services.blitz.impl.ConfigI
-
- getConnectCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getConnection() - Method in class ome.services.db.SelfCorrectingDataSource
-
- getConnection(String, String) - Method in class ome.services.db.SelfCorrectingDataSource
-
- getContainerCache() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the current container cache.
- getContainerCache() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getContainers() - Method in class ome.formats.importer.ImportCandidates
-
- getContainers() - Method in class ome.services.blitz.repo.ImportableFiles
-
- getContainerService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getContainerService() - Method in class ome.system.ServiceFactory
-
- getContainerTypes() - Method in class ome.logic.TypesImpl
-
- getContent() - Method in class pojos.AnnotationData
-
Returns the content of the annotation.
- getContent() - Method in class pojos.BooleanAnnotationData
-
Returns the textual content of the annotation.
- getContent() - Method in class pojos.DoubleAnnotationData
-
Returns the value.
- getContent() - Method in class pojos.FileAnnotationData
-
Returns the original file.
- getContent() - Method in class pojos.LongAnnotationData
-
Returns the rating value.
- getContent() - Method in class pojos.RatingAnnotationData
-
Returns the rating value.
- getContent() - Method in class pojos.TagAnnotationData
-
Returns the textual content of the annotation.
- getContent() - Method in class pojos.TermAnnotationData
-
Returns the textual content of the annotation.
- getContent() - Method in class pojos.TextualAnnotationData
-
Returns the textual content of the annotation.
- getContent() - Method in class pojos.TimeAnnotationData
-
Returns the timestamp of the annotation.
- getContent() - Method in class pojos.XMLAnnotationData
-
Returns the content of the annotation.
- getContentAsString() - Method in class pojos.AnnotationData
-
Returns the content of the annotation as a
String
, which is
parsed on a
Class
-by-
Class
basis.
- getContentAsString() - Method in class pojos.BooleanAnnotationData
-
Returns the textual content of the annotation.
- getContentAsString() - Method in class pojos.DoubleAnnotationData
-
Returns the value as a string.
- getContentAsString() - Method in class pojos.FileAnnotationData
-
Returns the absolute path to the file
- getContentAsString() - Method in class pojos.LongAnnotationData
-
Returns the value as a string.
- getContentAsString() - Method in class pojos.RatingAnnotationData
-
Returns the rating value as a string.
- getContentAsString() - Method in class pojos.TagAnnotationData
-
Returns the textual content of the annotation.
- getContentAsString() - Method in class pojos.TermAnnotationData
-
Returns the textual content of the annotation.
- getContentAsString() - Method in class pojos.TextualAnnotationData
-
Returns the textual content of the annotation.
- getContentAsString() - Method in class pojos.TimeAnnotationData
-
Returns the time as a string.
- getContentAsString() - Method in class pojos.XMLAnnotationData
-
Returns the textual content of the annotation.
- getContentLength() - Method in class ome.formats.importer.util.FileUploadCounter
-
- getContentMap(long) - Method in interface ome.api.IShare
-
Returns the contents of the share keyed by type.
- getContentMap(long) - Method in class ome.services.sharing.ShareBean
-
- getContentMap_async(AMD_IShare_getContentMap, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getContents(long) - Method in interface ome.api.IShare
-
Looks up all items
belong to the
share
.
- getContents(long) - Method in class ome.services.sharing.ShareBean
-
- getContents_async(AMD_IShare_getContents, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getContentSize(long) - Method in interface ome.api.IShare
-
Returns the number of items in the share.
- getContentSize(long) - Method in class ome.services.sharing.ShareBean
-
- getContentSize_async(AMD_IShare_getContentSize, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getContentSubList(long, int, int) - Method in interface ome.api.IShare
-
Returns a range of items from the share.
- getContentSubList(long, int, int) - Method in class ome.services.sharing.ShareBean
-
- getContentSubList_async(AMD_IShare_getContentSubList, long, int, int, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getContentType() - Method in class ome.formats.importer.util.FileUploadCounter
-
- getContext() - Method in class ome.security.basic.CurrentDetails
-
- getContext() - Method in interface ome.services.util.Executor
-
Provides access to the context for Work-API consumers who need to publish
events, etc.
- getContext() - Method in class ome.services.util.Executor.Impl
-
- 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.
- getContext() - Method in class ome.system.ServiceFactory
-
Deprecated.
- getContrastMethod() - Method in class pojos.ChannelAcquisitionData
-
Returns the contrast method.
- getContrastMethod() - Method in class pojos.ChannelData
-
Returns the contrast method.
- getContrastMethodAsEnum() - Method in class pojos.ChannelData
-
Returns the contrast method enumeration value.
- getControls() - Method in class ome.security.auth.PersonContextMapper
-
- getCorrection() - Method in class pojos.ObjectiveData
-
Returns the correction value of the objective.
- getCorrectionCollar() - Method in class pojos.ImageAcquisitionData
-
Returns the correction collar of the objective.
- getCount() - Method in class ome.io.nio.SimpleBackOff
-
- getCount(String) - Method in class ome.services.export.ExporterStepFactory
-
- getCountQuery(String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Returns the query for obtaining the number of collection items to a
particular instance.
- getCountQuery(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
Returns the query for obtaining the number of collection items to a
particular instance.
- getCreated() - Method in class pojos.DataObject
-
Returns the creation time of the object.
- getCreationEvent(Current) - Method in class omero.model.DetailsI
-
- getCurrent() - Method in class ome.services.blitz.util.RegisterServantMessage
-
- getCurrent() - Method in class ome.services.blitz.util.UnregisterServantMessage
-
- getCurrentEventContext() - Method in interface ome.api.StatefulServiceInterface
-
- getCurrentEventContext() - Method in class ome.security.basic.CurrentDetails
-
Public view on the data contained here.
- getCurrentEventContext() - Method in class ome.services.AbstractStatefulBean
-
- getCurrentEventContext() - Method in class ome.services.RenderingBean
-
- getCurrentEventContext() - Method in class ome.services.ThumbnailBean
-
- getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
-
- getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getCurrentEventId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentEventId() - Method in interface ome.system.EventContext
-
- getCurrentEventId() - Method in class ome.system.SimpleEventContext
-
- getCurrentEventType() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentEventType() - Method in interface ome.system.EventContext
-
- getCurrentEventType() - Method in class ome.system.SimpleEventContext
-
- getCurrentGroupId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentGroupId() - Method in interface ome.system.EventContext
-
- getCurrentGroupId() - Method in class ome.system.SimpleEventContext
-
- getCurrentGroupName() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentGroupName() - Method in interface ome.system.EventContext
-
- getCurrentGroupName() - Method in class ome.system.SimpleEventContext
-
- getCurrentGroupPermissions() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentGroupPermissions() - Method in interface ome.system.EventContext
-
- getCurrentGroupPermissions() - Method in class ome.system.SimpleEventContext
-
- getCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader
-
Get current EventLog
id.
- getCurrentSessionId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentSessionId() - Method in interface ome.system.EventContext
-
- getCurrentSessionId() - Method in class ome.system.SimpleEventContext
-
- getCurrentSessionUuid() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentSessionUuid() - Method in interface ome.system.EventContext
-
- getCurrentSessionUuid() - Method in class ome.system.SimpleEventContext
-
- getCurrentShareId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentShareId() - Method in interface ome.system.EventContext
-
- getCurrentShareId() - Method in class ome.system.SimpleEventContext
-
- getCurrentUmask() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentUmask() - Method in class ome.system.SimpleEventContext
-
- getCurrentUserId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentUserId() - Method in interface ome.system.EventContext
-
- getCurrentUserId() - Method in class ome.system.SimpleEventContext
-
- getCurrentUserName() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentUserName() - Method in interface ome.system.EventContext
-
- getCurrentUserName() - Method in class ome.system.SimpleEventContext
-
- getCurrentUserNames() - Method in class ome.services.util.DropBoxDirectoryCheck
-
- getCurveCoefficient() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the coefficient identifying a curve within a given family.
- getCustomAnnotationList() - Method in class ome.formats.importer.ImportContainer
-
The list of custom, user specified, annotations to link to all images
represented by this container.
- getCustomImageDescription() - Method in class ome.formats.importer.ImportContainer
-
Retrieves the current custom image description string.
- getCustomImageName() - Method in class ome.formats.importer.ImportContainer
-
Retrieves the current custom image name string.
- getCustomImageNaming() - Method in class ome.formats.importer.ImportConfig
-
- getCustomImageNaming() - Method in class ome.formats.importer.util.IniFileLoader
-
- getCustomPlateDescription() - Method in class ome.formats.importer.ImportContainer
-
Retrieves the current custom plate description string.
- getCustomPlateName() - Method in class ome.formats.importer.ImportContainer
-
Retrieves the current custom plate name string.
- getCutIn() - Method in class pojos.FilterData
-
Returns the cut in value or null
.
- getCutInTolerance() - Method in class pojos.FilterData
-
Returns the cut in tolerance value or null
.
- getCutOut() - Method in class pojos.FilterData
-
Returns the cut out value or null
.
- getCutOutTolerance() - Method in class pojos.FilterData
-
Returns the cut out tolerance value or null
.
- getData() - Method in class ome.io.nio.ReorderedPixelData
-
Returns the backing buffer for the pixel data.
- getData() - Method in class omeis.providers.re.data.Plane2D
-
Returns the pixel data that is used to back this Plane.
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
-
- getDatabaseTime() - Method in interface ome.api.IConfig
-
checks the database for it's time using a SELECT statement.
- getDatabaseTime() - Method in class ome.logic.ConfigImpl
-
- getDatabaseTime_async(AMD_IConfig_getDatabaseTime, Current) - Method in class ome.services.blitz.impl.ConfigI
-
- getDatabaseUuid() - Method in interface ome.api.IConfig
-
Provides the UUID for this OMERO (database) instance.
- getDatabaseUuid() - Method in class ome.logic.ConfigImpl
-
- getDatabaseUuid_async(AMD_IConfig_getDatabaseUuid, Current) - Method in class ome.services.blitz.impl.ConfigI
-
- getDatabaseVersion() - Method in interface ome.api.local.LocalConfig
-
Retrieves the newest database patch.
- getDatabaseVersion() - Method in class ome.logic.ConfigImpl
-
- 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.
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
-
- getDataObjects() - Method in class pojos.TagAnnotationData
-
Returns the collection of data objects related to this tag.
- getDataService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
- getDataset() - Method in class ome.formats.importer.util.TinyImportFixture
-
provides access to the created Dataset
instance.
- getDataset(long, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getDatasets(Project) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getDatasets(List<Long>, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getDatasets(List<Long>, boolean) - Method in interface ome.services.blitz.gateway.services.DataService
-
Get the Datasets with id's passed as list in ids.
- getDatasets(List<Long>, boolean) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
-
- getDatasets() - Method in class pojos.ImageData
-
Returns the datasets containing this image.
- getDatasets() - Method in class pojos.ProjectData
-
Returns the datasets contained in this project.
- getDatasetsForProject(long) - Method in interface ome.api.IAnalysis
-
- getDatasetsWithoutProjects() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getDataValue() - Method in class pojos.DoubleAnnotationData
-
Returns the value.
- getDataValue() - Method in class pojos.LongAnnotationData
-
Returns the value.
- getDate(Class) - Static method in class ome.system.Version
-
- getDebugLevel() - Method in class ome.formats.importer.ImportConfig
-
- getDebugLevel() - Method in class ome.formats.importer.util.IniFileLoader
-
Returns the level of debugging which should be set on
ImportConfig
Any value lower than null will not call configureDebug.
- getDefaultCondition() - Method in class ome.security.basic.AllGroupsSecurityFilter
-
- getDefaultCondition() - Method in class ome.security.basic.OneGroupSecurityFilter
-
- getDefaultCondition() - Method in interface ome.security.SecurityFilter
-
Return the string to be used as the condition.
- getDefaultCondition() - Method in class ome.security.SecurityFilterHolder
-
- getDefaultContext() - Method in class ome.system.ServiceFactory
-
used when no
context
name is provided to the
constructor.
- getDefaultContext() - Method in class ome.tools.spring.InternalServiceFactory
-
returns null to prevent the lookup of any context, but rather wait on
injection as a ApplicationContextAware
- getDefaultContext() - Method in class ome.tools.spring.ManagedServiceFactory
-
returns null to prevent the lookup of any context, but rather wait on
injection as a ApplicationContextAware
- getDefaultGroup(long) - Method in interface ome.api.IAdmin
-
retrieve the default group
for the given user
id.
- getDefaultGroup(long) - Method in class ome.logic.AdminImpl
-
- getDefaultGroup() - Method in class pojos.ExperimenterData
-
Returns the default Group for this Experimenter
- getDefaultGroup_async(AMD_IAdmin_getDefaultGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI
-
- getDefaultGroupLevel() - Method in class ome.formats.OMEROMetadataStoreClient
-
Retrieve the default group's permission 'level'.
- getDefaultGroupName() - Method in class ome.formats.OMEROMetadataStoreClient
-
Retrieve the default group's name
- getDefaultPixels() - Method in class pojos.ImageData
-
Returns the default set of pixels.
- getDefaultSample() - Method in class pojos.PlateData
-
Returns the currently selected field or 0
.
- getDefaultScriptDir() - Static method in class ome.services.scripts.ScriptRepoHelper
-
Directory which will be used as the root of this repository if no
directory is passed to a constructor.
- getDefaultT(Long) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
- getDefaultT(Long) - Method in interface ome.services.blitz.gateway.services.RenderingService
-
Get the default T point of the image
- getDefaultT() - Method in class ome.services.RenderingBean
-
- getDefaultT() - Method in interface omeis.providers.re.RenderingEngine
-
Returns the default timepoint index.
- getDefaultT_async(AMD_RenderingEngine_getDefaultT, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getDefaultT_async(AMD_RenderingEngine_getDefaultT, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getDefaultZ(Long) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
- getDefaultZ(Long) - Method in interface ome.services.blitz.gateway.services.RenderingService
-
Get the default Z section of the image
- getDefaultZ() - Method in class ome.services.RenderingBean
-
- getDefaultZ() - Method in interface omeis.providers.re.RenderingEngine
-
Returns the index of the default focal section.
- getDefaultZ_async(AMD_RenderingEngine_getDefaultZ, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getDefaultZ_async(AMD_RenderingEngine_getDefaultZ, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getDeleteReport() - Method in class omero.cmd.graphs.DeleteI
-
- getDeleteService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getDeleteService() - Method in class ome.system.ServiceFactory
-
- getDeletion() - Method in class omero.cmd.graphs.DeleteI
-
- getDescription(Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- getDescription(long) - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- getDescription() - Method in class pojos.DatasetData
-
Returns the description of the dataset.
- getDescription() - Method in class pojos.FileAnnotationData
-
Returns the description of the annotation.
- getDescription() - Method in class pojos.FileData
-
Returns the description of the file.
- getDescription() - Method in class pojos.GroupData
-
Returns the description of the group.
- getDescription() - Method in class pojos.ImageData
-
Returns the description of the image.
- getDescription() - Method in class pojos.PlateAcquisitionData
-
Returns the description of the plate acquisition.
- getDescription() - Method in class pojos.PlateData
-
Returns the description of the plate.
- getDescription() - Method in class pojos.ProjectData
-
Returns the description of the project.
- getDescription() - Method in class pojos.ScreenData
-
Returns the description of the screen.
- getDescription() - Method in class pojos.XMLAnnotationData
-
Returns the description of the annotation.
- getDetails(Object[], String[]) - Static method in class ome.tools.hibernate.HibernateUtils
-
- getDetails() - Method in class pojos.DataObject
-
Returns the details of the object.
- getDetector(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getDetector() - Method in class pojos.ChannelAcquisitionData
-
Returns the detector used for that channel.
- getDetectorBinningAsEnum() - Method in class pojos.ChannelAcquisitionData
-
Returns the binning enumeration value.
- getDetectors() - Method in class pojos.InstrumentData
-
Returns the collection of detectors.
- getDetectorSettingsBinning() - Method in class pojos.ChannelAcquisitionData
-
Returns the Binning factor.
- getDetectorSettingsGain() - Method in class pojos.ChannelAcquisitionData
-
Returns the gain set on the detector.
- getDetectorSettingsOffset() - Method in class pojos.ChannelAcquisitionData
-
Returns the offset set on the detector.
- getDetectorSettingsReadOutRate() - Method in class pojos.ChannelAcquisitionData
-
Returns the Read out rate set on the detector.
- getDetectorSettingsVoltage() - Method in class pojos.ChannelAcquisitionData
-
Returns the voltage set on the detector.
- getDichroic() - Method in class pojos.FilterSetData
-
Returns the dichroic if any.
- getDichroic() - Method in class pojos.LightPathData
-
Returns the dichroic if any.
- getDichroics() - Method in class pojos.InstrumentData
-
Returns the collection of dichroics.
- getDir() - Method in class ome.services.blitz.repo.FileMaker
-
- getDirectProxy() - Method in class ome.services.blitz.fire.Ring
-
- getDirectProxy() - Method in interface ome.services.blitz.redirect.Redirector.Context
-
String representation of the proxy to the local node which may be
contacted to create new sessions.
- getDirectProxy() - Method in class ome.services.blitz.util.BlitzConfiguration
-
Return a direct proxy to the session manager in this object adapter.
- getDisabledSubsystems() - Method in class ome.security.basic.BasicEventContext
-
- getDn(Experimenter) - Method in class ome.security.auth.PersonContextMapper
-
- getDnById(Long) - Method in class ome.security.auth.PasswordUtil
-
- getDoThumbnails() - Method in class ome.formats.importer.ImportContainer
-
Retrieves whether or not we are performing thumbnail creation upon
import completion.
- getDoubleAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getDoubleAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getDoubleAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getDoubleAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getDoubleAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getEffectiveUID() - Method in class ome.security.basic.BasicSecuritySystem
-
Returns the Id of the currently logged in user.
- getEffectiveUID() - Method in interface ome.security.SecuritySystem
-
Returns UID based on whether a share is active, etc.
- getEffectiveUID() - Method in class ome.security.SecuritySystemHolder
-
- getEffectiveUID() - Method in class ome.security.sharing.SharingSecuritySystem
-
- getEmail() - Method in class ome.formats.importer.util.ErrorContainer
-
- getEmail() - Method in class pojos.ExperimenterData
-
Returns the e-mail of the experimenter.
- getEmissionFilters() - Method in class pojos.FilterSetData
-
Returns the collections of emission filters if any.
- getEmissionFilters() - Method in class pojos.LightPathData
-
Returns the collections of emission filters if any.
- getEmissionWavelength() - Method in class pojos.ChannelData
-
Returns the emission wavelength of the channel.
- getEndTime() - Method in class omero.sys.ParametersI
-
Returns the value of the end time
parameter.
- getEndTime() - Method in class pojos.PlateAcquisitionData
-
Returns the time when the last image was collected.
- getEntity(String, Serializable) - Method in class ome.security.basic.OmeroInterceptor
-
- getEntityDeleteCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getEntityFetchCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getEntityInsertCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getEntityLoadCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getEntityName(Object) - Method in class ome.security.basic.OmeroInterceptor
-
- getEntityNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
Get the names of all entities
- getEntityStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
find entity statistics per name
- getEntityUpdateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- 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.
- getEnumeration(Class<T>, String, boolean) - Method in interface ome.formats.enums.EnumerationProvider
-
Retrieves an enumeration.
- getEnumeration(Class<T>, String, boolean) - Method in class ome.formats.enums.IQueryEnumProvider
-
- getEnumeration(Class<T>, String) - Method in class ome.logic.PixelsImpl
-
- getEnumeration(Class<T>, String) - Method in class ome.logic.TypesImpl
-
- getEnumeration_async(AMD_IPixels_getEnumeration, String, String, Current) - Method in class ome.services.blitz.impl.PixelsI
-
- getEnumeration_async(AMD_ITypes_getEnumeration, String, String, Current) - Method in class ome.services.blitz.impl.TypesI
-
- getEnumerationProvider() - Method in class ome.formats.OMEROMetadataStoreClient
-
Retrieves the active enumeration provider.
- getEnumerations(Class<T>) - Method in interface ome.formats.enums.EnumerationProvider
-
Retrieves all enumerations of a specific type.
- getEnumerations(Class<T>) - Method in class ome.formats.enums.IQueryEnumProvider
-
- getEnumerationsWithEntries() - Method in interface ome.api.ITypes
-
Gets all metadata classes which are IEnum type with contained objects.
- getEnumerationsWithEntries() - Method in class ome.logic.TypesImpl
-
- getEnumerationsWithEntries_async(AMD_ITypes_getEnumerationsWithEntries, Current) - Method in class ome.services.blitz.impl.TypesI
-
- getEnumerationTypes() - Method in interface ome.api.ITypes
-
Gets all metadata classes which are IEnum type.
- getEnumerationTypes() - Method in class ome.logic.TypesImpl
-
- getEnumerationTypes_async(AMD_ITypes_getEnumerationTypes, Current) - Method in class ome.services.blitz.impl.TypesI
-
- getError() - Method in class ome.formats.importer.util.ErrorContainer
-
- getError() - Method in class ome.services.delete.Deletion
-
- getEvent() - Method in class ome.security.basic.BasicEventContext
-
- getEvent() - Method in class ome.security.basic.CurrentDetails
-
- getEvent(Current) - Method in class ome.services.blitz.fire.SessionManagerI
-
- 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.
- getEventContext() - Method in class ome.logic.AdminImpl
-
- getEventContext() - Method in class ome.security.basic.BasicACLVoter
-
- getEventContext(boolean) - Method in class ome.security.basic.BasicSecuritySystem
-
- getEventContext() - Method in class ome.security.basic.BasicSecuritySystem
-
- getEventContext() - Method in interface ome.security.SecuritySystem
-
- getEventContext(boolean) - Method in interface ome.security.SecuritySystem
-
If refresh is false, returns the current
EventContext
stored
in the session.
- getEventContext() - Method in class ome.security.SecuritySystemHolder
-
- getEventContext(boolean) - Method in class ome.security.SecuritySystemHolder
-
- getEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
-
- getEventContext(boolean) - Method in class ome.security.sharing.SharingSecuritySystem
-
- getEventContext() - Method in class ome.services.blitz.impl.ServiceFactoryI
-
Doesn't take current into account
- getEventContext(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
Takes current into account
- getEventContext(Principal) - Method in interface ome.services.sessions.SessionManager
-
- getEventContext(Principal) - Method in class ome.services.sessions.SessionManagerImpl
-
- getEventContext() - Method in class omero.cmd.Helper
-
- getEventContext() - Method in class omero.model.DetailsI
-
- getEventContext_async(AMD_IAdmin_getEventContext, Current) - Method in class ome.services.blitz.impl.AdminI
-
- getEventContextQuiet() - Method in interface ome.api.local.LocalAdmin
-
- getEventContextQuiet() - Method in class ome.logic.AdminImpl
-
- getEventLogsByPeriod_async(AMD_ITimeline_getEventLogsByPeriod, RTime, RTime, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
-
- getEvents(long, Experimenter, Timestamp, Timestamp) - Method in interface ome.api.IShare
-
Gets events for share
per
experimenter
for period of time.
- getEvents(long, Experimenter, Timestamp, Timestamp) - Method in class ome.services.sharing.ShareBean
-
- getEvents_async(AMD_IShare_getEvents, long, Experimenter, RTime, RTime, Current) - Method in class ome.services.blitz.impl.ShareI
-
- 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
-
- getExcitationFilters() - Method in class pojos.FilterSetData
-
Returns the collections of excitation filters if any.
- getExcitationFilters() - Method in class pojos.LightPathData
-
Returns the collections of excitation filters if any.
- getExcitationWavelength() - Method in class pojos.ChannelData
-
Returns the excitation wavelength of the channel.
- getExclude(int) - Method in class ome.services.graphs.AnnotationGraphSpec
-
Returns the value from "...
- getExecutor() - Method in class ome.services.scheduler.ThreadPool
-
- getExecutor() - Method in class omero.cmd.SessionI
-
- getExperimenter(long) - Method in interface ome.api.IAdmin
-
fetch an Experimenter
and all related
groups
.
- getExperimenter(long) - Method in class ome.logic.AdminImpl
-
- getExperimenter() - Method in class omero.sys.ParametersI
-
Returns the value of the experimenter
parameter.
- getExperimenter_async(AMD_IAdmin_getExperimenter, long, Current) - Method in class ome.services.blitz.impl.AdminI
-
- getExperimenterID() - Method in class ome.formats.importer.ImportLibrary
-
- getExperimenterID() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getExperimenters() - Method in class pojos.GroupData
-
Returns the experimenters contained in this group.
- getExtendedMetadata() - Method in class ome.logic.AbstractLevel2Service
-
- getExternalDescription() - Method in class pojos.WellData
-
Returns the external description of the well.
- getExternalIdentifier() - Method in class pojos.PlateData
-
Returns the external identifier of the plate.
- getExternalInfo(Current) - Method in class omero.model.DetailsI
-
- getExtra() - Method in class ome.formats.importer.util.ErrorContainer
-
- getFailureClass() - Method in exception ome.formats.enums.EnumerationException
-
- getFailureClass() - Method in exception ome.formats.model.ModelException
-
Returns the class that was used during a failed instantiation.
- getFamily(String) - Method in class omeis.providers.re.quantum.QuantumFactory
-
Helper method to retrieve a Family enumeration from the database.
- getFamily() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the mapping family.
- getFeedbackUrl() - Method in class ome.formats.importer.ImportConfig
-
- getFilament(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getFile() - Method in class ome.formats.importer.ImportContainer
-
- getFile(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder
-
- getFileBuffer(OriginalFile) - Method in class ome.io.nio.OriginalFilesService
-
Returns FileBuffer based on OriginalFile path
- getFileFormat() - Method in class ome.formats.importer.util.ErrorContainer
-
get the file format for import
- getFileFormat() - Method in class pojos.FileAnnotationData
-
Returns the format of the uploaded file.
- getFileID() - Method in class pojos.FileAnnotationData
-
Returns the id of the file.
- getFileIds() - Method in class ome.tools.RepositoryTask
-
This public method is used to return a list of file ids that require
deletion from the disk repository.
- getFileKind() - Method in class pojos.FileAnnotationData
-
Returns a user readable description of the file.
- getFileName() - Method in class pojos.FileAnnotationData
-
Returns the name of the file.
- getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.InternalRepositoryI
-
- getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.LegacyRepositoryI
-
- getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.ScriptRepositoryI
-
- getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.TemporaryRepositoryI
-
- getFilePath() - Method in class pojos.FileAnnotationData
-
Returns the absolute path to the file.
- getFileRepo(OriginalFile) - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- getFiles() - Method in class ome.formats.importer.util.ErrorContainer
-
- getFileSize() - Method in class pojos.FileAnnotationData
-
Returns the size of the file.
- getFilesPath(Long) - Method in class ome.io.nio.AbstractFileSystemService
-
Returns a numbered path relative to the root of this service, but is
ignorant of FS and similar constructs.
- getFileType() - Method in class ome.formats.importer.util.ErrorContainer
-
- getFill() - Method in class pojos.ShapeSettingsData
-
Returns the fill color.
- getFillRule() - Method in class pojos.ShapeSettingsData
-
Returns the fill rule.
- getFilteredCompanionFiles() - Method in class ome.formats.OMEROMetadataStoreClient
-
Returns the current set of filtered companion files that the Bio-Formats
image reader contains.
- getFilteredSeriesCompanionFiles() - Method in class ome.formats.OMEROMetadataStoreClient
-
Returns the current set of filtered companion files that the Bio-Formats
image reader contains for the current series.
- getFilters() - Method in class pojos.InstrumentData
-
Returns the collection of filters.
- getFilterSet() - Method in class ome.formats.model.ChannelData
-
Returns the filter set for the logical channel of this channel data.
- getFilterSet(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getFilterSet() - Method in class pojos.ChannelAcquisitionData
-
Returns the filter set or null
.
- getFilterSet() - Method in class pojos.OTFData
-
Returns the associated filter set.
- getFilterSetEmissionFilter() - Method in class ome.formats.model.ChannelData
-
Returns the filter set's emission filter for the logical channel of
this channel data.
- getFilterSetExcitationFilter() - Method in class ome.formats.model.ChannelData
-
Returns the filter set's excitation filter for the logical channel of
this channel data.
- getFilterSets() - Method in class pojos.InstrumentData
-
Returns the collection of filter sets.
- getFilterWheel() - Method in class pojos.FilterData
-
Returns the wheel.
- getFirst(String) - Method in class ome.security.auth.AttributeSet
-
- getFirstName() - Method in class pojos.ExperimenterData
-
Returns the first name of the experimenter.
- getFluor() - Method in class pojos.ChannelData
-
Returns the Fluorophore used.
- getFlushCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getFont() - Method in class pojos.ShapeSettingsData
-
Get the style of the font for Shape.
- getFontFamily() - Method in class pojos.ShapeSettingsData
-
Returns the stroke.
- getFontSize() - Method in class pojos.ShapeSettingsData
-
Returns the stroke.
- getFontStyle() - Method in class pojos.ShapeSettingsData
-
Returns the font style.
- getForceFileArchiveOn() - Method in class ome.formats.importer.ImportConfig
-
- getForceFileArchiveOn() - Method in class ome.formats.importer.util.IniFileLoader
-
- getFormat() - Method in class pojos.ImageData
-
Returns the format of the image.
- getForumUrl() - Method in class ome.formats.importer.ImportConfig
-
- getForumUrl() - Method in class ome.formats.importer.util.IniFileLoader
-
- getFreeSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo
-
This method returns the free or available space on this file system
including nested subdirectories.
- getFreeSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl
-
- getFreeSpaceInKilobytes_async(AMD_IRepositoryInfo_getFreeSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
-
- getGain() - Method in class pojos.DetectorData
-
Returns the gain of the detector.
- getGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the maximum of all maxima.
- getGlobalMax() - Method in class pojos.ChannelData
-
Returns the global maximum of the channel i.e. the maximum of all maxima.
- getGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the minimum of all minima.
- getGlobalMin() - Method in class pojos.ChannelData
-
Returns the global minimum of the channel i.e. the minimum of all minima.
- getGreen() - Method in class pojos.WellData
-
Returns the green component of the color associated to the well,
or -1
.
- 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.
- getGridQuery() - Method in interface ome.services.blitz.fire.Registry
-
Returns an active QueryPrx
or null if none is available.
- getGridQuery() - Method in class ome.services.blitz.fire.Registry.Impl
-
- getGroup(long) - Method in interface ome.api.IAdmin
-
fetch an ExperimenterGroup
and all contained
users
.
- getGroup(long) - Method in class ome.logic.AdminImpl
-
- getGroup() - Method in class ome.security.basic.BasicEventContext
-
- getGroup() - Method in class ome.security.basic.CurrentDetails
-
- getGroup(Current) - Method in class ome.services.blitz.fire.SessionManagerI
-
- 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(Current) - Method in class omero.model.DetailsI
-
- getGroup() - Method in class omero.sys.ParametersI
-
Returns the value of the group
parameter.
- getGroup_async(AMD_IAdmin_getGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI
-
- getGroupAttribute(String) - Method in class ome.security.auth.LdapConfig
-
- getGroupFilter() - Method in class ome.security.auth.LdapConfig
-
- getGroupId() - Method in class pojos.DataObject
-
Returns the id of the group.
- getGroupId() - Method in class pojos.ExperimenterData
-
Overridden to return the id of the default group.
- getGroupId() - Method in class pojos.GroupData
-
Overridden to return the id of the object.
- getGroups() - Method in class pojos.ExperimenterData
-
Returns the groups the experimenter is a member of.
- 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
-
- getHandler(Class<? extends IObject>) - Method in class ome.formats.enums.handler.EnumHandlerFactory
-
Returns an enumeration handler for a specific enumeration type.
- getHandler(Class<? extends IObject>) - Method in class ome.formats.model.handler.ModelObjectHandlerFactory
-
Returns an enumeration handler for a specific enumeration type.
- getHeight() - Method in class omeis.providers.re.data.RegionDef
-
Returns the height of the region.
- getHeight() - Method in class pojos.MaskData
-
Returns the height of the mask.
- getHeight() - Method in class pojos.RectangleData
-
Returns the height untransformed rectangle.
- getHibernateClass(String) - Method in class ome.services.graphs.BaseGraphSpec
-
- getHibernateClass(String) - Method in interface ome.services.graphs.GraphSpec
-
Return the Hibernate type (ome.model.*) for the given table.
- getHibernateClass(String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Given the name of a database table or alternatively the simple class name
(non-fully qualified) of an IObject, this method returns the class which
Hibernate will map that table to.
- getHibernateClass(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getHolder() - Method in class ome.services.blitz.util.RegisterServantMessage
-
- getHolder() - Method in class ome.services.blitz.util.UnregisterServantMessage
-
- getHomeUrl() - Method in class ome.formats.importer.ImportConfig
-
- getHomeUrl() - Method in class ome.formats.importer.util.IniFileLoader
-
- getHost() - Method in class ome.system.Server
-
simple getter for the server host passed into the constructor
- getHttpClient() - Method in class ome.formats.importer.util.HtmlMessenger
-
- getHumidity() - Method in class pojos.ImageAcquisitionData
-
Returns the humidity level, this is a value in the interval [0, 1]
- getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.api.RawPixelsStore
-
- getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getHypercube(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a hypercube from this pixel buffer.
- getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.RomioPixelBuffer
-
- getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.services.RawPixelsBean
-
- getHypercube_async(AMD_RawPixelsStore_getHypercube, List<Integer>, List<Integer>, List<Integer>, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getHypercube_async(AMD_RawPixelsStore_getHypercube, List<Integer>, List<Integer>, List<Integer>, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a hypercube from the given pixels directly.
- getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
-
- getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a the size of a hypercube from this pixel buffer.
- getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.RomioPixelBuffer
-
- getIContainer() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Return the IContainer service.
- getId() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getId() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getId() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getId() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getId() - Method in interface ome.io.nio.PixelBuffer
-
Delegates to Pixels.getId()
.
- getId() - Method in class ome.io.nio.RomioPixelBuffer
-
- getId() - Method in class ome.services.graphs.GraphEntry
-
- getId() - Method in class pojos.DataObject
-
Returns the database id of the IObject or -1
if
null
- getIdByOrder(int) - Method in class ome.services.export.ExporterIndex
-
Returns the id of an object based on the order in which it was added.
- getIdentity(String) - Method in class omero.cmd.SessionI
-
- getIdentity(String) - Method in class omero.util.ServantHolder
-
Constructs an
Identity
from the current session
and from the given
String
which for
stateless services are defined by the instance fields
#adminKey
,
#configKey
, etc. and for stateful services are UUIDs.
- getIds() - Method in class ome.services.graphs.GraphStep
-
Currently returns the ID array without copying
therefore values should not be leaked to code outside
of the ome.services.graphs hierarchy.
- getIds() - Method in class ome.services.sessions.state.SessionCache
-
Since all methods which use
SessionCache.getIds()
will subsequently check for
the existing session, we do not block here.
- getIllumination() - Method in class pojos.ChannelAcquisitionData
-
Returns the illumination.
- getIllumination() - Method in class pojos.ChannelData
-
Returns the illumination.
- getIlluminationAsEnum() - Method in class pojos.ChannelData
-
Returns the illumination enumeration value.
- getImage(long, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getImage(long) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Get the image information for an image.
- getImage(long) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- getImage(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImage() - Method in class pojos.PixelsData
-
Returns the image linked to this pixels' set.
- getImage() - Method in class pojos.ROIData
-
Returns the image for the ROI.
- getImage() - Method in class pojos.WellSampleData
-
Returns the image related to that sample if any.
- getImageAcquisitionDate(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImageAndCount(Image[], long, UnloadedCollector) - Method in class ome.services.delete.DeleteBean
-
- getImageAnnotationRef(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImageAnnotationRefCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImageByName(String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getImageByName(String) - Method in interface ome.services.blitz.gateway.services.DataService
-
Get the list of images with name containing imageName.
- getImageByName(String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
-
- getImageCount() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImageDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImageFromDatasetByName(long, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getImageFromDatasetByName(Long, String) - Method in interface ome.services.blitz.gateway.services.DataService
-
Get the images from the dataset with name, this can use wild cards.
- getImageFromDatasetByName(Long, String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
-
- getImageID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImageName(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImageNames() - Method in class ome.formats.ImageNameMetadataStore
-
Retrieves the current map of Image names held.
- getImageReader() - Method in class ome.formats.importer.OMEROWrapper
-
Return the base image reader
- getImages(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer
-
Retrieve a user's (or all users') images within any given container.
- getImages(Class, Set, Parameters) - Method in class ome.logic.PojosImpl
-
- getImages(ContainerClass, List<Long>, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getImages(ContainerClass, List<Long>) - Method in interface ome.services.blitz.gateway.services.DataService
-
Retrieves the images contained in containers specified by the
node type.
- getImages(ContainerClass, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
-
- getImages() - Method in class pojos.DatasetData
-
Returns a set of images contained in the dataset.
- getImages_async(AMD_IContainer_getImages, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
-
- getImagesByOptions(Parameters) - Method in interface ome.api.IContainer
-
Retrieve images by options.
- getImagesByOptions(Parameters) - Method in class ome.logic.PojosImpl
-
- getImagesByOptions_async(AMD_IContainer_getImagesByOptions, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
-
- getImageService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
- getImagesForDataset(long) - Method in interface ome.api.IAnalysis
-
- getImageSize(PlaneDef) - Method in class omeis.providers.re.Renderer
-
Returns the size, in bytes, of the
RGBBuffer
that would be
rendered from the plane selected by
pd
.
- getImagingEnvironment(int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getImagingEnvironmentId() - Method in class pojos.ImageAcquisitionData
-
Returns the id of the StageLabel
or -1
if not already linked to the image.
- getImmersion() - Method in class pojos.ObjectiveData
-
Returns the immersion value of the objective.
- getImmutableFields() - Method in class ome.tools.hibernate.ExtendedMetadata.Immutables
-
- getImmutableFields(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getImplicitContext() - Method in class omero.client
-
Returns the ImplicitContext
which defines what properties
will be sent on every method invocation.
- getImportTypes() - Method in class ome.logic.TypesImpl
-
- getIndex() - Method in class ome.formats.importer.util.ErrorContainer
-
get the index for this error container
- getIndex() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
- getIndex() - Method in class pojos.ChannelData
-
Returns the channel's index.
- getIndex() - Method in class pojos.ImageData
-
Returns the index of the image within the multi-images file.
- getIniVersionNumber() - Method in class ome.formats.importer.ImportConfig
-
- getInput(String, String) - Method in interface ome.api.ISession
-
Retrieves an entry from the given session's
input
environment.
- getInput(String, String) - Method in class ome.services.sessions.SessionBean
-
- getInput(String, String) - Method in interface ome.services.sessions.SessionManager
-
Returns the input environment
Object
stored under the given key
or null if none present.
- getInput(String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getInput(String) - Method in class omero.client
-
Retrieves an item from the "input" shared (session) memory.
- getInput_async(AMD_ISession_getInput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getInputEnd() - Method in class omeis.providers.re.metadata.StatsFactory
-
Returns the input end.
- getInputKeys(String) - Method in interface ome.api.ISession
-
Retrieves all keys in the sesson's
input environment.
- getInputKeys(String) - Method in class ome.services.sessions.SessionBean
-
- getInputKeys() - Method in class omero.client
-
Returns a list of keys for all items in the "input" shared (session)
memory
- getInputKeys_async(AMD_ISession_getInputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getInputs(String) - Method in interface ome.api.ISession
-
Retrieves all inputs from the given session's
input
environment.
- getInputs(String) - Method in class ome.services.sessions.SessionBean
-
- getInputs_async(AMD_ISession_getInputs, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getInputStart() - Method in class omeis.providers.re.metadata.StatsFactory
-
Returns the input start.
- getInserted() - Method in class pojos.ImageData
-
Returns the insertion time of the image.
- getInstance(Class<T>) - Method in class ome.formats.model.BlitzInstanceProvider
-
- getInstance(Class<T>) - Method in interface ome.formats.model.InstanceProvider
-
Retrieves an instance.
- getInstance(String) - Static method in class ome.system.OmeroContext
-
create (if necessary) and return the single default OmeroContext named by
the beanFactoryName parameter.
- getInstanceProvider() - Method in class ome.formats.importer.ImportLibrary
-
- getInstanceProvider() - Method in class ome.formats.OMEROMetadataStoreClient
-
Retrieves the active enumeration provider.
- getInstitution() - Method in class pojos.ExperimenterData
-
Returns the institution where the experimenter works.
- getInstrumentId() - Method in class pojos.ImageData
-
Returns the id of the instrument if any.
- getInternalServiceFactory(String, String, int, int, String) - Method in interface ome.services.blitz.fire.Registry
-
Try to return a ServiceFactory from the grid.
- getInternalServiceFactory(String, String, int, int, String) - Method in class ome.services.blitz.fire.Registry.Impl
-
- getInternalValue(String) - Method in interface ome.api.local.LocalConfig
-
Provides a configuration value, ignoring the visibility of the given
value.
- getInternalValue(String) - Method in class ome.logic.ConfigImpl
-
- getIntervalEnd() - Method in class omeis.providers.re.codomain.CodomainChain
-
Returns the upper bound of the codomain interval.
- getIntervalStart() - Method in class omeis.providers.re.codomain.CodomainChain
-
Returns the lower bound of the codomain interval.
- getIObjectContainer(Class<? extends IObject>, LinkedHashMap<Index, Integer>) - Method in interface ome.formats.model.IObjectContainerStore
-
Retrieves an IObject container for a given class and location within the
OME-XML data model.
- getIObjectContainer(Class<? extends IObject>, LinkedHashMap<Index, Integer>) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getIObjectContainers(Class<? extends IObject>) - Method in interface ome.formats.model.IObjectContainerStore
-
Retrieves all IObject containers of a given class.
- getIObjectContainers(Class<? extends IObject>) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getIPixels() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Get the iPixels Service.
- getIQuery() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getIQuery() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Get the IQuery Service.
- getIScript() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Return the IScript service.
- getIsSPW() - Method in class ome.formats.importer.ImportContainer
-
- getIterator() - Method in class pojos.ROIData
-
Returns the iterator of the collection of the map.
- getITypes() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Get the types service.
- getIUpdate() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Get the iUpdate Service.
- getJavaClasspath() - Method in class ome.formats.importer.util.ErrorContainer
-
- getJavaVersion() - Method in class ome.formats.importer.util.ErrorContainer
-
- getJob() - Method in interface ome.api.JobHandle
-
- getJob(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
-
- getJob() - Method in class ome.services.JobBean
-
- getJob(Current) - Method in class omero.grid.InteractiveProcessorI
-
- getJob_async(AMD_JobHandle_getJob, Current) - Method in class ome.services.blitz.impl.JobHandleI
-
- getKeepAlive() - Method in class ome.formats.OMEROMetadataStoreClient
-
Returns clientKeepAlive created in store
- getKeywords() - Method in class pojos.WorkflowData
-
Returns the keywords of this workflow.
- getKeywordsAsList() - Method in class pojos.WorkflowData
-
Returns the keywords of this workflow as a list.
- getKind() - Method in class pojos.LightSourceData
-
Returns the kind of light source.
- getLabel() - Method in class pojos.PlateAcquisitionData
-
Returns the label associated to the plate acquisition.
- getLabelName() - Method in class pojos.ImageAcquisitionData
-
Returns the name of the stage label.
- getLaser(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getLaserFrequencyMultiplication() - Method in class pojos.LightSourceData
-
Returns the frequency multiplication of the laser.
- getLaserMedium() - Method in class pojos.LightSourceData
-
Returns the laser's medium.
- getLaserPockelCell() - Method in class pojos.LightSourceData
-
Returns the pockel cell flag of the laser.
- getLaserPulse() - Method in class pojos.LightSourceData
-
Returns the pulse of the laser.
- getLaserPump() - Method in class pojos.LightSourceData
-
Returns the pump.
- getLaserRepetitionRate() - Method in class pojos.LightSourceData
-
Returns the repetition rate (Hz) if the laser is repetitive.
- getLaserTuneable() - Method in class pojos.LightSourceData
-
Returns the value of the tuneable
field or null
if no value set.
- getLaserWavelength() - Method in class pojos.LightSourceData
-
Returns the laser's wavelength.
- getLast() - Method in class ome.security.basic.CurrentDetails
-
- getLast() - Method in interface ome.security.basic.PrincipalHolder
-
Get the last, i.e. currently active, principal.
- getLastModified() - Method in class pojos.AnnotationData
-
Returns the time when the annotation was last modified.
- getLastName() - Method in class pojos.ExperimenterData
-
Returns the last name of the experimenter.
- getLastUpdated() - Method in class ome.services.sessions.state.SessionCache
-
- getLdapService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- 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.
- getLeaderOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
-
- getLeaderOfGroupIds_async(AMD_IAdmin_getLeaderOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
-
- getLeaderOfGroupsList() - Method in class ome.security.basic.BasicEventContext
-
- getLeaderOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
-
- getLeaderOfGroupsList() - Method in interface ome.system.EventContext
-
- getLeaderOfGroupsList() - Method in class ome.system.SimpleEventContext
-
- getLeaders() - Method in class pojos.GroupData
-
Returns the experimenters contained in this group.
- getLeaves() - Method in class omero.sys.ParametersI
-
- getLensNA() - Method in class pojos.ObjectiveData
-
Returns the objective's LensNA.
- getLightEmittingDiode(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getLightPath() - Method in class pojos.ChannelAcquisitionData
-
Returns the light path or null
.
- getLightPathEmissionFilters() - Method in class ome.formats.model.ChannelData
-
Returns the collection of emission filters in the light path.
- getLightPathExcitationFilters() - Method in class ome.formats.model.ChannelData
-
Returns the collection of excitation filters in the light path.
- getLightSource() - Method in class ome.formats.model.ChannelData
-
Returns the light source for the light source settings of this channel
data.
- getLightSource() - Method in class pojos.ChannelAcquisitionData
-
Returns the source of light.
- getLightSourceModel() - Method in class pojos.LightSourceData
-
Returns the model of the light source.
- getLightSources() - Method in class pojos.InstrumentData
-
Returns the collection of light sources.
- getLightSourceSettings() - Method in class ome.formats.model.ChannelData
-
Returns the light source settings for the logical channel of this
channel data.
- getLigthSettingsAttenuation() - Method in class pojos.ChannelAcquisitionData
-
Returns the attenuation of the light source, percent value
between 0 and 1.
- getLigthSettingsWavelength() - Method in class pojos.ChannelAcquisitionData
-
Returns the wavelength of the light source.
- getLimit() - Method in class omero.sys.ParametersI
-
Returns the value of the limit
parameter.
- getLine(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getLine() - Method in class ome.services.blitz.repo.FileMaker
-
- getLineCap() - Method in class pojos.ShapeSettingsData
-
Returns the shape of the end of the line..
- getListAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getLocationStats() - Method in class omeis.providers.re.metadata.StatsFactory
-
Returns the statistics.
- getLockCandidateChecks(Class<? extends IObject>, boolean) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
- getLockCandidateChecks(Class<? extends IObject>, boolean) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getLockCandidateChecks(boolean) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
- getLockCandidates() - Method in class ome.security.basic.BasicEventContext
-
- getLockCandidates(IObject) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
walks the IObject
argument non-recursively and gathers
all IObject
instances which will be linked to by the
creation or updating of the argument.
- getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
walks the IObject
argument non-recursively and gathers
all IObject
instances which will be linkd to by the
creation or updating of the argument.
- getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
- getLockChecks(Class<? extends IObject>) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
returns all class/field name pairs which may possibly link to an object
of type klass
.
- getLockChecks(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
returns all class/field name pairs which may possibly link to an object
of type klass
.
- getLockingIds(Class<IObject>, long, Long) - Method in interface ome.api.local.LocalAdmin
-
Returns a map from
Class
(as string) to a count for all entities
which point to the given
IObject
.
- getLockingIds(IObject) - Method in class ome.logic.AdminImpl
-
- getLockingIds(Class<IObject>, long, Long) - Method in class ome.logic.AdminImpl
-
- getLogFile() - Method in class ome.formats.importer.ImportConfig
-
- getLogFile() - Method in class ome.formats.importer.util.IniFileLoader
-
- getLogger() - Method in class ome.services.util.BeanHelper
-
- getLogicalChannel() - Method in class ome.formats.model.ChannelData
-
Returns the logical channel for this channel data.
- getLogs() - Method in class ome.security.basic.BasicEventContext
-
- getLogs() - Method in class ome.security.basic.BasicSecuritySystem
-
- getLogs() - Method in class ome.security.basic.CurrentDetails
-
- getLogString(SelfConfigurableService) - Method in class ome.services.util.BeanHelper
-
- getLongAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getLongAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getLongAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getLongAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getLongAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getLongAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getLotNumber() - Method in class pojos.DetectorData
-
Returns the lot number of the detector.
- getLotNumber() - Method in class pojos.DichroicData
-
Returns the lot number.
- getLotNumber() - Method in class pojos.FilterData
-
Returns the lot number.
- getLotNumber() - Method in class pojos.FilterSetData
-
Returns the lot number.
- getLotNumber() - Method in class pojos.LightSourceData
-
Returns the lot of number the light source.
- getLotNumber() - Method in class pojos.ObjectiveData
-
Returns the lot number of the detector.
- getLowerLimit() - Method in class omeis.providers.re.codomain.PlaneSlicingContext
-
Returns the constant level for bit-planes < planeSelected w.r.t the
higher-order bits.
- getManagedServerContext() - Static method in class ome.system.OmeroContext
-
create (if necessary) and return the single default managed OmeroContext.
- getManagerList(boolean) - Method in class ome.services.blitz.fire.Ring
-
- getManagerList(boolean) - Method in interface ome.services.blitz.redirect.Redirector.Context
-
Return all known managers in the current cluster context, possibly
filtering out the inactive ones.
- getManufacturer() - Method in class pojos.DetectorData
-
Returns the manufacturer of the detector.
- getManufacturer() - Method in class pojos.DichroicData
-
Returns the manufacturer.
- getManufacturer() - Method in class pojos.FilterData
-
Returns the manufacturer.
- getManufacturer() - Method in class pojos.FilterSetData
-
Returns the manufacturer.
- getManufacturer() - Method in class pojos.LightSourceData
-
Returns the manufacturer of the light source.
- getManufacturer() - Method in class pojos.ObjectiveData
-
Returns the manufacturer of the detector.
- getMarkerEnd() - Method in class pojos.ShapeSettingsData
-
Returns the marker end.
- getMarkerStart() - Method in class pojos.ShapeSettingsData
-
Returns the marker start.
- getMask(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getMask() - Method in class pojos.MaskData
-
Returns the mask as a byte array.
- getMaskAsBinaryArray() - Method in class pojos.MaskData
-
Returns the mask image.
- getMaskAsBufferedImage() - Method in class pojos.MaskData
-
Returns the mask image.
- getMaskPoints() - Method in class pojos.PolygonData
-
Returns the points in the polygon.
- getMaskPoints() - Method in class pojos.PolylineData
-
Returns the points in the Polyline.
- getMatcher(String) - Method in class ome.services.graphs.GraphEntry
-
- getMaximumFieldCount() - Method in class pojos.PlateAcquisitionData
-
Returns the maximum number of fields in any well.
- getMaxPlaneHeight() - Method in class ome.io.nio.ConfiguredTileSizes
-
- getMaxPlaneHeight() - Method in interface ome.io.nio.TileSizes
-
- getMaxPlaneWidth() - Method in class ome.io.nio.ConfiguredTileSizes
-
- getMaxPlaneWidth() - Method in interface ome.io.nio.TileSizes
-
- getMeasuredRois_async(AMD_IRoi_getMeasuredRois, long, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
-
- getMeasuredRoisMap_async(AMD_IRoi_getMeasuredRoisMap, long, List<Long>, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
-
- getMedium() - Method in class pojos.ImageAcquisitionData
-
Returns the medium of the objective.
- getMediumAsEnum() - Method in class pojos.ImageAcquisitionData
-
Returns the medium enumeration value.
- getMemberCount(Set<Long>) - Method in interface ome.api.IShare
-
Returns a map from share id to the count of total members (including the
owner).
- getMemberCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
-
- getMemberCount_async(AMD_IShare_getMemberCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getMemberOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin
-
Finds the ids for all groups for which the given Experimenter
is
a member.
- getMemberOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
-
- getMemberOfGroupIds_async(AMD_IAdmin_getMemberOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
-
- getMemberOfGroupsList() - Method in class ome.security.basic.BasicEventContext
-
- getMemberOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
-
- getMemberOfGroupsList() - Method in interface ome.system.EventContext
-
- getMemberOfGroupsList() - Method in class ome.system.SimpleEventContext
-
- getMemberShares(boolean) - Method in interface ome.api.IShare
-
Gets all shares where current Experimenter
is a member.
- getMemberShares(boolean) - Method in class ome.services.sharing.ShareBean
-
- getMemberShares_async(AMD_IShare_getMemberShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getMemberSharesFor(Experimenter, boolean) - Method in interface ome.api.IShare
-
Gets all shares where given Experimenter
is a member.
- getMemberSharesFor(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
-
- getMemberSharesFor_async(AMD_IShare_getMemberSharesFor, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getMembersOnly() - Method in class pojos.GroupData
-
Returns the list of experimenters that are not owners of the group.
- getMessage() - Method in exception ome.io.nio.PixelBufferException
-
- getMessageDigest() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getMetadata(long) - Method in class ome.services.ThumbnailCtx
-
Retrieves the Thumbnail object for a given Pixels ID.
- getMetadata() - Method in class omeis.providers.re.Renderer
-
Returns the Pixels
set the rendering engine is for.
- getMetadataOnly() - Method in class ome.formats.importer.ImportContainer
-
Retrieves the metadata only flag.
- getMetadataOptions() - Method in class ome.formats.importer.OMEROWrapper
-
- getMetadataService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getMetadataService() - Method in class ome.system.ServiceFactory
-
- getMethod(String) - Method in class ome.services.blitz.util.IceMethodInvoker
-
For testing the cached method.
- getMethodCount() - Method in class ome.services.messages.stats.MethodStatsMessage
-
- getMicrobeamManipulation(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getMicrobeamManipulationLightSourceSettings(int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getMicroscopeLotNumber() - Method in class pojos.InstrumentData
-
Returns the lot number of the microscope.
- getMicroscopeManufacturer() - Method in class pojos.InstrumentData
-
Returns the model of the microscope.
- getMicroscopeModel() - Method in class pojos.InstrumentData
-
Returns the model of the microscope.
- getMicroscopeSerialNumber() - Method in class pojos.InstrumentData
-
Returns the serial number of the microscope.
- getMicroscopeType() - Method in class pojos.InstrumentData
-
Returns the type of microscope.
- getMiddleName() - Method in class pojos.ExperimenterData
-
Returns the middle name of the experimenter.
- getMode() - Method in class pojos.ChannelAcquisitionData
-
Returns the mode.
- getMode() - Method in class pojos.ChannelData
-
Returns the mode.
- getModeAsEnum() - Method in class pojos.ChannelData
-
Returns the acquisition enumeration value.
- getModel() - Method in class ome.services.RenderingBean
-
- 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.
- getModel() - Method in class pojos.DetectorData
-
Returns the manufacturer of the detector.
- getModel() - Method in class pojos.DichroicData
-
Returns the model.
- getModel() - Method in class pojos.FilterData
-
Returns the model.
- getModel() - Method in class pojos.FilterSetData
-
Returns the model.
- getModel() - Method in class pojos.ObjectiveData
-
Returns the model of the objective.
- getModel_async(AMD_RenderingEngine_getModel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getModel_async(AMD_RenderingEngine_getModel, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getModelProcessors() - Method in class ome.formats.OMEROMetadataStoreClient
-
Retrieves the current list of model processors the metadata store is
using.
- getMostRecentAnnotationLinks_async(AMD_ITimeline_getMostRecentAnnotationLinks, List<String>, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
-
- getMostRecentObjects_async(AMD_ITimeline_getMostRecentObjects, List<String>, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI
-
- getMostRecentShareCommentLinks_async(AMD_ITimeline_getMostRecentShareCommentLinks, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
-
- getMyOpenAgentSessions(String) - Method in interface ome.api.ISession
-
- getMyOpenAgentSessions(String) - Method in class ome.services.sessions.SessionBean
-
- getMyOpenAgentSessions_async(AMD_ISession_getMyOpenAgentSessions, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getMyOpenClientSessions() - Method in interface ome.api.ISession
-
- getMyOpenClientSessions() - Method in class ome.services.sessions.SessionBean
-
- getMyOpenClientSessions_async(AMD_ISession_getMyOpenClientSessions, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getMyOpenSessions() - Method in interface ome.api.ISession
-
Returns a list of open sessions for the current user.
- getMyOpenSessions() - Method in class ome.services.sessions.SessionBean
-
- getMyOpenSessions_async(AMD_ISession_getMyOpenSessions, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getMyUserPhotos() - Method in interface ome.api.IAdmin
-
Retrieve the OriginalFile
objectd attached to this
user as specified by {@link #uploadMyUserPhoto(String, String, byte[]).
- getMyUserPhotos() - Method in class ome.logic.AdminImpl
-
- getMyUserPhotos_async(AMD_IAdmin_getMyUserPhotos, Current) - Method in class ome.services.blitz.impl.AdminI
-
- getName() - Method in class ome.logic.HardWiredInterceptor
-
- getName() - Method in class ome.security.basic.AbstractSecurityFilter
-
- getName() - Method in class ome.security.basic.BasicSecurityWiring
-
Lookup name.
- getName() - Method in interface ome.security.SecurityFilter
-
Name of this security filter.
- getName() - Method in class ome.security.SecurityFilterHolder
-
- getName() - Method in class ome.services.graphs.BaseGraphSpec
-
- getName() - Method in class ome.services.graphs.GraphEntry
-
- getName(Matcher) - Method in class ome.services.graphs.GraphEntry
-
- getName() - Method in interface ome.services.graphs.GraphSpec
-
The name of this specification.
- getName() - Method in class ome.services.roi.PopulateRoiJob
-
- getName() - Method in class ome.services.scripts.ScriptFinder
-
Subclasses should override to return the name of the file under scripts/
which should be uploaded.
- getName() - Method in interface ome.services.sessions.SessionCallback
-
- getName() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
-
- 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
-
- getName() - Method in class pojos.ChannelData
-
Returns the name of the channel.
- getName() - Method in class pojos.DatasetData
-
Returns the name of the dataset.
- getName() - Method in class pojos.FileData
-
Returns the name of the file.
- getName() - Method in class pojos.GroupData
-
Returns the name of the group.
- getName() - Method in class pojos.ImageData
-
Returns the name of the image.
- getName() - Method in class pojos.PlateAcquisitionData
-
Returns the name of the plate acquisition.
- getName() - Method in class pojos.PlateData
-
Returns the name of the plate.
- getName() - Method in class pojos.ProjectData
-
Returns the name of the project.
- getName() - Method in class pojos.ScreenData
-
Returns the name of the screen.
- getNameSpace() - Method in class pojos.AnnotationData
-
Retrieves the nameSpace
of the underlying
Annotation
instance.
- getNameSpace() - Method in class pojos.WorkflowData
-
Returns the namespace of this workflow.
- getNamespaceKeywords(String) - Method in class pojos.ROIData
-
Returns the keywords of the namespace on the ROI.
- getNamespaceKeywords() - Method in class pojos.ROIData
-
Returns the keywords of the ROI.
- getNamespaces() - Method in class pojos.ROIData
-
Returns the namespace of the ROI.
- getNDFilter() - Method in class pojos.ChannelData
-
Returns the ND filter wavelength of the channel.
- getNewUserGroup() - Method in class ome.security.auth.LdapConfig
-
- getNodeUuid(Current) - Method in class ome.services.blitz.fire.Ring
-
- getNoiseReduction() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns true
if the noise reduction algorithm
is turned on, false
if turned off.
- getNominalMagnification() - Method in class pojos.ObjectiveData
-
Returns the objective's nominal magnification factor.
- getNumOfDirectories() - Method in class ome.formats.importer.ImportConfig
-
- getNumOfDirectories() - Method in class ome.formats.importer.util.IniFileLoader
-
- getObject(String, int) - Method in class ome.services.export.ExporterStepFactory
-
- getObject() - Method in interface ome.services.sessions.SessionCallback
-
- getObject() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
-
- getObject() - Method in class ome.services.sessions.state.CacheFactory
-
- getObjectAdapter() - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- getObjectAdapter() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
-
- getObjectByLSID(LSID) - Method in class ome.formats.OMEROMetadataStore
-
Retrieves an object from the internal object graph by LSID.
- getObjective(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getObjective() - Method in class pojos.ImageAcquisitionData
-
Returns the objective used to capture the image.
- getObjective() - Method in class pojos.OTFData
-
Returns the associated objective.
- getObjectives() - Method in class pojos.InstrumentData
-
Returns the collection of objectives.
- getObjectiveSettings(int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getObjectiveSettingsId() - Method in class pojos.ImageAcquisitionData
-
Returns the id of the Objective settings
or -1
if not already linked to the image.
- getObjectsRead() - Method in class ome.services.messages.stats.ObjectsReadStatsMessage
-
- getObjectsWritten() - Method in class ome.services.messages.stats.ObjectsWrittenStatsMessage
-
- getObjectType() - Method in class ome.security.basic.EventListenersFactoryBean
-
this
FactoryBean
produces a
Map
instance for use in
LocalSessionFactoryBean.setEventListeners(Map)
- getObjectType() - Method in class ome.services.delete.Deletion.Builder
-
- getOffset() - Method in class omero.sys.ParametersI
-
Returns the value of the offset
parameter.
- getOffset() - Method in class pojos.DetectorData
-
Returns the offset of the detector.
- getOp(Matcher) - Method in class ome.services.graphs.GraphEntry
-
- getOpString() - Method in class ome.services.graphs.GraphEntry
-
Primarily used for passing back a string representation of the default
operation to users for setting options.
- getOptimisticFailureCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getOptimizations() - Method in class omeis.providers.re.Renderer
-
Returns the optimizations that the renderer currently has enabled.
- getOrCreateParams(long, Current) - Method in class omero.grid.ParamsHelper
-
Get the script params for the file.
- getOrder() - Method in class ome.io.nio.ReorderedPixelData
-
Returns the byte order of the backing buffer.
- getOriginalEnumerations() - Method in interface ome.api.ITypes
-
Gets all original values.
- getOriginalEnumerations() - Method in class ome.logic.TypesImpl
-
- getOriginalEnumerations_async(AMD_ITypes_getOriginalEnumerations, Current) - Method in class ome.services.blitz.impl.TypesI
-
- getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in interface ome.io.nio.FilePathResolver
-
Retrieves the original file path for a given set of pixels.
- getOriginalFilePath(Pixels) - Method in class ome.io.nio.PixelsService
-
Retrieves the original file path for a given set of pixels.
- getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in class ome.services.OmeroFilePathResolver
-
- getOriginalGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the original maximum of all minima.
- getOriginalGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the original minimum of all minima.
- getOriginalMimetype() - Method in class pojos.FileAnnotationData
-
Returns the format of the original file.
- getOrphan() - Method in class omero.sys.ParametersI
-
- getOSArch() - Method in class ome.formats.importer.util.ErrorContainer
-
- getOSName() - Method in class ome.formats.importer.util.ErrorContainer
-
- getOSVersion() - Method in class ome.formats.importer.util.ErrorContainer
-
- getOTF() - Method in class pojos.ChannelAcquisitionData
-
Returns the OTF used for that channel.
- getOTF() - Method in class pojos.InstrumentData
-
Returns the collection of OTFs.
- getOutput(String, String) - Method in interface ome.api.ISession
-
Retrieves an entry from the session's
output environment.
- getOutput(String, String) - Method in class ome.services.sessions.SessionBean
-
- getOutput(String, String) - Method in interface ome.services.sessions.SessionManager
-
Returns the output environment
Object
stored under the given key
or null if none present.
- getOutput(String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getOutput(String) - Method in class omero.client
-
Retrieves an item from the "output" shared (session) memory.
- getOutput_async(AMD_ISession_getOutput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getOutputKeys(String) - Method in interface ome.api.ISession
-
Retrieves all keys in the sesson's
output environment.
- getOutputKeys(String) - Method in class ome.services.sessions.SessionBean
-
- getOutputKeys() - Method in class omero.client
-
Returns a list of keys for all items in the "output" shared (session)
memory
- getOutputKeys_async(AMD_ISession_getOutputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getOutputs(String) - Method in interface ome.api.ISession
-
Retrieves all outputs from the given session's
input
environment.
- getOutputs(String) - Method in class ome.services.sessions.SessionBean
-
- getOutputs_async(AMD_ISession_getOutputs, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getOverlays() - Method in class omeis.providers.re.Renderer
-
Returns the current set of overlays to be rendered.
- getOwner() - Method in class ome.security.basic.BasicEventContext
-
- getOwner() - Method in class ome.security.basic.CurrentDetails
-
- getOwner(Current) - Method in class omero.model.DetailsI
-
- getOwner() - Method in class pojos.DataObject
-
Returns the owner of the object.
- getOwnShares(boolean) - Method in interface ome.api.IShare
-
Gets all owned shares for the current Experimenter
- getOwnShares(boolean) - Method in class ome.services.sharing.ShareBean
-
- getOwnShares_async(AMD_IShare_getOwnShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getParameterTypes() - Method in class ome.security.basic.AllGroupsSecurityFilter
-
- getParameterTypes() - Method in class ome.security.basic.OneGroupSecurityFilter
-
- getParameterTypes() - Method in interface ome.security.SecurityFilter
-
Return a mapping of the hibernate types for each of the parameters
that the condition takes.
- getParameterTypes() - Method in class ome.security.SecurityFilterHolder
-
- getParams_async(AMD_IScript_getParams, long, Current) - Method in class ome.services.blitz.impl.ScriptI
-
Get the Parameters of the script.
- getParentFilePath() - Method in class pojos.ImageData
-
Returns the path to the file hosting the image.
- getParentTransformer(Class) - Static method in class ome.services.query.Hierarchy
-
- getPassword() - Method in class ome.system.Login
-
simple getter for the password passed into the constructor
- getPasswordAuthentication() - Method in class ome.security.SmtpAuthenticator
-
- getPastConnections(long) - Method in interface ome.api.IShare
-
Gets previous connections to share
.
- getPastConnections(long) - Method in class ome.services.sharing.ShareBean
-
- getPastConnections_async(AMD_IShare_getPastConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getPath() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getPath() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getPath() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getPath() - Method in class ome.io.nio.AbstractBuffer
-
- getPath() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getPath() - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the full path to this pixel buffer on disk
- getPath(Matcher) - Method in class ome.services.graphs.GraphEntry
-
- getPath() - Method in class pojos.FileData
-
Returns the (relative) path of the file.
- getPath() - Method in class pojos.OTFData
-
Returns the path.
- getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- getPaths() - Method in class ome.formats.importer.ImportCandidates
-
- getPathToFile() - Method in class pojos.ImageData
-
Returns the path to the file.
- getPerm1(Current) - Method in class omero.model.PermissionsI
-
- getPermissions(Current) - Method in class omero.model.DetailsI
-
- getPermissions() - Method in class pojos.DataObject
-
Returns the permission of the object.
- getPermissionsForGroup(Long) - Method in class ome.security.basic.BasicEventContext
-
- getPermissionsLevel() - Method in class pojos.PermissionData
-
Returns the permissions level.
- getPhysicalMemory() - Static method in class ome.services.util.JvmSettingsCheck
-
- getPinholeSize() - Method in class pojos.ChannelData
-
Returns the pin hole size of the channel.
- getPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService
-
- getPixelBuffer(Pixels, boolean) - Method in class ome.io.nio.PixelsService
-
Returns a pixel buffer for a given set of pixels.
- getPixelIds() - Method in class ome.tools.RepositoryTask
-
This public method is used to return a list of pixel ids that require
deletion from the disk repository.
- getPixels() - Method in class ome.formats.importer.util.TinyImportFixture
-
- getPixels() - Method in class ome.formats.OMEROImportFixture
-
Accessor for the created pixels.
- getPixels(long, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getPixels(long) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Get the pixels information for an image.
- getPixels(long) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- getPixels(Long) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
- getPixels(Long) - Method in interface ome.services.blitz.gateway.services.RenderingService
-
Get the pixels of the Rendering engine.
- getPixels(Long, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler
-
- getPixels() - Method in class ome.services.RenderingBean
-
- getPixels(long) - Method in class ome.services.ThumbnailCtx
-
Retrieves the Pixels object for a given Pixels ID.
- getPixels() - Method in class omeis.providers.re.Renderer
-
Returns the object that allows to access the pixels raw data.
- getPixels() - Method in interface omeis.providers.re.RenderingEngine
-
Returns the Pixels
set the Rendering engine is for.
- getPixels() - Method in class omero.util.RPSTileLoop
-
After saving the binary data, the update event of the
Pixels
instance will be updated and therefore
need to be reloaded.
- getPixels_async(AMD_RenderingEngine_getPixels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getPixels_async(AMD_RenderingEngine_getPixels, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getPixelsBinDataBigEndian(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsDimensionOrder(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsFromImage(long, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getPixelsFromImage(long) - Method in interface ome.services.blitz.gateway.services.DataService
-
Get the pixels associated with the image.
- getPixelsFromImage(long) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
-
- getPixelsId() - Method in interface ome.api.RawPixelsStore
-
Returns the current Pixels set identifier.
- getPixelsID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsId() - Method in class ome.services.RawPixelsBean
-
- getPixelsId_async(AMD_RawPixelsStore_getPixelsId, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getPixelsId_async(AMD_RawPixelsStore_getPixelsId, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getPixelSizeX() - Method in class pojos.PixelsData
-
Returns the dimension of a pixel along the X-axis, dimension is in
microns.
- getPixelSizeY() - Method in class pojos.PixelsData
-
Returns the dimension of a pixel along the Y-axis, dimension is in
microns.
- getPixelSizeZ() - Method in class pojos.PixelsData
-
Returns the dimension of a pixel along the Z-axis, dimension is in
microns.
- getPixelsParams(Pixels) - Method in interface ome.io.nio.FilePathResolver
-
Retrieves the pixels set's stored parameters.
- getPixelsParams(Pixels) - Method in class ome.services.OmeroFilePathResolver
-
- getPixelsPath(Long) - Method in class ome.io.nio.AbstractFileSystemService
-
Returns a numbered path relative to the root of this service, but is
ignorant of FS and similar constructs.
- getPixelsPhysicalSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsPhysicalSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsPhysicalSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getPixelsService() - Method in class ome.system.ServiceFactory
-
- getPixelsSizeC(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsSizeT(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsTimeIncrement(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsType() - Method in class ome.io.bioformats.BfPixelsWrapper
-
cgb - created from the methods below?
- getPixelsType(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsType() - Method in class omeis.providers.re.Renderer
-
Returns the pixels type.
- getPixelsType() - Method in class pojos.OTFData
-
Returns the pixels type.
- getPixelsTypeLowerBound(int) - Method in class ome.services.RenderingBean
-
- getPixelsTypeLowerBound(int) - Method in class omeis.providers.re.Renderer
-
Returns the minimum value for that channels depending on the pixels
type and the original range (globalmax, globalmin)
- 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)
- getPixelsTypeLowerBound_async(AMD_RenderingEngine_getPixelsTypeLowerBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getPixelsTypeLowerBound_async(AMD_RenderingEngine_getPixelsTypeLowerBound, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getPixelsTypeMax() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the upper bound of the pixels range or 0
if the value couldn't be set.
- getPixelsTypeMin() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the lower bound of the pixels range or 0
if the value couldn't be set.
- getPixelsTypeUpperBound(int) - Method in class ome.services.RenderingBean
-
- getPixelsTypeUpperBound(int) - Method in class omeis.providers.re.Renderer
-
Returns the maximum 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)
- getPixelsTypeUpperBound_async(AMD_RenderingEngine_getPixelsTypeUpperBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getPixelsTypeUpperBound_async(AMD_RenderingEngine_getPixelsTypeUpperBound, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getPixelType(String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getPixelType(String) - Method in interface ome.services.blitz.gateway.services.DataService
-
Get the pixelsType with type.
- getPixelType(String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
-
- getPixelType() - Method in class pojos.PixelsData
-
Returns the pixels type.
- getPixelTypes(Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getPixelTypes() - Method in interface ome.services.blitz.gateway.services.DataService
-
Get the PixelTypes available in the system.
- getPixelTypes() - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
-
- getPixelValue(int, int) - Method in class omeis.providers.re.data.Plane2D
-
Returns the pixel intensity value of the pixel at (x1, x2)
.
- getPixelValue(int) - Method in class omeis.providers.re.data.Plane2D
-
Returns the pixel intensity value of the pixel at a given offset within
the backing buffer.
- getPixelValueDirect(int) - Method in class ome.io.nio.ReorderedPixelData
-
Returns the pixel intensity value of the pixel at a given offset within
the backing buffer.
- getPlane(int, int, int) - Method in interface ome.api.RawPixelsStore
-
- getPlane(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getPlane(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getPlane(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getPlane(Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a particular 2D image plane from this pixel buffer.
- getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getPlane(long, int, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
Get the raw plane for the pixels pixelsId, this returns a 2d array
representing the plane, it returns doubles but will not lose data.
- getPlane(long, int, int, int) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
-
- getPlane(long, int, int, int) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService
-
get bytes to the plane c, t, z
- getPlane(int, int, int) - Method in class ome.services.RawPixelsBean
-
- getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getPlaneCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPlaneCount() - Method in class pojos.ROIData
-
Returns the number of planes occupied by the ROI.
- getPlaneDeltaT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPlaneDimsAsString(PlaneDef) - Method in class omeis.providers.re.Renderer
-
Returns a string with the dimensions of the specified plane.
- getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a particular 2D image plane from this pixel buffer.
- getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
-
- getPlaneExposureTime(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPlaneOffset(int, int, int) - Method in interface ome.api.RawPixelsStore
-
- getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getPlaneOffset(Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the offset for a particular 2D image plane in this pixel
buffer.
- getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getPlaneOffset(int, int, int) - Method in class ome.services.RawPixelsBean
-
- getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getPlanePositionX(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPlanePositionY(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPlanePositionZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- 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
-
- getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getPlaneRegion(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a particular region of a 2D image plane from this pixel buffer.
- getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getPlaneRegion(int, int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a region from a given plane directly.
- getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
-
- 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
-
- getPlaneSize() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getPlaneSize() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getPlaneSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getPlaneSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getPlaneSize() - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the in memory size of a 2D image plane in this pixel buffer.
- getPlaneSize() - Method in class ome.io.nio.RomioPixelBuffer
-
- getPlaneSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
-
- getPlaneSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService
-
Get the plane size of the current image.
- getPlaneSize() - Method in class ome.services.RawPixelsBean
-
- getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getPlaneTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPlaneTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPlaneTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPlate() - Method in class pojos.WellData
-
Returns the plate containing this Well.
- getPlateAcquisitions() - Method in class pojos.PlateData
-
Returns the plate acquisitions related to this plate.
- getPlates() - Method in class pojos.ScreenData
-
Returns the plates contained in this screen.
- getPlateType() - Method in class pojos.PlateData
-
Returns the type of plate e.g.
- getPockelCell() - Method in class pojos.ChannelData
-
Returns the Pockels cell settings.
- getPoint(double) - Method in class ome.util.math.geom2D.Line
-
Returns the point of this line defined by k
.
- getPoint(double) - Method in class ome.util.math.geom2D.Segment
-
Returns the point of this line defined by k
.
- getPoints(long, Session) - Method in class ome.services.roi.GeomTool
-
- getPoints() - Method in class ome.util.math.geom2D.EllipseArea
-
Implemented as specified by the
PlaneArea
I/F.
- getPoints() - Method in interface ome.util.math.geom2D.PlaneArea
-
Returns an array of
PlanePoint
contained in the PlaneArea.
- getPoints() - Method in class ome.util.math.geom2D.RectangleArea
-
Implemented as specified by the
PlaneArea
I/F.
- getPoints() - Method in class pojos.PolygonData
-
Returns the points in the polygon.
- getPoints() - Method in class pojos.PolylineData
-
Returns the points in the Polyline.
- getPoints1() - Method in class pojos.PolygonData
-
Returns the points in the polygon.
- getPoints1() - Method in class pojos.PolylineData
-
Returns the points in the Polyline.
- getPoints2() - Method in class pojos.PolygonData
-
Returns the points in the polygon.
- getPoints2() - Method in class pojos.PolylineData
-
Returns the points in the Polyline.
- getPoints_async(AMD_IRoi_getPoints, long, Current) - Method in class ome.services.blitz.impl.RoiI
-
- getPojoTypes() - Method in class ome.logic.TypesImpl
-
- getPort() - Method in class ome.system.Server
-
simple getter for the port passed into the constructor or the default
port if none.
- getPositionX() - Method in class pojos.ImageAcquisitionData
-
Returns the x-coordinate in the frame microscope.
- getPositionX() - Method in class pojos.WellSampleData
-
Returns the position X.
- getPositionY() - Method in class pojos.ImageAcquisitionData
-
Returns the y-coordinate in the frame microscope.
- getPositionY() - Method in class pojos.WellSampleData
-
Returns the position Y.
- getPositionZ() - Method in class pojos.ImageAcquisitionData
-
Returns the z-coordinate in the frame microscope.
- getPower() - Method in class pojos.LightSourceData
-
Returns the power of the light source.
- getPrefix() - Method in class ome.system.ServiceFactory
-
- getPrefix() - Method in class ome.tools.spring.InternalServiceFactory
-
- getPrefix() - Method in class ome.tools.spring.ManagedServiceFactory
-
- getPrepareStatementCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getPrincipal(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
-
- getPrincipal() - Method in class ome.security.basic.BasicEventContext
-
- getPrincipal() - Method in class ome.services.util.ExecutionThread
-
- getPrincipal() - Method in class omero.cmd.SessionI
-
- getProcessedIds(String) - Method in class ome.services.graphs.GraphState
-
Get the set of ids which were actually processed.
- getProject(long) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getProjectID() - Method in class ome.formats.importer.ImportContainer
-
- getProjections(IObject) - Method in class ome.services.search.FullText
-
- getProjectionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getProjectionService() - Method in class ome.system.ServiceFactory
-
- getProjects() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getProjects(List<Long>, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getProjects(List<Long>, boolean) - Method in interface ome.services.blitz.gateway.services.DataService
-
Get the projects in the users.
- getProjects(List<Long>, boolean) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
-
- getProjects() - Method in class pojos.DatasetData
-
Returns a set of projects containing the dataset.
- getProjectsForDataset(long) - Method in interface ome.api.IAnalysis
-
- getProjectsForUser(long) - Method in interface ome.api.IAnalysis
-
- getProperties() - Method in class ome.security.auth.FilePasswordProvider
-
- getProperties() - Method in class omero.client
-
Returns the active properties
for this instance.
- 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.
- getProperty(String) - Method in class omero.client
-
Returns the property value for this key or the empty string if none.
- getPropertyMap() - Method in class omero.client
-
Returns all properties which are prefixed with "omero." or "Ice."
- getPropertyMap(Properties) - Method in class omero.client
-
Returns all properties which are prefixed with "omero." or "Ice."
- getProtocolDescription() - Method in class pojos.ScreenData
-
Returns the description of the protocol.
- getProtocolIdentifier() - Method in class pojos.ScreenData
-
Returns the identifier of the protocol.
- getProvider(ChecksumType) - Method in interface ome.util.checksum.ChecksumProviderFactory
-
- getProvider(ChecksumType) - Method in class ome.util.checksum.ChecksumProviderFactoryImpl
-
- getProxiedObject(T) - Static method in class ome.services.fulltext.BridgeHelper
-
Simpler wrapper to handle superclass proxy objects (e.g.
- getProxy() - Method in class ome.services.blitz.impl.ScriptProcessI
-
- getProxy(Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- getProxy() - Method in class ome.services.blitz.util.RegisterServantMessage
-
- getProxyOrNull(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.Ring
-
- getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
-
Returns null early if the
Current
has already once been
routed by a
Redirector
implementation, returns an existing
session if it can be found, or returns a null.
- getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ConfigRedirector
-
Create or retrieve and returns a SessionPrx
which the current
method takes control of.
- getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.NullRedirector
-
Always returns null
- getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in interface ome.services.blitz.redirect.Redirector
-
Create or retrieve and returns a SessionPrx
which the current
method takes control of.
- getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ScaleRedirector
-
- getQuantumDef() - Method in class ome.services.RenderingBean
-
- getQuantumDef() - Method in interface omeis.providers.re.RenderingEngine
-
Returns the quantization object.
- getQuantumDef_async(AMD_RenderingEngine_getQuantumDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getQuantumDef_async(AMD_RenderingEngine_getQuantumDef, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getQuantumManager() - Method in class omeis.providers.re.Renderer
-
Returns the object that manages and allows to retrieve the objects that
are used to quantize wavelength data.
- getQueries() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
Get all executed query strings
- getQueryCacheHitCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getQueryCacheMissCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getQueryCachePutCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getQueryExecutionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getQueryExecutionMaxTime() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getQueryExecutionMaxTimeQueryString() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getQueryFactory() - Method in class ome.logic.AbstractLevel1Service
-
- getQueryFactory() - Method in class ome.logic.AbstractLevel2Service
-
- getQueryService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getQueryService() - Method in class ome.system.ServiceFactory
-
- getQueryStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
Query statistics from query string (HQL or SQL)
- getRadiusX() - Method in class pojos.EllipseData
-
Returns the radius along the X-axis.
- getRadiusY() - Method in class pojos.EllipseData
-
Returns the radius along the Y-axis.
- getRating() - Method in class pojos.RatingAnnotationData
-
Returns the rating value.
- getRawFileStoreService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Return the raw file store service.
- getRawPixelsStoreService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Return the raw pixels store service.
- getRawPlane(long, int, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Get the raw plane from the server with id pixelsId, and channels, c, timepoint
t, and z-section z.
- getRawPlane(long, int, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- getReader() - Method in class ome.formats.importer.ImportContainer
-
- getReader() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the current Bio-Formats reader that has been used to populate
the container store.
- getReader() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getReaderNames() - Static method in class ome.services.util.DBEnumCheck
-
- getReaderType(String) - Method in class ome.formats.importer.ImportCandidates
-
Retrieve reader type for file specified in path
- getReagentsCounts() - Method in class pojos.WellData
-
Returns the number of reagents linked to the object, key: id of the user,
value: number of annotation.
- getReagentSetDescripion() - Method in class pojos.ScreenData
-
Returns the description of the reagent set.
- getReagentSetIdentifier() - Method in class pojos.ScreenData
-
Returns the identifier of the Reagent set.
- getRed() - Method in class pojos.WellData
-
Returns the red component of the color associated to the well,
or -1
.
- getRedBand() - Method in class omeis.providers.re.RGBBuffer
-
Returns the data buffer for the red band.
- getRedirect(Redirector.Context) - Method in class ome.services.blitz.redirect.AbstractRedirector
-
Returns the current redirect, to which all calls to
#getProxyOrNull(String, Glacier2.SessionControlPrx, Ice.Current)
will be pointed.
- 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.
- getReference() - Method in class pojos.ImageData
-
Returns the reference to the file to register.
- getReferenceCache() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the current reference cache.
- getReferenceCache() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getReferenceCount(String) - Method in interface ome.api.ISession
-
Retrieves the current reference count for the given uuid.
- getReferenceCount(String) - Method in class ome.services.sessions.SessionBean
-
- getReferenceCount(String) - Method in interface ome.services.sessions.SessionManager
-
Return the number of client which are presumed to be attached to this
session or throw an exception if there's no such session.
- getReferenceCount(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getReferenceCount_async(AMD_ISession_getReferenceCount, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getReferenceStringCache() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the current string based reference cache.
- getReferenceStringCache() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getRefPlateId() - Method in class pojos.PlateAcquisitionData
-
Returns the id of the plate of reference.
- getRefractiveIndex() - Method in class pojos.ImageAcquisitionData
-
Returns the refractive index of the objective.
- getRegion(int, long) - Method in interface ome.api.RawPixelsStore
-
- getRegion(Integer, Long) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getRegion(Integer, Long) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getRegion(Integer, Long) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getRegion(Integer, Long) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a region from this pixel buffer.
- getRegion(Integer, Long) - Method in class ome.io.nio.RomioPixelBuffer
-
- getRegion(int, long) - Method in class ome.services.RawPixelsBean
-
- getRegion() - Method in class omeis.providers.re.data.PlaneDef
-
Returns the region to render.
- getRegion_async(AMD_RawPixelsStore_getRegion, int, long, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getRegion_async(AMD_RawPixelsStore_getRegion, int, long, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getRegionDirect(Integer, Long, byte[]) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a region from this pixel buffer directly.
- getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
-
- getRegistry() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
-
- getRegistry() - Method in class ome.services.blitz.util.BlitzConfiguration
-
- getRelationship(String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Walks both the #locksHolder
and the #lockedByHolder
data
for "from" argument to see if there is any direct relationship to the
"to" argument.
- getRelationship(String, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getRenderedImage(long, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getRenderedImage(long, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Render image as Buffered image.
- getRenderedImage(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- getRenderedImage(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
- getRenderedImage(long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService
-
Render image as Buffered image.
- getRenderedImageMatrix(long, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getRenderedImageMatrix(long, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Render image as 3d matrix.
- getRenderedImageMatrix(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- getRenderedImageMatrix(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
- getRenderedImageMatrix(long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService
-
Render image as 3d matrix.
- getRenderingDef() - Method in class omeis.providers.re.Renderer
-
Returns the settings that define the transformation context.
- getRenderingDefId() - Method in interface ome.api.ThumbnailStore
-
Return the id of the RenderingDef
loaded in this instance.
- getRenderingDefId() - Method in class ome.services.RenderingBean
-
- getRenderingDefId() - Method in class ome.services.ThumbnailBean
-
- getRenderingDefId() - Method in interface omeis.providers.re.RenderingEngine
-
- getRenderingDefId_async(AMD_RenderingEngine_getRenderingDefId, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getRenderingDefId_async(AMD_ThumbnailStore_getRenderingDefId, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- getRenderingDefId_async(AMD_RenderingEngine_getRenderingDefId, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getRenderingService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Return the rendering service.
- getRenderingSettings(long) - Method in interface ome.api.IRenderingSettings
-
Returns the default rendering settings for a given pixels for the
current user.
- getRenderingSettings(long) - Method in class ome.logic.RenderingSettingsImpl
-
- getRenderingSettings_async(AMD_IRenderingSettings_getRenderingSettings, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
-
- getRenderingSettingsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getRenderingSettingsService() - Method in class ome.system.ServiceFactory
-
- getReorderedPixelOffset(int, int, int) - Static method in class ome.io.nio.ReorderedPixelData
-
Returns the re-ordered pixel offset.
- getRepositoryInfoService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getRepositoryInfoService() - Method in class ome.system.ServiceFactory
-
- getRepositorySpace() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getRepoUuid() - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- getRequest(Current) - Method in class omero.cmd.HandleI
-
- getResolutionLevel() - Method in interface ome.api.RawPixelsStore
-
- getResolutionLevel() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getResolutionLevel() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getResolutionLevel() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getResolutionLevel() - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the active resolution level.
- getResolutionLevel() - Method in class ome.io.nio.RomioPixelBuffer
-
- getResolutionLevel() - Method in class ome.services.RawPixelsBean
-
- getResolutionLevel() - Method in class ome.services.RenderingBean
-
- getResolutionLevel() - Method in class omeis.providers.re.Renderer
-
Retrieves the active resolution level.
- getResolutionLevel() - Method in interface omeis.providers.re.RenderingEngine
-
- getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
-
- getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getResolutionLevels() - Method in interface ome.api.RawPixelsStore
-
- getResolutionLevels() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getResolutionLevels() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getResolutionLevels() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getResolutionLevels() - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the number of resolution levels that the backing
pixels pyramid contains.
- getResolutionLevels() - Method in class ome.io.nio.RomioPixelBuffer
-
- getResolutionLevels() - Method in class ome.services.RawPixelsBean
-
- getResolutionLevels() - Method in class ome.services.RenderingBean
-
- getResolutionLevels() - Method in class omeis.providers.re.Renderer
-
Retrieves the number of resolution levels that the backing
pixels pyramid contains.
- getResolutionLevels() - Method in interface omeis.providers.re.RenderingEngine
-
- getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
-
- getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getResponse() - Method in class ome.services.blitz.impl.commands.SaveI
-
- getResponse() - Method in class omero.cmd.basic.DoAllI
-
- getResponse() - Method in class omero.cmd.basic.ListRequestsI
-
- getResponse() - Method in class omero.cmd.basic.TimingI
-
- getResponse() - Method in class omero.cmd.CmdCallbackI
-
Returns possibly null Response value.
- getResponse() - Method in class omero.cmd.graphs.ChgrpI
-
- getResponse() - Method in class omero.cmd.graphs.ChmodI
-
- getResponse() - Method in class omero.cmd.graphs.ChownI
-
- getResponse() - Method in class omero.cmd.graphs.DeleteI
-
- getResponse() - Method in class omero.cmd.graphs.GraphSpecListI
-
- getResponse(Current) - Method in class omero.cmd.HandleI
-
- getResponse() - Method in class omero.cmd.Helper
-
- getResponse() - Method in interface omero.cmd.IRequest
-
Returns the current response value.
- getResponses() - Method in class ome.services.blitz.impl.ProcessorCallbackI
-
Return the number of times this instance has been called in a thread
safe manner.
- getResults(int, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
-
- getResults() - Method in class ome.services.delete.QueryConstraints
-
- getResults(ProcessPrx, Current) - Method in class omero.grid.InteractiveProcessorI
-
- getResultSet() - Method in class ome.tools.hibernate.SqlArray
-
- getResultSet(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
-
- getResultSet(long, int) - Method in class ome.tools.hibernate.SqlArray
-
- getResultSet(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
-
- getResultsString(Object, IdentityHashMap<Object, String>) - Method in class ome.services.util.ServiceHandler
-
public for testing purposes.
- getResultTypes() - Method in class ome.logic.TypesImpl
-
- getRevision(Class) - Static method in class ome.system.Version
-
- getRGBA(int) - Method in class ome.services.RenderingBean
-
- getRGBA(int) - Method in interface omeis.providers.re.RenderingEngine
-
Returns a 4D-array representing the color associated to the specified
channel.
- getRGBA_async(AMD_RenderingEngine_getRGBA, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- getRGBA_async(AMD_RenderingEngine_getRGBA, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getRing() - Method in class ome.services.blitz.util.BlitzConfiguration
-
- getROI() - Method in class pojos.util.ROIComponent
-
Returns all the ROI in the component as a list.
- getROI() - Method in class pojos.util.UploadMask
-
Returns the ROIs created from uploading the images.
- getROICoordinate() - Method in class pojos.ShapeData
-
Returns the ROICoordinate for the ShapeData.
- getRoiIds() - Method in class ome.services.blitz.measurements.MeasurementStore
-
- getRoiIds() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
-
Returns the ids of all Roi instances created during the save method.
- getRoiMeasurements_async(AMD_IRoi_getRoiMeasurements, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
-
- getRoiService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getRoiStats_async(AMD_IRoi_getRoiStats, long, Current) - Method in class ome.services.blitz.impl.RoiI
-
- getRoot() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getRoot() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getRoot() - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
-
Return the root class for this hierarchy.
- getRoot() - Method in class ome.services.graphs.AnnotationGraphSpec
-
- getRoot() - Method in class ome.services.graphs.LightSourceGraphSpec
-
- getRootId() - Method in class ome.system.Roles
-
- getRootName() - Method in class ome.system.Roles
-
- getRouter(Communicator) - Static method in class omero.client
-
Acquires the default router
,
and throws an exception if it is not of type {Glacier2.RouterPrx}.
- getRow(int, int, int, int) - Method in interface ome.api.RawPixelsStore
-
- getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getRow(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getRow(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a particular row or scanline from this pixel buffer.
- getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getRow(int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- getRow() - Method in class pojos.WellData
-
Returns the row used to indicate the location of the well on the grid.
- getRow_async(AMD_RawPixelsStore_getRow, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getRow_async(AMD_RawPixelsStore_getRow, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a particular row or scanline from this pixel buffer.
- getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
-
- getRowOffset(int, int, int, int) - Method in interface ome.api.RawPixelsStore
-
- getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getRowOffset(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the offset for a particular row or scanline in this pixel
buffer.
- getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getRowOffset(int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- getRowOffset_async(AMD_RawPixelsStore_getRowOffset, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getRowOffset_async(AMD_RawPixelsStore_getRowOffset, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getRowSequenceIndex() - Method in class pojos.PlateData
-
Returns the index indicating how to label a row.
- getRowSize() - Method in interface ome.api.RawPixelsStore
-
- getRowSize() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getRowSize() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getRowSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getRowSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getRowSize() - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the in memory size of a row or scanline of pixels in this
pixel buffer.
- getRowSize() - Method in class ome.io.nio.RomioPixelBuffer
-
- getRowSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
-
- getRowSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService
-
Get the plane size of the current image.
- getRowSize() - Method in class ome.services.RawPixelsBean
-
- getRowSize_async(AMD_RawPixelsStore_getRowSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getRowSize_async(AMD_RawPixelsStore_getRowSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getScalingFactor() - Method in class ome.io.nio.SimpleBackOff
-
- getScheduledDeletes() - Method in class ome.services.delete.Deletion
-
- getScore(IObject) - Method in class ome.services.search.FullText
-
- getScreens() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getScreens() - Method in class pojos.PlateData
-
Returns a set of screens containing the plate.
- getScriptDir() - Method in class ome.services.scripts.ScriptRepoHelper
-
Returns the actual root of this repository.
- getScriptID_async(AMD_IScript_getScriptID, String, Current) - Method in class ome.services.blitz.impl.ScriptI
-
Get the id of the official script with given path.
- getScriptRepository(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
-
- getScripts_async(AMD_IScript_getScripts, Current) - Method in class ome.services.blitz.impl.ScriptI
-
Get Scripts will return all the scripts by id and name available on the
server.
- getScriptService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getScriptText_async(AMD_IScript_getScriptText, long, Current) - Method in class ome.services.blitz.impl.ScriptI
-
Return the script with the name to the user.
- getScriptWithDetails_async(AMD_IScript_getScriptWithDetails, long, Current) - Method in class ome.services.blitz.impl.ScriptI
-
Return the script with the name to the user.
- getSecondLevelCacheHitCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getSecondLevelCacheMissCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getSecondLevelCachePutCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getSecondLevelCacheRegionNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
Get all second-level cache region names
- getSecondLevelCacheStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
Second level cache statistics per region
- getSecurityContexts(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getSecurityRoles() - Method in interface ome.api.IAdmin
-
returns the active
Roles
in use by the server.
- getSecurityRoles() - Method in class ome.logic.AdminImpl
-
- getSecurityRoles() - Method in class ome.security.basic.BasicSecuritySystem
-
- getSecurityRoles() - Method in interface ome.security.SecuritySystem
-
- getSecurityRoles() - Method in class ome.security.SecuritySystemHolder
-
- getSecurityRoles() - Method in class ome.security.sharing.SharingSecuritySystem
-
- getSecurityRoles_async(AMD_IAdmin_getSecurityRoles, Current) - Method in class ome.services.blitz.impl.AdminI
-
- getSecuritySystem() - Method in class ome.logic.AbstractLevel2Service
-
- getSelectedFile() - Method in class ome.formats.importer.util.ErrorContainer
-
- getSerialNumber() - Method in class pojos.DetectorData
-
Returns the serial number of the detector.
- getSerialNumber() - Method in class pojos.DichroicData
-
Returns the serial number.
- getSerialNumber() - Method in class pojos.FilterData
-
Returns the serial number.
- getSerialNumber() - Method in class pojos.FilterSetData
-
Returns the serial number.
- getSerialNumber() - Method in class pojos.LightSourceData
-
Returns the serial number of the light source.
- getSerialNumber() - Method in class pojos.ObjectiveData
-
Returns the serial number of the objective.
- getSeries() - Method in class ome.io.bioformats.BfPixelBuffer
-
Retrieves the current series of the underlying Bio-Formats reader.
- getSeries(Pixels) - Method in class ome.io.nio.PixelsService
-
Retrieves the series for a given set of pixels.
- getServant(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getServant() - Method in class ome.services.blitz.util.RegisterServantMessage
-
- getServantList() - Method in class omero.util.ServantHolder
-
- getServerFileMimetype() - Method in class pojos.FileAnnotationData
-
Returns the file format as defined by the specification, corresponding to
the file extension.
- getServerList() - Method in class ome.formats.importer.ImportConfig
-
- getServerPort() - Method in class ome.formats.importer.util.IniFileLoader
-
- getServerTime() - Method in interface ome.api.IConfig
-
checks the current server for it's time.
- getServerTime() - Method in class ome.logic.ConfigImpl
-
- getServerTime_async(AMD_IConfig_getServerTime, Current) - Method in class ome.services.blitz.impl.ConfigI
-
- getService() - Method in interface ome.services.util.Executor
-
- getService() - Method in class ome.services.util.Executor.Impl
-
- 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.
- getServiceCleanups() - Method in class ome.security.basic.BasicEventContext
-
- getServiceFactory() - Method in class ome.formats.OMEROMetadataStoreClient
-
Returns the currently active service factory.
- getServiceFactory(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
-
- getServiceFactory(String, String) - Method in class ome.services.blitz.fire.SessionManagerI
-
- getServiceFactory(Identity) - Method in class ome.services.blitz.fire.SessionManagerI
-
- getServiceFactory() - Method in class omero.client
-
Deprecated.
- getServiceFactory() - Method in class omero.cmd.Helper
-
- getServiceFactoryIdentity(Current) - Method in class ome.services.blitz.fire.SessionManagerI
-
- getServiceInterface() - Method in class ome.logic.AdminImpl
-
- getServiceInterface() - Method in class ome.logic.ConfigImpl
-
- getServiceInterface() - Method in class ome.logic.LdapImpl
-
- getServiceInterface() - Method in class ome.logic.MetadataImpl
-
Returns the Interface implemented by this class.
- getServiceInterface() - Method in class ome.logic.PixelsImpl
-
Returns the interface this implementation is for.
- getServiceInterface() - Method in class ome.logic.PojosImpl
-
Returns the Interface implemented by this class.
- getServiceInterface() - Method in class ome.logic.QueryImpl
-
- getServiceInterface() - Method in class ome.logic.RenderingSettingsImpl
-
Returns the interface this implementation is for.
- getServiceInterface() - Method in class ome.logic.RepositoryInfoImpl
-
- getServiceInterface() - Method in class ome.logic.TypesImpl
-
- getServiceInterface() - Method in class ome.logic.UpdateImpl
-
- getServiceInterface() - Method in class ome.services.delete.DeleteBean
-
- getServiceInterface() - Method in class ome.services.JobBean
-
- getServiceInterface() - Method in class ome.services.projection.ProjectionBean
-
Returns the interface this implementation is for.
- getServiceInterface() - Method in class ome.services.RawFileBean
-
- getServiceInterface() - Method in class ome.services.RawPixelsBean
-
- getServiceInterface() - Method in class ome.services.RenderingBean
-
Returns the service corresponding to this class.
- getServiceInterface() - Method in class ome.services.SearchBean
-
- getServiceInterface() - Method in class ome.services.sessions.SessionBean
-
- getServiceInterface() - Method in class ome.services.sharing.ShareBean
-
- getServiceInterface() - Method in class ome.services.ThumbnailBean
-
- getServiceInterface() - Method in interface ome.system.SelfConfigurableService
-
- getServiceKey() - Method in class ome.services.blitz.util.ExpiredServantMessage
-
- getSession(String) - Method in interface ome.api.ISession
-
Retrieves the session associated with this uuid, updating the last access
time as well.
- getSession(String) - Method in class ome.services.sessions.SessionBean
-
- getSession() - Method in interface ome.services.sessions.SessionContext
-
- getSession() - Method in class ome.services.sessions.SessionContextImpl
-
- getSession() - Method in class ome.system.ServiceFactory
-
- getSession() - Method in class ome.system.SessionInitializer
-
- getSession() - Method in class ome.tools.hibernate.SessionFactory
-
Returns a session active for the current thread.
- getSession() - Method in class omero.client
-
- getSession() - Method in class omero.cmd.Helper
-
- getSession() - Method in class omero.model.DetailsI
-
- getSession() - Method in class omero.util.RPSTileLoop
-
- getSession() - Method in class omero.util.ServantHolder
-
- getSession_async(AMD_ISession_getSession, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- getSessionCloseCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getSessionContext(String) - Method in class ome.services.sessions.state.SessionCache
-
Retrieve a session possibly raising either
RemovedSessionException
or SessionTimeoutException
.
- getSessionFactory() - Method in class ome.logic.AbstractLevel1Service
-
delegates to HibernateDaoSupport
to get the current
SessionFactory
- getSessionId() - Method in class ome.formats.importer.util.FileUploader
-
- getSessionId() - Method in class ome.services.messages.AbstractSessionMessage
-
- getSessionId() - Method in class omero.client
-
Returns the UUID for the current session without making a remote call.
- getSessionInitializer() - Method in class ome.system.ServiceFactory
-
- getSessionOpenCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getSessionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getSessionService() - Method in class ome.system.ServiceFactory
-
- getSessionStats(String) - Method in interface ome.services.sessions.SessionManager
-
Return the
SessionStats
which are being counted for the given
session or throw an exception if it has been removed.
- getSessionStats(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getSetting() - Method in interface ome.api.ILdap
-
Gets config value from properties.
- getSetting() - Method in class ome.logic.LdapImpl
-
- getSetting_async(AMD_ILdap_getSetting, Current) - Method in class ome.services.blitz.impl.LdapI
-
- getSettings(long) - Method in class ome.services.ThumbnailCtx
-
Retrieves the RenderingDef object for a given Pixels ID.
- getSha1() - Method in class ome.io.nio.RomioPixelBuffer
-
- getShapeCount() - Method in class pojos.ROIData
-
Returns the number of shapes in the ROI.
- getShapes(int, int) - Method in class pojos.ROIData
-
Returns the list of shapes on a given plane.
- getShapeSettings() - Method in class pojos.ShapeData
-
Returns the settings associated to the shape.
- getShapesInRange(ROICoordinate, ROICoordinate) - Method in class pojos.ROIData
-
Returns an iterator of the Shapes in the ROI in the range [start, end].
- getShapeStats_async(AMD_IRoi_getShapeStats, long, Current) - Method in class ome.services.blitz.impl.RoiI
-
- getShapeStatsList_async(AMD_IRoi_getShapeStatsList, List<Long>, Current) - Method in class ome.services.blitz.impl.RoiI
-
- getShare(long) - Method in interface ome.api.IShare
-
Gets a share as a Session
with all related:
comments
,
members
, fully loaded.
- getShare(long) - Method in class ome.services.sharing.ShareBean
-
- getShare_async(AMD_IShare_getShare, long, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getShareIfAccessible(long) - Method in class ome.services.sharing.ShareBean
-
Loads share and checks it's owner and member data against the current
context (owner/member/admin).
- getShareIfAccessible(long, boolean, long) - Method in class ome.services.sharing.ShareStore
-
Loads share and checks it's owner and member data against the current
context (owner/member/admin).
- getShares(long, boolean, boolean) - Method in class ome.services.sharing.BlobShareStore
-
- getShares(long, boolean, boolean) - Method in class ome.services.sharing.ShareStore
-
- getShareService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getShareService() - Method in class ome.system.ServiceFactory
-
- getSharesOwnedBy(Experimenter, boolean) - Method in interface ome.api.IShare
-
Gets all shares owned by the given Experimenter
.
- getSharesOwnedBy(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
-
- getSharesOwnedBy_async(AMD_IShare_getSharesOwnedBy, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
-
- getSize() - Method in class ome.util.mem.CopiableArray
-
Returns the number of elements in the array.
- getSizeC() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getSizeC() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getSizeC() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getSizeC() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getSizeC() - Method in interface ome.io.nio.PixelBuffer
-
Delegates to Pixels.getSizeC()
.
- getSizeC() - Method in class ome.io.nio.RomioPixelBuffer
-
- getSizeC() - Method in class pojos.PixelsData
-
Returns the number of channels.
- getSizeT() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getSizeT() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getSizeT() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getSizeT() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getSizeT() - Method in interface ome.io.nio.PixelBuffer
-
Delegates to Pixels.getSizeT()
.
- getSizeT() - Method in class ome.io.nio.RomioPixelBuffer
-
- getSizeT() - Method in class pojos.PixelsData
-
Returns the number of time-points.
- getSizeX() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getSizeX() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getSizeX() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getSizeX() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getSizeX() - Method in interface ome.io.nio.PixelBuffer
-
Delegates to Pixels.getSizeX()
.
- getSizeX() - Method in class ome.io.nio.RomioPixelBuffer
-
- getSizeX() - Method in class pojos.OTFData
-
Returns the size along the X-axis.
- getSizeX() - Method in class pojos.PixelsData
-
Returns the number of pixels along the X-axis.
- 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.
- getSizeY() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getSizeY() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getSizeY() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getSizeY() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getSizeY() - Method in interface ome.io.nio.PixelBuffer
-
Delegates to Pixels.getSizeY()
.
- getSizeY() - Method in class ome.io.nio.RomioPixelBuffer
-
- getSizeY() - Method in class pojos.OTFData
-
Returns the size along the Y-axis.
- getSizeY() - Method in class pojos.PixelsData
-
Returns the number of pixels along the Y-axis.
- getSizeZ() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getSizeZ() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getSizeZ() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getSizeZ() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getSizeZ() - Method in interface ome.io.nio.PixelBuffer
-
Delegates to Pixels.getSizeZ()
.
- getSizeZ() - Method in class ome.io.nio.RomioPixelBuffer
-
- getSizeZ() - Method in class pojos.PixelsData
-
Returns the number of pixels along the Z-axis.
- getSlice() - Method in class omeis.providers.re.data.PlaneDef
-
Returns an identifier to tell which kind of plane this object identifies.
- getSourceObject(LSID) - Method in interface ome.formats.model.IObjectContainerStore
-
Retrieves an OMERO Blitz source object for a given LSID.
- getSourceObject(LSID) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getSourceObjects(Class<T>) - Method in interface ome.formats.model.IObjectContainerStore
-
Retrieves all OMERO Blitz source objects of a given class.
- getSourceObjects(Class<T>) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getSql() - Method in class omero.cmd.Helper
-
- getSqlAction() - Method in class ome.services.util.Executor.SimpleWork
-
- getStack(int, int) - Method in interface ome.api.RawPixelsStore
-
- getStack(Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getStack(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getStack(Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getStack(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getStack(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the the entire number of optical sections for a single
wavelength or channel at a particular timepoint in this pixel buffer.
- getStack(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getStack(int, int) - Method in class ome.services.RawPixelsBean
-
- getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getStackDirect(Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the the entire number of optical sections for a single
wavelength or channel at a particular timepoint in this pixel buffer.
- getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
-
- getStackOffset(int, int) - Method in interface ome.api.RawPixelsStore
-
- getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getStackOffset(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getStackOffset(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the offset for the entire number of optical sections
for a single wavelength or channel at a particular timepoint in
this pixel buffer.
- getStackOffset(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getStackOffset(int, int) - Method in class ome.services.RawPixelsBean
-
- getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getStackSize() - Method in interface ome.api.RawPixelsStore
-
- getStackSize() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getStackSize() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getStackSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getStackSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getStackSize() - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the in memory size of the entire number of optical sections
for a single wavelength or channel at a particular timepoint in
this pixel buffer.
- getStackSize() - Method in class ome.io.nio.RomioPixelBuffer
-
- getStackSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
-
- getStackSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService
-
Get the stack size of the current image.
- getStackSize() - Method in class ome.services.RawPixelsBean
-
- getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getStackTrace(Throwable) - Static method in class ome.formats.importer.util.ErrorHandler
-
Return stack trace from throwable
- getStageLabelId() - Method in class pojos.ImageAcquisitionData
-
Returns the id of the StageLabel
or -1
if not already linked to the image.
- getStart() - Method in class ome.services.delete.Deletion
-
- getStartTime() - Method in class omero.sys.ParametersI
-
Returns the value of the start time
parameter.
- getStartTime() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getStartTime() - Method in class pojos.PlateAcquisitionData
-
Returns the time when the first image was collected.
- getStartTime() - Method in class pojos.WellSampleData
-
Returns the time at which the field was acquired.
- getStatefulServiceCount() - Method in class ome.services.blitz.impl.ServiceFactoryI
-
NB: Much of the logic here is similar to
SessionI.doClose
and should be
pushed down.
- getStatefulServiceCount() - Method in class omero.util.ServantHolder
-
- getStatefulServices() - Method in class omero.client
-
Returns all active StatefulServiceInterface
proxies.
- getStaticDisableHistory() - Method in class ome.formats.importer.ImportConfig
-
- getStaticDisableHistory() - Method in class ome.formats.importer.util.IniFileLoader
-
- getStaticDisableUpgradeCheck() - Method in class ome.formats.importer.ImportConfig
-
- getStaticDisableUpgradeCheck() - Method in class ome.formats.importer.util.IniFileLoader
-
- getStats() - Method in class ome.security.basic.BasicEventContext
-
- getStats() - Method in class ome.security.basic.CurrentDetails
-
- getStats(List<Long>) - Method in class ome.services.roi.GeomTool
-
- getStats() - Method in class omeis.providers.re.Renderer
-
Returns a
RenderingStats
object that the rendering strategy can
use to track performance.
- getStats() - Method in class omeis.providers.re.RenderingStats
-
Returns a stats report ready to be written to the log file.
- getStatus() - Method in class ome.formats.importer.util.ErrorContainer
-
return the error status
- getStatus() - Method in class omero.cmd.CmdCallbackI
-
Returns possibly null Status value.
- getStatus(Current) - Method in class omero.cmd.HandleI
-
- getStatus() - Method in class omero.cmd.Helper
-
- getStatus() - Method in class pojos.PlateData
-
Returns the status of the plate.
- getStatus() - Method in class pojos.WellData
-
Returns the status of the well.
- getStatusOrThrow() - Method in class omero.cmd.CmdCallbackI
-
- getSteps() - Method in class ome.services.delete.Deletion
-
- getSteps() - Method in class omero.cmd.Helper
-
- getStop() - Method in class ome.services.delete.Deletion
-
- getStore() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
- getStrategy(QuantumDef, PixelsType) - Method in class omeis.providers.re.quantum.QuantumFactory
-
Returns a strategy to carry out the quantization process whose context is
defined by pd
.
- getStride() - Method in class omeis.providers.re.data.PlaneDef
-
Returns the stride.
- getStroke() - Method in class pojos.ShapeSettingsData
-
Returns the color of the stroke.
- getStrokeDashArray() - Method in class pojos.ShapeSettingsData
-
Returns the stroke dashes.
- getStrokeWidth() - Method in class pojos.ShapeSettingsData
-
Returns the stroke's width.
- getSubSpec() - Method in class ome.services.graphs.GraphEntry
-
- getSubtypeValue(int, int, Object) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
- getSuccessfulTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getSuperSpec() - Method in class ome.services.graphs.BaseGraphSpec
-
- getSuperSpec() - Method in class ome.services.graphs.GraphEntry
-
- getSuperSpec() - Method in interface ome.services.graphs.GraphSpec
-
Specification of where this
GraphSpec
is attached under another
.
- getSupportedMetadataLevels() - Method in class ome.formats.importer.OMEROWrapper
-
- 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.
- getT() - Method in class pojos.ShapeData
-
Returns the time-point.
- getTable() - Method in class ome.services.blitz.measurements.MeasurementStore
-
- getTable() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
-
Returns the Table proxy which is in use by this service.
- getTable_async(AMD_IRoi_getTable, long, Current) - Method in class ome.services.blitz.impl.RoiI
-
- getTagAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTagAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTagAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTagAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTagAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTagDescription() - Method in class pojos.TagAnnotationData
-
Returns the description of the tag.
- getTagDescriptions() - Method in class pojos.TagAnnotationData
-
Returns the descriptions linked to that tag.
- 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.
- getTaggedObjectsCount(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
-
Implemented as specified by the
IMetadata
I/F
- getTaggedObjectsCount_async(AMD_IMetadata_getTaggedObjectsCount, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
-
- getTags() - Method in class pojos.TagAnnotationData
-
Returns the collection of tags related to this tag.
- getTagValue() - Method in class pojos.TagAnnotationData
-
Returns the text of the tag.
- getTarget() - Method in class ome.formats.importer.ImportContainer
-
- getTarget(Class<T>, long) - Method in class ome.formats.OMEROMetadataStoreClient
-
Helper method to retrieve an object from iQuery
- getTargetType(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
Returns the IObject
type which a given field points to.
- getTempDir() - Method in class omero.util.TempFileManager
-
Returns the directory under which all temporary files and folders will be
created.
- gettempdir() - Static method in class omero.util.TempFileManager
-
- getTemperature() - Method in class pojos.ImageAcquisitionData
-
Returns the temperature in Celcius.
- getTerm() - Method in class pojos.TermAnnotationData
-
Returns the term
.
- getTermAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTermAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTermAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTermAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTermAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTermDescription() - Method in class pojos.TermAnnotationData
-
Returns the description of the term.
- getTermVector() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
- getTestIds() - Method in class ome.tools.RepositoryTask
-
Private method used for testing only.
- getText() - Method in class pojos.EllipseData
-
Returns the text of the shape.
- getText() - Method in class pojos.LineData
-
Returns the text of the shape.
- getText() - Method in class pojos.MaskData
-
Returns the text of the shape.
- getText() - Method in class pojos.PointData
-
Returns the text of the shape.
- getText() - Method in class pojos.PolygonData
-
Returns the text of the shape.
- getText() - Method in class pojos.PolylineData
-
Returns the text of the shape.
- getText() - Method in class pojos.RectangleData
-
Returns the text of the shape.
- getText() - Method in class pojos.TextData
-
Returns the text of the shape.
- getText() - Method in class pojos.TextualAnnotationData
-
Returns the text of this annotation.
- getText() - Method in class pojos.XMLAnnotationData
-
Returns the text of this annotation.
- getThumbnail(Integer, Integer) - Method in interface ome.api.ThumbnailStore
-
Retrieves a thumbnail for a pixels set using a given set of rendering
settings (RenderingDef).
- getThumbnail(Thumbnail) - Method in class ome.io.nio.ThumbnailService
-
Return byte array of Thumbnail
- getThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService
-
Return byte array of Thumbnail, providing byte array
- getThumbnail(long, RInt, RInt, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getThumbnail(long, RInt, RInt) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Get the thumbnail of the image.
- getThumbnail(long, RInt, RInt) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- getThumbnail(long, RInt, RInt) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl
-
- getThumbnail(long, RInt, RInt) - Method in interface ome.services.blitz.gateway.services.ThumbnailService
-
Get the thumbnail of the image.
- getThumbnail(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Get (the path of) the thumbnail image for an image file on the repository.
- getThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnail_async(AMD_ThumbnailStore_getThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- getThumbnailByIndex(String, int, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Get (the path of) the thumbnail image for an image file on the repository.
- getThumbnailByLongestSide(Integer) - Method in interface ome.api.ThumbnailStore
-
Retrieves a thumbnail for a pixels set using a given set of rendering
settings (RenderingDef).
- getThumbnailByLongestSide(long, RInt) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl
-
- getThumbnailByLongestSide(long, RInt) - Method in interface ome.services.blitz.gateway.services.ThumbnailService
-
Get the thumbnail of the image, maintain aspect ratio.
- getThumbnailByLongestSide(Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnailByLongestSide_async(AMD_ThumbnailStore_getThumbnailByLongestSide, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- getThumbnailByLongestSideDirect(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 class ome.services.ThumbnailBean
-
- getThumbnailByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailByLongestSideDirect, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- 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).
- getThumbnailByLongestSideSet(RInt, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl
-
- getThumbnailByLongestSideSet(RInt, List<Long>) - Method in interface ome.services.blitz.gateway.services.ThumbnailService
-
Get a set of thumbnails, maintaining aspect ratio.
- getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
-
- getThumbnailByLongestSideSet_async(AMD_ThumbnailStore_getThumbnailByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- getThumbnailDirect(Integer, Integer) - Method in interface ome.api.ThumbnailStore
-
Retrieves a thumbnail for a pixels set using a given set of rendering
settings (RenderingDef).
- getThumbnailDirect(Integer, Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnailDirect_async(AMD_ThumbnailStore_getThumbnailDirect, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- getThumbnailExists(Thumbnail) - Method in class ome.io.nio.ThumbnailService
-
Returns whether or not a thumbnail exists on disk.
- 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.
- getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnailForSectionByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailForSectionByLongestSideDirect, int, int, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- 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.
- getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnailForSectionDirect_async(AMD_ThumbnailStore_getThumbnailForSectionDirect, int, int, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- getThumbnailIds() - Method in class ome.tools.RepositoryTask
-
This public method is used to return a list of thumbnail ids that require
deletion from the disk repository.
- getThumbnailLength(Thumbnail) - Method in class ome.io.nio.ThumbnailService
-
Returns length of Thumbnail on disk
- getThumbnailOutputStream(Thumbnail) - Method in class ome.io.nio.ThumbnailService
-
Return FileOutputStream of Thumbnail
- getThumbnailPath(Long) - Method in class ome.io.nio.AbstractFileSystemService
-
Returns a numbered path relative to the root of this service, but is
ignorant of FS and similar constructs.
- 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).
- getThumbnailSet(RInt, RInt, List<Long>, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- getThumbnailSet(RInt, RInt, List<Long>) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Get a set of thumbnails.
- getThumbnailSet(RInt, RInt, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- getThumbnailSet(RInt, RInt, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl
-
- getThumbnailSet(RInt, RInt, List<Long>) - Method in interface ome.services.blitz.gateway.services.ThumbnailService
-
Get a set of thumbnails.
- getThumbnailSet(Integer, Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
-
- getThumbnailSet_async(AMD_ThumbnailStore_getThumbnailSet, RInt, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- getThumbnailStoreService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
-
Return the thumbnail service.
- getTie(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getTile(int, int, int, int, int, int, int) - Method in interface ome.api.RawPixelsStore
-
- getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getTile(int, int, int, int, int, int, int, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a tile from this pixel buffer.
- getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getTile(int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- getTile(int, int, int, int, int, int, int) - Method in class omero.util.RPSTileData
-
- getTile(int, int, int, int, int, int, int) - Method in interface omero.util.TileData
-
- getTile_async(AMD_RawPixelsStore_getTile, int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getTile_async(AMD_RawPixelsStore_getTile, int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves a tile from this pixel buffer.
- getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
-
- getTileHeight() - Method in class ome.io.nio.ConfiguredTileSizes
-
- getTileHeight() - Method in interface ome.io.nio.TileSizes
-
- getTileSize() - Method in interface ome.api.RawPixelsStore
-
- getTileSize(Long) - Method in class ome.formats.OMEROMetadataStoreClient
-
Retrieves the suggested tile size for a pixels set.
- getTileSize() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getTileSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getTileSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getTileSize() - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the tile size for the pixel store.
- getTileSize() - Method in class ome.io.nio.RomioPixelBuffer
-
- getTileSize() - Method in class ome.services.RawPixelsBean
-
- getTileSize() - Method in class ome.services.RenderingBean
-
- getTileSize() - Method in class omeis.providers.re.Renderer
-
Retrieves the tile size for the pixel store.
- getTileSize() - Method in interface omeis.providers.re.RenderingEngine
-
- getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
-
- getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- getTileWidth() - Method in class ome.io.nio.ConfiguredTileSizes
-
- getTileWidth() - Method in interface ome.io.nio.TileSizes
-
- getTime() - Method in class pojos.TimeAnnotationData
-
Returns the time value.
- getTimelineService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getTimepoint(int) - Method in interface ome.api.RawPixelsStore
-
- getTimepoint(Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getTimepoint(Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getTimepoint(Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getTimepoint(Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getTimepoint(Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the entire number of optical sections for all
wavelengths or channels at a particular timepoint in this pixel buffer.
- getTimepoint(Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getTimepoint(int) - Method in class ome.services.RawPixelsBean
-
- getTimePoint() - Method in class pojos.ROICoordinate
-
Returns the timepoint.
- getTimepoint_async(AMD_RawPixelsStore_getTimepoint, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getTimepoint_async(AMD_RawPixelsStore_getTimepoint, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getTimepointDirect(Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getTimepointDirect(Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getTimepointDirect(Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the entire number of optical sections for all
wavelengths or channels at a particular timepoint in this pixel buffer.
- getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
-
- getTimepointOffset(int) - Method in interface ome.api.RawPixelsStore
-
- getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPixelBuffer
-
- getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getTimepointOffset(Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getTimepointOffset(Integer) - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the in memory size of the entire number of optical sections for
all wavelengths or channels at a particular timepoint in this
pixel buffer.
- getTimepointOffset(Integer) - Method in class ome.io.nio.RomioPixelBuffer
-
- getTimepointOffset(int) - Method in class ome.services.RawPixelsBean
-
- getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getTimepointSize() - Method in interface ome.api.RawPixelsStore
-
- getTimepointSize() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getTimepointSize() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getTimepointSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getTimepointSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getTimepointSize() - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the in memory size of the entire number of optical sections for
all wavelengths or channels at a particular timepoint in this
pixel buffer.
- getTimepointSize() - Method in class ome.io.nio.RomioPixelBuffer
-
- getTimepointSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
-
- getTimepointSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService
-
Get the timepoint size of the current image.
- getTimepointSize() - Method in class ome.services.RawPixelsBean
-
- getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getTimestampAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTimestampAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTimestampAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTimestampAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getTimestampAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getToken() - Method in class ome.formats.importer.util.ErrorContainer
-
- getTokenUrl() - Method in class ome.formats.importer.ImportConfig
-
- getTopicManager() - Method in class ome.services.blitz.util.BlitzConfiguration
-
- getTotalFoundCount() - Method in class ome.services.graphs.GraphState
-
Return the total number of ids loaded into this instance.
- getTotalProcessedCount() - Method in class ome.services.graphs.GraphState
-
Return the total number of ids which were processed.
- getTotalSize() - Method in interface ome.api.RawPixelsStore
-
- getTotalSize() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getTotalSize() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getTotalSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getTotalSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getTotalSize() - Method in interface ome.io.nio.PixelBuffer
-
Retrieves the in memory size of the entire pixel buffer.
- getTotalSize() - Method in class ome.io.nio.RomioPixelBuffer
-
- getTotalSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
-
- getTotalSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService
-
Get the total size of the current image.
- getTotalSize() - Method in class ome.services.RawPixelsBean
-
- getTotalSize(IObject) - Method in class ome.services.search.FullText
-
- getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- getTransactionAttribute(Method, Class) - Method in class ome.services.sharing.ShareRestrictionTransactionAttributeSource
-
- getTransactionAttribute(Method, Class) - Method in class ome.tools.spring.ForceTransactionAttributeSource
-
- getTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getTransform() - Method in class pojos.ShapeData
-
Returns the transformation.
- getTransmittance() - Method in class pojos.FilterData
-
Returns the cut out tolerance value or -1
.
- getType(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
-
- getType() - Method in class pojos.DetectorData
-
Returns the type of the detector.
- getType() - Method in class pojos.FilterData
-
Returns the type.
- getType() - Method in class pojos.LightSourceData
-
Returns the type of light.
- getTypes(ExtendedMetadata) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
-
Returns all the types that are known for this hierarcy.
- getTypes(ExtendedMetadata) - Method in class ome.services.graphs.AnnotationGraphSpec
-
- getTypes(ExtendedMetadata) - Method in class ome.services.graphs.LightSourceGraphSpec
-
- getTypesService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getTypesService() - Method in class ome.system.ServiceFactory
-
- getUIBounds() - Method in class ome.formats.importer.ImportConfig
-
- getUIBounds() - Method in class ome.formats.importer.util.IniFileLoader
-
- getUndeletedFiles() - Method in class ome.services.delete.Deletion
-
- getUnique() - Method in class omero.sys.ParametersI
-
- getUntied(Identity) - Method in class omero.util.ServantHolder
-
- getUpdated() - Method in class pojos.DataObject
-
Returns the updated time of the object.
- getUpdateEvent(Current) - Method in class omero.model.DetailsI
-
- getUpdateService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- getUpdateService() - Method in class ome.system.ServiceFactory
-
- getUpgradeUrl() - Method in class ome.system.UpgradeCheck
-
- getUploaderTokenURL() - Method in class ome.formats.importer.util.IniFileLoader
-
- getUploaderUrl() - Method in class ome.formats.importer.ImportConfig
-
- getUploaderURL() - Method in class ome.formats.importer.util.IniFileLoader
-
- getUploadUrl() - Method in class ome.formats.importer.util.ErrorContainer
-
- 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.
- getUsageFraction() - Method in class ome.logic.RepositoryInfoImpl
-
Deprecated.
- getUsageFraction_async(AMD_IRepositoryInfo_getUsageFraction, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
-
- getUsedFiles(String) - Method in class ome.formats.importer.ImportCandidates
-
Return string of files used by container item at path
- getUsedFiles() - Method in class ome.formats.importer.ImportContainer
-
- getUsedSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo
-
This method returns the total space in bytes for this file system
including nested subdirectories.
- getUsedSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl
-
Deprecated.
- getUsedSpaceInKilobytes_async(AMD_IRepositoryInfo_getUsedSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
-
- getUseMetadataFile() - Method in class ome.formats.importer.ImportContainer
-
Whether or not we're using an original metadata file.
- getUseQuaqua() - Method in class ome.formats.importer.ImportConfig
-
- getUseQuaqua() - Method in class ome.formats.importer.util.IniFileLoader
-
- getUserAttribute(String) - Method in class ome.security.auth.LdapConfig
-
- getUserDisableHistory() - Method in class ome.formats.importer.ImportConfig
-
- getUserDisableHistory() - Method in class ome.formats.importer.util.IniFileLoader
-
- getUserFilter() - Method in class ome.security.auth.LdapConfig
-
- getUserFullPath() - Method in class ome.formats.importer.ImportConfig
-
- getUserFullPath() - Method in class ome.formats.importer.util.IniFileLoader
-
- getUserGroupId() - Method in class ome.system.Roles
-
- getUserGroupName() - Method in class ome.system.Roles
-
- getUserId() - Method in class ome.services.ThumbnailCtx
-
Retrieves the current user ID to use for queries.
- getUserImages(Parameters) - Method in interface ome.api.IContainer
-
Retrieve a user's images.
- getUserImages(Parameters) - Method in class ome.logic.PojosImpl
-
- getUserImages_async(AMD_IContainer_getUserImages, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
-
- getUserName() - Method in class pojos.ExperimenterData
-
Returns the last name of the experimenter.
- getUserPasswordHash(Long) - Method in class ome.security.auth.PasswordUtil
-
- getUserPixels() - Method in class ome.formats.importer.ImportContainer
-
- getUserRoles(Experimenter) - Method in interface ome.api.local.LocalAdmin
-
Finds the group names for all groups for which the given Experimenter
is
a member.
- getUserRoles(Experimenter) - Method in class ome.logic.AdminImpl
-
- getUserRoles() - Method in interface ome.services.sessions.SessionContext
-
- getUserRoles() - Method in class ome.services.sessions.SessionContextImpl
-
- getUserRoles(String) - Method in interface ome.services.sessions.SessionManager
-
- getUserRoles(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getUserScripts_async(AMD_IScript_getUserScripts, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI
-
- getUserSettingsDirectory() - Method in class ome.formats.importer.ImportConfig
-
- getUserSettingsDirectory() - Method in class ome.formats.importer.util.IniFileLoader
-
- getUserSpecifiedAnnotations() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the user specified annotations.
- getUserSpecifiedAnnotations() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getUserSpecifiedImageDescription() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the user specified image description.
- getUserSpecifiedImageDescription() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getUserSpecifiedImageName() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the user specified image name.
- getUserSpecifiedImageName() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getUserSpecifiedPhysicalPixelSizes() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the user specified physical pixel sizes.
- getUserSpecifiedPhysicalPixelSizes() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getUserSpecifiedPlateDescription() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the user specified plate description.
- getUserSpecifiedPlateDescription() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getUserSpecifiedPlateName() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the user specified plate name.
- getUserSpecifiedPlateName() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getUserSpecifiedTarget() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the user specified linkage target (usually a Dataset for Images
and a Screen for Plates).
- getUserSpecifiedTarget() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getUuid() - Method in class ome.services.db.DatabaseIdentity
-
- getUuid() - Method in class ome.services.scripts.ScriptRepoHelper
-
Uuid of this repository.
- getUuid() - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
-
- getValue() - Method in exception ome.formats.enums.EnumerationException
-
- getValue() - Method in enum ome.formats.Index
-
- getValue(Class<? extends IObject>, int) - Method in class ome.formats.OMEXMLModelComparator
-
Assigns a value to a particular class based on its location in the
OME-XML hierarchy.
- getValue() - Method in class pojos.BooleanAnnotationData
-
Returns the text of this annotation.
- getVersion() - Method in interface ome.api.IConfig
-
Provides the release version.
- getVersion() - Method in class ome.logic.ConfigImpl
-
- getVersion() - Method in class pojos.DataObject
-
Returns the version of the object if the object is immutable,
false
otherwise.
- getVersion_async(AMD_IConfig_getVersion, Current) - Method in class ome.services.blitz.impl.ConfigI
-
- getVersionNote() - Method in class ome.formats.importer.util.IniFileLoader
-
- getVersionNumber() - Method in class ome.formats.importer.ImportConfig
-
- getVersionNumber() - Method in class ome.formats.importer.util.IniFileLoader
-
- getVisibility() - Method in class ome.system.Preference
-
- getVoltage() - Method in class pojos.DetectorData
-
Returns the voltage of the detector.
- getWarmUpFactor() - Method in class ome.io.nio.SimpleBackOff
-
- getWarning() - Method in class ome.services.delete.Deletion
-
- getWavelength() - Method in exception omeis.providers.re.quantum.QuantizationException
-
Returns the index of the wavelength that couldn't be rendered.
- getWellOriginX() - Method in class pojos.PlateData
-
Returns the x-coordinate in 2D-space of the well.
- getWellOriginY() - Method in class pojos.PlateData
-
Returns the y-coordinate in 2D-space of the well.
- getWellSamples() - Method in class pojos.WellData
-
Returns the well samples linked to the well.
- getWellType() - Method in class pojos.WellData
-
Returns a human readable identifier for the screening status e.g. empty,
positive control, etc.
- getWidth() - Method in class omeis.providers.re.data.RegionDef
-
Returns the width of the region.
- getWidth() - Method in class pojos.MaskData
-
Returns the width of the mask.
- getWidth() - Method in class pojos.RectangleData
-
Returns the width untransformed rectangle.
- getWindowEnd() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the upper bound of the input interval.
- getWindowStart() - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the lower bound of the input interval.
- getWorkingDistance() - Method in class pojos.ObjectiveData
-
Returns the working distance.
- 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.
- getX() - Method in class pojos.EllipseData
-
Returns the x-coordinate of the center of the ellipse.
- getX() - Method in class pojos.MaskData
-
Returns the x-coordinate of the top-left corner of the mask.
- getX() - Method in class pojos.PointData
-
Returns the x-coordinate of the shape.
- getX() - Method in class pojos.RectangleData
-
Returns the x-coordinate of the top-left corner of an untransformed
rectangle.
- getX() - Method in class pojos.TextData
-
Returns the x-coordinate text field.
- getX1() - Method in class pojos.LineData
-
Returns the x-coordinate of the starting point of an untransformed line.
- getX2() - Method in class pojos.LineData
-
Returns the x-coordinate of the end point of an untransformed line.
- getXEnd() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
-
Returns the x-coordinate of the pEnd
point.
- getXMLAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getXMLAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getXMLAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getXMLAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getXMLAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- 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.
- getY() - Method in class pojos.EllipseData
-
Returns the y-coordinate of the center of the ellipse.
- getY() - Method in class pojos.MaskData
-
Returns the y-coordinate of the top-left corner of the mask.
- getY() - Method in class pojos.PointData
-
Returns the y coordinate of the shape.
- getY() - Method in class pojos.RectangleData
-
Returns the y-coordinate of the top-left corner of an
untransformed rectangle.
- getY() - Method in class pojos.TextData
-
Returns the y-coordinate text field.
- getY1() - Method in class pojos.LineData
-
Returns the y-coordinate of the starting point of an untransformed line.
- getY2() - Method in class pojos.LineData
-
Returns the y-coordinate of the end point of an untransformed line.
- 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.
- getZ() - Method in class pojos.ShapeData
-
Returns the z-section.
- getZoom() - Method in class pojos.DetectorData
-
Returns the offset of the detector.
- getZSection() - Method in class pojos.ROICoordinate
-
Returns the z-section.
- GlobalMulticaster - Class in ome.services.messages
-
Global
ApplicationEventMulticaster
which can be used to integrate
parent and child
OmeroContext
instances.
- GlobalMulticaster() - Constructor for class ome.services.messages.GlobalMulticaster
-
Keeps track of which instance this is.
- granted(int, int) - Method in class omero.model.PermissionsI
-
- GraphEntry - Class in ome.services.graphs
-
Single value of the map entries from spec.xml.
- GraphEntry(GraphSpec, String) - Constructor for class ome.services.graphs.GraphEntry
-
- GraphEntry(GraphSpec, String, GraphEntry) - Constructor for class ome.services.graphs.GraphEntry
-
- GraphException - Exception in ome.services.graphs
-
Exception which will be thrown by activities within
GraphSpec
implementations.
- GraphException(String) - Constructor for exception ome.services.graphs.GraphException
-
- GraphOpts - Class in ome.services.graphs
-
Manager for option instances for an entire action graph.
- GraphOpts() - Constructor for class ome.services.graphs.GraphOpts
-
- GraphOpts.Op - Enum in ome.services.graphs
-
- GraphSpec - Interface in ome.services.graphs
-
Specification of a graph operation.
- GraphSpecListI - Class in omero.cmd.graphs
-
- GraphSpecListI(OmeroContext) - Constructor for class omero.cmd.graphs.GraphSpecListI
-
- GraphSpecPostProcessor - Class in ome.services.graphs
-
post processor which should be included in all Spring context files with
- GraphSpecPostProcessor() - Constructor for class ome.services.graphs.GraphSpecPostProcessor
-
- GraphState - Class in ome.services.graphs
-
Tree-structure containing all scheduled actions which closely resembles the
tree structure of the
GraphSpec
itself.
- GraphState(EventContext, GraphStepFactory, SqlAction, Session, GraphSpec) - Constructor for class ome.services.graphs.GraphState
-
- GraphStep - Class in ome.services.graphs
-
- GraphStep(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.graphs.GraphStep
-
- GraphStep.Callback - Interface in ome.services.graphs
-
- GraphStepFactory - Interface in ome.services.graphs
-
- GraphTables - Class in ome.services.graphs
-
- GraphTables() - Constructor for class ome.services.graphs.GraphTables
-
- GREEN_INDEX - Static variable in class ome.formats.model.ColorsFactory
-
Index of the red component of a color.
- GREEN_INDEX - Static variable in class omeis.providers.re.ColorsFactory
-
Index of the red component of a color.
- GREEN_TEXT - Static variable in class ome.formats.model.ChannelProcessor
-
Name of the green
component when it is a graphics image.
- group - Variable in class ome.formats.importer.ImportConfig
-
- group - Variable in class ome.system.Principal
-
- GROUP_COLLAB_READ - Static variable in class ome.formats.importer.ImportEvent
-
- GROUP_COLLAB_READ_LINK - Static variable in class ome.formats.importer.ImportEvent
-
- GROUP_EXPERIMENTER_MAP - Static variable in class pojos.ExperimenterData
-
Identifies the Experimenter#GROUPEXPERIMENTERMAP
field.
- GROUP_EXPERIMENTER_MAP - Static variable in class pojos.GroupData
-
Identifies the ExperimenterGroup#GROUPEXPERIMENTERMAP
field.
- GROUP_PRIVATE - Static variable in class ome.formats.importer.ImportEvent
-
- GROUP_PUBLIC - Static variable in class ome.formats.importer.ImportEvent
-
- GROUP_SYSTEM - Static variable in class ome.formats.importer.ImportEvent
-
- GroupAttributeMapper - Class in ome.security.auth
-
- GroupAttributeMapper(LdapConfig) - Constructor for class ome.security.auth.GroupAttributeMapper
-
- GroupChmodStrategy - Class in ome.security.basic
-
ChmodStrategy
which only permits modifying
the permissions on groups.
- GroupChmodStrategy(BasicACLVoter, SessionFactory, SqlAction, ExtendedMetadata) - Constructor for class ome.security.basic.GroupChmodStrategy
-
- GroupData - Class in pojos
-
The data that makes up an OME Group along with the various members of
the Group
- GroupData() - Constructor for class pojos.GroupData
-
Creates a new instance.
- GroupData(ExperimenterGroup) - Constructor for class pojos.GroupData
-
Creates a new instance.
- groupInfo(SqlAction) - Method in class ome.services.graphs.BaseGraphSpec
-
- groupInfo(SqlAction) - Method in interface ome.services.graphs.GraphSpec
-
- groupName - Variable in class ome.formats.importer.ImportEvent.GROUP_SET
-
- groupProxy(Long) - Method in interface ome.api.local.LocalAdmin
-
returns a possibly uninitialized proxy for the given
group id
.
- groupProxy(String) - Method in interface ome.api.local.LocalAdmin
-
returns a possibly uninitialized proxy for the given
group name
.
- groupProxy(Long) - Method in class ome.logic.AdminImpl
-
- groupProxy(String) - Method in class ome.logic.AdminImpl
-
- groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.AttributeNewUserGroupBean
-
- groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in interface ome.security.auth.NewUserGroupBean
-
- groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.OrgUnitNewUserGroupBean
-
- groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.QueryNewUserGroupBean
-
- groupType - Variable in class ome.formats.importer.ImportEvent.GROUP_SET
-
- grp(RLong) - Method in class omero.sys.ParametersI
-
Sets the value of the group
parameter.
- GUEST - Static variable in class ome.system.Login
-
CopyOfLogin
constant which has username and password values set
to null and other values set to their default.
- GUEST - Static variable in class pojos.GroupData
-
Identifies the Guest
group.
- 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.
- ic - Variable in class ome.services.sharing.ShareStore
-
- ice_postUnmarshal() - Method in class omero.model.PermissionsI
-
Called as Ice converts from a binary stream to a PermissionsI object.
- IceMapper - Class in omero.util
-
Responsible for the mapping of ome.* types to omero.* types and back again.
- IceMapper() - Constructor for class omero.util.IceMapper
-
- IceMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.IceMapper
-
- IceMapper.ReturnMapping - Interface in omero.util
-
- IceMethodInvoker - Class in ome.services.blitz.util
-
- IceMethodInvoker(ServiceInterface, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker
-
Create an
IceMethodInvoker
instance using the
Class
of
the passed argument to call
IceMethodInvoker#IceMethodInvoker(Class)
.
- IceMethodInvoker(Class<S>, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker
-
- IceUtil - Class in ome.services.util
-
Methods for working with Ice.
- IceUtil() - Constructor for class ome.services.util.IceUtil
-
- IConfig - Interface in ome.api
-
Access to server configuration.
- IContainer - Interface in ome.api
-
Provides methods for dealing with the core "Pojos" of OME.
- id - Variable in class ome.services.graphs.BaseGraphSpec
-
The id of the root type which will be processed.
- id - Variable in class ome.services.graphs.GraphStep
-
The actual id to be processed as opposed to
GraphEntry.getId()
which is the id of the root object.
- 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
-
- idEqual(IObject, IObject) - Static method in class ome.tools.hibernate.HibernateUtils
-
returns true under the following circumstatnces:
both arguments are null, or
both arguments are identical (==), or
both arguments have the same id value(equals)
- idOnly - Variable in class ome.services.search.SearchValues
-
- ids(Criteria) - Method in class ome.services.search.SearchAction
-
- ids(QueryBuilder, String) - Method in class ome.services.search.SearchAction
-
- idsInDb() - Method in class ome.services.scripts.ScriptRepoHelper
-
- idsInDb(SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper
-
- idToUuid(long) - Method in class ome.services.sharing.ShareBean
-
- idx - Variable in class ome.services.graphs.GraphStep
-
- IFD_TAG_PLANE_NUMBER - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter
-
TIFF tag we're using to store the Bio-Formats plane number.
- IFD_TAG_SERIES - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter
-
TIFF tag we're using to store the Bio-Formats series.
- ignoreUnknown - Variable in class ome.security.auth.ConfigurablePasswordProvider
-
If true, this implementation should return a null on
#checkPassword(String, String)
if the user is unknown, otherwise
a
Boolean.FALSE
.
- IHandle - Interface in omero.cmd
-
SPIOrthogonal interface hierarchy of types for working with the
Request
hierarchy.
- ILdap - Interface in ome.api
-
Administration interface providing access to admin-only functionality as well
as JMX-based server access and selected user functions.
- IllegalArgumentException - Exception in omero
-
- IllegalArgumentException(String) - Constructor for exception omero.IllegalArgumentException
-
- IMAGE - Static variable in class pojos.PixelsData
-
Identifies the Pixels#IMAGE
field.
- IMAGE_DESCRIPTION - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter
-
Current TIFF image comment for OMERO pixels pyramid TIFFs.
- IMAGE_LINKS - Static variable in class pojos.DatasetData
-
Identifies the Dataset#IMAGELINKS
field.
- IMAGE_QUERY - Static variable in class ome.services.delete.DeleteBean
-
Loads an Image
graph including: Pixels, Channel, LogicalChannel,
StatsInfo, PlaneInfo, Thumbnails, file maps, OriginalFiles, and Settings
- ImageAcquisitionData - Class in pojos
-
Object hosting the acquisition metadata.
- ImageAcquisitionData(Image) - Constructor for class pojos.ImageAcquisitionData
-
Creates a new instance.
- imageCount - Variable in class ome.formats.importer.ImportSize
-
- ImageData - Class in pojos
-
The data that makes up an OME Image along with links to its Pixels,
enclosing Datasets, and the Experimenter that owns this Image.
- ImageData() - Constructor for class pojos.ImageData
-
Creates a new instance.
- ImageData(Image) - Constructor for class pojos.ImageData
-
Creates a new instance.
- imageDescription - Variable in class ome.formats.importer.ImportConfig
-
- imageName - Variable in class ome.formats.importer.ImportConfig
-
- ImageNameMetadataStore - Class in ome.formats
-
Stores all Image names consumed by the interface.
- ImageNameMetadataStore() - Constructor for class ome.formats.ImageNameMetadataStore
-
- ImageService - Interface in ome.services.blitz.gateway.services
-
- ImageServiceImpl - Class in ome.services.blitz.gateway.services.impl
-
- ImageServiceImpl(GatewayFactory) - Constructor for class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
Instantiate the imageService with the serviceFactory.
- IMetadata - Interface in ome.api
-
Provides method to interact with acquisition metadata and
annotations.
- img - Variable in class ome.services.SVGRasterizer
-
The image that represents the SVG document.
- ImportableFiles - Class in ome.services.blitz.repo
-
A helper class used to obtain the import candidates
- ImportCandidates - Class in ome.formats.importer
-
Utility class which given any
File
object will determine the correct
number and members of a given import.
- ImportCandidates(OMEROWrapper, String[], IObserver) - Constructor for class ome.formats.importer.ImportCandidates
-
- ImportCandidates(int, OMEROWrapper, String[], IObserver) - Constructor for class ome.formats.importer.ImportCandidates
-
Main constructor which iterates over all the paths calling
DirectoryWalker.walk(File, Collection)
and permitting a descent to the given
depth.
- importCandidates(ImportConfig, ImportCandidates) - Method in class ome.formats.importer.ImportLibrary
-
Primary user method for importing a number
- ImportCandidates.CANCEL - Exception in ome.formats.importer
-
- ImportCandidates.CANCEL() - Constructor for exception ome.formats.importer.ImportCandidates.CANCEL
-
- ImportCandidates.SCANNING - Class in ome.formats.importer
-
Event raised during a pass through the directory structure given to
ImportCandidates
.
- ImportCandidates.SCANNING(File, int, int, int) - Constructor for class ome.formats.importer.ImportCandidates.SCANNING
-
- ImportConfig - Class in ome.formats.importer
-
Utility class which configures the Import.
- ImportConfig() - Constructor for class ome.formats.importer.ImportConfig
-
- ImportConfig(File) - Constructor for class ome.formats.importer.ImportConfig
-
- ImportConfig(Preferences, IniFileLoader, Properties) - Constructor for class ome.formats.importer.ImportConfig
-
Complete constructor.
- ImportConfig.AnnotationListValue - Class in ome.formats.importer
-
- ImportConfig.AnnotationListValue(String, ImportConfig, List<Annotation>) - Constructor for class ome.formats.importer.ImportConfig.AnnotationListValue
-
- ImportConfig.BoolValue - Class in ome.formats.importer
-
- ImportConfig.BoolValue(String, ImportConfig, boolean) - Constructor for class ome.formats.importer.ImportConfig.BoolValue
-
- ImportConfig.DoubleArrayValue - Class in ome.formats.importer
-
- ImportConfig.DoubleArrayValue(String, ImportConfig, Double[]) - Constructor for class ome.formats.importer.ImportConfig.DoubleArrayValue
-
- ImportConfig.FileValue - Class in ome.formats.importer
-
- ImportConfig.FileValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.FileValue
-
- ImportConfig.IntValue - Class in ome.formats.importer
-
- ImportConfig.IntValue(String, ImportConfig, int) - Constructor for class ome.formats.importer.ImportConfig.IntValue
-
- ImportConfig.IntValue(String, ImportConfig, int, String) - Constructor for class ome.formats.importer.ImportConfig.IntValue
-
- ImportConfig.LongValue - Class in ome.formats.importer
-
- ImportConfig.LongValue(String, ImportConfig, Long) - Constructor for class ome.formats.importer.ImportConfig.LongValue
-
- ImportConfig.PassValue - Class in ome.formats.importer
-
- ImportConfig.PassValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.PassValue
-
- ImportConfig.StrValue - Class in ome.formats.importer
-
- ImportConfig.StrValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.StrValue
-
- ImportConfig.StrValue(String, ImportConfig, String) - Constructor for class ome.formats.importer.ImportConfig.StrValue
-
- ImportConfig.StrValue(String, ImportConfig, String, String) - Constructor for class ome.formats.importer.ImportConfig.StrValue
-
- ImportConfig.Value<T> - Class in ome.formats.importer
-
Container which thread-safely makes a generic configuration value
available, without requiring getters and setters.
- ImportContainer - Class in ome.formats.importer
-
- ImportContainer(File, Long, IObject, Boolean, Double[], String, String[], Boolean) - Constructor for class ome.formats.importer.ImportContainer
-
- importData(Long, String, int, ImportSize) - Method in class ome.formats.importer.ImportLibrary
-
saves the binary data to the server.
- ImportEvent - Class in ome.formats.importer
-
- ImportEvent() - Constructor for class ome.formats.importer.ImportEvent
-
- ImportEvent.ADD - Class in ome.formats.importer
-
- ImportEvent.ADD() - Constructor for class ome.formats.importer.ImportEvent.ADD
-
- ImportEvent.BEGIN_POST_PROCESS - Class in ome.formats.importer
-
- ImportEvent.BEGIN_POST_PROCESS(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_POST_PROCESS
-
- ImportEvent.BEGIN_SAVE_TO_DB - Class in ome.formats.importer
-
- ImportEvent.BEGIN_SAVE_TO_DB(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_SAVE_TO_DB
-
- ImportEvent.COUNT_EVENT - Class in ome.formats.importer
-
- ImportEvent.DATA_STORED - Class in ome.formats.importer
-
- ImportEvent.DATA_STORED(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.DATA_STORED
-
- ImportEvent.DATASET_STORED - Class in ome.formats.importer
-
- ImportEvent.DATASET_STORED(int, String, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.DATASET_STORED
-
- ImportEvent.DEBUG_SEND - Class in ome.formats.importer
-
- ImportEvent.DEBUG_SEND(boolean, boolean) - Constructor for class ome.formats.importer.ImportEvent.DEBUG_SEND
-
- ImportEvent.END_POST_PROCESS - Class in ome.formats.importer
-
- ImportEvent.END_POST_PROCESS(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_POST_PROCESS
-
- ImportEvent.END_SAVE_TO_DB - Class in ome.formats.importer
-
- ImportEvent.END_SAVE_TO_DB(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_SAVE_TO_DB
-
- ImportEvent.ERRORS_CLEARED - Class in ome.formats.importer
-
- ImportEvent.ERRORS_CLEARED(int) - Constructor for class ome.formats.importer.ImportEvent.ERRORS_CLEARED
-
- ImportEvent.ERRORS_COMPLETE - Class in ome.formats.importer
-
- ImportEvent.ERRORS_COMPLETE() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_COMPLETE
-
- ImportEvent.ERRORS_FAILED - Class in ome.formats.importer
-
- ImportEvent.ERRORS_FAILED() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_FAILED
-
- ImportEvent.ERRORS_PENDING - Class in ome.formats.importer
-
- ImportEvent.ERRORS_PENDING() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_PENDING
-
- ImportEvent.ERRORS_SEND - Class in ome.formats.importer
-
- ImportEvent.ERRORS_SEND() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_SEND
-
- ImportEvent.ERRORS_UPLOAD_CANCELLED - Class in ome.formats.importer
-
- ImportEvent.ERRORS_UPLOAD_CANCELLED() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_UPLOAD_CANCELLED
-
- ImportEvent.FILE_SIZE_STEP - Class in ome.formats.importer
-
- ImportEvent.FILE_SIZE_STEP(long, long) - Constructor for class ome.formats.importer.ImportEvent.FILE_SIZE_STEP
-
- ImportEvent.FILE_UPLOAD_BYTES - Class in ome.formats.importer
-
- ImportEvent.FILE_UPLOAD_BYTES(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES
-
- ImportEvent.FILE_UPLOAD_CANCELLED - Class in ome.formats.importer
-
- ImportEvent.FILE_UPLOAD_CANCELLED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_CANCELLED
-
- ImportEvent.FILE_UPLOAD_COMPLETE - Class in ome.formats.importer
-
- ImportEvent.FILE_UPLOAD_COMPLETE(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_COMPLETE
-
- ImportEvent.FILE_UPLOAD_ERROR - Class in ome.formats.importer
-
- ImportEvent.FILE_UPLOAD_ERROR(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_ERROR
-
- ImportEvent.FILE_UPLOAD_EVENT - Class in ome.formats.importer
-
- ImportEvent.FILE_UPLOAD_FAILED - Class in ome.formats.importer
-
- ImportEvent.FILE_UPLOAD_FAILED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_FAILED
-
- ImportEvent.FILE_UPLOAD_FINISHED - Class in ome.formats.importer
-
- ImportEvent.FILE_UPLOAD_FINISHED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_FINISHED
-
- ImportEvent.FILE_UPLOAD_STARTED - Class in ome.formats.importer
-
- ImportEvent.FILE_UPLOAD_STARTED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_STARTED
-
- ImportEvent.GROUP_SET - Class in ome.formats.importer
-
- ImportEvent.GROUP_SET(String, int) - Constructor for class ome.formats.importer.ImportEvent.GROUP_SET
-
- ImportEvent.IMPORT_ARCHIVING - Class in ome.formats.importer
-
- ImportEvent.IMPORT_ARCHIVING(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_ARCHIVING
-
- ImportEvent.IMPORT_DONE - Class in ome.formats.importer
-
- ImportEvent.IMPORT_DONE(int, String, IObject, Long, int, ImportSize, List<Pixels>) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_DONE
-
- ImportEvent.IMPORT_OVERLAYS - Class in ome.formats.importer
-
- ImportEvent.IMPORT_OVERLAYS(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_OVERLAYS
-
- ImportEvent.IMPORT_PROCESSING - Class in ome.formats.importer
-
- ImportEvent.IMPORT_PROCESSING(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_PROCESSING
-
- ImportEvent.IMPORT_QUEUE_DONE - Class in ome.formats.importer
-
- ImportEvent.IMPORT_QUEUE_DONE() - Constructor for class ome.formats.importer.ImportEvent.IMPORT_QUEUE_DONE
-
- ImportEvent.IMPORT_QUEUE_STARTED - Class in ome.formats.importer
-
- ImportEvent.IMPORT_QUEUE_STARTED() - Constructor for class ome.formats.importer.ImportEvent.IMPORT_QUEUE_STARTED
-
- ImportEvent.IMPORT_STEP - Class in ome.formats.importer
-
- ImportEvent.IMPORT_STEP(int, int, int) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_STEP
-
- ImportEvent.LOADED_IMAGE - Class in ome.formats.importer
-
- ImportEvent.LOADED_IMAGE(String, Integer, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.LOADED_IMAGE
-
- ImportEvent.LOADING_IMAGE - Class in ome.formats.importer
-
- ImportEvent.LOADING_IMAGE(String, Integer, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.LOADING_IMAGE
-
- ImportEvent.LOGGED_IN - Class in ome.formats.importer
-
- ImportEvent.LOGGED_IN() - Constructor for class ome.formats.importer.ImportEvent.LOGGED_IN
-
- ImportEvent.LOGGED_OUT - Class in ome.formats.importer
-
- ImportEvent.LOGGED_OUT() - Constructor for class ome.formats.importer.ImportEvent.LOGGED_OUT
-
- ImportEvent.PROGRESS_EVENT - Class in ome.formats.importer
-
- ImportEvent.QUICKBAR_UPDATE - Class in ome.formats.importer
-
- ImportEvent.QUICKBAR_UPDATE() - Constructor for class ome.formats.importer.ImportEvent.QUICKBAR_UPDATE
-
- ImportEvent.REIMPORT - Class in ome.formats.importer
-
- ImportEvent.REIMPORT() - Constructor for class ome.formats.importer.ImportEvent.REIMPORT
-
- importFile(File, String, Map<Integer, Image>) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
- importFileSet(OriginalFile, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Import an image set's metadata.
- ImportFixture - Class in ome.formats.importer
-
test fixture for importing files without a GUI.
- ImportFixture(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportFixture
-
- importImage(ImportContainer, int, int, int) - Method in class ome.formats.importer.ImportLibrary
-
Perform an image import.
- ImportLibrary - Class in ome.formats.importer
-
- ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportLibrary
-
The library will not close the client instance.
- ImportProcessor - Class in ome.services.procs
-
- ImportProcessor() - Constructor for class ome.services.procs.ImportProcessor
-
- ImportSize - Class in ome.formats.importer
-
Calculates the various dimensions of an image from a Pixels
instance.
- ImportSize(String, Pixels, String) - Constructor for class ome.formats.importer.ImportSize
-
- in(PixelsType, String[]) - Static method in class omeis.providers.re.data.PlaneFactory
-
A static helper method to check if a type is one of the elements in an
array.
- include(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
returns true if this offset points to a field which may contain an
IObject
instance
- increment() - Method in class ome.services.sessions.SessionContext.Count
-
Increment the current reference count
and return the
new value atomically.
- increment(int) - Method in class ome.services.sessions.stats.LongCounter
-
- index - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
-
- index - Variable in class ome.formats.importer.ImportEvent.ERRORS_CLEARED
-
- index - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
-
- Index - Enum in ome.formats
-
- index(String, String[]) - Static method in class ome.tools.hibernate.HibernateUtils
-
- indexAllEvents() - Static method in class ome.services.fulltext.Main
-
- indexByClass(Set<String>) - Static method in class ome.services.fulltext.Main
-
- indexer - Variable in class ome.services.fulltext.FullTextThread
-
- indexFullDb() - Static method in class ome.services.fulltext.Main
-
- indexObject(IObject) - Method in interface ome.api.IUpdate
-
Initiates full-text indexing for the given object.
- indexObject(IObject) - Method in class ome.logic.UpdateImpl
-
- indexObject_async(AMD_IUpdate_indexObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
-
- info(String, Object...) - Method in class omero.cmd.Helper
-
- IniFileLoader - Class in ome.formats.importer.util
-
This class loads in the default importer.ini file (or one specified from the
command line when starting the app)
- IniFileLoader(File) - Constructor for class ome.formats.importer.util.IniFileLoader
-
Load given file
- init(String, boolean) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- init(ObjectAdapter, String) - Method in class ome.services.blitz.fire.Ring
-
Typically called from within
BlitzConfiguration
after the
communicator and adapter have been properly setup.
- init(Helper) - Method in class ome.services.blitz.impl.commands.SaveI
-
- init(String) - Method in class ome.services.blitz.repo.FileMaker
-
- init() - Static method in class ome.services.fulltext.Main
-
- init() - Method in class ome.services.sessions.SessionManagerImpl
-
Initialization method called by the Spring run-time to acquire an initial
Session
.
- init() - Method in class ome.services.sharing.ShareStore
-
Calls
ShareStore.doInit()
within a transaction with a session available to
all
HibernateTemplate
callbacks.
- init(Helper) - Method in class omero.cmd.basic.DoAllI
-
- init(Helper) - Method in class omero.cmd.basic.ListRequestsI
-
- init(Helper) - Method in class omero.cmd.basic.TimingI
-
- init(Helper) - Method in class omero.cmd.graphs.ChgrpI
-
- init(Helper) - Method in class omero.cmd.graphs.ChmodI
-
- init(Helper) - Method in class omero.cmd.graphs.ChownI
-
- init(Helper) - Method in class omero.cmd.graphs.DeleteI
-
- init(Helper) - Method in class omero.cmd.graphs.GraphSpecListI
-
- init(Helper) - Method in interface omero.cmd.IRequest
-
Method called within the thread boundaries before any processing occurs.
- initFile(String) - Method in class ome.services.formats.OmeroReader
-
- INITIAL_DELAY - Static variable in class ome.logic.RepositoryInfoImpl
-
- initialize(Object) - Method in interface ome.api.local.LocalQuery
-
Uses the Hibernate static method initialize
to prepare an
object for shipping over the wire.
- initialize(ServiceFactoryPrx) - Method in class ome.formats.OMEROMetadataStoreClient
-
Initializes the MetadataStore with an already logged in, ready to go
service factory.
- initialize(client) - Method in class ome.formats.OMEROMetadataStoreClient
-
Initializes the MetadataStore with an already logged in, ready to go
service factory.
- initialize(String, String, String, int) - Method in class ome.formats.OMEROMetadataStoreClient
-
Initializes the MetadataStore taking string parameters to feed to the
OMERO Blitz client object.
- initialize(String, String, String, int, boolean) - Method in class ome.formats.OMEROMetadataStoreClient
-
Initializes the MetadataStore taking string parameters to feed to the
OMERO Blitz client object.
- initialize(String, String, String, int, Long, boolean) - Method in class ome.formats.OMEROMetadataStoreClient
-
Initializes the MetadataStore taking string parameters to feed to the
OMERO Blitz client object.
- initialize(String, int, String) - Method in class ome.formats.OMEROMetadataStoreClient
-
Initializes the MetadataStore by joining an existing session.
- initialize(String, int, String, boolean) - Method in class ome.formats.OMEROMetadataStoreClient
-
Initializes the MetadataStore by joining an existing session.
- initialize(ServiceFactoryPrx, List<Pixels>, List<Long>) - Method in class ome.formats.OverlayMetadataStore
-
Initializes the metadata store implementation.
- initialize(Object) - Method in class ome.logic.QueryImpl
-
- initialize(Session) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- initialize(String[], String[], Class[], Map<String, Object>) - Method in class ome.services.blitz.measurements.MeasurementStore
-
- initialize(String[], String[], Class[], Map<String, Object>) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
-
- initialize() - Method in class ome.services.eventlogs.PersistentEventLogLoader
-
Called when the configuration database does not contain a valid
current_id.
- initialize() - Method in class ome.services.fulltext.PersistentEventLogLoader
-
Called when the configuration database does not contain a valid
current_id.
- initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
-
In order to allow subclasses like the AnnotationGraphSpec to make use
of this method, hooks have been added.
- initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.BaseGraphSpec
-
- initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.GraphEntry
-
- initialize(long, String, Map<String, String>) - Method in interface ome.services.graphs.GraphSpec
-
Called as each action is started.
- initialize() - Method in class ome.services.pixeldata.PersistentEventLogLoader
-
- initialize(Identity, IRequest, Map<String, String>) - Method in class omero.cmd.HandleI
-
- initialize(Identity, IRequest, Map<String, String>) - Method in interface omero.cmd.IHandle
-
Must be called on all instances exactly once before processing.
- initializeQuery(FullTextQuery) - Method in class ome.services.search.FullText
-
Allows settings offset and limit on the query.
- initializeReader() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
If the pyramid file exists (which the constructor guarantees) then we
assume that even if a lock file is present, that it's no longer valid.
- initializeRedirect(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
-
Set the new redirect value if null, or if the uuid is null or empty, then
the existing redirect will be removed.
- initializeUserAttributes(MethodInvocation, ServiceFactory, Principal, AtomicBoolean) - Static method in class ome.logic.HardWiredInterceptor
-
Adds the given environment context objects to the
ReflectiveMethodInvocation.getUserAttributes()
Map
for lookup in subclasses
- initializeWriter(String, String, boolean, int, int) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
Initializes the writer.
- initPixelsRange(PixelsType) - Method in class omeis.providers.re.metadata.StatsFactory
-
Determines the minimum and maximum corresponding to the passed
pixels type.
- inMemoryCache(String) - Method in interface ome.services.sessions.SessionManager
-
Returns after possibly creating an in-memory cache
which
can be used throughout the session.
- inMemoryCache(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- inMemoryCache(String) - Method in class ome.services.sessions.state.SessionCache
-
- InMemoryPlanarPixelBuffer - Class in ome.io.nio
-
Class implementation of the PixelBuffer interface for in memory planar pixel
data.
- InMemoryPlanarPixelBuffer(Pixels, byte[][][][]) - Constructor for class ome.io.nio.InMemoryPlanarPixelBuffer
-
Constructs an in memory pixel buffer based on a defined dimensionality.
- INNER_JOIN - Static variable in class ome.services.query.Query
-
imported constant for ease of use
- input - Variable in class ome.services.SVGRasterizer
-
The transcoder input.
- inputEnvironment(String) - Method in interface ome.services.sessions.SessionManager
-
Returns a copy of the input environment.
- inputEnvironment(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- insertEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- INSIGHT_PUBLISHED_NS - Static variable in class pojos.BooleanAnnotationData
-
The name space used to indicate that the tag is used a tag set.
- INSIGHT_RATING_NS - Static variable in class pojos.RatingAnnotationData
-
The name space used to identify the archived annotation linked to a set
of pixels.
- INSIGHT_TAGSET_NS - Static variable in class pojos.TagAnnotationData
-
The name space used to indicate that the tag is used a tag set.
- InstanceProvider - Interface in ome.formats.model
-
An instance provider, whose job is to make OMERO Blitz classes available
to a consumer based on a set of criteria.
- instantiate(String, EntityMode, Serializable) - Method in class ome.security.basic.OmeroInterceptor
-
default logic, but we may want to use them eventually for
dependency-injection.
- INSTITUTION - Static variable in class pojos.ExperimenterData
-
Identifies the Experimenter#INSTITUTION
field.
- InstrumentData - Class in pojos
-
Hosts the instrument used to capture an image.
- InstrumentData(Instrument) - Constructor for class pojos.InstrumentData
-
Creates a new instance.
- InstrumentProcessor - Class in ome.formats.model
-
Processes the members of an Instrument (Objective, OTF, Arc Laser and
Filament) and ensures that the Instrument containers are present in the
container cache, adding them if they are missing.
- InstrumentProcessor() - Constructor for class ome.formats.model.InstrumentProcessor
-
- INT - Static variable in class omeis.providers.re.data.PlaneFactory
-
Identifies the type used to store pixel values.
- INT16 - Static variable in class omeis.providers.re.data.PlaneFactory
-
Identifies the INT16 data type used to store pixel values,
as per OME spec.
- INT16_TYPE - Static variable in class pojos.PixelsData
-
Identifies the type used to store pixel values.
- INT32 - Static variable in class omeis.providers.re.data.PlaneFactory
-
Identifies the INT32 data type used to store pixel values,
as per OME spec.
- INT32_TYPE - Static variable in class pojos.PixelsData
-
Identifies the type used to store pixel values.
- INT8 - Static variable in class omeis.providers.re.data.PlaneFactory
-
Identifies the INT8 data type used to store pixel values,
as per OME spec.
- INT8_TYPE - Static variable in class pojos.PixelsData
-
Identifies the type used to store pixel values.
- INTEGER(Connection, List<Integer>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
-
- InteractiveProcessorI - Class in omero.grid
-
Processor
implementation which delegates to an omero.grid.Processor
servant.
- InteractiveProcessorI(Principal, SessionManager, Executor, ProcessorPrx, Job, long, SessionControlPrx, ParamsHelper, Current) - Constructor for class omero.grid.InteractiveProcessorI
-
- interceptor - Variable in class ome.security.basic.BasicSecuritySystem
-
- internalDelete(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl
-
- internalMerge(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl
-
Note if we use anything other than merge here, functionality from
ome.tools.hibernate.MergeEventListener
needs to be moved to
UpdateFilter
or to another event listener.
- InternalMessage - Class in ome.util.messages
-
- InternalMessage(Object) - Constructor for class ome.util.messages.InternalMessage
-
Sole constructor which takes the "source" of this
EventObject
.
- InternalRepositoryConfig - Class in ome.services.blitz.repo
-
Simple configuration class which is created via repository.xml Spring
configuration file after the OMERO.repository context is loaded.
- InternalRepositoryConfig(String) - Constructor for class ome.services.blitz.repo.InternalRepositoryConfig
-
- InternalRepositoryI - Class in ome.services.blitz.repo
-
Standalone repository service.
- InternalRepositoryI(ObjectAdapter, Registry, Executor, SqlAction, String, String) - Constructor for class ome.services.blitz.repo.InternalRepositoryI
-
- internalSave(IObject, ReloadFilter, Session) - Method in class ome.logic.UpdateImpl
-
Note if we use anything other than merge here, functionality from
ome.tools.hibernate.MergeEventListener
needs to be moved to
UpdateFilter
or to another event listener.
- internalServantConfig(Object) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- internalServantConfig(Object) - Method in class omero.cmd.SessionI
-
- InternalServiceFactory - Class in ome.tools.spring
-
subclass of ome.system.ServiceFactory which retrieves unmanaged ("internal")
service-
instances.
- InternalServiceFactory() - Constructor for class ome.tools.spring.InternalServiceFactory
-
default construtor
- InternalServiceFactory(OmeroContext) - Constructor for class ome.tools.spring.InternalServiceFactory
-
- internalSession - Variable in class ome.services.sessions.SessionManagerImpl
-
- Intersection - Class in ome.services.search
-
Intersection
SearchAction
which combines two other search actions
into one logical unit, e.g.
- Intersection(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Intersection
-
- intersects(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- intersects(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- intersects(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- intersects(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- 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.
- InThreadThrottlingStrategy - Class in ome.services.throttling
-
Throttling implementation which uses the calling server
Thread
for
execution.
- InThreadThrottlingStrategy(CurrentDetails) - Constructor for class ome.services.throttling.InThreadThrottlingStrategy
-
- invalidateConnection(long, Experimenter) - Method in interface ome.api.IShare
-
Makes the connection invalid for share
for
specifiec user.
- invalidateConnection(long, Experimenter) - Method in class ome.services.sharing.ShareBean
-
- invalidateConnection_async(AMD_IShare_invalidateConnection, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
-
- invalidateCurrentEventContext() - Method in class ome.security.basic.CurrentDetails
-
It suffices to set the Details
to a new instance to make this
context unusable.
- invalidateEventContext() - Method in class ome.security.basic.BasicSecuritySystem
-
- invalidateEventContext() - Method in interface ome.security.SecuritySystem
-
- invalidateEventContext() - Method in class ome.security.SecuritySystemHolder
-
- invalidateEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
-
- invertPDI(Set<Image>, CBlock<T>) - Static method in class ome.tools.HierarchyTransformations
-
- invoke(MethodInvocation) - Method in class ome.security.basic.BasicSecurityWiring
-
Wraps all OMERO invocations with login/logout semantics.
- invoke(MethodInvocation) - Method in class ome.security.basic.EventHandler
-
invocation interceptor for prepairing this
Thread
for execution
and subsequently reseting it.
- invoke(MethodInvocation) - Method in class ome.security.basic.NullEventHandler
-
- invoke(MethodInvocation) - Method in class ome.services.blitz.fire.AopContextInitializer
-
- invoke(Object, Current, IceMapper, Object...) - Method in class ome.services.blitz.util.IceMethodInvoker
-
Calls the method named in
Current.operation
with the
arguments provided mapped via the
IceMapper
instance.
- invoke(MethodInvocation) - Method in class ome.services.util.ServiceHandler
-
- invoke(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor
-
- invoke(MethodInvocation) - Method in class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
-
- invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionFactory
-
Wraps all invocations to Session to prevent certain usages.
- invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
-
delegates to HibernateInterceptor
or manages sessions internally,
based on the type of service.
- invoke(MethodInvocation) - Method in class omero.cmd.CallContext
-
- invoker - Variable in class ome.services.blitz.impl.AbstractAmdServant
-
If a service is provided, then an invoker will be created to cache all of
its methods.
- IObjectClassQuery - Class in ome.services.query
-
simple query subclass which uses the Parameters.CLASS
parameter value to create a Criteria
and then adds
Expression
instances based on all other
parameter names.
- IObjectClassQuery(Parameters) - Constructor for class ome.services.query.IObjectClassQuery
-
- IObjectContainerStore - Interface in ome.formats.model
-
An object that handles the storage and manipulation of IObject containers
and their references.
- iObjectType - Variable in class ome.services.graphs.GraphStep
-
Type of object which is being processed, using during
GraphState#release(String)
to send an
EventLogMessage
.
- IObservable - Interface in ome.formats.importer
-
- IObserver - Interface in ome.formats.importer
-
- IPixels - Interface in ome.api
-
- iPixels - Variable in class ome.services.projection.ProjectionBean
-
Reference to the service used to retrieve the pixels metadata.
- IProcessManager - Interface in ome.services.procs
-
Manages asynchronous processing logic for all Job
instances created
- 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.
- iQuery - Variable in class ome.logic.AbstractLevel2Service
-
- iQuery - Variable in class ome.services.AbstractStatefulBean
-
- IQueryEnumProvider - Class in ome.formats.enums
-
An enumeration provider which uses IQuery and a cache to fulfill the
contract of an EnumerationProvider.
- IQueryEnumProvider(IQueryPrx) - Constructor for class ome.formats.enums.IQueryEnumProvider
-
Default IQuery based enumeration provider constructor.
- 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.
- IRequest - Interface in omero.cmd
-
SPI Orthogonal interface hierarchy of types for working with the
Request
hierarchy.
- IResults - Interface in ome.api
-
Provides methods for storing, quering, and retrieving analysis results.
- IResults.PixelSet - Class in ome.api
-
- IResults.PixelSet() - Constructor for class ome.api.IResults.PixelSet
-
- IResults.Result - Interface in ome.api
-
- is_admin - Static variable in class ome.security.basic.AllGroupsSecurityFilter
-
- is_adminorpi - Static variable in interface ome.security.SecurityFilter
-
- is_nonprivate - Static variable in interface ome.security.SecurityFilter
-
- IS_ROOT_USER - Variable in class ome.system.Roles
-
- is_share - Static variable in interface ome.security.SecurityFilter
-
- IS_SYSTEM_GROUP - Variable in class ome.system.Roles
-
- IS_USER_GROUP - Variable in class ome.system.Roles
-
- isAbstract - Variable in class ome.services.graphs.AbstractHierarchyGraphSpec
-
Whether or not the type of types[i] is abstract.
- isAccepted(boolean, String, String, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
-
Deprecated.
- isActive() - Method in class ome.security.basic.BasicMethodSecurity
-
- isActive() - Method in interface ome.security.MethodSecurity
-
Indicates whether or not method security is active.
- isActive(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
- isActive(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService
-
Is the channel active.
- isActive() - Method in interface ome.services.procs.Process
-
- isActive() - Method in class ome.services.procs.ProcessSkeleton
-
- isActive(int) - Method in class ome.services.RenderingBean
-
- isActive(int) - Method in interface omeis.providers.re.RenderingEngine
-
Returns true
if the channel is mapped, false
otherwise.
- isActive() - Method in class pojos.ExperimenterData
-
Returns true
if the experimenter is active,
false
otherwise.
- isActive_async(AMD_RenderingEngine_isActive, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- isActive_async(AMD_RenderingEngine_isActive, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- isAdmin - Variable in class ome.system.SimpleEventContext
-
- isAdminOrPi(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
-
- isAllowLeadingWildcard() - Method in interface ome.api.Search
-
Returns the current leading-wildcard setting.
- isAllowLeadingWildcard() - Method in class ome.services.SearchBean
-
- isAllowLeadingWildcard_async(AMD_Search_isAllowLeadingWildcard, Current) - Method in class ome.services.blitz.impl.SearchI
-
- isAlphalessRendering() - Method in class omeis.providers.re.Optimizations
-
Returns true
if the alphaless rendering optimization is
enabled, and false
if it is not.
- isArchived() - Method in class pojos.ImageData
-
Returns true
if the image has been archived,
false
otherwise.
- isAutoCloseEnabled() - Method in class ome.tools.hibernate.CurrentSessionContext
-
- IScale - Interface in ome.api
-
Provides methods for performing scaling (change of the image size through
interpolation or other means) on BufferedImages.
- isCancelled() - Method in class omero.cmd.CmdCallbackI
-
Returns whether Status::CANCELLED is contained in
the flags variable of the Status instance.
- isCaseSensitive() - Method in interface ome.api.Search
-
Returns the current case sensitivity setting.
- isCaseSensitive() - Method in class ome.services.SearchBean
-
- isCaseSensitive_async(AMD_Search_isCaseSensitive, Current) - Method in class ome.services.blitz.impl.SearchI
-
- isClientObject() - Method in class pojos.ShapeData
-
Returns true
if the object one that has been created client
side.
- isClientSide() - Method in class pojos.ROIData
-
Returns true
if the object a client-side object,
false
otherwise.
- IsConstant() - Method in class omeis.providers.re.codomain.PlaneSlicingContext
-
Returns the type of bit-planes mapping.
- isCurrentUserAdmin() - Method in class ome.services.sessions.SessionContextImpl
-
- isCurrentUserAdmin() - Method in interface ome.system.EventContext
-
- isCurrentUserAdmin() - Method in class ome.system.SimpleEventContext
-
- isDb() - Method in class ome.system.Preference
-
- isDebugConsole() - Method in class ome.formats.importer.util.IniFileLoader
-
- isDebugUI() - Method in class ome.formats.importer.util.IniFileLoader
-
- isDetectorSettingsDirty() - Method in class pojos.ChannelAcquisitionData
-
Returns true
if the detector settings has been updated,
false
otherwise.
- isDirectory() - Method in class pojos.FileData
-
Returns true
if the file is a directory, false
otherwise.
- isDirty() - Method in class pojos.DataObject
-
Returns true
if setter value has modified the value of the
stored IObject, false
otherwise.
- isDisabled(String) - Method in class ome.security.basic.BasicSecuritySystem
-
- isDisabled(String) - Method in class ome.security.basic.CurrentDetails
-
- isDisabled(String) - Method in interface ome.security.SecuritySystem
-
checks if the listed id is disabled for the current Thread.
- isDisabled(String) - Method in class ome.security.SecuritySystemHolder
-
- isDisabled(String) - Method in class ome.security.sharing.SharingSecuritySystem
-
- isDisallow(int, Current) - Method in class omero.model.PermissionsI
-
- isDiskSpaceChecking() - Method in class ome.services.RawFileBean
-
getter disk overflow checking
- isDiskSpaceChecking() - Method in class ome.services.RawPixelsBean
-
- isDiskSpaceChecking() - Method in class ome.services.ThumbnailBean
-
- isEmpty() - Method in class ome.services.query.Definitions
-
- isEmptyEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
-
- isEnabled() - Method in class ome.security.auth.LdapConfig
-
- isEncryptedConnection() - Method in class ome.formats.OMEROMetadataStoreClient
-
- isEndTime() - Method in class omero.sys.ParametersI
-
Returns true
if the map contains the end time
parameter, false
otherwise.
- ISession - Interface in ome.api
-
Start here: Session
creation service for OMERO.
- isExceptionThrown() - Method in class ome.system.UpgradeCheck
-
- isExperimenter() - Method in class omero.sys.ParametersI
-
Returns true
if the filter contains and ownerId
parameter, false
otherwise.
- isExtendedGraphCritical(Set<Long>) - Method in class ome.services.ThumbnailCtx
-
Whether or not we're extended graph critical for a given set of
dimension pools.
- isf - Variable in class ome.services.util.Executor.Impl
-
- isFailure() - Method in class omero.cmd.CmdCallbackI
-
Returns whether Status::FAILURE is contained in
the flags variable of the Status instance.
- isFloat() - Method in interface ome.api.RawPixelsStore
-
- isFloat() - Method in class ome.io.bioformats.BfPixelBuffer
-
- isFloat() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- isFloat() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- isFloat() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- isFloat() - Method in interface ome.io.nio.PixelBuffer
-
Returns whether or not the pixel buffer has floating point pixels.
- isFloat() - Method in class ome.io.nio.RomioPixelBuffer
-
- isFloat(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
-
- isFloat(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService
-
Are the bytes in the image floats.
- isFloat() - Method in class ome.services.RawPixelsBean
-
- isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- isFontBold() - Method in class pojos.ShapeSettingsData
-
Returns true
if it is bold, false
otherwise.
- isFontItalic() - Method in class pojos.ShapeSettingsData
-
Returns true
if it is italic, false
otherwise.
- isForce() - Method in class ome.services.graphs.GraphOpts
-
- isGranted(Permissions.Role, Permissions.Right) - Static method in class ome.security.basic.AllGroupsSecurityFilter
-
- isGraphCritical(Details) - Method in class ome.security.basic.BasicSecuritySystem
-
- isGraphCritical(Details) - Method in class ome.security.basic.CurrentDetails
-
- isGraphCritical(Details) - Method in interface ome.security.SecuritySystem
-
Determines if the current security context has the possibility of
corrupting consistent graphs.
- isGraphCritical(Details) - Method in class ome.security.SecuritySystemHolder
-
- isGraphCritical(Details) - Method in class ome.security.sharing.SharingSecuritySystem
-
- isGroup() - Method in class omero.sys.ParametersI
-
Returns true
if the filter contains an groupId
,
false
otherwise.
- isGroupAnnotate(Current) - Method in class omero.model.PermissionsI
-
- isGroupAnnotate() - Method in class pojos.PermissionData
-
Returns true
if the group has annotate access i.e.
- isGroupRead(Current) - Method in class omero.model.PermissionsI
-
- isGroupRead() - Method in class pojos.PermissionData
-
Returns true
if the group has read access
i.e.
- isGroupWrite(Current) - Method in class omero.model.PermissionsI
-
- isGroupWrite() - Method in class pojos.PermissionData
-
Returns true
if the group has write access i.e.
- isHard() - Method in class ome.services.messages.stats.AbstractStatsMessage
-
- IShare - Interface in ome.api
-
Provides method for sharing - collaboration process for images, datasets,
projects.
- isHidden() - Method in class pojos.FileData
-
Returns true
if the file is hidden, false
otherwise.
- isImagingEnvironmentDirty() - Method in class pojos.ImageAcquisitionData
-
Returns true
if the StageLabel has been updated,
false
otherwise.
- isImmutable(Object) - Method in class omero.util.IceMapper
-
- isInProgress() - Method in interface ome.api.ThumbnailStore
-
This returns the last available in progress state for a
thumbnail.
- isInProgress() - Method in class ome.services.ThumbnailBean
-
- isInProgress_async(AMD_ThumbnailStore_isInProgress, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- isInRepo(long) - Method in class ome.services.scripts.ScriptRepoHelper
-
- isInRepo(SqlAction, long) - Method in class ome.services.scripts.ScriptRepoHelper
-
- isInSystemGroup(Long) - Method in class ome.security.SystemTypes
-
- isInSystemGroup(Details) - Method in class ome.security.SystemTypes
-
- isInUserGroup(Long) - Method in class ome.security.SystemTypes
-
- isInUserGroup(Details) - Method in class ome.security.SystemTypes
-
- isKeep() - Method in class ome.services.graphs.GraphEntry
-
- isLast(int) - Method in class omero.cmd.Helper
-
Returns true if this is the last step for the given request.
- isLeicaReader() - Method in class ome.formats.importer.OMEROWrapper
-
- isLifetime() - Method in class pojos.ImageData
-
Returns true
if the image is a lifetime image,
false
otherwise.
- isLightSourceSettingsDirty() - Method in class pojos.ChannelAcquisitionData
-
Returns true
if the light source settings has been updated,
false
otherwise.
- isLittleEndian() - Method in class ome.io.bioformats.BfPixelBuffer
-
Delegates to IFormatReader.isLittleEndian()
.
- isLoaded() - Method in class pojos.DataObject
-
Returns true
if the object is loaded, false
otherwise.
- isLockedByOthers() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- isMemberOfGroup(long) - Method in class pojos.ExperimenterData
-
Checks if supplied group id matches any group to which the current
experimenter belongs to.
- isMergedBatches() - Method in interface ome.api.Search
-
Returns the current merged-batches setting.
- isMergedBatches() - Method in class ome.services.SearchBean
-
- isMergedBatches_async(AMD_Search_isMergedBatches, Current) - Method in class ome.services.blitz.impl.SearchI
-
- isMetadataOnly() - Method in class ome.formats.importer.ImportLibrary
-
Retrieves the metadata only flag.
- isMinMaxSet() - Method in class ome.formats.importer.OMEROWrapper
-
- isModified() - Method in class ome.services.AbstractStatefulBean
-
- isMovieFile() - Method in class pojos.FileAnnotationData
-
Returns true
if it is a movie file.
- isMutable() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- isNoiseReduction() - Method in class omeis.providers.re.metadata.StatsFactory
-
Returns true
if the flag is on, false
otherwise.
- isNonPrivate(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
-
- isNull() - Method in class ome.services.graphs.GraphEntry
-
- isNullablePrimitive(Class<?>) - Static method in class omero.util.IceMapper
-
- isObjectiveSettingsDirty() - Method in class pojos.ImageAcquisitionData
-
Returns true
if the objective settings has been updated,
false
otherwise.
- isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
-
- isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.AnnotationGraphSpec
-
- isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.LightSourceGraphSpec
-
- isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.BasicSecuritySystem
-
tests whether or not the current user is either the owner of this entity,
or the superivsor of this entity, for example as root or as group owner.
- isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.CurrentDetails
-
- isPagination() - Method in class omero.sys.ParametersI
-
Returns true
if the filter contains a limit
OR a offset
, false
otherwise.
- isPasswordRequired(Long) - Method in class ome.security.auth.PasswordUtil
-
Returns a boolean based on the supplied user ID and system property
setting.
- isPixelsTypeSigned() - Method in class ome.services.RenderingBean
-
- isPixelsTypeSigned() - Method in class omeis.providers.re.Renderer
-
Returns true
if the pixels type is signed,
false
otherwise.
- isPixelsTypeSigned() - Method in interface omeis.providers.re.RenderingEngine
-
Returns true
if the pixels type is signed,
false
otherwise.
- isPixelsTypeSigned_async(AMD_RenderingEngine_isPixelsTypeSigned, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- isPixelsTypeSigned_async(AMD_RenderingEngine_isPixelsTypeSigned, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- isPrefs() - Method in class ome.system.Preference
-
- isPrimaryColorEnabled() - Method in class omeis.providers.re.Optimizations
-
Returns true
if the primary color optimization is enabled,
and false
if it is not.
- isPrimitive(Class<?>) - Method in class omero.util.IceMapper
-
- isProxyAccepted(boolean, String, ProcessorPrx, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
-
Callback method called by the remote processor instance.
- isReadOnly() - Method in class ome.services.sessions.SessionContextImpl
-
- isReadOnly() - Method in interface ome.system.EventContext
-
- isReadOnly - Variable in class ome.system.SimpleEventContext
-
- isReadOnly() - Method in class ome.system.SimpleEventContext
-
- isReadOnly() - Method in class pojos.ShapeData
-
Returns true
if the object a read-only object,
false
otherwise.
- isReady() - Method in class ome.security.basic.BasicSecuritySystem
-
- isReady() - Method in class ome.security.basic.CurrentDetails
-
Checks if the current
Thread
has non-null
Experimenter
,
Event
, and
ExperimenterGroup
, required for proper
functioning of the security system.
- isReady() - Method in interface ome.security.SecuritySystem
-
- isReady() - Method in class ome.security.SecuritySystemHolder
-
- isReady() - Method in class ome.security.sharing.SharingSecuritySystem
-
- isRepeatable() - Method in class ome.formats.importer.util.FileUploadCounter
-
- isRetry() - Method in class ome.io.messages.MissingPyramidMessage
-
- isReturnUnloaded() - Method in interface ome.api.Search
-
Returns the current return-unloaded setting.
- isReturnUnloaded() - Method in class ome.services.SearchBean
-
- isReturnUnloaded_async(AMD_Search_isReturnUnloaded, Current) - Method in class ome.services.blitz.impl.SearchI
-
- isRootUser(Experimenter) - Method in class ome.system.Roles
-
- isSecure() - Method in class omero.client
-
- isSend(int) - Method in class ome.formats.importer.util.ErrorHandler
-
Check if files need sending at error container index
- isShare(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
-
- isSigned() - Method in interface ome.api.RawPixelsStore
-
- isSigned() - Method in class ome.io.bioformats.BfPixelBuffer
-
- isSigned() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- isSigned() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- isSigned() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- isSigned() - Method in interface ome.io.nio.PixelBuffer
-
Returns whether or not the pixel buffer has signed pixels.
- isSigned() - Method in class ome.io.nio.RomioPixelBuffer
-
- isSigned(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
-
- isSigned(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService
-
Are the bytes in the image signed.
- isSigned() - Method in class ome.services.RawPixelsBean
-
- isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- isSingleton() - Method in class ome.security.basic.EventListenersFactoryBean
-
being a singleton implies that this FactoryBean
will only ever
create one instance.
- isSoft() - Method in class ome.services.graphs.GraphEntry
-
- isSPWReader() - Method in class ome.formats.importer.OMEROWrapper
-
- isStageLabelDirty() - Method in class pojos.ImageAcquisitionData
-
Returns true
if the position has been updated,
false
otherwise.
- isStartTime() - Method in class omero.sys.ParametersI
-
Returns true
if the map contains the start time
parameter, false
otherwise.
- isStatisticsEnabled() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
Are statistics logged
- isSyncOnLogin() - Method in class ome.security.auth.LdapConfig
-
- isSystemGroup(ExperimenterGroup) - Method in class ome.system.Roles
-
- isSystemGroup() - Method in class pojos.GroupData
-
Returns true
if the group is a system group,
false
otherwise.
- isSystemType(Class<? extends IObject>) - Method in class ome.security.basic.BasicSecuritySystem
-
classes which cannot be created by regular users.
- isSystemType(Class<? extends IObject>) - Method in interface ome.security.SecuritySystem
-
checks if instances of the given type are "System-Types".
- isSystemType(Class<? extends IObject>) - Method in class ome.security.SecuritySystemHolder
-
- isSystemType(Class<? extends IObject>) - Method in class ome.security.sharing.SharingSecuritySystem
-
- isSystemType(Class<?>) - Method in class ome.security.SystemTypes
-
classes which cannot be created by regular users.
- isThisType(String, boolean) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
-
- isThisType(String, boolean) - Method in class ome.services.formats.OmeroReader
-
- isThisType(RandomAccessInputStream) - Method in class ome.services.formats.OmeroReader
-
- isThreadSafe() - Method in class ome.services.messages.AbstractSessionMessage
-
- isThreadSafe() - Method in class ome.util.messages.InternalMessage
-
Returns true if this message can safely be passed to another
Thread
.
- isThumbnailCached(long) - Method in class ome.services.ThumbnailCtx
-
Checks to see if a thumbnail is in the on disk cache or not.
- isTransient(Object) - Method in class ome.security.basic.OmeroInterceptor
-
- isTypeSigned(PixelsType) - Static method in class omeis.providers.re.data.PlaneFactory
-
A static helper method to retrieve pixel byte signage.
- isUnloaded(Object) - Static method in class ome.tools.hibernate.HibernateUtils
-
- isUpgradeNeeded() - Method in class ome.formats.importer.ImportConfig
-
Check online to see if this is the current version
- isUpgradeNeeded() - Method in class ome.system.UpgradeCheck
-
- isUseProjections() - Method in interface ome.api.Search
-
Returns the current use-projection setting.
- isUseProjections() - Method in class ome.services.SearchBean
-
- isUseProjections_async(AMD_Search_isUseProjections, Current) - Method in class ome.services.blitz.impl.SearchI
-
- isUserAnnotate(Current) - Method in class omero.model.PermissionsI
-
- isUserGroup(ExperimenterGroup) - Method in class ome.system.Roles
-
- isUserRead(Current) - Method in class omero.model.PermissionsI
-
- isUserRead() - Method in class pojos.PermissionData
-
Returns true
if the user has read access,
false
otherwise.
- isUserWrite(Current) - Method in class omero.model.PermissionsI
-
- isUserWrite() - Method in class pojos.PermissionData
-
Returns true
if the user has write access,
false
otherwise.
- isVisible() - Method in class pojos.ShapeData
-
Returns true
if the shape is visible, false
otherwise.
- isVoid(Current) - Method in class ome.services.blitz.util.IceMethodInvoker
-
Checks for a void return type, which is needed to know what type of
ice_response() method to invoke.
- isVoid - Variable in class ome.services.throttling.Task
-
- isVoid() - Method in class omero.util.IceMapper
-
Returns true only if the current mapping is the
IceMapper.VOID
mapping.
- isWorldAnnotate(Current) - Method in class omero.model.PermissionsI
-
- isWorldRead(Current) - Method in class omero.model.PermissionsI
-
- isWorldRead() - Method in class pojos.PermissionData
-
Returns true
if the world has read access,
false
otherwise.
- isWorldWrite(Current) - Method in class omero.model.PermissionsI
-
- isWorldWrite() - Method in class pojos.PermissionData
-
Returns true
if the world has write access,
false
otherwise.
- isWrapperArray(Class<?>) - Static method in class omero.util.IceMapper
-
- isWrite() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
Whether or not this instance is in writing-mode.
- isXYPlanar() - Method in class omeis.providers.re.data.Plane2D
-
Returns true
if the plane is an XY-plane
,
false
otherwise.
- iterate() - Method in class ome.services.scripts.ScriptRepoHelper
-
- iterator() - Method in class ome.services.eventlogs.EventLogLoader
-
- iterator() - Method in class ome.services.messages.ShapeChangeMessage
-
- ITypes - Interface in ome.api
-
Access to reflective type information.
- IUpdate - Interface in ome.api
-
Provides methods for directly updating object graphs.
- iUpdate - Variable in class ome.logic.AbstractLevel2Service
-
- iUpdate - Variable in class ome.services.AbstractStatefulBean
-
- R_BAND - Static variable in class omeis.providers.re.RGBBuffer
-
Index of the red band in the image's data buffer.
- random(int) - Method in class ome.services.roi.GeomTool
-
- randomize(Random) - Method in class omero.model.SmartEllipseI
-
- randomize(Random) - Method in class omero.model.SmartLineI
-
- randomize(Random) - Method in class omero.model.SmartMaskI
-
- randomize(Random) - Method in class omero.model.SmartPathI
-
- randomize(Random) - Method in class omero.model.SmartPointI
-
- randomize(Random) - Method in class omero.model.SmartPolygonI
-
- randomize(Random) - Method in class omero.model.SmartPolylineI
-
- randomize(Random) - Method in class omero.model.SmartRectI
-
- randomize(Random) - Method in interface omero.model.SmartShape
-
Initializes this shape with completely random data.
- randomize(Random) - Method in class omero.model.SmartTextI
-
- rarray(RType...) - Static method in class omero.rtypes
-
- rarray(Collection<RType>) - Static method in class omero.rtypes
-
- RatingAnnotationData - Class in pojos
-
Annotation used to rate an object.
- RatingAnnotationData() - Constructor for class pojos.RatingAnnotationData
-
Creates a new instance of value LEVEL_ZERO
.
- RatingAnnotationData(int) - Constructor for class pojos.RatingAnnotationData
-
Creates a new instance.
- RatingAnnotationData(LongAnnotation) - Constructor for class pojos.RatingAnnotationData
-
Creates a new instance.
- RawFileBean - Class in ome.services
-
Raw file gateway which provides access to the OMERO file repository.
- RawFileBean() - Constructor for class ome.services.RawFileBean
-
default constructor
- RawFileBean(boolean) - Constructor for class ome.services.RawFileBean
-
overridden to allow Spring to set boolean
- RawFileStore - Interface in ome.api
-
Raw file gateway which provides access to the OMERO file repository.
- RawFileStoreI - Class in ome.services.blitz.impl
-
Implementation of the RawFileStore service.
- RawFileStoreI(RawFileStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawFileStoreI
-
- RawFileStoreService - Interface in ome.services.blitz.gateway.services
-
- RawFileStoreServiceImpl - Class in ome.services.blitz.gateway.services.impl
-
- RawFileStoreServiceImpl(RawFileStorePrx) - Constructor for class ome.services.blitz.gateway.services.impl.RawFileStoreServiceImpl
-
Create the ImageService passing the gateway.
- rawOption - Variable in class ome.services.graphs.AbstractHierarchyGraphSpec
-
Original string contained in the options
Map
before parsing.
- RawPixelsBean - Class in ome.services
-
Implementation of the RawPixelsStore stateful service.
- RawPixelsBean() - Constructor for class ome.services.RawPixelsBean
-
default constructor
- RawPixelsBean(boolean, String) - Constructor for class ome.services.RawPixelsBean
-
overridden to allow Spring to set boolean
- RawPixelsStore - Interface in ome.api
-
Binary data provider.
- RawPixelsStoreI - Class in ome.services.blitz.impl
-
Implementation of the RawPixelsStore service.
- RawPixelsStoreI(RawPixelsStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawPixelsStoreI
-
- RawPixelsStoreService - Interface in ome.services.blitz.gateway.services
-
- RawPixelsStoreServiceImpl - Class in ome.services.blitz.gateway.services.impl
-
- RawPixelsStoreServiceImpl(RawPixelsStorePrx) - Constructor for class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
-
Create the ImageService passing the gateway.
- rbool(boolean) - Static method in class omero.rtypes
-
- rclass(String) - Static method in class omero.rtypes
-
- rdouble(double) - Static method in class omero.rtypes
-
- read(long, int) - Method in interface ome.api.RawFileStore
-
- read(ByteBuffer) - Method in class ome.io.nio.FileBuffer
-
- read(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer
-
- read(long, long, int) - Method in class ome.services.blitz.gateway.services.impl.RawFileStoreServiceImpl
-
- read(long, long, int) - Method in interface ome.services.blitz.gateway.services.RawFileStoreService
-
Read from the file in the rawFileStore.
- read(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
- read(long, int) - Method in class ome.services.RawFileBean
-
- read(String) - Method in class ome.services.scripts.ScriptRepoHelper
-
- read_async(AMD_Exporter_read, long, int, Current) - Method in class ome.services.blitz.impl.ExporterI
-
- read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
-
- read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
-
- readBytes(int) - Method in class ome.services.sessions.stats.DelegatingStats
-
- readBytes(int) - Method in class ome.services.sessions.stats.NullSessionStats
-
- readBytes(int) - Method in interface ome.services.sessions.stats.SessionStats
-
- readBytes(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
-
- reader - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
-
- reader - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
-
- reader - Variable in class ome.io.bioformats.BfPixelBuffer
-
- reader() - Method in class ome.io.bioformats.BfPixelBuffer
-
- reader - Variable in class ome.io.bioformats.BfPyramidPixelBuffer
-
Bio-Formats implementation the delegate uses to read the backing TIFF.
- readerClass - Static variable in class ome.services.util.DBEnumCheck
-
- READERS_KEY - Static variable in class ome.formats.importer.ImportConfig
-
- readersPath - Variable in class ome.formats.importer.ImportConfig
-
- readOnly - Variable in class ome.security.basic.EventHandler
-
- readOnly - Variable in class ome.services.sessions.SessionManagerImpl
-
- READONLY_FLAG - Static variable in class pojos.ShapeData
-
Flag stating that the ROI is read only.
- ReadOnlyByteArray - Class in ome.util.mem
-
A read-only slice of a given array.
- ReadOnlyByteArray(byte[], int, int) - Constructor for class ome.util.mem.ReadOnlyByteArray
-
Creates a read-only slice of base
.
- reapSession(String) - Method in class ome.services.blitz.fire.SessionManagerI
-
- recompressSeries(TiffReader, int) - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter
-
Re-compresses a source series, that is JPEG 2000 compressed, via its
resolution level.
- recreateCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- rect(double, double, double, double) - Method in class ome.services.roi.GeomTool
-
- RectangleArea - Class in ome.util.math.geom2D
-
Represents a rectangle in the Euclidean space R2.
- RectangleArea() - Constructor for class ome.util.math.geom2D.RectangleArea
-
Constructs a new RectangleAreaAdapter
whose top-left corner is
(0, 0) and whose width and height are both zero.
- RectangleArea(int, int, int, int) - Constructor for class ome.util.math.geom2D.RectangleArea
-
Constructs a new RectangleAreaAdapter
whose top-left corner is
specified as (x, y) and whose width and height are specified by the
arguments of the same name.
- RectangleData - Class in pojos
-
Represents a rectangle in the Euclidean space R2.
- RectangleData(Shape) - Constructor for class pojos.RectangleData
-
Creates a new instance.
- RectangleData() - Constructor for class pojos.RectangleData
-
Creates a new instance with a default rectangle.
- RectangleData(double, double, double, double) - Constructor for class pojos.RectangleData
-
Creates a new instance of the RectangleData.
- RED_INDEX - Static variable in class ome.formats.model.ColorsFactory
-
Index of the red component of a color.
- RED_INDEX - Static variable in class omeis.providers.re.ColorsFactory
-
Index of the red component of a color.
- RED_TEXT - Static variable in class ome.formats.model.ChannelProcessor
-
Name of the red
component when it is a graphics image.
- Redirector - Interface in ome.services.blitz.redirect
-
Strategy interface for helping a
Ring
instance decide whether to
redirect
SessionPrx
creation to another
SessionManagerI
instance.
- Redirector.Context - Interface in ome.services.blitz.redirect
-
Interface implemented by Ring instances to allow passing in the context
necessary for making strategy decisions.
- ReferenceProcessor - Class in ome.formats.model
-
Processes the references of an IObjectContainerStore and ensures
that container references are consistent with the LSID stored in the
IObjectContainer itself.
- ReferenceProcessor() - Constructor for class ome.formats.model.ReferenceProcessor
-
- 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.
- refresh(T) - Method in class ome.logic.QueryImpl
-
- refresh(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache
-
Used externally to refresh the
SessionContext
instance
associated with the session uuid
- refresh_async(AMD_IQuery_refresh, IObject, Current) - Method in class ome.services.blitz.impl.QueryI
-
- refreshAll() - Method in class ome.system.OmeroContext
-
refreshes all the nested OmeroContexts within this instance.
- refreshAllIfNecessary() - Method in class ome.system.OmeroContext
-
Calls #refreshAll() if {@link #isRunning()} throws an
{@link 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.
- register(String, ObjectPrx, boolean) - Method in class ome.services.blitz.fire.TopicManager.Impl
-
- register(String, ObjectPrx, boolean) - Method in interface ome.services.blitz.fire.TopicManager
-
Enforces no security constraints.
- register(String, RString, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Register an OriginalFile using its path
- register(Log, Communicator, boolean) - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
-
- registerAll(Ehcache, CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
-
- registerCallback(ProcessCallbackPrx, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
-
- registerCallback(ProcessCallback) - Method in interface ome.services.procs.Process
-
- registerCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton
-
- registerFileSet(OriginalFile, List<Image>, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Register the Images in a list of Images, a single image will be a one-element list
- registerOriginalFile(OriginalFile, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Register an OriginalFile object
- registerServant(Identity, Object) - Method in class omero.cmd.SessionI
-
Registers the servant with the adapter (or throws an exception if one is
already registered) as well as configures the servant in any post-Spring
way necessary, based on the type of the servant.
- RegisterServantMessage - Class in ome.services.blitz.util
-
- RegisterServantMessage(Object, Object, Current) - Constructor for class ome.services.blitz.util.RegisterServantMessage
-
Create a new message
- RegisterServiceCleanupMessage - Class in ome.services.messages
-
Published when some resource must be cleaned up after method execution.
- RegisterServiceCleanupMessage(Object, Object) - Constructor for class ome.services.messages.RegisterServiceCleanupMessage
-
- registerTrigger(String, Trigger) - Method in class ome.services.scheduler.SchedulerFactoryBean
-
Registers a JobDetailAwareTrigger
.
- Registry - Interface in ome.services.blitz.fire
-
Helper class which makes the RegistryPrx
available within
OmeroBlitz.
- registry - Variable in class ome.services.blitz.fire.SessionManagerI
-
- Registry.Impl - Class in ome.services.blitz.fire
-
- Registry.Impl(Communicator) - Constructor for class ome.services.blitz.fire.Registry.Impl
-
- reindex(T) - Method in class ome.services.fulltext.BridgeHelper
-
- reindexAll(List<T>) - Method in class ome.services.fulltext.BridgeHelper
-
- ReindexMessage<T extends ome.model.IObject> - Class in ome.services.messages
-
Published when one or more IObject
instances must be re-indexed.
- ReindexMessage(Object, List<T>) - Constructor for class ome.services.messages.ReindexMessage
-
- relativeDN(String) - Method in class ome.security.auth.LdapConfig
-
Calculate the relative DN based on the current base.
- release(String, int) - Method in class ome.services.graphs.GraphState
-
- release(String, int) - Method in interface ome.services.graphs.GraphStep.Callback
-
- release(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep
-
- releaseDate - Static variable in class ome.formats.importer.Version
-
The data of the last release date.
- releaseLock(String) - Method in class omero.util.ServantHolder
-
Releases the given lock if found, otherwise throws an
InternalException
- reload(String) - Method in interface ome.services.sessions.SessionManager
-
- reload(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- reload(SessionContext) - Method in class ome.services.sessions.SessionManagerImpl
-
Will be called in a synchronized block by
SessionCache
in order
to allow for an update.
- reload(String) - Method in class ome.services.sessions.state.SessionCache
-
Provides the reloading logic of the
SessionCache
for the
SessionManagerImpl
to use.
- reload(SessionContext) - Method in interface ome.services.sessions.state.SessionCache.StaleCacheListener
-
Method called for every active session in the cache.
- ReloadFilter - Class in ome.tools.hibernate
-
UpdateFilter
subclass specialized for use with the
Session.save(Object)
(as opposed to
Session.merge(Object)
)
method.
- ReloadFilter(Session) - Constructor for class ome.tools.hibernate.ReloadFilter
-
- ReloadingRefreshEventListener - Class in ome.tools.hibernate
-
responsible for responding to RefreshEvent
. in particular in
reloading the unloaded
entities.
- ReloadingRefreshEventListener() - Constructor for class ome.tools.hibernate.ReloadingRefreshEventListener
-
- remove() - Method in interface ome.api.Search
-
Unsupported operation.
- remove() - Method in class ome.services.eventlogs.EventBacklog
-
Removes and returns the next EventLog
instance or null if none is
present.
- remove() - Method in class ome.services.eventlogs.EventLogLoader
-
- remove() - Method in class ome.services.graphs.BaseGraphSpec.SubSpecIterator
-
- remove() - Method in class ome.services.SearchBean
-
- remove() - Method in class omeis.providers.re.codomain.CodomainChain
-
- remove(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain
-
Removes a map context from the chain.
- remove(Resources.Entry) - Method in class omero.util.Resources
-
- remove(Identity) - Method in class omero.util.ServantHolder
-
- remove_async(AMD_Search_remove, Current) - Method in class ome.services.blitz.impl.SearchI
-
- remove_path(File) - Static method in class omero.util.TempFileManager
-
- removeAllDisabled(String...) - Method in class ome.security.basic.CurrentDetails
-
- removeAllListeners() - Method in class ome.services.messages.GlobalMulticaster
-
- removeApplicationListener(ApplicationListener) - Method in class ome.services.messages.GlobalMulticaster
-
- removeApplicationListenerBean(String) - Method in class ome.services.messages.GlobalMulticaster
-
- removeCallback(CmdCallbackPrx, Current) - Method in class omero.cmd.HandleI
-
- removeClientId(String) - Method in class omero.util.ServantHolder
-
- removeCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean
-
- removeCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine
-
Removes the specified context from the chain.
- removeCodomainMap_async(AMD_RenderingEngine_removeCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- removeCodomainMap_async(AMD_RenderingEngine_removeCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- removeCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- removeDisabled(String) - Method in class ome.security.basic.CurrentDetails
-
- removeFiles(List<Long>) - Method in class ome.io.nio.OriginalFilesService
-
Removes files from data repository based on a parameterized List of
Long file ids
- removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in interface ome.api.IAdmin
-
removes the given users from the owner list for this group.
- removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in class ome.logic.AdminImpl
-
- removeGroupOwners_async(AMD_IAdmin_removeGroupOwners, ExperimenterGroup, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.AdminI
-
- removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.api.IAdmin
-
Removes an experimenter from the given groups.
- removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
-
- removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
-
- removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
-
- removeGroups_async(AMD_IAdmin_removeGroups, Experimenter, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
-
- removeGuest(long, String) - Method in interface ome.api.IShare
-
Removes guest email address from share.
- removeGuest(long, String) - Method in class ome.services.sharing.ShareBean
-
- removeGuest_async(AMD_IShare_removeGuest, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
-
- removeGuests(long, String...) - Method in interface ome.api.IShare
-
Removes guest email addresses from the share.
- removeGuests(long, String...) - Method in class ome.services.sharing.ShareBean
-
- removeGuests_async(AMD_IShare_removeGuests, long, List<String>, Current) - Method in class ome.services.blitz.impl.ShareI
-
- removeIObjectContainer(LSID) - Method in interface ome.formats.model.IObjectContainerStore
-
Removes an IObject container from within the OME-XML data model store.
- removeIObjectContainer(LSID) - Method in class ome.formats.OMEROMetadataStoreClient
-
- removeMissingFilesFromDb(SqlAction, Session, List<OriginalFile>) - Method in class ome.services.scripts.ScriptRepoHelper
-
Given the current files on disk, #unregister(Long, Session)
all files which have been removed from disk.
- removeModelProcessor(ModelProcessor) - Method in class ome.formats.OMEROMetadataStoreClient
-
Removes a model processor from use.
- removeNamespace(String) - Method in class pojos.ROIData
-
Removes the namespace from the ROI.
- removeObject(long, T) - Method in interface ome.api.IShare
-
Removes existing item
from the
share
.
- removeObject(Identity) - Method in class ome.services.blitz.fire.Registry.Impl
-
- removeObject(Identity) - Method in interface ome.services.blitz.fire.Registry
-
- removeObject(long, T) - Method in class ome.services.sharing.ShareBean
-
- removeObject_async(AMD_IShare_removeObject, long, IObject, Current) - Method in class ome.services.blitz.impl.ShareI
-
- removeObjects(long, T...) - Method in interface ome.api.IShare
-
Remove existing items from the share.
- removeObjects(long, T...) - Method in class ome.services.sharing.ShareBean
-
- removeObjects_async(AMD_IShare_removeObjects, long, List<IObject>, Current) - Method in class ome.services.blitz.impl.ShareI
-
- removeObjectSafely(Identity) - Method in class ome.services.blitz.fire.Registry.Impl
-
- removeObjectSafely(Identity) - Method in interface ome.services.blitz.fire.Registry
-
- removePath(File) - Method in class omero.util.TempFileManager
-
- removePixels(List<Long>) - Method in class ome.io.nio.PixelsService
-
Removes files from data repository based on a parameterized List of Long
pixels ids
- removeProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
-
- removeServer(String) - Method in class ome.formats.importer.ImportConfig
-
- removeSession(String) - Method in class ome.services.sessions.state.SessionCache
-
- removeSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache
-
- removeShapeData(ShapeData) - Method in class pojos.ROIData
-
Removes the ShapeData object from ROIData.
- removeThumbnails(List<Long>) - Method in class ome.io.nio.ThumbnailService
-
Removes files from data repository based on a parameterized List of Long
thumbnail ids
- 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.
- removeUnusedFiles() - Method in class ome.logic.RepositoryInfoImpl
-
- removeUnusedFiles_async(AMD_IRepositoryInfo_removeUnusedFiles, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
-
- removeUser(long, Experimenter) - Method in interface ome.api.IShare
-
Removes experimenter
from
share
- removeUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean
-
- removeUser_async(AMD_IShare_removeUser, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
-
- removeUsers(long, List<Experimenter>) - Method in interface ome.api.IShare
-
Removes experimenters
from
share
- removeUsers(long, List<Experimenter>) - Method in class ome.services.sharing.ShareBean
-
- removeUsers_async(AMD_IShare_removeUsers, long, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.ShareI
-
- removingOnly() - Method in class ome.services.eventlogs.EventBacklog
-
- rename(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
- render(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
- render(PlaneDef) - Method in class ome.services.RenderingBean
-
- render(PlaneDef) - Method in class omeis.providers.re.Renderer
-
Renders the data selected by pd
according to the current
rendering settings.
- render(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine
-
Renders the data selected by pd
according to the current
rendering settings.
- render_async(AMD_RenderingEngine_render, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- render_async(AMD_RenderingEngine_render, PlaneDef, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- renderAsPackedInt(Long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
- renderAsPackedInt(Long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService
-
Render as a packedInt
- renderAsPackedInt(PlaneDef) - Method in class ome.services.RenderingBean
-
- renderAsPackedInt(PlaneDef, PixelBuffer) - Method in class omeis.providers.re.Renderer
-
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.
- renderAsPackedInt_async(AMD_RenderingEngine_renderAsPackedInt, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- renderAsPackedInt_async(AMD_RenderingEngine_renderAsPackedInt, PlaneDef, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- renderAsPackedIntAsRGBA(long, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
-
- renderAsPackedIntAsRGBA(long, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService
-
Render image as Buffered image.
- renderAsPackedIntAsRGBA(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
-
- renderAsPackedIntAsRGBA(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
- renderAsPackedIntAsRGBA(long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService
-
Render image as Buffered image.
- renderAsPackedIntAsRGBA(PlaneDef) - Method in class ome.services.RenderingBean
-
- renderAsPackedIntAsRGBA(PlaneDef, PixelBuffer) - Method in class omeis.providers.re.Renderer
-
Renders the data selected by pd
according to the current
rendering settings.
- renderAsPackedIntAsRGBA(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine
-
Renders the data selected by pd
according to the current
rendering settings.
- renderAsPackedIntAsRGBA_async(AMD_RenderingEngine_renderAsPackedIntAsRGBA, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- renderAsPackedIntAsRGBA_async(AMD_RenderingEngine_renderAsPackedIntAsRGBA, PlaneDef, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- renderCompressed(PlaneDef) - Method in class ome.services.RenderingBean
-
- 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.
- renderCompressed_async(AMD_RenderingEngine_renderCompressed, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- renderCompressed_async(AMD_RenderingEngine_renderCompressed, PlaneDef, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- Renderer - Class in omeis.providers.re
-
Transforms raw image data into an RGB image that can be displayed on
screen.
- Renderer(QuantumFactory, List<RenderingModel>, Pixels, RenderingDef, PixelBuffer) - Constructor for class omeis.providers.re.Renderer
-
Creates a new instance to render the specified pixels set and get this
new instance ready for rendering.
- RENDERING_DEF_QUERY_PREFIX - Static variable in class ome.logic.PixelsImpl
-
Standard rendering definition HQL query prefix
- RenderingBean - Class in ome.services
-
- RenderingBean(PixelsService, LocalCompress, Executor, SecuritySystem) - Constructor for class ome.services.RenderingBean
-
Compression service Bean injector.
- RenderingDefGraphSpec - Class in ome.services.graphs
-
- RenderingDefGraphSpec(List<String>) - Constructor for class ome.services.graphs.RenderingDefGraphSpec
-
Creates a new instance.
- RenderingEngine - Interface in omeis.providers.re
-
Defines a service to render a given pixels set.
- RenderingEngineI - Class in ome.services.blitz.impl
-
Implementation of the RenderingEngine service.
- RenderingEngineI(RenderingEngine, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingEngineI
-
- RenderingService - Interface in ome.services.blitz.gateway.services
-
- RenderingServiceImpl - Class in ome.services.blitz.gateway.services.impl
-
- RenderingServiceImpl(RenderingEnginePrx) - Constructor for class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
-
Create the ImageService passing the gateway.
- RenderingSettingsI - Class in ome.services.blitz.impl
-
Implementation of the IRenderingSettings service.
- RenderingSettingsI(IRenderingSettings, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingSettingsI
-
- RenderingSettingsImpl - Class in ome.logic
-
- RenderingSettingsImpl() - Constructor for class ome.logic.RenderingSettingsImpl
-
- RenderingStats - Class in omeis.providers.re
-
Exposes methods to time the various steps in the rendering process and
provides a stats report.
- RenderingStats(Renderer, PlaneDef) - Constructor for class omeis.providers.re.RenderingStats
-
Creates a new instance.
- RenderingTask - Interface in omeis.providers.re
-
This interface represents a rendering operation task.
- renderProjectedAsPackedInt(int, int, int, int, int) - Method in class ome.services.RenderingBean
-
- 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.
- renderProjectedAsPackedInt_async(AMD_RenderingEngine_renderProjectedAsPackedInt, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- renderProjectedAsPackedInt_async(AMD_RenderingEngine_renderProjectedAsPackedInt, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- renderProjectedCompressed(int, int, int, int, int) - Method in class ome.services.RenderingBean
-
- 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.
- renderProjectedCompressed_async(AMD_RenderingEngine_renderProjectedCompressed, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- renderProjectedCompressed_async(AMD_RenderingEngine_renderProjectedCompressed, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- ReorderedPixelData - Class in ome.io.nio
-
Represents a block of pixel data that needs to be re-ordered in accordance
with a DeltaVision file.
- ReorderedPixelData(String, ByteBuffer, int) - Constructor for class ome.io.nio.ReorderedPixelData
-
Default constructor.
- replace(Object, Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- repo - Variable in class ome.services.pixeldata.PersistentEventLogLoader
-
- RepoFile - Class in ome.services.scripts
-
File type wrapper for paths which are intended for being stored in the
database as a part of this repository.
- RepoFile(File, String) - Constructor for class ome.services.scripts.RepoFile
-
- RepoFile(File, File) - Constructor for class ome.services.scripts.RepoFile
-
Both root and file are absolute paths to files.
- RepoFile.FsFile - Class in ome.services.scripts
-
File type wrapper for actual OS files.
- RepoRawFileStoreI - Class in ome.services.blitz.repo
-
An implementation of the RepoRawFileStore interface
- RepoRawFileStoreI(long, File) - Constructor for class ome.services.blitz.repo.RepoRawFileStoreI
-
- report(Current) - Method in class ome.services.blitz.impl.DeleteHandleI
-
- reportForgottenPassword(String, String) - Method in interface ome.api.IAdmin
-
Can be used after repeated AuthenticationException
instances are
thrown, to request that an email with a temporary password be sent.
- reportForgottenPassword(String, String) - Method in class ome.logic.AdminImpl
-
- reportForgottenPassword_async(AMD_IAdmin_reportForgottenPassword, String, String, Current) - Method in class ome.services.blitz.impl.AdminI
-
- repositories(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
-
- RepositoryInfoI - Class in ome.services.blitz.impl
-
Implementation of the IRepositoryInfo service.
- RepositoryInfoI(IRepositoryInfo, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RepositoryInfoI
-
- RepositoryInfoImpl - Class in ome.logic
-
Class implementation of the IRepositoryInfo service interface.
- RepositoryInfoImpl() - Constructor for class ome.logic.RepositoryInfoImpl
-
- RepositoryTask - Class in ome.tools
-
Class implementation of various mechanised tasks, database queries, file I/O,
etc.
- RepositoryTask(SqlAction) - Constructor for class ome.tools.RepositoryTask
-
Constructor
- reps - Variable in class ome.services.fulltext.FullTextIndexer
-
- reps - Variable in class ome.services.pixeldata.PixelDataHandler
-
- requestFromUser() - Method in class ome.formats.importer.ImportConfig
-
if can't log in request needed information
- requestHeartBeats() - Method in class ome.services.blitz.fire.SessionManagerI
-
- RequestObjectFactoryRegistry - Class in ome.services.blitz.impl.commands
-
Types which rely on the omero.model and omero.api objects rather than just
the omero.cmd types.
- RequestObjectFactoryRegistry() - Constructor for class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
-
- RequestObjectFactoryRegistry - Class in omero.cmd
-
SPI type picked up from the Spring configuration and given a chance to
register all its ObjectFactory
instances with the
Communicator
.
- RequestObjectFactoryRegistry(ExtendedMetadata, Roles) - Constructor for class omero.cmd.RequestObjectFactoryRegistry
-
- REQUEUED - Static variable in interface ome.api.JobHandle
-
- requiresCompanion(String) - Static method in class ome.services.util.DBEnumCheck
-
- requiresPixelsPyramid() - Method in interface ome.api.RawPixelsStore
-
- requiresPixelsPyramid(Pixels) - Method in class ome.io.nio.PixelsService
-
Returns true if a pyramid should be used for the given Pixels
.
- requiresPixelsPyramid() - Method in class ome.services.RawPixelsBean
-
- requiresPixelsPyramid() - Method in class ome.services.RenderingBean
-
- requiresPixelsPyramid() - Method in interface omeis.providers.re.RenderingEngine
-
- requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
-
- requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- 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.
- 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 class ome.logic.RenderingSettingsImpl
-
- resetDefaults() - Method in class ome.services.RenderingBean
-
- resetDefaults() - Method in class ome.services.SearchBean
-
- resetDefaults() - Method in class ome.services.ThumbnailBean
-
- resetDefaults() - Method in interface omeis.providers.re.RenderingEngine
-
Resets the default settings i.e. the default values internal to the
Rendering engine.
- resetDefaults_async(AMD_RenderingEngine_resetDefaults, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- resetDefaults_async(AMD_IRenderingSettings_resetDefaults, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
-
- resetDefaults_async(AMD_Search_resetDefaults, Current) - Method in class ome.services.blitz.impl.SearchI
-
- resetDefaults_async(AMD_ThumbnailStore_resetDefaults, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- resetDefaults_async(AMD_RenderingEngine_resetDefaults, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- resetDefaultsAndGenerateThumbnails(List<Long>, List<Long>) - Method in class ome.formats.OMEROMetadataStoreClient
-
Resets the defaults and generates thumbnails for a given set of Pixels
IDs.
- 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).
- resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
-
- resetDefaultsByOwnerInSet_async(AMD_IRenderingSettings_resetDefaultsByOwnerInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
-
- 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.
- resetDefaultsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl
-
- resetDefaultsForPixels_async(AMD_IRenderingSettings_resetDefaultsForPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
-
- 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.
- resetDefaultsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl
-
- resetDefaultsInDataset_async(AMD_IRenderingSettings_resetDefaultsInDataset, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
-
- 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.
- resetDefaultsInImage(long) - Method in class ome.logic.RenderingSettingsImpl
-
- resetDefaultsInImage_async(AMD_IRenderingSettings_resetDefaultsInImage, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
-
- 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.
- resetDefaultsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
-
- resetDefaultsInSet_async(AMD_IRenderingSettings_resetDefaultsInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
-
- 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.
- resetDefaultsNoSave(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl
-
- resetDefaultsNoSave() - Method in class ome.services.RenderingBean
-
- resetDefaultsNoSave() - Method in interface omeis.providers.re.RenderingEngine
-
Resets the default settings i.e. the default values internal to the
Rendering engine.
- resetDefaultsNoSave_async(AMD_RenderingEngine_resetDefaultsNoSave, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- resetDefaultsNoSave_async(AMD_IRenderingSettings_resetDefaultsNoSave, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
-
- resetDefaultsNoSave_async(AMD_RenderingEngine_resetDefaultsNoSave, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI
-
- resetDetails(IObject, Object[], Object[], int, Details) - Method in class ome.security.basic.OmeroInterceptor
-
asks
BasicSecuritySystem
to create a new managed
Details
based on the previous state of this entity.
- resetEnumerations(Class<T>) - Method in interface ome.api.ITypes
-
- resetEnumerations(Class<T>) - Method in class ome.logic.TypesImpl
-
- resetEnumerations_async(AMD_ITypes_resetEnumerations, String, Current) - Method in class ome.services.blitz.impl.TypesI
-
- 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.
- resetMinMaxInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
-
- resetMinMaxInSet_async(AMD_IRenderingSettings_resetMinMaxInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
-
- resetReadFilter(Session) - Method in interface ome.api.local.LocalShare
-
- resetReadFilter(Session) - Method in class ome.services.sharing.ShareBean
-
- resolveAlias(String) - Method in class ome.system.PreferenceContext
-
- resolveConfigFile(String) - Method in class ome.services.blitz.util.BlitzConfiguration
-
Resolve the given config file to a concrete location, possibly throwing
an exception if stored in a jar.
- resolver - Variable in class ome.io.nio.PixelsService
-
Resolver of archived original file paths for pixels sets.
- resource - Variable in class ome.services.messages.RegisterServiceCleanupMessage
-
- Resources - Class in omero.util
-
Container class for storing resources which should be cleaned up on close and
periodically checked.
- Resources() - Constructor for class omero.util.Resources
-
- Resources(int) - Constructor for class omero.util.Resources
-
- Resources(int, ScheduledExecutorService) - Constructor for class omero.util.Resources
-
- Resources.Entry - Interface in omero.util
-
Interface to be implemented by any object which wants to be managed by
the
Resources
class.
- response - Variable in class ome.services.throttling.Task
-
- response(Object, OmeroContext) - Method in class ome.services.throttling.Task
-
Calls the response method
- responseRunning(List<Long>, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
-
Callback method which should not be called for this instance.
- restartIfNeeded() - Method in class ome.services.scheduler.SchedulerFactoryBean
-
Similar to the SchedulerFactoryBean.isRunning()
method, but properly handles the
situation where the Scheduler
has been completely shutdown and
therefore must be replaced.
- RESUBMITTED - Static variable in interface ome.api.JobHandle
-
- ResultHolder<U> - Class in ome.services.blitz.util
-
- ResultHolder(long) - Constructor for class ome.services.blitz.util.ResultHolder
-
- results() - Method in interface ome.api.Search
-
Returns up to
batch size
number of results along
with the related query metadata.
- results() - Method in class ome.services.SearchBean
-
- results_async(AMD_Search_results, Current) - Method in class ome.services.blitz.impl.SearchI
-
- 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
- retrieveAllRndSettings(long, long) - Method in class ome.logic.PixelsImpl
-
Implemented as specified by the
IPixels
I/F.
- retrieveAllRndSettings_async(AMD_IPixels_retrieveAllRndSettings, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI
-
- retrieveCollection(IObject, String, Parameters) - Method in interface ome.api.IContainer
-
Retrieves a collection with all members initialized ("loaded").
- retrieveCollection(IObject, String, Parameters) - Method in class ome.logic.PojosImpl
-
- retrieveCollection_async(AMD_IContainer_retrieveCollection, IObject, String, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
-
- 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
- retrievePixDescription(long) - Method in class ome.logic.PixelsImpl
-
- retrievePixDescription_async(AMD_IPixels_retrievePixDescription, long, Current) - Method in class ome.services.blitz.impl.PixelsI
-
- retrieveResult(int, List) - Method in interface ome.api.IResults
-
retrieving data for PixelSet
- retrieveResultPrimitive(int, String[]) - Method in interface ome.api.IResults
-
- retrieveResultsBulk(int[], List[]) - Method in interface ome.api.IResults
-
- retrieveResultsBulkPrimitive(int[], String[][]) - Method in interface ome.api.IResults
-
- retrieveRndSettings(long) - Method in interface ome.api.IPixels
-
Retrieves the rendering settings for a given pixels set and the currently
logged in user.
- retrieveRndSettings(long) - Method in class ome.logic.PixelsImpl
-
Implemented as specified by the
IPixels
I/F.
- retrieveRndSettings_async(AMD_IPixels_retrieveRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI
-
- 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
- retrieveRndSettingsFor(long, long) - Method in class ome.logic.PixelsImpl
-
Implemented as specified by the
IPixels
I/F.
- retrieveRndSettingsFor_async(AMD_IPixels_retrieveRndSettingsFor, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI
-
- returnedClass() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- returnSeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
-
- returnUnloaded - Variable in class ome.services.search.SearchValues
-
- reusedSession - Variable in class omero.cmd.SessionI
-
- reverse(Object) - Method in class omero.util.IceMapper
-
- reverse(Collection) - Method in class omero.util.IceMapper
-
Copied from ModelMapper.findCollection(Collection)
This could be
unified in that a method findCollection(Collection, Map) was added with
ModelMapper
calling findCollection(source,model2target) and
#reverseCollection(Collection)
calling
findCollection(source,target2model).
- reverse(Collection, Class) - Method in class omero.util.IceMapper
-
Creates a collection assignable to the given type.
- reverse(Map) - Method in class omero.util.IceMapper
-
- reverse(ModelBased) - Method in class omero.util.IceMapper
-
Copied from ReverseModelMapper#map(ModelBased)
- reverseArray(List, Class) - Method in class omero.util.IceMapper
-
Supports the separate case of reversing for arrays.
- ReverseIntensityContext - Class in omeis.providers.re.codomain
-
The empty context of the reverse intensity map.
- ReverseIntensityContext() - Constructor for class omeis.providers.re.codomain.ReverseIntensityContext
-
- revision - Static variable in class ome.formats.importer.Version
-
The repository revision.
- RevisionDate - Annotation Type in ome.annotations
-
annotation used for tracking source code changes.
- revisionDate - Static variable in class ome.formats.importer.Version
-
The data of the last repository revision.
- RevisionNumber - Annotation Type in ome.annotations
-
annotation used for tracking source code changes.
- rfloat(float) - Static method in class omero.rtypes
-
- 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.
- Ring - Class in ome.services.blitz.fire
-
Distributed ring of
BlitzConfiguration
objects which manages lookups
of sessions and other resources from all the blitzes which take part in the
cluster.
- Ring(String, Executor) - Constructor for class ome.services.blitz.fire.Ring
-
- Ring(String, Executor, Redirector) - Constructor for class ome.services.blitz.fire.Ring
-
- ring - Variable in class ome.services.blitz.fire.SessionManagerI
-
- rint(int) - Static method in class omero.rtypes
-
- rinternal(Internal) - Static method in class omero.rtypes
-
- rlist(RType...) - Static method in class omero.rtypes
-
- rlist(Collection<RType>) - Static method in class omero.rtypes
-
- rlong(long) - Static method in class omero.rtypes
-
- rmap() - Static method in class omero.rtypes
-
- rmap(Map<String, RType>) - Static method in class omero.rtypes
-
- rmap(String, RType) - Static method in class omero.rtypes
-
- robject(IObject) - Static method in class omero.rtypes
-
- ROIComponent - Class in pojos.util
-
Component hosting the ROI.
- ROIComponent(long) - Constructor for class pojos.util.ROIComponent
-
Instantiate the ROIComponent.
- ROICoordinate - Class in pojos
-
Defines a plane.
- ROICoordinate() - Constructor for class pojos.ROICoordinate
-
Creates a default instance.
- ROICoordinate(int, int) - Constructor for class pojos.ROICoordinate
-
Creates a new instance.
- ROIData - Class in pojos
-
Converts the ROI object.
- ROIData(Roi) - Constructor for class pojos.ROIData
-
Creates a new instance.
- ROIData() - Constructor for class pojos.ROIData
-
Create a new instance of an ROIData object.
- RoiI - Class in ome.services.blitz.impl
-
implementation of the IRoi service interface.
- RoiI(BlitzExecutor, GeomTool, SqlAction) - Constructor for class ome.services.blitz.impl.RoiI
-
- RoiI.RoiResultMapper - Class in ome.services.blitz.impl
-
- RoiI.RoiResultMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultMapper
-
- RoiI.RoiResultMapReturnMapper - Class in ome.services.blitz.impl
-
- RoiI.RoiResultMapReturnMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultMapReturnMapper
-
- RoiI.RoiResultReturnMapper - Class in ome.services.blitz.impl
-
- RoiI.RoiResultReturnMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultReturnMapper
-
- RoiTypes - Class in ome.services.roi
-
Intelligent server-side representations of the Roi
and Shape
types.
- RoiTypes() - Constructor for class ome.services.roi.RoiTypes
-
- RoiTypes.RoiTypesObjectFactoryRegistry - Class in ome.services.roi
-
- RoiTypes.RoiTypesObjectFactoryRegistry() - Constructor for class ome.services.roi.RoiTypes.RoiTypesObjectFactoryRegistry
-
- roleProvider - Variable in class ome.logic.AdminImpl
-
- RoleProvider - Interface in ome.security.auth
-
Provides user
and group
creation, deletion, and modification for use by services.
- roles - Variable in class ome.security.basic.AbstractSecurityFilter
-
- roles - Variable in class ome.security.basic.BasicACLVoter
-
- roles - Variable in class ome.security.basic.BasicSecuritySystem
-
- roles - Variable in class ome.services.sessions.SessionManagerImpl
-
- 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.
- rollback(EventLog) - Method in class ome.services.eventlogs.EventLogLoader
-
- rollback(String, int) - Method in class ome.services.graphs.GraphState
-
- rollback(String, int) - Method in interface ome.services.graphs.GraphStep.Callback
-
- rollback(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep
-
- rollbackOnly() - Method in class ome.services.graphs.GraphStep
-
- RomioPixelBuffer - Class in ome.io.nio
-
Class implementation of the PixelBuffer interface for standard "proprietary"
ROMIO/OMEIS data format.
- RomioPixelBuffer(String, Pixels) - Constructor for class ome.io.nio.RomioPixelBuffer
-
Creates a new instance.
- RomioPixelBuffer(String, Pixels, boolean) - Constructor for class ome.io.nio.RomioPixelBuffer
-
- root(Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
- ROOT - Static variable in class prefs
-
"omero.prefs", the value of the root
Preferences
node used for
all configuration work.
- ROOT_DEFAULT - Static variable in class ome.io.nio.AbstractFileSystemService
-
- ROUTED_FROM - Static variable in class ome.services.blitz.redirect.AbstractRedirector
-
- Router - Class in ome.services.blitz
-
Wrapper around a call to 'glacier2router' to permit Java control over the
process.
- Router() - Constructor for class ome.services.blitz.Router
-
- rps - Variable in class omero.util.RPSTileData
-
- RPSTileData - Class in omero.util
-
Access strategy which can be implemented by diverse resources
- RPSTileData(RPSTileLoop, RawPixelsStorePrx) - Constructor for class omero.util.RPSTileData
-
- RPSTileLoop - Class in omero.util
-
Helper subclass of
TileLoop
which handles
unloaded
Pixels
instances and manages the
creation of the
RPSTileData
.
- RPSTileLoop(ServiceFactoryPrx, Pixels) - Constructor for class omero.util.RPSTileLoop
-
- rset(RType...) - Static method in class omero.rtypes
-
- rset(Collection<RType>) - Static method in class omero.rtypes
-
- rstring(String) - Static method in class omero.rtypes
-
- RTF - Static variable in class pojos.FileAnnotationData
-
Identifies the RTF
file formats.
- rtime(long) - Static method in class omero.rtypes
-
- rtime(Date) - Static method in class omero.rtypes
-
- rtime_max() - Static method in class omero.rtypes
-
- rtime_min() - Static method in class omero.rtypes
-
- rtime_str(String) - Static method in class omero.rtypes
-
- rtype(Object) - Static method in class omero.rtypes
-
Attempts to dispatch to the other omero.rtypes.* static methods
to create a proper RType
subclass by checking the type
of the input.
- RTYPEDICT - Static variable in class omero.util.IceMapper
-
- RTypeMapper - Class in omero.util
-
Extension of
IceMapper
which guarantees that
RCollection
and
RMap
instances are properly created.
- RTypeMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.RTypeMapper
-
- rtypes - Class in omero
-
Abstract class similar to
Arrays
or
Collections
which is responsible for creating RTypes from
static factory methods.
- rtypes() - Constructor for class omero.rtypes
-
- rtypes.Conversion - Interface in omero
-
SPI-style interface which helps the omero server to properly convert
omero.RType objects into Java-native objects for use in Hibernate.
- rtypes.RTypeObjectFactoryRegistry - Class in omero
-
- rtypes.RTypeObjectFactoryRegistry() - Constructor for class omero.rtypes.RTypeObjectFactoryRegistry
-
- run() - Method in class ome.formats.importer.util.ClientKeepAlive
-
- run(int, int, int, int, int, int, int, int) - Method in interface ome.io.nio.TileLoopIteration
-
Invoke a single loop iteration.
- run() - Method in class ome.services.blitz.impl.DeleteHandleI
-
- run() - Method in class ome.services.blitz.Status
-
- run() - Method in class ome.services.blitz.util.CheckAllJobs
-
- run() - Method in interface ome.services.procs.IProcessManager
-
Runs the processing phase as root.
- run(OmeroContext) - Method in class ome.services.throttling.Adapter
-
- run(OmeroContext) - Method in class ome.services.throttling.Callback
-
- run(OmeroContext) - Method in class ome.services.throttling.Callback2
-
- run() - Method in class ome.services.throttling.Slot
-
- run(OmeroContext) - Method in class ome.services.throttling.Task
-
- run() - Method in class ome.services.util.DropBoxDirectoryCheck
-
Synchronizes the ${omero.data.dir}/DropBox directory by creating a
directory for any user who does not have one.
- run() - Method in class ome.services.util.ExecutionThread
-
- run() - Method in class ome.services.util.ServerDirectoryCheck
-
Synchronizes the ${omero.data.dir}/Server directory by creating a
directory for any user who does not have one.
- run() - Method in class ome.system.UpgradeCheck
-
If the
UpgradeCheck.url
has been set to null or the empty string, then no
upgrade check will be performed (silently).
- run() - Method in class omero.cmd.HandleI
-
- run(TileData, int, int, int, int, int, int, int, int) - Method in interface omero.util.TileLoopIteration
-
Invoke a single loop iteration.
- runAsAdmin() - Method in interface ome.security.AdminAction
-
- runAsAdmin(AdminAction) - Method in class ome.security.basic.BasicSecuritySystem
-
- runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.basic.BasicSecuritySystem
-
- runAsAdmin(ExperimenterGroup, AdminAction) - Method in interface ome.security.SecuritySystem
-
- runAsAdmin(AdminAction) - Method in interface ome.security.SecuritySystem
-
- runAsAdmin(AdminAction) - Method in class ome.security.SecuritySystemHolder
-
- runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.SecuritySystemHolder
-
- runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
-
- runAsAdmin(AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
-
- runAsAdmin() - Method in class ome.services.delete.QueryConstraints
-
- runnableCall(Current, Task) - Method in class ome.services.blitz.impl.AbstractAmdServant
-
- runnableCall(Current, Task) - Method in interface ome.services.blitz.util.BlitzExecutor
-
- runnableCall(Current, Task) - Method in class ome.services.throttling.InThreadThrottlingStrategy
-
- runnableCall(Current, Task) - Method in class ome.services.throttling.SerialThrottlingStrategy
-
- RUNNING - Static variable in interface ome.api.JobHandle
-
- runningProcess(long) - Method in interface ome.services.procs.IProcessManager
-
Returns a running
Process
for the
id
or null.
- runningProcess(long) - Method in class ome.services.procs.ProcessManager
-
- runScript_async(AMD_IScript_runScript, long, Map<String, RType>, RInt, Current) - Method in class ome.services.blitz.impl.ScriptI
-