- 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, String) - Constructor for class omero.cmd.CallContext
-
- CallContext(CurrentDetails, String) - 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(IObject) - Method in interface ome.api.local.LocalAdmin
-
Companion to IAdmin#canUpdate(IObject)
but not yet remotely
accessible.
- canAnnotate(IObject) - Method in class ome.logic.AdminImpl
-
- 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(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() - Method in class ome.services.blitz.repo.CheckedPath
-
- 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() - Method in class ome.services.blitz.repo.CheckedPath
-
Check if this file is actually readable on the underlying filesystem.
- 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(IObject, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
-
Delegates to IAdmin#canUpdate
- canUpdate(IObject, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- canUpdate_async(AMD_IAdmin_canUpdate, IObject, Current) - Method in class ome.services.blitz.impl.AdminI
-
- canWriteParentDirectory(ServiceFactory, SqlAction, String, CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
Throw a SecurityViolation
if the current
context cannot write to the parent directory.
- caseSensitive - Variable in class ome.services.search.SearchValues
-
- castChildOptions(Collection<ChildOption>) - Static method in class omero.cmd.graphs.ChildOptionI
-
Cast ChildOption[]
to ChildOptionI[]
.
- 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
-
- Channel_EmissionWavelength - Static variable in class ome.formats.model.UnitsFactory
-
- Channel_ExcitationWavelength - Static variable in class ome.formats.model.UnitsFactory
-
- Channel_PinholeSize - Static variable in class ome.formats.model.UnitsFactory
-
- 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
-
- checkAndCollapseGraph() - Method in class ome.formats.OMEROMetadataStore
-
Checks the entire object graph for sections that may be collapsed if
the data is derived from a Plate.
- checkAndRegister() - Method in class ome.services.JobBean
-
- checkArgs(Object...) - Method in class ome.services.graphs.GraphEntry
-
Deprecated.
- 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
-
- CheckedPath - Class in ome.services.blitz.repo
-
To prevent frequently re-calculating paths and re-creating File objects,
CheckedPath
objects store various interpretations of paths that
are passed in by users.
- CheckedPath(ServerFilePathTransformer, String, ChecksumProviderFactory, ChecksumAlgorithm) - Constructor for class ome.services.blitz.repo.CheckedPath
-
Construct a CheckedPath from a relative "/"-delimited path rooted at the repository.
- checkedPaths - Variable in class ome.services.blitz.repo.ManagedImportLocationI
-
- 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
-
- checkIndex(int) - Method in class ome.util.mem.ReadOnlyByteArray
-
Makes sure that i
is in [0, length)
.
- checkLocation(File, RawFileStorePrx) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
-
Check that the target location: 1) doesn't exist and 2) is properly
written to by the server.
- 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.
- checkPath(String, ChecksumAlgorithm, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Create a new
CheckedPath
object based on the given user input.
- 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
-
- checkRestriction(String, IObject) - Method in class ome.security.basic.BasicSecuritySystem
-
- checkRestriction(IObject) - Method in class ome.security.policy.BasePolicy
-
- checkRestriction(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
-
- checkRestriction(String, IObject) - Method in class ome.security.policy.DefaultPolicyService
-
- checkRestriction(IObject) - Method in interface ome.security.policy.Policy
-
Like #isRestricted(Policy)
but throws an appropriate
SecurityViolation
subclass if the restriction is active.
- checkRestriction(String, IObject) - Method in interface ome.security.policy.PolicyService
-
- checkRestriction(String, IObject) - Method in interface ome.security.SecuritySystem
-
Checks whether or not a ome.sercurity.Policy
instance of matching
name has been registered, considers itself active, and
considers the passed context object to be restricted.
- checkRestriction(String, IObject) - Method in class ome.security.SecuritySystemHolder
-
- checkRestriction(String, IObject) - Method in class ome.security.sharing.SharingSecuritySystem
-
- checkState() - Method in class ome.services.procs.ProcessSkeleton
-
- checksum(String, ChecksumAlgorithm) - Method in class ome.formats.importer.exclusions.AbstractFileExclusion
-
- CHECKSUM_ALGORITHM_NAMER - Static variable in class ome.services.blitz.util.ChecksumAlgorithmMapper
-
- checksumAlgorithm - Variable in class ome.formats.importer.ImportConfig
-
- ChecksumAlgorithmMapper - Class in ome.services.blitz.util
-
Work with
ChecksumAlgorithm
enumeration instances,
including mapping their values back to
ChecksumType
s.
- ChecksumAlgorithmMapper() - Constructor for class ome.services.blitz.util.ChecksumAlgorithmMapper
-
- checksumAlgorithms - Variable in class ome.services.blitz.repo.PublicRepositoryI
-
- checksumAsBytes() - Method in class ome.util.checksum.AbstractChecksumProvider
-
- checksumAsBytes() - Method in interface ome.util.checksum.ChecksumProvider
-
Returns a byte array representation of the calculated checksum.
- checksumAsBytes() - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
-
- checksumAsString() - Method in class ome.util.checksum.AbstractChecksumProvider
-
- checksumAsString() - Method in interface ome.util.checksum.ChecksumProvider
-
Returns a String
representing the checksum in hex form.
- checksumAsString() - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
-
- ChecksumProvider - Interface in ome.util.checksum
-
An interface producing checksums or message digests (depending on the
implementing class) of a given type of input.
- checksumProviderFactory - Variable in class ome.services.blitz.repo.PublicRepositoryI
-
- ChecksumProviderFactory - Interface in ome.util.checksum
-
- ChecksumProviderFactoryImpl - Class in ome.util.checksum
-
- ChecksumProviderFactoryImpl() - Constructor for class ome.util.checksum.ChecksumProviderFactoryImpl
-
- checksums - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
-
- 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
-
- checkUpgrade - Variable in class ome.formats.importer.ImportConfig
-
- checkWriteOperationAllowed(Session) - Method in class ome.tools.spring.ManualFlushHibernateTemplate
-
- Chgrp2I - Class in omero.cmd.graphs
-
Request to move model objects to a different experiment group, reimplementing
ChgrpI
.
- Chgrp2I(ACLVoter, SystemTypes, GraphPathBean, Deletion, GraphPolicy, SetMultimap<String, String>) - Constructor for class omero.cmd.graphs.Chgrp2I
-
- ChgrpFacadeI - Class in omero.cmd.graphs
-
- ChgrpFacadeI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.ChgrpFacadeI
-
Deprecated.
- ChgrpI - Class in omero.cmd.graphs
-
- ChgrpI(Communicator, ChgrpStepFactory, ApplicationContext) - Constructor for class omero.cmd.graphs.ChgrpI
-
Deprecated.
- chgrpQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.BaseGraphSpec
-
Deprecated.
- chgrpQuery(EventContext, String, GraphOpts) - Method in interface ome.services.graphs.GraphSpec
-
Deprecated.
- chgrpQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.LightSourceGraphSpec
-
Deprecated.
- ChgrpStep - Class in ome.services.chgrp
-
- ChgrpStep(OmeroContext, ExtendedMetadata, Roles, int, List<GraphStep>, GraphSpec, GraphEntry, long[], long) - Constructor for class ome.services.chgrp.ChgrpStep
-
Deprecated.
- ChgrpStepFactory - Class in ome.services.chgrp
-
- ChgrpStepFactory(OmeroContext, ExtendedMetadata, Roles) - Constructor for class ome.services.chgrp.ChgrpStepFactory
-
Deprecated.
- child(String) - Method in class ome.services.blitz.repo.CheckedPath
-
Returns a new
CheckedPath
that has the given path appended
to the end of this instances path.
- ChildOptionI - Class in omero.cmd.graphs
-
Child options adjust how child objects are treated according to their type and, if annotations, namespace,
overriding the default graph traversal policy for orphans.
- ChildOptionI(GraphPathBean, ImmutableSet<String>) - Constructor for class omero.cmd.graphs.ChildOptionI
-
Construct a new child option instance.
- ChildOptionI(ChildOptionI) - Constructor for class omero.cmd.graphs.ChildOptionI
-
Construct a new child option instance identical to that given.
- ChildOptionsPolicy - Class in omero.cmd.graphs
-
Adjust graph traversal policy for child objects according to their type and, if annotations, namespace.
- ChildOptionsPolicy() - Constructor for class omero.cmd.graphs.ChildOptionsPolicy
-
- 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(Communicator, ChmodStrategy) - Constructor for class omero.cmd.graphs.ChmodI
-
- chmodQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.BaseGraphSpec
-
Deprecated.
- chmodQuery(EventContext, String, GraphOpts) - Method in interface ome.services.graphs.GraphSpec
-
Deprecated.
- 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
-
- Chown2I - Class in omero.cmd.graphs
-
Request to give model objects to a different experimenter, reimplementing
ChownI
.
- Chown2I(ACLVoter, SystemTypes, GraphPathBean, Deletion, GraphPolicy, SetMultimap<String, String>) - Constructor for class omero.cmd.graphs.Chown2I
-
- ChownFacadeI - Class in omero.cmd.graphs
-
- ChownFacadeI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.ChownFacadeI
-
Deprecated.
- ChownI - Class in omero.cmd.graphs
-
- ChownI(Communicator, ChownStepFactory, ApplicationContext) - Constructor for class omero.cmd.graphs.ChownI
-
Deprecated.
- ChownStep - Class in ome.services.chown
-
- ChownStep(OmeroContext, ExtendedMetadata, Roles, int, List<GraphStep>, GraphSpec, GraphEntry, long[], long) - Constructor for class ome.services.chown.ChownStep
-
Deprecated.
- ChownStepFactory - Class in ome.services.chown
-
- ChownStepFactory(OmeroContext, ExtendedMetadata, Roles) - Constructor for class ome.services.chown.ChownStepFactory
-
Deprecated.
- 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.formats.importer.cli.CommandLineImporter
-
Cleans up after a successful or unsuccessful image import.
- 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
-
- CleanupFailure - Exception in ome.formats.importer.transfers
-
Exception
thrown when cleaning up resources after transfer fails
partially or completely.
- CleanupFailure(List<File>) - Constructor for exception ome.formats.importer.transfers.CleanupFailure
-
- cleanupSelf() - Method in class omero.cmd.SessionI
-
Called if this isn't a kill-everything event.
- cleanupUpload(RawFileStorePrx, FileInputStream) - Method in class ome.formats.importer.transfers.AbstractFileTransfer
-
Utility method for closing resources.
- 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
-
- ClientFilePathTransformer - Class in ome.services.blitz.repo.path
-
Transform client-local
File
to repository
FsFile
path.
- ClientFilePathTransformer(Function<String, String>) - Constructor for class ome.services.blitz.repo.path.ClientFilePathTransformer
-
Construct a new client-side file path transformer.
- 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
-
- close(boolean) - Method in class loci.ome.io.OmeroReader
-
- 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(Signal, Integer) - Static method in class ome.services.fulltext.Main
-
- close() - Method in class ome.services.JobBean
-
- close() - Method in class ome.services.messages.ParserOpenFileMessage
-
Used to close the passed in resource.
- 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(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
-
- 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.
- closeCalled(int) - Method in class ome.services.blitz.repo.ManagedImportProcessI
-
- closeCompleted(ImportConfig) - Static method in class ome.formats.importer.cli.CommandLineImporter
-
Look for all ImportProcessPrx
in the current session and close
them if they return a non-null Response
(i.e. they are done).
- closeOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
-
- closeParsedFiles() - Method in class ome.services.fulltext.ParserSession
-
- closeRaf() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- 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
-
Deprecated.
- collapse(boolean) - Method in interface ome.services.graphs.GraphStep.Callback
-
Deprecated.
- collect(UnloadedCollector, Image) - Method in class ome.services.delete.DeleteBean
-
Walks the Image
graph collecting unloaded instances of all
entities for later delete.
- 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
-
Deprecated.
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.
- combineFacadeRequests(List<Request>) - Static method in class omero.cmd.graphs.GraphUtil
-
Deprecated.
because facade classes are deprecated
- combineFilePathRestrictions(FilePathRestrictions...) - Static method in class ome.services.blitz.repo.path.FilePathRestrictions
-
Combine sets of rules to form a set that satisfies them all and that
include transformations away from Unicode control characters.
- CommandLineImporter - Class in ome.formats.importer.cli
-
The base entry point for the CLI version of the OMERO importer.
- CommandLineImporter(ImportConfig, String[], boolean) - Constructor for class ome.formats.importer.cli.CommandLineImporter
-
- CommandLineImporter(ImportConfig, String[], boolean, FileTransfer, int) - Constructor for class ome.formats.importer.cli.CommandLineImporter
-
Legacy constructor without any file exclusions.
- CommandLineImporter(ImportConfig, String[], boolean, FileTransfer, List<FileExclusion>, int) - Constructor for class ome.formats.importer.cli.CommandLineImporter
-
Main entry class for the application.
- commonRoot(List<FsFile>) - Method in class ome.services.blitz.repo.ManagedRepositoryI
-
From a list of paths, calculate the common root path that all share.
- COMPANION_FILE_NS - Static variable in class pojos.FileAnnotationData
-
The name space used to indicate that the FileAnnotation
is a companion file.
- 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.
- completeFast - Variable in class ome.services.fulltext.FullTextIndexer
-
- completeSlow - Variable in class ome.services.fulltext.FullTextIndexer
-
- 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.
- concatenate(FsFile...) - Static method in class ome.services.blitz.repo.path.FsFile
-
Concatenate paths.
- 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.cli.CommandLineImporter
-
Configuration used by all components
- 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(String) - Method in class ome.formats.importer.ImportConfig
-
Modifies the logging level of everything under the
ome.formats
, ome.services.blitz
,
ome.system
and loci
packages 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
-
- configureServant(Object) - Method in class omero.cmd.SessionI
-
Apply proper AOP and call setters for any known injection properties.
- 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
-
- container - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
-
- 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.blitz.repo.PublicRepositoryI
-
- context - Variable in class ome.services.fulltext.FileParser
-
- context - Variable in class ome.services.fulltext.FullTextIndexer
-
- 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(ElectricPotential) - Static method in class omero.model.ElectricPotentialI
-
FIXME: this should likely take a default so that locations which don't
want an exception can have
log.warn("Using new PositiveFloat(1.0)!"
- convert(Frequency) - Static method in class omero.model.FrequencyI
-
FIXME: this should likely take a default so that locations which don't
want an exception can have
log.warn("Using new PositiveFloat(1.0)!"
- convert(Length) - Static method in class omero.model.LengthI
-
FIXME: this should likely take a default so that locations which don't
want an exception can have
log.warn("Using new PositiveFloat(1.0)!"
- convert(Power) - Static method in class omero.model.PowerI
-
FIXME: this should likely take a default so that locations which don't
want an exception can have
log.warn("Using new PositiveFloat(1.0)!"
- convert(Pressure) - Static method in class omero.model.PressureI
-
FIXME: this should likely take a default so that locations which don't
want an exception can have
log.warn("Using new PositiveFloat(1.0)!"
- convert(Temperature) - Static method in class omero.model.TemperatureI
-
FIXME: this should likely take a default so that locations which don't
want an exception can have
log.warn("Using new PositiveFloat(1.0)!"
- convert(Time) - Static method in class omero.model.TimeI
-
FIXME: this should likely take a default so that locations which don't
want an exception can have
log.warn("Using new PositiveFloat(1.0)!"
- 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
-
- convertElectricPotential(ElectricPotential) - Static method in class ome.formats.model.UnitsFactory
-
Convert a Bio-Formats ElectricPotential
to an OMERO ElectricPotential.
- convertElectricPotential(ElectricPotential) - Static method in class ome.formats.model.UnitsFactory
-
- convertElectricPotential(ElectricPotential, Unit<ElectricPotential>) - Static method in class ome.formats.model.UnitsFactory
-
- convertElectricPotentialXML(ElectricPotential, String) - Static method in class ome.formats.model.UnitsFactory
-
- convertFrequency(Frequency) - Static method in class ome.formats.model.UnitsFactory
-
Convert a Bio-Formats Frequency
to an OMERO Frequency.
- convertFrequency(Frequency) - Static method in class ome.formats.model.UnitsFactory
-
- convertFrequency(Frequency, Unit<Frequency>) - Static method in class ome.formats.model.UnitsFactory
-
- convertFrequencyXML(Frequency, String) - Static method in class ome.formats.model.UnitsFactory
-
- convertLength(Length) - Static method in class ome.formats.model.UnitsFactory
-
Convert a Bio-Formats Length
to an OMERO Length.
- convertLength(Length) - Static method in class ome.formats.model.UnitsFactory
-
- convertLength(Length, Unit<Length>) - Static method in class ome.formats.model.UnitsFactory
-
- convertLengthXML(Length, String) - Static method in class ome.formats.model.UnitsFactory
-
- convertMapPairs(List<MapPair>) - Static method in class omero.util.IceMapper
-
- convertNamedValueList(List<NamedValue>) - Static method in class omero.util.IceMapper
-
- convertPower(Power) - Static method in class ome.formats.model.UnitsFactory
-
Convert a Bio-Formats Power
to an OMERO Power.
- convertPower(Power) - Static method in class ome.formats.model.UnitsFactory
-
- convertPower(Power, Unit<Power>) - Static method in class ome.formats.model.UnitsFactory
-
- convertPowerXML(Power, String) - Static method in class ome.formats.model.UnitsFactory
-
- convertPressure(Pressure) - Static method in class ome.formats.model.UnitsFactory
-
Convert a Bio-Formats Pressure
to an OMERO Pressure.
- convertPressure(Pressure) - Static method in class ome.formats.model.UnitsFactory
-
- convertPressure(Pressure, Unit<Pressure>) - Static method in class ome.formats.model.UnitsFactory
-
- convertPressureXML(Pressure, String) - Static method in class ome.formats.model.UnitsFactory
-
- convertStringStringMap(Map<String, String>) - Static method in class omero.util.IceMapper
-
Convert a String→String map's values to RString
s.
- convertTemperature(Temperature) - Static method in class ome.formats.model.UnitsFactory
-
Convert a Bio-Formats Temperature
to an OMERO Temperature.
- convertTemperature(Temperature) - Static method in class ome.formats.model.UnitsFactory
-
- convertTemperature(Temperature, Unit<Temperature>) - Static method in class ome.formats.model.UnitsFactory
-
- convertTemperatureXML(Temperature, String) - Static method in class ome.formats.model.UnitsFactory
-
- convertTime(Time) - Static method in class ome.formats.model.UnitsFactory
-
Convert a Bio-Formats Time
to an OMERO Time.
- convertTime(Time) - Static method in class ome.formats.model.UnitsFactory
-
- convertTime(Time, Unit<Time>) - Static method in class ome.formats.model.UnitsFactory
-
- convertTimeXML(Time, String) - Static method in class ome.formats.model.UnitsFactory
-
- 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.
- copy() - Method in class omero.cmd.graphs.ChgrpI
-
Deprecated.
- copy() - Method in class omero.cmd.graphs.ChmodI
-
Deprecated.
- copy() - Method in class omero.cmd.graphs.ChownI
-
Deprecated.
- copy() - Method in class omero.cmd.graphs.DeleteI
-
Deprecated.
- copy() - Method in interface omero.cmd.graphs.IGraphModifyRequest
-
Deprecated.
Produce a clone of this object.
- copy(Current) - Method in class omero.model.ElectricPotentialI
-
- copy(Current) - Method in class omero.model.FrequencyI
-
- copy(Current) - Method in class omero.model.LengthI
-
- copy(Current) - Method in class omero.model.PowerI
-
- copy(Current) - Method in class omero.model.PressureI
-
- copy(Current) - Method in class omero.model.TemperatureI
-
- copy(Current) - Method in class omero.model.TimeI
-
- 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
-
- copyFieldsTo(Chgrp2) - Method in class omero.cmd.graphs.Chgrp2I
-
- copyFieldsTo(Chown2) - Method in class omero.cmd.graphs.Chown2I
-
- copyFieldsTo(Delete2) - Method in class omero.cmd.graphs.Delete2I
-
- copyFieldsTo(X) - Method in interface omero.cmd.graphs.WrappableRequest
-
Copy the fields of this request to that of the given request.
- CopyFileTransfer - Class in ome.formats.importer.transfers
-
Local-only file transfer mechanism which makes use of the plaform
copy command.
- CopyFileTransfer() - Constructor for class ome.formats.importer.transfers.CopyFileTransfer
-
- copyGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
-
- copyList(List<T>) - Static method in class ome.services.search.SearchValues
-
- CopyMoveFileTransfer - Class in ome.formats.importer.transfers
-
Local-only file transfer mechanism which makes use of the
local copy command followed by the deletion of the original
source file.
- CopyMoveFileTransfer() - Constructor for class ome.formats.importer.transfers.CopyMoveFileTransfer
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.DetailsI
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.ElectricPotentialI
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.FrequencyI
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.LengthI
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.PermissionsI
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.PowerI
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.PressureI
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.TemperatureI
-
- copyObject(Filterable, ModelMapper) - Method in class omero.model.TimeI
-
- copyOfValues() - Method in class ome.services.search.SearchAction
-
- 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 class ome.services.messages.DeleteLogMessage
-
- 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
-
- Counter - Interface in ome.system.metrics
-
Thin wrapper around Counter
- counter(Object, String) - Method in class ome.system.metrics.DefaultMetrics
-
- counter(Object, String) - Method in interface ome.system.metrics.Metrics
-
- counter(Object, String) - Method in class ome.system.metrics.NullMetrics
-
- 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
-
- CRC32ChecksumProviderImpl - Class in ome.util.checksum
-
An implementation of the
ChecksumProvider
interface using
CRC32 as the message digest algorithm.
- CRC32ChecksumProviderImpl() - Constructor for class ome.util.checksum.CRC32ChecksumProviderImpl
-
- create(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.SessionManagerI
-
- create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.chgrp.ChgrpStepFactory
-
Deprecated.
- create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.chown.ChownStepFactory
-
Deprecated.
- create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.delete.DeleteStepFactory
-
Deprecated.
- create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.export.ExporterStepFactory
-
Deprecated.
- create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in interface ome.services.graphs.GraphStepFactory
-
Deprecated.
- 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.
- createBfReader() - Method in class ome.io.nio.PixelsService
-
Create an IFormatReader
with the appropriate ReaderWrapper
instances and IFormatReader.setFlattenedResolutions(boolean)
set to false.
- 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
-
- createCallback(ImportProcessPrx, HandlePrx, ImportContainer) - Method in class ome.formats.importer.ImportLibrary
-
- createChildOption() - Method in class omero.cmd.graphs.GraphRequestFactory
-
- 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
-
- createExclusion(String) - Static method in class ome.formats.importer.exclusions.AbstractFileExclusion
-
Factory method for instantiating
FileTransfer
objects from
a string.
- 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(Communicator) - Method in class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
-
- createFactories(Communicator) - Method in class ome.services.blitz.repo.RequestObjectFactoryRegistry
-
- createFactories(Communicator) - Method in class ome.services.roi.RoiTypes.RoiTypesObjectFactoryRegistry
-
- createFactories(Communicator) - Method in class omero.cmd.RequestObjectFactoryRegistry
-
- createFactories(Communicator) - Method in class omero.rtypes.RTypeObjectFactoryRegistry
-
- createFactories(Communicator) - Method in class omero.util.ObjectFactoryRegistry
-
- createFromRequest(SessionManager.CreationRequest) - Method in interface ome.services.sessions.SessionManager
-
- createFromRequest(SessionManager.CreationRequest) - Method in class ome.services.sessions.SessionManagerImpl
-
- createFullTextThread(EventLogLoader) - Static method in class ome.services.fulltext.Main
-
- createFullTextThread(EventLogLoader, boolean) - Static method in class ome.services.fulltext.Main
-
- 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, boolean) - Method in interface ome.security.auth.RoleProvider
-
- createGroup(String, Permissions, boolean) - Method in class ome.security.auth.SimpleRoleProvider
-
- createGroup(String, Permissions, boolean, 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) - 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
-
- createImport(ImportContainer) - Method in class ome.formats.importer.ImportLibrary
-
Provide initial configuration to the server in order to create the
ImportProcessPrx
which will manage state server-side.
- createImportProcess(Fileset, ImportLocation, ImportSettings, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
-
Creating the process will register itself in an appropriate
container (i.e. a SessionI or similar) for the current
user and therefore this instance no longer needs to worry
about the maintenance of the object.
- createInstance() - Method in class ome.security.basic.EventListenersFactoryBean
-
First, adds all default listeners.
- createInstance() - Method in class ome.services.delete.Deletion.Builder
-
Deprecated.
- 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
-
- createOrFixUserDir(String, List<CheckedPath>, Session, ServiceFactory, SqlAction) - Method in interface ome.services.blitz.repo.RepositoryDao
-
- createOrFixUserDir(String, List<CheckedPath>, Session, ServiceFactory, SqlAction) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- createOriginalFile(ServiceFactory, SqlAction, String, List<CheckedPath>, ChecksumAlgorithm, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
Primary location for creating original files from a
CheckedPath
instance.
- 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
-
- createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
-
- createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.CopyFileTransfer
-
Executes "cp file location" (Unix) or "cp file location" (Windows)
and fails on non-0 return codes.
- createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.HardlinkFileTransfer
-
Executes "ln file location" (Unix) or "mklink /H location file" (Windows)
and fails on non-0 return codes.
- createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.SymlinkFileTransfer
-
Executes "ln -s file location" (Unix) or "mklink location file" (Windows)
and fails on non-0 return codes.
- createPyramidPixelBuffer(Pixels, String, boolean) - Method in class ome.io.nio.PixelsService
-
Helper method to properly log any exceptions raised by Bio-Formats.
- createQueryBuilder(String[], GraphEntry) - Method in class ome.services.graphs.BaseGraphSpec
-
Deprecated.
- 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
-
- createRepoRFS(CheckedPath, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Create, initialize, and register an
RepoRawFileStoreI
with the proper setting (read or write).
- 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
-
- createTemplatePath(Object, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
-
Expand the template path and create its directories with the correct ownership.
- 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
-
- createTransfer(String) - Static method in class ome.formats.importer.transfers.AbstractFileTransfer
-
Factory method for instantiating
FileTransfer
objects from
a string.
- createUploadProcess(Fileset, ImportLocation, ImportSettings, Current, boolean) - Method in class ome.services.blitz.repo.ManagedRepositoryI
-
Creating the process will register itself in an appropriate
container (i.e. a SessionI or similar) for the current
user and therefore this instance no longer needs to worry
about the maintenance of the object.
- createUser(Experimenter, String) - Method in interface ome.api.IAdmin
-
create and return a new user.
- createUser(String) - Method in interface ome.api.ILdap
-
Creates an Experimenter
entry in the OMERO DB
based on the supplied LDAP username.
- createUser(Experimenter, String) - Method in class ome.logic.AdminImpl
-
- createUser(String) - Method in class ome.logic.LdapImpl
-
Creates an Experimenter
based on the supplied LDAP username.
- createUser(String, String) - Method in class ome.logic.LdapImpl
-
Creates an Experimenter
based on the supplied LDAP username.
- createUser(String, String, boolean) - Method in class ome.logic.LdapImpl
-
Creates an Experimenter
based on the supplied LDAP username.
- createUser_async(AMD_IAdmin_createUser, Experimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI
-
- createUser_async(AMD_ILdap_createUser, String, Current) - Method in class ome.services.blitz.impl.LdapI
-
- createUserFromLdap(String, String) - Method in class ome.logic.LdapImpl
-
Deprecated.
- 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, String) - Method in interface ome.services.sessions.SessionManager
-
- createWithAgent(Principal, String, String) - Method in interface ome.services.sessions.SessionManager
-
- createWithAgent(Principal, String, String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- createWithAgent(Principal, String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- credentials - Variable in class ome.services.sessions.SessionManager.CreationRequest
-
- 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
-
Deprecated.
- 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
-
- curr - Variable in class ome.services.blitz.util.FindServiceFactoryMessage
-
- current - Variable in class ome.security.SecurityFilterHolder
-
- current - Variable in class ome.security.SecuritySystemHolder
-
- current - Variable in class ome.services.throttling.Task
-
- current - Variable in class ome.tools.hibernate.ProxyCleanupFilter
-
- current_group - Static variable in class ome.security.basic.OneGroupSecurityFilter
-
- current_user - Static variable in interface ome.security.SecurityFilter
-
- currentContext(Principal) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- 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
-
- CurrentPlatform - Class in ome.services.blitz.util
-
Test under which platform OMERO is currently running.
- CurrentPlatform() - Constructor for class ome.services.blitz.util.CurrentPlatform
-
- 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
-
- currentUser(Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- G_BAND - Static variable in class omeis.providers.re.RGBBuffer
-
Index of the green band in the image's data buffer.
- 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
-
- generateThumbnails(ThumbnailGenerationJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
-
- 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.GroupContextMapper
-
- 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(int) - Method in class ome.services.graphs.GraphSteps
-
Deprecated.
- 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).
- get75thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
-
- get75thPercentile() - Method in interface ome.system.metrics.Snapshot
-
- get95thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
-
- get95thPercentile() - Method in interface ome.system.metrics.Snapshot
-
- get98thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
-
- get98thPercentile() - Method in interface ome.system.metrics.Snapshot
-
- get999thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
-
- get999thPercentile() - Method in interface ome.system.metrics.Snapshot
-
- get99thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
-
- get99thPercentile() - Method in interface ome.system.metrics.Snapshot
-
- 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.
- getAbsolutePaths() - Method in class pojos.FilesetData
-
Returns the collections of absolute paths.
- getAcquisitionData() - Method in class omero.sys.ParametersI
-
- getAcquisitionDate() - Method in class pojos.ImageData
-
Returns the acquisition date.
- getAction() - Method in class ome.services.mail.ObjectMailSender
-
- getActionForStarting() - Method in class omero.cmd.graphs.Chgrp2I
-
- getActionForStarting() - Method in class omero.cmd.graphs.Chown2I
-
- getActionForStarting() - Method in class omero.cmd.graphs.Delete2I
-
- getActionForStarting() - Method in interface omero.cmd.graphs.WrappableRequest
-
- 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
-
Deprecated.
- getAdapter() - Method in class omero.client
-
- getAdapter() - Method in class omero.cmd.SessionI
-
- 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(UnitsPressure) - Method in class pojos.ImageAcquisitionData
-
Returns the air pressure in bar
- getAirPressure() - Method in class pojos.ImageAcquisitionData
-
- getAll(String) - Method in class ome.security.auth.AttributeSet
-
- getAllChecksumAlgorithms() - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
-
- 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.
- getAllSystemUsers(boolean) - Method in class ome.services.mail.MailSender
-
- 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
-
- 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(T) - Method in class ome.security.auth.OmeroModelContextMapper
-
- getAttributeSet(T) - Method in class ome.security.auth.OmeroModelContextMapper
-
- 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
-
- 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
-
- getAvailableTypes() - Method in interface ome.util.checksum.ChecksumProviderFactory
-
- getAvailableTypes() - Method in class ome.util.checksum.ChecksumProviderFactoryImpl
-
- getB0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
-
Returns the y-intercept of the first line.
- getB1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
-
Returns the y-intercept of the second line.
- getB2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
-
Returns the y-intercept of the third line.
- 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
-
- getBfReader(Pixels) - Method in class ome.io.nio.PixelsService
-
Short-cut in the FS case where we know that we are dealing with a FS-lite
file, and want to retrieve the actual file as opposed to a pyramid or anything
else.
- getBioFormatsVersion() - Method in class ome.formats.importer.ImportConfig
-
- 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() - Method in class ome.formats.importer.transfers.TransferState
-
(Not thread safe) Get a moderately large buffer for use in
reading/writing data.
- getBuffer(long) - Method in class ome.services.roi.PixelData
-
- 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.
- getBytesFailed() - Method in class ome.services.delete.files.AbstractFileDeletions
-
- 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() - 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 ome.services.blitz.repo.ManagedImportRequestI
-
- getCallContext() - Method in class ome.services.blitz.repo.RawAccessRequestI
-
- getCallContext() - Method in class omero.cmd.admin.ResetPasswordRequestI
-
- 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.fs.ManageImageBinariesI
-
- getCallContext() - Method in class omero.cmd.fs.OriginalMetadataRequestI
-
- getCallContext() - Method in class omero.cmd.fs.UsedFilesRequestI
-
- getCallContext() - Method in class omero.cmd.graphs.Chgrp2I
-
- getCallContext() - Method in class omero.cmd.graphs.ChgrpFacadeI
-
Deprecated.
- getCallContext() - Method in class omero.cmd.graphs.ChgrpI
-
Deprecated.
- getCallContext() - Method in class omero.cmd.graphs.ChmodI
-
- getCallContext() - Method in class omero.cmd.graphs.Chown2I
-
- getCallContext() - Method in class omero.cmd.graphs.ChownFacadeI
-
Deprecated.
- getCallContext() - Method in class omero.cmd.graphs.ChownI
-
Deprecated.
- getCallContext() - Method in class omero.cmd.graphs.Delete2I
-
- getCallContext() - Method in class omero.cmd.graphs.DeleteFacadeI
-
Deprecated.
- getCallContext() - Method in class omero.cmd.graphs.DeleteI
-
Deprecated.
- getCallContext() - Method in class omero.cmd.graphs.DiskUsageI
-
- getCallContext() - Method in class omero.cmd.graphs.GraphSpecListI
-
Deprecated.
- getCallContext() - Method in class omero.cmd.graphs.SkipHeadI
-
- getCallContext() - Method in interface omero.cmd.IRequest
-
Returns the desired call context for this request.
- getCallContext() - Method in class omero.cmd.mail.SendEmailRequestI
-
- 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
-
- 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
-
- 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.
- getChannelLookupTable(int) - Method in class ome.services.RenderingBean
-
- getChannelLookupTable(int) - Method in interface omeis.providers.re.RenderingEngine
-
- getChannelLookupTable_async(AMD_RenderingEngine_getChannelLookupTable, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
-
- 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
-
- 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
-
- 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
-
- 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
-
- getCheckDone() - Method in class ome.services.util.DBEnumCheck
-
- 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.
- getChecksum() - Method in class ome.formats.importer.transfers.TransferState
-
Get the digest string for the local file.
- getChecksumAlgorithm() - Method in class ome.formats.importer.ImportContainer
-
- getChecksumAlgorithm(String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
-
Retrieve the checksum algorithm of the given name.
- getChecksumAlgorithm(String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- getChecksumAlgorithm(String) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
-
- getChecksumProvider() - Method in class ome.formats.importer.transfers.TransferState
-
- getChecksumType(ChecksumAlgorithm) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
-
- getChecksumType(ChecksumAlgorithm) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
-
- getChildOptionsPolicy(GraphPolicy, GraphPathBean, Collection<ChildOptionI>, Set<GraphPolicy.Ability>) - Static method in class omero.cmd.graphs.ChildOptionsPolicy
-
Adjust an existing graph traversal policy so that child objects may be included or excluded
regardless of if they are truly orphans.
- getChildTransformer(Class) - Static method in class ome.services.query.Hierarchy
-
- getClass(String) - Method in class ome.services.graphs.GraphState
-
Deprecated.
- getClass(String) - Method in interface ome.services.graphs.GraphStep.Callback
-
Deprecated.
- getClasses() - Method in interface ome.tools.hibernate.ExtendedMetadata
-
- getClasses() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getClassForSimpleName(String) - Method in class ome.services.graphs.GraphPathBean
-
- getCleanInstance() - Method in class ome.services.graphs.GraphPolicy
-
A stateful graph policy must override this method to provide a clone that has fresh state.
- getClient() - Method in class ome.formats.importer.util.ClientKeepAlive
-
- getClient() - Method in class omero.model.DetailsI
-
- getClientConfigDefaults() - Method in interface ome.api.IConfig
-
reads the etc/omero.properties file and returns all the key/value
pairs that are found there which match the prefix "omero.client".
- getClientConfigDefaults() - Method in class ome.logic.ConfigImpl
-
- getClientConfigDefaults_async(AMD_IConfig_getClientConfigDefaults, Current) - Method in class ome.services.blitz.impl.ConfigI
-
- getClientConfigValues() - Method in interface ome.api.IConfig
-
- getClientConfigValues() - Method in class ome.logic.ConfigImpl
-
- getClientConfigValues_async(AMD_IConfig_getClientConfigValues, Current) - Method in class ome.services.blitz.impl.ConfigI
-
- 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
-
- getCommunicationLink(String) - Method in class ome.formats.importer.util.HtmlMessenger
-
Creates a client to communicate.
- 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 ome.services.blitz.repo.path.FsFile
-
Get the path components of this instance.
- 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
-
- getConfig() - Method in class ome.formats.importer.OMEROWrapper
-
- getConfigDefaults() - Method in interface ome.api.IConfig
-
reads the etc/omero.properties file and returns all the key/value
pairs that are found there.
- getConfigDefaults() - Method in class ome.logic.ConfigImpl
-
- getConfigDefaults_async(AMD_IConfig_getConfigDefaults, Current) - Method in class ome.services.blitz.impl.ConfigI
-
- 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
-
- getConfigValues(String) - Method in interface ome.api.IConfig
-
retrieves configuration values from the backend store which match the
given regex.
- getConfigValues(String) - Method in class ome.logic.ConfigImpl
-
- getConfigValues_async(AMD_IConfig_getConfigValues, 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
-
- getConstraints() - Method in exception ome.services.graphs.GraphConstraintException
-
Deprecated.
- 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
-
- 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.MapAnnotationData
-
- 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.MapAnnotationData
-
- 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.
- 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
-
- 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.GroupContextMapper
-
- 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
-
Deprecated.
- getCount() - Method in interface ome.system.metrics.Counter
-
- getCount() - Method in class ome.system.metrics.DefaultCounter
-
- getCount() - Method in class ome.system.metrics.DefaultTimer
-
- getCount() - Method in interface ome.system.metrics.Timer
-
- 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.FindServiceFactoryMessage
-
- 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
-
- 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
-
- 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.
- getCustomImageNaming() - Method in class ome.formats.importer.ImportConfig
-
- getCustomImageNaming() - Method in class ome.formats.importer.util.IniFileLoader
-
- getCutIn(UnitsLength) - Method in class pojos.FilterData
-
Returns the cut in value or null
.
- getCutIn() - Method in class pojos.FilterData
-
- getCutInTolerance(UnitsLength) - Method in class pojos.FilterData
-
Returns the cut in tolerance value or null
.
- getCutInTolerance() - Method in class pojos.FilterData
-
- getCutOut(UnitsLength) - Method in class pojos.FilterData
-
Returns the cut out value or null
.
- getCutOut() - Method in class pojos.FilterData
-
- getCutOutTolerance(UnitsLength) - Method in class pojos.FilterData
-
Returns the cut out tolerance value or null
.
- getCutOutTolerance() - Method in class pojos.FilterData
-
- 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.
- getDataset() - Method in class ome.formats.importer.util.TinyImportFixture
-
provides access to the created Dataset
instance.
- getDatasets(Project) - Method in class ome.formats.OMEROMetadataStoreClient
-
- 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.
- getDefaultBatchSize() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getDefaultBlockSize() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getDefaultBlockSize() - Method in class omero.client
-
Returns the user configured setting for "omero.block_size"
or DEFAULTBLOCKSIZE
if none is set.
- getDefaultBody() - Method in class ome.services.mail.MailSender
-
- 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
-
Deprecated.
- 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() - 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
-
- 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
-
- getDeleteService() - Method in class ome.system.ServiceFactory
-
- getDeletion() - Method in class omero.cmd.graphs.DeleteI
-
Deprecated.
- 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.AnnotationData
-
Retrieves the description
of the
underlying Annotation
instance.
- 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(UnitsFrequency) - Method in class pojos.ChannelAcquisitionData
-
Returns the Read out rate set on the detector.
- getDetectorSettingsReadOutRate() - Method in class pojos.ChannelAcquisitionData
-
- getDetectorSettingsVoltage(UnitsElectricPotential) - Method in class pojos.ChannelAcquisitionData
-
Returns the voltage set on the detector.
- getDetectorSettingsVoltage() - Method in class pojos.ChannelAcquisitionData
-
- 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.
- getDirname() - Method in class ome.services.blitz.repo.CheckedPath
-
Assuming this is a directory, return relative path plus name with a final
slash.
- getDisabledSubsystems() - Method in class ome.security.basic.BasicEventContext
-
- getDn(T) - Method in class ome.security.auth.OmeroModelContextMapper
-
- 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(UnitsLength) - Method in class pojos.ChannelData
-
Returns the emission wavelength of the channel.
- getEmissionWavelength() - Method in class pojos.ChannelData
-
- 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
-
Deprecated.
- 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(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(Current) - Method in interface ome.services.blitz.repo.RepositoryDao
-
Look up information for the current session as specified in the ctx
field of the current.
- getEventContext(Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- 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(UnitsLength) - Method in class pojos.ChannelData
-
Returns the excitation wavelength of the channel.
- getExcitationWavelength() - Method in class pojos.ChannelData
-
- getExclude(int) - Method in class ome.services.graphs.AnnotationGraphSpec
-
Deprecated.
Returns the value from "...
- getExecutor() - Method in class ome.services.mail.MailSender
-
- 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.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
-
- getFactory(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
- getFailedFiles() - Method in exception ome.formats.importer.transfers.CleanupFailure
-
- getFailedFilesCount() - Method in class ome.services.delete.files.FileDeleter
-
- 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() - Method in class ome.formats.importer.transfers.TransferState
-
Return the target file passed to the constructor.
- getFile(long, Current, String) - Method in interface ome.services.blitz.repo.RepositoryDao
-
Get an
FsFile
object based on its ID.
- getFile(long, Current, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- getFile(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder
-
- getFileBuffer(OriginalFile, String) - Method in class ome.io.nio.OriginalFilesService
-
Returns FileBuffer based on OriginalFile path
- getFileBuffer(String) - Method in class ome.services.blitz.repo.CheckedPath
-
- getFileFilter() - Method in class ome.services.scripts.ScriptFileType
-
A file-pattern (most likely of the form "*.EXT") which will be used
to determine if a file is of this type.
- 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 interface ome.api.RawFileStore
-
Returns the current file id or null if none has been set.
- getFileId() - Method in class ome.services.messages.DeleteLogMessage
-
- getFileId() - Method in class ome.services.RawFileBean
-
- getFileID() - Method in class pojos.FileAnnotationData
-
Returns the id of the file.
- getFileId_async(AMD_RawFileStore_getFileId, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
-
- 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.
- getFilePathRestrictions(String...) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
-
Get a set of rules by which local files may not be named on the file-system,
formed by combining the rules of the given names with rules against control characters.
- getFilePathRestrictions(FilePathRestrictionInstance...) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
-
Get a set of rules by which local files may not be named on the file-system,
formed by combining the given rules identifiers with rules against control characters.
- getFileRepo(OriginalFile) - Method in class ome.services.blitz.repo.AbstractRepositoryI
-
- getFiles() - Method in class ome.formats.importer.util.ErrorContainer
-
- getFileset() - Method in class ome.services.blitz.repo.ManagedImportProcessI
-
- getFileset() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
-
- getFilesetId() - Method in class ome.services.delete.DeleteStep
-
Deprecated.
- getFilesetId() - Method in class pojos.ImageData
-
Returns the ID of the fileset to which this image belongs.
- 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.
- 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
-
- getFontSize(UnitsLength) - 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
-
- getFsFileFromClientFile(File, int) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer
-
Given a client-local
File
, and a path component depth,
returns the corresponding repository path.
- getFsFileFromServerFile(File) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
-
Given a server-local
File
, returns the corresponding repository path.
- getFullFsPath() - Method in class ome.services.blitz.repo.CheckedPath
-
The full path of the entity to which this path corresponds.
- 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.
- getGraphPathBean() - Method in class omero.cmd.graphs.GraphRequestFactory
-
- 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.services.blitz.repo.ManagedImportProcessI
-
- getGroup() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
-
- 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
-
- getHandle(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
-
- 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
-
Deprecated.
- getHibernateClass(String) - Method in interface ome.services.graphs.GraphSpec
-
Deprecated.
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.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
- 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
-
- 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.blitz.repo.CheckedPath
-
- getId() - Method in class ome.services.graphs.GraphEntry
-
Deprecated.
- 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
-
Deprecated.
Returns the id of an object based on the order in which it was added.
- getIdentifierProperty(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the identifier property for the given class.
- 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
-
Deprecated.
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(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
-
- getImageCount() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImageDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImageID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getImageIds() - Method in class pojos.FilesetData
-
Returns the collection of images related to the file set.
- 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() - 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
-
- getImagesBySplitFilesets(Map<Class<? extends IObject>, List<Long>>, Parameters) - Method in interface ome.api.IContainer
-
Given a list of IDs of certain entity types, calculates which filesets are split such that
a non-empty proper subset of their images are referenced, directly or indirectly, as being
included.
- getImagesBySplitFilesets(Map<Class<? extends IObject>, List<Long>>, Parameters) - Method in class ome.logic.PojosImpl
-
- getImagesBySplitFilesets_async(AMD_IContainer_getImagesBySplitFilesets, Map<String, List<Long>>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
-
- 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.
- getImportResponse() - Method in class ome.formats.importer.ImportLibrary.ImportCallback
-
- getImportSettings(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
-
- 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.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
-
- getIP(Current) - Method in class ome.services.blitz.fire.SessionManagerI
-
- getIQuery() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getIsSPW() - Method in class ome.formats.importer.ImportContainer
-
Return true if this import container contains a Screen/Plate/Well image
group.
- getIterator() - Method in class pojos.ROIData
-
Returns the iterator of the collection of the map.
- 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
- getKey() - Method in class ome.services.eventlogs.PersistentEventLogLoader
-
- getKeySet() - Method in class ome.system.PreferenceContext
-
- 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(UnitsFrequency) - Method in class pojos.LightSourceData
-
Returns the repetition rate (Hz) if the laser is repetitive.
- getLaserRepetitionRate() - Method in class pojos.LightSourceData
-
- getLaserTuneable() - Method in class pojos.LightSourceData
-
Returns the value of the tuneable
field or null
if no value set.
- getLaserWavelength(UnitsLength) - Method in class pojos.LightSourceData
-
Returns the laser's wavelength.
- getLaserWavelength() - Method in class pojos.LightSourceData
-
- 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
-
- getLauncher() - Method in class ome.services.scripts.ScriptFileType
-
Return the name of the launcher (".
- getLauncher(String) - Method in class ome.services.scripts.ScriptRepoHelper
-
Find an "omero.launcher..." property string for the given mimetype or
return "" if none is found.
- 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
-
- getLength() - Method in class ome.formats.importer.transfers.TransferState
-
- 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.
- getLightSettingsAttenuation() - Method in class pojos.ChannelAcquisitionData
-
Returns the attenuation of the light source, percent value
between 0 and 1.
- getLightSettingsWavelength(UnitsLength) - Method in class pojos.ChannelAcquisitionData
-
Returns the wavelength of the light source.
- getLightSettingsWavelength() - Method in class pojos.ChannelAcquisitionData
-
- 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.
- 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..
- getLinkedBy(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the classes and properties that link to the given class.
- getLinkedTo(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the classes and properties to which the given class links.
- getListAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient
-
- getLocalLocation(OriginalFile, OriginalFile) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
-
Build a path of the form "root.path/root.name/file.path/file.name".
- 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
-
- getLogFile() - Method in class ome.services.blitz.repo.ManagedImportLocationI
-
Return the server-side
CheckedPath
instance which can be used
for writing a log file for a fileset.
- 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.
- getMailUtil() - Method in class ome.services.mail.MailSender
-
- 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.
- getMapProperties(String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Get the names of any String→RString map properties this class has, otherwise an empty set if none.
- getMapProperties(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- 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
-
Deprecated.
- getMax() - Method in class ome.system.metrics.DefaultSnapshot
-
- getMax() - Method in interface ome.system.metrics.Snapshot
-
- 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
-
- getMean() - Method in class ome.system.metrics.DefaultSnapshot
-
- getMean() - Method in interface ome.system.metrics.Snapshot
-
- 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
-
- getMedian() - Method in class ome.system.metrics.DefaultSnapshot
-
- getMedian() - Method in interface ome.system.metrics.Snapshot
-
- 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.
- getMemoizerDirectory() - Method in class ome.io.nio.PixelsService
-
- getMemoizerWait() - Method in class ome.io.nio.PixelsService
-
- getMessage() - Method in exception ome.io.nio.PixelBufferException
-
- getMessageDigest() - Method in class ome.io.bioformats.BfPixelsWrapper
-
- getMessages() - Method in class ome.services.messages.DeleteLogsMessage
-
- 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.
- 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.
- getMimetype() - Method in class ome.services.blitz.repo.CheckedPath
-
Get the mimetype for a file.
- getMimetype() - Method in class ome.services.scripts.ScriptFileType
-
Returns the mimetype that must be set on an original file instance
in order to be considered of this type.
- getMin() - Method in class ome.system.metrics.DefaultSnapshot
-
- getMin() - Method in interface ome.system.metrics.Snapshot
-
- getMinimumDepth(Collection<File>) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer
-
Get the smallest path component depth that allows the given set of
File
s
to be disambiguated.
- 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
-
- 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 class ome.security.policy.BasePolicy
-
- getName() - Method in class ome.security.policy.BinaryAccessPolicy
-
- getName() - Method in interface ome.security.policy.Policy
-
Unique name for a class of restrictions that this
Policy
will enforce.
- 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.blitz.repo.CheckedPath
-
Get the last component of this path, the entity to which the path corresponds.
- getName() - Method in class ome.services.graphs.BaseGraphSpec
-
Deprecated.
- getName() - Method in class ome.services.graphs.GraphEntry
-
Deprecated.
- getName(Matcher) - Method in class ome.services.graphs.GraphEntry
-
Deprecated.
- getName() - Method in interface ome.services.graphs.GraphSpec
-
Deprecated.
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.
- getNoStatsInfo() - Method in class ome.formats.importer.ImportContainer
-
Retrieves whether or not we disabling StatsInfo
population.
- 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
-
Deprecated.
- 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.
- getObjectClass() - Method in class ome.services.mail.ObjectMailSender
-
- 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
-
Deprecated.
- 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.
- getOmeroVersion() - Method in class ome.formats.importer.ImportConfig
-
- getOp(Matcher) - Method in class ome.services.graphs.GraphEntry
-
Deprecated.
- getOpString() - Method in class ome.services.graphs.GraphEntry
-
Deprecated.
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.
- getOpts() - Method in class ome.services.graphs.GraphState
-
Deprecated.
- 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
-
- getOriginalFile() - Method in class ome.formats.importer.transfers.TransferState
-
Find original file as defined by the ID in the RawFileStorePrx
regardless of group.
- getOriginalFile(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
-
Gets the original file instance for a given file ID.
- getOriginalFile(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- 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
-
- getOriginalFiles(String, CheckedPath, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
-
Return a non-null, possibly empty list of OriginalFile
elements
which are accessible to the given user at the given path.
- getOriginalFiles(String, CheckedPath, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- getOriginalFiles(ServiceFactory, SqlAction, String, CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- getOriginalFileWithHasher(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
-
Retrieve the original file of the given ID.
- getOriginalFileWithHasher(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- 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
-
Deprecated.
- getPath() - Method in class pojos.FileData
-
Returns the (relative) path of the file.
- getPath() - Method in class pojos.OTFData
-
Returns the path.
- getPathFor(long) - Method in class ome.services.blitz.repo.path.MakeNextDirectory
-
Get the subdirectories to create for the given index,
the first directories to be created corresponding to index == 0
.
- getPathFrom(FsFile) - Method in class ome.services.blitz.repo.path.FsFile
-
Find the relative path of this path from a given parent.
- 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
-
- getPathSanitizer() - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
-
Get the string transformer that is used to make file-path components safe across platforms.
- 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
-
Never returns Permissions.DUMMY
.
- getPermissionsLevel() - Method in class pojos.PermissionData
-
Returns the permissions level.
- getPhysicalMemory() - Static method in class ome.services.util.JvmSettingsCheck
-
- getPinholeSize(UnitsLength) - Method in class pojos.ChannelData
-
Returns the pin hole size of the channel.
- getPinholeSize() - Method in class pojos.ChannelData
-
- 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, 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
-
- getPixelsBinDataBigEndian(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getPixelsDimensionOrder(int) - Method in class ome.services.blitz.impl.OmeroMetadata
-
- 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
-
- getPixelSizeX(UnitsLength) - Method in class pojos.PixelsData
-
Returns the dimension of a pixel along the X-axis
- getPixelSizeY() - Method in class pojos.PixelsData
-
- getPixelSizeY(UnitsLength) - Method in class pojos.PixelsData
-
Returns the dimension of a pixel along the Y-axis
- getPixelSizeZ() - Method in class pojos.PixelsData
-
- getPixelSizeZ(UnitsLength) - Method in class pojos.PixelsData
-
Returns the dimension of a pixel along the Z-axis
- getPixelsPath() - Method in interface ome.api.RawPixelsStore
-
Returns the current Pixels path.
- 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.
- getPixelsPath() - Method in class ome.services.RawPixelsBean
-
- getPixelsPath_async(AMD_RawPixelsStore_getPixelsPath, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
-
- getPixelsPath_async(AMD_RawPixelsStore_getPixelsPath, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- 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
-
- 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
-
- getPixelType() - Method in class pojos.PixelsData
-
Returns the pixels type.
- 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(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() - 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 Pockel 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(UnitsLength) - Method in class pojos.ImageAcquisitionData
-
Returns the x-coordinate in the frame microscope.
- getPositionX() - Method in class pojos.ImageAcquisitionData
-
- getPositionX(UnitsLength) - Method in class pojos.WellSampleData
-
Returns the position X.
- getPositionX() - Method in class pojos.WellSampleData
-
- getPositionY(UnitsLength) - Method in class pojos.ImageAcquisitionData
-
Returns the y-coordinate in the frame microscope.
- getPositionY() - Method in class pojos.ImageAcquisitionData
-
- getPositionY(UnitsLength) - Method in class pojos.WellSampleData
-
Returns the position Y.
- getPositionY() - Method in class pojos.WellSampleData
-
- getPositionZ(UnitsLength) - Method in class pojos.ImageAcquisitionData
-
Returns the z-coordinate in the frame microscope.
- getPositionZ() - Method in class pojos.ImageAcquisitionData
-
- getPower(UnitsPower) - Method in class pojos.LightSourceData
-
Returns the power of the light source.
- getPower() - Method in class pojos.LightSourceData
-
- 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
-
- getProcess() - Method in class ome.services.scripts.ScriptFileType
-
Return the import name of the process class which will be used
to invoke scripts of this type.
- getProcess(String) - Method in class ome.services.scripts.ScriptRepoHelper
-
Find an "omero.process..." property string for the given mimetype or
return "" if none is found.
- getProcessedIds(String) - Method in class ome.services.graphs.GraphState
-
Deprecated.
Get the set of ids which were actually processed.
- getProject(long) - Method in class ome.formats.OMEROMetadataStoreClient
-
- 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() - 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.
- getPropertyKind(String, String) - Method in class ome.services.graphs.GraphPathBean
-
Get what kind of property a specific class property is.
- 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.repo.ManagedImportProcessI
-
- getProxy() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
-
- 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
-
- 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.services.mail.MailSender
-
- getQueryService() - Method in class ome.system.ServiceFactory
-
- getQueryStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
Query statistics from query string (HQL or SQL)
- getQueryString() - Method in class ome.services.mail.ObjectMailSender
-
- 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.
- getRange(double) - Method in class omeis.providers.re.quantum.QuantumStrategy
-
Returns the range the values belongs to.
- getRating() - Method in class pojos.RatingAnnotationData
-
Returns the rating value.
- getRawFileStore(long, CheckedPath, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
-
Create a
RawFileBean
(i.e. an implementation of
RawFileStore
which can be passed to
RepoRawFileStore
for performing internal functions.
- getRawFileStore(long, CheckedPath, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- getReader() - Method in class ome.formats.importer.ImportContainer
-
Return the reader class name used for reading the contents of this
import container.
- 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
-
- getReaderClass(Fileset, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
-
Get the suggested BioFormats Reader for the given Fileset.
- 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
-
- getRelativePath() - Method in class ome.services.blitz.repo.CheckedPath
-
Get the parent path of the entity to which this path corresponds.
- 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
-
- 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
-
- getRenderShapes() - Method in class omeis.providers.re.data.PlaneDef
-
Returns whether or not the shapes (masks) will be rendered.
- 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
-
- getRepoUuid() - Method in class ome.services.blitz.repo.PublicRepositoryI
-
- getRequest(Class<R>) - Method in class omero.cmd.graphs.GraphRequestFactory
-
Construct a request.
- getRequest(Current) - Method in class omero.cmd.HandleI
-
- getRequests() - Method in class omero.cmd.graphs.Preprocessor
-
Deprecated.
Returns a copy of the requests field or an empty list if null.
- getRequiredPermissions() - Method in interface ome.services.graphs.GraphTraversal.Processor
-
- getRequiredPermissions() - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
-
- getResolutionDescriptions() - Method in interface ome.api.RawPixelsStore
-
- getResolutionDescriptions() - Method in class ome.io.bioformats.BfPixelBuffer
-
- getResolutionDescriptions() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
-
- getResolutionDescriptions() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
-
- getResolutionDescriptions() - Method in interface ome.io.nio.PixelBuffer
-
Return a list of lists each of which has sizeX, sizeY for the resolution
level matching the index of the outer index.
- getResolutionDescriptions() - Method in class ome.io.nio.RomioPixelBuffer
-
- getResolutionDescriptions() - Method in class ome.services.RawPixelsBean
-
- getResolutionDescriptions() - Method in class ome.services.RenderingBean
-
- getResolutionDescriptions() - Method in class omeis.providers.re.Renderer
-
Returns the image's size information per resolution level.
- getResolutionDescriptions() - Method in interface omeis.providers.re.RenderingEngine
-
- getResolutionDescriptions_async(AMD_PyramidService_getResolutionDescriptions, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
-
- getResolutionDescriptions_async(AMD_PyramidService_getResolutionDescriptions, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
-
- 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
-
- 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
-
- getResponse() - Method in class ome.services.blitz.impl.commands.SaveI
-
- getResponse() - Method in class ome.services.blitz.repo.ManagedImportRequestI
-
- getResponse() - Method in class ome.services.blitz.repo.RawAccessRequestI
-
- getResponse() - Method in class omero.cmd.admin.ResetPasswordRequestI
-
- 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.fs.ManageImageBinariesI
-
- getResponse() - Method in class omero.cmd.fs.OriginalMetadataRequestI
-
- getResponse() - Method in class omero.cmd.fs.UsedFilesRequestI
-
- getResponse() - Method in class omero.cmd.graphs.Chgrp2I
-
- getResponse() - Method in class omero.cmd.graphs.ChgrpFacadeI
-
Deprecated.
- getResponse() - Method in class omero.cmd.graphs.ChgrpI
-
Deprecated.
- getResponse() - Method in class omero.cmd.graphs.ChmodI
-
- getResponse() - Method in class omero.cmd.graphs.Chown2I
-
- getResponse() - Method in class omero.cmd.graphs.ChownFacadeI
-
Deprecated.
- getResponse() - Method in class omero.cmd.graphs.ChownI
-
Deprecated.
- getResponse() - Method in class omero.cmd.graphs.Delete2I
-
- getResponse() - Method in class omero.cmd.graphs.DeleteFacadeI
-
Deprecated.
- getResponse() - Method in class omero.cmd.graphs.DeleteI
-
Deprecated.
- getResponse() - Method in class omero.cmd.graphs.DiskUsageI
-
- getResponse() - Method in class omero.cmd.graphs.GraphSpecListI
-
Deprecated.
- getResponse() - Method in class omero.cmd.graphs.SkipHeadI
-
- 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.
- getResponse() - Method in class omero.cmd.mail.SendEmailRequestI
-
- 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>) - Static 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
-
- 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
-
- getRoles() - Method in class ome.services.mail.MailSender
-
- getRoles() - Method in class ome.services.util.DBUserCheck
-
- getRoot() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getRoot() - Method in class ome.services.blitz.impl.OmeroMetadata
-
- getRoot() - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
-
Deprecated.
Return the root class for this hierarchy.
- getRoot() - Method in class ome.services.graphs.AnnotationGraphSpec
-
Deprecated.
- getRoot() - Method in class ome.services.graphs.LightSourceGraphSpec
-
Deprecated.
- getRootFile() - Method in class ome.formats.importer.transfers.TransferState
-
Find original file represented by the managed repository that
import is taking place to.
- 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() - 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
-
Deprecated.
- 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
-
- getSender() - Method in class ome.services.mail.MailUtil
-
Helper method that returns value of omero.mail.from
.
- 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.
- getSeries() - Method in class pojos.ImageData
-
Returns the series.
- 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
-
- getServerFileFromFsFile(FsFile) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
-
Given a repository path, returns the corresponding server-local
File
.
- getServerFileMimetype() - Method in class pojos.FileAnnotationData
-
Returns the file format as defined by the specification, corresponding to
the file extension.
- 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 ome.services.blitz.impl.RawFileStoreI
-
- getServiceFactory() - Method in class ome.services.blitz.util.FindServiceFactoryMessage
-
- 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.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.
- getShapeIds() - Method in class omeis.providers.re.data.PlaneDef
-
Returns whether or not the shapes (masks) will be rendered.
- 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 its 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.
- getSkipHeadPolicyPerform(GraphPolicy, SetMultimap<String, Long>) - Static method in class omero.cmd.graphs.SkipHeadPolicy
-
Adjust an existing graph traversal policy so that for specific model objects permissions are not checked.
- getSkipHeadPolicySkip(GraphPolicy, GraphPathBean, Collection<String>, GraphPolicy.Action, SetMultimap<String, Long>) - Static method in class omero.cmd.graphs.SkipHeadPolicy
-
Adjust an existing graph traversal policy so that orphaned model objects will always or never be included,
according to their type.
- getSlice() - Method in class omeis.providers.re.data.PlaneDef
-
Returns an identifier to tell which kind of plane this object identifies.
- getSnapshot() - Method in class ome.system.metrics.DefaultHistogram
-
- getSnapshot() - Method in interface ome.system.metrics.Histogram
-
- 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
-
- getSQLJoin(String, String, String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
- getSQLJoin(String, String, String, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
Note: this implementation does not yet take into account the mapping
of joined subclasses like Job->UpdateJob.
- 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() - 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
-
Deprecated.
- getStartFrom(Response) - Method in class omero.cmd.graphs.Chgrp2I
-
- getStartFrom(Response) - Method in class omero.cmd.graphs.Chown2I
-
- getStartFrom(Response) - Method in class omero.cmd.graphs.Delete2I
-
- getStartFrom(Response) - Method in interface omero.cmd.graphs.WrappableRequest
-
From the response of the head-skipping request, determine which model objects are the targets of the operation.
- 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
-
- 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
-
- getStdDev() - Method in class ome.system.metrics.DefaultSnapshot
-
- getStdDev() - Method in interface ome.system.metrics.Snapshot
-
- getStep(int) - Method in class ome.services.graphs.GraphState
-
Deprecated.
- getSteps() - Method in class ome.services.delete.Deletion
-
Deprecated.
- getSteps() - Method in class omero.cmd.Helper
-
- getStop() - Method in class ome.services.delete.Deletion
-
Deprecated.
- getStore() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
- getStrategy(QuantumDef, Pixels) - 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
-
- getStrokeWidth(UnitsLength) - Method in class pojos.ShapeSettingsData
-
Returns the stroke's width (or 1 px if it's not set or <= 0)
- getSubclassesOf(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the subclasses of the given class, if any.
- getSubclassesOfReflexive(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the name of this class and of its mapped subclasses.
- getSubjectPrefix() - Method in class ome.services.mail.MailSender
-
- getSubSpec() - Method in class ome.services.graphs.GraphEntry
-
Deprecated.
- getSubtypeValue(int, int, Object) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
- getSuccessfulTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- getSuperclassesOf(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the superclasses of the given class, if any.
- getSuperclassesOfReflexive(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the name of this class and of its mapped superclasses.
- getSuperSpec() - Method in class ome.services.graphs.BaseGraphSpec
-
Deprecated.
- getSuperSpec() - Method in class ome.services.graphs.GraphEntry
-
Deprecated.
- getSuperSpec() - Method in interface ome.services.graphs.GraphSpec
-
Deprecated.
Specification of where this
GraphSpec
is attached under another
.
- getSupportedMetadataLevels() - Method in class ome.formats.importer.OMEROWrapper
-
- getSymbol(Current) - Method in class omero.model.ElectricPotentialI
-
- getSymbol(Current) - Method in class omero.model.FrequencyI
-
- getSymbol(Current) - Method in class omero.model.LengthI
-
- getSymbol(Current) - Method in class omero.model.PowerI
-
- getSymbol(Current) - Method in class omero.model.PressureI
-
- getSymbol(Current) - Method in class omero.model.TemperatureI
-
- getSymbol(Current) - Method in class omero.model.TimeI
-
- 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
- getTarget() - Method in class ome.services.blitz.repo.ManagedImportLocationI
-
Return the server-side
CheckedPath
instance which can be passed to
a Bio-Formats reader.
- 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(UnitsTemperature) - Method in class pojos.ImageAcquisitionData
-
Returns the temperature in Celcius.
- getTemperature() - Method in class pojos.ImageAcquisitionData
-
- 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.
- getThis() - Method in interface ome.services.util.Executor.StatefulWork
-
- getThis(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
-
- 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(Integer, Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnail_async(AMD_ThumbnailStore_getThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
-
- getThumbnailByLongestSide(Integer) - Method in interface ome.api.ThumbnailStore
-
Retrieves a thumbnail for a pixels set using a given set of rendering
settings (RenderingDef).
- getThumbnailByLongestSide(Integer) - Method in 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(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(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
-
- 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
-
- 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() - 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
-
- getTooSimilarFiles(Set<File>) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer
-
Get the files that are too similarly named.
- getTopicManager() - Method in class ome.services.blitz.util.BlitzConfiguration
-
- getTotalFoundCount() - Method in class ome.services.graphs.GraphState
-
Deprecated.
Return the total number of ids loaded into this instance.
- getTotalProcessedCount() - Method in class ome.services.graphs.GraphState
-
Deprecated.
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() - 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() - Method in class ome.security.policy.BasePolicy
-
- getTypes() - Method in interface ome.security.policy.Policy
-
- getTypes(ExtendedMetadata) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
-
Deprecated.
Returns all the types that are known for this hierarchy.
- getTypes(ExtendedMetadata) - Method in class ome.services.graphs.AnnotationGraphSpec
-
Deprecated.
- getTypes(ExtendedMetadata) - Method in class ome.services.graphs.LightSourceGraphSpec
-
Deprecated.
- 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
-
Deprecated.
- getUndeletedFiles() - Method in class ome.services.delete.files.AbstractFileDeletions
-
- getUndeletedFiles() - Method in class ome.services.delete.files.FileDeleter
-
- getUnique() - Method in class omero.sys.ParametersI
-
- getUnit(Current) - Method in class omero.model.ElectricPotentialI
-
- getUnit(Current) - Method in class omero.model.FrequencyI
-
- getUnit(Current) - Method in class omero.model.LengthI
-
- getUnit(Current) - Method in class omero.model.PowerI
-
- getUnit(Current) - Method in class omero.model.PressureI
-
- getUnit(Current) - Method in class omero.model.TemperatureI
-
- getUnit(Current) - Method in class omero.model.TimeI
-
- 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
-
- getUploader() - Method in class ome.formats.importer.transfers.TransferState
-
Return the RawFileStorePrx
instance for this index.
- getUploader(String) - Method in class ome.formats.importer.transfers.TransferState
-
Return the RawFileStorePrx
instance for this index setting
the mode if not null.
- getUploader(int, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
-
- getUploaderUrl() - Method in class ome.formats.importer.ImportConfig
-
- getUploadOffset(int, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
-
- getUploadTimeLeft() - Method in class ome.formats.importer.transfers.TransferState
-
- getUploadTimeLeft() - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
-
- getUploadTimeLeft() - Method in interface ome.formats.importer.util.TimeEstimator
-
Return the estimated time left in milliseconds based on the calls to
start
and
stop
methods.
- 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
-
- getUsedFilePaths() - Method in class pojos.FilesetData
-
Returns the collection of file paths used for importing the files
(in case of in-place imports these are the targets of the (sym)links)
- 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
-
Return a list of file names that belong to this import container.
- getUsedFilesTotalSize() - Method in class ome.formats.importer.ImportContainer
-
Returns the total size in bytes (based on File.length()
)
of all files in this import container.
- 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
-
- 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
-
- getUserEmail(String) - Method in class ome.services.mail.MailSender
-
- 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
-
- getUserInstitution(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
-
Get the current user's institution.
- getUserInstitution(long, ServiceFactory) - Method in interface ome.services.blitz.repo.RepositoryDao
-
Get the current user's institution.
- getUserInstitution(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- getUserInstitution(long, ServiceFactory) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
- 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
-
- getUserSpecifiedDescription() - Method in class ome.formats.importer.ImportContainer
-
Retrieves the current custom image/plate description string.
- getUserSpecifiedDescription() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the user specified image/plate description.
- getUserSpecifiedDescription() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getUserSpecifiedImageName() - Method in class ome.formats.OMEROMetadataStoreClient
-
- getUserSpecifiedName() - Method in class ome.formats.importer.ImportContainer
-
Retrieves the current custom image/plate name string.
- getUserSpecifiedName() - Method in interface ome.formats.model.IObjectContainerStore
-
Returns the user specified image/plate name.
- getUserSpecifiedName() - 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
-
- 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(double) - Method in class ome.system.metrics.DefaultSnapshot
-
- getValue(double) - Method in interface ome.system.metrics.Snapshot
-
- getValue(Current) - Method in class omero.model.ElectricPotentialI
-
- getValue(Current) - Method in class omero.model.FrequencyI
-
- getValue(Current) - Method in class omero.model.LengthI
-
- getValue(Current) - Method in class omero.model.PowerI
-
- getValue(Current) - Method in class omero.model.PressureI
-
- getValue(Current) - Method in class omero.model.TemperatureI
-
- getValue(Current) - Method in class omero.model.TimeI
-
- getValue() - Method in class pojos.BooleanAnnotationData
-
Returns the text of this annotation.
- getValues() - Method in class ome.system.metrics.DefaultSnapshot
-
- getValues() - Method in interface ome.system.metrics.Snapshot
-
- getVersion() - Method in interface ome.api.IConfig
-
Provides the release version.
- 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(UnitsElectricPotential) - Method in class pojos.DetectorData
-
Returns the voltage of the detector.
- getVoltage() - Method in class pojos.DetectorData
-
- getWarmUpFactor() - Method in class ome.io.nio.SimpleBackOff
-
- getWarning() - Method in class ome.services.delete.Deletion
-
Deprecated.
- getWarning() - Method in class ome.services.delete.files.FileDeleter
-
- getWavelength() - Method in exception omeis.providers.re.quantum.QuantizationException
-
Returns the index of the wavelength that couldn't be rendered.
- getWellOriginX(UnitsLength) - Method in class pojos.PlateData
-
Returns the x-coordinate in 2D-space of the well.
- getWellOriginX() - Method in class pojos.PlateData
-
- getWellOriginY(UnitsLength) - Method in class pojos.PlateData
-
Returns the y-coordinate in 2D-space of the well.
- getWellOriginY() - Method in class pojos.PlateData
-
- 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(UnitsLength) - Method in class pojos.ObjectiveData
-
Returns the working distance.
- getWorkingDistance() - Method in class pojos.ObjectiveData
-
- 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
-
- GraphConstraintException - Exception in ome.services.graphs
-
- GraphConstraintException(String, HashMultimap<String, Long>) - Constructor for exception ome.services.graphs.GraphConstraintException
-
Deprecated.
- GraphEntry - Class in ome.services.graphs
-
- GraphEntry(GraphSpec, String) - Constructor for class ome.services.graphs.GraphEntry
-
Deprecated.
- GraphEntry(GraphSpec, String, GraphEntry) - Constructor for class ome.services.graphs.GraphEntry
-
Deprecated.
- 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
-
- graphException(GraphException, long, long) - Method in class omero.cmd.Helper
-
Deprecated.
- GraphOpts - Class in ome.services.graphs
-
- GraphOpts() - Constructor for class ome.services.graphs.GraphOpts
-
Deprecated.
- GraphOpts.Op - Enum in ome.services.graphs
-
Deprecated.
- GraphPathBean - Class in ome.services.graphs
-
The graph path bean holds the Hiberate object mapping and assists navigation thereof.
- GraphPathBean() - Constructor for class ome.services.graphs.GraphPathBean
-
- GraphPathReport - Class in ome.services.graphs
-
A standalone tool for producing a summary of the Hibernate object mapping for our Sphinx documentation.
- GraphPathReport() - Constructor for class ome.services.graphs.GraphPathReport
-
- GraphPolicy - Class in ome.services.graphs
-
A policy guides how to traverse the graph.
- GraphPolicy() - Constructor for class ome.services.graphs.GraphPolicy
-
- GraphPolicy.Ability - Enum in ome.services.graphs
-
Abilities that the user may have to operate upon model objects.
- GraphPolicy.Action - Enum in ome.services.graphs
-
The action to take on an object instance.
- GraphPolicy.Details - Class in ome.services.graphs
-
A tuple noting the state of a mapped object instance in the current graph traversal.
- GraphPolicy.Orphan - Enum in ome.services.graphs
-
- GraphPolicyRule - Class in ome.services.graphs
-
A graph policy rule specifies a component of a
GraphPolicy
.
- GraphPolicyRule() - Constructor for class ome.services.graphs.GraphPolicyRule
-
- GraphRequestFactory - Class in omero.cmd.graphs
-
Create request objects that are executed using the
GraphPathBean
.
- GraphRequestFactory(ACLVoter, SystemTypes, GraphPathBean, Deletion, Map<Class<? extends Request>, List<GraphPolicyRule>>, List<String>, Set<String>, boolean) - Constructor for class omero.cmd.graphs.GraphRequestFactory
-
Construct a new graph request factory.
- GraphSpec - Interface in ome.services.graphs
-
- GraphSpecListI - Class in omero.cmd.graphs
-
- GraphSpecListI(OmeroContext) - Constructor for class omero.cmd.graphs.GraphSpecListI
-
Deprecated.
- GraphSpecPostProcessor - Class in ome.services.graphs
-
- GraphSpecPostProcessor() - Constructor for class ome.services.graphs.GraphSpecPostProcessor
-
Deprecated.
- GraphState - Class in ome.services.graphs
-
- GraphState(EventContext, GraphStepFactory, SqlAction, Session, GraphSpec) - Constructor for class ome.services.graphs.GraphState
-
Deprecated.
- GraphStep - Class in ome.services.graphs
-
- GraphStep(ExtendedMetadata, int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.graphs.GraphStep
-
Deprecated.
- GraphStep.Callback - Interface in ome.services.graphs
-
Deprecated.
- GraphStepFactory - Interface in ome.services.graphs
-
- GraphSteps - Class in ome.services.graphs
-
- GraphSteps(List<GraphStep>) - Constructor for class ome.services.graphs.GraphSteps
-
Deprecated.
- GraphTables - Class in ome.services.graphs
-
- GraphTables() - Constructor for class ome.services.graphs.GraphTables
-
Deprecated.
- GraphTraversal - Class in ome.services.graphs
-
An alternative implementation of model object graph traversal, relying on SELECTing in advance for making decisions,
instead of rolling back to savepoints to recover from failed attempts to act.
- GraphTraversal(Session, EventContext, ACLVoter, SystemTypes, GraphPathBean, SetMultimap<String, String>, GraphPolicy, GraphTraversal.Processor) - Constructor for class ome.services.graphs.GraphTraversal
-
Construct a new instance of a graph traversal manager.
- GraphTraversal.Processor - Interface in ome.services.graphs
-
Executes the planned operation.
- GraphUtil - Class in omero.cmd.graphs
-
Static utility methods for model graph operations.
- GraphUtil() - Constructor for class omero.cmd.graphs.GraphUtil
-
- graphValidation(Session) - Method in class ome.services.graphs.GraphStep
-
Deprecated.
Immediately we check that an object moved from GroupA to GroupB
is no longer pointed at by any objects in GroupA via foreign key
constraints.
- 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_SUDO_NS - Static variable in class ome.services.sessions.SessionManagerImpl
-
- 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
-
- groupContext(Long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
Creates a copy of the Current.ctx
map and if groupId is
not null, sets the "omero.group" key to be a string version of the
id.
- GroupContextMapper - Class in ome.security.auth
-
Specialized OME ExperimenterGroup context mapper.
- GroupContextMapper(LdapConfig, String) - Constructor for class ome.security.auth.GroupContextMapper
-
- GroupContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.GroupContextMapper
-
- 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.
- groupId - Variable in class ome.services.graphs.GraphPolicy.Details
-
the ID of the object's ExperimenterGroup
,
or null
if the object does not have a group
- groupInfo(SqlAction) - Method in class ome.services.graphs.BaseGraphSpec
-
Deprecated.
- groupInfo(SqlAction) - Method in interface ome.services.graphs.GraphSpec
-
Deprecated.
- groupnameFilter(String) - Method in class ome.security.auth.LdapConfig
-
- 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
-
- groupRestrictions(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
-
- 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
-
- groupsLed - Variable in class ome.services.sessions.SessionManager.CreationRequest
-
- 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_exception(Exception) - Method in class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
-
- ice_postUnmarshal() - Method in class omero.model.PermissionsI
-
Called as Ice converts from a binary stream to a PermissionsI object.
- ice_response(HandlePrx) - Method in class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
-
- 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
-
- icMap - Variable in class ome.formats.importer.util.ErrorHandler
-
Host information about the file and its corresponding import candidate.
- 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.blitz.repo.CheckedPath
-
- id - Variable in class ome.services.blitz.util.FindServiceFactoryMessage
-
- id - Variable in class ome.services.graphs.BaseGraphSpec
-
Deprecated.
The id of the root type which will be processed.
- id - Variable in class ome.services.graphs.GraphStep
-
Deprecated.
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
-
Deprecated.
- 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.
- ignoreAnnotator(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
-
For all cases of an annotator being ignore (WARN).
- ignoreInsecure(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
-
Called when saving a property to OMERO would result in a SecurityViolation
(DEBUG).
- ignoreMissing(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
-
Called when a property is missing from the OMERO model (WARN).
- 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
.
- ignoreUnneeded(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
-
Called when a property is not needed in OMERO since the data can
be gotten elsewhere, as in directly from the file itself (DEBUG).
- ignoreUnsupported(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
-
Called when a property is not expected in a file to be imported.
- IGraphModifyRequest - Interface in omero.cmd.graphs
-
- 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.
- imageID - Variable in class loci.ome.io.OMECredentials
-
- ImageNameMetadataStore - Class in ome.formats
-
Stores all Image names consumed by the interface.
- ImageNameMetadataStore() - Constructor for class ome.formats.ImageNameMetadataStore
-
- ImagingEnvironment_AirPressure - Static variable in class ome.formats.model.UnitsFactory
-
- ImagingEnvironment_Temperature - Static variable in class ome.formats.model.UnitsFactory
-
- 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.
- IMPORT_LOG_MIMETYPE - Static variable in class ome.services.blitz.repo.PublicRepositoryI
-
media type for import logs
- 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.
- ImportConfig.VersionInfo - Enum in ome.formats.importer
-
Keys for fileset version information entries.
- ImportContainer - Class in ome.formats.importer
-
- ImportContainer(File, IObject, Double[], String, String[], Boolean) - Constructor for class ome.formats.importer.ImportContainer
-
- ImportContainer(ImportConfig, File, IObject, Double[], String, String[], Boolean) - Constructor for class ome.formats.importer.ImportContainer
-
- 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, ImportContainer, 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, ImportContainer, 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, ImportContainer, 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, ImportContainer, 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, ImportContainer, 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, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_SAVE_TO_DB
-
- 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.FILE_UPLOAD_BYTES - Class in ome.formats.importer
-
- ImportEvent.FILE_UPLOAD_BYTES(String, int, int, Long, 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.FILESET_EXCLUSION - Class in ome.formats.importer
-
- ImportEvent.FILESET_EXCLUSION(String, int, int) - Constructor for class ome.formats.importer.ImportEvent.FILESET_EXCLUSION
-
- ImportEvent.FILESET_UPLOAD_END - Class in ome.formats.importer
-
- ImportEvent.FILESET_UPLOAD_END(String, int, int, Long, Long, String[], List<String>, Map<Integer, String>, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
-
- ImportEvent.FILESET_UPLOAD_PREPARATION - Class in ome.formats.importer
-
- ImportEvent.FILESET_UPLOAD_PREPARATION(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_PREPARATION
-
- ImportEvent.FILESET_UPLOAD_START - Class in ome.formats.importer
-
- ImportEvent.FILESET_UPLOAD_START(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_START
-
- ImportEvent.IMPORT_ARCHIVING - Class in ome.formats.importer
-
- ImportEvent.IMPORT_ARCHIVING(int, ImportContainer, 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, ImportContainer, IObject, Long, int, ImportSize, List<Pixels>, Fileset, List<IObject>) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_DONE
-
- ImportEvent.IMPORT_OVERLAYS - Class in ome.formats.importer
-
- ImportEvent.IMPORT_OVERLAYS(int, ImportContainer, 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, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_PROCESSING
-
- ImportEvent.IMPORT_STARTED - Class in ome.formats.importer
-
- ImportEvent.IMPORT_STARTED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_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.IMPORT_SUMMARY - Class in ome.formats.importer
-
- ImportEvent.IMPORT_SUMMARY(long, int) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
-
- 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.METADATA_IMPORTED - Class in ome.formats.importer
-
- ImportEvent.METADATA_IMPORTED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.METADATA_IMPORTED
-
- ImportEvent.METADATA_PROCESSED - Class in ome.formats.importer
-
- ImportEvent.METADATA_PROCESSED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.METADATA_PROCESSED
-
- ImportEvent.OBJECTS_RETURNED - Class in ome.formats.importer
-
- ImportEvent.OBJECTS_RETURNED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.OBJECTS_RETURNED
-
- ImportEvent.PIXELDATA_PROCESSED - Class in ome.formats.importer
-
- ImportEvent.PIXELDATA_PROCESSED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.PIXELDATA_PROCESSED
-
- ImportEvent.POST_UPLOAD_EVENT - Class in ome.formats.importer
-
- ImportEvent.POST_UPLOAD_EVENT(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.POST_UPLOAD_EVENT
-
- ImportEvent.PROGRESS_EVENT - Class in ome.formats.importer
-
- ImportEvent.PROGRESS_EVENT(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.PROGRESS_EVENT
-
- ImportEvent.REIMPORT - Class in ome.formats.importer
-
- ImportEvent.REIMPORT() - Constructor for class ome.formats.importer.ImportEvent.REIMPORT
-
- ImportEvent.THUMBNAILS_GENERATED - Class in ome.formats.importer
-
- ImportEvent.THUMBNAILS_GENERATED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.THUMBNAILS_GENERATED
-
- importFileset(Fileset, ImportSettings, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
-
Return a template based directory path.
- 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 uploading files if necessary.
- ImportLibrary - Class in ome.formats.importer
-
- ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportLibrary
-
- ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer) - Constructor for class ome.formats.importer.ImportLibrary
-
The library will not close the client instance.
- ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer, int) - Constructor for class ome.formats.importer.ImportLibrary
-
- ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer, List<FileExclusion>, int) - Constructor for class ome.formats.importer.ImportLibrary
-
- ImportLibrary.ImportCallback - Class in ome.formats.importer
-
- ImportLibrary.ImportCallback(ImportProcessPrx, HandlePrx, ImportContainer) - Constructor for class ome.formats.importer.ImportLibrary.ImportCallback
-
- importMetadata(MetadataImportJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
-
- importPaths(List<String>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
-
- 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
-
- importTime - Variable in class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
-
- 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.
- inc() - Method in interface ome.system.metrics.Counter
-
- inc() - Method in class ome.system.metrics.DefaultCounter
-
- 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.PROGRESS_EVENT
-
- Index - Enum in ome.formats
-
- index(IndexingJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
-
- 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(Helper) - Method in class ome.services.blitz.repo.ManagedImportRequestI
-
- init(Helper) - Method in class ome.services.blitz.repo.RawAccessRequestI
-
- 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.admin.ResetPasswordRequestI
-
- 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.fs.ManageImageBinariesI
-
- init(Helper) - Method in class omero.cmd.fs.OriginalMetadataRequestI
-
- init(Helper) - Method in class omero.cmd.fs.UsedFilesRequestI
-
- init(Helper) - Method in class omero.cmd.graphs.Chgrp2I
-
- init(Helper) - Method in class omero.cmd.graphs.ChgrpFacadeI
-
Deprecated.
- init(Helper) - Method in class omero.cmd.graphs.ChgrpI
-
Deprecated.
- init() - Method in class omero.cmd.graphs.ChildOptionI
-
Initialize this child option instance.
- init(Helper) - Method in class omero.cmd.graphs.ChmodI
-
- init(Helper) - Method in class omero.cmd.graphs.Chown2I
-
- init(Helper) - Method in class omero.cmd.graphs.ChownFacadeI
-
Deprecated.
- init(Helper) - Method in class omero.cmd.graphs.ChownI
-
Deprecated.
- init(Helper) - Method in class omero.cmd.graphs.Delete2I
-
- init(Helper) - Method in class omero.cmd.graphs.DeleteFacadeI
-
Deprecated.
- init(Helper) - Method in class omero.cmd.graphs.DeleteI
-
Deprecated.
- init(Helper) - Method in class omero.cmd.graphs.DiskUsageI
-
- init(Helper) - Method in class omero.cmd.graphs.GraphSpecListI
-
Deprecated.
- init(Helper) - Method in class omero.cmd.graphs.SkipHeadI
-
- init(Helper) - Method in interface omero.cmd.IRequest
-
Method called within the transaction boundaries before any processing occurs.
- init(Helper) - Method in class omero.cmd.mail.SendEmailRequestI
-
- initFile(String) - Method in class loci.ome.io.OmeroReader
-
- initFile(String) - Method in class ome.services.formats.OmeroReader
-
- INITIAL_DELAY - Static variable in class ome.logic.RepositoryInfoImpl
-
- INITIAL_FREE_PHYSICAL_MEMORY - Static variable in class ome.services.util.JvmSettingsCheck
-
FreePhysicalMemorySize value from the OperatingSystem JMX bean
at startup.
- initializationDone() - Method in class omero.cmd.CmdCallbackI
-
- 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(FileMaker, Long, String) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Called by the internal repository once initialization has taken place.
- initialize() - Method in class ome.services.eventlogs.EventLogQueue
-
Do nothing.
- 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
-
Deprecated.
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
-
Deprecated.
- initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.GraphEntry
-
Deprecated.
- initialize(long, String, Map<String, String>) - Method in interface ome.services.graphs.GraphSpec
-
Deprecated.
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(Pixels) - Method in class omeis.providers.re.metadata.StatsFactory
-
Determines the minimum and maximum corresponding to the passed
pixels.
- 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, ScriptRepoHelper, 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
.
- internalMkdir(CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
-
This method should only be used by the register public method in order to
guarantee that the DB is kept in sync with the file system.
- internalMoveToCommonSpace(IObject) - Method in interface ome.api.local.LocalAdmin
-
Unconditionally move an object into the user group (usually id=1).
- internalMoveToCommonSpace(IObject) - Method in class ome.logic.AdminImpl
-
Helpers which unconditionally moves the object to the common space.
- 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, Principal, String, PublicRepositoryI) - 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
-
- InvalidQueryException - Exception in ome.util.search
-
Exception to indicate that the query string was invalid
- InvalidQueryException() - Constructor for exception ome.util.search.InvalidQueryException
-
- InvalidQueryException(String, Throwable) - Constructor for exception ome.util.search.InvalidQueryException
-
- InvalidQueryException(String) - Constructor for exception ome.util.search.InvalidQueryException
-
- InvalidQueryException(Throwable) - Constructor for exception ome.util.search.InvalidQueryException
-
- 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
-
Deprecated.
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
-
- ip - Variable in class ome.services.sessions.SessionManager.CreationRequest
-
- 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
-
- iQuery - Variable in class ome.services.query.HierarchyNavigator
-
available query service
- 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
-
Deprecated.
Whether or not the type of types[i] is abstract.
- isAcceptable(List<String>) - Method in class ome.services.blitz.repo.path.MakeNextDirectory
-
If the circumstances (filesystem, etc.) are such that it is okay to use the given subdirectories.
- 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() - 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
-
- isAdjustedAfterReview(GraphPolicy.Details) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
-
An opportunity to adjust each model object after the graph policy reviews it.
- isAdjustedBeforeReview(GraphPolicy.Details) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
-
An opportunity to adjust each model object before the graph policy reviews it.
- 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
-
- isCheckPermissions - Variable in class ome.services.graphs.GraphPolicy.Details
-
- 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.
- isCondition(String) - Method in class ome.services.graphs.GraphPolicy
-
Check if a condition has been set.
- isCondition(String) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
-
- 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 ome.services.blitz.repo.CheckedPath
-
- 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
-
- isEnabled() - Method in class ome.services.mail.MailSender
-
- 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.
- isError(SqlAction.DeleteLog) - Method in class ome.services.messages.DeleteLogMessage
-
- 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() - 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
-
Deprecated.
- isFSImage() - Method in class pojos.ImageData
-
Returns true
is the image has been imported the new
import strategy known as FS import, false
if imported
using the previous import approach (data duplication).
- 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
-
- isGraphsWrap() - Method in class omero.cmd.graphs.GraphRequestFactory
-
- 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.
- isIgnoreCaseLookup() - Method in interface ome.security.auth.RoleProvider
-
- isIgnoreCaseLookup() - Method in class ome.security.auth.SimpleRoleProvider
-
- isImagingEnvironmentDirty() - Method in class pojos.ImageAcquisitionData
-
Returns true
if the StageLabel has been updated,
false
otherwise.
- isImmutable(Object) - Method in class omero.util.IceMapper
-
- isIncludeType(Class<? extends IObject>) - Method in class omero.cmd.graphs.ChildOptionI
-
Test if this child option adjusts graph traversal policy for the given child object class.
- 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
-
Deprecated.
- isLast(int) - Method in class omero.cmd.Helper
-
Returns true if this is the last step for the given request.
- isLDAP() - Method in class pojos.ExperimenterData
-
Returns true
if the user is connected via LDAP.
- isLegalFsFile(FsFile) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
-
Test if the given
FsFile
has been properly sanitized by the client.
- 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.
- isLinux() - Static method in class ome.services.blitz.util.CurrentPlatform
-
- 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
-
- isMacOSX() - Static method in class ome.services.blitz.util.CurrentPlatform
-
- 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
-
- isMinMaxSet() - Method in class ome.formats.importer.OMEROWrapper
-
- isModified() - Method in class ome.services.AbstractStatefulBean
-
- isModified() - Method in class ome.services.RawFileBean
-
Extends the check of the
AbstractStatefulBean.modified
flag performed by super
with an additional check of the actual file size against the value
stored in the database
- 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
-
Deprecated.
- 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.
- isOMERO - Variable in class loci.ome.io.OMECredentials
-
- isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
-
Deprecated.
- isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.AnnotationGraphSpec
-
Deprecated.
- isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.LightSourceGraphSpec
-
Deprecated.
- 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
-
- 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
-
- isPropertyAccessible(String, String) - Method in class ome.services.graphs.GraphPathBean
-
Find if the given property can be accessed.
- 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
-
- isReap() - Method in class ome.services.graphs.GraphEntry
-
Deprecated.
- isRestricted(IObject) - Method in class ome.security.policy.BasePolicy
-
- isRestricted(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
-
- isRestricted(String, IObject) - Method in class ome.security.policy.DefaultPolicyService
-
- isRestricted(IObject) - Method in interface ome.security.policy.Policy
-
- isRestricted(String, IObject) - Method in interface ome.security.policy.PolicyService
-
Ask each configured
Policy
instance with the given name argument
if it considers the restriction active for the given
IObject
argument.
- isRestricted(String, Current) - Method in class omero.model.PermissionsI
-
- 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
-
- isRoot - Variable in class ome.services.blitz.repo.CheckedPath
-
- 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() - 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
-
Deprecated.
- 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
- isStopSet() - Method in class ome.services.eventlogs.EventLogLoader
-
Returns true if the stop flag has been set on this instance.
- isSyncOnLogin() - Method in class ome.security.auth.LdapConfig
-
- isSystemGroup(ExperimenterGroup) - Method in class ome.system.Roles
-
- 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.
- isTargetNamespace(String) - Method in class omero.cmd.graphs.ChildOptionI
-
Test if this child option adjusts graph traversal policy for child objects that are annotations in the given namespace.
- isThisType(String, boolean) - Method in class loci.ome.io.OmeroReader
-
- 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.
- isUnknown() - Static method in class ome.services.blitz.util.CurrentPlatform
-
- 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.
- isWindows() - Method in class ome.formats.importer.transfers.AbstractFileTransfer
-
Uses os.name to determine whether or not this JVM is running
under Windows.
- isWindows() - Static method in class ome.services.blitz.util.CurrentPlatform
-
- 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
-
- 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
-