Index (omero-server 5.5.5 API)

A B C D E F G H I J K L M N O P Q R S T U V W _

A

AbstractClassIdsOptionsQuery - Class in ome.services.query: simple abstract class that provides a common Definitions containing: IdsQueryParameterDef and ClassQueryParameterDef.
AbstractClassIdsOptionsQuery(Parameters) - Constructor for class ome.services.query.AbstractClassIdsOptionsQuery
AbstractFileDeletions - Class in ome.services.delete.files: Base class for managing the removal of files from disk.
AbstractFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.AbstractFileDeletions
AbstractLevel1Service - Class in ome.logic: service level 1
AbstractLevel1Service() - Constructor for class ome.logic.AbstractLevel1Service
AbstractLevel2Service - Class in ome.logic: service level 2
AbstractLevel2Service() - Constructor for class ome.logic.AbstractLevel2Service
AbstractSecurityFilter - Class in ome.security.basic: overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.
AbstractSecurityFilter() - Constructor for class ome.security.basic.AbstractSecurityFilter: Default constructor which calls all the necessary setters for this FactoryBean.
AbstractSecurityFilter(Roles) - Constructor for class ome.security.basic.AbstractSecurityFilter
AbstractSessionMessage - Class in ome.services.messages: InternalMessage implementations which carry relate to some Session bound event.
AbstractSessionMessage(Object, String) - Constructor for class ome.services.messages.AbstractSessionMessage
AbstractStatefulBean - Class in ome.services: Base bean implementation for stateful services.
AbstractStatefulBean() - Constructor for class ome.services.AbstractStatefulBean
AbstractStatsMessage - Class in ome.services.messages.stats: Published when some limit in user/group/session activity has been reached.
AbstractStatsMessage(Object) - Constructor for class ome.services.messages.stats.AbstractStatsMessage
AbstractStatsMessage(Object, boolean) - Constructor for class ome.services.messages.stats.AbstractStatsMessage
accept(String, String) - Method in class ome.services.mail.MapAnnotationSubethaListener: Accepts all mails.
accept(Job) - Method in class ome.services.procs.ProcessorSkeleton
acl - Variable in class ome.tools.hibernate.ProxyCleanupFilter
ACLEventListener - Class in ome.security: responsible for intercepting all pre-INSERT, pre-UPDATE, pre-DELETE, and post-LOAD events to apply access control.
ACLEventListener(ACLVoter) - Constructor for class ome.security.ACLEventListener: main constructor.
aclVoter - Variable in class ome.logic.AdminImpl
ACLVoter - Interface in ome.security: helper security interface for all decisions on access control
aclVoter - Variable in class ome.security.basic.BasicSecuritySystem
acquireContext() - Method in class ome.services.util.BeanHelper: Lazy loads the application context, which means that if we're not in the application server, then the OmeroContext.MANAGED_CONTEXT should never get loaded.
action - Variable in class ome.services.graphs.GraphPolicy.Details: the current plan for the object, may be mutated by GraphPolicy.review(Map, Details, Map, Set, boolean)
action - Variable in class ome.services.messages.EventLogMessage
action - Variable in class ome.tools.hibernate.EventMethodInterceptor
Action() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.Action
activate() - Method in class ome.services.JobBean: Does almost nothing.
activate() - Method in class ome.services.RawFileBean
activate() - Method in class ome.services.RawPixelsBean
activate() - Method in class ome.services.RenderingBean
activate() - Method in class ome.services.SearchBean
activate(long) - Method in class ome.services.sharing.ShareBean
activate() - Method in class ome.services.ThumbnailBean
activeQueries() - Method in class ome.services.SearchBean
add(EventLog) - Method in class ome.services.eventlogs.EventBacklog: Adds the given EventLog instance to the end of a queue for later popping if no equivalent EventLog is present.
add(Document, String, String, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper: Deprecated.

Helper method which takes the parameters from the BridgeHelper.set(String, Object, Document, LuceneOptions) method (possibly modified) as well as the parsed String value which should be added to the index, and adds two fields.
addAction(SearchAction) - Method in class ome.services.SearchBean
addAllDisabled(String...) - Method in class ome.security.basic.CurrentDetails
addApplicationListener(ApplicationListener) - Method in class ome.services.messages.GlobalMulticaster
addApplicationListenerBean(String) - Method in class ome.services.messages.GlobalMulticaster
addCallback(String, SessionCallback) - Method in class ome.services.sessions.SessionManagerImpl
addCleanup(RegisterServiceCleanupMessage) - Method in class ome.security.basic.CurrentDetails: Add a RegisterServiceCleanupMessage to the current thread for cleanup by the ServiceHandler on exit.
addCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean: Deprecated.
addCodomainMapToChannel(CodomainMapContext, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
addComment(long, String) - Method in class ome.services.sharing.ShareBean
addContents(Document, String, OriginalFile, OriginalFilesService, Map<String, FileParser>, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper: Deprecated.

Second helper method used when parsing files.
addDisabled(String) - Method in class ome.security.basic.CurrentDetails
addEnumIfNotNull(Document, String, IEnum, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper: Deprecated.

Helper method which takes the parameters from the BridgeHelper.set(String, Object, Document, LuceneOptions) method (possibly modified) as well as the IEnum value which should be added to the index, and adds two fields.
addEventLog(Class<? extends IObject>, long) - Method in class ome.services.eventlogs.EventLogLoader: Adds an EventLog for the given Class and id to the backlog.
addEventLog(Class<? extends IObject>, long) - Method in class ome.services.eventlogs.EventLogQueue: Only schedule a new backlog event if there is no currently registered event of that type.
addFieldToDocument(String, String, Document) - Method in class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
addGroupOwners(ExperimenterGroup, Experimenter...) - Method in class ome.logic.AdminImpl
addGroups(Experimenter, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
addGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
addGroups(Experimenter, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
addGuest(long, String) - Method in class ome.services.sharing.ShareBean
addGuests(long, String...) - Method in class ome.services.sharing.ShareBean
addIfNotNull(Document, String, String, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper: Deprecated.

Helper method which takes the parameters from the BridgeHelper.set(String, Object, Document, LuceneOptions) method (possibly modified) as well as the parsed String value which should be added to the index, and adds two fields.
adding - Variable in class ome.services.eventlogs.EventBacklog: Switch between the adding and the removing states.
additions() - Method in class ome.security.basic.EventListenersFactoryBean
addLocalFile(File, long) - Method in class ome.services.delete.files.AbstractFileDeletions: Called during the creation of instances if a particular file should be handled by AbstractFileDeletions.deleteLocal().
addLog(String, Class, Long) - Method in class ome.security.basic.BasicSecuritySystem
addLog(String, Class, Long) - Method in class ome.security.basic.CurrentDetails
addManager(String, String) - Method in class ome.security.basic.NodeProviderInDb
addManager(String, String) - Method in class ome.security.basic.NodeProviderInMemory
addManager(String, String) - Method in class ome.security.basic.NodeProviderWrapper
addManager(String, String) - Method in interface ome.security.NodeProvider: Adds a manager node.
addNumericFieldToDocument(String, Object, Document) - Method in class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
addObject(long, T) - Method in class ome.services.sharing.ShareBean
addObjects(long, T...) - Method in class ome.services.sharing.ShareBean
addOrderByAsc(String) - Method in class ome.services.SearchBean
addOrderByDesc(String) - Method in class ome.services.SearchBean
addOrReplace(RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper
addOrReplace(Session, SqlAction, ServiceFactory, RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper
addParameters(Parameters) - Method in class ome.services.SearchBean
addReply(long, String, CommentAnnotation) - Method in class ome.services.sharing.ShareBean
addResult(List<IObject>) - Method in class ome.services.SearchBean
addSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache
addUser(Set<String>, Experimenter) - Method in class ome.services.mail.MailSender
addUser(Set<String>, Experimenter) - Method in class ome.services.mail.ObjectMailSender
addUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean
addUsers(long, Experimenter...) - Method in class ome.services.sharing.ShareBean
admin - Variable in class ome.services.delete.DeleteBean
admin - Variable in class ome.services.sharing.ShareBean
AdminAction - Interface in ome.security: action for passing to SecuritySystem.runAsAdmin(AdminAction).
adminFlush() - Method in class ome.services.sharing.ShareBean
AdminImpl - Class in ome.logic: Provides methods for administering user accounts, passwords, as well as methods which require special privileges.
AdminImpl(SqlAction, SessionFactory, MailSender, SimpleMailMessage, ACLVoter, PasswordProvider, RoleProvider, LdapImpl, PasswordUtil, ChmodStrategy, ChecksumProviderFactory, LightAdminPrivileges) - Constructor for class ome.logic.AdminImpl
adminPrivileges - Variable in class ome.logic.AdminImpl
adminPrivileges - Variable in class ome.services.sessions.SessionManagerImpl
advices - Variable in class ome.services.util.Executor.Impl
afs - Variable in class ome.services.delete.Deletion.Builder
afs - Variable in class ome.services.delete.files.AbstractFileDeletions
afterExecute(Runnable, Throwable) - Method in class ome.services.scheduler.ThreadPool: Standard ThreadPoolExecutor extension point which checks for the BackgroundFutureTask marker and releases a slot in the ThreadPool.maxBackground Semaphore.
afterPropertiesSet() - Method in class ome.security.KeyAndTrustStoreConfiguration
afterTransactionBegin(Transaction) - Method in class ome.security.basic.OmeroInterceptor
afterTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor
agent - Variable in class ome.services.sessions.SessionManager.CreationRequest
aggByQuery(String, String, String, Parameters) - Method in class ome.logic.QueryImpl
aggMapByQuery(String, String, String, String, Parameters) - Method in class ome.logic.QueryImpl
ALL_PROJECTIONS - Static variable in class ome.services.search.FullText
AllEntitiesPseudoLogLoader<T extends ome.model.IObject> - Class in ome.services.eventlogs: EventLogLoader which iterates through each object model type (in no particular order) and returns each object from lowest to highest id.
AllEntitiesPseudoLogLoader() - Constructor for class ome.services.eventlogs.AllEntitiesPseudoLogLoader
allEnumerations(Class<T>) - Method in class ome.logic.TypesImpl
AllEventsLogLoader - Class in ome.services.eventlogs
AllEventsLogLoader() - Constructor for class ome.services.eventlogs.AllEventsLogLoader
allgroups - Variable in class ome.security.SecurityFilterHolder
AllGroupsSecurityFilter - Class in ome.security.basic: overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.
AllGroupsSecurityFilter(SqlAction) - Constructor for class ome.security.basic.AllGroupsSecurityFilter: Default constructor which calls all the necessary setters for this FactoryBean.
AllGroupsSecurityFilter(SqlAction, Roles) - Constructor for class ome.security.basic.AllGroupsSecurityFilter
allObjects(Collection<Set<GraphPolicy.Details>>, GraphPolicy.Details, Collection<Set<GraphPolicy.Details>>) - Static method in class ome.services.graphs.GraphPolicy: Utility method to return all the objects for review as a single set of objects.
allowAnnotate(IObject, Details) - Method in interface ome.security.ACLVoter: test whether the given object should be annotatable given the trusted details.
allowAnnotate(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
allowAnnotate(IObject, Details) - Method in class ome.security.CompositeACLVoter
allowAnnotate(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
allowChmod(IObject) - Method in interface ome.security.ACLVoter: test whether the given object can have its Permissions changed within the current security context.
allowChmod(IObject) - Method in class ome.security.basic.BasicACLVoter
allowChmod(IObject) - Method in class ome.security.CompositeACLVoter
allowChmod(IObject) - Method in class ome.security.sharing.SharingACLVoter
allowCreation(IObject) - Method in interface ome.security.ACLVoter: test whether the given object should be insertable into the DB.
allowCreation(IObject) - Method in class ome.security.basic.BasicACLVoter
allowCreation(IObject) - Method in class ome.security.CompositeACLVoter
allowCreation(IObject) - Method in class ome.security.sharing.SharingACLVoter
allowDelete(IObject, Details) - Method in interface ome.security.ACLVoter: test whether the given object should be deleteable given the trusted details.
allowDelete(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
allowDelete(IObject, Details) - Method in class ome.security.CompositeACLVoter
allowDelete(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in interface ome.security.ACLVoter: test whether the object of the given Class with the given Details should be loadable in the current security context.
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.basic.BasicACLVoter: delegates to SecurityFilter because that is where the logic is defined for the read filter Ignores the id for the moment.
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.CompositeACLVoter
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.sharing.SharingACLVoter
allowUpdate(IObject, Details) - Method in interface ome.security.ACLVoter: test whether the given object should be updateable given the trusted details.
allowUpdate(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
allowUpdate(IObject, Details) - Method in class ome.security.CompositeACLVoter
allowUpdate(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
allTypes() - Method in class ome.services.SearchBean
alreadySeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
analyzer - Variable in class ome.logic.QueryImpl
and() - Method in class ome.services.SearchBean
and(String) - Method in class ome.tools.hibernate.QueryBuilder: Appends "and" plus your string unless this is the first where-spec in which case it is simply appended.
annotatedBetween(AnnotationCriteria) - Method in class ome.services.search.SearchAction
annotatedBetween(QueryBuilder, String) - Method in class ome.services.search.SearchAction
annotatedBy(AnnotationCriteria) - Method in class ome.services.search.SearchAction
annotatedBy(QueryBuilder, String) - Method in class ome.services.search.SearchAction
annotatedBy - Variable in class ome.services.search.SearchValues
annotatedStart - Variable in class ome.services.search.SearchValues
annotatedStop - Variable in class ome.services.search.SearchValues
AnnotatedWith - Class in ome.services.search: Query for Search which uses an example Annotation instance as the basis for comparison.
AnnotatedWith(SearchValues, Annotation[], boolean, boolean) - Constructor for class ome.services.search.AnnotatedWith
append(String, Object...) - Method in class ome.security.basic.EventListenersFactoryBean: appends the objects to the existing list identified by key.
append(String) - Method in class ome.tools.hibernate.QueryBuilder: Simple delegate method to allow appending arbitrary strings.
appendDate(StringBuilder, Date) - Method in class ome.tools.hibernate.SqlArray
appendSpace() - Method in class ome.tools.hibernate.QueryBuilder
applyContext(Details, boolean) - Method in class ome.security.basic.CurrentDetails
applyIfShareAccessible(QueryBuilder) - Method in class ome.services.sharing.ShareBean: If the current user is not an admin, then this methods adds a subclause to the HQL: AND ( share.owner.id = :userId or user.id = :userId ) QueryBuilder.where() should already have been called.
applySettingsToDataset(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
applySettingsToImage(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
applySettingsToImages(long, List<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
applySettingsToPixels(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
applySettingsToProject(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
applySettingsToSet(long, Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
asClassOrNull(String) - Method in class ome.services.fulltext.FullTextIndexer: Deprecated.
asroot - Variable in class ome.services.sessions.SessionManagerImpl: A private session for use only by this instance for running methods via Executor.
assemble(Serializable, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
assertManaged(IObject) - Method in class ome.logic.AdminImpl
assertMayProcess(String, long, Details) - Method in interface ome.services.graphs.GraphTraversal.Processor: Assert that an object with the given details may be processed.
assertNoPolicyViolations() - Method in class ome.services.graphs.GraphTraversal: Check that there are no policy violations matched by p:error policy rules.
assertNoUnlinking() - Method in class ome.services.graphs.GraphTraversal: Assert that GraphTraversal.unlinkTargets(boolean) need not be called.
attach(long) - Method in class ome.services.JobBean
AttributeNewUserGroupBean - Class in ome.security.auth: Handles the "*_attribute" specifiers from omero-server.properties.
AttributeNewUserGroupBean(String, boolean, boolean) - Constructor for class ome.security.auth.AttributeNewUserGroupBean
AttributeSet - Class in ome.security.auth: Specialized handling of all the attributes, multi or single valued.
AttributeSet(DirContextAdapter) - Constructor for class ome.security.auth.AttributeSet
available() - Method in class ome.services.pixeldata.PersistentEventLogLoader
AWTScaleService - Class in ome.logic: Provides methods for scaling buffered images.
AWTScaleService() - Constructor for class ome.logic.AWTScaleService

B

background(Callable<T>) - Method in class ome.services.scheduler.ThreadPool: Schedule a task in one of the limited background slots.
BASE_SCRIPT_FILTER - Static variable in class ome.services.scripts.ScriptRepoHelper: IOFileFilter instance used during ScriptRepoHelper.iterate() to find the matching scripts in the given directory.
basename() - Method in class ome.services.scripts.RepoFile
BasePolicy - Class in ome.security.policy: Simple base class for Policy implementations which always returns true for BasePolicy.isRestricted(IObject) and always fails on BasePolicy.checkRestriction(IObject).
BasePolicy(Set<Class<IObject>>) - Constructor for class ome.security.policy.BasePolicy
basic - Variable in class ome.security.SecuritySystemHolder
BasicACLVoter - Class in ome.security.basic
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter) - Constructor for class ome.security.basic.BasicACLVoter
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, SessionProvider, ReadOnlyStatus) - Constructor for class ome.security.basic.BasicACLVoter
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService) - Constructor for class ome.security.basic.BasicACLVoter: Deprecated.
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService, Roles) - Constructor for class ome.security.basic.BasicACLVoter
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService, Roles, SessionProvider, ReadOnlyStatus) - Constructor for class ome.security.basic.BasicACLVoter
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService, Roles, LightAdminPrivileges, SessionProvider, ReadOnlyStatus, Set<String>, Set<String>, String) - Constructor for class ome.security.basic.BasicACLVoter
BasicEventContext - Class in ome.security.basic: EventContext implementation for use within the security system.
BasicEventContext(Principal, SessionStats) - Constructor for class ome.security.basic.BasicEventContext
BasicEventContext(Principal, SessionStats, EventContext) - Constructor for class ome.security.basic.BasicEventContext: Copy-constructor to not have to allow the mutator SimpleEventContext.copy(EventContext) or copyContext(EventContext) out of the EventContext hierarchy.
BasicMethodSecurity - Class in ome.security.basic: Implementation of MethodSecurity which checks method security based on the RolesAllowed annotations of our implementation methods.
BasicMethodSecurity() - Constructor for class ome.security.basic.BasicMethodSecurity
BasicMethodSecurity(boolean) - Constructor for class ome.security.basic.BasicMethodSecurity
BasicSecuritySystem - Class in ome.security.basic: simplest implementation of SecuritySystem.
BasicSecuritySystem(OmeroInterceptor, SystemTypes, CurrentDetails, SessionManager, SessionProvider, EventProvider, Roles, ServiceFactory, TokenHolder, List<SecurityFilter>, PolicyService, ACLVoter) - Constructor for class ome.security.basic.BasicSecuritySystem: Main public constructor for this SecuritySystem implementation.
BasicSecurityWiring - Class in ome.security.basic: Responsible for logging users in and out via the Principal before and after the actual invocation of OMERO methods.
BasicSecurityWiring() - Constructor for class ome.security.basic.BasicSecurityWiring
BasicSecurityWiring.CloseOnNoSessionContext - Class in ome.security.basic
batch - Variable in class ome.services.fulltext.FullTextIndexer: Deprecated.
batchSize - Variable in class ome.services.eventlogs.EventLogLoader
batchSize - Variable in class ome.services.search.SearchValues
batchTimer - Variable in class ome.services.fulltext.FullTextIndexer: Deprecated.
BeanHelper - Class in ome.services.util: Helper for all bean implementations.
BeanHelper(Class) - Constructor for class ome.services.util.BeanHelper
BeanInstantiationGuard - Class in ome.services.util: Prevents creation of Spring beans based on read-only status.
BeanInstantiationGuard(ReadOnlyStatus, String) - Constructor for class ome.services.util.BeanInstantiationGuard: Construct a bean instantiation guard.
BeanInstantiationSubstituter - Class in ome.services.util: Adjusts instantiation class of Spring beans based on read-only status.
BeanInstantiationSubstituter(ReadOnlyStatus, String, String) - Constructor for class ome.services.util.BeanInstantiationSubstituter: Construct a bean instantiation substituter.
beforeTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor
BinaryAccessPolicy - Class in ome.security.policy: Policy which should be checked anytime access to original binary files in OMERO is being attempted.
BinaryAccessPolicy(Set<Class<IObject>>, ACLVoter) - Constructor for class ome.security.policy.BinaryAccessPolicy
BinaryAccessPolicy(Set<Class<IObject>>, ACLVoter, String[]) - Constructor for class ome.security.policy.BinaryAccessPolicy
BlobShareStore - Class in ome.services.sharing: Implements ShareStore and provides functionality to work with binary Ice data from the share.
BlobShareStore() - Constructor for class ome.services.sharing.BlobShareStore
BOOLEAN(Connection, List<Boolean>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
BOOLEAN() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
BOOLEAN(List<Boolean>) - Constructor for class ome.tools.hibernate.SqlArray.BOOLEAN
bridge - Variable in class ome.services.fulltext.FullTextThread: Deprecated.
BridgeHelper - Class in ome.services.fulltext: Deprecated.
BridgeHelper() - Constructor for class ome.services.fulltext.BridgeHelper: Deprecated.
Builder(AbstractFileSystemService, ExtendedMetadata) - Constructor for class ome.services.delete.Deletion.Builder
buildOrObtainSession() - Method in class ome.tools.hibernate.CurrentSessionContext
buildQuery(Session) - Method in class ome.services.query.CollectionCountQueryDefinition
buildQuery(Session) - Method in class ome.services.query.IObjectClassQuery
buildQuery(Session) - Method in class ome.services.query.PojosFindAnnotationsQueryDefinition
buildQuery(Session) - Method in class ome.services.query.PojosFindHierarchiesQueryDefinition
buildQuery(Session) - Method in class ome.services.query.PojosGetImagesByOptionsQueryDefinition
buildQuery(Session) - Method in class ome.services.query.PojosGetImagesQueryDefinition
buildQuery(Session) - Method in class ome.services.query.PojosGetUserImagesQueryDefinition
buildQuery(Session) - Method in class ome.services.query.PojosLoadHierarchyQueryDefinition
buildQuery(Session) - Method in class ome.services.query.Query: main point of entry for subclasses.
buildQuery(Session) - Method in class ome.services.query.StringQuery
buildQuery(QueryBuilder) - Method in class ome.services.scripts.ScriptRepoHelper: Adds a single clause of the form "AND (A OR B ...)" where each ScriptFileType A, B, etc.
byAnnotatedWith(Annotation...) - Method in class ome.services.SearchBean
byFullText(String) - Method in class ome.services.SearchBean
byGroupForTags(String) - Method in class ome.services.SearchBean
byHqlQuery(String, Parameters) - Method in class ome.services.SearchBean
byLuceneQueryBuilder(String, String, String, String, String) - Method in class ome.services.SearchBean
bySimilarTerms(String...) - Method in class ome.services.SearchBean
bySomeMustNone(String[], String[], String[]) - Method in class ome.services.SearchBean
byTagForGroups(String) - Method in class ome.services.SearchBean
byUUID(String[]) - Method in class ome.services.SearchBean

C

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
calculateBackOff(int) - Method in class ome.services.db.SelfCorrectingDataSource
calculateMessageDigest() - Method in class ome.services.RawPixelsBean
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
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
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
cancelJob() - Method in class ome.services.JobBean
canUpdate(IObject) - Method in class ome.logic.AdminImpl
caseSensitive - Variable in class ome.services.search.SearchValues
cd - Variable in class ome.security.basic.BasicSecuritySystem
cd - Variable in class ome.security.basic.EventLogListener
cd - Variable in class ome.security.SecurityFilterHolder
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 class ome.logic.AdminImpl
changeGroup(IObject, String) - Method in class ome.logic.AdminImpl
changeOwner(IObject, String) - Method in class ome.logic.AdminImpl
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
changePasswordWithOldPassword(String, String) - Method in class ome.logic.AdminImpl
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.
ChangeSecurityContextEvent - Class in ome.services.sessions.events: InternalMessage 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 class ome.logic.AdminImpl
changeUserPasswordById(Long, String) - Method in class ome.security.auth.PasswordUtil: Calls PasswordUtil.changeUserPasswordById(Long, String, METHOD) 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: Calls either PasswordUtil.preparePassword(String) or PasswordUtil.prepareSaltedPassword(Long, String) and passes the resulting value to SqlAction.setUserPassword(Long, String).
CHANNELID_QUERY - Static variable in class ome.services.delete.DeleteBean
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: Performs one of the checks returned by ChmodStrategy.getChecks(IObject obj, String permissions).
check(String) - Method in class ome.services.query.Query: check that there is a definition for this Query with the provided argument as its name.
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
checkDelayedCallContext(BasicEventContext) - Method in class ome.security.basic.CurrentDetails
checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper: Contacts the remote server to verify that the object implements this type.
checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ObjPrxHelper: Contacts the remote server to verify that the object implements this type.
checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ObjPrxHelper: Contacts the remote server to verify that a facet of the object implements this type.
checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ObjPrxHelper: Contacts the remote server to verify that a facet of the object implements this type.
checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper: Contacts the remote server to verify that the object implements this type.
checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ShareDataPrxHelper: Contacts the remote server to verify that the object implements this type.
checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareDataPrxHelper: Contacts the remote server to verify that a facet of the object implements this type.
checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ShareDataPrxHelper: Contacts the remote server to verify that a facet of the object implements this type.
checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper: Contacts the remote server to verify that the object implements this type.
checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ShareItemPrxHelper: Contacts the remote server to verify that the object implements this type.
checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareItemPrxHelper: Contacts the remote server to verify that a facet of the object implements this type.
checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ShareItemPrxHelper: Contacts the remote server to verify that a facet of the object implements this type.
checkForScriptUpdates() - Method in class ome.services.scripts.ScriptRepoHelper: Check for updates to scripts, modifying database accordingly.
checkImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean
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: Like OmeroInterceptor.checkManagedDetails(IObject, Details, Details) but allows passing in a specific Details instance.
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
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.
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: If this was constructed with the ignoreUnknown argument set to true, returns null, since the base class knows no users.
checkPassword(String, String, boolean) - Method in class ome.security.auth.FilePasswordProvider
checkPassword(String, String, boolean) - Method in class ome.security.auth.JdbcPasswordProvider: Retrieves password from the database and calls ConfigurablePasswordProvider.comparePasswords(String, String).
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
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: calls BasicSecuritySystem.isReady() and if not throws an ApiUsageException.
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 Policy.isRestricted(IObject) but throws an appropriate SecurityViolation subclass if the restriction is active.
checkRestriction(String, IObject) - Method in interface ome.security.policy.PolicyService: Give each configured Policy instance the chance to throw a SecurityViolation from its Policy.checkRestriction(IObject) method.
checkRestriction(String, IObject) - Method in interface ome.security.SecuritySystem: Checks whether or not a 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
checkType(String) - Method in interface ome.api.local.LocalQuery: Checks if a type has been mapped in Hibernate.
checkType(String) - Method in class ome.logic.PojosImpl
checkType(String) - Method in class ome.logic.QueryImpl
checkWriteOperationAllowed(Session) - Method in class ome.tools.spring.ManualFlushHibernateTemplate
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.
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
classes - Variable in class ome.services.fulltext.FullTextBridge: Deprecated.
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
cleanThread() - Method in class ome.tools.hibernate.SessionHandler
cleanup() - Method in class ome.services.util.ServiceHandler
clear() - Method in interface ome.api.local.LocalQuery
clear() - Method in class ome.logic.QueryImpl
clearDisabled() - Method in class ome.security.basic.CurrentDetails
clearLogs() - Method in class ome.security.basic.BasicSecuritySystem
clearLogs() - Method in class ome.security.basic.CurrentDetails
clearQueries() - Method in class ome.services.SearchBean
clearToken(GraphHolder) - Method in class ome.security.basic.TokenHolder
clone() - Method in class ome.services.sessions.state.CacheListener
clone() - Method in class ome.services.sharing.data.Obj
clone() - Method in class ome.services.sharing.data.ShareData
clone() - Method in class ome.services.sharing.data.ShareItem
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.RawFileBeanReadOnly
close() - Method in class ome.services.RawPixelsBean
close() - Method in class ome.services.RawPixelsBeanReadOnly
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
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
CloseOnNoSessionContext() - Constructor for class ome.security.basic.BasicSecurityWiring.CloseOnNoSessionContext
closeParsedFiles() - Method in class ome.services.fulltext.ParserSession: Deprecated.
closeSession(Session) - Method in class ome.services.sessions.SessionBean
closeSessionsForManager(String) - Method in class ome.security.basic.NodeProviderInDb: Assumes that the given manager is no longer available and so will not attempt to call cache.removeSession() since that requires the session to be in memory.
closeSessionsForManager(String) - Method in class ome.security.basic.NodeProviderInMemory: Assumes that the given manager is no longer available and will clean up all in-memory sessions.
closeSessionsForManager(String) - Method in class ome.security.basic.NodeProviderWrapper
closeSessionsForManager(String) - Method in interface ome.security.NodeProvider: Closes all sessions for a given manager node.
closeShare(long) - Method in class ome.services.sharing.ShareBean
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: extension of QueryParameterDef which restricts the type to a Collection, and specifies the element types of that Collection.
CollectionQueryParameterDef(String, boolean, Class) - Constructor for class ome.services.query.CollectionQueryParameterDef
COMBINED - Static variable in class ome.services.fulltext.BridgeHelper: Deprecated.

Name of the Field which contains the union of all fields.
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
completeFast - Variable in class ome.services.fulltext.FullTextIndexer: Deprecated.
completeSlow - Variable in class ome.services.fulltext.FullTextIndexer: Deprecated.
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
configGroup(EventContext, List<Long>) - Method in class ome.security.basic.AllGroupsSecurityFilter
ConfigImpl - Class in ome.logic: implementation of the IConfig service interface.
ConfigImpl() - Constructor for class ome.logic.ConfigImpl
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: Call ConfigurablePasswordProvider.ConfigurablePasswordProvider(PasswordUtil, boolean) with "ignoreUnknown" equal to false.
ConfigurablePasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider: Call ConfigurablePasswordProvider.ConfigurablePasswordProvider(PasswordUtil, boolean, boolean) with "salt" equal to false.
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.
containedExperimenters(long) - Method in class ome.logic.AdminImpl
containedGroups(long) - Method in class ome.logic.AdminImpl
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
containsKey(Object) - Method in class ome.services.query.Definitions
context - Variable in class ome.logic.AdminImpl
context - Variable in class ome.services.fulltext.FileParser
context - Variable in class ome.services.fulltext.FullTextIndexer: Deprecated.
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
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.Push - Class in ome.services.messages: Published when an internal service would like to modify the current EventContext.
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(Map) - Static method in class ome.tools.hibernate.HibernateUtils
copy(Collection) - Static method in class ome.tools.hibernate.HibernateUtils
copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
copyClassListToArray(List<Class>) - Static method in class ome.services.search.SearchValues
copyDetails(Details) - Static method in class ome.services.search.SearchValues
copyGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
copyList(List<T>) - Static method in class ome.services.search.SearchValues
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
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() - Method in class ome.services.messages.DeleteLogMessage
count() - Method in interface ome.services.sessions.SessionContext: Returns the SessionContext.Count instance held by this context.
Count(String) - Constructor for class ome.services.sessions.SessionContext.Count
count() - Method in class ome.services.sessions.SessionContextImpl
count - Variable in class ome.services.sessions.stats.LongCounter
countAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl
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: Takes the lock checks returned by ExtendedMetadata.getLockChecks(Class) and performs the actual check returning a map from class to total number of locks.
countLocks(Session, Long, String[][], String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
countOnDisk() - Method in class ome.services.scripts.ScriptRepoHelper: Returns the number of files which match ScriptRepoHelper.scriptFilter in ScriptRepoHelper.dir.
countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl
cpf - Variable in class ome.logic.AdminImpl
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.
createBufferedImage() - Method in class ome.services.SVGRasterizer: Returns the image that represents the SVG document.
createCache(CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
createCache(String, boolean, int) - Method in class ome.services.sessions.state.SessionCache
createDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl
createDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl
createDetails() - Method in class ome.security.basic.CurrentDetails: Creates a Details object for the current security context.
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 class ome.logic.TypesImpl
createException(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
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
createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
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 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
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
createInstance() - Method in class ome.security.basic.EventListenersFactoryBean: First, adds all default listeners.
createInstance() - Method in class ome.services.delete.Deletion.Builder
createJPEG(OutputStream) - Method in class ome.services.SVGRasterizer: Returns the image that represents the SVG document as a JPEG.
createNewRenderingDef(Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
createRestrictedSystemUser(Experimenter, List<AdminPrivilege>) - Method in class ome.logic.AdminImpl
createRestrictedSystemUserWithPassword(Experimenter, List<AdminPrivilege>, String) - Method in class ome.logic.AdminImpl
createRoot() - Method in class ome.formats.OMEROMetadataStore
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.
createSession(Principal, String) - Method in class ome.services.sessions.SessionBean
createSessionContext(List<?>, SessionContext) - Method in class ome.services.sessions.SessionManagerImpl: Takes a snapshot as from SessionManagerImpl.executeSessionContextLookup(ServiceFactory, Principal, Session) 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 class ome.services.sessions.SessionBean
createSessionWithTimeouts(Principal, long, long) - Method in class ome.services.sessions.SessionBean
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
createStats() - Method in class ome.services.sessions.stats.CounterFactory
createSystemUser(Experimenter) - Method in class ome.logic.AdminImpl
createThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
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 class ome.services.ThumbnailBean
createThumbnailsByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
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.
createUserFromLdap(String, String) - Method in class ome.logic.LdapImpl: Deprecated.
createUserSession(long, long, String) - Method in class ome.services.sessions.SessionBean
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
CreationRequest() - Constructor for class ome.services.sessions.SessionManager.CreationRequest
credentials - Variable in class ome.services.sessions.SessionManager.CreationRequest
CRITICAL_USAGE - Static variable in class ome.logic.RepositoryInfoImpl: Percentage (100.0 - 0.0) of disk use which will cause an exception during RepositoryInfoImpl.sanityCheckRepository()
ctx - Variable in class ome.security.auth.ConfigurablePasswordProvider
ctx - Variable in class ome.security.basic.BasicSecuritySystem
ctx - Variable in class ome.services.delete.Deletion.Builder
ctx - Variable in class ome.services.sharing.BlobShareStore
current - Variable in class ome.security.SecurityFilterHolder
current - Variable in class ome.security.SecuritySystemHolder
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
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, SystemTypes, LightAdminPrivileges, Set<String>, Set<String>) - Constructor for class ome.security.basic.CurrentDetails
currentMetadata() - Method in class ome.services.SearchBean
currentMetadataList() - Method in class ome.services.SearchBean
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

D

DatabaseIdentity - Class in ome.services.db: Represents the unique identity of this database, consisting of the omero.db.authority and omero.db.uuid properties.
DatabaseIdentity(String, SqlAction) - Constructor for class ome.services.db.DatabaseIdentity
DatabaseIdentity(String, String) - Constructor for class ome.services.db.DatabaseIdentity
dataPerUser - Variable in class ome.services.pixeldata.PersistentEventLogLoader
DATE(Connection, List<Date>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
DATE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
DATE(List<Date>) - Constructor for class ome.tools.hibernate.SqlArray.DATE
DBEnumCheck - Class in ome.services.util: Hook run by the context to guarantee that various enumerations are up to date.
DBEnumCheck(Executor, PreferenceContext, EnsureEnum, ReadOnlyStatus) - Constructor for class ome.services.util.DBEnumCheck
DBMappedEnumCheck - Class in ome.services.util: When a new version of the OMERO server starts up check that the database includes an enumeration instance for every value mapped for code generation.
DBMappedEnumCheck(Executor, PreferenceContext, EnsureEnum, ReadOnlyStatus) - Constructor for class ome.services.util.DBMappedEnumCheck
DBPatchCheck - Class in ome.services.util: Hook run by the context.
DBPatchCheck(SqlAction, PreferenceContext) - Constructor for class ome.services.util.DBPatchCheck
DBUnicodeUnitsCheck - Class in ome.services.util: Checks that the database contains correctly encoded enumerations for units of measure.
DBUnicodeUnitsCheck(Executor, PreferenceContext, ReadOnlyStatus) - Constructor for class ome.services.util.DBUnicodeUnitsCheck
DBUserCheck - Class in ome.services.util: Hook run by the context.
DBUserCheck(SqlAction, PreferenceContext, ReadOnlyStatus) - Constructor for class ome.services.util.DBUserCheck
deactivate() - Method in class ome.services.sharing.ShareBean
debugAll - Variable in class ome.security.basic.EventListenersFactoryBean
decrement() - Method in class ome.services.sessions.SessionContext.Count: Decrement the current reference count and return the new value atomically.
deepCopy(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
DEFAULT_BATCH_SIZE - Static variable in class ome.services.eventlogs.EventLogLoader: Currently 100.
DEFAULT_COMPRESSION_QUALITY - Static variable in class ome.services.ThumbnailBean: The default compression quality in fractional percent.
DEFAULT_ENCODING - Static variable in class ome.security.auth.PasswordUtil: The default encoding for converting plain text passwords to byte arrays (UTF-8)
DEFAULT_MAX - Static variable in class ome.services.eventlogs.EventLogQueue: Default maximum for the number of rows that will be loaded in a single call to SqlAction.getEventLogPartitions(java.util.Collection, java.util.Collection, long, long) .
DEFAULT_MIME_TYPE - Static variable in class ome.services.ThumbnailBean: The default MIME type.
DEFAULT_MIME_TYPE - Static variable in class ome.services.ThumbnailCtx: Default thumbnail MIME type.
DEFAULT_PORT - Static variable in class ome.services.mail.SubethaSMTP
DEFAULT_REPORTING_LOOPS - Static variable in class ome.services.fulltext.FullTextIndexer: Deprecated.

Default number of loops to wait if no external value is set.
DEFAULT_X_WIDTH - Static variable in class ome.services.ThumbnailBean: The default X-width for a thumbnail.
DEFAULT_Y_WIDTH - Static variable in class ome.services.ThumbnailBean: The default Y-width for a thumbnail.
DefaultPolicyService - Class in ome.security.policy: PolicyService which is configured with all Policy instances which are discovered in the Spring context and only focuses on a small subset of IObject types as specified by DefaultPolicyService.filterObject(IObject).
DefaultPolicyService() - Constructor for class ome.security.policy.DefaultPolicyService
defaultTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl
defaultTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl
define(Session, String, String, long, SessionManager.CreationRequest) - Method in class ome.services.sessions.SessionManagerImpl
define(Session, String, String, long, long, long, String, String, String) - Method in class ome.services.sessions.SessionManagerImpl
Definitions - Class in ome.services.query: container for QueryParameterDef instances.
Definitions(QueryParameterDef...) - Constructor for class ome.services.query.Definitions
defs - Variable in class ome.services.query.Query: container of QueryParameterDef instances.
DelegatingStats - Class in ome.services.sessions.stats: Delegates to a SessionStats which is acquired from DelegatingStats.stats().
DelegatingStats() - Constructor for class ome.services.sessions.stats.DelegatingStats
DelegatingStats(SessionStats[]) - Constructor for class ome.services.sessions.stats.DelegatingStats
delete(long) - Method in class ome.services.scripts.ScriptRepoHelper
delete(String) - Method in class ome.tools.hibernate.QueryBuilder
DeleteBean - Class in ome.services.delete: Strict implementation of the IDelete service interface which will use the SecuritySystem via SecuritySystem.runAsAdmin(AdminAction) to forcibly delete instances.
DeleteBean(LocalAdmin, SessionFactory) - Constructor for class ome.services.delete.DeleteBean
deleteChannels(long) - Method in class ome.services.delete.DeleteBean
deleteComment(Annotation) - Method in class ome.services.sharing.ShareBean
deleteCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader
deletedIds - Variable in class ome.services.delete.files.AbstractFileDeletions
deleteEnumeration(T) - Method in class ome.logic.TypesImpl
deleteExperimenter(Experimenter) - Method in class ome.logic.AdminImpl
deleteFiles(SetMultimap<String, Long>) - Method in class ome.services.delete.Deletion: For each Report use the map of tables to deleted ids to remove the files under Files, Pixels and Thumbnails if the ids no longer exist in the db.
deleteGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
deleteImage(long, boolean) - Method in class ome.services.delete.DeleteBean
deleteImages(Set<Long>, boolean) - Method in class ome.services.delete.DeleteBean
deleteImagesByDataset(long, boolean) - Method in class ome.services.delete.DeleteBean
deleteInstances(String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor: Delete the given instances.
deleteLocal() - Method in class ome.services.delete.files.AbstractFileDeletions: Helper to delete and log.
DeleteLogMessage - Class in ome.services.messages
DeleteLogMessage(Object, long) - Constructor for class ome.services.messages.DeleteLogMessage
DeleteLogsMessage - Class in ome.services.messages
DeleteLogsMessage(Object, List<Long>) - Constructor for class ome.services.messages.DeleteLogsMessage
deleteObject(IObject) - Method in class ome.logic.UpdateImpl
deletePlate(long) - Method in class ome.services.delete.DeleteBean
deleteSettings(long) - Method in class ome.services.delete.DeleteBean
Deletion - Class in ome.services.delete: Maintain state about a delete itself.
Deletion(AbstractFileSystemService, OmeroContext) - Constructor for class ome.services.delete.Deletion
Deletion.Builder - Class in ome.services.delete: Inner class which can be used to generate a Deletion.
deliver(String, String, InputStream) - Method in class ome.services.mail.MapAnnotationSubethaListener: Stores each email as a map annotation with MapAnnotationSubethaListener.NAMESPACE set.
description() - Method in class ome.services.procs.ProcessManager.Work
description() - Method in class ome.services.search.SearchAction: Returns the SearchAction subclass as the description.
description - Variable in class ome.services.util.Executor.Descriptive
description() - Method in class ome.services.util.Executor.Descriptive
description() - Method in interface ome.services.util.Executor.LoggedWork: Returns a description of what this work will be doing for logging purposes.
description() - Method in interface ome.services.util.Executor.SqlWork: Return a description of what this work will be doing for logging purposes.
Descriptive(Object, String, Object...) - Constructor for class ome.services.util.Executor.Descriptive
Descriptive(String, String, Object...) - Constructor for class ome.services.util.Executor.Descriptive
destroy() - Method in class ome.services.util.SleepTimer: This method is called by Spring during server shut-down.
destroy() - Method in class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean
DestroySessionMessage - Class in ome.services.messages: Published before a session destruction.
DestroySessionMessage(Object, String) - Constructor for class ome.services.messages.DestroySessionMessage
detach(String) - Method in interface ome.services.sessions.SessionManager: Allows decrementing the reference count for a session without calling the actual SessionManager.close(String) logic.
detach(String) - Method in class ome.services.sessions.SessionManagerImpl
detailsIndex(String[]) - Static method in class ome.tools.hibernate.HibernateUtils
dirname() - Method in class ome.services.scripts.RepoFile
dirtyMetadata(long) - Method in class ome.services.ThumbnailCtx: Whether or not the thumbnail metadata for a given Pixels ID is dirty (the RenderingDef has been updated since the Thumbnail was).
disable(Session) - Method in class ome.security.basic.AbstractSecurityFilter
disable(String...) - Method in class ome.security.basic.BasicSecuritySystem
disable(Session) - Method in interface ome.security.SecurityFilter: Reverts the call to SecurityFilter.enable(Session, EventContext).
disable(Session) - Method in class ome.security.SecurityFilterHolder
disable(String...) - Method in interface ome.security.SecuritySystem: disables components of the backend for the current Thread.
disable(String...) - Method in class ome.security.SecuritySystemHolder
disable(String...) - Method in class ome.security.sharing.SharingSecuritySystem
DisableAction() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.DisableAction
disableBaseFilters(Session) - Method in class ome.security.basic.AbstractSecurityFilter
disabled(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
disableFilters(Session) - Method in class ome.services.query.Query: turns the filters off that are listed in Query.newlyEnabledFilters
disableQueryCache() - Method in class ome.services.query.Query: Disable the Hibernate level 2 cache for this query.
disableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem: disable this filer.
disassemble(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
discover() - Method in class ome.logic.LdapImpl
discoverGroups() - Method in class ome.logic.LdapImpl
dispose() - Method in class ome.services.sessions.state.CacheListener
doAction(SecureAction, T...) - Method in class ome.security.basic.BasicSecuritySystem: It would be better to catch the SecureAction.updateObject(IObject...) method in a try/finally block, but since flush can be so poorly controlled that's not possible.
doAction(SecureAction, T...) - Method in interface ome.security.SecuritySystem
doAction(SecureAction, T...) - Method in class ome.security.SecuritySystemHolder
doAction(SecureAction, T...) - Method in class ome.security.sharing.SharingSecuritySystem
doCheck() - Method in class ome.services.util.DBEnumCheck
doCheck() - Method in class ome.services.util.DBMappedEnumCheck
doCheck() - Method in class ome.services.util.DBUnicodeUnitsCheck
doCheckPassword(String, String, Properties, boolean) - Method in class ome.security.auth.FilePasswordProvider
doClose() - Method in class ome.services.sharing.BlobShareStore
doClose() - Method in class ome.services.sharing.ShareStore
doContains(long, Class<T>, long) - Method in class ome.services.sharing.BlobShareStore
doContains(ShareData, Class<T>, long) - Method in class ome.services.sharing.BlobShareStore
doContains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
doFilter(String, Object) - Method in class ome.tools.hibernate.ProxyCleanupFilter
doFilter(String, Filterable) - Method in class ome.tools.hibernate.ProxySafeFilter
doFilter(String, Collection) - Method in class ome.tools.hibernate.ProxySafeFilter
doImport() - Method in class ome.formats.importer.util.TinyImportFixture: Deprecated.
doIndexing(FullTextSession) - Method in class ome.services.fulltext.FullTextIndexer: Deprecated.
doInHibernate(Session) - Method in class ome.services.query.Query: template method defined by HibernateTemplate.
doInit() - Method in class ome.services.sharing.BlobShareStore
doInit() - Method in class ome.services.sharing.ShareStore
doLogin(boolean, boolean) - Method in class ome.security.basic.EventHandler
doLookup(String, String, Long) - Method in class ome.services.query.HierarchyNavigator: Look up which objects of a given type relate to the given query object.
doLookup(T, E) - Method in class ome.services.query.HierarchyNavigatorWrap: Look up which objects of a given type relate to the given query object.
doMore(int) - Method in class ome.services.fulltext.FullTextIndexer: Deprecated.

Default implementation suggests doing more if fewer than FullTextIndexer.reps runs have been made and if there are still more than EventLogLoader.batchSize x 100 backlog entries.
doParse(File) - Method in class ome.services.fulltext.FileParser: Template method to parse a File into manageable chunks.
doParse(File) - Method in class ome.services.fulltext.PdfParser
doRun() - Method in class ome.services.fulltext.FullTextThread: Deprecated.

Passes the FullTextIndexer instance to Executor.Work.doWork(Session, ServiceFactory) between calls to DetailsFieldBridge.lock() and DetailsFieldBridge.unlock() in order to guarantee that no other FieldBridge can edit the property.
doRun() - Method in class ome.services.pixeldata.PixelDataThread: Loads event logs from the PixelDataHandler processing them all then in a background thread via a ExecutorCompletionService.
doRun() - Method in class ome.services.procs.ProcessManager
doRun() - Method in class ome.services.util.ExecutionThread
doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.BlobShareStore
doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.ShareStore
DOUBLE(Connection, List<Double>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
DOUBLE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
DOUBLE(List<Double>) - Constructor for class ome.tools.hibernate.SqlArray.DOUBLE
doUpdate() - Method in class ome.services.sessions.state.SessionCache: Will only ever be accessed by a single thread.
doWork(Session, ServiceFactory) - Method in class ome.services.fulltext.FullTextIndexer: Deprecated.

Runs FullTextIndexer.doIndexing(FullTextSession) within a Lucene transaction.
doWork(Session, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler: Loads PixelDataHandler.reps EventLog instances and returns them.
doWork(Session, ServiceFactory) - Method in class ome.services.procs.ProcessManager.Work
doWork(Session, ServiceFactory) - Method in class ome.services.search.AnnotatedWith
doWork(Session, ServiceFactory) - Method in class ome.services.search.Complement
doWork(Session, ServiceFactory) - Method in class ome.services.search.FullText
doWork(Session, ServiceFactory) - Method in class ome.services.search.HqlQuery
doWork(Session, ServiceFactory) - Method in class ome.services.search.Intersection
doWork(Session, ServiceFactory) - Method in class ome.services.search.SimilarTerms
doWork(Session, ServiceFactory) - Method in class ome.services.search.TagsAndGroups
doWork(Session, ServiceFactory) - Method in class ome.services.search.Union
doWork(SqlAction) - Method in interface ome.services.util.Executor.SqlWork
doWork(Session, ServiceFactory) - Method in interface ome.services.util.Executor.Work: Work method.
dryRun - Variable in class ome.services.fulltext.FullTextIndexer: Deprecated.
dsAllQuery - Static variable in class ome.services.delete.QueryConstraints
dsNotOwnQuery - Static variable in class ome.services.delete.QueryConstraints

E

elementType - Variable in class ome.services.query.CollectionQueryParameterDef
em - Variable in class ome.services.delete.Deletion.Builder
EMPTY - Static variable in class ome.services.fulltext.FileParser: Iterable which returns an empty Iterator.
emptyCleanups() - Method in class ome.security.basic.CurrentDetails: Returns the current cleanups and resets the Set.
enable(Session, EventContext) - Method in class ome.security.basic.AllGroupsSecurityFilter: Since we assume that the group is "-1" for this method, we have to pass in lists of all groups as we did before group permissions (~4.2).
enable(String...) - Method in class ome.security.basic.BasicSecuritySystem
enable(Session, EventContext) - Method in class ome.security.basic.LightAdminPrivilegesSecurityFilter
enable(Session, EventContext) - Method in class ome.security.basic.OneGroupSecurityFilter
enable(Session, EventContext) - Method in class ome.security.basic.SharingSecurityFilter
enable(Session, EventContext) - Method in interface ome.security.SecurityFilter: Enables this filter with the settings from this filter.
enable(Session, EventContext) - Method in class ome.security.SecurityFilterHolder
enable(String...) - Method in interface ome.security.SecuritySystem: enables components of the backend for the current Thread.
enable(String...) - Method in class ome.security.SecuritySystemHolder
enable(String...) - Method in class ome.security.sharing.SharingSecuritySystem
enableBaseFilters(Session, int, Long) - Method in class ome.security.basic.AbstractSecurityFilter
enabled - Variable in class ome.services.sharing.data.ShareData
enableFilters(Session) - Method in class ome.services.query.PojosFindHierarchiesQueryDefinition
enableFilters(Session) - Method in class ome.services.query.PojosGetImagesByOptionsQueryDefinition
enableFilters(Session) - Method in class ome.services.query.PojosGetImagesQueryDefinition
enableFilters(Session) - Method in class ome.services.query.PojosGetUserImagesQueryDefinition
enableFilters(Session) - Method in class ome.services.query.PojosLoadHierarchyQueryDefinition
enableFilters(Session) - Method in class ome.services.query.Query: does nothing by default, but can be overridden by subclasses to enable particular filters.
enableQueryCache() - Method in class ome.services.query.Query: Enable the Hibernate level 2 cache for this query.
enableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem: enables the read filter such that graph queries will have non-visible entities silently removed from the return value.
encodePassword(String) - Method in class ome.security.auth.ConfigurablePasswordProvider: Encodes the password as it would be encoded for a check by ConfigurablePasswordProvider.comparePasswords(String, String)
encodePassword(Long, String, boolean, PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
encodePassword(String) - Method in interface ome.security.auth.PasswordUtility
encodeSaltedPassword(Long, String) - Method in class ome.security.auth.ConfigurablePasswordProvider: Encodes the password as it would be encoded for a check by ConfigurablePasswordProvider.comparePasswords(String, String) salting the password with the given userId if it's provided.
ensure(Class<E>, Collection<String>) - Method in class ome.services.util.EnsureEnum: Ensure that the given enumerations exist.
EnsureEnum - Class in ome.services.util: Utility bean for ensuring that enumeration values do exist in the database.
EnsureEnum(Executor, String, Roles, ReadOnlyStatus) - Constructor for class ome.services.util.EnsureEnum: Construct a new enumeration ensurer.
entityIds - Variable in class ome.services.messages.EventLogMessage
entityIsDetached(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
entityIsTransient(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
entityToStringLong(E) - Method in class ome.services.query.HierarchyNavigatorWrap: Convert a model object to the type string and database ID expected by HierarchyNavigator.
entityType - Variable in class ome.services.messages.EventLogMessage
ENUM(E[]) - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
environment(String, String) - Method in class ome.services.sessions.SessionManagerImpl
EPSILON - Static variable in class ome.logic.RenderingSettingsImpl: The value used to compare double and float.
equals(Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
error(SqlAction.DeleteLog, Throwable) - Method in class ome.services.messages.DeleteLogMessage
errorIfInvalid(QueryParameter) - Method in class ome.services.query.CollectionQueryParameterDef
errorIfInvalid(QueryParameter) - Method in class ome.services.query.QueryParameterDef: validation method called by Query.checkParameters().
errorIfInvalidState() - Method in class ome.services.JobBean
errorIfInvalidState() - Method in class ome.services.RenderingBean
errorIfInvalidState() - Method in class ome.services.ThumbnailBean
errorIfNullPixels() - Method in class ome.services.RenderingBean: Throws an ApiUsageException if the pixels are not set.
errorIfNullPixels() - Method in class ome.services.ThumbnailBean
errorIfNullPixelsAndRenderingDef() - Method in class ome.services.ThumbnailBean
errorIfNullRenderer() - Method in class ome.services.RenderingBean: Reloads the rendering engine if null and has been made passive or throws an ApiUsageException if the rendering engine is not set.
errorIfNullRenderingDef() - Method in class ome.services.RenderingBean: Throws an ApiUsageException if the rendering settings are not set.
errorIfNullRenderingDef() - Method in class ome.services.ThumbnailBean
evaluateLinkages(IObject) - Method in class ome.security.basic.OmeroInterceptor: Checks the details of the objects which the given object links to in order to guarantee that linkages are valid.
EventBacklog - Class in ome.services.eventlogs: Thread-safe java.util-like Container for storing EventLog instances for later parsing.
EventBacklog() - Constructor for class ome.services.eventlogs.EventBacklog
EventHandler - Class in ome.security.basic: method interceptor responsible for login and creation of Events.
EventHandler(SqlAction, BasicSecuritySystem, SessionFactory, TransactionAttributeSource) - Constructor for class ome.security.basic.EventHandler: Deprecated.
EventHandler(SqlAction, BasicSecuritySystem, SessionFactory, TransactionAttributeSource, ReadOnlyStatus) - Constructor for class ome.security.basic.EventHandler
EventListenersFactoryBean - Class in ome.security.basic: configuring all the possible event listeners within XML can be cumbersome.
EventListenersFactoryBean(CurrentDetails, TokenHolder, ACLVoter, OmeroInterceptor) - Constructor for class ome.security.basic.EventListenersFactoryBean
EventLogFailure - Class in ome.services.eventlogs: Signifies that the processing of a EventLog has failed.
EventLogFailure(EventLogLoader, EventLog, Throwable) - Constructor for class ome.services.eventlogs.EventLogFailure
EventLogListener - Class in ome.security.basic: responsible for responding to all Hibernate Events.
EventLogListener(CurrentDetails) - Constructor for class ome.security.basic.EventLogListener: main constructor.
EventLogLoader - Class in ome.services.eventlogs: Data access object for the FullTextIndexer which provides an Iterator interface for EventLog instances to be properly indexed.
EventLogLoader() - Constructor for class ome.services.eventlogs.EventLogLoader
EventLogMessage - Class in ome.services.messages: Published only when an event log should be saved at the end of a transaction.
EventLogMessage(Object, String, Class<? extends IObject>, List<Long>) - Constructor for class ome.services.messages.EventLogMessage
EventLogQueue - Class in ome.services.eventlogs: PersistentEventLogLoader implementation which loads many rows at the same time, culling out duplicates in order to speed up indexing.
EventLogQueue() - Constructor for class ome.services.eventlogs.EventLogQueue
EventLogQueue(Metrics, int, String[], String[]) - Constructor for class ome.services.eventlogs.EventLogQueue
EventLogsMessage - Class in ome.services.messages: Published with the final collection of EventLog instances which will be saved.
EventLogsMessage(Object, Multimap<String, EventLog>) - Constructor for class ome.services.messages.EventLogsMessage
EventMethodInterceptor - Class in ome.tools.hibernate: filter which can be added to any event type in order to catch execution.
EventMethodInterceptor() - Constructor for class ome.tools.hibernate.EventMethodInterceptor
EventMethodInterceptor(EventMethodInterceptor.Action) - Constructor for class ome.tools.hibernate.EventMethodInterceptor
EventMethodInterceptor.Action - Class in ome.tools.hibernate
EventMethodInterceptor.DisableAction - Class in ome.tools.hibernate
eventProvider - Variable in class ome.security.basic.BasicSecuritySystem
EventProvider - Interface in ome.security: Provider for Event objects which is responsible for persisting and populating such entities.
EventProviderInDb - Class in ome.security.basic: Provider for Event objects which is responsible for persisting and populating such entities using Hibernate in accordance with the currently available IUpdate implementation.
EventProviderInDb(ServiceFactory) - Constructor for class ome.security.basic.EventProviderInDb: Main public constructor for this EventProvider implementation.
EventProviderInMemory - Class in ome.security.basic: Provider for Event objects which is responsible for persisting and populating such entities in-memory.
EventProviderInMemory() - Constructor for class ome.security.basic.EventProviderInMemory
EventProviderWrapper - Class in ome.security.basic: An event provider that offers a unified view of multiple underlying event providers.
EventProviderWrapper(ReadOnlyStatus, List) - Constructor for class ome.security.basic.EventProviderWrapper: Construct a new event provider.
evict(Object) - Method in interface ome.api.local.LocalQuery: Removes an object graph from the session.
evict(Object) - Method in class ome.logic.QueryImpl
excludes - Variable in class ome.services.eventlogs.EventLogLoader: Array of class types which will get excluded from indexing.
execute(HibernateCallback) - Method in interface ome.api.local.LocalQuery: Executes a HibernateCallback
execute(Query<T>) - Method in interface ome.api.local.LocalQuery: Executes a locally defined Query.
execute(HibernateCallback) - Method in class ome.logic.QueryImpl
execute(Query<T>) - Method in class ome.logic.QueryImpl
execute() - Method in interface ome.services.graphs.GraphTraversal.PlanExecutor: Perform the planned action.
execute(Principal, Executor.Work<T>) - Method in interface ome.services.util.Executor: Call Executor.execute(Map, Principal, Work) with a null call context.
execute(Map<String, String>, Principal, Executor.Work<T>) - Method in interface ome.services.util.Executor: Executes a Executor.Work instance wrapped in two layers of AOP.
execute(Principal, Executor.Work<T>) - Method in class ome.services.util.Executor.Impl: Call Executor.execute(Map, Principal, Work) with a null call context.
execute(Map<String, String>, Principal, Executor.Work<T>) - Method in class ome.services.util.Executor.Impl: Executes a Executor.Work instance wrapped in two layers of AOP.
executeCloseSession(String) - Method in interface ome.services.sessions.SessionProvider: Loads a session directly, sets its "closed" value and immediately saves it.
executeCloseSession(String) - Method in class ome.services.sessions.SessionProviderInDb
executeCloseSession(String) - Method in class ome.services.sessions.SessionProviderInMemory
executeCloseSession(String) - Method in class ome.services.sessions.SessionProviderWrapper
executeInternalSession(String, Session) - Method in interface ome.services.sessions.SessionProvider
executeInternalSession(String, Session) - Method in class ome.services.sessions.SessionProviderInDb
executeInternalSession(String, Session) - Method in class ome.services.sessions.SessionProviderInMemory
executeInternalSession(String, Session) - Method in class ome.services.sessions.SessionProviderWrapper
executeNextSessionId() - Method in interface ome.services.sessions.SessionProvider: Added as an attempt to cure ticket:1176
executeNextSessionId() - Method in class ome.services.sessions.SessionProviderInDb
executeNextSessionId() - Method in class ome.services.sessions.SessionProviderInMemory
executeNextSessionId() - Method in class ome.services.sessions.SessionProviderWrapper
executePasswordCheck(String, String) - Method in interface ome.services.sessions.SessionManager: Executes a password check using the Executor framework.
executePasswordCheck(String, String) - Method in class ome.services.sessions.SessionManagerImpl
executeSql(Executor.SqlWork) - Method in interface ome.services.util.Executor: Executes a Executor.SqlWork wrapped with a transaction.
executeSql(Executor.SqlWork) - Method in class ome.services.util.Executor.Impl: Executes a Executor.SqlWork in transaction.
executeUpdate(ServiceFactory, Session, String, long, Long) - Method in interface ome.services.sessions.SessionProvider
executeUpdate(ServiceFactory, Session, String, long, Long) - Method in class ome.services.sessions.SessionProviderInDb
executeUpdate(ServiceFactory, Session, String, long, Long) - Method in class ome.services.sessions.SessionProviderInMemory
executeUpdate(ServiceFactory, Session, String, long, Long) - Method in class ome.services.sessions.SessionProviderWrapper
ExecutionThread - Class in ome.services.util: Thread which can be started and will appropriately acquire a session, then use the Executor to complete its work.
ExecutionThread(SessionManager, Executor, Executor.Work, Principal) - Constructor for class ome.services.util.ExecutionThread: Main constructor.
executor - Variable in class ome.logic.UpdateImpl
executor - Variable in class ome.services.sessions.SessionManagerImpl
executor - Variable in class ome.services.sharing.ShareBean
executor - Variable in class ome.services.util.ExecutionThread
Executor - Interface in ome.services.util: Simple execution/work interface which can be used for internal tasks which need to have a full working implementation.
Executor.Descriptive - Class in ome.services.util
Executor.Impl - Class in ome.services.util
Executor.LoggedWork<X> - Interface in ome.services.util
Executor.Priority - Enum in ome.services.util
Executor.SimpleSqlWork - Class in ome.services.util: Simple adapter which takes a String for Executor.Descriptive.description
Executor.SimpleWork<T> - Class in ome.services.util: Simple adapter which takes a String for Executor.Descriptive.description
Executor.SqlWork - Interface in ome.services.util: Work SPI to perform actions related to stateless sessions.
Executor.StatefulWork - Interface in ome.services.util: In the case of a stateful work order, the bean itself needs to be associated with the sessionHandler and thread rather than the word instance itself.
Executor.Work<X> - Interface in ome.services.util: Work SPI to perform actions within the server as if they were fully wrapped in our service logic.
exists() - Method in class ome.services.RawFileBean
expirationAsLong(long, Timestamp) - Static method in class ome.services.sharing.ShareBean: Convert a expiration into a long which can be set on Session.setTimeToLive(Long).
ExtendedMetadata - Interface in ome.tools.hibernate: extension of the model metadata provided by SessionFactory.
ExtendedMetadata.Immutables - Class in ome.tools.hibernate
ExtendedMetadata.Impl - Class in ome.tools.hibernate: Sole implementation of ExtendedMetadata.
ExtendedMetadata.Locks - Class in ome.tools.hibernate: inner class which wraps the information (index number, path, etc) related to what fields a particular object can lock.
ExtendedMetadata.Relationship - Class in ome.tools.hibernate: Simple value class to maintain all of the state for use by ExtendedMetadata.getRelationship(String, String) and ExtendedMetadata.getSQLJoin(String, String, String, String).

F

factory - Variable in class ome.security.basic.EventHandler
factory - Variable in class ome.services.sessions.SessionManagerImpl
factory - Variable in class ome.services.util.Executor.Impl
factory - Variable in class ome.tools.hibernate.ListAsSQLArrayUserType
FACTORY - Static variable in class ome.tools.hibernate.SqlArray
fail(File, Long, Long) - Method in class ome.services.delete.files.AbstractFileDeletions
FailedLoginMailSender - Class in ome.services.mail: On an LoginAttemptMessage potentially send an email to administrators or the user herself to alert of possible security issues.
FailedLoginMailSender() - Constructor for class ome.services.mail.FailedLoginMailSender
FETCH - Static variable in class ome.services.query.Query: imported constant for ease of use
fetchAlso(Map<T, String>) - Method in class ome.services.SearchBean
fetchAlso(String...) - Method in class ome.services.SearchBean
fetchAnnotations - Variable in class ome.services.search.SearchValues
fetchAnnotations(Class...) - Method in class ome.services.SearchBean
fetchChildren(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
fetches - Variable in class ome.services.search.SearchValues
fetchParents(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
file - Variable in class ome.security.auth.FilePasswordProvider: Flat file read on each invocation with name, value pairs in Java Properties notation.
file() - Method in class ome.services.scripts.RepoFile
FileDeleter - Class in ome.services.delete.files: Helper class which sorts through a number of file-based deletions before processing them.
FileDeleter(OmeroContext, AbstractFileSystemService, SetMultimap<String, Long>) - Constructor for class ome.services.delete.files.FileDeleter
FILENAME - Static variable in class ome.formats.importer.util.TinyImportFixture: Deprecated.

Hard-coded filename of the image to be imported
FileParser - Class in ome.services.fulltext: Object which attempts to parse any file given to it.
FileParser() - Constructor for class ome.services.fulltext.FileParser
FilePasswordProvider - Class in ome.security.auth: Example password provider which uses the given file as password lookup.
FilePasswordProvider(PasswordUtil, File) - Constructor for class ome.security.auth.FilePasswordProvider
FilePasswordProvider(PasswordUtil, File, boolean) - Constructor for class ome.security.auth.FilePasswordProvider
files - Variable in class ome.services.fulltext.FullTextBridge: Deprecated.
fillRelationships(SessionFactoryImplementor, Map<String, ExtendedMetadata.Relationship>) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: For each of the fields contained in this ExtendedMetadata.Locks object, parse out the type and the field name and store those as the key and value in the "value" argument.
fillReplacement(MergeEvent) - Method in class ome.security.basic.MergeEventListener
filter(String, Filterable) - Method in class ome.tools.hibernate.ProxyCleanupFilter
filter(String, Collection) - Method in class ome.tools.hibernate.ProxyCleanupFilter
filter(String, Map) - Method in class ome.tools.hibernate.ProxyCleanupFilter
filter(String, Filter) - Method in class ome.tools.hibernate.QueryBuilder
filter(String, Filterable) - Method in class ome.tools.hibernate.ReloadFilter
filter(String, Object) - Method in class ome.tools.hibernate.UpdateFilter: overrides ContextFilter.filter(String, Object) to allow only certain types to enter the Hibernate system
filter(String, Filterable) - Method in class ome.tools.hibernate.UpdateFilter: overrides ContextFilter.filter(String, Filterable) to return previously merged or previously checked items.
filter(String, Collection) - Method in class ome.tools.hibernate.UpdateFilter: overrides ContextFilter.filter(String, Collection) to return previously checked collections.
filter(String, Map) - Method in class ome.tools.hibernate.UpdateFilter: Prevents CountPerOwner from being loaded unnecessarily.
filterName - Static variable in class ome.security.basic.AllGroupsSecurityFilter
filterNow() - Method in class ome.tools.hibernate.QueryBuilder: In order to support the order() method in addition to a filter, we allow applying the filter and nulling the instance eagerly before the user calls order.
filterObject(IObject) - Method in class ome.security.policy.DefaultPolicyService: Limit the objects to which Policy instances are applied.
filters - Variable in class ome.security.basic.BasicSecuritySystem
find(Class, long) - Method in class ome.logic.QueryImpl
find(String) - Method in interface ome.services.sessions.SessionManager: Finds a Session and update the last access time.
find(String) - Method in class ome.services.sessions.SessionManagerImpl
findAll(Class<T>, Filter) - Method in class ome.logic.QueryImpl
findAllByExample(T, Filter) - Method in class ome.logic.QueryImpl
findAllByFullText(Class<T>, String, Parameters) - Method in class ome.logic.QueryImpl
findAllByQuery(String, Parameters) - Method in class ome.logic.QueryImpl
findAllByString(Class<T>, String, String, boolean, Filter) - Method in class ome.logic.QueryImpl
findByExample(T) - Method in class ome.logic.QueryImpl
findByMimetype(String) - Method in class ome.services.scripts.ScriptRepoHelper: Search through all ScriptFileType instances and find one with a matching mimetype string.
findByQuery(String, Parameters) - Method in class ome.logic.QueryImpl
findByString(Class<T>, String, String) - Method in class ome.logic.QueryImpl
findContainerHierarchies(Class, Set, Parameters) - Method in class ome.logic.PojosImpl
findDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: default logic
findDN(String) - Method in class ome.logic.LdapImpl
findExperimenter(String) - Method in class ome.logic.LdapImpl
findGroup(String) - Method in class ome.logic.LdapImpl
findGroupDN(String) - Method in class ome.logic.LdapImpl
findInDb(String, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
findInDb(RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
findInDb(SqlAction, RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper: Looks to see if a path is contained in the repository.
findMinMax(int[]) - Method in class ome.services.RawPixelsBean
findQuietly(String) - Method in interface ome.services.sessions.SessionManager: Finds a Session without updating the last access time.
findQuietly(String) - Method in class ome.services.sessions.SessionManagerImpl
findSameUser(String, String...) - Method in interface ome.services.sessions.SessionManager: Returns a non-null, possibly empty list of session instances belonging to the same user as the given session with one of the given agents.
findSameUser(String, String...) - Method in class ome.services.sessions.SessionManagerImpl
findSessionById(long, Session) - Method in interface ome.services.sessions.SessionProvider: Retrieves a session by ID.
findSessionById(long, ServiceFactory) - Method in interface ome.services.sessions.SessionProvider: Retrieves a session by ID.
findSessionById(long, Session) - Method in class ome.services.sessions.SessionProviderInDb
findSessionById(long, ServiceFactory) - Method in class ome.services.sessions.SessionProviderInDb
findSessionById(long, Session) - Method in class ome.services.sessions.SessionProviderInMemory
findSessionById(long, ServiceFactory) - Method in class ome.services.sessions.SessionProviderInMemory
findSessionById(long, Session) - Method in class ome.services.sessions.SessionProviderWrapper
findSessionById(long, ServiceFactory) - Method in class ome.services.sessions.SessionProviderWrapper
findSessionIdByUuid(String, ServiceFactory) - Method in interface ome.services.sessions.SessionProvider
findSessionIdByUuid(String) - Method in interface ome.services.sessions.SessionProvider
findSessionIdByUuid(String, ServiceFactory) - Method in class ome.services.sessions.SessionProviderInDb
findSessionIdByUuid(String) - Method in class ome.services.sessions.SessionProviderInDb
findSessionIdByUuid(String, ServiceFactory) - Method in class ome.services.sessions.SessionProviderInMemory
findSessionIdByUuid(String) - Method in class ome.services.sessions.SessionProviderInMemory
findSessionIdByUuid(String, ServiceFactory) - Method in class ome.services.sessions.SessionProviderWrapper
findSessionIdByUuid(String) - Method in class ome.services.sessions.SessionProviderWrapper
finish() - Method in interface ome.services.procs.Process
finish() - Method in class ome.services.procs.ProcessSkeleton
fixNulledOrFilteredCollections(IObject, IObject, EntityPersister, SessionImplementor) - Static method in class ome.tools.hibernate.HibernateUtils: loads collections which have been filtered or nulled by the user
flipState() - Method in class ome.services.eventlogs.EventBacklog: Flips the EventBacklog to the "adding" state if it is empty, otherwise to the "removing" state.
FLOAT(Connection, List<Float>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
FLOAT() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
FLOAT(List<Float>) - Constructor for class ome.tools.hibernate.SqlArray.FLOAT
flush() - Method in interface ome.api.local.LocalUpdate
flush() - Method in class ome.logic.UpdateImpl
ForceTransactionAttributeSource - Class in ome.tools.spring: Requires that all method calls have some other form of attribute source by throwing an exception if accessed;
ForceTransactionAttributeSource() - Constructor for class ome.tools.spring.ForceTransactionAttributeSource
foreground(boolean, String[]) - Static method in class ome.services.fulltext.Main: Uses a PersistentEventLogLoader and cycles through all the remaining logs.
free() - Method in class ome.tools.hibernate.SqlArray
FROM - Static variable in class ome.services.mail.MapAnnotationSubethaListener
from(String, String) - Method in class ome.tools.hibernate.QueryBuilder
fullname() - Method in class ome.services.scripts.RepoFile
FullText - Class in ome.services.search: Search based on Lucene's Query class.
FullText(SearchValues, String, String, String, String, String, Class<? extends Analyzer>) - Constructor for class ome.services.search.FullText: Constructs a new instance; Builds a Lucence query with the provided arguments and passes it on the Lucene parser
FullText(SearchValues, String, Class<? extends Analyzer>) - Constructor for class ome.services.search.FullText: Creates a new instance; Passes the query directly on to the Lucene parser.
FullTextAnalyzer - Class in ome.services.fulltext: Deprecated.
FullTextAnalyzer() - Constructor for class ome.services.fulltext.FullTextAnalyzer: Deprecated.
fullTextBridge - Variable in class ome.logic.UpdateImpl
FullTextBridge - Class in ome.services.fulltext: Deprecated.
FullTextBridge() - Constructor for class ome.services.fulltext.FullTextBridge: Deprecated.

Since this constructor provides the instance with no way of parsing OriginalFile binaries, all files will be assumed to have blank content.
FullTextBridge(OriginalFilesService, Map<String, FileParser>) - Constructor for class ome.services.fulltext.FullTextBridge: Deprecated.

Constructor which provides an empty set of custom bridges.
FullTextBridge(OriginalFilesService, Map<String, FileParser>, Class<FieldBridge>[]) - Constructor for class ome.services.fulltext.FullTextBridge: Deprecated.

Main constructor.
FullTextIndexer - Class in ome.services.fulltext: Deprecated.
FullTextIndexer(EventLogLoader) - Constructor for class ome.services.fulltext.FullTextIndexer: Deprecated.
FullTextIndexer(EventLogLoader, Metrics) - Constructor for class ome.services.fulltext.FullTextIndexer: Deprecated.
FullTextIndexer2 - Class in ome.services.fulltext: An indexer bean replacing the 5.4 full-text thread FullTextIndexer with adequate functionality.
FullTextIndexer2(Scheduler, SessionFactory, FieldBridge, String, String, String) - Constructor for class ome.services.fulltext.FullTextIndexer2: Construct a new indexer.
FullTextThread - Class in ome.services.fulltext: Deprecated.
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge) - Constructor for class ome.services.fulltext.FullTextThread: Deprecated.

Uses default Principal for indexing
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, boolean) - Constructor for class ome.services.fulltext.FullTextThread: Deprecated.

Uses default Principal for indexing
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal) - Constructor for class ome.services.fulltext.FullTextThread: Deprecated.

Main constructor.
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal, boolean) - Constructor for class ome.services.fulltext.FullTextThread: Deprecated.

Main constructor.

G

generateRandomPasswd() - Method in class ome.security.auth.PasswordUtil
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(Session, Class, long) - Method in class ome.services.fulltext.FullTextIndexer: 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() - 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
getAction() - Method in class ome.services.mail.ObjectMailSender
getActiveConnections(long) - Method in class ome.services.sharing.ShareBean
getAdminPrivileges(Experimenter) - Method in class ome.logic.AdminImpl
getAdminPrivileges() - Method in class ome.security.basic.BasicEventContext
getAdminPrivileges() - Method in class ome.security.basic.CurrentDetails
getAdminsWithPrivileges(List<AdminPrivilege>) - Method in class ome.logic.AdminImpl
getAll(String) - Method in class ome.security.auth.AttributeSet
getAllClasses() - Method in class ome.services.graphs.GraphPathBean: Get all the classes mapped by Hibernate.
getAllEnumerations(Class<T>) - Method in class ome.logic.PixelsImpl: Deprecated.
getAllGuests(long) - Method in class ome.services.sharing.ShareBean
getAllMembers(long) - Method in class ome.services.sharing.ShareBean
getAllPrivileges() - Static method in class ome.security.basic.LightAdminPrivileges
getAllSystemUsers(boolean) - Method in class ome.services.mail.MailSender
getAllUsers(long) - Method in class ome.services.sharing.ShareBean
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
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
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
getAttribute(T) - Method in class ome.security.auth.OmeroModelContextMapper
getAttributeSet(T) - Method in class ome.security.auth.OmeroModelContextMapper
getAuthority() - Method in class ome.services.db.DatabaseIdentity
getAvailableFamilies() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getAvailableModels() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getBaseType() - Method in class ome.tools.hibernate.SqlArray
getBaseTypeName() - Method in class ome.tools.hibernate.SqlArray
getBatchSize() - Method in class ome.services.eventlogs.EventLogLoader
getBatchSize() - Method in class ome.services.SearchBean
getBeanHelper() - Method in class ome.logic.AbstractLevel1Service
getBeanHelper() - Method in class ome.logic.AbstractLevel2Service
getBeanHelper() - Method in class ome.services.AbstractStatefulBean
getBitDepth(PixelsType) - Method in class ome.logic.PixelsImpl
getBoost() - Method in class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
getBytesFailed() - Method in class ome.services.delete.files.AbstractFileDeletions
getByteWidth() - Method in class ome.services.RawPixelsBean
getCallbackObject(String, String) - Method in class ome.services.sessions.SessionManagerImpl
getCallContext() - Method in class ome.security.basic.BasicEventContext
getChannelCurveCoefficient(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelFamily(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelLookupTable(int) - Method in class ome.services.RenderingBean
getChannelNoiseReduction(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelStats(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelWindowEnd(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelWindowStart(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getCheckDone() - Method in class ome.services.util.DBEnumCheck
getCheckDone() - Method in class ome.services.util.DBMappedEnumCheck
getChecks(IObject, String) - Method in class ome.security.basic.GroupChmodStrategy
getChecks(IObject, String) - Method in interface ome.security.ChmodStrategy: Return all the checks necessary to validate the given object if it were to have its permissions.
getChildTransformer(Class) - Static method in class ome.services.query.Hierarchy
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: Create a clone of this graph policy that has fresh state.
getClientConfigDefaults() - Method in class ome.logic.ConfigImpl
getClientConfigValues() - Method in class ome.logic.ConfigImpl
getCodomainMapContext(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getCol(int, int, int, int) - Method in class ome.services.RawPixelsBean
getCollectionCount(String, String, Set, Parameters) - Method in class ome.logic.PojosImpl
getCommentCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
getComments(long) - Method in class ome.services.sharing.ShareBean
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: Implemented as specified by the RenderingEngine interface.
getConfigDefaults() - Method in class ome.logic.ConfigImpl
getConfigNameForPrivilege(AdminPrivilege) - Method in class ome.security.basic.LightAdminPrivileges
getConfigValue(String) - Method in class ome.logic.ConfigImpl: see IConfig.getConfigValue(String)
getConfigValues(String) - Method in class ome.logic.ConfigImpl
getConnection() - Method in class ome.services.db.SelfCorrectingDataSource
getConnection(String, String) - Method in class ome.services.db.SelfCorrectingDataSource
getContainerTypes() - Method in class ome.logic.TypesImpl
getContentMap(long) - Method in class ome.services.sharing.ShareBean
getContents(long) - Method in class ome.services.sharing.ShareBean
getContentSize(long) - Method in class ome.services.sharing.ShareBean
getContentSubList(long, int, int) - Method in class ome.services.sharing.ShareBean
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
getControls() - Method in class ome.security.auth.GroupContextMapper
getControls() - Method in class ome.security.auth.PersonContextMapper
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.
getCurrentAdminPrivileges() - Method in class ome.logic.AdminImpl
getCurrentAdminPrivileges() - Method in class ome.services.sessions.SessionContextImpl
getCurrentEventContext() - Method in class ome.security.basic.CurrentDetails
getCurrentEventContext() - Method in class ome.services.AbstractStatefulBean
getCurrentEventContext() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getCurrentEventContext() - Method in class ome.services.ThumbnailBean
getCurrentEventId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentEventType() - Method in class ome.services.sessions.SessionContextImpl
getCurrentGroupId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentGroupName() - Method in class ome.services.sessions.SessionContextImpl
getCurrentGroupPermissions() - Method in class ome.services.sessions.SessionContextImpl
getCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader: Get current EventLog id.
getCurrentSessionId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentSessionUuid() - Method in class ome.services.sessions.SessionContextImpl
getCurrentShareId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentSudoerId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentSudoerName() - Method in class ome.services.sessions.SessionContextImpl
getCurrentUmask() - Method in class ome.services.sessions.SessionContextImpl
getCurrentUserId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentUserName() - Method in class ome.services.sessions.SessionContextImpl
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 class ome.logic.ConfigImpl: see IConfig.getDatabaseTime()
getDatabaseUuid() - Method in class ome.logic.ConfigImpl
getDatabaseVersion() - Method in interface ome.api.local.LocalConfig: Retrieves the newest database patch.
getDatabaseVersion() - Method in class ome.logic.ConfigImpl
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
getDataset() - Method in class ome.formats.importer.util.TinyImportFixture: Deprecated.

provides access to the created Dataset instance.
getDefaultBody() - Method in class ome.services.mail.MailSender
getDefaultCondition() - Method in class ome.security.basic.AllGroupsSecurityFilter
getDefaultCondition() - Method in class ome.security.basic.LightAdminPrivilegesSecurityFilter
getDefaultCondition() - Method in class ome.security.basic.OneGroupSecurityFilter
getDefaultCondition() - Method in class ome.security.basic.SharingSecurityFilter
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.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 class ome.logic.AdminImpl
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: Implemented as specified by the RenderingEngine interface.
getDefaultZ() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getDetails(Object[], String[]) - Static method in class ome.tools.hibernate.HibernateUtils
getDirectSubclassesOf(String) - Method in class ome.services.graphs.GraphPathBean: Get the direct subclasses of the given class, if any.
getDirectSuperclassOf(String) - Method in class ome.services.graphs.GraphPathBean: Get the direct superclass of the given class, if any.
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
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
getEntity(String, Serializable) - Method in class ome.security.basic.OmeroInterceptor
getEntityName(Object) - Method in class ome.security.basic.OmeroInterceptor
getEnumeration(Class<T>, String) - Method in class ome.logic.PixelsImpl: Deprecated.
getEnumeration(Class<T>, String) - Method in class ome.logic.TypesImpl
getEnumerationsWithEntries() - Method in class ome.logic.TypesImpl
getEnumerationTypes() - Method in class ome.logic.TypesImpl
getEvent() - Method in class ome.security.basic.BasicEventContext
getEvent() - Method in class ome.security.basic.CurrentDetails
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: Calls SecuritySystem.getEventContext(boolean) with a false as "refresh".
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(Principal) - Method in interface ome.services.sessions.SessionManager: Provides a partial EventContext for the current Session.
getEventContext(Principal) - Method in class ome.services.sessions.SessionManagerImpl
getEventContextQuiet() - Method in interface ome.api.local.LocalAdmin: Like IAdmin.getEventContext() but will not reload the context.
getEventContextQuiet() - Method in class ome.logic.AdminImpl
getEvents(long, Experimenter, Timestamp, Timestamp) - Method in class ome.services.sharing.ShareBean
getExecutor() - Method in class ome.services.mail.MailSender
getExecutor() - Method in class ome.services.scheduler.ThreadPool: Deprecated.
getExperimenter(long) - Method in class ome.logic.AdminImpl
getExtendedMetadata() - Method in class ome.logic.AbstractLevel2Service
getFailedFilesCount() - Method in class ome.services.delete.files.FileDeleter
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.
getFileId() - Method in class ome.services.messages.DeleteLogMessage
getFileId() - Method in class ome.services.RawFileBean
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.
getFirst(String) - Method in class ome.security.auth.AttributeSet
getFreeSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl
getGroup(long) - Method in class ome.logic.AdminImpl
getGroup() - Method in class ome.security.basic.BasicEventContext
getGroup() - Method in class ome.security.basic.CurrentDetails
getGroupAttribute(String) - Method in class ome.security.auth.LdapConfig
getGroupFilter() - Method in class ome.security.auth.LdapConfig
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
getHistogram(int[], int, boolean, PlaneDef) - Method in class ome.services.RawPixelsBean
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.services.RawPixelsBean
getIdentifierProperty(String) - Method in class ome.services.graphs.GraphPathBean: Get the identifier property for the given class.
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.
getImageAndCount(Image[], long, UnloadedCollector) - Method in class ome.services.delete.DeleteBean: Uses the locally defined query to load an Image and calls DeleteBean.collect(UnloadedCollector, Image) in order to define a list of what will be deleted.
getImages(Class, Set, Parameters) - Method in class ome.logic.PojosImpl
getImagesByOptions(Parameters) - Method in class ome.logic.PojosImpl
getImagesBySplitFilesets(Map<Class<? extends IObject>, List<Long>>, Parameters) - Method in class ome.logic.PojosImpl
getImmutableFields() - Method in class ome.tools.hibernate.ExtendedMetadata.Immutables
getImmutableFields(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
getImportTypes() - Method in class ome.logic.TypesImpl
getIndex() - Method in class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
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
getInputKeys(String) - Method in class ome.services.sessions.SessionBean
getInputs(String) - Method in class ome.services.sessions.SessionBean
getInterfaceImplemented(String, String) - Method in class ome.services.graphs.GraphPathBean: Get the interface whose method is implemented by a specific class property, if any.
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
getJob() - Method in class ome.services.JobBean
getKey() - Method in class ome.services.eventlogs.PersistentEventLogLoader
getLast() - Method in class ome.security.basic.CurrentDetails
getLast() - Method in interface ome.security.basic.PrincipalHolder: Get the last, i.e.
getLastUpdated() - Method in class ome.services.sessions.state.SessionCache
getLauncher() - Method in class ome.services.scripts.ScriptFileType: Return the name of the launcher ("./run.exe") that is used for scripts of this type.
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.
getLeaderOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
getLeaderOfGroupsList() - Method in class ome.security.basic.BasicEventContext
getLeaderOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
getLinkedBy(String) - Method in class ome.services.graphs.GraphPathBean: Get the classes and properties that link to the given class.
getLinkeds(String, String, Long) - Method in class ome.services.graphs.GraphTraversal: Get the model objects that are linked to by the given object via the given property.
getLinkedTo(String) - Method in class ome.services.graphs.GraphPathBean: Get the classes and properties to which the given class links.
getLinkers(String, String, Long) - Method in class ome.services.graphs.GraphTraversal: Get the model objects that link to the given object via the given property.
getLockCandidateChecks(Class<? extends IObject>, boolean) - Method in interface ome.tools.hibernate.ExtendedMetadata: Rather than iterating over an IObject like ExtendedMetadata.getLockCandidates(IObject) this method returns type/field name pairs (like ExtendedMetadata.getLockChecks(Class)) to allow performing the queries manually.
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 linked 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
getLogger() - Method in class ome.services.util.BeanHelper
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
getLutReaders(ChannelBinding[]) - Method in class ome.logic.LutProviderImpl
getMailUtil() - Method in class ome.services.mail.MailSender
getManagerByUuid(String, ServiceFactory) - Method in class ome.security.basic.NodeProviderInDb
getManagerByUuid(String, ServiceFactory) - Method in class ome.security.basic.NodeProviderInMemory
getManagerByUuid(String, ServiceFactory) - Method in class ome.security.basic.NodeProviderWrapper
getManagerByUuid(String, ServiceFactory) - Method in interface ome.security.NodeProvider: Retrieves a given manager node.
getManagerIdByUuid(String, SqlAction) - Method in class ome.security.basic.NodeProviderInDb
getManagerIdByUuid(String, SqlAction) - Method in class ome.security.basic.NodeProviderInMemory
getManagerIdByUuid(String, SqlAction) - Method in class ome.security.basic.NodeProviderWrapper
getManagerIdByUuid(String, SqlAction) - Method in interface ome.security.NodeProvider: Retrieves a given manager node ID.
getManagerList(boolean) - Method in class ome.security.basic.NodeProviderInDb
getManagerList(boolean) - Method in class ome.security.basic.NodeProviderInMemory
getManagerList(boolean) - Method in class ome.security.basic.NodeProviderWrapper
getManagerList(boolean) - Method in interface ome.security.NodeProvider
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
getMemberCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
getMemberOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
getMemberOfGroupsList() - Method in class ome.security.basic.BasicEventContext
getMemberOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
getMemberShares(boolean) - Method in class ome.services.sharing.ShareBean
getMemberSharesFor(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
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.
getMetadataSimple(long) - Method in class ome.services.ThumbnailCtx: Retrieves the Thumbnail object for a given Pixels ID.
getMethodCount() - Method in class ome.services.messages.stats.MethodStatsMessage
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.
getModel() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getMyOpenAgentSessions(String) - Method in class ome.services.sessions.SessionBean
getMyOpenClientSessions() - Method in class ome.services.sessions.SessionBean
getMyOpenSessions() - Method in class ome.services.sessions.SessionBean
getMyUserPhotos() - Method in class ome.logic.AdminImpl
getName() - Method in class ome.logic.HardWiredInterceptor: Can be implemented by all subclasses, so that they can configure themselves in HardWiredInterceptor.selfConfigure(OmeroContext).
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 interface ome.services.graphs.GraphPolicyRulePredicate
getName() - Method in class ome.services.graphs.GroupPredicate
getName() - Method in class ome.services.graphs.PermissionsPredicate
getName() - Method in interface ome.services.sessions.SessionCallback
getName() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
getNewUserGroup() - Method in class ome.security.auth.LdapConfig
getNewUserGroupOwner() - Method in class ome.security.auth.LdapConfig
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
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
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
getOriginalEnumerations() - Method in class ome.logic.TypesImpl
getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in class ome.services.OmeroFilePathResolver
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
getOutputKeys(String) - Method in class ome.services.sessions.SessionBean
getOutputs(String) - Method in class ome.services.sessions.SessionBean
getOwnedGroups() - Method in class ome.logic.LdapImpl.GroupLoader: Return the found owned groups for the given username.
getOwner() - Method in class ome.security.basic.BasicEventContext
getOwner() - Method in class ome.security.basic.CurrentDetails
getOwnShares(boolean) - Method in class ome.services.sharing.ShareBean
getParameterTypes() - Method in class ome.security.basic.AllGroupsSecurityFilter
getParameterTypes() - Method in class ome.security.basic.LightAdminPrivilegesSecurityFilter
getParameterTypes() - Method in class ome.security.basic.OneGroupSecurityFilter
getParameterTypes() - Method in class ome.security.basic.SharingSecurityFilter
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
getParentTransformer(Class) - Static method in class ome.services.query.Hierarchy
getPasswordAuthentication() - Method in class ome.security.SmtpAuthenticator
getPastConnections(long) - Method in class ome.services.sharing.ShareBean
getPermissionsForGroup(Long) - Method in class ome.security.basic.BasicEventContext: Never returns Permissions.DUMMY.
getPhysicalMemory() - Static method in class ome.services.util.JvmSettingsCheck
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: Deprecated.
getPixels(Long, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler
getPixels() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getPixels(long) - Method in class ome.services.ThumbnailCtx: Retrieves the Pixels object for a given Pixels ID.
getPixelsId() - Method in class ome.services.RawPixelsBean
getPixelsPath() - Method in class ome.services.RawPixelsBean
getPixelsTypeLowerBound(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getPixelsTypeUpperBound(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getPlane(int, int, int) - Method in class ome.services.RawPixelsBean
getPlaneOffset(int, int, int) - Method in class ome.services.RawPixelsBean
getPlaneRegion(int, int, int, int, int) - Method in class ome.services.RawPixelsBean
getPlaneSize() - Method in class ome.services.RawPixelsBean
getPojoTypes() - Method in class ome.logic.TypesImpl
getPrefix() - Method in class ome.tools.spring.InternalServiceFactory
getPrefix() - Method in class ome.tools.spring.ManagedServiceFactory
getPrincipal(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
getPrincipal() - Method in class ome.security.basic.BasicEventContext
getPrincipal() - Method in class ome.services.util.ExecutionThread
getPrivilege(String) - Method in class ome.security.basic.LightAdminPrivileges
getPrivilegeForConfigName(String) - Method in class ome.security.basic.LightAdminPrivileges
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.
getProjections(IObject) - Method in class ome.services.search.FullText
getProperties() - Method in class ome.security.auth.FilePasswordProvider
getPropertyKind(String, String) - Method in class ome.services.graphs.GraphPathBean: Get what kind of property a specific class property is.
getPropertyType(String, String) - Method in class ome.services.graphs.GraphPathBean: Get the Hibernate type of a specific class property.
getProxiedObject(T) - Static method in class ome.services.fulltext.BridgeHelper: Deprecated.

Simpler wrapper to handle superclass proxy objects (e.g.
getQuantumDef() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getQueryFactory() - Method in class ome.logic.AbstractLevel1Service
getQueryFactory() - Method in class ome.logic.AbstractLevel2Service
getQueryService() - Method in class ome.services.mail.MailSender
getQueryString() - Method in class ome.services.mail.ObjectMailSender
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
getRegion(int, long) - Method in class ome.services.RawPixelsBean
getRelationship(String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata: Walks the data on what locks what 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: Walks the data on what locks what for "from" argument to see if there is any direct relationship to the "to" argument.
getRenderingDefId() - Method in class ome.services.RenderingBean
getRenderingDefId() - Method in class ome.services.ThumbnailBean
getRenderingSettings(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
getRequiredPermissions() - Method in interface ome.services.graphs.GraphTraversal.Processor
getResolutionDescriptions() - Method in class ome.services.RawPixelsBean
getResolutionDescriptions() - Method in class ome.services.RenderingBean
getResolutionLevel() - Method in class ome.services.RawPixelsBean
getResolutionLevel() - Method in class ome.services.RenderingBean
getResolutionLevels() - Method in class ome.services.RawPixelsBean
getResolutionLevels() - Method in class ome.services.RenderingBean
getResults() - Method in class ome.services.delete.QueryConstraints
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
getRGBA(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getRoles() - Method in class ome.services.mail.MailSender
getRoles() - Method in class ome.services.util.DBUserCheck
getRow(int, int, int, int) - Method in class ome.services.RawPixelsBean
getRowOffset(int, int, int, int) - Method in class ome.services.RawPixelsBean
getRowSize() - Method in class ome.services.RawPixelsBean
getScore(IObject) - Method in class ome.services.search.FullText
getScriptDir() - Method in class ome.services.scripts.ScriptRepoHelper: Returns the actual root of this repository.
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
getSecuritySystem() - Method in class ome.logic.AbstractLevel2Service
getSender() - Method in class ome.services.mail.MailUtil: Helper method that returns value of omero.mail.from.
getServerTime() - Method in class ome.logic.ConfigImpl: see IConfig.getServerTime()
getService() - Method in interface ome.services.util.Executor: Returns the ExecutorService assigned to this instance.
getService() - Method in class ome.services.util.Executor.Impl
getServiceCleanups() - Method in class ome.security.basic.BasicEventContext
getServiceFactory(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
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
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.tools.hibernate.SessionFactory: Returns a session active for the current thread.
getSessionContext(String) - Method in class ome.services.sessions.state.SessionCache: Retrieve a session possibly raising either RemovedSessionException or SessionTimeoutException.
getSessionContext(String, boolean) - Method in class ome.services.sessions.state.SessionCache: Retrieve a session possibly raising either RemovedSessionException or SessionTimeoutException.
getSessionData() - Method in interface ome.services.sessions.SessionManager: Return all sessions that are active with associated possibly varying session data information.
getSessionData() - Method in class ome.services.sessions.SessionManagerImpl
getSessionData(String, boolean) - Method in class ome.services.sessions.state.SessionCache: Returns all the data contained in the internal implementation of this manager.
getSessionFactory() - Method in class ome.logic.AbstractLevel1Service: delegates to HibernateDaoSupport to get the current SessionFactory
getSessionId() - Method in class ome.services.messages.AbstractSessionMessage
getSessionPrivileges(Session) - Method in class ome.security.basic.LightAdminPrivileges: Determine the light administrator privileges associated with a session.
getSessionQuietly(String) - Method in interface ome.api.local.LocalSession: Lookups a Session without updating the last access time.
getSessionQuietly(String) - Method in class ome.services.sessions.SessionBean
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 class ome.logic.LdapImpl
getSettings(long) - Method in class ome.services.ThumbnailCtx: Retrieves the RenderingDef object for a given Pixels ID.
getShare(long) - Method in class ome.services.sharing.ShareBean
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
getSharesOwnedBy(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
getSimpleProperties(String) - Method in class ome.services.graphs.GraphPathBean: Deprecated.
instead use GraphPathBean.getSimpleProperties(String, boolean) setting isNested to false
getSimpleProperties(String, boolean) - Method in class ome.services.graphs.GraphPathBean: Get the simple properties for the given class, not linking to other mapped classes.
getSqlAction() - Method in class ome.services.util.Executor.SimpleWork
getSQLJoin(String, String, String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata: provides the link between two tables similar to {link ExtendedMetadata.getRelationship(String, String).
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 class ome.services.RawPixelsBean
getStackOffset(int, int) - Method in class ome.services.RawPixelsBean
getStackSize() - Method in class ome.services.RawPixelsBean
getStats() - Method in class ome.security.basic.BasicEventContext
getStats() - Method in class ome.security.basic.CurrentDetails
getStore() - Method in class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
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
getSubtypeValue(int, int, Object) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: uses the ClassMetadata for this ExtendedMetadata.Locks tp retrieve the component value.
getSudoer() - Method in class ome.security.basic.BasicEventContext
getSudoer() - Method in class ome.security.basic.CurrentDetails
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.
getTaggedObjectsCount(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
getTargetType(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Returns the IObject type which a given field points to.
getTermVector() - Method in class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
getThis() - Method in interface ome.services.util.Executor.StatefulWork
getThis(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
getThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
getThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBeanReadOnly
getThumbnailByLongestSide(Integer) - Method in class ome.services.ThumbnailBean
getThumbnailByLongestSide(Integer) - Method in class ome.services.ThumbnailBeanReadOnly
getThumbnailByLongestSideDirect(Integer) - Method in class ome.services.ThumbnailBean
getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBeanReadOnly
getThumbnailDirect(Integer, Integer) - Method in class ome.services.ThumbnailBean
getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in class ome.services.ThumbnailBean
getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in class ome.services.ThumbnailBean
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.
getThumbnailSet(Integer, Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
getThumbnailWithoutDefault(Integer, Integer) - Method in class ome.services.ThumbnailBean
getTile(int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean
getTileSize() - Method in class ome.services.RawPixelsBean
getTileSize() - Method in class ome.services.RenderingBean
getTimepoint(int) - Method in class ome.services.RawPixelsBean
getTimepointOffset(int) - Method in class ome.services.RawPixelsBean
getTimepointSize() - Method in class ome.services.RawPixelsBean
getTotalSize() - Method in class ome.services.RawPixelsBean
getTotalSize(IObject) - Method in class ome.services.search.FullText
getTransactionAttribute(Method, Class) - Method in class ome.services.sharing.ShareRestrictionTransactionAttributeSource
getTransactionAttribute(Method, Class) - Method in class ome.tools.spring.ForceTransactionAttributeSource
getType(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
getTypes() - Method in class ome.security.policy.BasePolicy
getTypes() - Method in interface ome.security.policy.Policy: Each Policy should tell the PolicyService which types of IObject instances it cares about.
getUndeletedFiles() - Method in class ome.services.delete.files.AbstractFileDeletions
getUndeletedFiles() - Method in class ome.services.delete.files.FileDeleter
getUsageFraction() - Method in class ome.logic.RepositoryInfoImpl: Deprecated.
getUsedSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl: Deprecated.
getUserAttribute(String) - Method in class ome.security.auth.LdapConfig
getUserEmail(String) - Method in class ome.services.mail.MailSender
getUserFilter() - Method in class ome.security.auth.LdapConfig
getUserId() - Method in class ome.services.ThumbnailCtx: Retrieves the current user ID to use for queries.
getUserImages(Parameters) - Method in class ome.logic.PojosImpl
getUserPasswordHash(Long) - Method in class ome.security.auth.PasswordUtil
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
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
getVersion() - Method in class ome.logic.ConfigImpl: see IConfig.getVersion()
getWarning() - Method in class ome.services.delete.files.FileDeleter
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.
GraphException - Exception in ome.services.graphs: Exception which will be thrown by traversing the graph if an error occurred.
GraphException(String) - Constructor for exception ome.services.graphs.GraphException
GraphPathBean - Class in ome.services.graphs: The graph path bean holds the Hibernate 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: If an object instance has any GraphPolicy.Action.EXCLUDEd parents that would prevent it from being orphaned.
GraphPolicyRule - Class in ome.services.graphs: A graph policy rule specifies a component of a GraphPolicy.
GraphPolicyRule() - Constructor for class ome.services.graphs.GraphPolicyRule
GraphPolicyRulePredicate - Interface in ome.services.graphs: A plug-in for graph policy rule matches whereby an object may be matched against named values.
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, GraphPathBean, SetMultimap<String, String>, GraphPolicy, GraphTraversal.Processor) - Constructor for class ome.services.graphs.GraphTraversal: Construct a new instance of a graph traversal manager.
GraphTraversal.PlanExecutor - Interface in ome.services.graphs: Executor that allows callers to actually perform the planned action.
GraphTraversal.Processor - Interface in ome.services.graphs: Executes the planned operation.
GROUP_SUDO_NS - Static variable in class ome.services.sessions.SessionManagerImpl
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
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
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
groupnameFilter(String) - Method in class ome.security.auth.LdapConfig
GroupPredicate - Class in ome.services.graphs: A predicate that allows group=system and similar to be used in graph policy rule matches.
GroupPredicate(Roles) - Constructor for class ome.services.graphs.GroupPredicate: Construct a new group predicate.
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
guests - Variable in class ome.services.sharing.data.ShareData
guests - Variable in class ome.services.sharing.data.ShareItem

H

handleAnnotated(IAnnotated, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge: Deprecated.

Responsible for iterating over any attached OMERO.tables and registering all appropriate row objects for later processing.
handleAnnotation(Annotation, TablesBridge.RowProcessor) - Method in class ome.services.fulltext.bridges.TablesBridge: Deprecated.

Detects if the given annotation contains an OMERO.table and if so, passes it off for further processing.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.security.policy.DefaultPolicyService: Loads all Policy instances from the context, and uses them to initialize this PolicyService.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.graphs.GraphPathBean: The application context after refresh should contain a usable Hibernate session factory.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.mail.ServerUpMailSender
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.scripts.ScriptRepoHelper: Loads all ScriptFileType instances from the context, and uses them to initialize all scripts in the repo.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Listener method which waits for a ContextRefreshedEvent and then extracts the SessionFactory from the ApplicationContext and pases it to ExtendedMetadata.Impl.setSessionFactory(SessionFactory).
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.tools.spring.OnContextRefreshedEventListener
handleEventLog(FullTextSession, EventLog) - Method in class ome.services.fulltext.FullTextIndexer: Deprecated.
handleEventLog(EventLog, Session, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler: Handles only single elements from the PersistentEventLogLoader in order to keep transactions short and safe.
handleHdf5(String, TablesBridge.RowProcessor) - Method in class ome.services.fulltext.bridges.TablesBridge: Deprecated.

Process a single OMERO.tables file.
handleImage(Image, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge: Deprecated.

Processes any annotations attached to the following types which contain this image: Plate, Dataset
HardWiredInterceptor - Class in ome.logic: Extension point for interceptors which should be compiled in from third-party code.
HardWiredInterceptor() - Constructor for class ome.logic.HardWiredInterceptor
hash - Variable in class ome.security.auth.ConfigurablePasswordProvider: Hash implementation to use for encoding passwords to check and changed passwords.
hash() - Method in class ome.services.scripts.RepoFile.FsFile
hash() - Method in class ome.services.scripts.RepoFile
hashCode(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
hasher() - Method in class ome.services.scripts.RepoFile.FsFile
hasher() - Method in class ome.services.scripts.RepoFile
hasMetadata(long) - Method in class ome.services.ThumbnailCtx: Whether or not thumbnail metadata is available for a given Pixels ID.
hasNext() - Method in class ome.services.eventlogs.EventLogLoader: Tests for available objects.
hasNext() - Method in class ome.services.eventlogs.EventLogQueue: Checks if either any EventLogQueue.Entry instances are available or tries to load them if not.
hasNext() - Method in class ome.services.SearchBean
hasPassword(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
hasPassword(String) - Method in class ome.security.auth.ConfigurablePasswordProvider: Always returns false, override with specific logic.
hasPassword(String) - Method in class ome.security.auth.FilePasswordProvider
hasPassword(String) - Method in class ome.security.auth.JdbcPasswordProvider
hasPassword(String) - Method in class ome.security.auth.LdapPasswordProvider: Only returns if the user is already in the database and has a DN value in the password table.
hasPassword(String) - Method in interface ome.security.auth.PasswordProvider: Returns true if this provider considers itself responsible for the given user name.
hasPassword(String) - Method in class ome.security.auth.PasswordProviders
hasPassword(String) - Method in class ome.security.auth.providers.LdapPasswordProvider431: Only returns if the user is already in the database and has a DN value in the password table.
hasPrivilegedToken(IObject) - Method in class ome.security.basic.BasicSecuritySystem
hasPrivilegedToken(IObject) - Method in class ome.security.basic.TokenHolder
hasPrivilegedToken(IObject) - Method in interface ome.security.SecuritySystem: checks that the IObject argument has been granted a Token by the SecuritySystem.
hasPrivilegedToken(IObject) - Method in class ome.security.SecuritySystemHolder
hasPrivilegedToken(IObject) - Method in class ome.security.sharing.SharingSecuritySystem
hasReplacement(Object) - Method in class ome.tools.hibernate.UpdateFilter
hasSettings(long) - Method in class ome.services.ThumbnailCtx: Whether or not settings are available for a given Pixels ID.
hasSubtypes(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: returns true if this offset points to a field which is an embedded component.
HibernateUtils - Class in ome.tools.hibernate: contains methods for reloading unloaded entities and nulled collections as well as determining the index of certain properties in a dehydrated Hibernate array.
HibernateUtils() - Constructor for class ome.tools.hibernate.HibernateUtils
Hierarchy - Class in ome.services.query: single-point of entry for walking of OME container hierarchies.
Hierarchy() - Constructor for class ome.services.query.Hierarchy
HierarchyNavigator - Class in ome.services.query: Query the database for relationships between model objects.
HierarchyNavigator(IQuery) - Constructor for class ome.services.query.HierarchyNavigator: Construct a new hierarchy navigator.
HierarchyNavigatorWrap<T,E> - Class in ome.services.query: Convenience class for creating versions of HierarchyNavigator with different model object representations.
HierarchyNavigatorWrap(IQuery) - Constructor for class ome.services.query.HierarchyNavigatorWrap
HierarchyTransformations - Class in ome.tools
HierarchyTransformations() - Constructor for class ome.tools.HierarchyTransformations
hints - Variable in class ome.services.SVGRasterizer: The transcoder hints.
HqlQuery - Class in ome.services.search: Delegate to IQuery.findAllByQuery(String, Parameters).
HqlQuery(SearchValues, String, Parameters) - Constructor for class ome.services.search.HqlQuery

I

ic - Variable in class ome.services.sharing.ShareStore
ice_factory() - Static method in class ome.services.sharing.data.Obj
ice_factory() - Static method in class ome.services.sharing.data.ShareData
ice_factory() - Static method in class ome.services.sharing.data.ShareItem
ice_id() - Method in class ome.services.sharing.data.Obj
ice_id(Current) - Method in class ome.services.sharing.data.Obj
ice_id() - Method in class ome.services.sharing.data.ShareData
ice_id(Current) - Method in class ome.services.sharing.data.ShareData
ice_id() - Method in class ome.services.sharing.data.ShareItem
ice_id(Current) - Method in class ome.services.sharing.data.ShareItem
ice_ids() - Method in class ome.services.sharing.data.Obj
ice_ids(Current) - Method in class ome.services.sharing.data.Obj
ice_ids() - Method in class ome.services.sharing.data.ShareData
ice_ids(Current) - Method in class ome.services.sharing.data.ShareData
ice_ids() - Method in class ome.services.sharing.data.ShareItem
ice_ids(Current) - Method in class ome.services.sharing.data.ShareItem
ice_isA(String) - Method in class ome.services.sharing.data.Obj
ice_isA(String, Current) - Method in class ome.services.sharing.data.Obj
ice_isA(String) - Method in class ome.services.sharing.data.ShareData
ice_isA(String, Current) - Method in class ome.services.sharing.data.ShareData
ice_isA(String) - Method in class ome.services.sharing.data.ShareItem
ice_isA(String, Current) - Method in class ome.services.sharing.data.ShareItem
ice_staticId() - Static method in class ome.services.sharing.data.Obj
ice_staticId() - Static method in class ome.services.sharing.data.ObjPrxHelper: Provides the Slice type ID of this type.
ice_staticId() - Static method in class ome.services.sharing.data.ShareData
ice_staticId() - Static method in class ome.services.sharing.data.ShareDataPrxHelper: Provides the Slice type ID of this type.
ice_staticId() - Static method in class ome.services.sharing.data.ShareItem
ice_staticId() - Static method in class ome.services.sharing.data.ShareItemPrxHelper: Provides the Slice type ID of this type.
IceUtil - Class in ome.services.util: Methods for working with Ice.
IceUtil() - Constructor for class ome.services.util.IceUtil
id - Variable in class ome.services.sharing.data.Obj
id - Variable in class ome.services.sharing.data.ShareData
id - Variable in class ome.services.sharing.data.ShareItem
idEqual(IObject, IObject) - Static method in class ome.tools.hibernate.HibernateUtils: returns true under the following circumstances: both arguments are null, or both arguments are identical (==), or both arguments have the same id value(equals)
IdMapHelper - Class in ome.services.sharing.data
IdMapHelper() - Constructor for class ome.services.sharing.data.IdMapHelper
IdMapHolder - Class in ome.services.sharing.data
IdMapHolder() - Constructor for class ome.services.sharing.data.IdMapHolder
IdMapHolder(Map<String, List<Long>>) - Constructor for class ome.services.sharing.data.IdMapHolder
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
ignoreUnknown - Variable in class ome.security.auth.ConfigurablePasswordProvider: If true, this implementation should return a null on ConfigurablePasswordProvider.checkPassword(String, String, boolean) if the user is unknown, otherwise a Boolean.FALSE.
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
img - Variable in class ome.services.SVGRasterizer: The image that represents the SVG document.
Impl(CurrentDetails, SessionFactory, SqlAction, String[]) - Constructor for class ome.services.util.Executor.Impl
Impl(CurrentDetails, SessionFactory, SqlAction, String[], ThreadPool) - Constructor for class ome.services.util.Executor.Impl
Impl() - Constructor for class ome.tools.hibernate.ExtendedMetadata.Impl
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() - Method in class ome.services.fulltext.FullTextIndexer2: Index a batch of model objects all at once.
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: Deprecated.
indexFullDb() - Static method in class ome.services.fulltext.Main
indexNullAs() - Method in class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
indexObject(IObject) - Method in class ome.logic.UpdateImpl
indexObject(IObject, long, long, long) - Method in class ome.services.search.IndexWatcher: Index the given object.
indexRetry() - Method in class ome.services.fulltext.FullTextIndexer2: Index a batch of model objects one by one.
indexWatcher - Variable in class ome.logic.UpdateImpl
IndexWatcher - Class in ome.services.search: The index watcher writes REINDEX entries to the event log and waits for the indexing thread to process them.
IndexWatcher(DataSource, String) - Constructor for class ome.services.search.IndexWatcher: Construct a new index watcher.
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.
INITIAL_DELAY - Static variable in class ome.logic.RepositoryInfoImpl: Time (2 minutes) between successive calls to RepositoryInfoImpl.sanityCheckRepository() needed to trigger an actual call to RepositoryInfoImpl.getUsageFraction()
INITIAL_FREE_PHYSICAL_MEMORY - Static variable in class ome.services.util.JvmSettingsCheck: FreePhysicalMemorySize value from the OperatingSystem JMX bean at startup.
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(Object) - Method in class ome.logic.QueryImpl
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: Deprecated.

Called when the configuration database does not contain a valid current_id.
initialize() - Method in class ome.services.pixeldata.PersistentEventLogLoader
initializeQuery(FullTextQuery) - Method in class ome.services.search.FullText: Allows settings offset and limit on the query.
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
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
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
instantiate(String, EntityMode, Serializable) - Method in class ome.security.basic.OmeroInterceptor: default logic, but we may want to use them eventually for dependency-injection.
INTEGER(Connection, List<Integer>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
INTEGER() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
INTEGER(List<Integer>) - Constructor for class ome.tools.hibernate.SqlArray.INTEGER
interceptor - Variable in class ome.security.basic.BasicSecuritySystem
Interceptor(ACLVoter, SessionHandler, CurrentDetails) - Constructor for class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
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 MergeEventListener needs to be moved to UpdateFilter or to another event listener.
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.
internalSave(IObject, ReloadFilter, Session) - Method in class ome.logic.UpdateImpl: Note if we use anything other than merge here, functionality from MergeEventListener needs to be moved to UpdateFilter or to another event listener.
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: Internal SessionContext created during SessionManagerImpl.init() which is used for all method calls internal to the session manager (see execute* methods)
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
invalidateConnection(long, Experimenter) - Method in class ome.services.sharing.ShareBean
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: Clears the content of the EventContextso that the SecuritySystem will no longer return true for SecuritySystem.isReady().
invalidateEventContext() - Method in class ome.security.SecuritySystemHolder
invalidateEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
invertPDI(Set<Image>, CBlock<T>) - Static method in class ome.tools.HierarchyTransformations
invoke(MethodInvocation) - Method in class ome.security.basic.BasicSecurityWiring: Wraps all OMERO invocations with login/logout semantics.
invoke(MethodInvocation) - Method in class ome.security.basic.EventHandler: Invocation interceptor for preparing this Thread for execution and subsequently resetting it.
invoke(MethodInvocation) - Method in class ome.security.basic.NullEventHandler
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.
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
ip - Variable in class ome.services.sessions.SessionManager.CreationRequest
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.
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
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_share - Static variable in interface ome.security.SecurityFilter
isActive() - Method in class ome.security.basic.BasicMethodSecurity: See MethodSecurity.isActive()
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: Implemented as specified by the RenderingEngine interface.
isAdminOrPi(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
isAllowLeadingWildcard() - Method in class ome.services.SearchBean
isAutoCloseEnabled() - Method in class ome.tools.hibernate.CurrentSessionContext
isCaseSensitive() - Method in class ome.services.SearchBean
isCheckPermissions - Variable in class ome.services.graphs.GraphPolicy.Details: if the user's permissions for the object should be checked before the GraphTraversal.Processor acts upon it
isCompressed() - Method in class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
isCondition(String) - Method in class ome.services.graphs.GraphPolicy: Check if a condition has been set.
isCurrentUserAdmin() - Method in class ome.services.sessions.SessionContextImpl
isCurrentUserGuest() - Method in class ome.security.basic.CurrentDetails
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
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
isError(SqlAction.DeleteLog) - Method in class ome.services.messages.DeleteLogMessage
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
isFloat() - Method in class ome.services.RawPixelsBean
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
isHard() - Method in class ome.services.messages.stats.AbstractStatsMessage
isIgnoreCaseLookup() - Method in interface ome.security.auth.RoleProvider
isIgnoreCaseLookup() - Method in class ome.security.auth.SimpleRoleProvider
isInert() - Method in class ome.services.scripts.ScriptFileType: Returns true if the script type cannot be executed, false otherwise.
isInert(OriginalFile) - Method in class ome.services.scripts.ScriptRepoHelper: Returns true if the file is an "inert" file e.g.
isInProgress() - Method in class ome.services.ThumbnailBean
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
isMatch(GraphPolicy.Details, String) - Method in interface ome.services.graphs.GraphPolicyRulePredicate: If this predicate is satisfied by the given object.
isMatch(GraphPolicy.Details, String) - Method in class ome.services.graphs.GroupPredicate
isMatch(GraphPolicy.Details, String) - Method in class ome.services.graphs.PermissionsPredicate
isMergedBatches() - Method in class ome.services.SearchBean
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
isMutable() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
isNonPrivate(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
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 supervisor of this entity, for example as root or as group owner.
isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.CurrentDetails
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: Implemented as specified by the RenderingEngine interface.
isProbablyTimeout(DataAccessResourceFailureException) - Static method in class ome.logic.QueryImpl
isPropertyAccessible(String, String) - Method in class ome.services.graphs.GraphPathBean: Find if the given property can be accessed.
isReadOnly(ReadOnlyStatus) - Method in class ome.security.basic.EventProviderInDb
isReadOnly(ReadOnlyStatus) - Method in class ome.security.basic.EventProviderInMemory
isReadOnly(ReadOnlyStatus) - Method in class ome.security.basic.NodeProviderInDb
isReadOnly(ReadOnlyStatus) - Method in class ome.security.basic.NodeProviderInMemory
isReadOnly() - Method in class ome.services.sessions.SessionContextImpl
isReadOnly(ReadOnlyStatus) - Method in class ome.services.sessions.SessionProviderInDb
isReadOnly(ReadOnlyStatus) - Method in class ome.services.sessions.SessionProviderInMemory
isReadOnly(ReadOnlyStatus) - Method in interface ome.services.util.ReadOnlyStatus.IsAware
isReadOnlyDb() - Method in class ome.services.util.ReadOnlyStatus
isReadOnlyRepo() - Method in class ome.services.util.ReadOnlyStatus
isReady() - Method in class ome.security.basic.BasicSecuritySystem: implements SecuritySystem.isReady().
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: checks if this SecuritySystem instance is in a valid state.
isReady() - Method in class ome.security.SecuritySystemHolder
isReady() - Method in class ome.security.sharing.SharingSecuritySystem
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: Checks whether or not this instance would throw a SecurityViolation if the same instance were passed to Policy.checkRestriction(IObject).
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.
isReturnUnloaded() - Method in class ome.services.SearchBean
isShare(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
isSigned() - Method in class ome.services.RawPixelsBean
isSingleton() - Method in class ome.security.basic.EventListenersFactoryBean: being a singleton implies that this FactoryBean will only ever create one instance.
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
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.
isThreadSafe() - Method in class ome.services.messages.AbstractSessionMessage
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
isUnloaded(Object) - Static method in class ome.tools.hibernate.HibernateUtils
isUseProjections() - Method in class ome.services.SearchBean
iterate() - Method in class ome.services.scripts.ScriptRepoHelper
iterator() - Method in class ome.services.eventlogs.EventLogLoader
iUpdate - Variable in class ome.logic.AbstractLevel2Service
iUpdate - Variable in class ome.services.AbstractStatefulBean

J

JavaImageScalingService - Class in ome.logic: Provides methods for scaling buffered images using Java Image Scaling.
JavaImageScalingService() - Constructor for class ome.logic.JavaImageScalingService
JdbcHashedPasswordProvider - Class in ome.security.auth: Central PasswordProvider which uses the "password" table in the central OMERO database.
JdbcHashedPasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.JdbcHashedPasswordProvider
JdbcHashedPasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.JdbcHashedPasswordProvider
JdbcPasswordProvider - Class in ome.security.auth: Central PasswordProvider which uses the "password" table in the central OMERO database.
JdbcPasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.JdbcPasswordProvider
JdbcPasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.JdbcPasswordProvider
JdbcPasswordProvider(PasswordUtil, boolean, boolean) - Constructor for class ome.security.auth.JdbcPasswordProvider
job(ServiceFactory, long) - Method in class ome.services.procs.ProcessManager.Work
JobBean - Class in ome.services: Provides methods for submitting asynchronous tasks.
JobBean() - Constructor for class ome.services.JobBean: default constructor
jobError() - Method in class ome.services.JobBean
jobFinished() - Method in class ome.services.JobBean
jobMessage() - Method in class ome.services.JobBean
jobRunning() - Method in class ome.services.JobBean
jobStatus() - Method in class ome.services.JobBean
join(String) - Method in interface ome.services.sessions.SessionCallback
join(String) - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
join(String, String, boolean, boolean) - Method in class ome.tools.hibernate.QueryBuilder
joinChildren(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
joinParents(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
JvmSettingsCheck - Class in ome.services.util: Hook run by the context which prints out JVM-related information, primarily Java version, max heap size and available processors.
JvmSettingsCheck() - Constructor for class ome.services.util.JvmSettingsCheck

K

key(String) - Method in class ome.security.auth.AttributeSet
key - Variable in class ome.services.eventlogs.PersistentEventLogLoader: Key used to look configuration value; 'name'
KeyAndTrustStoreConfiguration - Class in ome.security: Calls System.setProperty(String, String) for the "javax.net.ssl" properties needed to configure a trust store and a keystore for the Java process.
KeyAndTrustStoreConfiguration() - Constructor for class ome.security.KeyAndTrustStoreConfiguration
keys() - Method in class ome.services.sharing.BlobShareStore
keys() - Method in class ome.services.sharing.ShareStore
keySet() - Method in class ome.services.query.Definitions

L

lastEventLog() - Method in class ome.services.eventlogs.EventLogLoader
lastresultsAsWorkingGroup() - Method in class ome.services.SearchBean
LdapConfig - Class in ome.security.auth: Static methods for dealing with LDAP (DN) and the "password" table.
LdapConfig(boolean, String, String, String, String, String) - Constructor for class ome.security.auth.LdapConfig: As LdapConfig.LdapConfig(boolean, String, String, String, String, String, boolean, String) setting syncOnLogin to false and base to null.
LdapConfig(boolean, String, String, String, String, String, boolean) - Constructor for class ome.security.auth.LdapConfig: As LdapConfig.LdapConfig(boolean, String, String, String, String, String, boolean, String) setting base to null.
LdapConfig(boolean, String, String, String, String, String, boolean, String) - Constructor for class ome.security.auth.LdapConfig: As LdapConfig.LdapConfig(boolean, String, String, String, String, String, boolean, String, String) setting newUserGroupOwner to null.
LdapConfig(boolean, String, String, String, String, String, boolean, String, String) - Constructor for class ome.security.auth.LdapConfig: Base constructor which stores all LdapConfig.parse(String) and stores all values for later lookup.
LdapImpl - Class in ome.logic: Provides methods for administering user accounts, passwords, as well as methods which require special privileges.
LdapImpl(ContextSource, LdapOperations, Roles, LdapConfig, RoleProvider, SqlAction) - Constructor for class ome.logic.LdapImpl
LdapImpl.GroupLoader - Class in ome.logic: Data class which stores the state of the NewUserGroupBean and NewUserGroupOwnerBean operations.
LdapPasswordProvider - Class in ome.security.auth: LDAP PasswordProvider which can create users on request to synchronize with an LDAP directory.
LdapPasswordProvider(PasswordUtil, LdapImpl) - Constructor for class ome.security.auth.LdapPasswordProvider
LdapPasswordProvider(PasswordUtil, LdapImpl, boolean) - Constructor for class ome.security.auth.LdapPasswordProvider
LdapPasswordProvider431 - Class in ome.security.auth.providers: LDAP PasswordProvider which can create users on request to synchronize with an LDAP directory.
LdapPasswordProvider431(PasswordUtil, LdapImpl) - Constructor for class ome.security.auth.providers.LdapPasswordProvider431
LdapPasswordProvider431(PasswordUtil, LdapImpl, boolean) - Constructor for class ome.security.auth.providers.LdapPasswordProvider431
ldapUtil - Variable in class ome.logic.AdminImpl
ldapUtil - Variable in class ome.security.auth.LdapPasswordProvider
ldapUtil - Variable in class ome.security.auth.providers.LdapPasswordProvider431
leader_of_groups - Static variable in class ome.security.basic.AllGroupsSecurityFilter
leadingWildcard - Variable in class ome.services.search.SearchValues
LEFT_JOIN - Static variable in class ome.services.query.Query: imported constant for ease of use
legacyUtil - Variable in class ome.security.auth.ConfigurablePasswordProvider: Possibly null PasswordUtil instance which will be used as a fallback for password checks if the ConfigurablePasswordProvider.util instance fails.
length() - Method in class ome.services.scripts.RepoFile.FsFile
length() - Method in class ome.services.scripts.RepoFile
LightAdminPrivileges - Class in ome.security.basic: Report the light administrator privileges associated with a given session.
LightAdminPrivileges(Roles) - Constructor for class ome.security.basic.LightAdminPrivileges
LightAdminPrivilegesCleanup - Class in ome.security.basic: Periodically clean up old entries from the _current_admin_privileges database table.
LightAdminPrivilegesCleanup(SqlAction, int) - Constructor for class ome.security.basic.LightAdminPrivilegesCleanup: Start a new scheduled repeating task for cleaning up the _current_admin_privileges database table.
LightAdminPrivilegesSecurityFilter - Class in ome.security.basic: Filter database queries to respect light administrator privileges.
LightAdminPrivilegesSecurityFilter(Roles) - Constructor for class ome.security.basic.LightAdminPrivilegesSecurityFilter: Construct a new light administrator filter.
link(ILink[], Parameters) - Method in class ome.logic.PojosImpl
linkGroupAndUser(ExperimenterGroup, Experimenter, boolean) - Method in class ome.security.auth.SimpleRoleProvider
list(List<Obj>) - Method in class ome.services.sharing.ShareBean
listActiveRestrictions(IObject) - Method in class ome.security.policy.DefaultPolicyService
listActiveRestrictions(IObject) - Method in interface ome.security.policy.PolicyService: Return all identifier strings as would be passed as the first argument to PolicyService.isRestricted(String, IObject) or PolicyService.checkRestriction(String, IObject) which considers itself active for the given argument.
listAllRestrictions() - Method in class ome.security.policy.DefaultPolicyService
listAllRestrictions() - Method in interface ome.security.policy.PolicyService: Return all configured identifier strings as would be passed as the first argument to PolicyService.isRestricted(String, IObject) or PolicyService.checkRestriction(String, IObject).
ListAsSQLArrayUserType<T> - Class in ome.tools.hibernate: Hibernate type to store Lists of primitives using SQL ARRAY.
ListAsSQLArrayUserType() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType
ListAsSQLArrayUserType.ArrayFactory - Interface in ome.tools.hibernate
ListAsSQLArrayUserType.BOOLEAN - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$BOOLEAN" hibernate.column name="fieldName" sql-type="bool[]"
ListAsSQLArrayUserType.DATE - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$DATE" hibernate.column name="fieldName" sql-type="timestamp[]"
ListAsSQLArrayUserType.DOUBLE - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$DOUBLE" hibernate.column name="fieldName" sql-type="float8[]"
ListAsSQLArrayUserType.ENUM<E extends java.lang.Enum<E>> - Class in ome.tools.hibernate: Warning, this one is special.
ListAsSQLArrayUserType.FLOAT - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$FLOAT" hibernate.column name="fieldName" sql-type="real[]"
ListAsSQLArrayUserType.INTEGER - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$INTEGER" hibernate.column name="fieldName" sql-type="int[]"
ListAsSQLArrayUserType.STRING - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING" hibernate.column name="fieldName" sql-type="text[]"
ListAsSQLArrayUserType.STRING2 - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING2" hibernate.column name="fieldName" sql-type="text[]" Added by Josh
load(FileDeleter.Type) - Method in class ome.services.delete.files.FileDeleter: Lookup the ids which are scheduled for deletion.
load(List<Object[]>) - Method in class ome.services.eventlogs.EventLogQueue
load(Long, String, Long, String, Integer) - Method in class ome.services.eventlogs.EventLogQueue: Guarantees that the given arguments are available somewhere in the queue returning true if they were newly added.
load() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
load(long, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
load(long, Session, SqlAction, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
load() - Method in class ome.services.util.DBUserCheck
loadAll(boolean, String) - Method in class ome.services.scripts.ScriptRepoHelper: Walks all files in the repository (via ScriptRepoHelper.iterate() and adds them if not found in the database.
loadAll(boolean, String, Principal) - Method in class ome.services.scripts.ScriptRepoHelper
loadAll(boolean) - Method in class ome.services.scripts.ScriptRepoHelper: Walks all files in the repository (via ScriptRepoHelper.iterate() and adds them if not found in the database.
loadAllMetadata(long) - Method in class ome.services.ThumbnailCtx: Retrieves all thumbnail metadata available in the database for a given Pixels ID.
loadAndPrepareMetadata(Set<Long>, int) - Method in class ome.services.ThumbnailCtx: Bulk loads and prepares metadata for a group of pixels sets.
loadAndPrepareMetadata(Set<Long>, Dimension) - Method in class ome.services.ThumbnailCtx: Bulk loads and prepares metadata for a group of pixels sets.
loadAndPrepareMetadata(Set<Long>, Dimension, boolean) - Method in class ome.services.ThumbnailCtx: Bulk loads and prepares metadata for a group of pixels sets.
loadAndPrepareRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx: Bulk loads a set of rendering settings for a group of pixels sets and prepares our internal data structures.
loadAndPrepareRenderingSettings(long, long) - Method in class ome.services.ThumbnailCtx: Loads and prepares a rendering settings for a Pixels ID and RenderingDef ID.
loadAnnotation(Set<Long>) - Method in class ome.logic.MetadataImpl
loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
loadAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl
loadChannelAcquisitionData(Set<Long>) - Method in class ome.logic.MetadataImpl
loadContainerHierarchy(Class, Set, Parameters) - Method in class ome.logic.PojosImpl
loadedObjects(int) - Method in class ome.services.sessions.stats.DelegatingStats
loadedObjects(int) - Method in class ome.services.sessions.stats.NullSessionStats
loadedObjects(int) - Method in interface ome.services.sessions.stats.SessionStats
loadedObjects(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
loader - Variable in class ome.services.eventlogs.EventLogFailure
loader - Variable in class ome.services.fulltext.FullTextIndexer: Deprecated.
loader - Variable in class ome.services.pixeldata.PixelDataHandler
loadEventContext(boolean) - Method in class ome.security.basic.BasicSecuritySystem
loadEventContext(boolean, boolean) - Method in class ome.security.basic.BasicSecuritySystem
loadEventContext(boolean) - Method in interface ome.security.SecuritySystem: Prepares the current EventContext instance with the current Principal.
loadEventContext(boolean) - Method in class ome.security.SecuritySystemHolder
loadEventContext(boolean) - Method in class ome.security.sharing.SharingSecuritySystem
loadInstrument(long) - Method in class ome.logic.MetadataImpl
loadLdapGroups(String, DistinguishedName) - Method in class ome.logic.LdapImpl: Deprecated.
loadLogFiles(Class<? extends IObject>, Set<Long>) - Method in class ome.logic.MetadataImpl
loadMembers(ShareData) - Method in class ome.services.sharing.ShareBean
loadPermissions(Session) - Method in class ome.security.basic.BasicEventContext
loadPermissions(Session) - Method in class ome.security.basic.CurrentDetails: Checks the "groupPermissions" map in BasicEventContext which has been filled up by calls to BasicEventContext.setPermissionsForGroup(Long, Permissions) during BasicACLVoter.allowLoad(org.hibernate.Session, Class, Details, long).
loadRenderingDef(long) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
loadRndSettings(long) - Method in class ome.logic.PixelsImpl
loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl
loadSpecifiedAnnotationsLinkedTo(Class, Set<String>, Set<String>, Class, Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
loadTagContent(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
loadTagSets(Parameters) - Method in class ome.logic.MetadataImpl
LocalAdmin - Interface in ome.api.local: Provides local (internal) extensions for administration
localAdmin - Variable in class ome.logic.UpdateImpl
LocalCompress - Interface in ome.api.local: Provides methods for performing scaling (change of the image size through interpolation or other means) on BufferedImages.
LocalConfig - Interface in ome.api.local: Provides local (internal) extensions for configuration.
LocalQuery - Interface in ome.api.local: Provides local (internal) extensions for querying
localQuery - Variable in class ome.logic.UpdateImpl
LocalSession - Interface in ome.api.local: Provides local (internal) extensions for session management
LocalShare - Interface in ome.api.local: Provides local (internal) extensions for shares
LocalUpdate - Interface in ome.api.local: Provides local (internal) extensions for updating
log - Variable in class ome.security.auth.ConfigurablePasswordProvider
log - Variable in class ome.security.basic.AbstractSecurityFilter
log(String) - Method in class ome.security.basic.OmeroInterceptor
log - Static variable in class ome.services.delete.DeleteBean
log - Variable in class ome.services.eventlogs.EventLogFailure
log - Variable in class ome.services.eventlogs.EventLogLoader
log - Variable in class ome.services.fulltext.BridgeHelper: Deprecated.
log - Variable in class ome.services.mail.MailSender
log - Variable in class ome.services.scripts.ScriptRepoHelper
log - Static variable in class ome.services.sharing.ShareBean
log - Variable in class ome.services.sharing.ShareStore
log - Static variable in class ome.services.util.DBEnumCheck
log - Static variable in class ome.services.util.DBPatchCheck
log - Static variable in class ome.services.util.DBUserCheck
log - Static variable in class ome.services.util.JvmSettingsCheck
log - Static variable in class ome.services.util.ServerDirectoryCheck
log - Static variable in class ome.services.util.ServerVersionCheck
log(String) - Method in class ome.tools.hibernate.EventMethodInterceptor
logger() - Method in class ome.services.fulltext.BridgeHelper: Deprecated.
LOGGER - Static variable in class ome.services.util.DBUnicodeUnitsCheck
login(Principal) - Method in class ome.security.basic.BasicSecuritySystem
login(Principal) - Method in class ome.security.basic.CurrentDetails
login(BasicEventContext) - Method in class ome.security.basic.CurrentDetails: Login method which can be used by the security system to replace the existing BasicEventContext.
login(Principal) - Method in interface ome.security.basic.PrincipalHolder: Add a new principal context to the stack.
login(BasicEventContext) - Method in interface ome.security.basic.PrincipalHolder: Allow logging in directly with an event context.
login(Principal) - Method in interface ome.security.SecuritySystem: stores this Principal instance in the current thread context for authenticating and authorizing all actions.
login(Principal) - Method in class ome.security.SecuritySystemHolder
login(Principal) - Method in class ome.security.sharing.SharingSecuritySystem
loginAttempt(String, Boolean) - Method in class ome.security.auth.ConfigurablePasswordProvider
LoginAttemptListener - Class in ome.security.auth: Listens for any LoginAttemptMessage.
LoginAttemptListener(int, long) - Constructor for class ome.security.auth.LoginAttemptListener
LoginAttemptMessage - Class in ome.services.messages: Published when any check is performed against a password.
LoginAttemptMessage(Object, String, Boolean) - Constructor for class ome.services.messages.LoginAttemptMessage
logout() - Method in class ome.security.basic.BasicSecuritySystem
logout() - Method in class ome.security.basic.CurrentDetails
logout() - Method in interface ome.security.basic.PrincipalHolder: Pop the last created principal context and return the number of active contexts remaining.
logout() - Method in interface ome.security.SecuritySystem: clears the top Principal instance from the current thread context.
logout() - Method in class ome.security.SecuritySystemHolder
logout() - Method in class ome.security.sharing.SharingSecuritySystem
LongCounter - Class in ome.services.sessions.stats: Counter object which increments an internal long by some integer value, and according to some strategy publishes an InternalMessage subclass.
LongCounter(int) - Constructor for class ome.services.sessions.stats.LongCounter
LongSeqHelper - Class in ome.services.sharing.data
LongSeqHelper() - Constructor for class ome.services.sharing.data.LongSeqHelper
LongSeqHolder - Class in ome.services.sharing.data
LongSeqHolder() - Constructor for class ome.services.sharing.data.LongSeqHolder
LongSeqHolder(List<Long>) - Constructor for class ome.services.sharing.data.LongSeqHolder
lookup() - Method in class ome.services.eventlogs.EventLogQueue
lookup(long) - Method in class ome.services.procs.ProcessorSkeleton
lookup(String, Parameters) - Method in class ome.services.query.ClassQuerySource
lookup(String, Parameters) - Method in class ome.services.query.NullQuerySource
lookup(String, Parameters) - Method in class ome.services.query.QueryFactory
lookup(String, Parameters) - Method in class ome.services.query.QuerySource: map the queryID argument to some Query instance (including null).
lookup(String, Parameters) - Method in class ome.services.query.StringQuerySource
lookupExperimenter(String) - Method in class ome.logic.AdminImpl
lookupExperimenters() - Method in class ome.logic.AdminImpl
lookupGroup(String) - Method in class ome.logic.AdminImpl
lookupGroups() - Method in class ome.logic.AdminImpl
lookupLdapAuthExperimenter(long) - Method in class ome.logic.AdminImpl
lookupLdapAuthExperimenter(Long) - Method in class ome.logic.LdapImpl: Queries the LDAP server and returns the DN for the specified OMERO user ID.
lookupLdapAuthExperimenters() - Method in class ome.logic.AdminImpl
lookupLdapAuthExperimenters() - Method in class ome.logic.LdapImpl: Queries the LDAP server and returns the DN for all OMERO users that have the ldap flag enabled.
lookupPixels(long) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
lookupRenderingDef(long) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
lowestEntityId - Variable in class ome.services.pixeldata.PersistentEventLogLoader: The lowest entity id from a single dataPerUser set.
lsid(Class, long) - Method in class ome.services.db.DatabaseIdentity
lsid(Class, long, long) - Method in class ome.services.db.DatabaseIdentity
lsid(String, String) - Method in class ome.services.db.DatabaseIdentity
lsid(String, String, String) - Method in class ome.services.db.DatabaseIdentity
LsidUtils - Class in ome.tools.lsid
LsidUtils() - Constructor for class ome.tools.lsid.LsidUtils
LutProviderImpl - Class in ome.logic: Lookup table provider implementation.
LutProviderImpl(ScriptRepoHelper, ScriptFileType) - Constructor for class ome.logic.LutProviderImpl
lutReaders - Variable in class ome.logic.LutProviderImpl: Available readers, keyed off name.

M

mailSender - Variable in class ome.logic.AdminImpl
MailSender - Class in ome.services.mail: Basic bean with setter injection that can be used as a base class for other senders.
MailSender() - Constructor for class ome.services.mail.MailSender
mailSender - Variable in class ome.services.mail.MailUtil
MailUtil - Class in ome.services.mail: Methods for dealing with the preparation of JavaMail MIME messages.
MailUtil(String, JavaMailSender) - Constructor for class ome.services.mail.MailUtil
mailUtil - Variable in class ome.services.sharing.ShareBean
main(String[]) - Static method in class ome.security.auth.PasswordUtil: Main method which takes exactly one argument, passes it to PasswordUtil.preparePassword(String) and prints the results on System.out.
Main - Class in ome.services.fulltext: Commandline entry-point for various full text actions.
Main() - Constructor for class ome.services.fulltext.Main
main(String[]) - Static method in class ome.services.fulltext.Main
main(String[]) - Static method in class ome.services.graphs.GraphPathReport: Generate a Sphinx report of OMERO Hibernate entities.
main(String[]) - Static method in class ome.services.sharing.BlobShareStore
main(String[]) - Static method in class ome.services.util.JvmSettingsCheck
managedEvent(boolean, IObject, Details, Details, Details) - Method in class ome.security.basic.OmeroInterceptor
managedExternalInfo(boolean, IObject, Details, Details, Details) - Method in class ome.security.basic.OmeroInterceptor: Deprecated.
managedGroup(boolean, IObject, Details, Details, Details, BasicEventContext) - Method in class ome.security.basic.OmeroInterceptor
managedOwner(boolean, IObject, Details, Details, Details, BasicEventContext) - Method in class ome.security.basic.OmeroInterceptor
ManagedServiceFactory - Class in ome.tools.spring: subclass of ome.system.ServiceFactory which retrieves managed service-instances.
ManagedServiceFactory() - Constructor for class ome.tools.spring.ManagedServiceFactory
manager - Variable in class ome.services.util.ExecutionThread
ManualFlushHibernateTemplate - Class in ome.tools.spring
ManualFlushHibernateTemplate() - Constructor for class ome.tools.spring.ManualFlushHibernateTemplate
map(Map<String, List<Long>>) - Method in class ome.services.sharing.ShareBean
MapAnnotationSubethaListener - Class in ome.services.mail: Basic SimpleMessageListener which stores all received emails as MapAnnotation instances belong to root with the namespace MapAnnotationSubethaListener.NAMESPACE.
MapAnnotationSubethaListener(Executor, Principal) - Constructor for class ome.services.mail.MapAnnotationSubethaListener
MapAnnotationSubethaListener(Executor, String) - Constructor for class ome.services.mail.MapAnnotationSubethaListener
mapFromAttributes(Attributes) - Method in class ome.security.auth.GroupAttributeMapper
mapFromContext(Object) - Method in class ome.security.auth.GroupContextMapper
mapFromContext(Object) - Method in class ome.security.auth.OmeroModelContextMapper
mapFromContext(Object) - Method in class ome.security.auth.PersonContextMapper
markAndSweep() - Method in class ome.services.db.SelfCorrectingDataSource: First removes all entries in SelfCorrectingDataSource.errorTimes that are older than some given time and then uses the remaining number of errors to determine the backoff : (#^1/2)*1000 milliseconds.
matches(String, String) - Method in class ome.services.messages.EventLogsMessage
matches(File) - Method in class ome.services.scripts.RepoFile
maxFileSize - Variable in class ome.services.fulltext.FileParser
maxUserTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl
maxUserTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl
mayHaveMapProperties(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
mayHaveMapProperties(Class<? extends IObject>) - Method in interface ome.tools.hibernate.ExtendedMetadata: Check if an object of this class may have map properties.
member_of_groups - Static variable in class ome.security.basic.AllGroupsSecurityFilter
members - Variable in class ome.services.sharing.data.ShareData
members - Variable in class ome.services.sharing.data.ShareItem
MERGE_EVENT - Static variable in class ome.security.basic.MergeEventListener
mergedBatches - Variable in class ome.services.search.SearchValues
MergeEventListener - Class in ome.security.basic: responsible for responding to merge events.
MergeEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.MergeEventListener: main constructor.
message - Variable in exception ome.services.graphs.GraphException
message() - Method in class ome.services.sessions.stats.LongCounter
message() - Method in class ome.services.sessions.stats.MethodCounter
message() - Method in class ome.services.sessions.stats.ObjectsReadCounter
message() - Method in class ome.services.sessions.stats.ObjectsWrittenCounter
message() - Method in class ome.services.sessions.stats.SessionsCreatedCounter
metadata - Variable in class ome.logic.AbstractLevel2Service
MetadataImpl - Class in ome.logic: Implement the IMetadata I/F.
MetadataImpl() - Constructor for class ome.logic.MetadataImpl
methodCount() - Method in class ome.services.sessions.stats.DelegatingStats
methodCount() - Method in class ome.services.sessions.stats.NullSessionStats
methodCount() - Method in interface ome.services.sessions.stats.SessionStats
methodCount() - Method in class ome.services.sessions.stats.SimpleSessionStats
MethodCounter - Class in ome.services.sessions.stats: Counter for active methods for a given session.
MethodCounter(int) - Constructor for class ome.services.sessions.stats.MethodCounter
methodHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
methodIn() - Method in class ome.services.sessions.stats.DelegatingStats
methodIn() - Method in class ome.services.sessions.stats.NullSessionStats
methodIn() - Method in interface ome.services.sessions.stats.SessionStats
methodIn() - Method in class ome.services.sessions.stats.SimpleSessionStats
methodOut() - Method in class ome.services.sessions.stats.DelegatingStats
methodOut() - Method in class ome.services.sessions.stats.NullSessionStats
methodOut() - Method in interface ome.services.sessions.stats.SessionStats
methodOut() - Method in class ome.services.sessions.stats.SimpleSessionStats
methodSecurity - Variable in class ome.security.basic.BasicSecurityWiring
MethodSecurity - Interface in ome.security: Interface which allows security interceptors to check if a method should be executable for a given user.
MethodStatsMessage - Class in ome.services.messages.stats: Published when more than the specified number of active method calls is reached.
MethodStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.MethodStatsMessage
ModelObjectSequencer - Class in ome.services.graphs: Deprecated.
no longer used internally, replaced by GraphTraversal.orderFileDeletion()
ModelObjectSequencer() - Constructor for class ome.services.graphs.ModelObjectSequencer: Deprecated.
modificationCheck() - Method in class ome.services.scripts.ScriptRepoHelper: Checks if
modified - Variable in class ome.services.AbstractStatefulBean: True if any write operation took place on this bean.
modified() - Method in class ome.services.AbstractStatefulBean
modifiedStart - Variable in class ome.services.search.SearchValues
modifiedStop - Variable in class ome.services.search.SearchValues
more() - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader: Returns the number of classes which are still unprocessed as a proxy for how much is left to process.
more() - Method in class ome.services.eventlogs.AllEventsLogLoader
more() - Method in class ome.services.eventlogs.EventLogLoader: Should return an estimate of how many more EventLog instances are available for processing.
more() - Method in class ome.services.eventlogs.EventLogQueue: In general, EventLogQueue will intend to use much larger batch sizes, and so further loops should likely not be attempted.
more() - Method in class ome.services.eventlogs.PersistentEventLogLoader
moveToCommonSpace(IObject...) - Method in class ome.logic.AdminImpl
multicastEvent(ApplicationEvent) - Method in class ome.services.messages.GlobalMulticaster: Multicast only if this instance was the first created.
multicastEvent(ApplicationEvent, ResolvableType) - Method in class ome.services.messages.GlobalMulticaster
myFilterCondition() - Method in class ome.security.basic.AllGroupsSecurityFilter
myFilterCondition() - Method in class ome.security.basic.OneGroupSecurityFilter
MySeqGenerator - Class in ome.tools.hibernate: http://www.hibernate.org/296.html
MySeqGenerator() - Constructor for class ome.tools.hibernate.MySeqGenerator

N

NAME - Static variable in class ome.security.policy.BinaryAccessPolicy: This string can also be found in the Constants.ice file in the blitz package.
name - Variable in class ome.services.query.QueryParameterDef: name of this parameter.
name - Variable in class ome.services.scripts.RepoFile.FsFile
nameById(long) - Method in interface ome.security.auth.RoleProvider
nameById(long) - Method in class ome.security.auth.SimpleRoleProvider
NAMESPACE - Static variable in class ome.services.mail.MapAnnotationSubethaListener
neededRight(Class<?>, Class<?>) - Method in class ome.security.basic.OmeroInterceptor: The default right need for a linkage is Permissions.Right.WRITE.
needsSanityCheck() - Method in class ome.logic.RepositoryInfoImpl: Calculates based on the cached usage and the elapsed time whether or not a real RepositoryInfoImpl.sanityCheckRepository() should be calculated.
newEvent(Session, EventType, TokenHolder) - Method in class ome.security.basic.CurrentDetails
newlyEnabledFilters - Variable in class ome.services.query.Query: the set of filters that is being or has been enabled for this Query.
newTaskFor(Callable<T>) - Method in class ome.services.scheduler.ThreadPool: Overrides ThreadPoolExecutor to return our own instance of FutureTask so that we have a marker for when the background activity is completed in ThreadPool.afterExecute(Runnable, Throwable).
newTransientDetails(IObject) - Method in class ome.security.basic.BasicSecuritySystem
newTransientDetails(IObject) - Method in class ome.security.basic.OmeroInterceptor
newTransientDetails(IObject, Details) - Method in class ome.security.basic.OmeroInterceptor: Like OmeroInterceptor.newTransientDetails(IObject) but allows passing in a newDetails object with possibly preset values.
newTransientDetails(IObject) - Method in interface ome.security.SecuritySystem: creates a new secure details for transient entities.
newTransientDetails(IObject) - Method in class ome.security.SecuritySystemHolder
newTransientDetails(IObject) - Method in class ome.security.sharing.SharingSecuritySystem
NewUserGroupBean - Interface in ome.security.auth: Strategy for finding the appropriate groups for a given user in LDAP.
NewUserGroupOwnerBean - Interface in ome.security.auth: Strategy for finding the appropriate group owners for a given user in LDAP.
next() - Method in class ome.services.eventlogs.EventLogLoader: Returns the current EventLogLoader.log instance which may be loaded by a call to EventLogLoader.hasNext() if necessary.
next() - Method in class ome.services.eventlogs.EventLogQueue: Return a wrapped version of EventLogQueue.Data.next() which could possibly be null.
next() - Method in class ome.services.SearchBean
nextEventLog(long) - Method in class ome.services.eventlogs.EventLogLoader: Returns the EventLog with the next id after the given argument or null if none exists.
NodeProvider - Interface in ome.security: Provider for Node objects which is responsible for persisting and populating such entities.
NodeProviderInDb - Class in ome.security.basic: Provider for Node objects which is responsible for persisting and populating such entities.
NodeProviderInDb(String, Executor) - Constructor for class ome.security.basic.NodeProviderInDb
NodeProviderInMemory - Class in ome.security.basic: Provider for Node objects which is responsible for persisting and populating such entities.
NodeProviderInMemory(String) - Constructor for class ome.security.basic.NodeProviderInMemory
NodeProviderWrapper - Class in ome.security.basic: A node provider that offers a unified view of multiple underlying node providers.
NodeProviderWrapper(ReadOnlyStatus, List) - Constructor for class ome.security.basic.NodeProviderWrapper: Construct a new node provider.
norm(String) - Static method in class ome.services.scripts.RepoFile: Somewhat complicated method to turn any path into a unique like path rooted at "/".
not() - Method in class ome.services.SearchBean
notAnnotatedBy - Variable in class ome.services.search.SearchValues
notAnnotatedBy(Details) - Method in class ome.services.SearchBean
note() - Method in class ome.services.fulltext.FullTextIndexer2: Note which event log entries were processed.
noteDetails(Session, IObject, String, long) - Method in class ome.services.graphs.GraphPolicy: Any model object about which policy may be asked is first passed to GraphPolicy.noteDetails(Session, IObject, String, long) before GraphPolicy.review(Map, Details, Map, Set, boolean).
noteDetails(Session, IObject, String, long) - Method in interface ome.services.graphs.GraphPolicyRulePredicate: Once this instance is submitted to GraphPolicy.registerPredicate(GraphPolicyRulePredicate) then this method is called by GraphPolicy.noteDetails(org.hibernate.Session, IObject, String, long).
noteDetails(Session, IObject, String, long) - Method in class ome.services.graphs.GroupPredicate
noteDetails(Session, IObject, String, long) - Method in class ome.services.graphs.PermissionsPredicate
NoThumbnail(String) - Constructor for exception ome.services.ThumbnailCtx.NoThumbnail
notifications(String) - Method in class ome.services.sessions.SessionManagerImpl
notifyElementEvicted(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
notifyElementExpired(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
notifyElementPut(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
notifyElementRemoved(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
notifyElementUpdated(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
notifyMembersOfShare(long, String, String, boolean) - Method in class ome.services.sharing.ShareBean
notifyRemoveAll(Ehcache) - Method in class ome.services.sessions.state.CacheListener
notNullOrLikeOrEqual(QueryBuilder, String, Class, Object, boolean, boolean) - Static method in class ome.services.search.SearchAction
notNullOrLikeOrEqual(String, Class, Object, boolean, boolean) - Static method in class ome.services.search.SearchAction
notOwnedBy - Variable in class ome.services.search.SearchValues
notOwnedBy(Details) - Method in class ome.services.SearchBean
NS_COMMENT - Static variable in class ome.services.sharing.ShareBean
NS_ENABLED - Static variable in class ome.services.sharing.ShareBean
NSEXPERIMENTERPHOTO - Static variable in class ome.logic.AdminImpl
NULL_RENDERER - Static variable in class ome.services.RenderingBean: Message if the rendering engine is not ready.
NullEventHandler - Class in ome.security.basic: Provides only the bare minimum of functionality to allow methods to succeed.
NullEventHandler(SecuritySystem, SessionFactory) - Constructor for class ome.security.basic.NullEventHandler
nullProperties(String, String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor: Null the given property of the indicated instances.
NullQuerySource - Class in ome.services.query: always returns null for any id.
NullQuerySource() - Constructor for class ome.services.query.NullQuerySource
nullSafeGet(ResultSet, String[], Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
nullSafeGroupId(IObject) - Static method in class ome.tools.hibernate.HibernateUtils: returns the id of the group of this entity, or null if: (1) the object is null, (2) the Details is null, (3) the group is null.
nullSafeOwnerId(IObject) - Static method in class ome.tools.hibernate.HibernateUtils: returns the id of the owner of this entity, or null if: (1) the object is null, (2) the Details is null, (3) the owner is null.
nullSafeSet(PreparedStatement, Object, int) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
NullSessionStats - Class in ome.services.sessions.stats: Implementation of SessionStats which does nothing.
NullSessionStats() - Constructor for class ome.services.sessions.stats.NullSessionStats
numberOfSubtypes(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: returns the number of subtypes for iterating over this secondary array.
numThreads - Variable in class ome.services.pixeldata.PersistentEventLogLoader

O

Obj - Class in ome.services.sharing.data
Obj() - Constructor for class ome.services.sharing.data.Obj
Obj(String, long) - Constructor for class ome.services.sharing.data.Obj
objectList - Variable in class ome.services.sharing.data.ShareData
ObjectMailSender - Class in ome.services.mail: When an EventLogMessage of the specified type and kind is received, an email is sent to all users which are returned by a given query.
ObjectMailSender() - Constructor for class ome.services.mail.ObjectMailSender
objectMap - Variable in class ome.services.sharing.data.ShareData
objects - Variable in class ome.services.messages.ReindexMessage
ObjectsReadCounter - Class in ome.services.sessions.stats: Counter for all the objects read in a session.
ObjectsReadCounter(int) - Constructor for class ome.services.sessions.stats.ObjectsReadCounter
objectsReadHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
ObjectsReadStatsMessage - Class in ome.services.messages.stats: Published when some limit in user/group/session activity has been reached.
ObjectsReadStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.ObjectsReadStatsMessage
ObjectsWrittenCounter - Class in ome.services.sessions.stats: Counter for all the objects read in a session.
ObjectsWrittenCounter(int) - Constructor for class ome.services.sessions.stats.ObjectsWrittenCounter
objectsWrittenHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
ObjectsWrittenStatsMessage - Class in ome.services.messages.stats
ObjectsWrittenStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.ObjectsWrittenStatsMessage
ObjHolder - Class in ome.services.sharing.data
ObjHolder() - Constructor for class ome.services.sharing.data.ObjHolder
ObjHolder(Obj) - Constructor for class ome.services.sharing.data.ObjHolder
ObjPrx - Interface in ome.services.sharing.data
ObjPrxHelper - Class in ome.services.sharing.data: Provides type-specific helper functions.
ObjPrxHelper() - Constructor for class ome.services.sharing.data.ObjPrxHelper
ObjPrxHolder - Class in ome.services.sharing.data
ObjPrxHolder() - Constructor for class ome.services.sharing.data.ObjPrxHolder
ObjPrxHolder(ObjPrx) - Constructor for class ome.services.sharing.data.ObjPrxHolder
ObjSeqHelper - Class in ome.services.sharing.data
ObjSeqHelper() - Constructor for class ome.services.sharing.data.ObjSeqHelper
ObjSeqHolder - Class in ome.services.sharing.data
ObjSeqHolder() - Constructor for class ome.services.sharing.data.ObjSeqHolder
ObjSeqHolder(List<Obj>) - Constructor for class ome.services.sharing.data.ObjSeqHolder
obToImageCache - Variable in class ome.services.sharing.BlobShareStore
ome.api.local - package ome.api.local: Non-client service API for OMERO
ome.formats - package ome.formats
ome.formats.importer.util - package ome.formats.importer.util
ome.logic - package ome.logic: The central repository of implementations which will be accessible through this server.
ome.security - package ome.security: JBoss and OMERO security handling
ome.security.auth - package ome.security.auth
ome.security.auth.providers - package ome.security.auth.providers
ome.security.basic - package ome.security.basic: Basic OMERO security contextual classes
ome.security.policy - package ome.security.policy: Extensible service and security policies which can influence whether a user, group, or other agent can perform a certain action.
ome.security.sharing - package ome.security.sharing
ome.services - package ome.services: Base services package for OMERO API services
ome.services.db - package ome.services.db
ome.services.delete - package ome.services.delete: Implementations of the ome.api.IDelete service.
ome.services.delete.files - package ome.services.delete.files
ome.services.eventlogs - package ome.services.eventlogs
ome.services.fulltext - package ome.services.fulltext: All necessary classes for background indexing of metadata and attached binary files.
ome.services.fulltext.bridges - package ome.services.fulltext.bridges: Custom FieldBridge implementations which can be configured to be run on each indexing activity.
ome.services.graphs - package ome.services.graphs: Server classes for handling complicated graphs of model objects.
ome.services.mail - package ome.services.mail: General mail services.
ome.services.messages - package ome.services.messages: Message implementations used throughout the server for internal communication.
ome.services.messages.stats - package ome.services.messages.stats
ome.services.pixeldata - package ome.services.pixeldata
ome.services.procs - package ome.services.procs: Internal process and process management
ome.services.procs.scripts - package ome.services.procs.scripts: Script processor infrastructure.
ome.services.projection - package ome.services.projection
ome.services.query - package ome.services.query: facilitates the creation of Hibernate Queries and Criteria.
ome.services.scheduler - package ome.services.scheduler
ome.services.scripts - package ome.services.scripts
ome.services.search - package ome.services.search: Internal search implementation classes.
ome.services.sessions - package ome.services.sessions
ome.services.sessions.events - package ome.services.sessions.events
ome.services.sessions.state - package ome.services.sessions.state
ome.services.sessions.stats - package ome.services.sessions.stats
ome.services.sharing - package ome.services.sharing
ome.services.sharing.data - package ome.services.sharing.data
ome.services.util - package ome.services.util: Helper classes to support OMERO service beans
ome.tools - package ome.tools: OMERO Server Utility and Spring/Hibernate Tools
ome.tools.hibernate - package ome.tools.hibernate: Hibernate specific tools for the OMERO Server
ome.tools.lsid - package ome.tools.lsid: Life Science Identifier (LSID) tools
ome.tools.spring - package ome.tools.spring: OMERO Server tools specific to Spring
OMERO_TABLE - Variable in class ome.services.fulltext.bridges.TablesBridge: Deprecated.

Mimetype set on OriginalFile.mimetype (or in previous version, OriginalFile.format.value).
omeroDataDir - Variable in class ome.services.OmeroFilePathResolver: The server's OMERO data directory.
OmeroFilePathResolver - Class in ome.services: OMERO server based resolver for file paths.
OmeroFilePathResolver(SqlAction, String) - Constructor for class ome.services.OmeroFilePathResolver: Constructor.
OmeroInterceptor - Class in ome.security.basic: implements Interceptor for controlling various aspects of the Hibernate runtime.
OmeroInterceptor(Roles, SystemTypes, ExtendedMetadata, CurrentDetails, TokenHolder, SessionStats, LightAdminPrivileges, SqlAction, Set<String>, Set<String>) - Constructor for class ome.security.basic.OmeroInterceptor
OMEROMetadataStore - Class in ome.formats: An OMERO metadata store.
OMEROMetadataStore() - Constructor for class ome.formats.OMEROMetadataStore: Empty constructor for testing purposes.
OMEROMetadataStore(ServiceFactory, SqlAction) - Constructor for class ome.formats.OMEROMetadataStore: Creates a new instance.
OmeroModelContextMapper - Class in ome.security.auth: Parent class for any OMERO model-to-LDAP mappers.
OmeroModelContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.OmeroModelContextMapper
onApplicationEvent(LoginAttemptMessage) - Method in class ome.security.auth.LoginAttemptListener
onApplicationEvent(EventLogMessage) - Method in class ome.security.basic.BasicSecuritySystem
onApplicationEvent(ContextMessage) - Method in class ome.security.basic.EventHandler: If a ContextMessage is received then we need to either add a ContextMessage.Push login to the stack or ContextMessage.Pop remove one.
onApplicationEvent(UserSignalMessage) - Method in class ome.services.db.SelfCorrectingDataSource: Handles the USR1 posix signal by calling close on the underlying data source via reflection.
onApplicationEvent(ApplicationEvent) - Method in class ome.services.eventlogs.EventLogLoader
onApplicationEvent(ApplicationEvent) - Method in class ome.services.eventlogs.EventLogQueue
onApplicationEvent(ApplicationEvent) - Method in class ome.services.fulltext.ParserSession: Deprecated.
onApplicationEvent(ApplicationEvent) - Method in class ome.services.fulltext.PersistentEventLogLoader: Deprecated.
onApplicationEvent(LoginAttemptMessage) - Method in class ome.services.mail.FailedLoginMailSender
onApplicationEvent(EventLogsMessage) - Method in class ome.services.mail.ObjectMailSender
onApplicationEvent(ShutdownMessage) - Method in class ome.services.mail.ServerDownMailSender
onApplicationEvent(MissingPyramidMessage) - Method in class ome.services.pixeldata.PixelDataThread: Called in the main server (Blitz-0) in order to create a PIXELDATA EventLog which will get processed by PixelData-0.
onApplicationEvent(ContextRefreshedEvent) - Method in class ome.services.scheduler.SchedulerFactoryBean
onApplicationEvent(ApplicationEvent) - Method in class ome.services.sessions.SessionManagerImpl
onApplicationEvent(ApplicationEvent) - Method in class ome.services.util.ServiceHandler
onApplicationEvent(ContextRefreshedEvent) - Method in class ome.tools.spring.OnContextRefreshedEventListener
onCollectionRecreate(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
onCollectionRemove(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
onCollectionUpdate(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
OnContextRefreshedEventListener - Class in ome.tools.spring: ApplicationListener which only listens for ContextRefreshedEvent and only responds to the first one.
OnContextRefreshedEventListener() - Constructor for class ome.tools.spring.OnContextRefreshedEventListener
OnContextRefreshedEventListener(boolean, int) - Constructor for class ome.tools.spring.OnContextRefreshedEventListener
onDelete(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: default logic
onDiskCache(String) - Method in interface ome.services.sessions.SessionManager: Returns after possibly creating an on-disk cache which can be used throughout the session.
onDiskCache(String) - Method in class ome.services.sessions.SessionManagerImpl
onDiskCache(String) - Method in class ome.services.sessions.state.SessionCache
onegroup - Variable in class ome.security.SecurityFilterHolder
OneGroupSecurityFilter - Class in ome.security.basic: overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.
OneGroupSecurityFilter() - Constructor for class ome.security.basic.OneGroupSecurityFilter: Default constructor which calls all the necessary setters for this FactoryBean.
OneGroupSecurityFilter(Roles) - Constructor for class ome.security.basic.OneGroupSecurityFilter
onExecutionException(ExecutionException) - Method in class ome.services.pixeldata.PixelDataThread: Basic handling just logs at ERROR level.
onFlushDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: calls back to BasicSecuritySystem.checkManagedDetails(IObject, Details) for properly setting Details.
onLoad(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: default logic.
onlyAnnotatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
onlyAnnotatedBy(Details) - Method in class ome.services.SearchBean
onlyAnnotatedWith - Variable in class ome.services.search.SearchValues
onlyAnnotatedWith(Class...) - Method in class ome.services.SearchBean
onlyCreatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
onlyIds - Variable in class ome.services.search.SearchValues
onlyIds(Long...) - Method in class ome.services.SearchBean
onlyModifiedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
onlyOwnedBy(Details) - Method in class ome.services.SearchBean
onlyPermissionsChanged(Details, Details) - Static method in class ome.tools.hibernate.HibernateUtils
onlyType(Class<T>) - Method in class ome.services.SearchBean
onlyTypes - Variable in class ome.services.search.SearchValues
onlyTypes(Class<T>...) - Method in class ome.services.SearchBean
onMerge(MergeEvent) - Method in class ome.security.basic.MergeEventListener
onMerge(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
onPostDelete(PostDeleteEvent) - Method in class ome.security.ACLEventListener: unused
onPostDelete(PostDeleteEvent) - Method in class ome.security.basic.EventLogListener
onPostInsert(PostInsertEvent) - Method in class ome.security.ACLEventListener: unused
onPostInsert(PostInsertEvent) - Method in class ome.security.basic.EventLogListener
onPostLoad(PostLoadEvent) - Method in class ome.security.ACLEventListener: catches all load events after the fact, and tests the current users permissions to read that object.
onPostUpdate(PostUpdateEvent) - Method in class ome.security.ACLEventListener: unused
onPostUpdate(PostUpdateEvent) - Method in class ome.security.basic.EventLogListener
onPreDelete(PreDeleteEvent) - Method in class ome.security.ACLEventListener
onPreInsert(PreInsertEvent) - Method in class ome.security.ACLEventListener
onPreLoad(PreLoadEvent) - Method in class ome.security.ACLEventListener: unused
onPrepareStatement(String) - Method in class ome.security.basic.OmeroInterceptor
onPreUpdate(PreUpdateEvent) - Method in class ome.security.ACLEventListener
onPreUpdate(PreUpdateEvent) - Method in class ome.security.basic.UpdateEventListener: updates the update event field of an IObject instance.
onRefresh(RefreshEvent) - Method in class ome.tools.hibernate.ReloadingRefreshEventListener
onRefresh(RefreshEvent, Map) - Method in class ome.tools.hibernate.ReloadingRefreshEventListener
onSave(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: calls back to BasicSecuritySystem.newTransientDetails(IObject) for properly setting Details
onSaveOrUpdate(SaveOrUpdateEvent) - Method in class ome.security.basic.SaveEventListener
optimize() - Method in class ome.services.fulltext.FullTextIndexer2: Defragment the search index.
optional - Variable in class ome.services.query.QueryParameterDef: whether or not this QueryParameter can be omitted or its value null.
optlock - Variable in class ome.services.sharing.data.ShareData
or() - Method in class ome.services.SearchBean
or(String) - Method in class ome.tools.hibernate.QueryBuilder: Appends "or" plus your string unless this is the first where-spec in which case it is simply appended.
order(String, boolean) - Method in class ome.tools.hibernate.QueryBuilder
orderBy - Variable in class ome.services.search.SearchValues
orderByAscending(String) - Static method in class ome.services.search.SearchAction
orderByPath(String) - Static method in class ome.services.search.SearchAction
OrgUnitNewUserGroupBean - Class in ome.security.auth: Handles the ":ou:" specifier from omero-server.properties by adding the user to a group named by the final organizational unit.
OrgUnitNewUserGroupBean(DistinguishedName) - Constructor for class ome.security.auth.OrgUnitNewUserGroupBean
OriginalFileDeletions - Class in ome.services.delete.files: Deletes all repository files immediately.
OriginalFileDeletions(AbstractFileSystemService, Set<Long>, OmeroContext) - Constructor for class ome.services.delete.files.OriginalFileDeletions
orphan - Variable in class ome.services.graphs.GraphPolicy.Details: the current orphan state of the object, may be mutated by GraphPolicy.review(Map, Details, Map, Set, boolean); applies only if GraphPolicy.Details.action is GraphPolicy.Action.EXCLUDE
osf - Variable in class ome.logic.AdminImpl
outputEnvironment(String) - Method in interface ome.services.sessions.SessionManager: Returns a copy of the output environment.
outputEnvironment(String) - Method in class ome.services.sessions.SessionManagerImpl
override(String[], Object) - Method in class ome.security.basic.EventListenersFactoryBean: calls override for each key
override(String, Object) - Method in class ome.security.basic.EventListenersFactoryBean: first re-initializes the list for key, and then adds object
overrides() - Method in class ome.security.basic.EventListenersFactoryBean
own(String) - Method in class ome.services.db.DatabaseIdentity
ownedBy - Variable in class ome.services.search.SearchValues
owner - Variable in class ome.services.sharing.data.ShareData
ownerId - Variable in class ome.services.graphs.GraphPolicy.Details: the ID of the object's Experimenter, or null if the object does not have an owner
ownerOfGroups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in interface ome.security.auth.NewUserGroupOwnerBean
ownerOfGroups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.QueryNewUserGroupBean
ownerOrGroup(Class, Criteria) - Method in class ome.services.search.SearchAction
ownerOrGroup(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction
ownerOrGroupFilters(Session, String[], String[]) - Method in class ome.services.query.Query: standard filter used by many subclasses which uses the Parameters.isExperimenter() and Parameters.isGroup() booleans to see if a filter should be turned on.

P

param(int, Object) - Method in class ome.tools.hibernate.QueryBuilder
param(String, Object) - Method in class ome.tools.hibernate.QueryBuilder
paramList(String, Collection) - Method in class ome.tools.hibernate.QueryBuilder
params - Variable in class ome.services.query.Query: container of QueryParameter instances.
params(Parameters) - Method in class ome.tools.hibernate.QueryBuilder
parse(String[]) - Static method in class ome.logic.HardWiredInterceptor: Produces a List of instantiated interceptors from a list of HardWiredInterceptor subclass names.
parse(String) - Method in class ome.security.auth.LdapConfig
parse(OriginalFile, OriginalFilesService, Map<String, FileParser>) - Method in class ome.services.fulltext.BridgeHelper: Deprecated.

Attempts to parse the given OriginalFile.
parse(File) - Method in class ome.services.fulltext.FileParser: Uses FileParser.doParse(File) to create manageable chunks of a file for indexing.
parse(String[], String[], String[]) - Static method in class ome.services.search.SomeMustNone
parse(ShareData) - Method in class ome.services.sharing.ShareStore
parse(long, byte[]) - Method in class ome.services.sharing.ShareStore
parseField(String) - Static method in class ome.tools.lsid.LsidUtils: takes a field identifier as code-generated in each IObject class and produces a back-end useable name.
parseFilter(Criteria, Filter) - Method in class ome.logic.QueryImpl: Responsible for applying the information provided in a Filter to a Criteria instance.
ParserOpenFileMessage - Class in ome.services.messages: A trivial copy of RegisterServiceCleanupMessage with a different name so that we can catch files opened during search indexing and close them at the end of parsing.
ParserOpenFileMessage(Object, Object) - Constructor for class ome.services.messages.ParserOpenFileMessage
parsers - Variable in class ome.services.fulltext.FullTextBridge: Deprecated.
parserSession - Variable in class ome.services.fulltext.FullTextIndexer: Deprecated.
ParserSession - Class in ome.services.fulltext: Deprecated.
ParserSession() - Constructor for class ome.services.fulltext.ParserSession: Deprecated.
parseRules(GraphPathBean, Collection<GraphPolicyRule>) - Static method in class ome.services.graphs.GraphPolicyRule: Convert the text-based rules as specified in the configuration metadata into a policy applicable in model object graph traversal.
parseStream(InputStream) - Method in class ome.services.mail.MapAnnotationSubethaListener
parseType(String) - Static method in class ome.tools.lsid.LsidUtils: takes a field identifier as code-generated in each IObject class and produces a back-end useable type name.
passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.AllGroupsSecurityFilter: tests that the Details argument passes the security test that this filter defines.
passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.LightAdminPrivilegesSecurityFilter
passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.OneGroupSecurityFilter: tests that the Details argument passes the security test that this filter defines.
passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.SharingSecurityFilter
passesFilter(Session, Details, EventContext) - Method in interface ome.security.SecurityFilter: tests that the Details argument passes the security test that this filter defines.
passesFilter(Session, Details, EventContext) - Method in class ome.security.SecurityFilterHolder
passivate() - Method in class ome.services.JobBean: Does nothing.
passivate() - Method in class ome.services.RawFileBean
passivate() - Method in class ome.services.RawPixelsBean
passivate() - Method in class ome.services.RenderingBean
passivate() - Method in class ome.services.SearchBean
passivate() - Method in class ome.services.ThumbnailBean
passivationNotAllowed() - Method in class ome.services.util.BeanHelper
PasswordChangeException - Exception in ome.security.auth: Caught exception thrown from PasswordProvider.changePassword(String, String) to allow read-only implementations to refuse an action.
PasswordChangeException(String) - Constructor for exception ome.security.auth.PasswordChangeException
passwordDigest(String) - Method in class ome.security.auth.PasswordUtil: Creates an MD5 hash of the given clear text and base64 encodes it.
passwordDigest(Long, String, boolean) - Method in class ome.security.auth.PasswordUtil
passwordProvider - Variable in class ome.logic.AdminImpl
PasswordProvider - Interface in ome.security.auth: Authentication interface responsible for checking and changing passwords.
PasswordProviders - Class in ome.security.auth: Composite class which delegates to each of the configured providers in turn.
PasswordProviders(PasswordProvider...) - Constructor for class ome.security.auth.PasswordProviders
PasswordProviders(AtomicBoolean, PasswordProvider...) - Constructor for class ome.security.auth.PasswordProviders
passwordUtil - Variable in class ome.logic.AdminImpl
PasswordUtil - Class in ome.security.auth: Static methods for dealing with password hashes and the "password" table.
PasswordUtil(SqlAction) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil(SqlAction, boolean) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil(SqlAction, Charset) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil(SqlAction, boolean, Charset) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil(SqlAction, Roles, boolean) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil(SqlAction, Roles, boolean, Charset) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil.METHOD - Enum in ome.security.auth
PasswordUtility - Interface in ome.security.auth: Extension interface to PasswordProvider for methods which may or may not be available from a provider implementation.
patch(Object) - Method in class ome.services.sharing.data.ObjHolder
patch(Object) - Method in class ome.services.sharing.data.ShareDataHolder
patch(Object) - Method in class ome.services.sharing.data.ShareItemHolder
path - Variable in class ome.services.scripts.RepoFile.FsFile
PdfParser - Class in ome.services.fulltext: FileParser for "application/pdf" files using PDFBox.
PdfParser() - Constructor for class ome.services.fulltext.PdfParser
permissions(Class<T>) - Method in class ome.logic.TypesImpl
permissions - Variable in class ome.services.graphs.GraphPolicy.Details: the current permissions on the object
PermissionsPredicate - Class in ome.services.graphs: A predicate that allows perms=rwr--- and similar to be used in graph policy rule matches.
PermissionsPredicate() - Constructor for class ome.services.graphs.PermissionsPredicate
PerSessionStats - Class in ome.services.sessions.stats: Delegates to a SessionStats which is acquired on every method invocation.
PerSessionStats(CurrentDetails) - Constructor for class ome.services.sessions.stats.PerSessionStats
PersistentEventLogLoader - Class in ome.services.eventlogs: EventLogLoader implementation which keeps tracks of the last EventLog instance, and always provides the next unindexed instance.
PersistentEventLogLoader() - Constructor for class ome.services.eventlogs.PersistentEventLogLoader
PersistentEventLogLoader - Class in ome.services.fulltext: Deprecated.
PersistentEventLogLoader() - Constructor for class ome.services.fulltext.PersistentEventLogLoader: Deprecated.
PersistentEventLogLoader - Class in ome.services.pixeldata: EventLogLoader implementation which keeps tracks of the last EventLog instance, and always provides the next unindexed instance.
PersistentEventLogLoader(String, int) - Constructor for class ome.services.pixeldata.PersistentEventLogLoader
PersonContextMapper - Class in ome.security.auth: Specialized OME Experimenter context mapper.
PersonContextMapper(LdapConfig, String) - Constructor for class ome.security.auth.PersonContextMapper
PersonContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.PersonContextMapper
PerThreadStats - Class in ome.services.sessions.stats: Delegates to a SessionStats which is acquired on every method invocation.
PerThreadStats(CurrentDetails) - Constructor for class ome.services.sessions.stats.PerThreadStats
PixelDataHandler - Class in ome.services.pixeldata: Simple action which can be done in an asynchronous thread in order to process PIXELDATA event logs.
PixelDataHandler(EventLogLoader, PixelsService) - Constructor for class ome.services.pixeldata.PixelDataHandler
PixelDataThread - Class in ome.services.pixeldata
PixelDataThread(SessionManager, Executor, PixelDataHandler, String) - Constructor for class ome.services.pixeldata.PixelDataThread: Deprecated.
PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread: Deprecated.
PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread: Deprecated.
PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread: Deprecated.
PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int, Metrics, ReadOnlyStatus) - Constructor for class ome.services.pixeldata.PixelDataThread: Calculates PixelDataThread.performProcessing based on the existence of the "pixelDataTrigger" and passes all parameters to the main ctor.
PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread: Deprecated.
PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics, ReadOnlyStatus) - Constructor for class ome.services.pixeldata.PixelDataThread: Deprecated.
PixelDataThread(boolean, SessionManager, Executor, PixelDataHandler, Principal, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread: Calls main constructor with NullMetrics.
PixelDataThread(boolean, SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread: Calls main constructor with read-only status being all read-write.
PixelDataThread(boolean, SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics, ReadOnlyStatus) - Constructor for class ome.services.pixeldata.PixelDataThread: Main constructor.
pixelsData - Variable in class ome.logic.RenderingSettingsImpl: Reference to the service used to retrieve the pixels data.
PixelsFileDeletions - Class in ome.services.delete.files: Registers the given file paths as well as other Pixel-related files like Pyramids for later deletion via AbstractFileDeletions.deleteLocal().
PixelsFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.PixelsFileDeletions
PixelsImpl - Class in ome.logic: implementation of the Pixels service interface.
PixelsImpl() - Constructor for class ome.logic.PixelsImpl
pixelsMetadata - Variable in class ome.logic.RenderingSettingsImpl: Reference to the service used to retrieve the pixels metadata.
pixelsService - Variable in class ome.services.pixeldata.PixelDataHandler
pixelsService - Variable in class ome.services.projection.ProjectionBean: Reference to the service used to retrieve the pixels data.
pixToImageCache - Variable in class ome.services.sharing.BlobShareStore
planOperation(SetMultimap<String, Long>, boolean, boolean) - Method in class ome.services.graphs.GraphTraversal: Traverse model object graph to determine steps for the proposed operation.
planOperation(Collection<? extends IObject>, boolean, boolean) - Method in class ome.services.graphs.GraphTraversal: Traverse model object graph to determine steps for the proposed operation.
PLATEIMAGES_QUERY - Static variable in class ome.services.delete.DeleteBean
PojosFindAnnotationsQueryDefinition - Class in ome.services.query
PojosFindAnnotationsQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosFindAnnotationsQueryDefinition
PojosFindHierarchiesQueryDefinition - Class in ome.services.query: walks up the hierarchy tree starting at Image nodes while fetching various information.
PojosFindHierarchiesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosFindHierarchiesQueryDefinition
PojosGetImagesByOptionsQueryDefinition - Class in ome.services.query
PojosGetImagesByOptionsQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetImagesByOptionsQueryDefinition
PojosGetImagesQueryDefinition - Class in ome.services.query
PojosGetImagesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetImagesQueryDefinition
PojosGetUserImagesQueryDefinition - Class in ome.services.query
PojosGetUserImagesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetUserImagesQueryDefinition
PojosImpl - Class in ome.logic: implementation of the Pojos service interface.
PojosImpl() - Constructor for class ome.logic.PojosImpl
PojosLoadHierarchyQueryDefinition - Class in ome.services.query
PojosLoadHierarchyQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosLoadHierarchyQueryDefinition
Policy - Interface in ome.security.policy: Strategy to permit the flexible restriction of certain actions throughout OMERO.
policyService - Variable in class ome.security.basic.BasicACLVoter
policyService - Variable in class ome.security.basic.BasicSecuritySystem
PolicyService - Interface in ome.security.policy: Internal service containing a number of configured Policy instances.
poll() - Method in class ome.services.search.IndexWatcher: Check for new objects to index and for progress with indexing past objects.
Pop(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage.Pop
pop() - Method in class ome.services.pixeldata.PersistentEventLogLoader
pop(List<IObject>) - Method in class ome.services.SearchBean: Wrapper method which should be called on all results for the user.
populateMinMax(double[][][]) - Method in class ome.formats.OMEROMetadataStore: Synchronize the minimum and maximum intensity values with those specified by the client and save them in the DB.
postFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor
postProcess(IObject) - Method in interface ome.security.ACLVoter: Gives the ACLVoter instance a chance to act on the IObject after the transaction but before finishing the AOP stack.
postProcess(IObject) - Method in class ome.security.basic.BasicACLVoter
postProcess(IObject) - Method in class ome.security.CompositeACLVoter
postProcess(IObject) - Method in class ome.security.sharing.SharingACLVoter
postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ome.services.util.BeanInstantiationGuard
predicates - Variable in class ome.services.graphs.GraphPolicy: The predicates that have been registered with GraphPolicy.registerPredicate(GraphPolicyRulePredicate).
preFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor
prepare() - Method in class ome.services.fulltext.FullTextIndexer2: Query the database for new event log entries indicating model objects to process.
prepare(Set<Long>) - Method in class ome.services.RawPixelsBean
prepareLookups(String, String, Collection<Long>) - Method in class ome.services.query.HierarchyNavigator: Batch bulk database queries to prime the cache for HierarchyNavigator.doLookup(String, String, Long).
prepareLookups(T, Collection<E>) - Method in class ome.services.query.HierarchyNavigatorWrap: Batch bulk database queries to prime the cache for HierarchyNavigatorWrap.doLookup(Object, Object).
preparePassword(String) - Method in class ome.security.auth.PasswordUtil
preparePassword(Long, String, boolean) - Method in class ome.security.auth.PasswordUtil
prepareReload() - Method in class ome.services.sessions.SessionManagerImpl
prepareSaltedPassword(Long, String) - Method in class ome.security.auth.PasswordUtil
prepend(String, Object...) - Method in class ome.security.basic.EventListenersFactoryBean: adds the objects to the existing list identified by key.
previewImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean: This uses DeleteBean.IMAGE_QUERY to load all the subordinate metadata of the Image which will be deleted.
principal() - Method in class ome.security.basic.NodeProviderInDb
principal() - Method in class ome.security.basic.NodeProviderInMemory
principal() - Method in class ome.security.basic.NodeProviderWrapper
principal() - Method in interface ome.security.NodeProvider: Retrieves the current active principal.
principal - Variable in class ome.services.sessions.SessionManager.CreationRequest
principal - Variable in class ome.services.util.ExecutionThread
principal() - Method in class ome.services.util.Executor.Impl
principal() - Method in interface ome.services.util.Executor: Returns a Principal representing your current session or null, if none is active.
principalHolder - Variable in class ome.security.basic.BasicSecurityWiring
PrincipalHolder - Interface in ome.security.basic: Stack of active Principal instances.
principalHolder - Variable in class ome.services.sessions.SessionManagerImpl
principalHolder - Variable in class ome.services.util.Executor.Impl
process(Long, ServiceFactory, Session) - Method in class ome.services.pixeldata.PixelDataHandler: Here we assume that our log loader will only return us the proper types, since we are using the specific type defined in this package.
Process - Interface in ome.services.procs
process(long) - Method in interface ome.services.procs.Processor
process(long) - Method in class ome.services.procs.ProcessorSkeleton
process(Job) - Method in class ome.services.procs.ProcessorSkeleton
ProcessCallback - Interface in ome.services.procs
processCancelled(Process) - Method in class ome.services.JobBean
processCancelled(Process) - Method in interface ome.services.procs.ProcessCallback
processFinished(Process) - Method in class ome.services.JobBean
processFinished(Process) - Method in interface ome.services.procs.ProcessCallback
processInstances(String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor: Process the given instances.
ProcessManager - Class in ome.services.procs
ProcessManager(SessionManager, SecuritySystem, Executor, Processor...) - Constructor for class ome.services.procs.ProcessManager: main constructor which takes a non-null array of Processor instances as its only argument.
ProcessManager.Work - Class in ome.services.procs: Task performed by the ProcessManager on each invocation of ExecutionThread.run().
processor() - Method in interface ome.services.procs.Process
Processor - Interface in ome.services.procs
processor() - Method in class ome.services.procs.ProcessSkeleton
processors - Variable in class ome.services.procs.ProcessManager.Work: processors available for processing.
ProcessorSkeleton - Class in ome.services.procs
ProcessorSkeleton() - Constructor for class ome.services.procs.ProcessorSkeleton
ProcessSkeleton - Class in ome.services.procs
ProcessSkeleton(Processor) - Constructor for class ome.services.procs.ProcessSkeleton
processTargets() - Method in class ome.services.graphs.GraphTraversal: Prepare to process the targeted model objects.
procMap - Variable in class ome.services.procs.ProcessManager.Work: Map of all active processes.
projection(String, Parameters) - Method in class ome.logic.QueryImpl
ProjectionBean - Class in ome.services.projection: Implements projection functionality for Pixels sets as declared in IProjection.
ProjectionBean() - Constructor for class ome.services.projection.ProjectionBean
projectPixels(long, PixelsType, int, int, int, List<Integer>, int, int, int, String) - Method in class ome.services.projection.ProjectionBean
projectStack(long, PixelsType, int, int, int, int, int, int) - Method in class ome.services.projection.ProjectionBean
ProjectWithImageNameBridge - Class in ome.services.fulltext.bridges: Deprecated.
ProjectWithImageNameBridge() - Constructor for class ome.services.fulltext.bridges.ProjectWithImageNameBridge: Deprecated.
propagateHiddenValues(IObject, IObject) - Method in class ome.security.basic.MergeEventListener
ProxyCleanupFilter - Class in ome.tools.hibernate: removes all proxies from a return graph to prevent ClassCastExceptions and Session Closed exceptions.
ProxyCleanupFilter() - Constructor for class ome.tools.hibernate.ProxyCleanupFilter: Passes nulls to ProxyCleanupFilter.ProxyCleanupFilter(ACLVoter, CurrentDetails) such that all restricted objects will be unloaded.
ProxyCleanupFilter(ACLVoter, CurrentDetails) - Constructor for class ome.tools.hibernate.ProxyCleanupFilter: Construct a proxy cleanup filter that checks the security restrictions on certain objects.
ProxyCleanupFilter.Interceptor - Class in ome.tools.hibernate: wraps a filter for each invocation
proxyNames - Variable in class ome.services.util.Executor.Impl
ProxySafeFilter - Class in ome.tools.hibernate: extension to ContextFilter to check for uninitialized Hibernate proxies before stepping into an entity or collection.
ProxySafeFilter() - Constructor for class ome.tools.hibernate.ProxySafeFilter
publisher - Variable in class ome.services.fulltext.BridgeHelper: Deprecated.
publisher - Variable in class ome.services.sessions.stats.CounterFactory
purge() - Method in class ome.services.fulltext.FullTextIndexer2: Purge a batch of model objects.
Push(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage.Push
put(String, String) - Method in class ome.security.auth.AttributeSet
put(String, Object[]) - Method in class ome.security.basic.EventListenersFactoryBean: replaces the key with the provided objects or an empty list if none provided
putSession(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache: Puts a session blindly into the context.
putStatus(MethodInvocation, SessionStatus) - Method in class ome.tools.hibernate.SessionHandler

Q

query() - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
query() - Method in class ome.services.eventlogs.AllEventsLogLoader
query - Variable in class ome.services.eventlogs.EventLogLoader: Query string to be kept in sync with EventLogLoader.excludes.
query() - Method in class ome.services.eventlogs.EventLogLoader
query() - Method in class ome.services.eventlogs.EventLogQueue
query() - Method in class ome.services.eventlogs.PersistentEventLogLoader
query() - Method in class ome.services.pixeldata.PersistentEventLogLoader: Uses data from the PersistentEventLogLoader.dataPerUser "queue" to allow new requests to be processed even if one user adds a large number of PIXELDATA events.
Query<T> - Class in ome.services.query: base Query type to facilitate the creation of ORM queries.
Query(Definitions, Parameters) - Constructor for class ome.services.query.Query: main constructor used by subclasses.
query(Session) - Method in class ome.tools.hibernate.QueryBuilder
QueryBuilder - Class in ome.tools.hibernate: Very thin wrapper around a StringBuilder to generate HQL queries.
QueryBuilder() - Constructor for class ome.tools.hibernate.QueryBuilder
QueryBuilder(boolean) - Constructor for class ome.tools.hibernate.QueryBuilder: Whether Session.createSQLQuery(String) should be used or not during QueryBuilder.query(Session) and similar.
QueryBuilder(int) - Constructor for class ome.tools.hibernate.QueryBuilder
QueryConstraints - Class in ome.services.delete: AdminAction which queries all datasets and retrieve images linked to the datasets.
QueryConstraints(LocalAdmin, LocalQuery, long, boolean) - Constructor for class ome.services.delete.QueryConstraints
QueryException - Exception in ome.services.query: something failed in looking up a query
QueryException(String) - Constructor for exception ome.services.query.QueryException
queryFactory - Variable in class ome.logic.AbstractLevel1Service
queryFactory - Variable in class ome.logic.AbstractLevel2Service
QueryFactory - Class in ome.services.query: query locator which is configured by Spring.
QueryFactory(QuerySource...) - Constructor for class ome.services.query.QueryFactory: main constructor which takes a non-null array of query sources as its only argument.
QueryImpl - Class in ome.logic: Provides methods for directly querying object graphs.
QueryImpl() - Constructor for class ome.logic.QueryImpl
QueryNewUserGroupBean - Class in ome.security.auth: Handles the ":query:" specifier from omero-server.properties.
QueryNewUserGroupBean(String) - Constructor for class ome.security.auth.QueryNewUserGroupBean
QueryParameterDef - Class in ome.services.query: definition of a slot into which a QueryParameter must fit.
QueryParameterDef(String, Class, boolean) - Constructor for class ome.services.query.QueryParameterDef: main constructor.
queryService - Variable in class ome.services.eventlogs.EventLogLoader
QuerySource - Class in ome.services.query: contract for any source of queries.
QuerySource() - Constructor for class ome.services.query.QuerySource
queryString() - Method in class ome.tools.hibernate.QueryBuilder: Returns the current query as a String.
queryWithoutFilter(Session) - Method in class ome.tools.hibernate.QueryBuilder

R

Rasterizer() - Constructor for class ome.services.SVGRasterizer.Rasterizer
RawFileBean - Class in ome.services: Raw file gateway which provides access to the OMERO file repository.
RawFileBean() - Constructor for class ome.services.RawFileBean: default constructor
RawFileBean(boolean) - Constructor for class ome.services.RawFileBean: overridden to allow Spring to set boolean
RawFileBeanReadOnly - Class in ome.services: Raw file gateway which provides access to the OMERO file repository.
RawFileBeanReadOnly() - Constructor for class ome.services.RawFileBeanReadOnly: default constructor
RawFileBeanReadOnly(boolean) - Constructor for class ome.services.RawFileBeanReadOnly: overridden to allow Spring to set boolean
RawPixelsBean - Class in ome.services: Implementation of the RawPixelsStore stateful service.
RawPixelsBean() - Constructor for class ome.services.RawPixelsBean: default constructor
RawPixelsBean(boolean, String) - Constructor for class ome.services.RawPixelsBean: overridden to allow Spring to set boolean
RawPixelsBeanReadOnly - Class in ome.services: Implementation of the RawPixelsStore stateful service.
RawPixelsBeanReadOnly() - Constructor for class ome.services.RawPixelsBeanReadOnly: default constructor
RawPixelsBeanReadOnly(boolean, String) - Constructor for class ome.services.RawPixelsBeanReadOnly: overridden to allow Spring to set boolean
read(long, int) - Method in class ome.services.RawFileBean
read(String) - Method in class ome.services.scripts.ScriptRepoHelper
read(BasicStream) - Static method in class ome.services.sharing.data.IdMapHelper
read(BasicStream) - Static method in class ome.services.sharing.data.LongSeqHelper
read(BasicStream) - Static method in class ome.services.sharing.data.ObjSeqHelper
read(BasicStream) - Static method in class ome.services.sharing.data.StringSeqHelper
readBytes(int) - Method in class ome.services.sessions.stats.DelegatingStats
readBytes(int) - Method in class ome.services.sessions.stats.NullSessionStats
readBytes(int) - Method in interface ome.services.sessions.stats.SessionStats
readBytes(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
readOnly - Variable in class ome.security.basic.EventHandler
readOnly - Variable in class ome.services.sessions.SessionManagerImpl
ReadOnlyConfigInit - Class in ome.services.util: Propagate the server's read-only status into corresponding keys in the configuration service.
ReadOnlyConfigInit(IConfig, ReadOnlyStatus) - Constructor for class ome.services.util.ReadOnlyConfigInit: Set read-only status in the current configuration.
readOnlyStatus - Variable in class ome.logic.AbstractLevel2Service
ReadOnlyStatus - Class in ome.services.util: Hook run by the context as early as possible to detect if the DB connection is read-only.
ReadOnlyStatus(boolean, boolean) - Constructor for class ome.services.util.ReadOnlyStatus
ReadOnlyStatus(boolean, boolean, boolean, SqlAction, String, String) - Constructor for class ome.services.util.ReadOnlyStatus
ReadOnlyStatus.IsAware - Interface in ome.services.util: Implemented by classes that can report if a given read-only status would cause them to be in read-only mode.
refresh(T) - Method in class ome.logic.QueryImpl
refresh(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache: Used externally to refresh the SessionContext instance associated with the session uuid
registerAll(Ehcache, CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
registerCallback(ProcessCallback) - Method in interface ome.services.procs.Process
registerCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton
registerPredicate(GraphPolicyRulePredicate) - Method in class ome.services.graphs.GraphPolicy: Use the given predicate in executing this graph policy.
RegisterServiceCleanupMessage - Class in ome.services.messages: Published when some resource must be cleaned up after method execution.
RegisterServiceCleanupMessage(Object, Object) - Constructor for class ome.services.messages.RegisterServiceCleanupMessage
registerTrigger(String, Trigger) - Method in class ome.services.scheduler.SchedulerFactoryBean: Registers a Trigger.
reindex(T) - Method in class ome.services.fulltext.BridgeHelper: Deprecated.

Publishes a ReindexMessage which will get processed asynchronously.
reindexAll(List<T>) - Method in class ome.services.fulltext.BridgeHelper: Deprecated.

Publishes a ReindexMessage which will get processed asynchronously.
ReindexMessage<T extends ome.model.IObject> - Class in ome.services.messages: Published when one or more IObject instances must be re-indexed.
ReindexMessage(Object, List<T>) - Constructor for class ome.services.messages.ReindexMessage
relativeDN(String) - Method in class ome.security.auth.LdapConfig: Calculate the relative DN based on the current base.
reload(String) - Method in interface ome.services.sessions.SessionManager: Similar to SessionManager.getEventContext(Principal) but uses the internal reload logic to get a fresh representation of the context.
reload(String) - Method in class ome.services.sessions.SessionManagerImpl
reload(SessionContext) - Method in class ome.services.sessions.SessionManagerImpl: Will be called in a synchronized block by SessionCache in order to allow for an update.
reload(String) - Method in class ome.services.sessions.state.SessionCache: Provides the reloading logic of the SessionCache for the SessionManagerImpl to use.
reload(SessionContext) - Method in interface ome.services.sessions.state.SessionCache.StaleCacheListener: Method called for every active session in the cache.
ReloadFilter - Class in ome.tools.hibernate: UpdateFilter subclass specialized for use with the Session.save(Object) (as opposed to Session.merge(Object)) method.
ReloadFilter(Session) - Constructor for class ome.tools.hibernate.ReloadFilter
ReloadingRefreshEventListener - Class in ome.tools.hibernate: responsible for responding to RefreshEvent.
ReloadingRefreshEventListener() - Constructor for class ome.tools.hibernate.ReloadingRefreshEventListener
remove() - Method in class ome.services.eventlogs.EventBacklog: Removes and returns the next EventLog instance or null if none is present.
remove() - Method in class ome.services.eventlogs.EventLogLoader
remove() - Method in class ome.services.SearchBean
removeAllDisabled(String...) - Method in class ome.security.basic.CurrentDetails
removeAllListeners() - Method in class ome.services.messages.GlobalMulticaster
removeApplicationListener(ApplicationListener) - Method in class ome.services.messages.GlobalMulticaster
removeApplicationListenerBean(String) - Method in class ome.services.messages.GlobalMulticaster
removeCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean: Deprecated.
removeCodomainMapFromChannel(CodomainMapContext, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
removeDisabled(String) - Method in class ome.security.basic.CurrentDetails
removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in class ome.logic.AdminImpl
removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
removeGuest(long, String) - Method in class ome.services.sharing.ShareBean
removeGuests(long, String...) - Method in class ome.services.sharing.ShareBean
removeMissingFilesFromDb(SqlAction, Session, List<OriginalFile>) - Method in class ome.services.scripts.ScriptRepoHelper: Given the current files on disk, ScriptRepoHelper.unregister(Long, SqlAction) all files which have been removed from disk.
removeObject(long, T) - Method in class ome.services.sharing.ShareBean
removeObjects(long, T...) - Method in class ome.services.sharing.ShareBean
removeSession(String) - Method in class ome.services.sessions.state.SessionCache
removeSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache
removeStatus(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
removeUnusedFiles() - Method in class ome.logic.RepositoryInfoImpl
removeUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean
removeUsers(long, List<Experimenter>) - Method in class ome.services.sharing.ShareBean
removingOnly() - Method in class ome.services.eventlogs.EventBacklog: Check the current state of the EventBacklog.
render(PlaneDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderAsPackedInt(PlaneDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderCompressed(PlaneDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
RENDERING_DEF_QUERY_PREFIX - Static variable in class ome.logic.PixelsImpl: Standard rendering definition HQL query prefix
RenderingBean - Class in ome.services: Provides the RenderingEngine service.
RenderingBean(PixelsService, LocalCompress, Executor, SecuritySystem, LutProvider) - Constructor for class ome.services.RenderingBean: Compression service Bean injector.
RenderingSettingsImpl - Class in ome.logic: Implementation of the IRenderingSettings I/F.
RenderingSettingsImpl() - Constructor for class ome.logic.RenderingSettingsImpl
renderProjectedAsPackedInt(int, int, int, int, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderProjectedCompressed(int, int, int, int, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
replace(Object, Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
repo - Variable in class ome.services.pixeldata.PersistentEventLogLoader
RepoFile - Class in ome.services.scripts: File type wrapper for paths which are intended for being stored in the database as a part of this repository.
RepoFile(File, String) - Constructor for class ome.services.scripts.RepoFile: Assumes that path is relative under root, and constructs a new File and calls RepoFile.RepoFile(File, File)
RepoFile(File, File) - Constructor for class ome.services.scripts.RepoFile: Both root and file are absolute paths to files.
RepoFile.FsFile - Class in ome.services.scripts: File type wrapper for actual OS files.
reportForgottenPassword(String, String) - Method in class ome.logic.AdminImpl
reportingLoops - Variable in class ome.services.fulltext.FullTextIndexer: Deprecated.

Frequency with which the percentage done should be calculated.
RepositoryInfoImpl - Class in ome.logic: Class implementation of the IRepositoryInfo service interface.
RepositoryInfoImpl() - Constructor for class ome.logic.RepositoryInfoImpl
RepositoryTask - Class in ome.tools: Class implementation of various mechanized tasks, database queries, file I/O, etc.
RepositoryTask(SqlAction) - Constructor for class ome.tools.RepositoryTask
reps - Variable in class ome.services.fulltext.FullTextIndexer: Deprecated.
reps - Variable in class ome.services.pixeldata.PixelDataHandler
requiresPixelsPyramid() - Method in class ome.services.RawPixelsBean
requiresPixelsPyramid() - Method in class ome.services.RenderingBean
reset(String[]) - Static method in class ome.services.fulltext.Main: Can be used to reset the value that the PersistentEventLogLoader would read if started now.
resetDefaults(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
resetDefaults() - Method in class ome.services.SearchBean
resetDefaults() - Method in class ome.services.ThumbnailBean
resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultSettings(boolean) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
resetDefaultsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInImage(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsNoSave(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
resetDetails(IObject, Object[], Object[], int, Details) - Method in class ome.security.basic.OmeroInterceptor: asks BasicSecuritySystem to create a new managed Details based on the previous state of this entity.
resetEnumerations(Class<T>) - Method in class ome.logic.TypesImpl
resetMinMaxInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetReadFilter(Session) - Method in interface ome.api.local.LocalShare
resetReadFilter(Session) - Method in class ome.services.sharing.ShareBean
resource - Variable in class ome.services.messages.ParserOpenFileMessage
resource - Variable in class ome.services.messages.RegisterServiceCleanupMessage
restartIfNeeded() - Method in class ome.services.scheduler.SchedulerFactoryBean: Similar to the SchedulerFactoryBean.isRunning() method, but properly handles the situation where the Scheduler has been completely shutdown and therefore must be replaced.
restrictions(IObject) - Method in interface ome.security.ACLVoter: Provide the active restrictions for this IObject.
restrictions(IObject) - Method in class ome.security.basic.BasicACLVoter
restrictions(IObject) - Method in class ome.security.CompositeACLVoter
restrictions(IObject) - Method in class ome.security.sharing.SharingACLVoter
results() - Method in class ome.services.SearchBean
retrieveAllRndSettings(long, long) - Method in class ome.logic.PixelsImpl
retrieveCollection(IObject, String, Parameters) - Method in class ome.logic.PojosImpl
retrievePixDescription(long) - Method in class ome.logic.PixelsImpl
retrieveRndSettings(long) - Method in class ome.logic.PixelsImpl
retrieveRndSettingsFor(long, long) - Method in class ome.logic.PixelsImpl
returnedClass() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
returnSeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
returnUnloaded - Variable in class ome.services.search.SearchValues
review(Map<String, Set<GraphPolicy.Details>>, GraphPolicy.Details, Map<String, Set<GraphPolicy.Details>>, Set<String>, boolean) - Method in class ome.services.graphs.GraphPolicy: The action to take about the link between the mapped objects.
roleProvider - Variable in class ome.logic.AdminImpl
RoleProvider - Interface in ome.security.auth: Provides user and group creation, deletion, and modification for use by services.
roles - Variable in class ome.security.basic.AbstractSecurityFilter
roles - Variable in class ome.security.basic.BasicACLVoter
roles - Variable in class ome.security.basic.BasicSecuritySystem
roles - Variable in class ome.services.sessions.SessionManagerImpl
rollback(EventLog) - Method in class ome.services.eventlogs.EventLogLoader
run() - Method in class ome.security.basic.LightAdminPrivilegesCleanup
run() - Method in class ome.services.delete.files.FileDeleter
run() - Method in interface ome.services.procs.IProcessManager: Runs the processing phase as root.
run() - Method in class ome.services.util.ExecutionThread: Initializes the Session for this Thread if necessary, then calls ExecutionThread.doRun().
run() - Method in class ome.services.util.ServerDirectoryCheck: Ensures that directories exist corresponding to, ${omero.data.dir}/FullText ${omero.managed.dir}
runAsAdmin() - Method in interface ome.security.AdminAction: executes with special privileges within the SecuritySystem.
runAsAdmin(AdminAction) - Method in class ome.security.basic.BasicSecuritySystem: Calls BasicSecuritySystem.runAsAdmin(AdminAction) with a null-group id.
runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.basic.BasicSecuritySystem: merge event is disabled for BasicSecuritySystem.runAsAdmin(AdminAction) because passing detached (client-side) entities to this method is particularly dangerous.
runAsAdmin(ExperimenterGroup, AdminAction) - Method in interface ome.security.SecuritySystem: Allows actions to be performed with the EventContext.isCurrentUserAdmin() flag enabled but without changing the value of EventContext.getCurrentUserId(), so that ownerships are properly handled.
runAsAdmin(AdminAction) - Method in interface ome.security.SecuritySystem: Calls SecuritySystem.runAsAdmin(ExperimenterGroup, AdminAction) with a null group.
runAsAdmin(AdminAction) - Method in class ome.security.SecuritySystemHolder
runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.SecuritySystemHolder
runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
runAsAdmin(AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
runAsAdmin() - Method in class ome.services.delete.QueryConstraints
runningProcess(long) - Method in interface ome.services.procs.IProcessManager: Returns a running Process for the id or null.
runningProcess(long) - Method in class ome.services.procs.ProcessManager

S

salt - Variable in class ome.security.auth.ConfigurablePasswordProvider: Whether or not salting based on the user ID should be attempted.
saltedPasswordDigest(Long, String) - Method in class ome.security.auth.PasswordUtil: Creates an MD5 hash of the given clear text and base64 encodes it.
sanityCheckPixels(Pixels, Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
sanityCheckRepository() - Method in class ome.logic.RepositoryInfoImpl
save() - Method in class ome.services.RawFileBean
save() - Method in class ome.services.RawPixelsBean
SAVE_EVENT - Static variable in class ome.security.basic.SaveEventListener
saveAndReturnArray(IObject[]) - Method in class ome.logic.UpdateImpl
saveAndReturnIds(IObject[]) - Method in class ome.logic.UpdateImpl
saveAndReturnObject(IObject) - Method in class ome.logic.UpdateImpl
saveArray(IObject[]) - Method in class ome.logic.UpdateImpl
saveAsNewSettings() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
saveCollection(Collection) - Method in class ome.logic.UpdateImpl
saveCurrentSettings() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
SaveEventListener - Class in ome.security.basic: event listener which will only handle newly created (transient) objects in a given graph.
SaveEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.SaveEventListener: main constructor.
saveObject(IObject) - Method in class ome.logic.UpdateImpl
saveRndSettings(RenderingDef) - Method in class ome.logic.PixelsImpl
saveToDB(FilesetJobLink) - Method in class ome.formats.OMEROMetadataStore: Saves the current object graph to the database.
scaleBufferedImage(BufferedImage, float, float) - Method in class ome.logic.AWTScaleService
scaleBufferedImage(BufferedImage, float, float) - Method in class ome.logic.JavaImageScalingService
SchedulerFactoryBean - Class in ome.services.scheduler: Produces a Scheduler which automatically loads all the triggers it can find.
SchedulerFactoryBean() - Constructor for class ome.services.scheduler.SchedulerFactoryBean
SCRIPT_REPO - Static variable in class ome.services.scripts.ScriptRepoHelper: Id used by all script repositories.
ScriptFileType - Class in ome.services.scripts: Definition of the script types that will be accepted by the server.
ScriptFileType(String, String) - Constructor for class ome.services.scripts.ScriptFileType
ScriptFileType(String, String, String, String) - Constructor for class ome.services.scripts.ScriptFileType
ScriptProcess - Class in ome.services.procs.scripts
ScriptProcess(Processor) - Constructor for class ome.services.procs.scripts.ScriptProcess
ScriptProcessor - Class in ome.services.procs.scripts
ScriptProcessor() - Constructor for class ome.services.procs.scripts.ScriptProcessor
ScriptRepoHelper - Class in ome.services.scripts: Strategy used by the ScriptRepository for registering, loading, and saving files.
ScriptRepoHelper(Executor, String, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper: Deprecated.
ScriptRepoHelper(Executor, String, Roles, ReadOnlyStatus) - Constructor for class ome.services.scripts.ScriptRepoHelper
ScriptRepoHelper(File, Executor, String, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper: Deprecated.
ScriptRepoHelper(String, File, Executor, String, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper: Deprecated.
ScriptRepoHelper(File, Executor, String, Principal, Roles, ReadOnlyStatus) - Constructor for class ome.services.scripts.ScriptRepoHelper: Deprecated.
ScriptRepoHelper(String, File, Executor, String, Principal, Roles, ReadOnlyStatus) - Constructor for class ome.services.scripts.ScriptRepoHelper
SearchAction - Class in ome.services.search: Serializable action used by SearchBean to generate results lazily.
SearchAction(SearchValues) - Constructor for class ome.services.search.SearchAction
searchAll() - Method in class ome.logic.LdapImpl
SearchBean - Class in ome.services: Implements the Search interface.
SearchBean(Executor, Class<? extends Analyzer>) - Constructor for class ome.services.SearchBean
SearchBean() - Constructor for class ome.services.SearchBean: Empty constructor required by EJB and self configuration.
searchByAttribute(String, String, String) - Method in class ome.logic.LdapImpl
searchByAttributes(String, String[], String[]) - Method in class ome.logic.LdapImpl
searchByDN(String) - Method in class ome.logic.LdapImpl
searchDnInGroups(String, String) - Method in class ome.logic.LdapImpl
SearchValues - Class in ome.services.search: Values used by SearchBean to store user requests.
SearchValues() - Constructor for class ome.services.search.SearchValues
sec - Variable in class ome.logic.AbstractLevel2Service
sec - Variable in class ome.security.auth.SimpleRoleProvider
sec - Variable in class ome.services.AbstractStatefulBean
sec - Variable in class ome.services.procs.ProcessManager.Work: SecuritySystem in order to perform a secure save on the Job instance.
secSys - Variable in class ome.security.basic.EventHandler
SecureAction - Interface in ome.security: Action for passing to SecuritySystem.doAction(SecureAction, IObject...).
SecureMerge - Class in ome.tools.hibernate: Helper originally from SimpleRoleProvider for merging admin objects.
SecureMerge(Session) - Constructor for class ome.tools.hibernate.SecureMerge
SecureMerge(Session, boolean) - Constructor for class ome.tools.hibernate.SecureMerge
securityFilter - Variable in class ome.security.basic.BasicACLVoter
SecurityFilter - Interface in ome.security: Base filter interface ...
SecurityFilterHolder - Class in ome.security: Security dispatcher holding each currently active SecurityFilter instance and allowing dispatching between them.
SecurityFilterHolder(CurrentDetails, OneGroupSecurityFilter, AllGroupsSecurityFilter, SharingSecurityFilter) - Constructor for class ome.security.SecurityFilterHolder
SecuritySystem - Interface in ome.security: central security interface.
SecuritySystemHolder - Class in ome.security: Security dispatcher holding each currently active SecuritySystem instance and allowing dispatching between them.
SecuritySystemHolder(BasicSecuritySystem, SharingSecuritySystem) - Constructor for class ome.security.SecuritySystemHolder
select(String...) - Method in class ome.tools.hibernate.QueryBuilder
selfConfigure() - Method in class ome.logic.AbstractLevel1Service: This method was previously called by the EJB container, but is no longer needed.
selfConfigure() - Method in class ome.logic.AbstractLevel2Service: This method was previously called by the EJB container, but is no longer needed.
selfConfigure(OmeroContext) - Method in class ome.logic.HardWiredInterceptor: Calls OmeroContext.applyBeanPropertyValues(Object, String) to have properties injected.
selfConfigure(SessionManager, ServiceFactory, SessionCache) - Static method in class ome.security.basic.BasicSecuritySystem: Simplified factory method which generates all the security primitives internally.
selfConfigure() - Method in class ome.services.AbstractStatefulBean
SelfCorrectingDataSource - Class in ome.services.db: DataSource delegate which wraps the
SelfCorrectingDataSource(DataSource, long) - Constructor for class ome.services.db.SelfCorrectingDataSource
SelfCorrectingDataSource(DataSource, long, int, long) - Constructor for class ome.services.db.SelfCorrectingDataSource
sendBlind(Set<String>, String) - Method in class ome.services.mail.MailSender
sendBlind(Set<String>, String, String) - Method in class ome.services.mail.MailSender
sendEmail(String, String, String, String, boolean, List<String>, List<String>) - Method in class ome.services.mail.MailUtil: Main method which takes typical email fields as arguments, to prepare and populate the given new MimeMessage instance and send.
sendEmail(String, String, String, boolean, List<String>, List<String>) - Method in class ome.services.mail.MailUtil: Overloaded method which takes typical email fields as arguments, to prepare and populate the given new MimeMessage instance and send.
sendEmail(Collection<EventLog>) - Method in class ome.services.mail.ObjectMailSender
sender - Variable in class ome.services.mail.MailUtil
sender - Variable in class ome.services.mail.ServerUpMailSender
serialVersionUID - Static variable in class ome.services.sharing.data.Obj
serialVersionUID - Static variable in class ome.services.sharing.data.ObjPrxHelper
serialVersionUID - Static variable in class ome.services.sharing.data.ShareData
serialVersionUID - Static variable in class ome.services.sharing.data.ShareDataPrxHelper
serialVersionUID - Static variable in class ome.services.sharing.data.ShareItem
serialVersionUID - Static variable in class ome.services.sharing.data.ShareItemPrxHelper
ServerDirectoryCheck - Class in ome.services.util: Hook run by the context at startup to create needed directories for the server.
ServerDirectoryCheck(String, String, ReadOnlyStatus) - Constructor for class ome.services.util.ServerDirectoryCheck
ServerDownMailSender - Class in ome.services.mail: Send an email to all members of the system group when the server is shutting down.
ServerDownMailSender() - Constructor for class ome.services.mail.ServerDownMailSender
ServerUpMailSender - Class in ome.services.mail: Announces to all members of the system group that the server has come up.
ServerUpMailSender(MailSender) - Constructor for class ome.services.mail.ServerUpMailSender
ServerVersionCheck - Class in ome.services.util: Hook run by the context.
ServerVersionCheck(String) - Constructor for class ome.services.util.ServerVersionCheck
service - Variable in class ome.services.util.Executor.Impl
ServiceHandler - Class in ome.services.util
ServiceHandler(CurrentDetails) - Constructor for class ome.services.util.ServiceHandler
ServiceHandler(CurrentDetails, long, long) - Constructor for class ome.services.util.ServiceHandler
SessionBean - Class in ome.services.sessions: Implementation of ISession.
SessionBean(SessionManager, Executor, CurrentDetails, LightAdminPrivileges) - Constructor for class ome.services.sessions.SessionBean
SessionCache - Class in ome.services.sessions.state: Synchronized and lockable state for the SessionManager.
SessionCache() - Constructor for class ome.services.sessions.state.SessionCache
SessionCache.StaleCacheListener - Interface in ome.services.sessions.state: Observer pattern used to refresh sessions in doUpdate.
SessionCallback - Interface in ome.services.sessions
SessionCallback.SimpleCloseCallback - Class in ome.services.sessions: Assumes that only close() will be called.
SessionContext - Interface in ome.services.sessions: Extends EventContext to hold a Session.
SessionContext.Count - Class in ome.services.sessions: Synchronized counter which can be passed between SessionContext instances as they are recreated.
SessionContextImpl - Class in ome.services.sessions
SessionContextImpl(Session, List<Long>, List<Long>, List<String>, SessionStats, SessionContext) - Constructor for class ome.services.sessions.SessionContextImpl
SessionContextImpl(Session, Set<AdminPrivilege>, List<Long>, List<Long>, List<String>, SessionStats, Roles, SessionContext) - Constructor for class ome.services.sessions.SessionContextImpl
sessionFactory - Variable in class ome.logic.AbstractLevel1Service
SessionFactory - Class in ome.tools.hibernate: Simple source of Thread-aware Session instances.
SessionFactory(SessionFactory, SqlAction) - Constructor for class ome.tools.hibernate.SessionFactory
SessionHandler - Class in ome.tools.hibernate: interceptor which delegates to HibernateInterceptor for stateless services but which keeps a WeakHashMap of sessions keyed by the stateful service reference.
SessionHandler(SessionFactory) - Constructor for class ome.tools.hibernate.SessionHandler: Constructor taking a SessionFactory.
sessionInit() - Method in class ome.services.util.ExecutionThread
sessionManager - Variable in class ome.logic.UpdateImpl
sessionManager - Variable in class ome.security.basic.BasicSecuritySystem
SessionManager - Interface in ome.services.sessions: Responsible for holding onto Session instances for optimized login.
sessionManager - Variable in class ome.services.sharing.ShareBean
SessionManager.CreationRequest - Class in ome.services.sessions: Extensible data object which can be passed to create* methods to stop the explosion of different methods.
SessionManagerImpl - Class in ome.services.sessions: Is for ISession a cache and will be kept there in sync? OR Factors out the logic from ISession and SessionManagerI Therefore either called directly, or via synchronous messages.
SessionManagerImpl() - Constructor for class ome.services.sessions.SessionManagerImpl
sessionProvider - Variable in class ome.security.basic.BasicSecuritySystem
sessionProvider - Variable in class ome.services.sessions.SessionManagerImpl
SessionProvider - Interface in ome.services.sessions: Provides SessionManagerImpl with wrapper around session storage backends.
SessionProviderInDb - Class in ome.services.sessions: Is for ISession a cache and will be kept there in sync? OR Factors out the logic from ISession and SessionManagerI Therefore either called directly, or via synchronous messages.
SessionProviderInDb(Roles, NodeProvider, Executor) - Constructor for class ome.services.sessions.SessionProviderInDb
SessionProviderInMemory - Class in ome.services.sessions: In-memory implementation of SessionProviderInDb.
SessionProviderInMemory(Roles, NodeProvider, Executor) - Constructor for class ome.services.sessions.SessionProviderInMemory
SessionProviderWrapper - Class in ome.services.sessions: A session provider that offers a unified view of multiple underlying session providers.
SessionProviderWrapper(ReadOnlyStatus, List) - Constructor for class ome.services.sessions.SessionProviderWrapper: Construct a new Session provider.
SessionsCreatedCounter - Class in ome.services.sessions.stats: Counter for all the objects read in a session.
SessionsCreatedCounter(int) - Constructor for class ome.services.sessions.stats.SessionsCreatedCounter
SessionsCreatedStatsMessage - Class in ome.services.messages.stats: Published when some limit in user/group/session activity has been reached.
SessionsCreatedStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.SessionsCreatedStatsMessage
SessionStats - Interface in ome.services.sessions.stats: Thread-safe counter for all
set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper: Deprecated.

Method to be implemented by all bridges.
set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.ProjectWithImageNameBridge: Deprecated.

If the "value" argument is a Project, this bridge gathers all images and adds them to the index with a slightly reduced boost value.
set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge: Deprecated.

Primary entry point for all bridges.
set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge: Deprecated.

Default implementation of the FullTextBridge.set(String, Object, Document, LuceneOptions) method which calls FullTextBridge.set_file(String, IObject, Document, LuceneOptions) FullTextBridge.set_annotations(String, IObject, Document, LuceneOptions), FullTextBridge.set_acquisition(String, IObject, Document, LuceneOptions), FullTextBridge.set_details(String, IObject, Document, LuceneOptions), FullTextBridge.set_fileset(String, IObject, Document, LuceneOptions), FullTextBridge.set_folders(String, IObject, Document, LuceneOptions), and finally FullTextBridge.set_custom(String, IObject, Document, LuceneOptions).
set(Share, long, List<T>, List<Long>, List<String>, boolean) - Method in class ome.services.sharing.ShareStore
set_acquisition(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge: Deprecated.

Walks the acquisition related metadata including channel names.
set_annotations(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge: Deprecated.

Walks the various Annotation instances attached to the object argument and adds various levels to the index.
set_custom(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge: Deprecated.

Loops over each field bridge class and calls its FieldBridge.set(String, Object, Document, LuceneOptions) method.
set_details(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge: Deprecated.

Parses all ownership and time-based details to the index for the given object.
set_file(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge: Deprecated.

Uses BridgeHelper.parse(OriginalFile, OriginalFilesService, Map) to get a Reader for the given file which is then passed to BridgeHelper.addContents(Document, String, OriginalFile, OriginalFilesService, Map, LuceneOptions) using the field name "file.contents".
set_fileset(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge: Deprecated.

Walks the Fileset instances attached to an Image.
set_folders(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge: Deprecated.

Walks the various Folder instances attached to the object argument so that it may be found via its immediate parent folder.
setAction(String) - Method in class ome.services.mail.ObjectMailSender
setActive(int, boolean) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setActive(long, boolean) - Method in class ome.services.sharing.ShareBean
setAdmin(boolean) - Method in class ome.security.basic.BasicEventContext
setAdminPrivileges(Experimenter, List<AdminPrivilege>) - Method in class ome.logic.AdminImpl
setAdminPrivileges(Set<AdminPrivilege>) - Method in class ome.security.basic.BasicEventContext
setAdminPrivileges(LightAdminPrivileges) - Method in class ome.services.sessions.SessionManagerImpl
setAdminService(LocalAdmin) - Method in class ome.logic.UpdateImpl
setAdminService(IAdmin) - Method in class ome.services.RawFileBean
setAllowLeadingWildcard(boolean) - Method in class ome.services.SearchBean
setAlternateStylesheet(String) - Method in class ome.services.SVGRasterizer: Sets the alternate stylesheet to use.
setAnalyzer(Class<? extends Analyzer>) - Method in class ome.logic.QueryImpl
setAnalyzer(Class<? extends Analyzer>) - Method in class ome.services.SearchBean: Injector used by Spring.
setApplicationContext(ApplicationContext) - Method in class ome.logic.AdminImpl
setApplicationContext(ApplicationContext) - Method in class ome.logic.ConfigImpl
setApplicationContext(ApplicationContext) - Method in class ome.logic.LdapImpl
setApplicationContext(ApplicationContext) - Method in class ome.security.auth.ConfigurablePasswordProvider
setApplicationContext(ApplicationContext) - Method in class ome.security.basic.BasicSecuritySystem
setApplicationContext(ApplicationContext) - Method in class ome.security.basic.GroupChmodStrategy
setApplicationContext(ApplicationContext) - Method in class ome.services.delete.Deletion.Builder
setApplicationContext(ApplicationContext) - Method in class ome.services.fulltext.FileParser
setApplicationContext(ApplicationContext) - Method in class ome.services.fulltext.FullTextIndexer: Deprecated.
setApplicationContext(ApplicationContext) - Method in class ome.services.scheduler.SchedulerFactoryBean
setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.SessionManagerImpl
setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.state.CacheFactory
setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.state.SessionCache: Context injector.
setApplicationContext(ApplicationContext) - Method in class ome.services.sharing.BlobShareStore: Because there is a cyclic dependency (SF -> ACLVoter -> BlobStore -> SF), we have to lazy-load the session factory via the context.
setApplicationContext(ApplicationContext) - Method in class ome.services.ThumbnailBean
setApplicationContext(ApplicationContext) - Method in class ome.services.util.Executor.Impl
setApplicationContext(ApplicationContext) - Method in class ome.tools.hibernate.SessionHandler
setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.InternalServiceFactory: simple injector for the ApplicationContext
setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.ManagedServiceFactory: simple injector for the ApplicationContext
setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.OnContextRefreshedEventListener
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.BridgeHelper: Deprecated.
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.bridges.TablesBridge: Deprecated.
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.CounterFactory
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.LongCounter
setBackgroundColor(Paint) - Method in class ome.services.SVGRasterizer: Sets the Paint to use for the background of the image.
setBatchSize(int) - Method in class ome.services.eventlogs.EventLogLoader: Set the number of EventLog instances will be loaded in a single run.
setBatchSize(int) - Method in class ome.services.SearchBean
setBeanDefinitionForReadOnly(BeanDefinitionRegistry) - Method in class ome.services.util.BeanInstantiationGuard: Act on the bean definition registry to make the target bean suitable for read-only mode.
setBeanDefinitionForReadOnly(BeanDefinitionRegistry) - Method in class ome.services.util.BeanInstantiationSubstituter
setBeanFactory(BeanFactory) - Method in class ome.services.messages.GlobalMulticaster
setCacheEventListeners(CacheEventListener[]) - Method in class ome.services.sessions.state.CacheFactory
setCacheManager(CacheManager) - Method in class ome.services.sessions.state.SessionCache: Injection method, also performs the creation of SessionCache.sessions
setCallContext(Map<String, String>) - Method in class ome.security.basic.BasicEventContext
setCaseSensitive(boolean) - Method in class ome.services.SearchBean
setCaseSentivice(boolean) - Method in class ome.services.SearchBean
setChanges(String) - Method in class ome.services.graphs.GraphPolicyRule
setChannelGlobalMinMax(long, int, double, double) - Method in class ome.logic.PixelsImpl
setChannelLookupTable(int, String) - Method in class ome.services.RenderingBean
setChannelWindow(int, double, double) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setChecksumProviderFactory(ChecksumProviderFactory) - Method in class ome.services.RawFileBean: ChecksumProviderFactory Bean injector
setClasses(Set<String>) - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
setCodomainInterval(int, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setCompressionLevel(float) - Method in interface ome.api.local.LocalCompress: Sets the current compression level for the service.
setCompressionLevel(float) - Method in class ome.logic.CompressImpl
setCompressionLevel(float) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setCompressionService(LocalCompress) - Method in class ome.services.ThumbnailBean: Compression service Bean injector.
setCondition(String) - Method in class ome.services.graphs.GraphPolicy: Set a named condition,
setConfigValue(String, String) - Method in class ome.logic.ConfigImpl: see IConfig.setConfigValue(String, String)
setConfigValueIfEquals(String, String, String) - Method in class ome.logic.ConfigImpl: see IConfig.setConfigValueIfEquals(String, String, String)
setContactSystem(boolean) - Method in class ome.services.mail.FailedLoginMailSender
setContactUser(boolean) - Method in class ome.services.mail.FailedLoginMailSender
setContext(Map<String, String>) - Method in class ome.security.basic.CurrentDetails
setCounterFactory(CounterFactory) - Method in class ome.services.sessions.SessionManagerImpl
setCriteria(Criteria) - Method in class ome.services.query.Query: provide this Query instance with a Criteria to be used for retrieving data.
setCronExpression(String) - Method in class ome.services.fulltext.FullTextIndexer2
setCurrentDetails(CurrentDetails) - Method in class ome.logic.ConfigImpl: CurrentDetails setter for dependency injection.
setCurrentId(long) - Method in class ome.services.eventlogs.PersistentEventLogLoader
setDatabaseIdentity(DatabaseIdentity) - Method in class ome.logic.ConfigImpl
setDatadir(String) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for data repository directory
setDebug(boolean) - Method in class ome.tools.hibernate.EventMethodInterceptor
setDebugAll(boolean) - Method in class ome.security.basic.EventListenersFactoryBean: for setter injection
setDefaultBody(String) - Method in class ome.services.mail.MailSender
setDefaultGroup(Experimenter, ExperimenterGroup) - Method in class ome.logic.AdminImpl
setDefaultGroup(Experimenter, ExperimenterGroup) - Method in interface ome.security.auth.RoleProvider
setDefaultGroup(Experimenter, ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
setDefaultT(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setDefaultTimeToIdle(long) - Method in class ome.services.sessions.SessionManagerImpl
setDefaultTimeToLive(long) - Method in class ome.services.sessions.SessionManagerImpl
setDefaultZ(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setDescription(long, String) - Method in class ome.services.sharing.ShareBean
setDisabledSubsystems(Set<String>) - Method in class ome.security.basic.BasicEventContext
setDiskSpaceChecking(boolean) - Method in class ome.services.RawFileBean: setter disk overflow checking
setDiskSpaceChecking(boolean) - Method in class ome.services.RawPixelsBean
setDiskSpaceChecking(boolean) - Method in class ome.services.ThumbnailBean
setDN(Long, String) - Method in class ome.logic.LdapImpl: Deprecated.
setDryRun(boolean) - Method in class ome.services.fulltext.FullTextIndexer: Deprecated.
setEnabled(boolean) - Method in class ome.services.mail.MailSender
setError(String) - Method in class ome.services.graphs.GraphPolicyRule
setEvent(Event) - Method in class ome.security.basic.BasicEventContext
setExcludes(String[]) - Method in class ome.services.eventlogs.EventLogLoader: Spring injector
setExecutor(Executor) - Method in class ome.logic.UpdateImpl
setExecutor(Executor) - Method in class ome.services.mail.MailSender
setExecutor(Executor) - Method in class ome.services.SearchBean: Injector used by Spring, currently, since SelfConfigurableService.selfConfigure() requires it.
setExecutor(Executor) - Method in class ome.services.sessions.SessionManagerImpl
setExpiration(long, Timestamp) - Method in class ome.services.sharing.ShareBean
setExtendedMetadata(ExtendedMetadata) - Method in class ome.logic.AbstractLevel2Service
setFileId(long) - Method in class ome.services.RawFileBean
setFileIdWithBuffer(long, FileBuffer) - Method in class ome.services.RawFileBean
setFileService(OriginalFilesService) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for ROMIO file service
setFullTextBridge(FullTextBridge) - Method in class ome.logic.UpdateImpl
setGroup(ExperimenterGroup, Permissions) - Method in class ome.security.basic.BasicEventContext
setGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl
setGroupOwner(Experimenter, ExperimenterGroup, boolean) - Method in interface ome.security.auth.RoleProvider
setGroupOwner(Experimenter, ExperimenterGroup, boolean) - Method in class ome.security.auth.SimpleRoleProvider
setIContainer(IContainer) - Method in class ome.logic.MetadataImpl: IContainer bean injector.
setIdOnly() - Method in class ome.services.SearchBean
setImageHeight(float) - Method in class ome.services.SVGRasterizer: Sets the height of the image to rasterize.
setImageWidth(float) - Method in class ome.services.SVGRasterizer: Sets the width of the image to rasterize.
setIndexWatcher(IndexWatcher) - Method in class ome.logic.UpdateImpl
setInProgressImageResource(Resource) - Method in class ome.services.ThumbnailBean: In-progress image resource Bean injector.
setInput(String, String, Object) - Method in class ome.services.sessions.SessionBean
setInput(String, String, Object) - Method in interface ome.services.sessions.SessionManager: Places the argument in the input environment under the given key, possibly initializing the Map Throws an exception if there is no Session with the given identifier.
setInput(String, String, Object) - Method in class ome.services.sessions.SessionManagerImpl
setIoService(ThumbnailService) - Method in class ome.services.ThumbnailBean: I/O service (ThumbnailService) Bean injector.
setIPixels(IPixels) - Method in class ome.services.projection.ProjectionBean: IPixels bean injector.
setIPixels(IPixels) - Method in class ome.services.ThumbnailBean: Pixels service Bean injector.
setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.RawFileBean: Disk Space Usage service Bean injector
setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.RawPixelsBean: Disk Space Usage service Bean injector
setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.ThumbnailBean: Disk Space Usage service Bean injector
setIsWriteDb(boolean) - Method in class ome.services.util.BeanInstantiationGuard
setIsWriteRepo(boolean) - Method in class ome.services.util.BeanInstantiationGuard
setKey(String) - Method in class ome.services.eventlogs.PersistentEventLogLoader
setKeyStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
setKeyStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
setLanguages(String) - Method in class ome.services.SVGRasterizer: Sets the preferred language to use.
setLeaderOfGroups(List<Long>) - Method in class ome.security.basic.BasicEventContext
setLegacyUtil(PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
setLockCandidates(Set<IObject>) - Method in class ome.security.basic.BasicEventContext
setLogs(List<EventLog>) - Method in class ome.security.basic.BasicEventContext
setLutProvider(LutProvider) - Method in class ome.services.ThumbnailBean: Lookup table provider Bean injector.
setMailUtil(MailUtil) - Method in class ome.services.mail.MailSender
setManagerDown(String) - Method in class ome.security.basic.NodeProviderInDb
setManagerDown(String) - Method in class ome.security.basic.NodeProviderInMemory
setManagerDown(String) - Method in class ome.security.basic.NodeProviderWrapper
setManagerDown(String) - Method in interface ome.security.NodeProvider: Sets a given manager node as down.
setMatches(String) - Method in class ome.services.graphs.GraphPolicyRule
setMaxClauseCount(Integer) - Method in class ome.services.SearchBean: Deprecated.
setMaxFileSize(Long) - Method in class ome.services.fulltext.FileParser
setMedia(String) - Method in class ome.services.SVGRasterizer: Sets the media to rasterize.
setMemberOfGroups(List<Long>) - Method in class ome.security.basic.BasicEventContext
setMergedBatches(boolean) - Method in class ome.services.SearchBean
setMessage(String) - Method in class ome.services.JobBean
setMethodHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
setMethodSecurity(MethodSecurity) - Method in class ome.security.basic.BasicSecurityWiring: Setter injection.
setMimetype(OriginalFile) - Method in class ome.services.scripts.ScriptFileType: Sets the mimetype on the given OriginalFile if the name field matches the wildcard pattern for this instance.
setMimetype(OriginalFile) - Method in class ome.services.scripts.ScriptRepoHelper
setModel(RenderingModel) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setObjectClass(Class<IObject>) - Method in class ome.services.mail.ObjectMailSender
setObjectsReadHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
setObjectsWrittenHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
setOnAllUsers(boolean) - Method in class ome.services.mail.FailedLoginMailSender
setOnSpecificUsers(Set<String>) - Method in class ome.services.mail.FailedLoginMailSender
setOriginalFilesService(OriginalFilesService) - Method in class ome.services.RawFileBean: I/O service (OriginalFilesService) Bean injector.
setOriginalSettingsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsInImage(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
setOutput(String, String, Object) - Method in class ome.services.sessions.SessionBean
setOutput(String, String, Object) - Method in interface ome.services.sessions.SessionManager: Places the argument in the output environment under the given key, possibly initializing the Map Throws an exception if there is no Session with the given identifier.
setOutput(String, String, Object) - Method in class ome.services.sessions.SessionManagerImpl
setOverlays(Map<byte[], Integer>) - Method in class ome.services.RenderingBean: Deprecated.
As of release 5.1.0, replaced by PlaneDef.setShapeIds(List).
setOwner(Experimenter) - Method in class ome.security.basic.BasicEventContext
setOwnsAll() - Method in class ome.services.graphs.GraphTraversal: Deprecated.
An ugly expedient hack that requires review and may be removed without notice.
setParameterValues(Properties) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
setPermissionsForGroup(Long, Permissions) - Method in class ome.security.basic.BasicEventContext: Called during BasicACLVoter.allowLoad(org.hibernate.Session, Class, ome.model.internal.Details, long) to track groups that will need resolving later.
setPermittedClasses(Map<Integer, Set<Class<? extends IObject>>>) - Method in interface ome.security.ACLVoter: Specify object classes based on restriction constants in Permissions that do not always have those restrictions.
setPermittedClasses(Map<Integer, Set<Class<? extends IObject>>>) - Method in class ome.security.basic.BasicACLVoter
setPermittedClasses(Map<Integer, Set<Class<? extends IObject>>>) - Method in class ome.security.CompositeACLVoter
setPermittedClasses(Map<Integer, Set<Class<? extends IObject>>>) - Method in class ome.security.sharing.SharingACLVoter
setPixelDataService(PixelsService) - Method in class ome.services.ThumbnailBean: Pixels data service Bean injector.
setPixelsData(PixelsService) - Method in class ome.logic.RenderingSettingsImpl: Sets injector.
setPixelsData(PixelsService) - Method in class ome.services.RawPixelsBean
setPixelsId(long, boolean) - Method in class ome.services.RawPixelsBean
setPixelsId(long) - Method in class ome.services.ThumbnailBean
setPixelsId(long) - Method in class ome.services.ThumbnailBeanReadOnly
setPixelsMetadata(IPixels) - Method in class ome.logic.RenderingSettingsImpl: Sets injector.
setPixelsMetadata(IPixels) - Method in class ome.services.RawPixelsBean
setPixelsService(PixelsService) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for ROMIO pixels service
setPixelsService(PixelsService) - Method in class ome.services.projection.ProjectionBean: PixelsService bean injector.
setPixelToMMFactor(float) - Method in class ome.services.SVGRasterizer: Sets the unit conversion factor to the specified value.
setPlane(byte[], int, int, int) - Method in class ome.services.RawPixelsBean
setPreferenceContext(PreferenceContext) - Method in class ome.logic.ConfigImpl: PreferenceContext setter for dependency injection.
setPrincipalHolder(PrincipalHolder) - Method in class ome.security.basic.BasicSecurityWiring: Setter injection.
setPrincipalHolder(PrincipalHolder) - Method in class ome.services.sessions.SessionManagerImpl
setProcessManager(IProcessManager) - Method in class ome.services.JobBean: Process Manager Bean injector.
setQuality(float) - Method in class ome.services.SVGRasterizer: Sets the quality of the image to rasterize when rasterizing to a JPEG.
setQuantizationMap(int, Family, double, boolean) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setQuantumStrategy(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setQuery(Query) - Method in class ome.services.query.Query: provide this Query instance with a Query to be used for retrieving data.
setQueryFactory(QueryFactory) - Method in class ome.logic.AbstractLevel1Service
setQueryFactory(QueryFactory) - Method in class ome.logic.AbstractLevel2Service
setQueryService(LocalQuery) - Method in class ome.logic.AbstractLevel2Service
setQueryService(LocalQuery) - Method in class ome.logic.UpdateImpl
setQueryService(IQuery) - Method in class ome.security.auth.PasswordUtil
setQueryService(LocalQuery) - Method in class ome.services.AbstractStatefulBean: Query service Bean injector.
setQueryService(IQuery) - Method in class ome.services.eventlogs.EventLogLoader: Spring injector
setQueryService(IQuery) - Method in class ome.services.mail.MailSender
setQueryService(IQuery) - Method in class ome.services.procs.ProcessorSkeleton
setQueryString(String) - Method in class ome.services.mail.ObjectMailSender
setRawPixelsStore(RawPixelsStore) - Method in class ome.logic.RenderingSettingsImpl: Sets injector.
setReadOnly(boolean) - Method in class ome.security.basic.BasicEventContext
setReadOnly(ReadOnlyStatus) - Method in class ome.services.sessions.SessionManagerImpl
setReadOnlyStatus(ReadOnlyStatus) - Method in class ome.logic.AbstractLevel2Service
setRegion(int, long, byte[]) - Method in class ome.services.RawPixelsBean
setRenderingDefId(long) - Method in class ome.services.ThumbnailBean
setRepetitions(int) - Method in class ome.services.fulltext.FullTextIndexer: Deprecated.

Spring injector.
setRepetitions(int) - Method in class ome.services.pixeldata.PixelDataHandler: Spring injector.
setReportingLoops(int) - Method in class ome.services.fulltext.FullTextIndexer: Deprecated.
setResolutionLevel(int) - Method in class ome.services.RawPixelsBean
setResolutionLevel(int) - Method in class ome.services.RenderingBean
setReturnUnloaded(boolean) - Method in class ome.services.SearchBean
setRGBA(int, int, int, int, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setRoles(Roles) - Method in class ome.services.mail.MailSender
setRoles(Roles) - Method in class ome.services.sessions.SessionManagerImpl
setRow(byte[], int, int, int, int) - Method in class ome.services.RawPixelsBean
setScaleService(IScale) - Method in class ome.services.ThumbnailBean: Scale service Bean injector.
setSecurityContext(Principal, IObject) - Method in interface ome.services.sessions.SessionManager: Sets the context for the current session to the given value.
setSecurityContext(Principal, IObject) - Method in class ome.services.sessions.SessionManagerImpl
setSecuritySystem(SecuritySystem) - Method in class ome.logic.AbstractLevel2Service
setSecuritySystem(SecuritySystem) - Method in class ome.services.AbstractStatefulBean
setServiceCleanups(Set<RegisterServiceCleanupMessage>) - Method in class ome.security.basic.BasicEventContext
setSessionCache(SessionCache) - Method in class ome.services.sessions.SessionManagerImpl
setSessionFactory(SessionFactory) - Method in class ome.logic.AbstractLevel1Service: delegates to HibernateDaoSupport.
setSessionFactory(SessionFactory) - Method in class ome.logic.TypesImpl: injector for usage by the container.
setSessionFactory(SessionFactory) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Initializes the metadata needed by this instance.
setSessionManager(SessionManager) - Method in class ome.logic.UpdateImpl
setSessionManager(SessionManager) - Method in class ome.security.basic.BasicMethodSecurity
setSessionProvider(SessionProvider) - Method in class ome.services.sessions.SessionManagerImpl
setSettingsService(IRenderingSettings) - Method in class ome.services.ThumbnailBean: Rendering settings service Bean injector.
setShareId(Long) - Method in class ome.security.basic.BasicEventContext
setShareId(Long) - Method in interface ome.services.sessions.SessionContext: The Share id is the only mutable bit in the SessionContext.
setShareId(Long) - Method in class ome.services.sessions.SessionContextImpl
setSqlAction(SqlAction) - Method in class ome.logic.ConfigImpl: SqlAction setter for dependency injection.
setSqlAction(SqlAction) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for SQL operations
setSqlAction(SqlAction) - Method in class ome.services.eventlogs.PersistentEventLogLoader
setSqlAction(SqlAction) - Method in class ome.services.fulltext.FullTextIndexer: Deprecated.

Since these instances are used repeatedly, we need to check for already set SqlAction
setSqlAction(SqlAction) - Method in class ome.services.pixeldata.PixelDataHandler: Since these instances are used repeatedly, we need to check for already set SqlAction
setSqlAction(SqlAction) - Method in class ome.services.RawPixelsBean: SQL action Bean injector
setSqlAction(SqlAction) - Method in class ome.services.sharing.BlobShareStore
setSqlAction(SqlAction) - Method in class ome.services.util.Executor.SimpleWork
setStack(byte[], int, int, int) - Method in class ome.services.RawPixelsBean
setStaleCacheListener(SessionCache.StaleCacheListener) - Method in class ome.services.sessions.state.SessionCache
setStatus(String) - Method in class ome.services.JobBean
setStatusAndMessage(String, String) - Method in class ome.services.JobBean
setStop(boolean) - Method in class ome.services.eventlogs.EventLogLoader: Called by controlling objects (a worker thread) in order to free up the thread.
setSubjectPrefix(String) - Method in class ome.services.mail.MailSender
setSudoer(Experimenter) - Method in class ome.security.basic.BasicEventContext
setThumbnailService(ThumbnailService) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for ROMIO thumbnail service
setTile(byte[], int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean
setTimeout(int) - Method in class ome.services.query.Query
setTimeout(int) - Method in class ome.services.search.SearchAction
setTimeout(Consumer<Integer>) - Method in class ome.services.util.TimeoutSetter: Set the timeout on the given query.
setTimeoutSetter(TimeoutSetter) - Method in class ome.logic.QueryImpl
setTimeoutSetter(TimeoutSetter) - Method in class ome.services.SearchBean
setTimepoint(byte[], int) - Method in class ome.services.RawPixelsBean
SETTINGSID_QUERY - Static variable in class ome.services.delete.DeleteBean
setToken(GraphHolder) - Method in class ome.security.basic.TokenHolder
setTrustStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
setTrustStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
setTypes(ITypes) - Method in class ome.services.eventlogs.PersistentEventLogLoader
setTypesService(ITypes) - Method in class ome.services.JobBean: Types service Bean injector.
setTypesService(ITypes) - Method in class ome.services.procs.ProcessorSkeleton
setUmask(Permissions) - Method in class ome.security.basic.BasicEventContext
setUp() - Method in class ome.formats.importer.util.TinyImportFixture: Deprecated.

Creates a dataset and locates the test image file.
setUpdateInterval(long) - Method in class ome.services.sessions.state.SessionCache: Inject time in milliseconds between updates.
setUpdateService(LocalUpdate) - Method in class ome.logic.AbstractLevel2Service
setUpdateService(LocalUpdate) - Method in class ome.services.AbstractStatefulBean
setUpdateService(IUpdate) - Method in class ome.services.procs.ProcessorSkeleton
setUseProjections(boolean) - Method in class ome.services.SearchBean
setUserId(long) - Method in class ome.services.ThumbnailCtx: Sets the user ID to use for queries.
setUserStyleSheetURI(String) - Method in class ome.services.SVGRasterizer: Sets the uri of the user stylesheet.
setUuid(String) - Method in class ome.services.sessions.SessionManagerImpl
setXMLParserValidating(boolean) - Method in class ome.services.SVGRasterizer: Sets whether or not the XML parser used to parse SVG document should be validating or not, depending on the specified parameter.
sf - Variable in class ome.logic.TypesImpl
sf - Variable in class ome.security.auth.SimpleRoleProvider
sf - Variable in class ome.security.basic.BasicSecuritySystem
sf - Variable in class ome.services.delete.DeleteBean
share - Variable in class ome.security.SecurityFilterHolder
share - Variable in class ome.services.sharing.data.ShareItem
ShareBean - Class in ome.services.sharing: Note: SessionManager should not be used to obtain the Share data since it may not be completely in sync.
ShareBean(LocalAdmin, SessionManager, ShareStore, Executor, MailUtil) - Constructor for class ome.services.sharing.ShareBean
ShareData - Class in ome.services.sharing.data
ShareData() - Constructor for class ome.services.sharing.data.ShareData
ShareData(long, long, List<Long>, List<String>, Map<String, List<Long>>, List<Obj>, boolean, long) - Constructor for class ome.services.sharing.data.ShareData
ShareDataHolder - Class in ome.services.sharing.data
ShareDataHolder() - Constructor for class ome.services.sharing.data.ShareDataHolder
ShareDataHolder(ShareData) - Constructor for class ome.services.sharing.data.ShareDataHolder
ShareDataPrx - Interface in ome.services.sharing.data
ShareDataPrxHelper - Class in ome.services.sharing.data: Provides type-specific helper functions.
ShareDataPrxHelper() - Constructor for class ome.services.sharing.data.ShareDataPrxHelper
ShareDataPrxHolder - Class in ome.services.sharing.data
ShareDataPrxHolder() - Constructor for class ome.services.sharing.data.ShareDataPrxHolder
ShareDataPrxHolder(ShareDataPrx) - Constructor for class ome.services.sharing.data.ShareDataPrxHolder
ShareItem - Class in ome.services.sharing.data
ShareItem() - Constructor for class ome.services.sharing.data.ShareItem
ShareItem(long, String, long, List<Long>, List<String>) - Constructor for class ome.services.sharing.data.ShareItem
ShareItemHolder - Class in ome.services.sharing.data
ShareItemHolder() - Constructor for class ome.services.sharing.data.ShareItemHolder
ShareItemHolder(ShareItem) - Constructor for class ome.services.sharing.data.ShareItemHolder
ShareItemPrx - Interface in ome.services.sharing.data
ShareItemPrxHelper - Class in ome.services.sharing.data: Provides type-specific helper functions.
ShareItemPrxHelper() - Constructor for class ome.services.sharing.data.ShareItemPrxHelper
ShareItemPrxHolder - Class in ome.services.sharing.data
ShareItemPrxHolder() - Constructor for class ome.services.sharing.data.ShareItemPrxHolder
ShareItemPrxHolder(ShareItemPrx) - Constructor for class ome.services.sharing.data.ShareItemPrxHolder
ShareRestrictionTransactionAttributeSource - Class in ome.services.sharing: Prevents methods from setting the transaction to readOnly = false when a share is activated.
ShareRestrictionTransactionAttributeSource(CurrentDetails, SessionCache) - Constructor for class ome.services.sharing.ShareRestrictionTransactionAttributeSource
ShareStore - Class in ome.services.sharing: Entry to the Ice code generated data/ directory.
ShareStore() - Constructor for class ome.services.sharing.ShareStore
sharesToSessions(List<ShareData>) - Method in class ome.services.sharing.ShareBean
shareToSession(ShareData) - Method in class ome.services.sharing.ShareBean
sharing - Variable in class ome.security.SecuritySystemHolder
SharingACLVoter - Class in ome.security.sharing
SharingACLVoter(CurrentDetails, SystemTypes, ShareStore, TokenHolder) - Constructor for class ome.security.sharing.SharingACLVoter
SharingSecurityFilter - Class in ome.security.basic: The sharing security filter provides database-level access protection for share contexts.
SharingSecurityFilter(Roles, ShareStore) - Constructor for class ome.security.basic.SharingSecurityFilter: Construct a new sharing security filter.
SharingSecuritySystem - Class in ome.security.sharing: central security interface.
SharingSecuritySystem(BasicSecuritySystem) - Constructor for class ome.security.sharing.SharingSecuritySystem
ShutdownSafeEhcacheManagerFactoryBean - Class in ome.tools.spring: Workaround for the Spring/EHCache shutdown sequence.
ShutdownSafeEhcacheManagerFactoryBean() - Constructor for class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean
SimilarTerms - Class in ome.services.search: Search to find similar terms to some given terms.
SimilarTerms(SearchValues, String...) - Constructor for class ome.services.search.SimilarTerms
SimpleCloseCallback() - Constructor for class ome.services.sessions.SessionCallback.SimpleCloseCallback
simpleDelete(Map<String, String>, Executor, Principal, long) - Method in class ome.services.scripts.ScriptRepoHelper: Unlike ScriptRepoHelper.delete(long) this method simply performs the DB delete on the given original file id.
SimpleLuceneOptions - Class in ome.services.fulltext: Deprecated.
SimpleLuceneOptions(LuceneOptions, Float) - Constructor for class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
SimpleLuceneOptions(LuceneOptions, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
SimpleLuceneOptions(LuceneOptions, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
SimpleLuceneOptions(LuceneOptions, Float, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions: Deprecated.
SimpleRoleProvider - Class in ome.security.auth: Implements RoleProvider.
SimpleRoleProvider(SecuritySystem, SessionFactory) - Constructor for class ome.security.auth.SimpleRoleProvider
SimpleRoleProvider(SecuritySystem, SessionFactory, AtomicBoolean) - Constructor for class ome.security.auth.SimpleRoleProvider
SimpleSessionStats - Class in ome.services.sessions.stats
SimpleSessionStats(ObjectsReadCounter, ObjectsWrittenCounter, MethodCounter) - Constructor for class ome.services.sessions.stats.SimpleSessionStats
SimpleSqlWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleSqlWork
SimpleWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleWork
size(String) - Method in class ome.security.auth.AttributeSet
size() - Method in class ome.security.basic.CurrentDetails
size() - Method in interface ome.security.basic.PrincipalHolder: Get the number of active principal contexts.
size() - Method in class ome.services.query.Definitions
size() - Method in class ome.services.RawFileBean
size() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: the total number of fields for this entity.
skipFrom() - Method in class ome.tools.hibernate.QueryBuilder
skipWhere() - Method in class ome.tools.hibernate.QueryBuilder
sleepFor(long) - Static method in class ome.services.util.SleepTimer: Sleep for the given number of milliseconds.
SleepTimer - Class in ome.services.util: Provides a timer for having a thread sleep that prematurely awakens when the server is to shut down, so the sleeping does not keep the server running.
SleepTimer() - Constructor for class ome.services.util.SleepTimer
SmtpAuthenticator - Class in ome.security
SmtpAuthenticator(String, String) - Constructor for class ome.security.SmtpAuthenticator
SomeMustNone - Class in ome.services.search: FullText subclass which parses 3 arrays of strings into into a single Lucene query.
SomeMustNone(SearchValues, String[], String[], String[], Class<? extends Analyzer>) - Constructor for class ome.services.search.SomeMustNone
sortOriginalFileIds(Session, Collection<Long>) - Static method in class ome.services.graphs.ModelObjectSequencer: Deprecated.

Sort a list of original file IDs such that files precede containing directories.
sources - Variable in class ome.services.query.QueryFactory: sources available for lookups.
sql - Variable in class ome.logic.AdminImpl
sql - Variable in class ome.security.basic.EventHandler
sql - Variable in class ome.services.eventlogs.PersistentEventLogLoader
sql - Variable in class ome.services.OmeroFilePathResolver: SQL action instance for this class.
sqlAction - Variable in class ome.services.sharing.BlobShareStore
sqlAction - Variable in class ome.services.util.Executor.Impl
SqlArray<T> - Class in ome.tools.hibernate: Hibernate type to store a java array using SQL ARRAY.
SqlArray(List<T>, int) - Constructor for class ome.tools.hibernate.SqlArray
SqlArray(List<T>, int, String) - Constructor for class ome.tools.hibernate.SqlArray
SqlArray.BOOLEAN - Class in ome.tools.hibernate
SqlArray.DATE - Class in ome.tools.hibernate
SqlArray.DOUBLE - Class in ome.tools.hibernate
SqlArray.FLOAT - Class in ome.tools.hibernate
SqlArray.INTEGER - Class in ome.tools.hibernate
SqlArray.STRING - Class in ome.tools.hibernate
SqlArray.STRING2 - Class in ome.tools.hibernate
sqlTypes() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
standalone(String[]) - Static method in class ome.services.fulltext.Main: Starts up and simply waits until told by the grid to disconnect.
start() - Method in class ome.services.fulltext.FullTextIndexer2: Start the indexer.
start() - Method in class ome.services.fulltext.FullTextThread: Deprecated.

Called by Spring on creation.
start() - Method in class ome.services.mail.SubethaSMTP
start() - Method in class ome.services.pixeldata.PixelDataThread: Called by Spring on creation.
start() - Method in class ome.services.util.DBPatchCheck
start() - Method in class ome.services.util.ServerVersionCheck: Prints simple banner with OMERO version.
startProcess(ServiceFactory, long) - Method in class ome.services.procs.ProcessManager.Work
stats() - Method in interface ome.services.sessions.SessionContext: Return a SessionStats implementation for this session.
stats() - Method in class ome.services.sessions.SessionContextImpl
stats() - Method in class ome.services.sessions.stats.CurrentSessionStats
stats() - Method in class ome.services.sessions.stats.DelegatingStats: Intended to be overwritten by subclasses.
stats() - Method in class ome.services.sessions.stats.PerSessionStats
stats() - Method in class ome.services.sessions.stats.PerThreadStats
stop() - Method in class ome.services.fulltext.FullTextIndexer2: Stop the indexer.
stop() - Method in class ome.services.fulltext.FullTextThread: Deprecated.

Called by Spring on destruction.
stop() - Method in class ome.services.mail.SubethaSMTP
stop() - Method in class ome.services.pixeldata.PixelDataThread: Called by Spring on destruction.
stop() - Method in class ome.services.util.ServerVersionCheck: Prints simple banner with "Stopping OMERO"
store - Variable in class ome.security.basic.BasicSecuritySystem
store - Variable in class ome.services.sharing.ShareBean
storeShareData(long, ShareData) - Method in class ome.services.sharing.ShareBean
STRING - Static variable in class ome.services.query.StringQuery: parameter name for the definition of the HQL string.
STRING(Connection, List<String>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
STRING() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
STRING(List<String>) - Constructor for class ome.tools.hibernate.SqlArray.STRING
STRING2(Connection, List<String[]>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
STRING2() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
STRING2(List<String[]>) - Constructor for class ome.tools.hibernate.SqlArray.STRING2
stringLongToEntity(String, long) - Method in class ome.services.query.HierarchyNavigatorWrap: Convert the given type string and database ID to the model object.
StringQuery - Class in ome.services.query: simple HQL query.
StringQuery(Parameters) - Constructor for class ome.services.query.StringQuery: Default constructor, used primarily for testing.
StringQuery(SqlAction, Parameters) - Constructor for class ome.services.query.StringQuery
StringQuerySource - Class in ome.services.query: interprets the query id as an HQL query.
StringQuerySource() - Constructor for class ome.services.query.StringQuerySource: Default constructor, used primarily for testing.
StringQuerySource(SqlAction) - Constructor for class ome.services.query.StringQuerySource
StringSeqHelper - Class in ome.services.sharing.data
StringSeqHelper() - Constructor for class ome.services.sharing.data.StringSeqHelper
StringSeqHolder - Class in ome.services.sharing.data
StringSeqHolder() - Constructor for class ome.services.sharing.data.StringSeqHolder
StringSeqHolder(List<String>) - Constructor for class ome.services.sharing.data.StringSeqHolder
stringToType(String) - Method in class ome.services.query.HierarchyNavigatorWrap: Convert the given type string to the object type.
SubethaSMTP - Class in ome.services.mail: Simple server bean which can be started on Spring context creation and shutdown when the application is editing.
SubethaSMTP(MessageHandlerFactory) - Constructor for class ome.services.mail.SubethaSMTP
SubethaSMTP(MessageHandlerFactory, int) - Constructor for class ome.services.mail.SubethaSMTP
subject - Variable in class ome.services.graphs.GraphPolicy.Details: the unloaded instance
submit(Job) - Method in class ome.services.JobBean
submit(Callable<T>) - Method in class ome.services.util.Executor.Impl
submit(Map<String, String>, Callable<T>) - Method in class ome.services.util.Executor.Impl
submit(Executor.Priority, Callable<T>) - Method in class ome.services.util.Executor.Impl
submit(Executor.Priority, Map<String, String>, Callable<T>) - Method in class ome.services.util.Executor.Impl
submit(Callable<T>) - Method in interface ome.services.util.Executor: Call Executor.submit(Map, Callable) with a null callContext.
submit(Map<String, String>, Callable<T>) - Method in interface ome.services.util.Executor: Simple submission method which can be used in conjunction with a call to Executor.execute(Principal, Work) to overcome the no-multiple-login rule.
submit(Executor.Priority, Callable<T>) - Method in interface ome.services.util.Executor: Simple submission method with a Executor.Priority.
submit(Executor.Priority, Map<String, String>, Callable<T>) - Method in interface ome.services.util.Executor: Like Executor.submit(Map, Callable) but provide info to which priority queue should be used.
subselect(QueryBuilder) - Method in class ome.tools.hibernate.QueryBuilder: Appends the string representation of the QueryBuilder argument inside of parentheses.
subtypeEquals(int, int, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: returns true is the indexed subtype returns the same class type as the klass argument.
subtypeName(int, int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: retrieves the full Hibernate path for this component field.
success(SqlAction.DeleteLog) - Method in class ome.services.messages.DeleteLogMessage
success - Variable in class ome.services.messages.LoginAttemptMessage
sudoer - Variable in class ome.services.sessions.SessionManager.CreationRequest
SVGRasterizer - Class in ome.services: This class provides a simple and method based API for converting a SVG document fragment to a BufferedImage.
SVGRasterizer(String) - Constructor for class ome.services.SVGRasterizer: Constructs a new SVGRasterizer.
SVGRasterizer(URL) - Constructor for class ome.services.SVGRasterizer: Constructs a new SVGRasterizer.
SVGRasterizer(InputStream) - Constructor for class ome.services.SVGRasterizer: Constructs a new SVGRasterizer converter.
SVGRasterizer(Reader) - Constructor for class ome.services.SVGRasterizer: Constructs a new SVGRasterizer converter.
SVGRasterizer.Rasterizer - Class in ome.services: An image transcoder that stores the resulting image.
synchronizeLdapUser(String) - Method in class ome.logic.LdapImpl
synchronizeLoginCache() - Method in class ome.logic.AdminImpl
systemService - Variable in class ome.services.util.Executor.Impl
SystemTypes - Class in ome.security: Defines what IObject classes are considered "system" types.
SystemTypes() - Constructor for class ome.security.SystemTypes
SystemTypes(Roles) - Constructor for class ome.security.SystemTypes
sysTypes - Variable in class ome.security.basic.BasicACLVoter
sysTypes - Variable in class ome.security.basic.BasicSecuritySystem

T

TablesBridge - Class in ome.services.fulltext.bridges: Deprecated.
TablesBridge() - Constructor for class ome.services.fulltext.bridges.TablesBridge: Deprecated.
TagsAndGroups - Class in ome.services.search: Query template used by SearchBean to store user requests.
TagsAndGroups(SearchValues, String, boolean) - Constructor for class ome.services.search.TagsAndGroups
targetName - Variable in class ome.services.util.BeanInstantiationGuard
tearDown() - Method in class ome.formats.importer.util.TinyImportFixture: Deprecated.
templateMessage - Variable in class ome.logic.AdminImpl
ThreadPool - Class in ome.services.scheduler: An internal implementation of ThreadPoolExecutor that additionally handles the submission of ThreadPool.background(Callable) tasks at a lower priority and with more limited slots.
ThreadPool() - Constructor for class ome.services.scheduler.ThreadPool
ThreadPool(int, int, long, int, long) - Constructor for class ome.services.scheduler.ThreadPool
throwable - Variable in class ome.services.eventlogs.EventLogFailure
throwCreationViolation(IObject) - Method in interface ome.security.ACLVoter: throws a SecurityViolation based on the given IObject and the context of the current user.
throwCreationViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
throwCreationViolation(IObject) - Method in class ome.security.CompositeACLVoter
throwCreationViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
throwDeleteViolation(IObject) - Method in interface ome.security.ACLVoter: throws a SecurityViolation based on the given IObject and the context of the current user.
throwDeleteViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
throwDeleteViolation(IObject) - Method in class ome.security.CompositeACLVoter
throwDeleteViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
throwDisabled(String) - Method in class ome.security.sharing.SharingACLVoter
throwIfAlreadySet(Object, Object) - Method in class ome.services.util.BeanHelper
throwIfCancelled() - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
throwLoadViolation(IObject) - Method in interface ome.security.ACLVoter: throws a SecurityViolation based on the given IObject and the context of the current user.
throwLoadViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
throwLoadViolation(IObject) - Method in class ome.security.CompositeACLVoter
throwLoadViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
throwOnNullData(long, ShareData) - Method in class ome.services.sharing.ShareBean
throwUpdateViolation(IObject) - Method in interface ome.security.ACLVoter: throws a SecurityViolation based on the given IObject and the context of the current user.
throwUpdateViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
throwUpdateViolation(IObject) - Method in class ome.security.CompositeACLVoter
throwUpdateViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
ThumbnailBean - Class in ome.services: Provides methods for directly querying object graphs.
ThumbnailBean(boolean) - Constructor for class ome.services.ThumbnailBean: overridden to allow Spring to set boolean
ThumbnailBeanReadOnly - Class in ome.services: Provides methods for directly querying object graphs.
ThumbnailBeanReadOnly(boolean) - Constructor for class ome.services.ThumbnailBeanReadOnly: overridden to allow Spring to set boolean
ThumbnailCtx - Class in ome.services
ThumbnailCtx(IQuery, IUpdate, IPixels, IRenderingSettings, ThumbnailService, OmeroContext, SecuritySystem, long) - Constructor for class ome.services.ThumbnailCtx: Default constructor.
ThumbnailCtx.NoThumbnail - Exception in ome.services: Marker exception which is thrown by all methods which wish to tell their callers that for whatever reason the desired Thumbnail is not available, in which case the caller can use a *Direct method instead.
thumbnailExists(Integer, Integer) - Method in class ome.services.ThumbnailBean
ThumbnailFileDeletions - Class in ome.services.delete.files: Helper class which sorts through a number of file-based deletions before processing them.
ThumbnailFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.ThumbnailFileDeletions
timeout - Variable in class ome.services.search.SearchAction
timeoutSetter - Variable in class ome.logic.QueryImpl
TimeoutSetter - Class in ome.services.util: Sets timeouts for queries according to event context.
TimeoutSetter(SecuritySystem, int, int) - Constructor for class ome.services.util.TimeoutSetter: Construct the timeout setter.
timeToIdle - Variable in class ome.services.sessions.SessionManager.CreationRequest
timeToLive - Variable in class ome.services.sessions.SessionManager.CreationRequest
TinyImportFixture - Class in ome.formats.importer.util: Deprecated.
TinyImportFixture(ServiceFactory) - Constructor for class ome.formats.importer.util.TinyImportFixture: Deprecated.
TO - Static variable in class ome.services.mail.MapAnnotationSubethaListener
tokenHolder - Variable in class ome.security.basic.BasicACLVoter
tokenHolder - Variable in class ome.security.basic.BasicSecuritySystem
TokenHolder - Class in ome.security.basic: Manages a special token (a unique object) which can be inserted into IObject instances for special almost-administrative handling.
TokenHolder() - Constructor for class ome.security.basic.TokenHolder
tokenStream(String, Reader) - Method in class ome.services.fulltext.FullTextAnalyzer: Deprecated.

Returns a FullTextAnalyzer.LowercaseAlphaNumericTokenizer
toString() - Method in class ome.security.basic.BasicEventContext
toString() - Method in exception ome.services.graphs.GraphException
toString() - Method in class ome.services.graphs.GraphPolicyRule
toString() - Method in class ome.services.scripts.RepoFile.FsFile
toString() - Method in class ome.services.scripts.RepoFile
toString() - Method in class ome.tools.hibernate.QueryBuilder
toString() - Method in class ome.tools.hibernate.SqlArray
toString() - Method in class ome.tools.spring.InternalServiceFactory
total() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: as opposed to ExtendedMetadata.Locks.size(), the returns the actual number of fields that will need to be checked.
TOTAL_PHYSICAL_MEMORY - Static variable in class ome.services.util.JvmSettingsCheck: TotalPhysicalMemorySize value from the OperatingSystem JMX bean at startup.
TOTAL_SIZE - Static variable in class ome.services.search.FullText
totalSharedItems() - Method in class ome.services.sharing.BlobShareStore
totalSharedItems() - Method in class ome.services.sharing.ShareStore
totalShares() - Method in class ome.services.sharing.BlobShareStore
totalShares() - Method in class ome.services.sharing.ShareStore
translateException(Throwable) - Method in class ome.services.util.BeanHelper
truncate(long) - Method in class ome.services.RawFileBean
txSource - Variable in class ome.security.basic.EventHandler
type - Variable in class ome.services.query.QueryParameterDef: type of this parameter.
type - Variable in class ome.services.sharing.data.Obj
type() - Method in class ome.services.sharing.data.ObjHolder
type() - Method in class ome.services.sharing.data.ShareDataHolder
type - Variable in class ome.services.sharing.data.ShareItem
type() - Method in class ome.services.sharing.data.ShareItemHolder
types - Variable in class ome.security.policy.BasePolicy
types - Variable in class ome.services.eventlogs.PersistentEventLogLoader
TypesImpl - Class in ome.logic: implementation of the ITypes service interface.
TypesImpl() - Constructor for class ome.logic.TypesImpl
typeToString(T) - Method in class ome.services.query.HierarchyNavigatorWrap: Convert the given object type to the type strings expected by HierarchyNavigator.

U

uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper: Downcasts the given proxy to this type without contacting the remote server.
uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ObjPrxHelper: Downcasts the given proxy to this type without contacting the remote server.
uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper: Downcasts the given proxy to this type without contacting the remote server.
uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareDataPrxHelper: Downcasts the given proxy to this type without contacting the remote server.
uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper: Downcasts the given proxy to this type without contacting the remote server.
uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareItemPrxHelper: Downcasts the given proxy to this type without contacting the remote server.
Union - Class in ome.services.search: Union SearchAction which combines two other search actions into one logical unit, e.g.
Union(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Union
unique_alias(String) - Method in class ome.tools.hibernate.QueryBuilder: Obtain a unique alias to be used in the SQL.
unlink(ILink[], Parameters) - Method in class ome.logic.PojosImpl
unlinkTargets(boolean) - Method in class ome.services.graphs.GraphTraversal: Prepare to remove links between the targeted model objects and the remainder of the model object graph.
unloadedObjectCache - Variable in class ome.tools.hibernate.ProxyCleanupFilter
unloadReplacedObjects() - Method in class ome.tools.hibernate.UpdateFilter: provides an external hook to unload all files which have already been merged.
unordered() - Method in class ome.services.SearchBean
unregister(Long, SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper: Unregisters a given file from the script repository by setting its Repo uuid to null.
unregisterCallback(ProcessCallback) - Method in interface ome.services.procs.Process
unregisterCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton
unsetGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl
update(RepoFile, Long, Map<String, String>) - Method in class ome.services.scripts.ScriptRepoHelper
update(Session) - Method in interface ome.services.sessions.SessionManager: Certain fields from the Session instance will be copied and then saved to the db, as well as a new SessionContext created.
update(Session, boolean) - Method in interface ome.services.sessions.SessionManager: Same as SessionManager.update(Session) but some security checks can be overridden.
update(Session) - Method in class ome.services.sessions.SessionManagerImpl
update(Session, boolean) - Method in class ome.services.sessions.SessionManagerImpl
update(Share, ShareData) - Method in class ome.services.sharing.ShareStore
update(String) - Method in class ome.tools.hibernate.QueryBuilder
UPDATE_EVENT - Static variable in class ome.security.basic.UpdateEventListener
updateCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean: Deprecated.
updateDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl
updateDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl
updatedObjects(int) - Method in class ome.services.sessions.stats.DelegatingStats
updatedObjects(int) - Method in class ome.services.sessions.stats.NullSessionStats
updatedObjects(int) - Method in interface ome.services.sessions.stats.SessionStats
updatedObjects(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
updateEnumeration(T) - Method in class ome.logic.TypesImpl
updateEnumerations(List<T>) - Method in class ome.logic.TypesImpl
updateEvent(Event) - Method in class ome.security.basic.EventProviderInDb: Persists a given Event.
updateEvent(Event) - Method in class ome.security.basic.EventProviderInMemory: Persists a given Event.
updateEvent(Event) - Method in class ome.security.basic.EventProviderWrapper
updateEvent(Event) - Method in interface ome.security.EventProvider: Persists a given Event.
updateEvent(UserGroupUpdateEvent) - Method in class ome.services.sessions.state.SessionCache: Adds a new entry to SessionCache.state.
UpdateEventListener - Class in ome.security.basic: responsible for setting the updat event on all events shortly before being saved.
UpdateEventListener(CurrentDetails) - Constructor for class ome.security.basic.UpdateEventListener: main constructor.
updateExperimenter(Experimenter) - Method in class ome.logic.AdminImpl
updateExperimenterWithPassword(Experimenter, String) - Method in class ome.logic.AdminImpl
UpdateFilter - Class in ome.tools.hibernate: responsible for correlating entity identities during multiple calls to merge.
UpdateFilter() - Constructor for class ome.tools.hibernate.UpdateFilter
updateGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
UpdateImpl - Class in ome.logic: implementation of the IUpdate service interface
UpdateImpl() - Constructor for class ome.logic.UpdateImpl
updateObject(String, IObject, Map<String, Integer>) - Method in class ome.formats.OMEROMetadataStore: Updates a given model object in our object graph.
updateObject(T...) - Method in interface ome.security.SecureAction: executes with special privileges within the SecuritySystem.
updateObject(T...) - Method in class ome.tools.hibernate.SecureMerge
updateReadFilter(Session) - Method in class ome.security.basic.BasicSecuritySystem
updateReferences(Map<String, String[]>) - Method in class ome.formats.OMEROMetadataStore: Updates our object graph references.
updateSelf(Experimenter) - Method in class ome.logic.AdminImpl
updateSession(Session) - Method in class ome.services.sessions.SessionBean
updateSettings(RenderingDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
uploadMyUserPhoto(String, String, byte[]) - Method in class ome.logic.AdminImpl
usage() - Static method in class ome.services.fulltext.Main
useProjections - Variable in class ome.services.search.SearchValues
user - Variable in class ome.services.messages.LoginAttemptMessage
userGroups(String) - Method in class ome.security.auth.PasswordUtil
UserGroupUpdateEvent - Class in ome.services.sessions.events: InternalMessage published by the SecuritySystem when an Experimenter, ExperimenterGroup, or GroupExperimenterMap is inserted or updated.
UserGroupUpdateEvent(Object) - Constructor for class ome.services.sessions.events.UserGroupUpdateEvent
userId(String) - Method in class ome.security.auth.PasswordUtil: Get the user's ID
userName(long) - Method in class ome.security.auth.PasswordUtil: Get the user's name
usernameFilter(String) - Method in class ome.security.auth.LdapConfig
userProxy(String) - Method in interface ome.api.local.LocalAdmin: returns a possibly uninitialized proxy for the given user name.
userProxy(Long) - Method in interface ome.api.local.LocalAdmin: returns a possibly uninitialized proxy for the given user id.
userProxy(Long) - Method in class ome.logic.AdminImpl
userProxy(String) - Method in class ome.logic.AdminImpl
util - Variable in class ome.security.auth.ConfigurablePasswordProvider
uuid - Variable in class ome.security.basic.NodeProviderInDb: UUID for this cluster node.
uuid - Variable in class ome.security.basic.NodeProviderInMemory: UUID for this cluster node.

V

valid(String) - Method in class ome.services.db.DatabaseIdentity
validateEmail(String) - Method in class ome.services.mail.MailUtil: Helper Validate that this address conforms to the syntax rules of RFC 822.
validatePassword(String, String) - Method in class ome.logic.LdapImpl: Validates password for base.
value(String) - Method in class ome.services.query.Query: get the Object value for this name argument.
value - Variable in class ome.services.sharing.data.ObjPrxHolder
value - Variable in class ome.services.sharing.data.ShareDataPrxHolder
value - Variable in class ome.services.sharing.data.ShareItemPrxHolder
valueOf(String) - Static method in enum ome.security.auth.PasswordUtil.METHOD: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Ability: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Action: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Orphan: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.util.Executor.Priority: Returns the enum constant of this type with the specified name.
values() - Static method in enum ome.security.auth.PasswordUtil.METHOD: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.graphs.GraphPolicy.Ability: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.graphs.GraphPolicy.Action: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.graphs.GraphPolicy.Orphan: Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class ome.services.search.SearchAction
values() - Static method in enum ome.services.util.Executor.Priority: Returns an array containing the constants of this enum type, in the order they are declared.
verbose - Variable in class ome.tools.hibernate.EventMethodInterceptor

W

waitForLock - Variable in class ome.services.fulltext.FullTextThread: Deprecated.
wasSource(EventLogLoader) - Method in class ome.services.eventlogs.EventLogFailure
where() - Method in class ome.tools.hibernate.QueryBuilder: Marks the end of all fetches by adding a "where" clause to the string.
whereClause() - Method in class ome.tools.hibernate.QueryBuilder: Similar to how skipFrom and skipWhere were previously used, this sets the current builder to QueryBuilder.where() but without prefacing the "where " string.
Work(SecuritySystem, Processor...) - Constructor for class ome.services.procs.ProcessManager.Work
work - Variable in class ome.services.util.ExecutionThread
wrap(String, IObject) - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
wrap(Iterator<Reader>) - Method in class ome.services.fulltext.FileParser: Wraps an Iterator with an Iterable instance.
wrap(Reader) - Method in class ome.services.fulltext.FileParser
write(byte[], long, int) - Method in class ome.services.RawFileBean
write(String, String) - Method in class ome.services.scripts.ScriptRepoHelper
write(RepoFile, String) - Method in class ome.services.scripts.ScriptRepoHelper
write(BasicStream, Map<String, List<Long>>) - Static method in class ome.services.sharing.data.IdMapHelper
write(BasicStream, List<Long>) - Static method in class ome.services.sharing.data.LongSeqHelper
write(BasicStream, List<Obj>) - Static method in class ome.services.sharing.data.ObjSeqHelper
write(BasicStream, List<String>) - Static method in class ome.services.sharing.data.StringSeqHelper
writeImage(BufferedImage, TranscoderOutput) - Method in class ome.services.SVGRasterizer.Rasterizer
WriteStrategy - Interface in ome.security: Responsible for determining which users can modify which objects in which contexts.
writtenBytes(int) - Method in class ome.services.sessions.stats.DelegatingStats
writtenBytes(int) - Method in class ome.services.sessions.stats.NullSessionStats
writtenBytes(int) - Method in interface ome.services.sessions.stats.SessionStats
writtenBytes(int) - Method in class ome.services.sessions.stats.SimpleSessionStats

_

__dont_use_me_factory - Variable in class ome.services.sharing.BlobShareStore: Used indirectly to obtain sessions for querying and updating the store during normal operation.
__ids - Static variable in class ome.services.sharing.data.Obj
__ids - Static variable in class ome.services.sharing.data.ObjPrxHelper
__ids - Static variable in class ome.services.sharing.data.ShareData
__ids - Static variable in class ome.services.sharing.data.ShareDataPrxHelper
__ids - Static variable in class ome.services.sharing.data.ShareItem
__ids - Static variable in class ome.services.sharing.data.ShareItemPrxHelper
__read(BasicStream) - Static method in class ome.services.sharing.data.ObjPrxHelper
__read(BasicStream) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
__read(BasicStream) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
__readImpl(BasicStream) - Method in class ome.services.sharing.data.Obj
__readImpl(BasicStream) - Method in class ome.services.sharing.data.ShareData
__readImpl(BasicStream) - Method in class ome.services.sharing.data.ShareItem
__write(BasicStream, ObjPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper
__write(BasicStream, ShareDataPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
__write(BasicStream, ShareItemPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
__writeImpl(BasicStream) - Method in class ome.services.sharing.data.Obj
__writeImpl(BasicStream) - Method in class ome.services.sharing.data.ShareData
__writeImpl(BasicStream) - Method in class ome.services.sharing.data.ShareItem
_addGraph(ShareData, ShareBean.Graph) - Method in class ome.services.sharing.ShareBean

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