Index (OMERO (OME Remote Objects) Server)

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AbstractAmdServant - Class in ome.services.blitz.impl: throttled implementation base class which can be used by _ServiceInterfaceOperations implementors and injected into a tie servant.
AbstractAmdServant(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AbstractAmdServant
AbstractBuffer - Class in ome.io.nio
AbstractClassIdsOptionsQuery - Class in ome.services.query: simple abstract class that provides a common Definitions containing: IdsQueryParameterDef, ome.services.query.OptionsQueryParameterDef, and ClassQueryParameterDef.
AbstractClassIdsOptionsQuery(Parameters) - Constructor for class ome.services.query.AbstractClassIdsOptionsQuery
AbstractFileSystemService - Class in ome.io.nio
AbstractFileSystemService(String) - Constructor for class ome.io.nio.AbstractFileSystemService
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
AbstractRedirector - Class in ome.services.blitz.redirect: Base Redirector
AbstractRedirector(Executor) - Constructor for class ome.services.blitz.redirect.AbstractRedirector
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
AbstractThrottlingStrategy - Class in ome.services.throttling: Throttling implementation which uses the calling server Thread for execution.
AbstractThrottlingStrategy() - Constructor for class ome.services.throttling.AbstractThrottlingStrategy
accept(Job) - Method in class ome.services.procs.ProcessorSkeleton
access(File) - Method in class omero.util.TempFileManager: Returns true if the current user can write to the give directory.
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. controls access to individual db rows..
aclVoter - Variable in class ome.logic.AdminImpl
ACLVoter - Interface in ome.security: helper security interface for all decisions on access control
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.
acquireLock(String) - Method in class ome.services.blitz.util.ServantHolder: Acquires the given lock or if necessary creates a new one.
acquireProcessor(Job, int, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
acquireProcessor(Job, int, Current) - Method in interface omero.grid.ParamsHelper.Acquirer
acquisitionData() - Method in class omero.sys.ParametersI: Sets the acquisition data parameter to true.
action - Variable in class ome.services.messages.EventLogMessage
action - Variable in class ome.tools.hibernate.EventMethodInterceptor
activate(long) - Method in interface ome.api.IShare: Turns on the access control lists attached to the given share for the current session.
activate() - Method in interface ome.api.StatefulServiceInterface: Completely restore this service for active use from whatever passivation it has implemented.
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
activate_async(AMD_StatefulServiceInterface_activate, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
activate_async(AMD_IShare_activate, long, Current) - Method in class ome.services.blitz.impl.ShareI
activateAndWait(Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI: Generates a UUID-based Identity with the category of PROCESSORCALLBACK.value and then calls {@link #activateAndWait(Current, Ice.Identity).
activateAndWait(Current, Identity) - Method in class ome.services.blitz.impl.ProcessorCallbackI: Primary method which adds this instance to IceStorm, waits for a response from any active processor services, and finally unregister itself before returning the first processor instance which responded.
activeQueries() - Method in interface ome.api.Search: Returns the number of active queries.
activeQueries() - Method in class ome.services.SearchBean
activeQueries_async(AMD_Search_activeQueries, Current) - Method in class ome.services.blitz.impl.SearchI
activeServices(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
adapter - Variable in class ome.services.blitz.fire.SessionManagerI
Adapter - Class in ome.services.throttling: Simple adapter which takes a Executor.Work instance and executes it as a BlitzExecutor task.
Adapter(Object, Current, IceMapper, Executor, Principal, Executor.Work) - Constructor for class ome.services.throttling.Adapter
add(Document, String, String, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper: Helper method which takes the parameters from the #set(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float) method (possibly modified) as well as the parsed String value which should be added to the index, and adds two fields.
add(EventLog) - Method in class ome.services.fulltext.EventBacklog: Adds the given EventLog instance to the end of a queue for later popping if no equivalent EventLog is present.
add(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain: Adds a map context to the chain.
add(String, RType) - Method in class omero.sys.ParametersI
add(Resources.Entry) - Method in class omero.util.Resources
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
addArray(int[][], int, int, int) - Method in class pojos.util.UploadMask: Adds a Mask Shape to the appropriate ROIClass, creating one if necessary.
addCallback(String, SessionCallback) - Method in class ome.services.sessions.SessionManagerImpl
addCircle(String, double, double, double) - Method in class ome.services.blitz.measurements.MeasurementStore
addCircle(String, double, double, double) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
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: Implemented as specified by the RenderingEngine interface.
addCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine: Adds the context to the mapping chain.
addCodomainMap_async(AMD_RenderingEngine_addCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
addComment(long, String) - Method in interface ome.api.IShare: Creates comment for share.
addComment(long, String) - Method in class ome.services.sharing.ShareBean
addComment_async(AMD_IShare_addComment, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
addContents(Document, String, OriginalFile, OriginalFilesService, Map<String, FileParser>, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper: Second helper method used when parsing files.
addDisabled(String) - Method in class ome.security.basic.CurrentDetails
addEventLog(Class<? extends IObject>, long) - Method in class ome.services.fulltext.EventLogLoader: Adds an EventLog for the given Class and id to the backlog.
addGroupOwners(ExperimenterGroup, Experimenter...) - Method in interface ome.api.IAdmin: adds the given users to the owner list for this group.
addGroupOwners(ExperimenterGroup, Experimenter...) - Method in class ome.logic.AdminImpl
addGroupOwners_async(AMD_IAdmin_addGroupOwners, ExperimenterGroup, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.AdminI
addGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.api.IAdmin: adds a user to the given groups.
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
addGroups_async(AMD_IAdmin_addGroups, Experimenter, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
addGuest(long, String) - Method in interface ome.api.IShare: Add guest email address to the share.
addGuest(long, String) - Method in class ome.services.sharing.ShareBean
addGuest_async(AMD_IShare_addGuest, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
addGuests(long, String...) - Method in interface ome.api.IShare: Adds guest email addresses to the share.
addGuests(long, String...) - Method in class ome.services.sharing.ShareBean
addGuests_async(AMD_IShare_addGuests, long, List<String>, Current) - Method in class ome.services.blitz.impl.ShareI
addId(long) - Method in class omero.sys.ParametersI
addId(RLong) - Method in class omero.sys.ParametersI
addIds(Collection<Long>) - Method in class omero.sys.ParametersI
addImage(Image) - Method in class ome.services.blitz.impl.OmeroMetadata
addImage(byte[], int, int, int) - Method in class pojos.util.UploadMask: Adds a Mask Shape to the appropriate ROIClass, creating one if necessary.
addImage_async(AMD_Exporter_addImage, long, Current) - Method in class ome.services.blitz.impl.ExporterI
adding - Variable in class ome.services.fulltext.EventBacklog: Switch between the adding and the removing states.
additions() - Method in class ome.security.basic.EventListenersFactoryBean
addKeyword(String) - Method in class pojos.WorkflowData: Adds a new keyword to the workflow.
addLog(String, Class, Long) - Method in class ome.security.basic.BasicSecuritySystem
addLog(String, Class, Long) - Method in class ome.security.basic.CurrentDetails
addLong(String, long) - Method in class omero.sys.ParametersI
addLong(String, RLong) - Method in class omero.sys.ParametersI
addLongs(String, Collection<Long>) - Method in class omero.sys.ParametersI
addMasks(Map<Integer, MaskData>) - Method in class pojos.util.ROIComponent: Adds the Masks in the maskSet to the component.
addObject(long, T) - Method in interface ome.api.IShare: Adds new item to share.
addObject(ObjectPrx) - Method in interface ome.services.blitz.fire.Registry
addObject(ObjectPrx) - Method in class ome.services.blitz.fire.Registry.Impl
addObject(String, IObject) - Method in class ome.services.blitz.measurements.MeasurementStore
addObject(String, IObject) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
addObject(long, T) - Method in class ome.services.sharing.ShareBean
addObject_async(AMD_IShare_addObject, long, IObject, Current) - Method in class ome.services.blitz.impl.ShareI
addObjects(long, T...) - Method in interface ome.api.IShare: Adds new items to share.
addObjects(Map<String, IObject>) - Method in class ome.services.blitz.measurements.MeasurementStore
addObjects(Map<String, IObject>) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
addObjects(long, T...) - Method in class ome.services.sharing.ShareBean
addObjects_async(AMD_IShare_addObjects, long, List<IObject>, Current) - Method in class ome.services.blitz.impl.ShareI
addOrderByAsc(String) - Method in interface ome.api.Search: A path from the target entity which will be added to the current stack of order statements applied to the query.
addOrderByAsc(String) - Method in class ome.services.SearchBean
addOrderByAsc_async(AMD_Search_addOrderByAsc, String, Current) - Method in class ome.services.blitz.impl.SearchI
addOrderByDesc(String) - Method in interface ome.api.Search: A path from the target entity which will be added to the current stack of order statements applied to the query.
addOrderByDesc(String) - Method in class ome.services.SearchBean
addOrderByDesc_async(AMD_Search_addOrderByDesc, String, Current) - Method in class ome.services.blitz.impl.SearchI
addOrReplace(RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper
addOrReplace(Session, ServiceFactory, RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper
addProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
addReply(long, String, CommentAnnotation) - Method in interface ome.api.IShare: Creates comment which replies to an existing comment.
addReply(long, String, CommentAnnotation) - Method in class ome.services.sharing.ShareBean
addReply_async(AMD_IShare_addReply, long, String, TextAnnotation, Current) - Method in class ome.services.blitz.impl.ShareI
addResult(List<IObject>) - Method in class ome.services.SearchBean
addRows(Object[][]) - Method in class ome.services.blitz.measurements.MeasurementStore
addRows(Object[][]) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore: Adds an array of rows (Object[]) to the store.
addSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache
addShapeData(ShapeData) - Method in class pojos.ROIData: Adds ShapeData object to ROIData.
addUser(long, Experimenter) - Method in interface ome.api.IShare: Adds experimenter to share
addUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean
addUser_async(AMD_IShare_addUser, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
addUsers(long, Experimenter...) - Method in interface ome.api.IShare: Adds experimenters to share
addUsers(long, Experimenter...) - Method in class ome.services.sharing.ShareBean
addUsers_async(AMD_IShare_addUsers, long, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.ShareI
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
AdminI - Class in ome.services.blitz.impl: Implementation of the IAdmin service.
AdminI(IAdmin, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AdminI
AdminImpl - Class in ome.logic: Provides methods for administering user accounts, passwords, as well as methods which require special privileges.
AdminImpl(SimpleJdbcOperations, SessionFactory, MailSender, SimpleMailMessage, ACLVoter, PasswordProvider, RoleProvider, LdapImpl, PasswordUtil) - Constructor for class ome.logic.AdminImpl
advices - Variable in class ome.services.util.Executor.Impl
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
aggByQuery(String, String, String, Parameters) - Method in class ome.logic.QueryImpl
aggMapByQuery(String, String, String, String, Parameters) - Method in class ome.logic.QueryImpl
all(String[]) - Static method in class prefs: Calls Preferences.childrenNames() and returns the array.
AllEntitiesPseudoLogLoader<T extends ome.model.IObject> - Class in ome.services.fulltext: 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.fulltext.AllEntitiesPseudoLogLoader
allEnumerations(Class<T>) - Method in interface ome.api.ITypes
allEnumerations(Class<T>) - Method in class ome.logic.TypesImpl
allEnumerations_async(AMD_ITypes_allEnumerations, String, Current) - Method in class ome.services.blitz.impl.TypesI
AllEventsLogLoader - Class in ome.services.fulltext
AllEventsLogLoader() - Constructor for class ome.services.fulltext.AllEventsLogLoader
allExps() - Method in class omero.sys.ParametersI: Removes the experimenter parameter from the map.
allGrps() - Method in class omero.sys.ParametersI: Removes the group parameter from the map.
allow(ObjectPrx) - Method in class ome.services.blitz.impl.ServiceFactoryI
ALLOW_LEADING_WILDCARD - Static variable in interface ome.api.Search: Default leading-wildcard setting
allowAdministration() - Method in class ome.services.blitz.Router
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(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(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(Class<? extends IObject>, Details, long) - Method in class ome.security.CompositeACLVoter
allowLoad(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
allTimes() - Method in class omero.sys.ParametersI: Removes the time parameters from the map.
allTypes() - Method in interface ome.api.Search: Permits all types to be returned.
allTypes() - Method in class ome.services.SearchBean
allTypes_async(AMD_Search_allTypes, Current) - Method in class ome.services.blitz.impl.SearchI
ALPHA_INDEX - Static variable in class omeis.providers.re.ColorsFactory: Index of the red component of a color.
alphalessRendering - Variable in class omeis.providers.re.Optimizations: We can do alphaless rendering
alreadyRouted(Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
alreadySeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
analyzer - Variable in class ome.logic.QueryImpl
and() - Method in interface ome.api.Search: Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the intersection of the two calls.
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.
and_async(AMD_Search_and, Current) - Method in class ome.services.blitz.impl.SearchI
angle(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the angle between this vector and the specified argument, provided none of these vectors is the null vector.
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
AnnotationData - Class in pojos: Holds a textual annotation of a given data object and a reference to the Experimenter that wrote it.
AnnotationData(Class<? extends Annotation>) - Constructor for class pojos.AnnotationData: Creates a new instance.
AnnotationData(A) - Constructor for class pojos.AnnotationData: Creates a new instance.
AnnotationDeleteSpec - Class in ome.services.delete: DeleteSpec specialized for deleting annotations.
AnnotationDeleteSpec(List<String>) - Constructor for class ome.services.delete.AnnotationDeleteSpec: Creates a new instance.
AnnotationDeleteSpec(Map<String, String>, List<String>) - Constructor for class ome.services.delete.AnnotationDeleteSpec: Creates a new instance.
ANNOTATIONS - Static variable in class pojos.ChannelData: Identifies the Channel#ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class pojos.DatasetData: Identifies the Dataset#ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class pojos.ImageData: Identifies the Image#ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class pojos.PlateData: Identifies the Plate#ANNOTATIONLINKS field.
AnnotationUtils - Class in ome.annotations: Checks metadata constraints on API calls.
AnnotationUtils() - Constructor for class ome.annotations.AnnotationUtils
AopContextInitializer - Class in ome.services.blitz.fire
AopContextInitializer(ServiceFactory, Principal, boolean) - Constructor for class ome.services.blitz.fire.AopContextInitializer
ApiConsistencyCheck - Class in ome.services.blitz.util: Checks all servant definitions (see: ome/services/blitz-servantDefinitions.xml) to guarantee that the RMI and the Blitz APIs match.
ApiConsistencyCheck() - Constructor for class ome.services.blitz.util.ApiConsistencyCheck
ApiConstraintChecker - Class in ome.annotations: Checks metadata constraints on API calls.
ApiConstraintChecker() - Constructor for class ome.annotations.ApiConstraintChecker
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
appendDbPoint(StringBuilder, Point) - Static method in class omero.model.SmartShape.Util
appendDbPoint(StringBuilder, double, double) - Static method in class omero.model.SmartShape.Util
appendSegement(StringBuilder, boolean, double, double) - Static method in class omero.model.SmartShape.Util
appendSpace() - Method in class ome.tools.hibernate.QueryBuilder
appendSvgPoint(StringBuilder, Point) - Static method in class omero.model.SmartShape.Util
appendSvgPoint(StringBuilder, double, double) - Static method in class omero.model.SmartShape.Util
applyBeanPropertyValues(Object, String) - Method in class ome.system.OmeroContext: Uses the methods of this context's BeanFactory to autowire any Object based on the given beanName.
applyBeanPropertyValues(Object, Class<? extends ServiceInterface>) - Method in class ome.system.OmeroContext: Uses the methods of this context's BeanFactory to autowire any Object based on the service class.
applyHardWiredInterceptors(List<HardWiredInterceptor>, AopContextInitializer) - Method in class ome.services.blitz.impl.AbstractAmdServant: Applies the hard-wired intercepting to this instance.
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 interface ome.api.IRenderingSettings: Applies rendering settings to all images in a given Dataset.
applySettingsToDataset(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
applySettingsToDataset_async(AMD_IRenderingSettings_applySettingsToDataset, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
applySettingsToImage(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to a given Image.
applySettingsToImage(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
applySettingsToImage_async(AMD_IRenderingSettings_applySettingsToImage, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
applySettingsToImages(long, List<Long>) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to a given Image.
applySettingsToImages(long, List<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
applySettingsToImages_async(AMD_IRenderingSettings_applySettingsToImages, long, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
applySettingsToPixels(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to a given Pixels.
applySettingsToPixels(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
applySettingsToPixels_async(AMD_IRenderingSettings_applySettingsToPixels, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
applySettingsToProject(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to all images in all Datasets of a given Project.
applySettingsToProject(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
applySettingsToProject_async(AMD_IRenderingSettings_applySettingsToProject, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
applySettingsToSet(long, Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to one or many containers.
applySettingsToSet(long, Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
applySettingsToSet_async(AMD_IRenderingSettings_applySettingsToSet, long, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
ARC - Static variable in class pojos.LightSourceData: Indicates that the light source is a arc.
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartEllipseI
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartLineI
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartMaskI
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPathI
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPointI
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPolygonI
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPolylineI
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartRectI
areaPoints(SmartShape.PointCallback) - Method in interface omero.model.SmartShape: Calls the SmartShape.PointCallback with all of the x/y coordinates which are within the shape.
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartTextI
areTablesEnabled(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
args(String...) - Static method in class prefs: Converts varargs to a String-array.
ArrayStringType - Class in ome.tools.hibernate
ArrayStringType() - Constructor for class ome.tools.hibernate.ArrayStringType
asAnnotation() - Method in class pojos.DataObject: Returns the hosted IObject as an Annotation.
asAwtShape() - Method in class omero.model.SmartEllipseI
asAwtShape() - Method in class omero.model.SmartLineI
asAwtShape() - Method in class omero.model.SmartMaskI
asAwtShape() - Method in class omero.model.SmartPathI
asAwtShape() - Method in class omero.model.SmartPointI
asAwtShape() - Method in class omero.model.SmartPolygonI
asAwtShape() - Method in class omero.model.SmartPolylineI
asAwtShape() - Method in class omero.model.SmartRectI
asAwtShape() - Method in interface omero.model.SmartShape: Converst the current SmartShape to a Shape.
asAwtShape() - Method in class omero.model.SmartTextI
ASCENDING_LETTER - Static variable in class pojos.PlateData: Indicates that the column or row is a letter starting from A.
ASCENDING_NUMBER - Static variable in class pojos.PlateData: Indicates that the column or row is a number starting from 1.
asChannel() - Method in class pojos.DataObject: Returns the hosted IObject as a Well.
asClassOrNull(String) - Method in class ome.services.fulltext.FullTextIndexer
asDataset() - Method in class pojos.DataObject: Returns the hosted IObject as a Dataset.
asExperimenter() - Method in class pojos.DataObject: Returns the hosted IObject as an Experimenter.
asGroup() - Method in class pojos.DataObject: Returns the hosted IObject as an Experimenter Group.
asIAnnotated() - Method in class pojos.DataObject: not null; may through class-cast exception
asImage() - Method in class pojos.DataObject: Returns the hosted IObject as an Image.
asIObject() - Method in class pojos.DataObject: not null; no exceptions.
asPixels() - Method in class pojos.DataObject: Returns the hosted IObject as a Pixels.
asPlate() - Method in class pojos.DataObject: Returns the hosted IObject as a Plate.
asPoints() - Method in class omero.model.SmartEllipseI
asPoints() - Method in class omero.model.SmartLineI
asPoints() - Method in class omero.model.SmartMaskI
asPoints() - Method in class omero.model.SmartPathI
asPoints() - Method in class omero.model.SmartPointI
asPoints() - Method in class omero.model.SmartPolygonI
asPoints() - Method in class omero.model.SmartPolylineI
asPoints() - Method in class omero.model.SmartRectI
asPoints() - Method in interface omero.model.SmartShape: Provides some, possibly lossy, bounding polygon of this SmartShape via points.
asPoints() - Method in class omero.model.SmartTextI
asPojo(IObject) - Static method in class pojos.DataObject: Converts the passed IObject into its corresponding Pojo object.
asPojos(Collection) - Static method in class pojos.DataObject: Converts the collection of IObjects into the corresponding DataObjects
asPojos(Map) - Static method in class pojos.DataObject: Converts the map of IObjects into the corresponding DataObjects
asProject() - Method in class pojos.DataObject: Returns the hosted IObject as a Project.
asProperties() - Method in class ome.system.Login: produces a copy of the internal fields as a Properties instance.
asProperties() - Method in class ome.system.Server: produces a copy of the internal fields as a Properties instance.
asroot - Variable in class ome.services.sessions.SessionManagerImpl: A private session for use only by this instance for running methods via Executor.
asScreen() - Method in class pojos.DataObject: Returns the hosted IObject as a Screen.
assemble(Serializable, Object) - Method in class ome.tools.hibernate.ArrayStringType
assemble(Serializable, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
assemble(Serializable, Object) - Method in class ome.tools.hibernate.PermissionsType
assertManaged(IObject) - Method in class ome.logic.AdminImpl
assertNodes(Set<String>) - Method in class ome.services.blitz.fire.Ring
asWell() - Method in class pojos.DataObject: Returns the hosted IObject as a Well.
asWellSample() - Method in class pojos.DataObject: Returns the hosted IObject as a Well.
attach(long) - Method in interface ome.api.JobHandle
attach(long) - Method in class ome.services.JobBean
attach_async(AMD_JobHandle_attach, long, Current) - Method in class ome.services.blitz.impl.JobHandleI
attachImageToDataset(Dataset, Image, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
attachImageToDataset(Dataset, Image) - Method in interface ome.services.blitz.gateway.services.DataService: Attach an image to a dataset.
attachImageToDataset(Dataset, Image) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
AttributeNewUserGroupBean - Class in ome.security.auth: Handles the ":attribute:" specifier from etc/omero.properties.
AttributeNewUserGroupBean(String) - 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
availableCommands_async(AMD_IDelete_availableCommands, Current) - Method in class ome.services.blitz.impl.DeleteI
AWTScaleService - Class in ome.logic: Provides methods for scaling buffered images.
AWTScaleService() - Constructor for class ome.logic.AWTScaleService

B

B_BAND - Static variable in class omeis.providers.re.RGBBuffer: Index of the blue band in the image's data buffer.
backgroundSynchronizeShapeGeometries() - Method in class ome.services.roi.GeomTool
base - Variable in class ome.util.mem.ReadOnlyByteArray: The original array.
base - Variable in class omerojava.util.ReadOnlyByteArray: The original array.
BaseDeleteSpec - Class in ome.services.delete: DeleteSpec which takes the id of some id as the root of deletion.
BaseDeleteSpec(String, String...) - Constructor for class ome.services.delete.BaseDeleteSpec: Simplified constructor, primarily used for testing.
BaseDeleteSpec(List<String>) - Constructor for class ome.services.delete.BaseDeleteSpec
BaseDeleteSpec.SubSpecIterator - Class in ome.services.delete: Iterator which walks returns all DeleteSpecs which are reachable from the given spec, depth first including the spec itself.
BaseDeleteSpec.SubSpecIterator(DeleteSpec) - Constructor for class ome.services.delete.BaseDeleteSpec.SubSpecIterator
basename() - Method in class ome.services.scripts.RepoFile
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
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, Roles, ServiceFactory, TokenHolder) - 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
batchSize - Variable in class ome.services.fulltext.EventLogLoader
batchSize - Variable in class ome.services.search.SearchValues
be - Variable in class ome.services.blitz.impl.AbstractAmdServant
BeanHelper - Class in ome.services.util: Helper for all bean implementations.
BeanHelper(Class) - Constructor for class ome.services.util.BeanHelper
beforeTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor
BinaryMaskQuantizer - Class in omeis.providers.re.quantum: Quantization process for binary masks.
BinaryMaskQuantizer(QuantumDef, PixelsType) - Constructor for class omeis.providers.re.quantum.BinaryMaskQuantizer: Creates a new strategy.
BIT - Static variable in class ome.io.nio.PixelData: Identifies the type used to store pixel values.
BIT_EIGHT - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 8 i.e.
BIT_FIVE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 5 i.e.
BIT_FOUR - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 4 i.e.
BIT_ONE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 1 i.e.
BIT_SEVEN - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 7 i.e.
BIT_SIX - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 6 i.e.
BIT_THREE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 3 i.e.
BIT_TWO - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 2 i.e.
BIT_ZERO - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext: Identifies the bit-plane 0 i.e.
BlitzConfiguration - Class in ome.services.blitz.util: Factory bean which creates an instance as well as the proper ObjectAdapter and adds initial, well-known servants.
BlitzConfiguration(Ring, SessionManager, SecuritySystem, Executor) - Constructor for class ome.services.blitz.util.BlitzConfiguration: Single constructor which builds all Ice instances needed for the server runtime based on arguments provided.
BlitzConfiguration(InitializationData, Ring, SessionManager, SecuritySystem, Executor) - Constructor for class ome.services.blitz.util.BlitzConfiguration: Like #BlitzConfiguration(ome.services.sessions.SessionManager, SecuritySystem, Executor) but allows properties to be specified via an InitializationData instance.
BlitzConfiguration(Ring, SessionManager, SecuritySystem, Executor, Map<String, ObjectFactory>) - Constructor for class ome.services.blitz.util.BlitzConfiguration: Like #BlitzConfiguration(ome.services.sessions.SessionManager, SecuritySystem, Executor) but allows ObjectFactory instances to be specified via a Map.
BlitzConfiguration(InitializationData, Ring, SessionManager, SecuritySystem, Executor, Map<String, ObjectFactory>) - Constructor for class ome.services.blitz.util.BlitzConfiguration: Full constructor
BlitzExecutor - Interface in ome.services.blitz.util: Single-point of execution for all AMD blitz calls.
BlitzOnly - Interface in ome.services.blitz.util: Marker interface which specifies that an servant should not be checked for api consistency via ApiConsistencyCheck.
BlobShareStore - Class in ome.services.sharing
BlobShareStore() - Constructor for class ome.services.sharing.BlobShareStore
block(long) - Method in class omero.grid.DeleteCallbackI: Should only be used if the default logic of the process methods is kept in place.
block(long) - Method in class omero.grid.ProcessCallbackI: Should only be used if the default logic of the process methods is kept in place.
BLUE_INDEX - Static variable in class omeis.providers.re.ColorsFactory: Index of the red component of a color.
BooleanAnnotationData - Class in pojos: Boolean annotation.
BooleanAnnotationData() - Constructor for class pojos.BooleanAnnotationData: Creates a new instance.
BooleanAnnotationData(boolean) - Constructor for class pojos.BooleanAnnotationData: Creates a new instance.
BooleanAnnotationData(BooleanAnnotation) - Constructor for class pojos.BooleanAnnotationData: Creates a new instance.
breakSharing() - Method in class ome.util.mem.Handle: Subclasses must call this method before forwarding any call that modifies the Body's state.
bridge - Variable in class ome.services.fulltext.FullTextThread
BridgeHelper - Class in ome.services.fulltext: Base class for building custom FieldBridge implementations.
BridgeHelper() - Constructor for class ome.services.fulltext.BridgeHelper
buf - Variable in class ome.io.nio.DeltaVision
buildOrObtainSession() - Method in class ome.tools.hibernate.CurrentSessionContext
buildParseJob(long) - Method in class omero.grid.ParamsHelper: Build a job for the script with id.
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
byAnnotatedWith(Annotation...) - Method in interface ome.api.Search: Finds entities annotated with an Annotation similar to the example.
byAnnotatedWith(Annotation...) - Method in class ome.services.SearchBean
byAnnotatedWith_async(AMD_Search_byAnnotatedWith, List<Annotation>, Current) - Method in class ome.services.blitz.impl.SearchI
byFullText(String) - Method in interface ome.api.Search: Passes the query as is to the Lucene backend.
byFullText(String) - Method in class ome.services.SearchBean
byFullText_async(AMD_Search_byFullText, String, Current) - Method in class ome.services.blitz.impl.SearchI
byGroupForTags(String) - Method in interface ome.api.Search: Returns transient (without ID) TagAnnotation instances which represent all the tags in the given group.
byGroupForTags(String) - Method in class ome.services.SearchBean
byGroupForTags_async(AMD_Search_byGroupForTags, String, Current) - Method in class ome.services.blitz.impl.SearchI
byHqlQuery(String, Parameters) - Method in interface ome.api.Search: Delegates to IQuery.findAllByQuery(String, Parameters) method to take advantage of the Search.and(), Search.or(), and Search.not() methods, or queue-semantics.
byHqlQuery(String, Parameters) - Method in class ome.services.SearchBean
byHqlQuery_async(AMD_Search_byHqlQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.SearchI
bySimilarTerms(String...) - Method in interface ome.api.Search: Returns transient (without ID) TextAnnotation instances which represent terms which are similar to the give terms.
bySimilarTerms(String...) - Method in class ome.services.SearchBean
bySimilarTerms_async(AMD_Search_bySimilarTerms, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
bySomeMustNone(String[], String[], String[]) - Method in interface ome.api.Search: Builds a Lucene query and passes it to Search.byFullText(String).
bySomeMustNone(String[], String[], String[]) - Method in class ome.services.SearchBean
bySomeMustNone_async(AMD_Search_bySomeMustNone, List<String>, List<String>, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
byTagForGroups(String) - Method in interface ome.api.Search: Creates a query which will return transient (without ID) TagAnnotation instances which represent all the tag groups which the given tag belongs to.
byTagForGroups(String) - Method in class ome.services.SearchBean
byTagForGroups_async(AMD_Search_byTagForGroups, String, Current) - Method in class ome.services.blitz.impl.SearchI
BYTE - Static variable in class ome.io.nio.PixelData: Identifies the type used to store pixel values.
BYTE - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
ByteArray - Class in ome.util.mem: A read-write slice of a given array.
ByteArray(byte[], int, int) - Constructor for class ome.util.mem.ByteArray: Creates a read-write slice of base.
bytesPerPixel - Variable in class ome.io.nio.PixelData: The number of bytes per pixel.
bytesPerPixel() - Method in class ome.io.nio.PixelData: Returns the number of byte per pixel for the pixel data.
bytesPerPixel - Variable in class omeis.providers.re.data.Plane2D: How many bytes make up a pixel value.
byUUID(String[]) - Method in class ome.services.SearchBean

C

c2c() - Method in class omero.util.IceMapper
cache - Variable in class ome.services.sessions.SessionManagerImpl
CacheFactory - Class in ome.services.sessions.state
CacheFactory() - Constructor for class ome.services.sessions.state.CacheFactory
CacheListener - Class in ome.services.sessions.state: Basic CacheEventListener which does nothing.
CacheListener() - Constructor for class ome.services.sessions.state.CacheListener
calculateBackOff(int) - Method in class ome.services.db.SelfCorrectingDataSource
calculateMessageDigest() - Method in interface ome.api.RawPixelsStore
calculateMessageDigest() - Method in class ome.io.nio.DeltaVision
calculateMessageDigest() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
calculateMessageDigest() - Method in interface ome.io.nio.PixelBuffer: Calculates a SHA-1 message digest for the entire pixel buffer.
calculateMessageDigest() - Method in class ome.io.nio.RomioPixelBuffer
calculateMessageDigest() - Method in class ome.services.RawPixelsBean
calculateMessageDigest_async(AMD_RawPixelsStore_calculateMessageDigest, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
calculateXYWidths(Pixels, int) - Method in class ome.services.ThumbnailCtx: Calculates the ratio of the two sides of a Pixel set and returns the X and Y widths based on the longest side maintaining aspect ratio.
call(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource
call(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.Action
call(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
call() - Method in interface omeis.providers.re.RenderingTask: Renders wavelength.
Callback - Class in ome.services.throttling: Manages AMD-based method dispatches from blitz.
Callback(Boolean, Boolean, ServiceInterface, IceMethodInvoker, Object, IceMapper, Current, Object...) - Constructor for class ome.services.throttling.Callback
Callback(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Constructor for class ome.services.throttling.Callback
Callback2<R> - Class in ome.services.throttling: Callable-based callback which guarantees that ice_response or ice_exception is called.
Callback2(Current, Object, boolean, Callable<R>) - Constructor for class ome.services.throttling.Callback2
callInvokerOnMappedArgs(IceMapper, Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant
callInvokerOnRawArgs(Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor: Uses the given IceMethodInvoker to make the method call.
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor: Passes the given arguments to IceMethodInvoker with the assumption that all conversion from omero.* to ome.* has taken place.
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy
callWithRetries(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource
cancel(Current) - Method in class ome.services.blitz.impl.DeleteHandleI
cancel(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
cancel() - Method in interface ome.services.procs.Process
cancel() - Method in class ome.services.procs.ProcessSkeleton
cancel(String) - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
cancelJob() - Method in interface ome.api.JobHandle: Marks a job for cancellation.
cancelJob() - Method in class ome.services.JobBean
cancelJob_async(AMD_JobHandle_cancelJob, Current) - Method in class ome.services.blitz.impl.JobHandleI
CANCELLED - Static variable in interface ome.api.JobHandle
canMapReturnValue() - Method in class omero.util.IceMapper: True if this instance has a IceMapper.ReturnMapping
canRead(EventContext, String) - Method in class ome.system.PreferenceContext
canRunScript_async(AMD_IScript_canRunScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI
canUpdate(IObject) - Method in interface ome.api.IAdmin: Returns true if the currently logged in user can modify the given IObject.
canUpdate(IObject) - Method in class ome.logic.AdminImpl
canUpdate_async(AMD_IAdmin_canUpdate, IObject, Current) - Method in class ome.services.blitz.impl.AdminI
caseSensitive - Variable in class ome.services.search.SearchValues
cause(Throwable) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities
cb - Variable in class ome.services.throttling.Task
cd - Variable in class ome.security.basic.BasicSecuritySystem
cd - Variable in class ome.security.basic.EventLogListener
ceId - Variable in class ome.system.SimpleEventContext
ceType - Variable in class ome.system.SimpleEventContext
cgId - Variable in class ome.system.SimpleEventContext
cgName - Variable in class ome.system.SimpleEventContext
chainedList - Variable in class ome.services.search.SearchAction: List of IObject instances which have currently been found.
chainedSearch(List<IObject>) - Method in class ome.services.search.SearchAction: Set the current list of found ids from previous searches, which should be chained in this search.
changeDistinguisedName(String, String) - Method in class ome.security.auth.PasswordProviders
changeExpiredCredentials(String, String, String) - Method in interface ome.api.IAdmin: Used after an ExpiredCredentialsException instance is thrown.
changeExpiredCredentials(String, String, String) - Method in class ome.logic.AdminImpl
changeExpiredCredentials_async(AMD_IAdmin_changeExpiredCredentials, String, String, String, Current) - Method in class ome.services.blitz.impl.AdminI
changeGroup(IObject, String) - Method in interface ome.api.IAdmin: call details.setGroup() on this instance.
changeGroup(IObject, String) - Method in class ome.logic.AdminImpl
changeGroup_async(AMD_IAdmin_changeGroup, IObject, String, Current) - Method in class ome.services.blitz.impl.AdminI
changeOwner(IObject, String) - Method in interface ome.api.IAdmin: call details.setOwner() on this instance.
changeOwner(IObject, String) - Method in class ome.logic.AdminImpl
changeOwner_async(AMD_IAdmin_changeOwner, IObject, String, Current) - Method in class ome.services.blitz.impl.AdminI
changePassword(String) - Method in interface ome.api.IAdmin: change the password for the current user.
changePassword(String) - Method in class ome.logic.AdminImpl
changePassword(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider: Throws by default.
changePassword(String, String) - Method in class ome.security.auth.JdbcPasswordProvider
changePassword(String, String) - Method in interface ome.security.auth.PasswordProvider: Attempts to change the password for the given user.
changePassword(String, String) - Method in class ome.security.auth.PasswordProviders
changePassword_async(AMD_IAdmin_changePassword, RString, Current) - Method in class ome.services.blitz.impl.AdminI
changePasswordWithOldPassword(String, String) - Method in interface ome.api.IAdmin: change the password for the current user by passing the old password.
changePasswordWithOldPassword(String, String) - Method in class ome.logic.AdminImpl
changePasswordWithOldPassword_async(AMD_IAdmin_changePasswordWithOldPassword, RString, RString, Current) - Method in class ome.services.blitz.impl.AdminI
changePermissions(IObject, Permissions) - Method in interface ome.api.IAdmin: call defaults.setPermissions() on this instance.
changePermissions(IObject, Permissions) - Method in class ome.logic.AdminImpl: the implementation of this method is somewhat tricky in that Permissions changes must be allowed even when other updates are not.
changePermissions_async(AMD_IAdmin_changePermissions, IObject, Permissions, Current) - Method in class ome.services.blitz.impl.AdminI
ChangeSecurityContextEvent - Class in ome.services.sessions.events: InteralMessage published by the SessionManager when setSecurityContext() is called.
ChangeSecurityContextEvent(Object, String, IObject, IObject) - Constructor for class ome.services.sessions.events.ChangeSecurityContextEvent
changeUserPassword(String, String) - Method in interface ome.api.IAdmin: change the password for the a given user.
changeUserPassword(String, String) - Method in class ome.logic.AdminImpl
changeUserPassword_async(AMD_IAdmin_changeUserPassword, String, RString, Current) - Method in class ome.services.blitz.impl.AdminI
changeUserPasswordById(Long, String) - Method in class ome.security.auth.PasswordUtil
ChannelAcquisitionData - Class in pojos: Object hosting the acquisition related to a logical channel.
ChannelAcquisitionData(LogicalChannel) - Constructor for class pojos.ChannelAcquisitionData: Creates a new instance.
ChannelData - Class in pojos: The data that makes up an OME Channel along with links to its logical channel.
ChannelData(int) - Constructor for class pojos.ChannelData: Creates a new instance.
ChannelData(int, Channel) - Constructor for class pojos.ChannelData: Creates a new instance.
CHANNELID_QUERY - Static variable in class ome.services.delete.DeleteBean
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.
check() - Method in interface omero.util.Resources.Entry: Called during each cycle.
CheckAllJobs - Class in ome.services.blitz.util
CheckAllJobs(Executor, ObjectAdapter, TopicManager) - Constructor for class ome.services.blitz.util.CheckAllJobs
CheckAllJobs(Executor, ObjectAdapter, TopicManager, long) - Constructor for class ome.services.blitz.util.CheckAllJobs
checkAndRegister() - Method in class ome.services.JobBean
checkArgs(Object...) - Method in class ome.services.delete.DeleteEntry
checkBounds(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision
checkBounds(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
checkBounds(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Checks to ensure that no one particular axis has an offset out of bounds.
checkBounds(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
checkCluster() - Method in class ome.services.blitz.fire.Ring: Method called during initialization to get all the active uuids within the cluster, and remove any dead nodes.
checkDatabase(String) - Method in class ome.system.PreferenceContext
checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper
checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ObjPrxHelper
checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ObjPrxHelper
checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ObjPrxHelper
checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
checkImageDelete(long, boolean) - Method in interface ome.api.IDelete: Returns all entities which would prevent the given Image id from being deleted.
checkImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean
checkImageDelete_async(AMD_IDelete_checkImageDelete, long, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI
checkIndex(int) - Method in class ome.util.mem.ReadOnlyByteArray: Makes sure that i is in [0, length).
checkIndex(int) - Method in class omerojava.util.ReadOnlyByteArray: Makes sure that i is in [0, length).
checkManagedDetails(IObject, Details) - Method in class ome.security.basic.BasicSecuritySystem
checkManagedDetails(IObject, Details) - Method in class ome.security.basic.OmeroInterceptor
checkManagedDetails(IObject, Details) - Method in interface ome.security.SecuritySystem: checks that a non-privileged user has not attempted to edit the entity's security details.
checkManagedDetails(IObject, Details) - Method in class ome.security.SecuritySystemHolder
checkManagedDetails(IObject, Details) - Method in class ome.security.sharing.SharingSecuritySystem
checkMethod(Object, Method, Principal, boolean) - Method in class ome.security.basic.BasicMethodSecurity: See MethodSecurity#checkMethod(Object, Method, Principal)
checkMethod(Object, Method, Principal, boolean) - Method in interface ome.security.MethodSecurity: Throws a SecurityViolation exception if the given Principal does not have the proper permissions to execute the given method.
checkNeedsUpdateWithoutLock() - Method in class ome.services.sessions.state.SessionCache: Whether or not SessionCache.doUpdate() should run.
checkNonNull(List<Point>) - Static method in class omero.model.SmartShape.Util: Used from assert statements of the form: assert Util.checkNonNull(points) : "Null points in " + this; in all the implementations of SmartShape.asPoints().
checkParameters() - Method in class ome.services.query.Query: check the Parameters instance against the Definitions instance for this Query.
checkPassword(String, String) - Method in interface ome.api.local.LocalAdmin: Checks password for given user.
checkPassword(String, String) - Method in class ome.logic.AdminImpl: Jumps through some hurdles (see PasswordUtil#userId(SimpleJdbcTemplate, String) to not have to use Hibernate in order to prevent unauthorized access to Hibernate.
checkPassword(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider: If ConfigurablePasswordProvider.ignoreUnknown is true, returns null, since the base class knows no users.
checkPassword(String, String) - Method in class ome.security.auth.FilePasswordProvider
checkPassword(String, String) - Method in class ome.security.auth.JdbcPasswordProvider: Retrieves password from the database and calls ConfigurablePasswordProvider.comparePasswords(String, String).
checkPassword(String, String) - Method in class ome.security.auth.LdapPasswordProvider
checkPassword(String, String) - Method in interface ome.security.auth.PasswordProvider: Authenticates the give user given the password token.
checkPassword(String, String) - Method in class ome.security.auth.PasswordProviders
checkPassword(String) - Method in class ome.services.blitz.fire.Ring: Currently only returns false since if the regular password check performed by SessionManager cannot find the session, then the cluster has no extra information.
checkPermissions(String, String, StringHolder, Current) - Method in class ome.services.blitz.fire.PermissionsVerifierI
checkProperty(String, String) - Method in interface ome.api.local.LocalQuery: Checks if a property is defined on a mapped Hibernate type.
checkProperty(String, String) - Method in class ome.logic.PojosImpl
checkProperty(String, String) - Method in class ome.logic.QueryImpl
checkReady(String) - Method in class ome.security.basic.BasicSecuritySystem: calls BasicSecuritySystem.isReady() and if not throws an ApiUsageException.
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
choose() - Method in class ome.security.CompositeACLVoter
choose() - Method in class ome.security.SecuritySystemHolder
chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.ConfigRedirector
chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.NullRedirector: Does nothing.
chooseNextRedirect(Redirector.Context, Set<String>) - Method in interface ome.services.blitz.redirect.Redirector: Gives the Redirector a chance to configure the next appropriate redirect based on the Set of current Node uuids.
chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.ScaleRedirector: Does nothing since all redirects are chosen during Redirector.getProxyOrNull(Context, String, Glacier2.SessionControlPrx, Ice.Current)
classes - Variable in class ome.services.fulltext.FullTextBridge
ClassQuerySource - Class in ome.services.query: creates a query based on the id string by interpreting it as a Class.
ClassQuerySource() - Constructor for class ome.services.query.ClassQuerySource
clean() - Method in class ome.services.RawFileBean
cleanTempDir() - Method in class omero.util.TempFileManager: Deletes TempFileManager.dir
cleanThread() - Method in class ome.tools.hibernate.SessionHandler
cleanup() - Method in class ome.services.util.ServiceHandler
cleanup() - Method in class omero.util.Resources
cleanup() - Method in interface omero.util.Resources.Entry: Gives an Resources.Entry a chance to cleanup resources before it is removed from checking.
cleanup() - Method in class omero.util.TempFileManager: Releases TempFileManager.lock and deletes TempFileManager.dir.
cleanUserDir() - Method in class omero.util.TempFileManager: Attempts to delete all directories under self.userdir other than the one owned by this process.
clear() - Method in interface ome.api.local.LocalQuery
clear() - Method in class ome.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 interface ome.api.Search: Removes all active queries (leaving settings alone), such that Search.activeQueries() will return 0.
clearQueries() - Method in class ome.services.SearchBean
clearQueries_async(AMD_Search_clearQueries, Current) - Method in class ome.services.blitz.impl.SearchI
clearToken(GraphHolder) - Method in class ome.security.basic.TokenHolder
client - Class in omero: Central client-side blitz entry point.
client() - Constructor for class omero.client: Calls client.client(Ice.InitializationData) with a new InitializationData
client(InitializationData) - Constructor for class omero.client: Creates an Communicator from a InitializationData instance.
client(String) - Constructor for class omero.client: Creates an Communicator pointing at the given server using the #DEFAULT_PORT.
client(String, int) - Constructor for class omero.client: Creates an Communicator pointing at the given server with the non-standard port.
client(String[]) - Constructor for class omero.client: Calls client.client(String[], Ice.InitializationData) with a new InitializationData
client(String[], InitializationData) - Constructor for class omero.client: Creates an Communicator from command-line arguments.
client(File...) - Constructor for class omero.client: Creates an Communicator from multiple files.
client(Map) - Constructor for class omero.client: Creates an Communicator from a Map instance.
CLIENT_CONTEXT - Static variable in class ome.system.OmeroContext: identifier for an OmeroContext configured in classpath*:beanRefContext.xml for use by remote (via JNDI/RMI) clients.
ClientError - Exception in omero: abstract superclass of all Omero exceptions.
ClientError(String) - Constructor for exception omero.ClientError
clientId - Variable in class ome.services.blitz.impl.ServiceFactoryI
clientId(Current) - Static method in class ome.services.blitz.impl.ServiceFactoryI: Helpers method to extract the CLIENTUUID out of the given Ice.Current.
clone() - Method in class ome.services.sessions.state.CacheListener
close() - Method in interface ome.api.StatefulServiceInterface: signals the end of the service lifecycle.
close() - Method in class ome.io.nio.DeltaVision
close() - Method in class ome.io.nio.FileBuffer: Closes the buffer, cleaning up file state.
close() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
close() - Method in interface ome.io.nio.PixelBuffer: Closes the buffer, cleaning up file state.
close() - Method in class ome.io.nio.RomioPixelBuffer: Closes the buffer, cleaning up file state.
close(Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
close(Current) - Method in interface ome.services.blitz.impl.CloseableServant
close(Current) - Method in class ome.services.blitz.impl.DeleteHandleI
close(boolean, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
close(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI: Deprecated.
close() - Method in class ome.services.delete.BaseDeleteSpec
close() - Method in interface ome.services.delete.DeleteSpec
close() - Method in class ome.services.formats.OmeroReader
close() - Method in class ome.services.JobBean
close() - Method in class ome.services.messages.RegisterServiceCleanupMessage: Used to close the passed in resource.
close() - Method in class ome.services.RawFileBean
close() - Method in class ome.services.RawPixelsBean
close() - Method in class ome.services.RenderingBean
close() - Method in class ome.services.SearchBean
close() - Method in interface ome.services.sessions.SessionCallback
close(String) - Method in interface ome.services.sessions.SessionManager: If reference count for the session is less than 1, close the session.
close(String) - Method in class ome.services.sessions.SessionManagerImpl
close() - Method in class ome.services.sharing.ShareStore
close() - Method in class ome.services.ThumbnailBean
close() - Method in class omeis.providers.re.Renderer: Closes the buffer, cleaning up file state.
close() - Method in class omero.grid.DeleteCallbackI
close(Current) - Method in class omero.grid.InteractiveProcessorI
close() - Method in class omero.grid.ProcessCallbackI
close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant: SessionHandler also specially catches close() calls, but cannot remove the servant from the ObjectAdapter and thereby prevent any further communication.
CloseableServant - Interface in ome.services.blitz.impl: Marker interface which distinguishes a servant which wants to have CloseableServant.close(Ice.Current) called on ServiceFactoryI.doDestroy()
closeAll() - Method in interface ome.services.sessions.SessionManager: Close all sessions with checking for the necessary reference counts.
closeAll() - Method in class ome.services.sessions.SessionManagerImpl
closeAll() - Method in class ome.system.OmeroContext: closes all the nested OmeroContexts within this instance.
closeOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
closeService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
closeService() - Method in interface ome.services.blitz.gateway.services.GatewayService: Close the service and all it's surrogate services.
closeSession(Session) - Method in interface ome.api.ISession: Closes session and releases all resources.
closeSession(Session) - Method in class ome.services.sessions.SessionBean
closeSession() - Method in class ome.system.ServiceFactory
closeSession() - Method in class omero.client: Closes the session and nulls out the communicator.
closeSession_async(AMD_ISession_closeSession, Session, Current) - Method in class ome.services.blitz.impl.SessionI
closeShare(long) - Method in interface ome.api.IShare: Closes share.
closeShare(long) - Method in class ome.services.sharing.ShareBean
closeShare_async(AMD_IShare_closeShare, long, Current) - Method in class ome.services.blitz.impl.ShareI
CodomainChain - Class in omeis.providers.re.codomain: Queues the contexts that define the spatial domain transformations that have to be applied to the image.
CodomainChain(int, int) - Constructor for class omeis.providers.re.codomain.CodomainChain: Creates a new chain.
CodomainChain(int, int, List) - Constructor for class omeis.providers.re.codomain.CodomainChain: Creates a new chain.
CodomainMap - Interface in omeis.providers.re.codomain: Declares the interface common to all codomain maps.
CodomainMapContext - Class in omeis.providers.re.codomain: Each concrete subclass defines transformation parameters for a CodomainMap implementation.
CodomainMapContext() - Constructor for class omeis.providers.re.codomain.CodomainMapContext
collect(UnloadedCollector, Image) - Method in class ome.services.delete.DeleteBean: Walks the Image graph collecting unloaded instances of all entities for later delete.
collectionCast(Class<T>, List<IObject>) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities: Helper method for the conversion of base types in containers(normally of type IObject) to a concrete type.
CollectionCountQueryDefinition - Class in ome.services.query: counts the number of members in a collection.
CollectionCountQueryDefinition(Parameters) - Constructor for class ome.services.query.CollectionCountQueryDefinition
CollectionQueryParameterDef - Class in ome.services.query: 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
ColorsFactory - Class in omeis.providers.re: Utility class to determine the color usually associated to a specified channel depending on its emission wavelength.
ColorsFactory() - Constructor for class omeis.providers.re.ColorsFactory
COMBINED - Static variable in class ome.services.fulltext.BridgeHelper: Name of the Field which contains the union of all fields.
commands(Current) - Method in class ome.services.blitz.impl.DeleteHandleI
CommonsLoggingAdapter - Class in ome.services.blitz.util: A simple Adapter to have the ICE runtime log to our log file.
CommonsLoggingAdapter(Log) - Constructor for class ome.services.blitz.util.CommonsLoggingAdapter
COMPANION_FILE_NS - Static variable in class pojos.FileAnnotationData: The name space used to indicate that the FileAnnotation is a companion file.
compare(Object, Object) - Method in class pojos.ROICoordinate: Implemented as specified by the Comparator I/F.
comparePasswords(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider: Compares the password provided by the user (unhashed) against the given trusted password.
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
COMPLEX_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
CompositeACLVoter - Class in ome.security
CompositeACLVoter(CurrentDetails, BasicACLVoter, SharingACLVoter) - Constructor for class ome.security.CompositeACLVoter
CompressImpl - Class in ome.logic
CompressImpl() - Constructor for class ome.logic.CompressImpl
compressToStream(BufferedImage, OutputStream) - Method in interface ome.api.local.LocalCompress: Compresses a buffered image to an output stream.
compressToStream(BufferedImage, OutputStream) - Method in class ome.logic.CompressImpl
computeLocationStats(Pixels, PixelBuffer, PlaneDef, int) - Method in class omeis.providers.re.metadata.StatsFactory: Helper object to determine the location of the pixels' values, the inputWindow i.e.
ConfigI - Class in ome.services.blitz.impl: Implementation of the IConfig service.
ConfigI(IConfig, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ConfigI
ConfigImpl - Class in ome.logic: implementation of the IConfig service interface.
ConfigImpl() - Constructor for class ome.logic.ConfigImpl
ConfigRedirector - Class in ome.services.blitz.redirect: Redirector implementation which uses the REDIRECT config key via LocalConfig to know which Node is currently active.
ConfigRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ConfigRedirector
ConfigurablePasswordProvider - Class in ome.security.auth: Base class for most PasswordProvider implementations, providing configuration for default behaviors.
ConfigurablePasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
ConfigurablePasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
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.
configureLogging() - Static method in class ome.services.blitz.Entry: Most ome/omero classes use the Log and LogFactory classes for logging.
conn - Variable in class ome.services.sharing.FreezeShareStore
containedExperimenters(long) - Method in interface ome.api.IAdmin: fetch all users contained in this group.
containedExperimenters(long) - Method in class ome.logic.AdminImpl
containedExperimenters_async(AMD_IAdmin_containedExperimenters, long, Current) - Method in class ome.services.blitz.impl.AdminI
containedGroups(long) - Method in interface ome.api.IAdmin: fetch all groups of which the given user is a member.
containedGroups(long) - Method in class ome.logic.AdminImpl
containedGroups_async(AMD_IAdmin_containedGroups, long, Current) - Method in class ome.services.blitz.impl.AdminI
ContainerI - Class in ome.services.blitz.impl: Implementation of the IContainer service.
ContainerI(IContainer, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ContainerI
contains(Object) - Method in interface ome.api.local.LocalQuery: Tests if an object is currently contained in the session.
contains(Object) - Method in class ome.logic.QueryImpl
contains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
contains(double, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(Point2D) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(double, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(Point2D) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(String) - Method in class pojos.WorkflowData: Returns true if the keyword exist in the workflow, false otherwise.
containsKey(Object) - Method in class ome.services.query.Definitions
context - Variable in class ome.logic.AdminImpl
context - Variable in class ome.services.blitz.fire.SessionManagerI
context - Variable in class ome.services.fulltext.FileParser
context - Variable in class ome.services.sessions.SessionManagerImpl
context - Variable in class ome.services.util.Executor.Impl
ContrastStretchingContext - Class in omeis.providers.re.codomain: Two points pStart and pEnd define the context of this transformation.
ContrastStretchingContext() - Constructor for class omeis.providers.re.codomain.ContrastStretchingContext
control - Variable in class ome.services.blitz.impl.ServiceFactoryI
convert(IceMapper) - Method in interface omero.rtypes.Conversion: Convert the "val" field on the given RType instance to an ome.model.* representation.
convert(EventContext) - Static method in class omero.util.IceMapper
convert(RGBBuffer) - Static method in class omero.util.IceMapper
convert(PlaneDef) - Static method in class omero.util.IceMapper
convert(Principal) - Static method in class omero.util.IceMapper
convert(Roles) - Static method in class omero.util.IceMapper
convert(Date) - Static method in class omero.util.IceMapper
convert(RTime) - Static method in class omero.util.IceMapper
convert(Parameters) - Method in class omero.util.IceMapper
convert(String, Object) - Method in class omero.util.IceMapper
convert(Options) - Static method in class omero.util.IceMapper
convert(Filter) - Static method in class omero.util.IceMapper
convert(Permissions) - Static method in class omero.util.IceMapper
convert(Permissions) - Static method in class omero.util.IceMapper
convertClientToServer(Pixels, double[][]) - Static method in class omerojava.util.GatewayUtils: convert the client data pixels to server byte array, also sets the data pixel size to the size of the pixels in the pixels Id param.
convertPojos(ContainerClass) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities: Converts the specified POJO into the corresponding model.
ConvertToBlitzExceptionMessage - Class in ome.services.blitz.util: Internal event which gives third party services a chance to map their exceptions to a blitz exception.
ConvertToBlitzExceptionMessage(Object, Throwable) - Constructor for class ome.services.blitz.util.ConvertToBlitzExceptionMessage
convertXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI
Copiable - Interface in ome.util.mem: Requires an implementing class to provide deep copies of its instances.
CopiableArray - Class in ome.util.mem: This abstract class provides an implementation of the Copiable interface.
CopiableArray(int) - Constructor for class ome.util.mem.CopiableArray: Creates a new instance.
copy(SearchValues) - Method in class ome.services.search.SearchValues
copy(Parameters) - Method in class ome.services.search.SearchValues: Copies all known values from Parameters
copy(Session) - Method in class ome.services.sessions.SessionManagerImpl
copy(EventContext) - Method in class ome.system.SimpleEventContext: Copies all values directly from the given instance into this instance.
copy(Map) - Static method in class ome.tools.hibernate.HibernateUtils
copy(Collection) - Static method in class ome.tools.hibernate.HibernateUtils
copy() - Method in interface ome.util.mem.Copiable: Makes a copy of this object.
copy(int, int) - Method in class ome.util.mem.CopiableArray: Copies the Copiable from the specified position from into the specified position to.
copy() - Method in class ome.util.mem.CopiableArray: Implements the method as specified by Copiable.
copy() - Method in class ome.util.mem.Handle: Returns a deep copy of this object.
copy() - Method in class omeis.providers.re.codomain.CodomainMapContext: Returns a deep copy of this object.
copy() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Implemented as specified by superclass.
copy() - Method in class omeis.providers.re.codomain.IdentityMapContext: Implemented as specified by superclass.
copy() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Implemented as specified by superclass.
copy() - Method in class omeis.providers.re.codomain.ReverseIntensityContext: Implemented as specified by superclass.
copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in interface ome.api.IPixels: Copies the metadata, and only the metadata linked to a Image object into a new Image object of equal or differing size across one or many of its three physical dimensions or temporal dimension.
copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
copyAndResizeImage_async(AMD_IPixels_copyAndResizeImage, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI
copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in interface ome.api.IPixels: Copies the metadata, and only the metadata linked to a Pixels object into a new Pixels object of equal or differing size across one or many of its three physical dimensions or temporal dimension.
copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
copyAndResizePixels_async(AMD_IPixels_copyAndResizePixels, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI
copyClassListToArray(List<Class>) - Static method in class ome.services.search.SearchValues
copyDetails(Details) - Static method in class ome.services.search.SearchValues
copyGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
copyImage(long, int, int, int, int, List<Integer>, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
copyImage(long, int, int, int, int, List<Integer>, String) - Method in interface ome.services.blitz.gateway.services.ImageService: Copy the image and pixels from image.
copyImage(long, int, int, int, int, List<Integer>, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
copyList(List<T>) - Static method in class ome.services.search.SearchValues
copyObject(Filterable, ModelMapper) - Method in class omero.model.DetailsI
copyObject(Filterable, ModelMapper) - Method in class omero.model.PermissionsI
copyOfValues() - Method in class ome.services.search.SearchAction
copyPixels(long, List<Integer>, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
copyPixels(long, int, int, int, int, List<Integer>, String) - Method in interface ome.services.blitz.gateway.services.ImageService: Copy the pixels set from pixels to a new set.
copyPixels(long, List<Integer>, String) - Method in interface ome.services.blitz.gateway.services.ImageService: Copy the pixels set from pixels to a new set.
copyPixels(long, int, int, int, int, List<Integer>, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
copyPixels(long, List<Integer>, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
copyPixelsXYTZ(long, int, int, int, int, List<Integer>, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
copyTimestamp(Timestamp) - Static method in class ome.services.search.SearchValues
copyToken(IObject, IObject) - Method in class ome.security.basic.BasicSecuritySystem: See {@link TokenHolder#copyToken(IObject, IObject)
copyToken(IObject, IObject) - Method in class ome.security.basic.TokenHolder: copy a token from one IObject to another.
copyUser(Experimenter) - Method in class ome.security.auth.SimpleRoleProvider
copyValues(EntityPersister, Object, Object, SessionImplementor, Map) - Method in class ome.security.basic.MergeEventListener
copyValues(EntityPersister, Object, Object, SessionImplementor, Map, ForeignKeyDirection) - Method in class ome.security.basic.MergeEventListener
count() - Method in interface ome.services.sessions.SessionContext: Returns the SessionContext.Count instance held by this context.
count() - Method in class ome.services.sessions.SessionContextImpl
count - Variable in class ome.services.sessions.stats.LongCounter
countAnnotationsUsedNotOwned(Class, long) - Method in interface ome.api.IMetadata: Counts the number of annotation of a given type used by the specified user but not owned by the user.
countAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
countAnnotationsUsedNotOwned_async(AMD_IMetadata_countAnnotationsUsedNotOwned, String, long, Current) - Method in class ome.services.blitz.impl.MetadataI
countByPeriod_async(AMD_ITimeline_countByPeriod, List<String>, RTime, RTime, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
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(SimpleJdbcOperations) - Method in class ome.services.scripts.ScriptRepoHelper
countOnDisk() - Method in class ome.services.scripts.ScriptRepoHelper: Returns the number of files which match ScriptRepoHelper.SCRIPT_FILTER in ScriptRepoHelper.dir.
countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata: Counts the number of annotation of a given type.
countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
countSpecifiedAnnotations_async(AMD_IMetadata_countSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
create(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.SessionManagerI
create(String) - Method in class ome.services.roi.RoiTypes.ObjectFactory
create(String) - Method in class omero.rtypes.ObjectFactory
create(File) - Method in class omero.util.TempFileManager: If the given directory doesn't exist, creates it and returns true.
create_path() - Static method in class omero.util.TempFileManager: Calls TempFileManager.createPath(String, String, boolean) on TempFileManager.manager with defaults of "omero", ".tmp", and false.
create_path(String) - Static method in class omero.util.TempFileManager: Calls TempFileManager.createPath(String, String, boolean) on TempFileManager.manager with defaults of ".tmp", and false.
create_path(String, String) - Static method in class omero.util.TempFileManager: Calls TempFileManager.createPath(String, String, boolean) on TempFileManager.manager with ".tmp", and false arguments.
create_path(String, String, boolean) - Static method in class omero.util.TempFileManager: Calls TempFileManager.createPath(String, String, boolean) on TempFileManager.manager.
createAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration: Creates an adapter with the name "BlitzAdapter", which must be properly configured via --Ice.Config or ICE_CONFIG or similar.
createAndPrepareMissingRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx: Resets a given set of Pixels rendering settings to the default effectively creating any which do not exist.
createAndRegisterManager(SessionManager, SecuritySystem, Executor) - Method in class ome.services.blitz.util.BlitzConfiguration
createAndRegisterVerifier(SessionManager) - Method in class ome.services.blitz.util.BlitzConfiguration
createByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createCache(CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
createCache(String, boolean, int) - Method in class ome.services.sessions.state.SessionCache
createClient(boolean) - Method in class omero.client: Creates a possibly insecure client instance and calls client.joinSession(String) using the current session id.
createCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration
createCommunicator(String, String[]) - Method in class ome.services.blitz.util.BlitzConfiguration
createDataObject(T, Parameters) - Method in interface ome.api.IContainer: Creates the specified data object.
createDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
createDataObject_async(AMD_IContainer_createDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
createDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer: convenience method to save network calls.
createDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
createDataObjects_async(AMD_IContainer_createDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
createDetails() - Method in class ome.security.basic.CurrentDetails: Creates a Details object for the current security context.
createdOrModified(Class, Criteria) - Method in class ome.services.search.SearchAction
createdOrModified(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction
createdStart - Variable in class ome.services.search.SearchValues
createdStop - Variable in class ome.services.search.SearchValues
createEnumeration(T) - Method in interface ome.api.ITypes
createEnumeration(T) - Method in class ome.logic.TypesImpl
createEnumeration_async(AMD_ITypes_createEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
createException(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin: create and return a new user in the given groups.
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
createExperimenter_async(AMD_IAdmin_createExperimenter, Experimenter, ExperimenterGroup, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin: create and return a new user in the given groups with password.
createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
createExperimenterWithPassword_async(AMD_IAdmin_createExperimenterWithPassword, Experimenter, RString, ExperimenterGroup, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
createExporter(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createFullTextThread(EventLogLoader) - Static method in class ome.services.fulltext.Main
createGateway(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin: create and return a new group.
createGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
createGroup(ExperimenterGroup) - Method in interface ome.security.auth.RoleProvider
createGroup(String, Permissions, boolean) - Method in interface ome.security.auth.RoleProvider
createGroup(String, Permissions, boolean) - Method in class ome.security.auth.SimpleRoleProvider
createGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
createGroup_async(AMD_IAdmin_createGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in interface ome.api.IPixels: Creates the metadata, and only the metadata linked to an Image object.
createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in class ome.logic.PixelsImpl
createImage(int, int, int, int, List<Integer>, PixelsType, String, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in interface ome.services.blitz.gateway.services.ImageService: Create a new image of specified X,Y, Z, T and channels plus pixelsType with name and description
createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
createImage_async(AMD_IPixels_createImage, int, int, int, int, List<Integer>, PixelsType, String, String, Current) - Method in class ome.services.blitz.impl.PixelsI
createInstance() - Method in class ome.security.basic.EventListenersFactoryBean: First, adds all default listeners.
createJob(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder: Returns a fresh (unsaved) ScriptJob which can be passed to acquireProcessor for background processing.
createJobHandle(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createJobHandle() - Method in class ome.system.ServiceFactory: create a new JobHandle proxy.
createNewRenderingDef(Pixels) - Method in interface ome.api.IRenderingSettings: Creates a new rendering definition object along with its sub-objects.
createNewRenderingDef(Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
createNewRenderingDef_async(AMD_IRenderingSettings_createNewRenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
createPath(String, String, boolean) - Method in class omero.util.TempFileManager: Uses File.createTempFile(String, String, File) to create temporary files and folders under TempFileManager.dir.
createPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService: Creates a PixelBuffer for a given pixels set.
createPlane(PlaneDef, int, Pixels, PixelBuffer) - Static method in class omeis.providers.re.data.PlaneFactory: Factory method to fetch plane data and create an object to access it.
createPrincipal() - Method in class ome.system.SessionInitializer
createRawFileStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createRawFileStore() - Method in class ome.system.ServiceFactory: create a new RawFileStore proxy.
createRawPixelsStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createRawPixelsStore() - Method in class ome.system.ServiceFactory: create a new RawPixelsStore proxy.
createRenderingEngine(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createRenderingEngine() - Method in class ome.system.ServiceFactory: create a new RenderingEngine proxy.
createRoot() - Method in class ome.formats.OMEROMetadataStore
createRoot_async(AMD_MetadataStore_createRoot, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
createSearchService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createSearchService() - Method in class ome.system.ServiceFactory: create a new Search proxy.
createServantDelegate(String) - Method in class ome.services.blitz.impl.ServiceFactoryI: Creates a proxy according to the ServantDefinition for the given name.
createSession(Principal, String) - Method in interface ome.api.ISession: Creates a new session and returns it to the user.
createSession(Principal, String) - Method in class ome.services.sessions.SessionBean
createSession() - Method in class omero.client: Calls client.createSession(String, String) with null values
createSession(String, String) - Method in class omero.client: Performs the actual logic of logging in, which is done via the #getRouter().
createSession_async(AMD_ISession_createSession, Principal, String, Current) - Method in class ome.services.blitz.impl.SessionI
createSessionContext(List<?>, SessionContext) - Method in class ome.services.sessions.SessionManagerImpl: Takes a snapshot as from #executeSessionContextLookup(ServiceFactory, Principal) and turns it into a SessionContext instance.
CreateSessionMessage - Class in ome.services.messages: Published after a successful session creation.
CreateSessionMessage(Object, String) - Constructor for class ome.services.messages.CreateSessionMessage
createSessionWithTimeout(Principal, long) - Method in interface ome.api.ISession: Allows an admin to create a Session for the give Principal
createSessionWithTimeout(Principal, long) - Method in class ome.services.sessions.SessionBean
createSessionWithTimeout_async(AMD_ISession_createSessionWithTimeout, Principal, long, Current) - Method in class ome.services.blitz.impl.SessionI
createSessionWithTimeouts(Principal, long, long) - Method in interface ome.api.ISession: Allows an admin to create a Session for the give Principal
createSessionWithTimeouts(Principal, long, long) - Method in class ome.services.sessions.SessionBean
createSessionWithTimeouts_async(AMD_ISession_createSessionWithTimeouts, Principal, long, long, Current) - Method in class ome.services.blitz.impl.SessionI
createShare(String, Timestamp, List<T>, List<Experimenter>, List<String>, boolean) - Method in interface ome.api.IShare: Creates share with all related: items, members, and guests.
createShare(Principal, boolean, long, String, String, long) - Method in interface ome.services.sessions.SessionManager
createShare(Principal, boolean, long, String, String, long) - Method in class ome.services.sessions.SessionManagerImpl
createShare(String, Timestamp, List<T>, List<Experimenter>, List<String>, boolean) - Method in class ome.services.sharing.ShareBean
createShare_async(AMD_IShare_createShare, String, RTime, List<IObject>, List<Experimenter>, List<String>, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
createStats() - Method in class ome.services.sessions.stats.CounterFactory
createSubpath(String) - Method in class ome.io.nio.AbstractFileSystemService: Makes sure that for a given path, it's subpath exists.
createSystemUser(Experimenter) - Method in interface ome.api.IAdmin: create and return a new system user.
createSystemUser(Experimenter) - Method in class ome.logic.AdminImpl
createSystemUser_async(AMD_IAdmin_createSystemUser, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
createTempFile(String, String) - Static method in class omero.util.TempFileManager: Emulates File.createTempFile(String, String) by calling TempFileManager.create_path(String, String).
createThumbnail(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Creates a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) in the on-disk cache.
createThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService: Creates thumbnail on disk using byte array
createThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
createThumbnail_async(AMD_ThumbnailStore_createThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
createThumbnailMetadata(Pixels, Dimension) - Method in class ome.services.ThumbnailCtx: Creates metadata for a thumbnail of a given set of pixels set and X-Y dimensions.
createThumbnails() - Method in interface ome.api.ThumbnailStore: Creates thumbnails for a pixels set using a given set of rendering settings (RenderingDef) in the on-disk cache for every sizeX/sizeY combination already cached.
createThumbnails() - Method in class ome.services.ThumbnailBean
createThumbnails_async(AMD_ThumbnailStore_createThumbnails, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
createThumbnailsByLongestSideSet(Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore: Creates thumbnails for a number of pixels sets using a given set of rendering settings (RenderingDef) in the on-disk cache.
createThumbnailsByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
createThumbnailsByLongestSideSet_async(AMD_ThumbnailStore_createThumbnailsByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
createThumbnailService() - Method in class ome.system.ServiceFactory: create a new ThumbnailStore proxy.
createThumbnailStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createUser(Experimenter, String) - Method in interface ome.api.IAdmin: create and return a new user.
createUser(Experimenter, String) - Method in class ome.logic.AdminImpl
createUser_async(AMD_IAdmin_createUser, Experimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI
createUserDirectories(Set<String>) - Method in class ome.services.util.DropBoxDirectoryCheck
createUserFromLdap(String, String) - Method in class ome.logic.LdapImpl: Gets user from LDAP for checking him by requirements and setting his details on DB
createUserSession(long, long, String) - Method in interface ome.api.ISession: Allows a user to open up another session for him/herself with the given defaults without needing to re-enter password.
createUserSession(long, long, String) - Method in class ome.services.sessions.SessionBean
createUserSession_async(AMD_ISession_createUserSession, long, long, String, Current) - Method in class ome.services.blitz.impl.SessionI
createWithAgent(Principal, String, String) - Method in interface ome.services.sessions.SessionManager
createWithAgent(Principal, String) - Method in interface ome.services.sessions.SessionManager
createWithAgent(Principal, String, String) - Method in class ome.services.sessions.SessionManagerImpl
createWithAgent(Principal, String) - Method in class ome.services.sessions.SessionManagerImpl
credentials - Variable in class ome.system.SessionInitializer
CRITICAL_USAGE - Static variable in class ome.logic.RepositoryInfoImpl: Percentage (100.0 - 0.0) of disk use which will cause an exception during RepositoryInfoImpl.sanityCheckRepository()
csId - Variable in class ome.system.SimpleEventContext
csName - Variable in class ome.system.SimpleEventContext
CSV - Static variable in class pojos.FileAnnotationData: Identifies the CSV file formats.
ctx - Variable in class ome.security.auth.ConfigurablePasswordProvider
ctx - Variable in class ome.security.basic.BasicSecuritySystem
ctx - Variable in class ome.services.blitz.impl.AbstractAmdServant
ctx - Variable in class ome.services.sharing.BlobShareStore
ctx - Variable in class ome.services.throttling.AbstractThrottlingStrategy
ctx - Variable in class ome.system.ServiceFactory: the context instance which this ServiceFactory uses to look up all of its state.
cuId - Variable in class ome.system.SimpleEventContext
cuName - Variable in class ome.system.SimpleEventContext
current - Variable in class ome.security.SecuritySystemHolder
current - Variable in class ome.services.throttling.Task
current_group - Static variable in class ome.tools.hibernate.SecurityFilter
current_user - Static variable in class ome.tools.hibernate.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 - Variable in class ome.tools.hibernate.ProxyCleanupFilter
currentMetadata() - Method in interface ome.api.Search: Provides access to the extra query information (for example Lucene score and boost values) for a single call to Search.next().
currentMetadata() - Method in class ome.services.SearchBean
currentMetadata_async(AMD_Search_currentMetadata, Current) - Method in class ome.services.blitz.impl.SearchI
currentMetadataList() - Method in interface ome.api.Search: Provides access to the extra query information (for example Lucene score and boost values) for a single call to Search.results().
currentMetadataList() - Method in class ome.services.SearchBean
currentMetadataList_async(AMD_Search_currentMetadataList, Current) - Method in class ome.services.blitz.impl.SearchI
CurrentSessionContext - Class in ome.tools.hibernate: Implementation of Hibernate's current_session_context_class extension point.
CurrentSessionContext(SessionFactoryImplementor) - Constructor for class ome.tools.hibernate.CurrentSessionContext
CurrentSessionStats - Class in ome.services.sessions.stats: Wrapper which delegates to a SessionStats instance acquired during construction.
CurrentSessionStats(CurrentDetails, SessionManager) - Constructor for class ome.services.sessions.stats.CurrentSessionStats
currentUser - Variable in class ome.security.basic.BasicACLVoter

D

data - Variable in class ome.io.nio.PixelData: The pixels data backing buffer.
data - Variable in class ome.services.roi.GeomTool
data - Variable in class ome.services.roi.PixelData
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, SimpleJdbcTemplate) - Constructor for class ome.services.db.DatabaseIdentity
DatabaseIdentity(String, String) - Constructor for class ome.services.db.DatabaseIdentity
DataObject - Class in pojos: Abstract superclass for objects that hold OMEDS data.
DataObject() - Constructor for class pojos.DataObject
DataService - Interface in ome.services.blitz.gateway.services
DataServiceImpl - Class in ome.services.blitz.gateway.services.impl
DataServiceImpl(GatewayFactory) - Constructor for class ome.services.blitz.gateway.services.impl.DataServiceImpl: Instantiate the imageService with the serviceFactory.
DATASET_LINKS - Static variable in class pojos.ImageData: Identifies the Image#DATASETLINKS field.
DATASET_LINKS - Static variable in class pojos.ProjectData: Identifies the Project#DATASETLINKS field.
DatasetData - Class in pojos: The data that makes up an OME Dataset along with links to its contained Images and enclosing Project as well as the Experimenter that owns this Dataset.
DatasetData() - Constructor for class pojos.DatasetData: Creates a new instance.
DatasetData(Dataset) - Constructor for class pojos.DatasetData: Creates a new instance.
DataSink - Class in omerojava.util: Encapsulates access to the image raw data.
DbCreate - Class in ome.services.blitz: Database creation driver used by Entry when called from the command line.
DbCreate(String[]) - Constructor for class ome.services.blitz.DbCreate
DbCreate(File, Executor) - Constructor for class ome.services.blitz.DbCreate
DBEnumCheck - Class in ome.services.util: Hook run by the context to guarantee that various enumerations are up to date.
DBEnumCheck(Executor) - Constructor for class ome.services.util.DBEnumCheck
DBPatchCheck - Class in ome.services.util: Hook run by the context.
DBPatchCheck(Executor, LocalConfig) - Constructor for class ome.services.util.DBPatchCheck
dbPath(Shape) - Method in class ome.services.roi.GeomTool
DbUpdateTask - Class in ome.tools: An ant task for checking the current database version.
DbUpdateTask() - Constructor for class ome.tools.DbUpdateTask
deactivate() - Method in interface ome.api.IShare: Turns off the access control lists with the current share.
deactivate() - Method in class ome.services.sharing.ShareBean
deactivate_async(AMD_IShare_deactivate, Current) - Method in class ome.services.blitz.impl.ShareI
DEBUG - Static variable in class prefs: Activated by setting DBEUG=true in the environment.
debugAll - Variable in class ome.security.basic.EventListenersFactoryBean
DECILE - Static variable in class omeis.providers.re.quantum.QuantumStrategy: Determines the number of sub-intervals of the [globalMin, globalMax] interval.
decodeKey(byte[], Communicator) - Method in class ome.services.sharing.data.ShareItems
decodeKey(byte[], Communicator) - Method in class ome.services.sharing.data.ShareMap
decodeValue(byte[], Communicator) - Method in class ome.services.sharing.data.ShareItems
decodeValue(byte[], Communicator) - Method in class ome.services.sharing.data.ShareMap
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.ArrayStringType
deepCopy(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
deepCopy(Object) - Method in class ome.tools.hibernate.PermissionsType
def(String[]) - Static method in class prefs: Returns the current default if no argument is given, or sets the default to the given string (or "" if null) otherwise returing "Default set to: ... ".
DEFAULT - Static variable in class ome.services.delete.DeleteEntry
DEFAULT - Static variable in class pojos.GroupData: Identifies the default group.
DEFAULT - Static variable in class prefs: Key (and default value) of the property under prefs.ROOT which defines which "profile" (subnode} is in effect.
DEFAULT_BATCH_SIZE - Static variable in interface ome.api.Search: Default batch size
DEFAULT_BATCH_SIZE - Static variable in class ome.services.fulltext.EventLogLoader: Currently 100.
DEFAULT_CASE_SENSITIVTY - Static variable in interface ome.api.Search: Default case sensitivity
DEFAULT_COMPRESSION_QUALITY - Static variable in class ome.services.ThumbnailBean: The default compression quality in fractional percent.
DEFAULT_FILL_COLOUR - Static variable in class pojos.ShapeSettingsData: The default fill color.
DEFAULT_FILL_COLOUR_ALPHA - Static variable in class pojos.ShapeSettingsData: The default fill color.
DEFAULT_FONT_FAMILY - Static variable in class pojos.ShapeSettingsData: The default font family.
DEFAULT_FONT_SIZE - Static variable in class pojos.ShapeSettingsData: The default font size.
DEFAULT_FONT_STYLE - Static variable in class pojos.ShapeSettingsData: The default font style.
DEFAULT_FONT_WEIGHT - Static variable in class pojos.ShapeSettingsData: The default font weight.
DEFAULT_MERGED_BATCHES - Static variable in interface ome.api.Search: Default merged-batches
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.system.Server
DEFAULT_RETURN_UNLOADED - Static variable in interface ome.api.Search: Default return-unloaded
DEFAULT_STROKE_COLOUR - Static variable in class pojos.ShapeSettingsData: The default stroke color.
DEFAULT_STROKE_WIDTH - Static variable in class pojos.ShapeSettingsData: The default stroke width.
DEFAULT_TIMEOUT - Static variable in class ome.system.UpgradeCheck: Default timeout is 10 seconds.
DEFAULT_USE_PROJECTIONS - Static variable in interface ome.api.Search: Default use-projections
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.
defaultTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl
defaultTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl
DEFAULTWORKFLOW - Static variable in class pojos.WorkflowData: The default workflow, i.e. nothing .
define(Session, String, String, long, long, long, 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 - Variable in class ome.services.fulltext.PersistentEventLogLoader: String used with parameter 'name' to drop the current id;
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
DeleteCallbackI - Class in omero.grid: Callback used for waiting until DeleteHandlePrx will return true on DeleteHandlePrx.finished().
DeleteCallbackI(client, DeleteHandlePrx) - Constructor for class omero.grid.DeleteCallbackI
deleteChannels(long) - Method in class ome.services.delete.DeleteBean
deleteComment(Annotation) - Method in interface ome.api.IShare: Deletes comment from the database.
deleteComment(Annotation) - Method in class ome.services.sharing.ShareBean
deleteComment_async(AMD_IShare_deleteComment, Annotation, Current) - Method in class ome.services.blitz.impl.ShareI
deleteCurrentId() - Method in class ome.services.fulltext.PersistentEventLogLoader
deleteDataObject(IObject, Parameters) - Method in interface ome.api.IContainer: Deletes a data object.
deleteDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
deleteDataObject_async(AMD_IContainer_deleteDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
deleteDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer: convenience method to save network calls.
deleteDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
deleteDataObjects_async(AMD_IContainer_deleteDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
DeleteEntry - Class in ome.services.delete: Single value of the map entries from spec.xml.
DeleteEntry(DeleteSpec, String) - Constructor for class ome.services.delete.DeleteEntry
DeleteEntry(DeleteSpec, String, DeleteEntry) - Constructor for class ome.services.delete.DeleteEntry
deleteEnumeration(T) - Method in interface ome.api.ITypes: deletes enumeration value specified by object
deleteEnumeration(T) - Method in class ome.logic.TypesImpl
deleteEnumeration_async(AMD_ITypes_deleteEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
DeleteException - Exception in ome.services.delete: Exception which will be thrown by activities within DeleteSpec implementations.
DeleteException(String) - Constructor for exception ome.services.delete.DeleteException
deleteExperimenter(Experimenter) - Method in interface ome.api.IAdmin: removes a user by removing the password information for that user as well as all GroupExperimenterMap instances.
deleteExperimenter(Experimenter) - Method in class ome.logic.AdminImpl
deleteExperimenter_async(AMD_IAdmin_deleteExperimenter, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
deleteGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin: removes a group by first removing all users in the group, and then deleting the actual ExperimenterGroup instance.
deleteGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
deleteGroup_async(AMD_IAdmin_deleteGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
DeleteHandleI - Class in ome.services.blitz.impl: Servant for the handle proxy from the IDelete service.
DeleteHandleI(Identity, ServiceFactoryI, AbstractFileSystemService, DeleteCommand[], int) - Constructor for class ome.services.blitz.impl.DeleteHandleI: Create and
DeleteI - Class in ome.services.blitz.impl: Implementation of the IDelete service.
DeleteI(IDelete, BlitzExecutor, ThreadPool, int, String) - Constructor for class ome.services.blitz.impl.DeleteI
deleteImage(long, boolean) - Method in interface ome.api.IDelete: Deletes an Image and all related (subordinate) metadata as defined below.
deleteImage(long, boolean) - Method in class ome.services.delete.DeleteBean
deleteImage_async(AMD_IDelete_deleteImage, long, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI
deleteImages(Set<Long>, boolean) - Method in interface ome.api.IDelete: Deletes several Image instances within a single transaction via the IDelete.deleteImage(long, boolean) method.
deleteImages(Set<Long>, boolean) - Method in class ome.services.delete.DeleteBean
deleteImages_async(AMD_IDelete_deleteImages, List<Long>, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI
deleteImagesByDataset(long, boolean) - Method in interface ome.api.IDelete: Deletes the user-visible Image instances of the given Dataset within a single transaction via the IDelete.deleteImage(long, boolean).
deleteImagesByDataset(long, boolean) - Method in class ome.services.delete.DeleteBean
deleteImagesByDataset_async(AMD_IDelete_deleteImagesByDataset, long, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI
deleteObject(IObject) - Method in interface ome.api.IUpdate: Deletes a single entity.
deleteObject(IObject) - Method in class ome.logic.UpdateImpl
deleteObject(IObject, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
deleteObject(IObject) - Method in interface ome.services.blitz.gateway.services.DataService: Delete the object.
deleteObject(IObject) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
deleteObject_async(AMD_IUpdate_deleteObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
DeleteOpts - Class in ome.services.delete: Manager for option instances for an entire delete graph.
DeleteOpts() - Constructor for class ome.services.delete.DeleteOpts
DeleteOpts.Op - Enum in ome.services.delete
deletePlate(long) - Method in interface ome.api.IDelete: Deletes all the images contained in a plate as if deleted by: deleteImage(id, true) so that all Dataset and Annotation links are broken, with WellSamples removed first.
deletePlate(long) - Method in class ome.services.delete.DeleteBean
deletePlate_async(AMD_IDelete_deletePlate, long, Current) - Method in class ome.services.blitz.impl.DeleteI
deleteScript_async(AMD_IScript_deleteScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI: Delete the script with id from the server.
deleteSettings(long) - Method in interface ome.api.IDelete: Deletes all rendering settings for the given Pixel id.
deleteSettings(long) - Method in class ome.services.delete.DeleteBean
deleteSettings_async(AMD_IDelete_deleteSettings, long, Current) - Method in class ome.services.blitz.impl.DeleteI
DeleteSpec - Interface in ome.services.delete: Specification of a delete operation.
DeleteSpecFactory - Class in ome.services.delete: Container which is loaded with stateful DeleteSpec instances for use in a multi-threaded environment.
DeleteSpecFactory() - Constructor for class ome.services.delete.DeleteSpecFactory
DeleteState - Class in ome.services.delete: Tree-structure containing all scheduled deletes which closely resembles the tree structure of the DeleteSpec itself.
DeleteState(OmeroContext, Session, DeleteSpec) - Constructor for class ome.services.delete.DeleteState
DeleteStep - Class in ome.services.delete: Single action performed by DeleteState.
DeltaVision - Class in ome.io.nio: Class implementation of the PixelBuffer interface for a DeltaVision specific image file.
DeltaVision(String, OriginalFile) - Constructor for class ome.io.nio.DeltaVision: Constructor.
DeltaVisionHeader - Class in ome.io.nio: Temporary class implementation of an image file header for the server-side import of a DeltaVision file.
DeltaVisionHeader(ByteBuffer, boolean) - Constructor for class ome.io.nio.DeltaVisionHeader: Constructor
DEPTH_1BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 1-bit depth (=2^1-1) output interval.
DEPTH_2BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 2-bit depth (=2^2-1) output interval.
DEPTH_3BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 3-bit depth (=2^3-1) output interval.
DEPTH_4BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 4-bit depth (=2^4-1) output interval.
DEPTH_5BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 5-bit depth (=2^5-1) output interval.
DEPTH_6BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 6-bit depth (=2^6-1) output interval.
DEPTH_7BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 7-bit depth (=2^7-1) output interval.
DEPTH_8BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 8-bit depth (=2^8-1) output interval.
DESCENDING_LETTER - Static variable in class pojos.PlateData: Indicates that the column or row is a letter starting from Z or P.
DESCENDING_NUMBER - Static variable in class pojos.PlateData: Indicates that the column or row is a letter starting from 26 or 16.
description() - Method in class ome.services.fulltext.FullTextIndexer
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.StatelessWork: Return a description of what this work will be doing for logging purposes.
description() - Method in interface ome.services.util.Executor.Work: Returns a description of what this work will be doing for logging purposes.
DESCRIPTION - Static variable in class pojos.DatasetData: Identifies the Dataset#DESCRIPTION field.
DESCRIPTION - Static variable in class pojos.GroupData: Identifies the ExperimenterGroup#DESCRIPTION field.
DESCRIPTION - Static variable in class pojos.ImageData: Identifies the Image#DESCRIPTION field.
DESCRIPTION - Static variable in class pojos.PlateData: Identifies the Plate#DESCRIPTION field.
DESCRIPTION - Static variable in class pojos.ProjectData: Identifies the Project#DESCRIPTION field.
DESCRIPTION - Static variable in class pojos.ScreenData: Identifies the Screen#DESCRIPTION field.
destroy() - Method in class ome.services.blitz.fire.Ring
destroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI: Destruction simply decrements the reference count for a session to allow reconnecting to it.
destroy() - Method in class ome.services.blitz.util.BlitzConfiguration
destroy() - Method in class ome.services.roi.RoiTypes.ObjectFactory
destroy() - Method in class ome.services.throttling.Queue
destroy() - Method in class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean
destroy() - Method in class omero.rtypes.ObjectFactory
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
detachOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
DetailsI - Class in omero.model
DetailsI() - Constructor for class omero.model.DetailsI
detailsIndex(String[]) - Static method in class ome.tools.hibernate.HibernateUtils
DetectorData - Class in pojos: Hosts a detector.
DetectorData(Detector) - Constructor for class pojos.DetectorData: Creates a new instance.
DichroicData - Class in pojos: Hosts the dichroic.
DichroicData(Dichroic) - Constructor for class pojos.DichroicData: Creates a new instance.
diff(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the sum of this vector with the reciprocal of the specified argument.
DimensionsOutOfBoundsException - Exception in ome.io.nio
DimensionsOutOfBoundsException(String) - Constructor for exception ome.io.nio.DimensionsOutOfBoundsException
direction - Variable in class ome.util.math.geom2D.Line: The unit vector that, given the Line.origin point, identifies this line.
directionX1 - Variable in class ome.util.math.geom2D.Segment: The end point of the segment's first element.
directionX2 - Variable in class ome.util.math.geom2D.Segment: The end point of the segment's second element.
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(String...) - Method in class ome.security.basic.BasicSecuritySystem
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
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
disableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem: disable this filer.
disassemble(Object) - Method in class ome.tools.hibernate.ArrayStringType
disassemble(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
disassemble(Object) - Method in class ome.tools.hibernate.PermissionsType
discriminator(String) - Method in class ome.services.roi.GeomTool: Maps from multiple possible user-provided names of shapes (e.g.
dispatch(String[]) - Static method in class prefs: Uses the first string in the argument array to reflectively invoke another method with the same signature on prefs.
dispose() - Method in class ome.services.sessions.state.CacheListener
distance(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the distance between this point and the specified argument.
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. instead, we use the one time token which is removed this Object is checked for privileges.
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
doCheckPassword(String, String, Properties) - Method in class ome.security.auth.FilePasswordProvider
doClose() - Method in class ome.services.sharing.BlobShareStore
doClose() - Method in class ome.services.sharing.FreezeShareStore
doClose() - Method in class ome.services.sharing.ShareStore
doContains(long, Class<T>, long) - Method in class ome.services.sharing.BlobShareStore
doContains(long, Class<T>, long) - Method in class ome.services.sharing.FreezeShareStore
doContains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
doDestroy() - Method in class ome.services.blitz.impl.ServiceFactoryI: Performs the actual cleanup operation on all the resources shared between this and other ServiceFactoryI instances in the same Session.
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
doIndexing(FullTextSession) - Method in class ome.services.fulltext.FullTextIndexer
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.FreezeShareStore
doInit() - Method in class ome.services.sharing.ShareStore
doMore(int) - Method in class ome.services.fulltext.FullTextIndexer: 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(Session) - Method in class ome.services.blitz.impl.DeleteHandleI
doRun() - Method in class ome.services.fulltext.FullTextThread: Passes the FullTextIndexer instance to Executor.Work#doWork(org.springframework.transaction.TransactionStatus, org.hibernate.Session, ome.system.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.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.FreezeShareStore
doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.ShareStore
doStop() - Method in class omero.grid.InteractiveProcessorI
dot(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calulates the dot product of this vector by the specified argument.
DOUBLE - Static variable in class ome.io.nio.PixelData: Identifies the type used to store pixel values.
DOUBLE - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
DOUBLE - Static variable in class omerojava.util.PixelTypes: Identifies the type used to store pixel values.
DOUBLE_COMPLEX_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
DOUBLE_TYPE - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the DOUBLE data type used to store pixel values, as per OME spec.
DOUBLE_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
DoubleAnnotationData - Class in pojos: Wraps a double annotation.
DoubleAnnotationData(double) - Constructor for class pojos.DoubleAnnotationData: Creates a new instance.
DoubleAnnotationData() - Constructor for class pojos.DoubleAnnotationData: Creates a new instance.
DoubleAnnotationData(DoubleAnnotation) - Constructor for class pojos.DoubleAnnotationData: Creates a new instance.
DoubleConverter - Class in omerojava.util: Packs a sequence of bytes representing a big-endian double into a double value of appropriate integer type.
DoubleConverter() - Constructor for class omerojava.util.DoubleConverter
doUpdate() - Method in class ome.services.sessions.state.SessionCache: Will only ever be accessed by a single thread.
down(String, Current) - Method in class ome.services.blitz.fire.Ring: Called when any node goes down.
download(long, File) - Method in class omero.client
download(long, File, int) - Method in class omero.client
doWork(Session, ServiceFactory) - Method in class ome.services.fulltext.FullTextIndexer: Runs FullTextIndexer.doIndexing(FullTextSession) within a Lucene transaction.
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(SimpleJdbcOperations) - Method in interface ome.services.util.Executor.StatelessWork
doWork(Session, ServiceFactory) - Method in interface ome.services.util.Executor.Work: Work method.
drop(String[]) - Static method in class prefs: Drops the entire profile (subnode) via Preferences.removeNode().
DropBoxDirectoryCheck - Class in ome.services.util: Hook run by the context at startup to create a drop-box directory per user.
DropBoxDirectoryCheck(String, SimpleJdbcOperations) - Constructor for class ome.services.util.DropBoxDirectoryCheck
dsAllQuery - Static variable in class ome.services.delete.QueryConstraints
dsNotOwnQuery - Static variable in class ome.services.delete.QueryConstraints
DV_FORMAT - Static variable in class ome.io.nio.PixelsService: The DeltaVision file format enumeration value

E

EDITOR_EXPERIMENT_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is an experiment.
EDITOR_EXPERIMENT_NS - Static variable in class pojos.FileAnnotationData: The name space used to indicate that the FileAnnotation is an experiment.
EDITOR_PROTOCOL_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is a protocol.
EDITOR_PROTOCOL_NS - Static variable in class pojos.FileAnnotationData: The name space used to indicate that the FileAnnotation is a protocol.
editScript_async(AMD_IScript_editScript, OriginalFile, String, Current) - Method in class ome.services.blitz.impl.ScriptI
elementType - Variable in class ome.services.query.CollectionQueryParameterDef
ellipse(double, double, double, double) - Method in class ome.services.roi.GeomTool
ellipse(double, double, double, double, int, int) - Method in class ome.services.roi.GeomTool
EllipseArea - Class in ome.util.math.geom2D: Represents an ellipse in the Euclidean space R².
EllipseArea(float, float, float, float) - Constructor for class ome.util.math.geom2D.EllipseArea: Creates a new instance.
EllipseData - Class in pojos: Represents an ellipse in the Euclidean space R².
EllipseData(Shape) - Constructor for class pojos.EllipseData: Creates a new instance of Ellipse data from an existing shape.
EllipseData() - Constructor for class pojos.EllipseData: Creates a new instance of EllipseData.
EllipseData(double, double, double, double) - Constructor for class pojos.EllipseData: Creates a new instance of the EllipseData.
EMAIL - Static variable in class pojos.ExperimenterData: Identifies the Experimenter#EMAIL field.
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(String...) - Method in class ome.security.basic.BasicSecuritySystem
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
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 overriden by subclasses to enable particular filters.
enableKeepAlive(int) - Method in class omero.client: Resets the "omero.keep_alive" property on the current Communicator which is used on initialization to determine the time-period between checks.
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.
encodeKey(Object, Communicator) - Method in class ome.services.sharing.data.ShareItems
encodeKey(Object, Communicator) - Method in class ome.services.sharing.data.ShareMap
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(String) - Method in interface ome.security.auth.PasswordUtility
encodeValue(Object, Communicator) - Method in class ome.services.sharing.data.ShareItems
encodeValue(Object, Communicator) - Method in class ome.services.sharing.data.ShareMap
endIO(int) - Method in class omeis.providers.re.RenderingStats: Notifies the end of pixels data retrieval for the specified wavelength (channel).
endMalloc() - Method in class omeis.providers.re.RenderingStats: Notifies the end of the allocation of an RGB memory buffers for the rendering process.
endRendering() - Method in class omeis.providers.re.RenderingStats: Notifies the end of the trasnformation of the raw pixels data.
endTime(RTime) - Method in class omero.sys.ParametersI: Sets the value of the end time parameter.
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
entityType - Variable in class ome.services.messages.EventLogMessage
entries - Variable in class ome.services.delete.BaseDeleteSpec: The paths which make up this delete specification.
entries() - Method in class ome.services.delete.BaseDeleteSpec
entries() - Method in interface ome.services.delete.DeleteSpec: Returns a copy of the list of DeleteEntry instances contained in this DeleteSpec
Entry - Class in ome.services.blitz: OMERO.blitz startup code.
Entry(String) - Constructor for class ome.services.blitz.Entry: Stores name of the OmeroContext which is to be used by this instance.
env() - Method in class omero.client: Helper method to access session environment
ENV - Static variable in class prefs: Environment variable which can be set to override the current, active profile.
environment(String, String) - Method in class ome.services.sessions.SessionManagerImpl
envItems - Variable in class ome.services.sharing.FreezeShareStore
envLocation - Variable in class ome.services.sharing.FreezeShareStore
envMap - Variable in class ome.services.sharing.FreezeShareStore
envRoot - Variable in class ome.services.sharing.FreezeShareStore
equals(Object) - Method in class ome.tools.FileSystem: Public equals implementation based on name only (very loose equals)
equals(Object, Object) - Method in class ome.tools.hibernate.ArrayStringType
equals(Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
equals(Object, Object) - Method in class ome.tools.hibernate.PermissionsType
equals(Object) - Method in class ome.util.math.geom2D.Line: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(Object) - Method in class ome.util.math.geom2D.PlanePoint: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(double, double) - Method in class ome.util.math.geom2D.PlanePoint: Check to see if the point values are equal.
equals(double, double, double) - Method in class ome.util.math.geom2D.Segment: Performs an equality test based on a point on this line defined by k as in getPoint() and another given point.
equals(Object) - Method in class ome.util.math.geom2D.Segment: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(Object) - Method in class omeis.providers.re.codomain.CodomainMapContext: This method is overridden so that objects of the same class are considered the same.
equals(Object) - Method in class omeis.providers.re.data.PlaneDef: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(Object) - Method in class pojos.ROICoordinate: Overridden to control if the passed object equals the current one.
ERROR - Static variable in interface ome.api.JobHandle
error(String) - Method in class ome.services.blitz.util.CommonsLoggingAdapter
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
errorIfNullPixels() - Method in class ome.services.ThumbnailBean
errorIfNullPixelsAndRenderingDef() - Method in class ome.services.ThumbnailBean
errorIfNullRenderer() - Method in class ome.services.RenderingBean
errorIfNullRenderingDef() - Method in class ome.services.RenderingBean
errorIfNullRenderingDef() - Method in class ome.services.ThumbnailBean
errorOnViolation(Class, Method, Object[]) - Static method in class ome.annotations.ApiConstraintChecker
errors(Current) - Method in class ome.services.blitz.impl.DeleteHandleI
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.fulltext: Thread-safe java.util-like Container for storing EventLog instances for later parsing.
EventBacklog() - Constructor for class ome.services.fulltext.EventBacklog
EventContext - Interface in ome.system: manages authenticated principals and other context for a given event.
EventHandler - Class in ome.security.basic: method interceptor responsible for login and creation of Events.
EventHandler(SimpleJdbcOperations, SimpleJdbcOperations, BasicSecuritySystem, SessionFactory, TransactionAttributeSource) - Constructor for class ome.security.basic.EventHandler: only public constructor, used for dependency injection.
EventHandler(SimpleJdbcOperations, SimpleJdbcOperations, BasicSecuritySystem, SessionFactory, TransactionAttributeSource, boolean) - 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
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.fulltext: Data access object for the FullTextIndexer which provides an Iterator interface for EventLog instances to be properly indexed.
EventLogLoader() - Constructor for class ome.services.fulltext.EventLogLoader
EventLogMessage - Class in ome.services.messages: Published when an event log should be saved at the end of a transaction.
EventLogMessage(Object, String, Class<IObject>, List<Long>) - Constructor for class ome.services.messages.EventLogMessage
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.Action() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.Action
EventMethodInterceptor.DisableAction - Class in ome.tools.hibernate
EventMethodInterceptor.DisableAction() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.DisableAction
evict(Object) - Method in interface ome.api.local.LocalQuery: Removes an object graph from the session.
evict(Object) - Method in class ome.logic.QueryImpl
ex - Variable in class ome.services.roi.GeomTool
exception - Variable in class ome.services.throttling.Task
exception(Throwable, OmeroContext) - Method in class ome.services.throttling.Task
excludes - Variable in class ome.services.fulltext.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(int) - Method in class ome.services.delete.DeleteState
execute(Principal, Executor.Work) - Method in interface ome.services.util.Executor: Executes a Executor.Work instance wrapped in two layers of AOP.
execute(Principal, Executor.Work) - Method in class ome.services.util.Executor.Impl: Executes a Executor.Work instance wrapped in two layers of AOP.
execute() - Method in class ome.tools.DbUpdateTask
execute(RMap, Current) - Method in class omero.grid.InteractiveProcessorI
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
executeStateless(Executor.StatelessWork) - Method in interface ome.services.util.Executor: Executes a Executor.StatelessWork wrapped with a transaction.
executeStateless(Executor.StatelessWork) - Method in class ome.services.util.Executor.Impl: Executes a Executor.StatelessWork in transaction.
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.blitz.fire.SessionManagerI
executor - Variable in class ome.services.blitz.redirect.AbstractRedirector
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.Descriptive(Object, String, Object...) - Constructor for class ome.services.util.Executor.Descriptive
Executor.Impl - Class in ome.services.util
Executor.Impl(CurrentDetails, SessionFactory, SimpleJdbcOperations, String[]) - Constructor for class ome.services.util.Executor.Impl
Executor.Impl(CurrentDetails, SessionFactory, SimpleJdbcOperations, String[], ExecutorService) - Constructor for class ome.services.util.Executor.Impl
Executor.SimpleStatelessWork - Class in ome.services.util: Simple adapter which takes a String for Executor.Descriptive.description
Executor.SimpleStatelessWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleStatelessWork
Executor.SimpleWork - Class in ome.services.util: Simple adapter which takes a String for Executor.Descriptive.description
Executor.SimpleWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleWork
Executor.StatelessWork - Interface in ome.services.util: Work SPI to perform actions related to stateless sessions.
Executor.Work - Interface in ome.services.util: Work SPI to perform actions within the server as if they were fully wrapped in our service logic.
executorWorkCall(Executor.Work) - Method in class ome.services.blitz.impl.AbstractAmdServant
exists() - Method in interface ome.api.RawFileStore: Checks to see if a raw file exists with the file ID that the service was initialized with.
exists(OriginalFile) - Method in class ome.io.nio.OriginalFilesService: Returns whether or not an OriginalFile exists on disk.
exists(long) - Method in class ome.services.blitz.gateway.services.impl.RawFileStoreServiceImpl
exists(long) - Method in interface ome.services.blitz.gateway.services.RawFileStoreService: Does the file exist in the RawFileStore.
exists() - Method in class ome.services.RawFileBean
exists_async(AMD_RawFileStore_exists, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
exit(String[]) - Static method in class prefs: Uses the length of the argument array as the exit code.
exp(RLong) - Method in class omero.sys.ParametersI: Sets the value of the experimenter parameter.
EXPERIMENTER_PHOTO_NS - Static variable in class pojos.FileAnnotationData: The name space used to identify the experimenter photo.
ExperimenterData - Class in pojos: The data that makes up an OME Experimenter along with information about the Group the Experimenter belongs in.
ExperimenterData() - Constructor for class pojos.ExperimenterData: Creates a new instance.
ExperimenterData(Experimenter) - Constructor for class pojos.ExperimenterData: Creates a new instance.
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).
ExpiredServantMessage - Class in ome.services.blitz.util: ApplicationEvent which gets raised on CacheEventListener.notifyElementExpired(net.sf.ehcache.Ehcache, net.sf.ehcache.Element)
ExpiredServantMessage(Object, String) - Constructor for class ome.services.blitz.util.ExpiredServantMessage
expires(Current) - Method in class omero.grid.InteractiveProcessorI
EXPONENTIAL - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a exponential map for the quantization process.
ExponentialMap - Class in omeis.providers.re.quantum: This class implements the QuantumMap interface.
ExponentialMap() - Constructor for class omeis.providers.re.quantum.ExponentialMap
export(String[]) - Static method in class prefs: Exports all properties in the current profile to System.out, or if a single argument is given, that is take to be the name of a target ouput file.
ExporterI - Class in ome.services.blitz.impl: Implementation of the Exporter service.
ExporterI(BlitzExecutor, DatabaseIdentity) - Constructor for class ome.services.blitz.impl.ExporterI
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 implementatino of ExtendedMetadata.
ExtendedMetadata.Impl() - Constructor for class ome.tools.hibernate.ExtendedMetadata.Impl
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.

F

factory - Variable in class ome.security.basic.EventHandler
factory - Variable in class ome.services.blitz.impl.RoiI
factory - Variable in class ome.services.blitz.impl.ScriptI
factory - Variable in class ome.services.blitz.impl.TimelineI
factory - Variable in class ome.services.roi.GeomTool
factory - Variable in class ome.services.sessions.SessionManagerImpl
factory - Variable in class ome.services.util.Executor.Impl
Factory - Static variable in class omero.model.DetailsI
Factory - Static variable in class omero.model.PermissionsI
FETCH - Static variable in class ome.services.query.Query: imported constant for ease of use
fetchAlso(String...) - Method in interface ome.api.Search: Adds a fetch clause for loading non-annotation fields of returned entities.
fetchAlso(Map<T, String>) - Method in class ome.services.SearchBean
fetchAlso(String...) - Method in class ome.services.SearchBean
fetchAlso_async(AMD_Search_fetchAlso, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
fetchAnnotations(Class...) - Method in interface ome.api.Search: Queries the database for all annotations of the given types for all returned instances.
fetchAnnotations - Variable in class ome.services.search.SearchValues
fetchAnnotations(Class...) - Method in class ome.services.SearchBean
fetchAnnotations_async(AMD_Search_fetchAnnotations, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
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
FILAMENT - Static variable in class pojos.LightSourceData: Indicates that the light source is a filament.
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
FileAnnotationData - Class in pojos: Annotation to upload files to the server.
FileAnnotationData(File) - Constructor for class pojos.FileAnnotationData: Creates a new instance.
FileAnnotationData(FileAnnotation) - Constructor for class pojos.FileAnnotationData: Creates a new instance.
FileBuffer - Class in ome.io.nio: Raw file buffer which provides I/O operations within the OMERO file repository.
FileData - Class in pojos: DataObject used to handle the file visible via FS.
FileData(OriginalFile) - Constructor for class pojos.FileData: Creates a new instance.
FileData(OriginalFile, boolean) - Constructor for class pojos.FileData: Creates a new instance.
FileData(OriginalFile, boolean, boolean) - Constructor for class pojos.FileData: Creates a new instance.
FILENAME - Static variable in class ome.formats.importer.util.TinyImportFixture: 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
FILES_PATH - Static variable in class ome.io.nio.AbstractFileSystemService
filesToString(File...) - Static method in class omero.client
FileSystem - Class in ome.tools: Extends Sun Microsystems java.io.File for J2SE 5 only.
FileSystem(String) - Constructor for class ome.tools.FileSystem: pass-thru constructor
FileSystem(URI) - Constructor for class ome.tools.FileSystem: pass-thru constructor
FileSystem(String, String) - Constructor for class ome.tools.FileSystem: pass-thru constructor
FileSystem(File, String) - Constructor for class ome.tools.FileSystem: pass-thru constructor
fillObject(ReverseModelMapper) - Method in class omero.model.DetailsI
fillObject(ReverseModelMapper) - Method in class omero.model.PermissionsI
fillRelationships(SessionFactoryImplementor, Map<String, String>) - 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
fillServerError(ServerError, Throwable) - Static method in class omero.util.IceMapper
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, Filterable) - Method in class omero.util.IceMapper
FILTERABLE - Static variable in class omero.util.IceMapper
FILTERABLE_ARRAY - Static variable in class omero.util.IceMapper
FILTERABLE_COLLECTION - Static variable in class omero.util.IceMapper
FILTERABLE_PRIMITIVE_MAP - Static variable in class omero.util.IceMapper
FilterData - Class in pojos: Object hosting a filter.
FilterData(Filter) - Constructor for class pojos.FilterData: Creates a new instance.
filterName - Static variable in class ome.tools.hibernate.SecurityFilter
FilterSetData - Class in pojos: Object hosting a filterSet.
FilterSetData(FilterSet) - Constructor for class pojos.FilterSetData: Creates a new instance.
find(Class<T>, long) - Method in interface ome.api.IQuery: lookup an entity by class and id.
find(Class, long) - Method in class ome.logic.QueryImpl
find(String) - Method in interface ome.services.sessions.SessionManager
find(String) - Method in class ome.services.sessions.SessionManagerImpl
find_async(AMD_IQuery_find, String, long, Current) - Method in class ome.services.blitz.impl.QueryI
findAll(Class<T>, Filter) - Method in interface ome.api.IQuery: lookup all entities that belong to this class and match filter.
findAll(Class<T>, Filter) - Method in class ome.logic.QueryImpl
findAll_async(AMD_IQuery_findAll, String, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
findAllByExample(T, Filter) - Method in interface ome.api.IQuery: search based on provided example entity.
findAllByExample(T, Filter) - Method in class ome.logic.QueryImpl
findAllByExample_async(AMD_IQuery_findAllByExample, IObject, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
findAllByFullText(Class<T>, String, Parameters) - Method in interface ome.api.IQuery: executes a full text search based on Lucene.
findAllByFullText(Class<T>, String, Parameters) - Method in class ome.logic.QueryImpl
findAllByFullText_async(AMD_IQuery_findAllByFullText, String, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
findAllByQuery(String, Parameters) - Method in interface ome.api.IQuery: executes the stored query with the given name.
findAllByQuery(String, Parameters) - Method in class ome.logic.QueryImpl
findAllByQuery(String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
findAllByQuery(String) - Method in interface ome.services.blitz.gateway.services.DataService: Run the query against the iQuery interface.
findAllByQuery(String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
findAllByQuery_async(AMD_IQuery_findAllByQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
findAllByString(Class<T>, String, String, boolean, Filter) - Method in interface ome.api.IQuery: search a given field matching against a String.
findAllByString(Class<T>, String, String, boolean, Filter) - Method in class ome.logic.QueryImpl
findAllByString_async(AMD_IQuery_findAllByString, String, String, String, boolean, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
findByAnyIntersection_async(AMD_IRoi_findByAnyIntersection, long, List<Shape>, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
findByExample(T) - Method in interface ome.api.IQuery: search based on provided example entity.
findByExample(T) - Method in class ome.logic.QueryImpl
findByExample_async(AMD_IQuery_findByExample, IObject, Current) - Method in class ome.services.blitz.impl.QueryI
findById(long, boolean) - Method in class ome.services.sharing.data.ShareMap
findById(long) - Method in class ome.services.sharing.data.ShareMap
findByImage_async(AMD_IRoi_findByImage, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
findByIntersection_async(AMD_IRoi_findByIntersection, long, Shape, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
findByOwner(long, boolean) - Method in class ome.services.sharing.data.ShareMap
findByOwner(long) - Method in class ome.services.sharing.data.ShareMap
findByPlane_async(AMD_IRoi_findByPlane, long, int, int, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
findByQuery(String, Parameters) - Method in interface ome.api.IQuery: executes the stored query with the given name.
findByQuery(String, Parameters) - Method in class ome.logic.QueryImpl
findByQuery(String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
findByQuery(String) - Method in interface ome.services.blitz.gateway.services.DataService: Run the query against the iQuery interface.
findByQuery(String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
findByQuery_async(AMD_IQuery_findByQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
findByRoi_async(AMD_IRoi_findByRoi, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
findByShare(long, boolean) - Method in class ome.services.sharing.data.ShareItems
findByShare(long) - Method in class ome.services.sharing.data.ShareItems
findByString(Class<T>, String, String) - Method in interface ome.api.IQuery: search a given field matching against a String.
findByString(Class<T>, String, String) - Method in class ome.logic.QueryImpl
findByString_async(AMD_IQuery_findByString, String, String, String, Current) - Method in class ome.services.blitz.impl.QueryI
findByType(String, boolean) - Method in class ome.services.sharing.data.ShareItems
findByType(String) - Method in class ome.services.sharing.data.ShareItems
findByUser(String) - Method in interface ome.services.sessions.SessionManager
findByUser(String) - Method in class ome.services.sessions.SessionManagerImpl
findByUserAndAgent(String, String...) - Method in interface ome.services.sessions.SessionManager: Returns a non-null, possibly empty list of session instances belonging to the given user and with one of the given agents.
findByUserAndAgent(String, String...) - Method in class ome.services.sessions.SessionManagerImpl
findCollection(Collection) - Method in class omero.util.IceMapper: Overrides the findCollection logic of ModelMapper, since all Collections should be Lists in Ice.
findCollectionTarget(Object) - Method in class omero.util.RTypeMapper
findContainerHierarchies(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer: Retrieves hierarchy trees in various hierarchies that contain the specified Images.
findContainerHierarchies(Class, Set, Parameters) - Method in class ome.logic.PojosImpl: Implemented as speficied by the IContainer I/F
findContainerHierarchies_async(AMD_IContainer_findContainerHierarchies, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
findDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: default logic
findDN(String) - Method in interface ome.api.ILdap: Searchs unique Distinguished Name - String in LDAP for Common Name equals username.
findDN(String) - Method in class ome.logic.LdapImpl
findDN_async(AMD_ILdap_findDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
findExperimenter(String) - Method in interface ome.api.ILdap: Searchs Experimenter by unique Distinguished Name - String in LDAP for Common Name equals username.
findExperimenter(String) - Method in class ome.logic.LdapImpl
findExperimenter_async(AMD_ILdap_findExperimenter, String, Current) - Method in class ome.services.blitz.impl.LdapI
findInDb(String, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
findInDb(RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
findInDb(SimpleJdbcOperations, RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper: Looks to see if a path is contained in the repository.
findIntersectingRois(long, Shape...) - Method in class ome.services.roi.GeomTool
findIntersectingRois(long, RoiOptions, Shape...) - Method in class ome.services.roi.GeomTool
findKeyTarget(Object) - Method in class omero.util.RTypeMapper
findMethodAnnotations(Class, Method) - Static method in class ome.annotations.AnnotationUtils: finds all parameter annotations for the given class including on all implemented interfaces.
findParameterAnnotations(Class, Method) - Static method in class ome.annotations.AnnotationUtils: finds all parameter annotations for the given class including on all implemented interfaces.
findPixelSets(int, Class, int, Map) - Method in interface ome.api.IResults: finding PixelSets.
findPixelSetsPrimitive(int, String, int, Map) - Method in interface ome.api.IResults
findProxy(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
finish() - Method in interface ome.services.procs.Process
finish() - Method in class ome.services.procs.ProcessSkeleton
FINISHED - Static variable in interface ome.api.JobHandle
finished(Current) - Method in class ome.services.blitz.impl.DeleteHandleI
finished(int) - Method in class omero.grid.DeleteCallbackI: Client method to be overwritten when block is returning a non-null.
FIRSTNAME - Static variable in class pojos.ExperimenterData: Identifies the Experimenter#FIRSTNAME field.
firstPlane() - Method in class pojos.ROIData: Return the first plane that the ROI starts on.
fixNulledOrFilteredCollections(IObject, IObject, EntityPersister, SessionImplementor) - Static method in class ome.tools.hibernate.HibernateUtils: loads collections which have been filtered or nulled by the user
FLIM - Static variable in class ome.services.util.NamespaceCheck
FLIM_NS - Static variable in class pojos.FileAnnotationData: Identifies the FLIM namespace.
flipState() - Method in class ome.services.fulltext.EventBacklog: Flips the EventBacklog to the "adding" state if it is empty, otherwise to the "removing" state.
FLOAT - Static variable in class ome.io.nio.PixelData: Identifies the type used to store pixel values.
FLOAT - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
FLOAT - Static variable in class omerojava.util.PixelTypes: Identifies the type used to store pixel values.
FLOAT_TYPE - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the FLOAT data type used to store pixel values, as per OME spec.
FLOAT_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
FloatConverter - Class in omerojava.util: Packs a sequence of bytes representing a big-endian float into a double value of appropriate integer type.
FloatConverter() - Constructor for class omerojava.util.FloatConverter
flush() - Method in interface ome.api.local.LocalUpdate
flush() - Method in class ome.logic.UpdateImpl
FONT_BOLD - Static variable in class pojos.ShapeSettingsData: Set if font bold.
FONT_ITALIC - Static variable in class pojos.ShapeSettingsData: Set if font italic.
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
free(String) - Method in class ome.tools.FileSystem: This method will return the free space in kilobytes TODO - resolve the slash mount
free() - Method in class ome.tools.hibernate.SqlArray
FreezeShareStore - Class in ome.services.sharing: Entry to the Ice code generated data/ directory.
FreezeShareStore(String, File) - Constructor for class ome.services.sharing.FreezeShareStore
from - Variable in class ome.services.blitz.util.ConvertToBlitzExceptionMessage
from(String, String) - Method in class ome.tools.hibernate.QueryBuilder
fromClass(Class) - Static method in class ome.services.blitz.measurements.Helper: Factory method to generate Helper instances from the Class of a given column.
fromLsid(String) - Static method in class ome.services.blitz.measurements.Helper: Factory method to generate Helper instances from the LSID of a given column.
fromPoints(String) - Method in class pojos.ShapeData: Parses out the type from the points string.
fromRType(RType) - Method in class omero.util.IceMapper: Uses the omero.rtypes hierarchy to properly convert any RType to its internal representation.
fullname() - Method in class ome.services.scripts.RepoFile
FullText - Class in ome.services.search: Search based on Lucene's Query class.
FullText(SearchValues, String, Class<? extends Analyzer>) - Constructor for class ome.services.search.FullText
FullTextAnalyzer - Class in ome.services.fulltext: Analyzer implementation based largely on SimpleAnalyzer, but with extensions for handling scientific and OS-type strings.
FullTextAnalyzer() - Constructor for class ome.services.fulltext.FullTextAnalyzer
fullTextBridge - Variable in class ome.logic.UpdateImpl
FullTextBridge - Class in ome.services.fulltext: Primary definition of what will be indexed via Hibernate Search.
FullTextBridge() - Constructor for class ome.services.fulltext.FullTextBridge: 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: Constructor which provides an empty set of custom bridges.
FullTextBridge(OriginalFilesService, Map<String, FileParser>, Class<FieldBridge>[]) - Constructor for class ome.services.fulltext.FullTextBridge: Main constructor.
FullTextIndexer - Class in ome.services.fulltext: Simple action which can be done in an asynchronous thread in order to index Hibernate entities.
FullTextIndexer(EventLogLoader) - Constructor for class ome.services.fulltext.FullTextIndexer
FullTextThread - Class in ome.services.fulltext: Library entry-point for indexing.
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge) - Constructor for class ome.services.fulltext.FullTextThread: Uses default Principal for indexing
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, boolean) - Constructor for class ome.services.fulltext.FullTextThread: Uses default Principal for indexing
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal) - Constructor for class ome.services.fulltext.FullTextThread: Main constructor.
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal, boolean) - Constructor for class ome.services.fulltext.FullTextThread: Main constructor.

G

G_BAND - Static variable in class omeis.providers.re.RGBBuffer: Index of the green band in the image's data buffer.
GatewayFactory - Class in ome.services.blitz.gateway.services
GatewayFactory(ServiceFactoryPrx) - Constructor for class ome.services.blitz.gateway.services.GatewayFactory: Create services from the serviceFactory.
GatewayHeartbeat - Class in omerojava.util
GatewayHeartbeat(GatewayPrx) - Constructor for class omerojava.util.GatewayHeartbeat: Create an instance of the OmeroJava class and create the heartbeat thread.
GatewayService - Interface in ome.services.blitz.gateway.services
GatewayUtils - Class in omerojava.util
GatewayUtils() - Constructor for class omerojava.util.GatewayUtils
generateRandomPasswd() - Method in class ome.security.auth.PasswordUtil
generateTiff_async(AMD_Exporter_generateTiff, Current) - Method in class ome.services.blitz.impl.ExporterI
generateXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI
generateXml_async(AMD_Exporter_generateXml, Current) - Method in class ome.services.blitz.impl.ExporterI: Generate XML and return the length
geomTool - Variable in class ome.services.blitz.impl.RoiI
GeomTool - Class in ome.services.roi: Strategy for handling the conversion between shapes and database-specific geometries.
GeomTool(PixelData, SimpleJdbcOperations, SessionFactory) - Constructor for class ome.services.roi.GeomTool
GeomTool(PixelData, SimpleJdbcOperations, SessionFactory, Executor, String) - Constructor for class ome.services.roi.GeomTool
get(Class<T>, long) - Method in interface ome.api.IQuery: lookup an entity by class and id.
get(Class, long) - Method in class ome.logic.QueryImpl
get(String, DirContextAdapter) - Method in class ome.security.auth.PersonContextMapper
get() - Method in class ome.services.blitz.util.ResultHolder
get(Identity) - Method in class ome.services.blitz.util.ServantHolder
get(String) - Method in class ome.services.delete.DeleteSpecFactory
get(Session, Class, long) - Method in class ome.services.fulltext.FullTextIndexer
get(Object) - Method in class ome.services.query.Definitions
get(String) - Method in class ome.services.query.Query: get the QueryParameter for this name argument.
get(long, int, int, int, int, int) - Method in class ome.services.roi.PixelData
get() - Method in class ome.services.sessions.SessionContext.Count: Return the current number of references which this session is aware of.
get(long) - Method in class ome.services.sharing.BlobShareStore
get(long) - Method in class ome.services.sharing.FreezeShareStore
get(long) - Method in class ome.services.sharing.ShareStore
get(Future<T>) - Method in interface ome.services.util.Executor: Helper method to perform Future.get() and properly unwrap the exceptions.
get(Future<T>) - Method in class ome.services.util.Executor.Impl
get(int) - Method in class ome.util.mem.CopiableArray: Return the Copiable at the specified position.
get(int) - Method in class ome.util.mem.ReadOnlyByteArray: Reads the element at the index position within this slice.
get(int) - Method in class omerojava.util.ReadOnlyByteArray: Reads the element at the index position within this slice.
get(String[]) - Static method in class prefs: Returns either the given key=value pairs (or all if no argument is given).
get_async(AMD_IQuery_get, String, long, Current) - Method in class ome.services.blitz.impl.QueryI
getA0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the slope of the first line.
getA1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the slope of the second line.
getA2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the slope of the third line.
getAbsolutePath() - Method in class pojos.FileData: Returns the absolute path.
getAcquisitionData() - Method in class omero.sys.ParametersI
getAcquisitionDate() - Method in class pojos.ImageData: Returns the acquisition date.
getActiveConnections(long) - Method in interface ome.api.IShare: Gets actual active connections to share.
getActiveConnections(long) - Method in class ome.services.sharing.ShareBean
getActiveConnections_async(AMD_IShare_getActiveConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI
getAdapter() - Method in class ome.services.blitz.impl.ServiceFactoryI
getAdapter() - Method in class omero.client
getAdminService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getAdminService() - Method in class ome.system.ServiceFactory
getAdminSession() - Method in interface ome.services.blitz.fire.Registry: Create a new AdminSessionPrx with the RegistryPrx.
getAdminSession() - Method in class ome.services.blitz.fire.Registry.Impl
getAgent(Current) - Method in class ome.services.blitz.fire.SessionManagerI
getAirPressure() - Method in class pojos.ImageAcquisitionData: Returns the air pressure in bar
getAll(String) - Method in class ome.security.auth.AttributeSet
getAllDatasets() - Method in interface ome.api.IAnalysis
getAllEnumerations(Class<T>) - Method in interface ome.api.IPixels: Retrieves the exhaustive list of enumerations for a given enumeration class.
getAllEnumerations(Class<T>) - Method in class ome.logic.PixelsImpl
getAllEnumerations_async(AMD_IPixels_getAllEnumerations, String, Current) - Method in class ome.services.blitz.impl.PixelsI
getAllForImage(long) - Method in interface ome.api.IAnalysis
getAllGuests(long) - Method in interface ome.api.IShare: Get the email addresses for all share guests.
getAllGuests(long) - Method in class ome.services.sharing.ShareBean
getAllGuests_async(AMD_IShare_getAllGuests, long, Current) - Method in class ome.services.blitz.impl.ShareI
getAllMembers(long) - Method in interface ome.api.IShare: Get all users who are a member of the share.
getAllMembers(long) - Method in class ome.services.sharing.ShareBean
getAllMembers_async(AMD_IShare_getAllMembers, long, Current) - Method in class ome.services.blitz.impl.ShareI
getAllPixels() - Method in class pojos.ImageData: Returns all the sets of pixels related to this image.
getAllUsers(long) - Method in interface ome.api.IShare: Get a single set containing the login names of the Experimenters as well email addresses for guests.
getAllUsers(long) - Method in class ome.services.sharing.ShareBean
getAllUsers_async(AMD_IShare_getAllUsers, long, Current) - Method in class ome.services.blitz.impl.ShareI
getAlpha() - Method in class pojos.WellData: Returns the alpha component of the color associated to the well, or -1.
getAmplificationGain() - Method in class pojos.DetectorData: Returns the amplification gain of the detector.
getAnalysisService() - Method in class ome.system.ServiceFactory
getAndLogException(Throwable) - Method in class ome.services.util.ServiceHandler
getAnnotatableTypes() - Method in interface ome.tools.hibernate.ExtendedMetadata: Returns all the classes which implement IAnnotated
getAnnotatableTypes() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
getAnnotations() - Method in class pojos.DatasetData: Returns the annotations related to this dataset.
getAnnotations() - Method in class pojos.ImageData: Returns the annotations
getAnnotationsCounts() - Method in class pojos.DatasetData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.ImageData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.PlateData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.ProjectData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.ScreenData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.WellData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationTypes() - Method in interface ome.api.ITypes: Returns a list of classes which implement IAnnotated.
getAnnotationTypes() - Method in class ome.logic.TypesImpl
getAnnotationTypes() - Method in interface ome.tools.hibernate.ExtendedMetadata: Returns all the classes which subclass Annotation
getAnnotationTypes() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
getAnnotationTypes_async(AMD_ITypes_getAnnotationTypes, Current) - Method in class ome.services.blitz.impl.TypesI
getArray() - Method in class ome.tools.hibernate.SqlArray
getArray(long, int) - Method in class ome.tools.hibernate.SqlArray
getArray(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
getArray(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
getAttachedFile() - Method in class pojos.FileAnnotationData: Returns the file to upload to the server.
getAttribute(Experimenter) - Method in class ome.security.auth.PersonContextMapper
getAttributeSet(Experimenter) - Method in class ome.security.auth.PersonContextMapper
getAuthority() - Method in class ome.services.db.DatabaseIdentity
getAvailableFamilies() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getAvailableFamilies() - Method in interface omeis.providers.re.RenderingEngine: Returns the list of mapping families supported by the Rendering engine.
getAvailableFamilies_async(AMD_RenderingEngine_getAvailableFamilies, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getAvailableModels() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getAvailableModels() - Method in interface omeis.providers.re.RenderingEngine: Returns the list of color models supported by the Rendering engine.
getAvailableModels_async(AMD_RenderingEngine_getAvailableModels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getB0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-intercept of the first line.
getB1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-intercept of the second line.
getB2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-intercept of the third line.
getBaseType() - Method in class ome.tools.hibernate.SqlArray
getBaseTypeName() - Method in class ome.tools.hibernate.SqlArray
getBatchSize() - Method in interface ome.api.Search: Returns the current batch size.
getBatchSize() - Method in class ome.services.SearchBean
getBatchSize_async(AMD_Search_getBatchSize, Current) - Method in class ome.services.blitz.impl.SearchI
getBeanHelper() - Method in class ome.logic.AbstractLevel1Service
getBeanHelper() - Method in class ome.logic.AbstractLevel2Service
getBeanHelper() - Method in class ome.services.AbstractStatefulBean
getBit(byte[], int) - Method in class pojos.MaskData: Sets the bit value in a byte array at position bit to be the value value.
getBitDepth(PixelsType) - Method in interface ome.api.IPixels: Bit depth for a given pixel type.
getBitDepth(PixelsType) - Static method in class ome.io.nio.PixelsService: Retrieves the bit width of a particular PixelsType.
getBitDepth(PixelsType) - Method in class ome.logic.PixelsImpl
getBitDepth_async(AMD_IPixels_getBitDepth, PixelsType, Current) - Method in class ome.services.blitz.impl.PixelsI
getBlitzAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration
getBlitzManager() - Method in class ome.services.blitz.util.BlitzConfiguration
getBlitzVerifier() - Method in class ome.services.blitz.util.BlitzConfiguration
getBlue() - Method in class pojos.WellData: Returns the blue component of the color associated to the well, or -1.
getBlueBand() - Method in class omeis.providers.re.RGBBuffer: Returns the data buffer for the blue band.
getBlueValue(int) - Method in class omeis.providers.re.RGBAIntBuffer: Retrieves the Blue value for a particular pixel index.
getBlueValue(int) - Method in class omeis.providers.re.RGBBuffer: Retrieves the Blue value for a particular pixel index.
getBlueValue(int) - Method in class omeis.providers.re.RGBIntBuffer: Retrieves the Blue value for a particular pixel index.
getBody() - Method in class ome.util.mem.Handle: Returns a reference to the Body object that is currently paired up with this handle.
getBooleanAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getBooleanAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getBooleanAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getBooleanAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getBooleanAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getBoost() - Method in class ome.services.fulltext.SimpleLuceneOptions
getBounds() - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
getBounds() - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
getBounds2D() - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
getBounds2D() - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
getByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getByPeriod_async(AMD_ITimeline_getByPeriod, List<String>, RTime, RTime, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI
getBytesPerPixel() - Method in class ome.io.nio.DeltaVisionHeader: Returns the number of bytes per pixel.
getBytesPerPixels(String) - Static method in class omerojava.util.GatewayUtils: Returns the number of bytes per pixel depending on the pixel type.
getByteWidth() - Method in interface ome.api.RawPixelsStore
getByteWidth() - Method in class ome.io.nio.DeltaVision
getByteWidth() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getByteWidth() - Method in interface ome.io.nio.PixelBuffer: Returns the byte width for the pixel buffer.
getByteWidth() - Method in class ome.io.nio.RomioPixelBuffer
getByteWidth(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
getByteWidth(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService: Get the bytewidth of the image
getByteWidth() - Method in class ome.services.RawPixelsBean
getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getC() - Method in class pojos.ShapeData: Returns the channel.
getCalibratedMagnification() - Method in class pojos.ObjectiveData: Returns the objective's calibrated magnification factor.
getCallbackObject(String, String) - Method in class ome.services.sessions.SessionManagerImpl
getCallGroup() - Method in class ome.security.basic.CurrentDetails
getChannelAcquisitionMode(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelBindings() - Method in class omeis.providers.re.Renderer: Returns an array containing the channel bindings.
getChannelBindingsAsList() - Method in class omeis.providers.re.Renderer: Returns a list containing the channel bindings.
getChannelColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelContrastMethod(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelCurveCoefficient(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelCurveCoefficient(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the coefficient identifying a map in the family.
getChannelCurveCoefficient_async(AMD_RenderingEngine_getChannelCurveCoefficient, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChannelEmissionWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelExcitationWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelFamily(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelFamily(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the family associated to the specified channel.
getChannelFamily_async(AMD_RenderingEngine_getChannelFamily, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChannelFluor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelIlluminationType(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelLabeling() - Method in class pojos.ChannelData: Returns the label of the channel.
getChannelName(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelNDFilter(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelNoiseReduction(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelNoiseReduction(int) - Method in interface omeis.providers.re.RenderingEngine: Returns true if the noise reduction algorithm used to map the pixels intensity values is turned on, false if the algorithm is turned off.
getChannelNoiseReduction_async(AMD_RenderingEngine_getChannelNoiseReduction, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChannelPinholeSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelPockelCellSetting(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelSamplesPerPixel(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelStats(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelStats(int) - Method in interface omeis.providers.re.RenderingEngine
getChannelStats_async(AMD_RenderingEngine_getChannelStats, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChannelWindowEnd(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
getChannelWindowEnd(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService: Get the channel max.
getChannelWindowEnd(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelWindowEnd(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the upper bound of the pixels intensity interval.
getChannelWindowEnd_async(AMD_RenderingEngine_getChannelWindowEnd, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChannelWindowStart(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
getChannelWindowStart(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService: Get the channel min.
getChannelWindowStart(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelWindowStart(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the lower bound of the pixels intensity interval.
getChannelWindowStart_async(AMD_RenderingEngine_getChannelWindowStart, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChildTransformer(Class) - Static method in class ome.services.query.Hierarchy
getClassName(Class) - Static method in class ome.tools.StringUtils
getClientContext() - Static method in class ome.system.OmeroContext: create (if necessary) and return the single default client OmeroContext.
getClientContext(Properties) - Static method in class ome.system.OmeroContext: initialize a new client OmeroContext (named OmeroContext.CLIENT_CONTEXT), using the OmeroContext.getContext(Properties, String) method.
getCo2Percent() - Method in class pojos.ImageAcquisitionData: Returns the Co2 level, this is a percent value in the interval [0, 1].
getCodomainChain() - Method in class omeis.providers.re.Renderer: Returns the object that defines the sequence of spatial transformations to be applied to quantized data.
getCol(int, int, int, int) - Method in interface ome.api.RawPixelsStore
getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision
getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getCol(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves a particular column from this pixel buffer.
getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
getCol(int, int, int, int) - Method in class ome.services.RawPixelsBean
getCol_async(AMD_RawPixelsStore_getCol, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.DeltaVision
getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves a particular column from this pixel buffer.
getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
getCollectionCount(String, String, Set<Long>, Parameters) - Method in interface ome.api.IContainer: Counts the number of members in a collection for a given object.
getCollectionCount(String, String, Set, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
getCollectionCount_async(AMD_IContainer_getCollectionCount, String, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
getColor(int, Channel) - Static method in class omeis.providers.re.ColorsFactory: Determines the color usually associated to the specified wavelength.
getColor(int, Channel, LogicalChannel) - Static method in class omeis.providers.re.ColorsFactory: Determines the color usually associated to the specified wavelength.
getColorArray(ChannelBinding) - Static method in class omeis.providers.re.Renderer: Returns an array whose ascending indices represent the color components Red, Green and Blue.
getColSize() - Method in class ome.io.nio.DeltaVision
getColSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getColSize() - Method in interface ome.io.nio.PixelBuffer: Retrieves the in memory size of a column of pixels in this pixel buffer.
getColSize() - Method in class ome.io.nio.RomioPixelBuffer
getColumn() - Method in class pojos.WellData: Returns the column used to indicate the location of the well on the grid.
getColumnSequenceIndex() - Method in class pojos.PlateData: Returns the index indicating how to label a column.
getCommentAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getCommentAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getCommentAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getCommentAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getCommentAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getCommentCount(Set<Long>) - Method in interface ome.api.IShare: Returns a map from share id to comment count.
getCommentCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
getCommentCount_async(AMD_IShare_getCommentCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI
getComments(long) - Method in interface ome.api.IShare: Looks up all comments which belong to the share.
getComments(long) - Method in class ome.services.sharing.ShareBean
getComments_async(AMD_IShare_getComments, long, Current) - Method in class ome.services.blitz.impl.ShareI
getCommunicator() - Method in class ome.services.blitz.fire.Ring
getCommunicator() - Method in interface ome.services.blitz.redirect.Redirector.Context: Active communicator for use by the Redirector instance.
getCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration
getCommunicator() - Method in class omero.client: Returns the Communicator for this instance or throws an exception if null.
getComponents() - Method in class pojos.MultiImageData: Returns the collection of images composing the file.
getCompressionLevel() - Method in interface ome.api.local.LocalCompress: Returns the current compression level for the service.
getCompressionLevel() - Method in class ome.logic.CompressImpl
getCompressionLevel() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getCompressionLevel() - Method in interface omeis.providers.re.RenderingEngine: Returns the current compression level for the service.
getCompressionLevel_async(AMD_RenderingEngine_getCompressionLevel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getConfigService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getConfigService() - Method in class ome.system.ServiceFactory
getConfigValue(String) - Method in interface ome.api.IConfig: retrieve a configuration value from the backend store.
getConfigValue(String) - Method in class ome.logic.ConfigImpl: see IConfig.getConfigValue(String)
getConfigValue_async(AMD_IConfig_getConfigValue, String, Current) - Method in class ome.services.blitz.impl.ConfigI
getConnection() - Method in class ome.services.db.SelfCorrectingDataSource
getConnection(String, String) - Method in class ome.services.db.SelfCorrectingDataSource
getContainerService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getContainerService() - Method in class ome.system.ServiceFactory
getContainerTypes() - Method in class ome.logic.TypesImpl
getContent() - Method in class pojos.AnnotationData: Returns the content of the annotation.
getContent() - Method in class pojos.BooleanAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class pojos.DoubleAnnotationData: Returns the value.
getContent() - Method in class pojos.FileAnnotationData: Returns the original file.
getContent() - Method in class pojos.LongAnnotationData: Returns the rating value.
getContent() - Method in class pojos.RatingAnnotationData: Returns the rating value.
getContent() - Method in class pojos.TagAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class pojos.TermAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class pojos.TextualAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class pojos.TimeAnnotationData: Returns the timestamp of the annotation.
getContentAsString() - Method in class pojos.AnnotationData: Returns the content of the annotation as a String, which is parsed on a Class-by-Class basis.
getContentAsString() - Method in class pojos.BooleanAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.DoubleAnnotationData: Returns the value as a string.
getContentAsString() - Method in class pojos.FileAnnotationData: Returns the absolute path to the file
getContentAsString() - Method in class pojos.LongAnnotationData: Returns the value as a string.
getContentAsString() - Method in class pojos.RatingAnnotationData: Returns the rating value as a string.
getContentAsString() - Method in class pojos.TagAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.TermAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.TextualAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.TimeAnnotationData: Returns the time as a string.
getContentMap(long) - Method in interface ome.api.IShare: Returns the contents of the share keyed by type.
getContentMap(long) - Method in class ome.services.sharing.ShareBean
getContentMap_async(AMD_IShare_getContentMap, long, Current) - Method in class ome.services.blitz.impl.ShareI
getContents(long) - Method in interface ome.api.IShare: Looks up all items belong to the share.
getContents(long) - Method in class ome.services.sharing.ShareBean
getContents_async(AMD_IShare_getContents, long, Current) - Method in class ome.services.blitz.impl.ShareI
getContentSize(long) - Method in interface ome.api.IShare: Returns the number of items in the share.
getContentSize(long) - Method in class ome.services.sharing.ShareBean
getContentSize_async(AMD_IShare_getContentSize, long, Current) - Method in class ome.services.blitz.impl.ShareI
getContentSubList(long, int, int) - Method in interface ome.api.IShare: Returns a range of items from the share.
getContentSubList(long, int, int) - Method in class ome.services.sharing.ShareBean
getContentSubList_async(AMD_IShare_getContentSubList, long, int, int, Current) - Method in class ome.services.blitz.impl.ShareI
getContext() - Method in interface ome.services.util.Executor: Provides access to the context for Work-API consumers who need to publish events, etc.
getContext() - Method in class ome.services.util.Executor.Impl
getContext(Properties, String) - Static method in class ome.system.OmeroContext: initialize a new client OmeroContext using the Properties provided as values for property (e.g.
getContext() - Method in class ome.system.ServiceFactory: Deprecated.
getContrastMethod() - Method in class pojos.ChannelAcquisitionData: Returns the contrast method.
getContrastMethod() - Method in class pojos.ChannelData: Returns the contrast method.
getContrastMethodAsEnum() - Method in class pojos.ChannelData: Returns the contrast method enumeration value.
getCorrection() - Method in class pojos.ObjectiveData: Returns the correction value of the objective.
getCorrectionCollar() - Method in class pojos.ImageAcquisitionData: Returns the correction collar of the objective.
getCountQuery(String) - Method in interface ome.tools.hibernate.ExtendedMetadata: Returns the query for obtaining the number of collection items to a particular instance.
getCountQuery(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Returns the query for obtaining the number of collection items to a particular instance.
getCreated() - Method in class pojos.DataObject: Returns the creation time of the object.
getCreationEvent(Current) - Method in class omero.model.DetailsI
getCurrent() - Method in class ome.services.blitz.util.RegisterServantMessage
getCurrent() - Method in class ome.services.blitz.util.UnregisterServantMessage
getCurrentDetails() - Method in class ome.services.delete.BaseDeleteSpec
getCurrentDetails() - Method in interface ome.services.delete.DeleteSpec
getCurrentEventContext() - Method in interface ome.api.StatefulServiceInterface: Returns the current EventContext for this instance.
getCurrentEventContext() - Method in class ome.security.basic.CurrentDetails: Public view on the data contained here.
getCurrentEventContext() - Method in class ome.services.AbstractStatefulBean
getCurrentEventContext() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getCurrentEventContext() - Method in class ome.services.ThumbnailBean
getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
getCurrentEventId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentEventId() - Method in interface ome.system.EventContext
getCurrentEventId() - Method in class ome.system.SimpleEventContext
getCurrentEventType() - Method in class ome.services.sessions.SessionContextImpl
getCurrentEventType() - Method in interface ome.system.EventContext
getCurrentEventType() - Method in class ome.system.SimpleEventContext
getCurrentGroupId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentGroupId() - Method in interface ome.system.EventContext
getCurrentGroupId() - Method in class ome.system.SimpleEventContext
getCurrentGroupName() - Method in class ome.services.sessions.SessionContextImpl
getCurrentGroupName() - Method in interface ome.system.EventContext
getCurrentGroupName() - Method in class ome.system.SimpleEventContext
getCurrentGroupPermissions() - Method in class ome.services.sessions.SessionContextImpl
getCurrentGroupPermissions() - Method in interface ome.system.EventContext
getCurrentGroupPermissions() - Method in class ome.system.SimpleEventContext
getCurrentId() - Method in class ome.services.fulltext.PersistentEventLogLoader: Get current EventLog id.
getCurrentSessionId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentSessionId() - Method in interface ome.system.EventContext
getCurrentSessionId() - Method in class ome.system.SimpleEventContext
getCurrentSessionUuid() - Method in class ome.services.sessions.SessionContextImpl
getCurrentSessionUuid() - Method in interface ome.system.EventContext
getCurrentSessionUuid() - Method in class ome.system.SimpleEventContext
getCurrentShareId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentShareId() - Method in interface ome.system.EventContext
getCurrentShareId() - Method in class ome.system.SimpleEventContext
getCurrentUmask() - Method in class ome.services.sessions.SessionContextImpl
getCurrentUmask() - Method in class ome.system.SimpleEventContext
getCurrentUserId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentUserId() - Method in interface ome.system.EventContext
getCurrentUserId() - Method in class ome.system.SimpleEventContext
getCurrentUserName() - Method in class ome.services.sessions.SessionContextImpl
getCurrentUserName() - Method in interface ome.system.EventContext
getCurrentUserName() - Method in class ome.system.SimpleEventContext
getCurrentUserNames() - Method in class ome.services.util.DropBoxDirectoryCheck
getCurveCoefficient() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the coefficient identifying a curve within a given family.
getCutIn() - Method in class pojos.FilterData: Returns the cut in value or null.
getCutInTolerance() - Method in class pojos.FilterData: Returns the cut in tolerance value or null.
getCutOut() - Method in class pojos.FilterData: Returns the cut out value or null.
getCutOutTolerance() - Method in class pojos.FilterData: Returns the cut out tolerance value or null.
getData() - Method in class ome.io.nio.PixelData: Returns the backing buffer for the pixel data.
getData() - Method in class ome.io.nio.ReorderedPixelData: Returns the backing buffer for the pixel data.
getData() - Method in class omeis.providers.re.data.Plane2D: Returns the pixel data that is used to back this Plane.
getDataAsArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
getDataAsArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
getDataAsArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
getDataAsArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
getDataAsArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
getDataAsArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
getDataAsArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
getDataAsArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
getDataAsArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
getDatabaseTime() - Method in interface ome.api.IConfig: checks the database for it's time using a SELECT statement.
getDatabaseTime() - Method in class ome.logic.ConfigImpl: see IConfig.getDatabaseTime()
getDatabaseTime_async(AMD_IConfig_getDatabaseTime, Current) - Method in class ome.services.blitz.impl.ConfigI
getDatabaseUuid() - Method in interface ome.api.IConfig: Provides the UUID for this OMERO (database) instance.
getDatabaseUuid() - Method in class ome.logic.ConfigImpl
getDatabaseUuid_async(AMD_IConfig_getDatabaseUuid, Current) - Method in class ome.services.blitz.impl.ConfigI
getDatabaseVersion() - Method in interface ome.api.local.LocalConfig: Retrieves the newest database patch.
getDatabaseVersion() - Method in class ome.logic.ConfigImpl
getDataBuffer() - Method in class omeis.providers.re.RGBAIntBuffer: Retrieves the data buffer that contains the pixel values.
getDataBuffer() - Method in class omeis.providers.re.RGBIntBuffer: Retrieves the data buffer that contains the pixel values.
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
getDataObjects() - Method in class pojos.TagAnnotationData: Returns the collection of data objects related to this tag.
getDataService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
getDataset() - Method in class ome.formats.importer.util.TinyImportFixture: provides access to the created Dataset instance.
getDataset(long, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getDatasets(List<Long>, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getDatasets(List<Long>, boolean) - Method in interface ome.services.blitz.gateway.services.DataService: Get the Datasets with id's passed as list in ids.
getDatasets(List<Long>, boolean) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
getDatasets() - Method in class pojos.ImageData: Returns the datasets containing this image.
getDatasets() - Method in class pojos.ProjectData: Returns the datasets contained in this project.
getDatasetsForProject(long) - Method in interface ome.api.IAnalysis
getDatasetsFromProject(Project) - Static method in class omerojava.util.GatewayUtils: Get the datasets from the project, the project must have the datasets loaded already.
getDataValue() - Method in class pojos.DoubleAnnotationData: Returns the value.
getDataValue() - Method in class pojos.LongAnnotationData: Returns the value.
getDate(Class) - Static method in class ome.system.Version: Parses the given class for its RevisionDate annotation.
getDefaultContext() - Method in class ome.system.ServiceFactory: used when no context name is provided to the constructor.
getDefaultContext() - Method in class ome.tools.spring.InternalServiceFactory: returns null to prevent the lookup of any context, but rather wait on injection as a ApplicationContextAware
getDefaultContext() - Method in class ome.tools.spring.ManagedServiceFactory: returns null to prevent the lookup of any context, but rather wait on injection as a ApplicationContextAware
getDefaultGroup(long) - Method in interface ome.api.IAdmin: retrieve the default group for the given user id.
getDefaultGroup(long) - Method in class ome.logic.AdminImpl
getDefaultGroup() - Method in class pojos.ExperimenterData: Returns the default Group for this Experimenter
getDefaultGroup_async(AMD_IAdmin_getDefaultGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI
getDefaultPixels() - Method in class pojos.ImageData: Returns the default set of pixels.
getDefaultSample() - Method in class pojos.PlateData: Returns the currently selected field or 0.
getDefaultScriptDir() - Static method in class ome.services.scripts.ScriptRepoHelper: Directory which will be used as the root of this repository if no directory is passed to a constructor.
getDefaultT(Long) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
getDefaultT(Long) - Method in interface ome.services.blitz.gateway.services.RenderingService: Get the default T point of the image
getDefaultT() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getDefaultT() - Method in interface omeis.providers.re.RenderingEngine: Returns the default timepoint index.
getDefaultT_async(AMD_RenderingEngine_getDefaultT, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getDefaultZ(Long) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
getDefaultZ(Long) - Method in interface ome.services.blitz.gateway.services.RenderingService: Get the default Z section of the image
getDefaultZ() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getDefaultZ() - Method in interface omeis.providers.re.RenderingEngine: Returns the index of the default focal section.
getDefaultZ_async(AMD_RenderingEngine_getDefaultZ, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getDeletedsIds(String) - Method in class ome.services.delete.DeleteState: Get the set of ids which were actually deleted.
getDeleteService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getDeleteService() - Method in class ome.system.ServiceFactory
getDescription() - Method in class pojos.DatasetData: Returns the description of the dataset.
getDescription() - Method in class pojos.FileAnnotationData: Returns the description of the annotation.
getDescription() - Method in class pojos.FileData: Returns the description of the file.
getDescription() - Method in class pojos.GroupData: Returns the description of the group.
getDescription() - Method in class pojos.ImageData: Returns the description of the image.
getDescription() - Method in class pojos.PlateAcquisitionData: Returns the description of the plate acquisition.
getDescription() - Method in class pojos.PlateData: Returns the description of the plate.
getDescription() - Method in class pojos.ProjectData: Returns the description of the project.
getDescription() - Method in class pojos.ScreenData: Returns the description of the screen.
getDetails(Object[], String[]) - Static method in class ome.tools.hibernate.HibernateUtils
getDetails() - Method in class pojos.DataObject: Returns the details of the object.
getDetector() - Method in class pojos.ChannelAcquisitionData: Returns the detector used for that channel.
getDetectorBinningAsEnum() - Method in class pojos.ChannelAcquisitionData: Returns the binning enumeration value.
getDetectors() - Method in class pojos.InstrumentData: Returns the collection of detectors.
getDetectorSettingsBinning() - Method in class pojos.ChannelAcquisitionData: Returns the Binning factor.
getDetectorSettingsGain() - Method in class pojos.ChannelAcquisitionData: Returns the gain set on the detector.
getDetectorSettingsOffset() - Method in class pojos.ChannelAcquisitionData: Returns the offset set on the detector.
getDetectorSettingsReadOutRate() - Method in class pojos.ChannelAcquisitionData: Returns the Read out rate set on the detector.
getDetectorSettingsVoltage() - Method in class pojos.ChannelAcquisitionData: Returns the voltage set on the detector.
getDichroic() - Method in class pojos.FilterSetData: Returns the dichroic if any.
getDichroic() - Method in class pojos.LightPathData: Returns the dichroic if any.
getDichroics() - Method in class pojos.InstrumentData: Returns the collection of dichroics.
getDirectProxy() - Method in class ome.services.blitz.fire.Ring: Returns the proxy information for the local SessionManager.
getDirectProxy() - Method in interface ome.services.blitz.redirect.Redirector.Context: String representation of the proxy to the local node which may be contacted to create new sessions.
getDirectProxy() - Method in class ome.services.blitz.util.BlitzConfiguration: Return a direct proxy to the session manager in this object adapter.
getDn(Experimenter) - Method in class ome.security.auth.PersonContextMapper
getDnById(Long) - Method in class ome.security.auth.PasswordUtil
getDoubleAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getDoubleAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getDoubleAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getDoubleAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getDoubleAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getEmail() - Method in class pojos.ExperimenterData: Returns the e-mail of the experimenter.
getEmissionFilters() - Method in class pojos.FilterSetData: Returns the collections of emission filters if any.
getEmissionFilters() - Method in class pojos.LightPathData: Returns the collections of emission filters if any.
getEmissionWavelength() - Method in class pojos.ChannelData: Returns the emission wavelength of the channel.
getEndTime() - Method in class omero.sys.ParametersI: Returns the value of the end time parameter.
getEndTime() - Method in class pojos.PlateAcquisitionData: Returns the time when the last image was collected.
getEntity(String, Serializable) - Method in class ome.security.basic.OmeroInterceptor
getEntityName(Object) - Method in class ome.security.basic.OmeroInterceptor
getEnumeration(Class<T>, String) - Method in interface ome.api.IPixels: Retrieves a particular enumeration for a given enumeration class.
getEnumeration(Class<T>, String) - Method in interface ome.api.ITypes: lookup an enumeration value.
getEnumeration(Class<T>, String) - Method in class ome.logic.PixelsImpl
getEnumeration(Class<T>, String) - Method in class ome.logic.TypesImpl
getEnumeration_async(AMD_IPixels_getEnumeration, String, String, Current) - Method in class ome.services.blitz.impl.PixelsI
getEnumeration_async(AMD_ITypes_getEnumeration, String, String, Current) - Method in class ome.services.blitz.impl.TypesI
getEnumerationsWithEntries() - Method in interface ome.api.ITypes: Gets all metadata classes which are IEnum type with contained objects.
getEnumerationsWithEntries() - Method in class ome.logic.TypesImpl
getEnumerationsWithEntries_async(AMD_ITypes_getEnumerationsWithEntries, Current) - Method in class ome.services.blitz.impl.TypesI
getEnumerationTypes() - Method in interface ome.api.ITypes: Gets all metadata classes which are IEnum type.
getEnumerationTypes() - Method in class ome.logic.TypesImpl
getEnumerationTypes_async(AMD_ITypes_getEnumerationTypes, Current) - Method in class ome.services.blitz.impl.TypesI
getEvent() - Method in class ome.security.basic.CurrentDetails
getEvent(Current) - Method in class ome.services.blitz.fire.SessionManagerI
getEvent() - Method in class ome.system.Login: simple getter for the event type passed into the constructor
getEventContext() - Method in interface ome.api.IAdmin: returns an implementation of EventContext loaded with the security for the current user and thread.
getEventContext() - Method in class ome.logic.AdminImpl
getEventContext() - Method in class ome.security.basic.BasicSecuritySystem
getEventContext() - Method in interface ome.security.SecuritySystem: Returns the current EventContext.
getEventContext() - Method in class ome.security.SecuritySystemHolder
getEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
getEventContext() - Method in class ome.services.blitz.impl.ServiceFactoryI
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
getEventContext_async(AMD_IAdmin_getEventContext, Current) - Method in class ome.services.blitz.impl.AdminI
getEventLogsByPeriod_async(AMD_ITimeline_getEventLogsByPeriod, RTime, RTime, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
getEvents(long, Experimenter, Timestamp, Timestamp) - Method in interface ome.api.IShare: Gets events for share per experimenter for period of time.
getEvents(long, Experimenter, Timestamp, Timestamp) - Method in class ome.services.sharing.ShareBean
getEvents_async(AMD_IShare_getEvents, long, Experimenter, RTime, RTime, Current) - Method in class ome.services.blitz.impl.ShareI
getEventType() - Method in class ome.system.Principal
getException() - Method in exception ome.util.messages.MessageException: Get the exception which this instance wraps.
getExceptionThrown() - Method in class ome.system.UpgradeCheck
getExcitationFilters() - Method in class pojos.FilterSetData: Returns the collections of excitation filters if any.
getExcitationFilters() - Method in class pojos.LightPathData: Returns the collections of excitation filters if any.
getExcitationWavelength() - Method in class pojos.ChannelData: Returns the excitation wavelength of the channel.
getExclude(int) - Method in class ome.services.delete.AnnotationDeleteSpec: Returns the value from "...
getExecutor() - Method in class ome.services.blitz.impl.ServiceFactoryI
getExecutor() - Method in class ome.services.scheduler.ThreadPool
getExperimenter(long) - Method in interface ome.api.IAdmin: fetch an Experimenter and all related groups.
getExperimenter(long) - Method in class ome.logic.AdminImpl
getExperimenter() - Method in class omero.sys.ParametersI: Returns the value of the experimenter parameter.
getExperimenter_async(AMD_IAdmin_getExperimenter, long, Current) - Method in class ome.services.blitz.impl.AdminI
getExperimenters() - Method in class pojos.GroupData: Returns the experimenters contained in this group.
getExtendedHeaderSize() - Method in class ome.io.nio.DeltaVisionHeader: Returns the size in bytes of the extended header
getExtendedMetadata() - Method in class ome.logic.AbstractLevel2Service
getExternalDescription() - Method in class pojos.WellData: Returns the external description of the well.
getExternalIdentifier() - Method in class pojos.PlateData: Returns the external identifier of the plate.
getExternalInfo(Current) - Method in class omero.model.DetailsI
getFamily(String) - Method in class omeis.providers.re.quantum.QuantumFactory: Helper method to retrieve a Family enumeration from the database.
getFamily() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the mapping family.
getFile(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder
getFileBuffer(OriginalFile) - Method in class ome.io.nio.OriginalFilesService: Returns FileBuffer based on OriginalFile path
getFileFormat() - Method in class pojos.FileAnnotationData: Returns the format of the uploaded file.
getFileID() - Method in class pojos.FileAnnotationData: Returns the id of the file.
getFileIds() - Method in class ome.tools.RepositoryTask: This public method is used to return a list of file ids that require deletion from the disk repository.
getFileKind() - Method in class pojos.FileAnnotationData: Returns a user readable description of the file.
getFileName() - Method in class pojos.FileAnnotationData: Returns the name of the file.
getFileParamKeys(long) - Method in class ome.services.db.PgArrayHelper: Returns only the (possibly empty) keys which are set on the given original file.
getFileParams(long) - Method in class ome.services.db.PgArrayHelper: Loads all the (possibly empty) params for the given original file.
getFilePath() - Method in class pojos.FileAnnotationData: Returns the absolute path to the file.
getFileSize() - Method in class pojos.FileAnnotationData: Returns the size of the file.
getFilesPath(Long) - Method in class ome.io.nio.AbstractFileSystemService
getFillColor() - Method in class pojos.ShapeSettingsData: Returns the fill color.
getFillRule() - Method in class pojos.ShapeSettingsData: Returns the fill rule.
getFilters() - Method in class pojos.InstrumentData: Returns the collection of filters.
getFilterSet() - Method in class pojos.ChannelAcquisitionData: Returns the filter set or null.
getFilterSet() - Method in class pojos.OTFData: Returns the associated filter set.
getFilterSets() - Method in class pojos.InstrumentData: Returns the collection of filter sets.
getFilterWheel() - Method in class pojos.FilterData: Returns the wheel.
getFirst(String) - Method in class ome.security.auth.AttributeSet
getFirstName() - Method in class pojos.ExperimenterData: Returns the first name of the experimenter.
getFirstPlaneOffset() - Method in class ome.io.nio.DeltaVision: Returns the offset of the first plane in the file.
getFluor() - Method in class pojos.ChannelData: Returns the Fluorophore used.
getFont() - Method in class pojos.ShapeSettingsData: Get the style of the font for Shape.
getFontFamily() - Method in class pojos.ShapeSettingsData: Returns the stroke.
getFontSize() - Method in class pojos.ShapeSettingsData: Returns the stroke.
getFontStyle() - Method in class pojos.ShapeSettingsData: Returns the font style.
getFontWeight() - Method in class pojos.ShapeSettingsData: Get the weight of the font.
getFreeSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo: This method returns the free or available space on this file system including nested subdirectories.
getFreeSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl
getFreeSpaceInKilobytes_async(AMD_IRepositoryInfo_getFreeSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
getGain() - Method in class pojos.DetectorData: Returns the gain of the detector.
getGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the maximum of all maxima.
getGlobalMax() - Method in class pojos.ChannelData: Returns the global maximum of the channel i.e. the maximum of all maxima.
getGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the minimum of all minima.
getGlobalMin() - Method in class pojos.ChannelData: Returns the global minimum of the channel i.e. the minimum of all minima.
getGreen() - Method in class pojos.WellData: Returns the green component of the color associated to the well, or -1.
getGreenBand() - Method in class omeis.providers.re.RGBBuffer: Returns the data buffer for the green band.
getGreenValue(int) - Method in class omeis.providers.re.RGBAIntBuffer: Retrieves the Green value for a particular pixel index.
getGreenValue(int) - Method in class omeis.providers.re.RGBBuffer: Retrieves the Green value for a particular pixel index.
getGreenValue(int) - Method in class omeis.providers.re.RGBIntBuffer: Retrieves the Green value for a particular pixel index.
getGridQuery() - Method in interface ome.services.blitz.fire.Registry: Returns an active QueryPrx or null if none is available.
getGridQuery() - Method in class ome.services.blitz.fire.Registry.Impl
getGroup(long) - Method in interface ome.api.IAdmin: fetch an ExperimenterGroup and all contained users.
getGroup(long) - Method in class ome.logic.AdminImpl
getGroup() - Method in class ome.security.basic.CurrentDetails
getGroup(Current) - Method in class ome.services.blitz.fire.SessionManagerI
getGroup() - Method in class ome.system.Login: simple getter for the group name passed into the constructor
getGroup() - Method in class ome.system.Principal
getGroup(Current) - Method in class omero.model.DetailsI
getGroup() - Method in class omero.sys.ParametersI: Returns the value of the group parameter.
getGroup_async(AMD_IAdmin_getGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI
getGroupAttribute(String) - Method in class ome.security.auth.LdapConfig
getGroupFilter() - Method in class ome.security.auth.LdapConfig
getGroups() - Method in class pojos.ExperimenterData: Returns the groups the experimenter is a member of.
getGuestGroupName() - Method in class ome.system.Roles
getHeader() - Method in class ome.io.nio.DeltaVision: Returns an object representing the header of this DeltaVision file.
getHeight() - Method in class pojos.MaskData: Returns the height of the mask.
getHeight() - Method in class pojos.RectangleData: Returns the height untransformed rectangle.
getHibernateClass(String) - Method in class ome.services.delete.BaseDeleteSpec
getHibernateClass(String) - Method in interface ome.services.delete.DeleteSpec: Return the Hibernate type (ome.model.*) for the given table.
getHibernateClass(String) - Method in interface ome.tools.hibernate.ExtendedMetadata: Given the name of a database table or alternatively the simple class name (non-fully qualified) of an IObject, this method returns the class which Hibernate will map that table to.
getHibernateClass(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
getHost() - Method in class ome.system.Server: simple getter for the server host passed into the constructor
getHumidity() - Method in class pojos.ImageAcquisitionData: Returns the humidity level, this is a value in the interval [0, 1]
getIContainer() - Method in class ome.services.blitz.gateway.services.GatewayFactory: Return the IContainer service.
getId() - Method in class ome.io.nio.DeltaVision
getId() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getId() - Method in interface ome.io.nio.PixelBuffer: Delegates to Pixels.getId().
getId() - Method in class ome.io.nio.RomioPixelBuffer
getId() - Method in class ome.services.delete.DeleteEntry
getId() - Method in class pojos.DataObject: Returns the database id of the IObject or -1 if null
getIdentity(String) - Method in class ome.services.blitz.impl.ServiceFactoryI: Constructs an Identity from the name of this ServiceFactoryI and from the given String which for stateless services are defined by the instance fields #adminKey, #configKey, etc. and for stateful services are UUIDs.
getIds() - Method in class ome.services.sessions.state.SessionCache: Since all methods which use SessionCache.getIds() will subsequently check for the existing session, we do not block here.
getIllumination() - Method in class pojos.ChannelAcquisitionData: Returns the illumination.
getIllumination() - Method in class pojos.ChannelData: Returns the illumination.
getIlluminationAsEnum() - Method in class pojos.ChannelData: Returns the illumination enumeration value.
getImage(long, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getImage(long) - Method in interface ome.services.blitz.gateway.services.ImageService: Get the image information for an image.
getImage(long) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
getImage(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImage() - Method in class pojos.PixelsData: Returns the image linked to this pixels' set.
getImage() - Method in class pojos.ROIData: Returns the image for the ROI.
getImage() - Method in class pojos.WellSampleData: Returns the image related to that sample if any.
getImageAcquiredDate(int) - Method in class ome.services.blitz.impl.OmeroMetadata
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.
getImageAnnotationRef(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImageAnnotationRefCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImageByName(String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getImageByName(String) - Method in interface ome.services.blitz.gateway.services.DataService: Get the list of images with name containing imageName.
getImageByName(String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
getImageCount() - Method in class ome.io.nio.DeltaVisionHeader: Returns the number of plane images
getImageCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getImageDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImageFromDatasetByName(long, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getImageFromDatasetByName(Long, String) - Method in interface ome.services.blitz.gateway.services.DataService: Get the images from the dataset with name, this can use wild cards.
getImageFromDatasetByName(Long, String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
getImageID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImageName(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImages(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer: Retrieve a user's (or all users') images within any given container.
getImages(Class, Set, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
getImages(ContainerClass, List<Long>, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getImages(ContainerClass, List<Long>) - Method in interface ome.services.blitz.gateway.services.DataService: Retrieves the images contained in containers specified by the node type.
getImages(ContainerClass, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
getImages() - Method in class pojos.DatasetData: Returns a set of images contained in the dataset.
getImages_async(AMD_IContainer_getImages, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
getImagesByOptions(Parameters) - Method in interface ome.api.IContainer: Retrieve images by options.
getImagesByOptions(Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
getImagesByOptions_async(AMD_IContainer_getImagesByOptions, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
getImageService() - Method in class ome.services.blitz.gateway.services.GatewayFactory
getImagesForDataset(long) - Method in interface ome.api.IAnalysis
getImagesFromDataset(Dataset) - Static method in class omerojava.util.GatewayUtils: Get the images from the Dataset, the Dataset must be loaded in the project beforehand.
getImagesFromProject(Project) - Static method in class omerojava.util.GatewayUtils: Get the images from the Project, the images must be loaded in the project beforehand.
getImageSize(PlaneDef) - Method in class omeis.providers.re.Renderer: Returns the size, in bytes, of the RGBBuffer that would be rendered from the plane selected by pd.
getImageTypeCode() - Method in class ome.io.nio.DeltaVisionHeader: Returns the numeric image type
getImagingEnvironmentId() - Method in class pojos.ImageAcquisitionData: Returns the id of the StageLabel or -1 if not already linked to the image.
getImmersion() - Method in class pojos.ObjectiveData: Returns the immersion value of the objective.
getImmutableFields() - Method in class ome.tools.hibernate.ExtendedMetadata.Immutables
getImmutableFields(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
getImplicitContext() - Method in class omero.client: Returns the ImplicitContext which defines what properties will be sent on every method invocation.
getImportTypes() - Method in class ome.logic.TypesImpl
getIndex() - Method in class ome.services.fulltext.SimpleLuceneOptions
getIndex() - Method in class pojos.ChannelData: Returns the channel's index.
getIndex() - Method in class pojos.ImageData: Returns the index of the image within the multi-images file.
getInput(String, String) - Method in interface ome.api.ISession: Retrieves an entry from the given session's input environment.
getInput(String, String) - Method in class ome.services.sessions.SessionBean
getInput(String, String) - Method in interface ome.services.sessions.SessionManager: Returns the input environment Object stored under the given key or null if none present.
getInput(String, String) - Method in class ome.services.sessions.SessionManagerImpl
getInput(String) - Method in class omero.client: Retrieves an item from the "input" shared (session) memory.
getInput_async(AMD_ISession_getInput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI
getInputEnd() - Method in class omeis.providers.re.metadata.StatsFactory: Returns the input end.
getInputKeys(String) - Method in interface ome.api.ISession: Retrieves all keys in the sesson's input environment.
getInputKeys(String) - Method in class ome.services.sessions.SessionBean
getInputKeys() - Method in class omero.client: Returns a list of keys for all items in the "input" shared (session) memory
getInputKeys_async(AMD_ISession_getInputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI
getInputs(String) - Method in interface ome.api.ISession: Retrieves all inputs from the given session's input environment.
getInputs(String) - Method in class ome.services.sessions.SessionBean
getInputs_async(AMD_ISession_getInputs, String, Current) - Method in class ome.services.blitz.impl.SessionI
getInputStart() - Method in class omeis.providers.re.metadata.StatsFactory: Returns the input start.
getInserted() - Method in class pojos.ImageData: Returns the insertion time of the image.
getInstance(String) - Static method in class ome.system.OmeroContext: create (if necessary) and return the single default OmeroContext named by the beanFactoryName parameter.
getInstitution() - Method in class pojos.ExperimenterData: Returns the institution where the experimenter works.
getInstrumentId() - Method in class pojos.ImageData: Returns the id of the instrument if any.
getInternalServiceFactory(String, String, int, int, String) - Method in interface ome.services.blitz.fire.Registry: Try to return a ServiceFactory from the grid.
getInternalServiceFactory(String, String, int, int, String) - Method in class ome.services.blitz.fire.Registry.Impl
getInternalValue(String) - Method in interface ome.api.local.LocalConfig: Provides a configuration value, ignoring the visibility of the given value.
getInternalValue(String) - Method in class ome.logic.ConfigImpl
getIntervalEnd() - Method in class omeis.providers.re.codomain.CodomainChain: Returns the upper bound of the codomain interval.
getIntervalStart() - Method in class omeis.providers.re.codomain.CodomainChain: Returns the lower bound of the codomain interval.
getIPixels() - Method in class ome.services.blitz.gateway.services.GatewayFactory: Get the iPixels Service.
getIQuery() - Method in class ome.services.blitz.gateway.services.GatewayFactory: Get the IQuery Service.
getIScript() - Method in class ome.services.blitz.gateway.services.GatewayFactory: Return the IScript service.
getIterator() - Method in class pojos.ROIData: Returns the iterator of the collection of the map.
getITypes() - Method in class ome.services.blitz.gateway.services.GatewayFactory: Get the types service.
getIUpdate() - Method in class ome.services.blitz.gateway.services.GatewayFactory: Get the iUpdate Service.
getJob() - Method in interface ome.api.JobHandle
getJob(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
getJob() - Method in class ome.services.JobBean
getJob(Current) - Method in class omero.grid.InteractiveProcessorI
getJob_async(AMD_JobHandle_getJob, Current) - Method in class ome.services.blitz.impl.JobHandleI
getKeywords() - Method in class pojos.WorkflowData: Returns the keywords of this workflow.
getKeywordsAsList() - Method in class pojos.WorkflowData: Returns the keywords of this workflow as a list.
getKind() - Method in class pojos.LightSourceData: Returns the kind of light source.
getLabel() - Method in class pojos.PlateAcquisitionData: Returns the label associated to the plate acquisition.
getLabelName() - Method in class pojos.ImageAcquisitionData: Returns the name of the stage label.
getLaserFrequencyMultiplication() - Method in class pojos.LightSourceData: Returns the frequency multiplication of the laser.
getLaserMedium() - Method in class pojos.LightSourceData: Returns the laser's medium.
getLaserPockelCell() - Method in class pojos.LightSourceData: Returns the pockel cell flag of the laser.
getLaserPulse() - Method in class pojos.LightSourceData: Returns the pulse of the laser.
getLaserRepetitionRate() - Method in class pojos.LightSourceData: Returns the repetition rate (Hz) if the laser is repetitive.
getLaserTuneable() - Method in class pojos.LightSourceData: Returns the value of the tuneable field or null if no value set.
getLaserWavelength() - Method in class pojos.LightSourceData: Returns the laser's wavelength.
getLast() - Method in class ome.security.basic.CurrentDetails
getLast() - Method in interface ome.security.basic.PrincipalHolder: Get the last, i.e. currently active, principal.
getLastModified() - Method in class pojos.AnnotationData: Returns the time when the annotation was last modified.
getLastName() - Method in class pojos.ExperimenterData: Returns the last name of the experimenter.
getLastUpdated() - Method in class ome.services.sessions.state.SessionCache
getLdapService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getLdapService() - Method in class ome.system.ServiceFactory
getLeaderOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin: Finds the ids for all groups for which the given Experimenter is owner/leader.
getLeaderOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
getLeaderOfGroupIds_async(AMD_IAdmin_getLeaderOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
getLeaderOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
getLeaderOfGroupsList() - Method in interface ome.system.EventContext
getLeaderOfGroupsList() - Method in class ome.system.SimpleEventContext
getLeaders() - Method in class pojos.GroupData: Returns the experimenters contained in this group.
getLeaves() - Method in class omero.sys.ParametersI
getLensNA() - Method in class pojos.ObjectiveData: Returns the objective's LensNA.
getLightPath() - Method in class pojos.ChannelAcquisitionData: Returns the light path or null.
getLightSource() - Method in class pojos.ChannelAcquisitionData: Returns the source of light.
getLightSourceModel() - Method in class pojos.LightSourceData: Returns the model of the light source.
getLightSources() - Method in class pojos.InstrumentData: Returns the collection of light sources.
getLigthSettingsAttenuation() - Method in class pojos.ChannelAcquisitionData: Returns the attenuation of the light source, percent value between 0 and 1.
getLigthSettingsWavelength() - Method in class pojos.ChannelAcquisitionData: Returns the wavelength of the light source.
getLimit() - Method in class omero.sys.ParametersI: Returns the value of the limit parameter.
getLineCap() - Method in class pojos.ShapeSettingsData: Returns the stroke.
getLocationStats() - Method in class omeis.providers.re.metadata.StatsFactory: Returns the statistics.
getLockCandidates(IObject) - Method in interface ome.tools.hibernate.ExtendedMetadata: walks the IObject argument non-recursively and gathers all IObject instances which will be linkd to by the creation or updating of the argument.
getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: walks the IObject argument non-recursively and gathers all IObject instances which will be linkd to by the creation or updating of the argument.
getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
getLockChecks(Class<? extends IObject>) - Method in interface ome.tools.hibernate.ExtendedMetadata: returns all class/field name pairs which may possibly link to an object of type klass.
getLockChecks(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: returns all class/field name pairs which may possibly link to an object of type klass.
getLockingIds(IObject) - 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(IObject, Long) - Method in class ome.logic.AdminImpl
getLogger() - Method in class ome.services.util.BeanHelper
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
getLongAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getLongAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getLongAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getLongAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getLongAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getLotNumber() - Method in class pojos.DetectorData: Returns the lot number of the detector.
getLotNumber() - Method in class pojos.DichroicData: Returns the lot number.
getLotNumber() - Method in class pojos.FilterData: Returns the lot number.
getLotNumber() - Method in class pojos.FilterSetData: Returns the lot number.
getLotNumber() - Method in class pojos.LightSourceData: Returns the lot of number the light source.
getLotNumber() - Method in class pojos.ObjectiveData: Returns the lot number of the detector.
getLowerLimit() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the constant level for bit-planes < planeSelected w.r.t the higher-order bits.
getManagedServerContext() - Static method in class ome.system.OmeroContext: create (if necessary) and return the single default managed OmeroContext.
getManagerList(boolean) - Method in class ome.services.blitz.fire.Ring
getManagerList(boolean) - Method in interface ome.services.blitz.redirect.Redirector.Context: Return all known managers in the current cluster context, possibly filtering out the inactive ones.
getManufacturer() - Method in class pojos.DetectorData: Returns the manufacturer of the detector.
getManufacturer() - Method in class pojos.DichroicData: Returns the manufacturer.
getManufacturer() - Method in class pojos.FilterData: Returns the manufacturer.
getManufacturer() - Method in class pojos.FilterSetData: Returns the manufacturer.
getManufacturer() - Method in class pojos.LightSourceData: Returns the manufacturer of the light source.
getManufacturer() - Method in class pojos.ObjectiveData: Returns the manufacturer of the detector.
getMarkerEnd() - Method in class pojos.ShapeSettingsData: Returns the stroke.
getMarkerStart() - Method in class pojos.ShapeSettingsData: Returns the stroke.
getMask() - Method in class pojos.MaskData: Returns the mask as a byte array.
getMaskAsBinaryArray() - Method in class pojos.MaskData: Returns the mask image.
getMaskAsBufferedImage() - Method in class pojos.MaskData: Returns the mask image.
getMaskPoints() - Method in class pojos.PolygonData: Returns the points in the polygon.
getMaskPoints() - Method in class pojos.PolylineData: Returns the points in the Polyline.
getMatcher(String) - Method in class ome.services.delete.DeleteEntry
getMaximum() - Method in class ome.io.nio.PixelData: Returns the minimum pixel value this pixel data supports.
getMaximumFieldCount() - Method in class pojos.PlateAcquisitionData: Returns the maximum number of fields in any well.
getMeasuredRois_async(AMD_IRoi_getMeasuredRois, long, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
getMeasuredRoisMap_async(AMD_IRoi_getMeasuredRoisMap, long, List<Long>, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
getMedium() - Method in class pojos.ImageAcquisitionData: Returns the medium of the objective.
getMediumAsEnum() - Method in class pojos.ImageAcquisitionData: Returns the medium enumeration value.
getMemberCount(Set<Long>) - Method in interface ome.api.IShare: Returns a map from share id to the count of total members (including the owner).
getMemberCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
getMemberCount_async(AMD_IShare_getMemberCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI
getMemberOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin: Finds the ids for all groups for which the given Experimenter is a member.
getMemberOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
getMemberOfGroupIds_async(AMD_IAdmin_getMemberOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
getMemberOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
getMemberOfGroupsList() - Method in interface ome.system.EventContext
getMemberOfGroupsList() - Method in class ome.system.SimpleEventContext
getMemberShares(boolean) - Method in interface ome.api.IShare: Gets all shares where current Experimenter is a member.
getMemberShares(boolean) - Method in class ome.services.sharing.ShareBean
getMemberShares_async(AMD_IShare_getMemberShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
getMemberSharesFor(Experimenter, boolean) - Method in interface ome.api.IShare: Gets all shares where given Experimenter is a member.
getMemberSharesFor(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
getMemberSharesFor_async(AMD_IShare_getMemberSharesFor, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
getMessage() - Method in exception ome.io.nio.DimensionsOutOfBoundsException
getMetadata(long) - Method in class ome.services.ThumbnailCtx: Retrieves the Thumbnail object for a given Pixels ID.
getMetadata() - Method in class omeis.providers.re.Renderer: Returns the Pixels set the rendering engine is for.
getMetadataService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getMetadataService() - Method in class ome.system.ServiceFactory
getMethod(String) - Method in class ome.services.blitz.util.IceMethodInvoker: For testing the cached method.
getMethodCount() - Method in class ome.services.messages.stats.MethodStatsMessage
getMicroscopeLotNumber() - Method in class pojos.InstrumentData: Returns the lot number of the microscope.
getMicroscopeManufacturer() - Method in class pojos.InstrumentData: Returns the model of the microscope.
getMicroscopeModel() - Method in class pojos.InstrumentData: Returns the model of the microscope.
getMicroscopeSerialNumber() - Method in class pojos.InstrumentData: Returns the serial number of the microscope.
getMicroscopeType() - Method in class pojos.InstrumentData: Returns the type of microscope.
getMiddleName() - Method in class pojos.ExperimenterData: Returns the middle name of the experimenter.
getMinimum() - Method in class ome.io.nio.PixelData: Returns the minimum pixel value this pixel data supports.
getMode() - Method in class pojos.ChannelAcquisitionData: Returns the mode.
getMode() - Method in class pojos.ChannelData: Returns the mode.
getModeAsEnum() - Method in class pojos.ChannelData: Returns the acquisition enumeration value.
getModel() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getModel() - Method in interface omeis.providers.re.RenderingEngine: Returns the model that dictates how transformed raw data has to be mapped onto a color space.
getModel() - Method in class pojos.DetectorData: Returns the manufacturer of the detector.
getModel() - Method in class pojos.DichroicData: Returns the model.
getModel() - Method in class pojos.FilterData: Returns the model.
getModel() - Method in class pojos.FilterSetData: Returns the model.
getModel() - Method in class pojos.ObjectiveData: Returns the model of the objective.
getModel_async(AMD_RenderingEngine_getModel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getMostRecentAnnotationLinks_async(AMD_ITimeline_getMostRecentAnnotationLinks, List<String>, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
getMostRecentObjects_async(AMD_ITimeline_getMostRecentObjects, List<String>, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI
getMostRecentShareCommentLinks_async(AMD_ITimeline_getMostRecentShareCommentLinks, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
getMyOpenAgentSessions(String) - Method in interface ome.api.ISession: Like ISession.getMyOpenSessions() but returns only those sessions with the given agent string.
getMyOpenAgentSessions(String) - Method in class ome.services.sessions.SessionBean
getMyOpenAgentSessions_async(AMD_ISession_getMyOpenAgentSessions, String, Current) - Method in class ome.services.blitz.impl.SessionI
getMyOpenClientSessions() - Method in interface ome.api.ISession: Like ISession.getMyOpenSessions() but returns only those sessions started by official OMERO clients.
getMyOpenClientSessions() - Method in class ome.services.sessions.SessionBean
getMyOpenClientSessions_async(AMD_ISession_getMyOpenClientSessions, Current) - Method in class ome.services.blitz.impl.SessionI
getMyOpenSessions() - Method in interface ome.api.ISession: Returns a list of open sessions for the current user.
getMyOpenSessions() - Method in class ome.services.sessions.SessionBean
getMyOpenSessions_async(AMD_ISession_getMyOpenSessions, Current) - Method in class ome.services.blitz.impl.SessionI
getMyUserPhotos() - Method in interface ome.api.IAdmin: Retrieve the OriginalFile objectd attached to this user as specified by {@link #uploadMyUserPhoto(String, String, byte[]).
getMyUserPhotos() - Method in class ome.logic.AdminImpl
getMyUserPhotos_async(AMD_IAdmin_getMyUserPhotos, Current) - Method in class ome.services.blitz.impl.AdminI
getName() - Method in class ome.logic.HardWiredInterceptor: Can be implemented by all subclasses, so that they can configure themselves in HardWiredInterceptor.selfConfigure(OmeroContext).
getName() - Method in class ome.security.basic.BasicSecurityWiring: Lookup name.
getName() - Method in class ome.services.delete.BaseDeleteSpec
getName() - Method in class ome.services.delete.DeleteEntry
getName(Matcher) - Method in class ome.services.delete.DeleteEntry
getName() - Method in interface ome.services.delete.DeleteSpec: The name of this specification.
getName() - Method in class ome.services.roi.PopulateRoiJob
getName() - Method in class ome.services.scripts.ScriptFinder: Subclasses should override to return the name of the file under scripts/ which should be uploaded.
getName() - Method in interface ome.services.sessions.SessionCallback
getName() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
getName() - Method in class ome.system.Login: simple getter for the user name passed into the constructor
getName() - Method in class ome.system.Preference
getName() - Method in class ome.system.Principal
getName() - Method in class pojos.ChannelData: Returns the name of the channel.
getName() - Method in class pojos.DatasetData: Returns the name of the dataset.
getName() - Method in class pojos.FileData: Returns the name of the file.
getName() - Method in class pojos.GroupData: Returns the name of the group.
getName() - Method in class pojos.ImageData: Returns the name of the image.
getName() - Method in class pojos.PlateAcquisitionData: Returns the name of the plate acquisition.
getName() - Method in class pojos.PlateData: Returns the name of the plate.
getName() - Method in class pojos.ProjectData: Returns the name of the project.
getName() - Method in class pojos.ScreenData: Returns the name of the screen.
getNameSpace() - Method in class pojos.AnnotationData: Retrieves the nameSpace of the underlying Annotation instance.
getNameSpace() - Method in class pojos.TermAnnotationData: Returns the namespace of the term.
getNameSpace() - Method in class pojos.WorkflowData: Returns the namespace of this workflow.
getNamespaceKeywords(String) - Method in class pojos.ROIData: Returns the keywords of the namespace on the ROI.
getNamespaceKeywords() - Method in class pojos.ROIData: Returns the keywords of the ROI.
getNamespaces() - Method in class pojos.ROIData: Returns the namespace of the ROI.
getNDFilter() - Method in class pojos.ChannelData: Returns the ND filter wavelength of the channel.
getNewUserGroup() - Method in class ome.security.auth.LdapConfig
getNodeUuid(Current) - Method in class ome.services.blitz.fire.Ring
getNoiseReduction() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns true if the noise reduction algorithm is turned on, false if turned off.
getNominalMagnification() - Method in class pojos.ObjectiveData: Returns the objective's nominal magnification factor.
getNullShapes() - Method in class ome.services.roi.GeomTool
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.
getObjective() - Method in class pojos.ImageAcquisitionData: Returns the objective used to capture the image.
getObjective() - Method in class pojos.OTFData: Returns the associated objective.
getObjectives() - Method in class pojos.InstrumentData: Returns the collection of objectives.
getObjectiveSettingsId() - Method in class pojos.ImageAcquisitionData: Returns the id of the Objective settings or -1 if not already linked to the image.
getObjectsRead() - Method in class ome.services.messages.stats.ObjectsReadStatsMessage
getObjectsWritten() - Method in class ome.services.messages.stats.ObjectsWrittenStatsMessage
getObjectType() - Method in class ome.security.basic.EventListenersFactoryBean: this FactoryBean produces a Map instance for use in LocalSessionFactoryBean.setEventListeners(Map)
getOffset() - Method in class omero.sys.ParametersI: Returns the value of the offset parameter.
getOffset() - Method in class pojos.DetectorData: Returns the offset of the detector.
getOmeroPixelType() - Method in class ome.io.nio.DeltaVisionHeader: Returns a new OMERO pixels type object which corresponds to the DeltaVision pixels type.
getOp(Matcher) - Method in class ome.services.delete.DeleteEntry
getOptimizations() - Method in class omeis.providers.re.Renderer: Returns the optimizations that the renderer currently has enabled.
getOrCreateParams(long, Current) - Method in class omero.grid.ParamsHelper: Get the script params for the file.
getOrder() - Method in class ome.io.nio.PixelData: Returns the byte order of the backing buffer.
getOrder() - Method in class ome.io.nio.ReorderedPixelData: Returns the byte order of the backing buffer.
getOriginalEnumerations() - Method in interface ome.api.ITypes: Gets all original values.
getOriginalEnumerations() - Method in class ome.logic.TypesImpl
getOriginalEnumerations_async(AMD_ITypes_getOriginalEnumerations, Current) - Method in class ome.services.blitz.impl.TypesI
getOriginalFileWhereFormatStartsWith(Pixels, String) - Method in interface ome.io.nio.OriginalFileMetadataProvider: Finds the first original file for a pixels set whose format starts with a given string.
getOriginalFileWhereFormatStartsWith(Pixels, String) - Method in class ome.services.OmeroOriginalFileMetadataProvider: Implemented as specified by the OriginalFileMetadataProvider I/F.
getOriginalGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the original maximum of all minima.
getOriginalGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the original minimum of all minima.
getOriginalMimetype() - Method in class pojos.FileAnnotationData: Returns the format of the original file.
getOrphan() - Method in class omero.sys.ParametersI
getOTF() - Method in class pojos.ChannelAcquisitionData: Returns the OTF used for that channel.
getOTF() - Method in class pojos.InstrumentData: Returns the collection of OTFs.
getOutput(String, String) - Method in interface ome.api.ISession: Retrieves an entry from the session's output environment.
getOutput(String, String) - Method in class ome.services.sessions.SessionBean
getOutput(String, String) - Method in interface ome.services.sessions.SessionManager: Returns the output environment Object stored under the given key or null if none present.
getOutput(String, String) - Method in class ome.services.sessions.SessionManagerImpl
getOutput(String) - Method in class omero.client: Retrieves an item from the "output" shared (session) memory.
getOutput_async(AMD_ISession_getOutput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI
getOutputKeys(String) - Method in interface ome.api.ISession: Retrieves all keys in the sesson's output environment.
getOutputKeys(String) - Method in class ome.services.sessions.SessionBean
getOutputKeys() - Method in class omero.client: Returns a list of keys for all items in the "output" shared (session) memory
getOutputKeys_async(AMD_ISession_getOutputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI
getOutputs(String) - Method in interface ome.api.ISession: Retrieves all outputs from the given session's input environment.
getOutputs(String) - Method in class ome.services.sessions.SessionBean
getOutputs_async(AMD_ISession_getOutputs, String, Current) - Method in class ome.services.blitz.impl.SessionI
getOverlays() - Method in class omeis.providers.re.Renderer: Returns the current set of overlays to be rendered.
getOwner() - Method in class ome.security.basic.CurrentDetails
getOwner(Current) - Method in class omero.model.DetailsI
getOwner() - Method in class pojos.DataObject: Returns the owner of the object.
getOwnShares(boolean) - Method in interface ome.api.IShare: Gets all owned shares for the current Experimenter
getOwnShares(boolean) - Method in class ome.services.sharing.ShareBean
getOwnShares_async(AMD_IShare_getOwnShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
getParams_async(AMD_IScript_getParams, long, Current) - Method in class ome.services.blitz.impl.ScriptI: Get the Parameters of the script.
getParentFilePath() - Method in class pojos.ImageData: Returns the path to the file hosting the image.
getParentTransformer(Class) - Static method in class ome.services.query.Hierarchy
getPassword() - Method in class ome.system.Login: simple getter for the password passed into the constructor
getPasswordAuthentication() - Method in class ome.security.SmtpAuthenticator
getPastConnections(long) - Method in interface ome.api.IShare: Gets previous connections to share.
getPastConnections(long) - Method in class ome.services.sharing.ShareBean
getPastConnections_async(AMD_IShare_getPastConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI
getPatcher() - Method in class ome.services.sharing.data.ObjHolder
getPatcher() - Method in class ome.services.sharing.data.ShareDataHolder
getPatcher() - Method in class ome.services.sharing.data.ShareItemHolder
getPath() - Method in class ome.io.nio.AbstractBuffer
getPath() - Method in class ome.io.nio.DeltaVision
getPath() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getPath() - Method in interface ome.io.nio.PixelBuffer: Retrieves the full path to this pixel buffer on disk
getPath(Matcher) - Method in class ome.services.delete.DeleteEntry
getPath() - Method in class pojos.FileData: Returns the (relative) path of the file.
getPath() - Method in class pojos.OTFData: Returns the path.
getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
getPathToFile() - Method in class pojos.ImageData: Returns the path to the file.
getPerm1(Current) - Method in class omero.model.PermissionsI
getPermissions(Current) - Method in class omero.model.DetailsI
getPermissions() - Method in class pojos.DataObject: Returns the permission of the object.
getPinholeSize() - Method in class pojos.ChannelData: Returns the pin hole size of the channel.
getPixelBeginOffset() - Method in class ome.io.nio.DeltaVisionHeader: Returns the number of bytes to the beginning of the Pixels
getPixelBuffer(Pixels, OriginalFileMetadataProvider, boolean) - Method in class ome.io.nio.PixelsService: Returns a pixel buffer for a given set of pixels.
getPixelIds() - Method in class ome.tools.RepositoryTask: This public method is used to return a list of pixel ids that require deletion from the disk repository.
getPixels() - Method in class ome.formats.importer.util.TinyImportFixture
getPixels(long, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getPixels(long) - Method in interface ome.services.blitz.gateway.services.ImageService: Get the pixels information for an image.
getPixels(long) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
getPixels(Long) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
getPixels(Long) - Method in interface ome.services.blitz.gateway.services.RenderingService: Get the pixels of the Rendering engine.
getPixels() - 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.
getPixels() - Method in class omeis.providers.re.Renderer: Returns the object that allows to access the pixels raw data.
getPixels() - Method in interface omeis.providers.re.RenderingEngine: Returns the Pixels set the Rendering engine is for.
getPixels_async(AMD_RenderingEngine_getPixels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getPixelsArrayAsByte() - Method in class omerojava.util.Plane1D: Return the pixels array of the mapped data.
getPixelsArrayAsByte(boolean) - Method in class omerojava.util.Plane2D: Return the pixels array of the mapped data.
getPixelsArrayAsDouble() - Method in class omerojava.util.Plane1D: Return the pixels array of the mapped data.
getPixelsArrayAsDouble(boolean) - Method in class omerojava.util.Plane2D: Return the pixels array of the mapped data.
getPixelsArrayAsInt() - Method in class omerojava.util.Plane1D: Return the pixels array of the mapped data.
getPixelsArrayAsInt(boolean) - Method in class omerojava.util.Plane2D: Return the pixels array of the mapped data.
getPixelsArrayAsLong() - Method in class omerojava.util.Plane1D: Return the pixels array of the mapped data.
getPixelsArrayAsLong(boolean) - Method in class omerojava.util.Plane2D: Return the pixels array of the mapped data.
getPixelsArrayAsShort() - Method in class omerojava.util.Plane1D: Return the pixels array of the mapped data.
getPixelsArrayAsShort(boolean) - Method in class omerojava.util.Plane2D: Return the pixels array of the mapped data.
getPixelsBinDataBigEndian(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsDimensionOrder(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsFromDataset(Dataset) - Static method in class omerojava.util.GatewayUtils: Get the pixels from the Dataset, the pixels must be loaded in the Dataset beforehand.
getPixelsFromImage(long, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getPixelsFromImage(long) - Method in interface ome.services.blitz.gateway.services.DataService: Get the pixels associated with the image.
getPixelsFromImage(long) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
getPixelsFromImageList(List<Image>) - Static method in class omerojava.util.GatewayUtils: Get the pixels from the list of images, these images must have the pixels loaded beforehand.
getPixelsFromProject(Project) - Static method in class omerojava.util.GatewayUtils: Get the pixels from the Project, the pixels must be loaded in the project beforehand.
getPixelsId() - Method in interface ome.api.RawPixelsStore: Returns the current Pixels set identifier.
getPixelsID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsId() - Method in class ome.services.RawPixelsBean
getPixelsId_async(AMD_RawPixelsStore_getPixelsId, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getPixelsImageMap(List<Image>) - Static method in class omerojava.util.GatewayUtils: create a map of pixelsId to pixels from the images in the image list.
getPixelSizeX() - Method in class pojos.PixelsData: Returns the dimension of a pixel along the X-axis, dimension is in microns.
getPixelSizeY() - Method in class pojos.PixelsData: Returns the dimension of a pixel along the Y-axis, dimension is in microns.
getPixelSizeZ() - Method in class pojos.PixelsData: Returns the dimension of a pixel along the Z-axis, dimension is in microns.
getPixelsParamKeys(long) - Method in class ome.services.db.PgArrayHelper: Returns only the (possibly empty) keys which are set on the given original file.
getPixelsParams(long) - Method in class ome.services.db.PgArrayHelper: Loads all the (possibly empty) params for the given original file.
getPixelsPath(Long) - Method in class ome.io.nio.AbstractFileSystemService
getPixelsPhysicalSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsPhysicalSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsPhysicalSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getPixelsService() - Method in class ome.system.ServiceFactory
getPixelsSizeC(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsSizeT(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsTimeIncrement(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsType(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsType() - Method in class omeis.providers.re.Renderer: Returns the pixels type.
getPixelsType() - Method in class pojos.OTFData: Returns the pixels type.
getPixelsTypeLowerBound(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getPixelsTypeLowerBound(int) - Method in class omeis.providers.re.Renderer: Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeLowerBound(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeLowerBound_async(AMD_RenderingEngine_getPixelsTypeLowerBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getPixelsTypeMax() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the upper bound of the pixels range or 0 if the value couldn't be set.
getPixelsTypeMin() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the lower bound of the pixels range or 0 if the value couldn't be set.
getPixelsTypeUpperBound(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getPixelsTypeUpperBound(int) - Method in class omeis.providers.re.Renderer: Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeUpperBound(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeUpperBound_async(AMD_RenderingEngine_getPixelsTypeUpperBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getPixelType() - Method in class ome.io.nio.DeltaVisionHeader: Returns a numeric value for the pixel type
getPixelType(String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getPixelType(String) - Method in interface ome.services.blitz.gateway.services.DataService: Get the pixelsType with type.
getPixelType(String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
getPixelType() - Method in class pojos.PixelsData: Returns the pixels type.
getPixelTypes(Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getPixelTypes() - Method in interface ome.services.blitz.gateway.services.DataService: Get the PixelTypes available in the system.
getPixelTypes() - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
getPixelValue(int) - Method in class ome.io.nio.PixelData: Returns the pixel intensity value of the pixel at a given offset within the backing buffer.
getPixelValue(int, int) - Method in class omeis.providers.re.data.Plane2D: Returns the pixel intensity value of the pixel at (x1, x2).
getPixelValue(int) - Method in class omeis.providers.re.data.Plane2D: Returns the pixel intensity value of the pixel at a given offset within the backing buffer.
getPixelValueDirect(int) - Method in class ome.io.nio.PixelData: Returns the pixel intensity value of the pixel at a given offset within the backing buffer.
getPixelValueDirect(int) - Method in class ome.io.nio.ReorderedPixelData: Returns the pixel intensity value of the pixel at a given offset within the backing buffer.
getPlane(int, int, int) - Method in interface ome.api.RawPixelsStore
getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision
getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getPlane(Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves a particular 2D image plane from this pixel buffer.
getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
getPlane(long, int, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway: Get the raw plane for the pixels pixelsId, this returns a 2d array representing the plane, it returns doubles but will not lose data.
getPlane(long, int, int, int) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
getPlane(long, int, int, int) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService: get bytes to the plane c, t, z
getPlane(int, int, int) - Method in class ome.services.RawPixelsBean
getPlane(int, int, int) - Method in class omerojava.util.DataSink: Extracts a 2D plane from the pixels set this object is working for.
getPlane1D(Pixels, byte[]) - Static method in class omerojava.util.GatewayUtils: Extracts a 1D plane from the pixels set this object is working for.
getPlane2D(Pixels, byte[]) - Static method in class omerojava.util.GatewayUtils: Extracts a 2D plane from the pixels set this object is working for.
getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getPlaneCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlaneCount() - Method in class pojos.ROIData: Returns the number of planes occupied by the ROI.
getPlaneDeltaT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlaneDimsAsString(PlaneDef) - Method in class omeis.providers.re.Renderer: Returns a string with the dimensions of the specified plane.
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.DeltaVision
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves a particular 2D image plane from this pixel buffer.
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
getPlaneExposureTime(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlaneOffset(int, int, int) - Method in interface ome.api.RawPixelsStore
getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision
getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getPlaneOffset(Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves the offset for a particular 2D image plane in this pixel buffer.
getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
getPlaneOffset(int, int, int) - Method in class ome.services.RawPixelsBean
getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getPlanePositionX(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlanePositionY(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlanePositionZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlanePrevious() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the value corresponding to the index of the bit-plane ranged just before the one selected.
getPlaneRegion(int, int, int, int, int) - Method in interface ome.api.RawPixelsStore
getPlaneRegion(int, int, int, int, int) - Method in class ome.services.RawPixelsBean
getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.DeltaVision
getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves a region from a given plane directly.
getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
getPlaneSelected() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the value corresponding to the index of the selected bit-plane.
getPlaneSize() - Method in interface ome.api.RawPixelsStore: delegates to PixelBuffer
getPlaneSize() - Method in class ome.io.nio.DeltaVision
getPlaneSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getPlaneSize() - Method in interface ome.io.nio.PixelBuffer: Retrieves the in memory size of a 2D image plane in this pixel buffer.
getPlaneSize() - Method in class ome.io.nio.RomioPixelBuffer
getPlaneSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
getPlaneSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService: Get the plane size of the current image.
getPlaneSize() - Method in class ome.services.RawPixelsBean
getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getPlaneTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlaneTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlaneTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlate() - Method in class pojos.WellData: Returns the plate containing this Well.
getPlateAcquisitions() - Method in class pojos.PlateData: Returns the plate acquisitions related to this plate.
getPlates() - Method in class pojos.ScreenData: Returns the plates contained in this screen.
getPlateType() - Method in class pojos.PlateData: Returns the type of plate e.g.
getPockelCell() - Method in class pojos.ChannelData: Returns the Pockels cell settings.
getPoint(double) - Method in class ome.util.math.geom2D.Line: Returns the point of this line defined by k.
getPoint(double) - Method in class ome.util.math.geom2D.Segment: Returns the point of this line defined by k.
getPoints(long, Session) - Method in class ome.services.roi.GeomTool
getPoints() - Method in class ome.util.math.geom2D.EllipseArea: Implemented as specified by the PlaneArea I/F.
getPoints() - Method in interface ome.util.math.geom2D.PlaneArea: Returns an array of PlanePoint contained in the PlaneArea.
getPoints() - Method in class ome.util.math.geom2D.RectangleArea: Implemented as specified by the PlaneArea I/F.
getPoints() - Method in class pojos.PolygonData: Returns the points in the polygon.
getPoints() - Method in class pojos.PolylineData: Returns the points in the Polyline.
getPoints1() - Method in class pojos.PolygonData: Returns the points in the polygon.
getPoints1() - Method in class pojos.PolylineData: Returns the points in the Polyline.
getPoints2() - Method in class pojos.PolygonData: Returns the points in the polygon.
getPoints2() - Method in class pojos.PolylineData: Returns the points in the Polyline.
getPoints_async(AMD_IRoi_getPoints, long, Current) - Method in class ome.services.blitz.impl.RoiI
getPojoTypes() - Method in class ome.logic.TypesImpl
getPort() - Method in class ome.system.Server: simple getter for the port passed into the constructor or the default port if none.
getPositionX() - Method in class pojos.ImageAcquisitionData: Returns the x-coordinate in the frame microscope.
getPositionX() - Method in class pojos.WellSampleData: Returns the position X.
getPositionY() - Method in class pojos.ImageAcquisitionData: Returns the y-coordinate in the frame microscope.
getPositionY() - Method in class pojos.WellSampleData: Returns the position Y.
getPositionZ() - Method in class pojos.ImageAcquisitionData: Returns the z-coordinate in the frame microscope.
getPower() - Method in class pojos.LightSourceData: Returns the power of the light source.
getPrefix() - Method in class ome.system.ServiceFactory: used by ServiceFactory.getServiceByClass(Class) to find the correct service proxy in the ServiceFactory.ctx
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.services.blitz.impl.ServiceFactoryI
getPrincipal() - Method in class ome.services.util.ExecutionThread
getProjectionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getProjectionService() - Method in class ome.system.ServiceFactory
getProjects(List<Long>, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getProjects(List<Long>, boolean) - Method in interface ome.services.blitz.gateway.services.DataService: Get the projects in the users.
getProjects(List<Long>, boolean) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
getProjects() - Method in class pojos.DatasetData: Returns a set of projects containing the dataset.
getProjectsForDataset(long) - Method in interface ome.api.IAnalysis
getProjectsForUser(long) - Method in interface ome.api.IAnalysis
getProperties() - Method in class ome.security.auth.FilePasswordProvider
getProperties() - Method in class omero.client: Returns the active properties for this instance.
getProperty(String) - Method in class ome.system.OmeroContext
getProperty(String) - Method in class ome.system.PreferenceContext: Lookup method for getting access to the merged properties for this instance.
getProperty(String) - Method in class omero.client: Returns the property value for this key or the empty string if none.
getPropertyMap() - Method in class omero.client: Returns all properties which are prefixed with "omero." or "Ice."
getPropertyMap(Properties) - Method in class omero.client: Returns all properties which are prefixed with "omero." or "Ice."
getProtocolDescription() - Method in class pojos.ScreenData: Returns the description of the protocol.
getProtocolIdentifier() - Method in class pojos.ScreenData: Returns the identifier of the protocol.
getProxy() - Method in class ome.services.blitz.impl.ScriptProcessI
getProxy() - Method in class ome.services.blitz.util.RegisterServantMessage
getProxyOrNull(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.Ring: Delegates to the Ring.redirector strategy configured for this instance.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector: Returns null early if the Current has already once been routed by a Redirector implementation, returns an existing session if it can be found, or returns a null.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ConfigRedirector: Create or retrieve and returns a SessionPrx which the current method takes control of.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.NullRedirector: Always returns null
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in interface ome.services.blitz.redirect.Redirector: Create or retrieve and returns a SessionPrx which the current method takes control of.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ScaleRedirector
getQuantumDef() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getQuantumDef() - Method in interface omeis.providers.re.RenderingEngine: Returns the quantization object.
getQuantumDef_async(AMD_RenderingEngine_getQuantumDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getQuantumManager() - Method in class omeis.providers.re.Renderer: Returns the object that manages and allows to retrieve the objects that are used to quantize wavelength data.
getQueryFactory() - Method in class ome.logic.AbstractLevel1Service
getQueryFactory() - Method in class ome.logic.AbstractLevel2Service
getQueryService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getQueryService() - Method in class ome.system.ServiceFactory
getRadiusX() - Method in class pojos.EllipseData: Returns the radius along the X-axis.
getRadiusY() - Method in class pojos.EllipseData: Returns the radius along the Y-axis.
getRating() - Method in class pojos.RatingAnnotationData: Returns the rating value.
getRawFileStoreService() - Method in class ome.services.blitz.gateway.services.GatewayFactory: Return the raw file store service.
getRawPixelsStoreService() - Method in class ome.services.blitz.gateway.services.GatewayFactory: Return the raw pixels store service.
getRawPlane(long, int, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService: Get the raw plane from the server with id pixelsId, and channels, c, timepoint t, and z-section z.
getRawPlane(long, int, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
getReaderNames() - Static method in class ome.services.util.DBEnumCheck
getReagentsCounts() - Method in class pojos.WellData: Returns the number of reagents linked to the object, key: id of the user, value: number of annotation.
getReagentSetDescripion() - Method in class pojos.ScreenData: Returns the description of the reagent set.
getReagentSetIdentifier() - Method in class pojos.ScreenData: Returns the identifier of the Reagent set.
getRed() - Method in class pojos.WellData: Returns the red component of the color associated to the well, or -1.
getRedBand() - Method in class omeis.providers.re.RGBBuffer: Returns the data buffer for the red band.
getRedirect(Redirector.Context) - Method in class ome.services.blitz.redirect.AbstractRedirector: Returns the current redirect, to which all calls to #getProxyOrNull(String, Glacier2.SessionControlPrx, Ice.Current) will be pointed.
getRedValue(int) - Method in class omeis.providers.re.RGBAIntBuffer: Retrieves the Red value for a particular pixel index.
getRedValue(int) - Method in class omeis.providers.re.RGBBuffer: Retrieves the Red value for a particular pixel index.
getRedValue(int) - Method in class omeis.providers.re.RGBIntBuffer: Retrieves the Red value for a particular pixel index.
getReference() - Method in class pojos.ImageData: Returns the reference to the file to register.
getReferenceCount(String) - Method in interface ome.api.ISession: Retrieves the current reference count for the given uuid.
getReferenceCount(String) - Method in class ome.services.sessions.SessionBean
getReferenceCount(String) - Method in interface ome.services.sessions.SessionManager: Return the number of client which are presumed to be attached to this session or throw an exception if there's no such session.
getReferenceCount(String) - Method in class ome.services.sessions.SessionManagerImpl
getReferenceCount_async(AMD_ISession_getReferenceCount, String, Current) - Method in class ome.services.blitz.impl.SessionI
getRefPlateId() - Method in class pojos.PlateAcquisitionData: Returns the id of the plate of reference.
getRefractiveIndex() - Method in class pojos.ImageAcquisitionData: Returns the refractive index of the objective.
getRegion(int, long) - Method in interface ome.api.RawPixelsStore
getRegion(Integer, Long) - Method in class ome.io.nio.DeltaVision
getRegion(Integer, Long) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getRegion(Integer, Long) - Method in interface ome.io.nio.PixelBuffer: Retrieves a region from this pixel buffer.
getRegion(Integer, Long) - Method in class ome.io.nio.RomioPixelBuffer
getRegion(int, long) - Method in class ome.services.RawPixelsBean
getRegion_async(AMD_RawPixelsStore_getRegion, int, long, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.DeltaVision
getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getRegionDirect(Integer, Long, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves a region from this pixel buffer directly.
getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
getRegistry() - Method in class ome.services.blitz.util.BlitzConfiguration
getRelationship(String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata: Walks both the #locksHolder and the #lockedByHolder data for "from" argument to see if there is any direct relationship to the "to" argument.
getRelationship(String, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Walks both the ExtendedMetadata.Impl.locksHolder and the ExtendedMetadata.Impl.lockedByHolder data for "from" argument to see if there is any direct relationship to th "to" argument.
getRenderedImage(long, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getRenderedImage(long, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService: Render image as Buffered image.
getRenderedImage(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
getRenderedImage(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
getRenderedImage(long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService: Render image as Buffered image.
getRenderedImageMatrix(long, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getRenderedImageMatrix(long, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService: Render image as 3d matrix.
getRenderedImageMatrix(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
getRenderedImageMatrix(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
getRenderedImageMatrix(long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService: Render image as 3d matrix.
getRenderingDef() - Method in class omeis.providers.re.Renderer: Returns the settings that define the transformation context.
getRenderingService() - Method in class ome.services.blitz.gateway.services.GatewayFactory: Return the rendering service.
getRenderingSettings(long) - Method in interface ome.api.IRenderingSettings: Returns the default rendering settings for a given pixels for the current user.
getRenderingSettings(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
getRenderingSettings_async(AMD_IRenderingSettings_getRenderingSettings, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
getRenderingSettingsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getRenderingSettingsService() - Method in class ome.system.ServiceFactory
getReorderedPixelOffset(int, int, int) - Static method in class ome.io.nio.ReorderedPixelData: Returns the re-ordered pixel offset.
getRepositoryInfoService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getRepositoryInfoService() - Method in class ome.system.ServiceFactory
getResults(int, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
getResults() - Method in class ome.services.delete.QueryConstraints
getResults(ProcessPrx, Current) - Method in class omero.grid.InteractiveProcessorI
getResultSet() - Method in class ome.tools.hibernate.SqlArray
getResultSet(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
getResultSet(long, int) - Method in class ome.tools.hibernate.SqlArray
getResultSet(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
getResultsString(Object, IdentityHashMap<Object, String>) - Method in class ome.services.util.ServiceHandler: public for testing purposes.
getResultTypes() - Method in class ome.logic.TypesImpl
getRevision(Class) - Static method in class ome.system.Version: Parses the given class for its RevisionNumber annotation.
getRGBA(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getRGBA(int) - Method in interface omeis.providers.re.RenderingEngine: Returns a 4D-array representing the color associated to the specified channel.
getRGBA_async(AMD_RenderingEngine_getRGBA, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getRing() - Method in class ome.services.blitz.util.BlitzConfiguration
getROI() - Method in class pojos.util.ROIComponent: Returns all the ROI in the component as a list.
getROI() - Method in class pojos.util.UploadMask: Returns the ROIs created from uploading the images.
getROICoordinate() - Method in class pojos.ShapeData: Get the ROICoordinate for the ShapeData
getRoiIds() - Method in class ome.services.blitz.measurements.MeasurementStore
getRoiIds() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore: Returns the ids of all Roi instances created during the save method.
getRoiMeasurements_async(AMD_IRoi_getRoiMeasurements, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
getRoiService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getRoiStats_async(AMD_IRoi_getRoiStats, long, Current) - Method in class ome.services.blitz.impl.RoiI
getRoot() - Method in class ome.services.blitz.impl.OmeroMetadata
getRootId() - Method in class ome.system.Roles
getRootName() - Method in class ome.system.Roles
getRouter(Communicator) - Static method in class omero.client: Acquires the default router, and throws an exception if it is not of type {Glacier2.RouterPrx}.
getRow(int, int, int, int) - Method in interface ome.api.RawPixelsStore
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getRow(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves a particular row or scanline from this pixel buffer.
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
getRow(int, int, int, int) - Method in class ome.services.RawPixelsBean
getRow() - Method in class pojos.WellData: Returns the row used to indicate the location of the well on the grid.
getRow_async(AMD_RawPixelsStore_getRow, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.DeltaVision
getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves a particular row or scanline from this pixel buffer.
getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
getRowOffset(int, int, int, int) - Method in interface ome.api.RawPixelsStore
getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision
getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getRowOffset(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves the offset for a particular row or scanline in this pixel buffer.
getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
getRowOffset(int, int, int, int) - Method in class ome.services.RawPixelsBean
getRowOffset_async(AMD_RawPixelsStore_getRowOffset, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getRowSequenceIndex() - Method in class pojos.PlateData: Returns the index indicating how to label a row.
getRowSize() - Method in interface ome.api.RawPixelsStore
getRowSize() - Method in class ome.io.nio.DeltaVision
getRowSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getRowSize() - Method in interface ome.io.nio.PixelBuffer: Retrieves the in memory size of a row or scanline of pixels in this pixel buffer.
getRowSize() - Method in class ome.io.nio.RomioPixelBuffer
getRowSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
getRowSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService: Get the plane size of the current image.
getRowSize() - Method in class ome.services.RawPixelsBean
getRowSize_async(AMD_RawPixelsStore_getRowSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getScreens() - Method in class pojos.PlateData: Returns a set of screens containing the plate.
getScriptDir() - Method in class ome.services.scripts.ScriptRepoHelper: Returns the actual root of this repository.
getScriptID_async(AMD_IScript_getScriptID, String, Current) - Method in class ome.services.blitz.impl.ScriptI: Get the id of the official script with given path.
getScriptRepository(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
getScripts_async(AMD_IScript_getScripts, Current) - Method in class ome.services.blitz.impl.ScriptI: Get Scripts will return all the scripts by id and name available on the server.
getScriptService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getScriptText_async(AMD_IScript_getScriptText, long, Current) - Method in class ome.services.blitz.impl.ScriptI: Return the script with the name to the user.
getScriptWithDetails_async(AMD_IScript_getScriptWithDetails, long, Current) - Method in class ome.services.blitz.impl.ScriptI: Return the script with the name to the user.
getSecurityContexts(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getSecurityRoles() - Method in interface ome.api.IAdmin: returns the active Roles in use by the server.
getSecurityRoles() - Method in class ome.logic.AdminImpl
getSecurityRoles() - Method in class ome.security.basic.BasicSecuritySystem
getSecurityRoles() - Method in interface ome.security.SecuritySystem
getSecurityRoles() - Method in class ome.security.SecuritySystemHolder
getSecurityRoles() - Method in class ome.security.sharing.SharingSecuritySystem
getSecurityRoles_async(AMD_IAdmin_getSecurityRoles, Current) - Method in class ome.services.blitz.impl.AdminI
getSecuritySystem() - Method in class ome.logic.AbstractLevel2Service
getSequence() - Method in class ome.io.nio.DeltaVisionHeader: Returns a numeric value that represents the Z,C, and T ordering
getSerialNumber() - Method in class pojos.DetectorData: Returns the serial number of the detector.
getSerialNumber() - Method in class pojos.DichroicData: Returns the serial number.
getSerialNumber() - Method in class pojos.FilterData: Returns the serial number.
getSerialNumber() - Method in class pojos.FilterSetData: Returns the serial number.
getSerialNumber() - Method in class pojos.LightSourceData: Returns the serial number of the light source.
getSerialNumber() - Method in class pojos.ObjectiveData: Returns the serial number of the objective.
getServant(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI
getServant() - Method in class ome.services.blitz.util.RegisterServantMessage
getServantList() - Method in class ome.services.blitz.util.ServantHolder
getServerFileMimetype() - Method in class pojos.FileAnnotationData: Returns the file format as defined by the specification, corresponding to the file extension.
getServerTime() - Method in interface ome.api.IConfig: checks the current server for it's time.
getServerTime() - Method in class ome.logic.ConfigImpl: see IConfig.getServerTime()
getServerTime_async(AMD_IConfig_getServerTime, Current) - Method in class ome.services.blitz.impl.ConfigI
getServiceByClass(Class<T>) - Method in class ome.system.ServiceFactory: looks up services based on the current prefix and the class name of the service type.
getServiceFactory(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
getServiceFactory(String, String) - Method in class ome.services.blitz.fire.SessionManagerI
getServiceFactory(Identity) - Method in class ome.services.blitz.fire.SessionManagerI
getServiceFactory() - Method in class omero.client: Deprecated.
getServiceFactoryIdentity(Current) - Method in class ome.services.blitz.fire.SessionManagerI
getServiceInterface() - Method in class ome.logic.AdminImpl
getServiceInterface() - Method in class ome.logic.ConfigImpl
getServiceInterface() - Method in class ome.logic.LdapImpl
getServiceInterface() - Method in class ome.logic.MetadataImpl: Returns the Interface implemented by this class.
getServiceInterface() - Method in class ome.logic.PixelsImpl: Returns the interface this implementation is for.
getServiceInterface() - Method in class ome.logic.PojosImpl: Returns the Interface implemented by this class.
getServiceInterface() - Method in class ome.logic.QueryImpl
getServiceInterface() - Method in class ome.logic.RenderingSettingsImpl: Returns the interface this implementation is for.
getServiceInterface() - Method in class ome.logic.RepositoryInfoImpl
getServiceInterface() - Method in class ome.logic.TypesImpl
getServiceInterface() - Method in class ome.logic.UpdateImpl
getServiceInterface() - Method in class ome.services.delete.DeleteBean
getServiceInterface() - Method in class ome.services.JobBean
getServiceInterface() - Method in class ome.services.projection.ProjectionBean: Returns the interface this implementation is for.
getServiceInterface() - Method in class ome.services.RawFileBean
getServiceInterface() - Method in class ome.services.RawPixelsBean
getServiceInterface() - Method in class ome.services.RenderingBean
getServiceInterface() - Method in class ome.services.SearchBean
getServiceInterface() - Method in class ome.services.sessions.SessionBean
getServiceInterface() - Method in class ome.services.sharing.ShareBean
getServiceInterface() - Method in class ome.services.ThumbnailBean
getServiceInterface() - Method in interface ome.system.SelfConfigurableService
getServiceKey() - Method in class ome.services.blitz.util.ExpiredServantMessage
getSession(String) - Method in interface ome.api.ISession: Retrieves the session associated with this uuid, updating the last access time as well.
getSession(String) - Method in class ome.services.sessions.SessionBean
getSession() - Method in interface ome.services.sessions.SessionContext
getSession() - Method in class ome.services.sessions.SessionContextImpl
getSession() - Method in class ome.system.ServiceFactory
getSession() - Method in class ome.system.SessionInitializer
getSession() - Method in class ome.tools.hibernate.SessionFactory
getSession() - Method in class omero.client: Returns the current active session or throws an exception if none has been created since the last client.closeSession()
getSession_async(AMD_ISession_getSession, String, Current) - Method in class ome.services.blitz.impl.SessionI
getSessionContext(String, boolean) - Method in class ome.services.sessions.state.SessionCache: Retrieve a session possibly raising either RemovedSessionException or SessionTimeoutException.
getSessionFactory() - Method in class ome.logic.AbstractLevel1Service: delegates to HibernateDaoSupport to get the current SessionFactory
getSessionId() - Method in class ome.services.messages.AbstractSessionMessage
getSessionId() - Method in class omero.client: Returns the UUID for the current session without making a remote call.
getSessionInitializer() - Method in class ome.system.ServiceFactory
getSessionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getSessionService() - Method in class ome.system.ServiceFactory
getSessionStats(String) - Method in interface ome.services.sessions.SessionManager: Return the SessionStats which are being counted for the given session or throw an exception if it has been removed.
getSessionStats(String) - Method in class ome.services.sessions.SessionManagerImpl
getSetting() - Method in interface ome.api.ILdap: Gets config value from properties.
getSetting() - Method in class ome.logic.LdapImpl
getSetting_async(AMD_ILdap_getSetting, Current) - Method in class ome.services.blitz.impl.LdapI
getSettings(long) - Method in class ome.services.ThumbnailCtx: Retrieves the RenderingDef object for a given Pixels ID.
getSha1() - Method in class ome.io.nio.RomioPixelBuffer
getShapeCount() - Method in class pojos.ROIData: Returns the number of shapes in the ROI.
getShapeIds(long) - Method in class ome.services.roi.GeomTool
getShapes(int, int) - Method in class pojos.ROIData: Returns the list of shapes on a given plane.
getShapeSettings() - Method in class pojos.ShapeData: Returns the settings associated to the shape.
getShapesInRange(ROICoordinate, ROICoordinate) - Method in class pojos.ROIData: Returns an iterator of the Shapes in the ROI in the range [start, end].
getShapeStats_async(AMD_IRoi_getShapeStats, long, Current) - Method in class ome.services.blitz.impl.RoiI
getShapeStatsList_async(AMD_IRoi_getShapeStatsList, List<Long>, Current) - Method in class ome.services.blitz.impl.RoiI
getShare(long) - Method in interface ome.api.IShare: Gets a share as a Session with all related: comments, members, fully loaded.
getShare(long) - Method in class ome.services.sharing.ShareBean
getShare_async(AMD_IShare_getShare, long, Current) - Method in class ome.services.blitz.impl.ShareI
getShareIfAccessible(long) - Method in class ome.services.sharing.ShareBean: Loads share and checks it's owner and member data against the current context (owner/member/admin).
getShares(long, boolean, boolean) - Method in class ome.services.sharing.BlobShareStore
getShares(long, boolean, boolean) - Method in class ome.services.sharing.FreezeShareStore
getShares(long, boolean, boolean) - Method in class ome.services.sharing.ShareStore
getShareService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getShareService() - Method in class ome.system.ServiceFactory
getSharesOwnedBy(Experimenter, boolean) - Method in interface ome.api.IShare: Gets all shares owned by the given Experimenter.
getSharesOwnedBy(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
getSharesOwnedBy_async(AMD_IShare_getSharesOwnedBy, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
getSize() - Method in class ome.util.mem.CopiableArray: Returns the number of elements in the array.
getSizeC() - Method in class ome.io.nio.DeltaVision
getSizeC() - Method in class ome.io.nio.DeltaVisionHeader: Returns the number of channels
getSizeC() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getSizeC() - Method in interface ome.io.nio.PixelBuffer: Delegates to Pixels.getSizeC().
getSizeC() - Method in class ome.io.nio.RomioPixelBuffer
getSizeC() - Method in class pojos.PixelsData: Returns the number of channels.
getSizeT() - Method in class ome.io.nio.DeltaVision
getSizeT() - Method in class ome.io.nio.DeltaVisionHeader: Returns the number of timepoints taken
getSizeT() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getSizeT() - Method in interface ome.io.nio.PixelBuffer: Delegates to Pixels.getSizeT().
getSizeT() - Method in class ome.io.nio.RomioPixelBuffer
getSizeT() - Method in class pojos.PixelsData: Returns the number of time-points.
getSizeX() - Method in class ome.io.nio.DeltaVision
getSizeX() - Method in class ome.io.nio.DeltaVisionHeader: Returns the width (no. of X pixels) of a single plane image
getSizeX() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getSizeX() - Method in interface ome.io.nio.PixelBuffer: Delegates to Pixels.getSizeX().
getSizeX() - Method in class ome.io.nio.RomioPixelBuffer
getSizeX() - Method in class pojos.OTFData: Returns the size along the X-axis.
getSizeX() - Method in class pojos.PixelsData: Returns the number of pixels along the X-axis.
getSizeX1() - Method in class omeis.providers.re.RGBBuffer: Returns the number of pixels on the X1-axis.
getSizeX2() - Method in class omeis.providers.re.RGBBuffer: Returns the number of pixels on the X2-axis.
getSizeY() - Method in class ome.io.nio.DeltaVision
getSizeY() - Method in class ome.io.nio.DeltaVisionHeader: Returns the height (no. of Y pixels) of a single plane image
getSizeY() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getSizeY() - Method in interface ome.io.nio.PixelBuffer: Delegates to Pixels.getSizeY().
getSizeY() - Method in class ome.io.nio.RomioPixelBuffer
getSizeY() - Method in class pojos.OTFData: Returns the size along the Y-axis.
getSizeY() - Method in class pojos.PixelsData: Returns the number of pixels along the Y-axis.
getSizeZ() - Method in class ome.io.nio.DeltaVision
getSizeZ() - Method in class ome.io.nio.DeltaVisionHeader: Returns the number of focal points (Z-dimension) taken
getSizeZ() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getSizeZ() - Method in interface ome.io.nio.PixelBuffer: Delegates to Pixels.getSizeZ().
getSizeZ() - Method in class ome.io.nio.RomioPixelBuffer
getSizeZ() - Method in class pojos.PixelsData: Returns the number of pixels along the Z-axis.
getSlice() - Method in class omeis.providers.re.data.PlaneDef: Returns an identifier to tell which kind of plane this object identifies.
getStack(int, int) - Method in interface ome.api.RawPixelsStore
getStack(Integer, Integer) - Method in class ome.io.nio.DeltaVision
getStack(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getStack(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStack(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
getStack(int, int) - Method in class ome.services.RawPixelsBean
getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.DeltaVision
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getStackDirect(Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
getStackOffset(int, int) - Method in interface ome.api.RawPixelsStore
getStackOffset(Integer, Integer) - Method in class ome.io.nio.DeltaVision
getStackOffset(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getStackOffset(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStackOffset(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
getStackOffset(int, int) - Method in class ome.services.RawPixelsBean
getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getStackSize() - Method in interface ome.api.RawPixelsStore
getStackSize() - Method in class ome.io.nio.DeltaVision
getStackSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getStackSize() - Method in interface ome.io.nio.PixelBuffer: Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStackSize() - Method in class ome.io.nio.RomioPixelBuffer
getStackSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
getStackSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService: Get the stack size of the current image.
getStackSize() - Method in class ome.services.RawPixelsBean
getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getStageLabelId() - Method in class pojos.ImageAcquisitionData: Returns the id of the StageLabel or -1 if not already linked to the image.
getStartTime() - Method in class omero.sys.ParametersI: Returns the value of the start time parameter.
getStartTime() - Method in class pojos.PlateAcquisitionData: Returns the time when the first image was collected.
getStartTime() - Method in class pojos.WellSampleData: Returns the time at which the field was acquired.
getStatefulServiceCount() - Method in class ome.services.blitz.impl.ServiceFactoryI: NB: Much of the logic here is similar to ServiceFactoryI.doClose and should be pushed down.
getStatefulServices() - Method in class omero.client: Returns all active StatefulServiceInterface proxies.
getStats() - Method in class ome.security.basic.CurrentDetails
getStats(List<Long>) - Method in class ome.services.roi.GeomTool
getStats() - Method in class omeis.providers.re.Renderer: Returns a RenderingStats object that the rendering strategy can use to track performance.
getStats() - Method in class omeis.providers.re.RenderingStats: Returns a stats report ready to be written to the log file.
getStatus() - Method in class pojos.PlateData: Returns the status of the plate.
getStore() - Method in class ome.services.fulltext.SimpleLuceneOptions
getStrategy(QuantumDef, PixelsType) - Method in class omeis.providers.re.quantum.QuantumFactory: Returns a strategy to carry out the quantization process whose context is defined by pd.
getStrokeColor() - Method in class pojos.ShapeSettingsData: Returns the color of the stroke.
getStrokeDashArray() - Method in class pojos.ShapeSettingsData: Returns the stroke dashes.
getStrokeWidth() - Method in class pojos.ShapeSettingsData: Returns the stroke's width.
getSubSpec() - Method in class ome.services.delete.DeleteEntry
getSubtypeValue(int, int, Object) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: uses the ClassMetadata for this ExtendedMetadata.Locks tp retrieve the component value.
getSuperSpec() - Method in class ome.services.delete.BaseDeleteSpec
getSuperSpec() - Method in class ome.services.delete.DeleteEntry
getSuperSpec() - Method in interface ome.services.delete.DeleteSpec: Specification of where this DeleteSpec is attached under another .
getSystemGroupId() - Method in class ome.system.Roles
getSystemGroupName() - Method in class ome.system.Roles
getT() - Method in class omeis.providers.re.data.PlaneDef: Returns the timepoint.
getT() - Method in class pojos.ShapeData: Returns the timepoint.
getTable() - Method in class ome.services.blitz.measurements.MeasurementStore
getTable() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore: Returns the Table proxy which is in use by this service.
getTable_async(AMD_IRoi_getTable, long, Current) - Method in class ome.services.blitz.impl.RoiI
getTagAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getTagAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTagAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTagAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTagAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTagDescription() - Method in class pojos.TagAnnotationData: Returns the description of the tag.
getTagDescriptions() - Method in class pojos.TagAnnotationData: Returns the descriptions linked to that tag.
getTaggedObjectsCount(Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Returns a map whose key is a tag's id and the value the number of Projects, Datasets, and Images linked to that tag.
getTaggedObjectsCount(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
getTaggedObjectsCount_async(AMD_IMetadata_getTaggedObjectsCount, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
getTags() - Method in class pojos.TagAnnotationData: Returns the collection of tags related to this tag.
getTagValue() - Method in class pojos.TagAnnotationData: Returns the text of the tag.
getTargetType(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Returns the IObject type which a given field points to.
getTempDir() - Method in class omero.util.TempFileManager: Returns the directory under which all temporary files and folders will be created.
getTemperature() - Method in class pojos.ImageAcquisitionData: Returns the temperature in Celcius.
getTerm() - Method in class pojos.TermAnnotationData: Returns the term.
getTermAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getTermAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTermAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTermAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTermAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTermDescription() - Method in class pojos.TermAnnotationData: Returns the description of the term.
getTermVector() - Method in class ome.services.fulltext.SimpleLuceneOptions
getTestIds() - Method in class ome.tools.RepositoryTask: Private method used for testing only.
getText() - Method in class pojos.EllipseData: Returns the text of the shape.
getText() - Method in class pojos.LineData: Returns the text of the shape.
getText() - Method in class pojos.MaskData: Returns the text of the shape.
getText() - Method in class pojos.PointData: Returns the text of the shape.
getText() - Method in class pojos.PolygonData: Returns the text of the shape.
getText() - Method in class pojos.PolylineData: Returns the text of the shape.
getText() - Method in class pojos.RectangleData: Returns the text of the shape.
getText() - Method in class pojos.ShapeSettingsData: Returns the stroke.
getText() - Method in class pojos.TextData: Returns the text of the shape.
getText() - Method in class pojos.TextualAnnotationData: Returns the text of this annotation.
getThumbnail(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnail(Thumbnail) - Method in class ome.io.nio.ThumbnailService: Return byte array of Thumbnail
getThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService: Return byte array of Thumbnail, providing byte array
getThumbnail(long, RInt, RInt, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getThumbnail(long, RInt, RInt) - Method in interface ome.services.blitz.gateway.services.ImageService: Get the thumbnail of the image.
getThumbnail(long, RInt, RInt) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
getThumbnail(long, RInt, RInt) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl
getThumbnail(long, RInt, RInt) - Method in interface ome.services.blitz.gateway.services.ThumbnailService: Get the thumbnail of the image.
getThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
getThumbnail_async(AMD_ThumbnailStore_getThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailByLongestSide(Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailByLongestSide(long, RInt) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl
getThumbnailByLongestSide(long, RInt) - Method in interface ome.services.blitz.gateway.services.ThumbnailService: Get the thumbnail of the image, maintain aspect ratio.
getThumbnailByLongestSide(Integer) - Method in class ome.services.ThumbnailBean
getThumbnailByLongestSide_async(AMD_ThumbnailStore_getThumbnailByLongestSide, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailByLongestSideDirect(Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailByLongestSideDirect(Integer) - Method in class ome.services.ThumbnailBean
getThumbnailByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailByLongestSideDirect, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore: Retrieves a number of thumbnails for pixels sets using given sets of rendering settings (RenderingDef).
getThumbnailByLongestSideSet(RInt, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl
getThumbnailByLongestSideSet(RInt, List<Long>) - Method in interface ome.services.blitz.gateway.services.ThumbnailService: Get a set of thumbnails, maintaining aspect ratio.
getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
getThumbnailByLongestSideSet_async(AMD_ThumbnailStore_getThumbnailByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailDirect(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailDirect(Integer, Integer) - Method in class ome.services.ThumbnailBean
getThumbnailDirect_async(AMD_ThumbnailStore_getThumbnailDirect, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailExists(Thumbnail) - Method in class ome.io.nio.ThumbnailService: Returns whether or not a thumbnail exists on disk.
getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) for a particular section.
getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in class ome.services.ThumbnailBean
getThumbnailForSectionByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailForSectionByLongestSideDirect, int, int, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) for a particular section.
getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in class ome.services.ThumbnailBean
getThumbnailForSectionDirect_async(AMD_ThumbnailStore_getThumbnailForSectionDirect, int, int, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailIds() - Method in class ome.tools.RepositoryTask: This public method is used to return a list of thumbnail ids that require deletion from the disk repository.
getThumbnailLength(Thumbnail) - Method in class ome.io.nio.ThumbnailService: Returns length of Thumbnail on disk
getThumbnailOutputStream(Thumbnail) - Method in class ome.io.nio.ThumbnailService: Return FileOutputStream of Thumbnail
getThumbnailPath(Long) - Method in class ome.io.nio.AbstractFileSystemService
getThumbnailSet(Integer, Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore: Retrieves a number of thumbnails for pixels sets using given sets of rendering settings (RenderingDef).
getThumbnailSet(RInt, RInt, List<Long>, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
getThumbnailSet(RInt, RInt, List<Long>) - Method in interface ome.services.blitz.gateway.services.ImageService: Get a set of thumbnails.
getThumbnailSet(RInt, RInt, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
getThumbnailSet(RInt, RInt, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl
getThumbnailSet(RInt, RInt, List<Long>) - Method in interface ome.services.blitz.gateway.services.ThumbnailService: Get a set of thumbnails.
getThumbnailSet(Integer, Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
getThumbnailSet_async(AMD_ThumbnailStore_getThumbnailSet, RInt, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailStoreService() - Method in class ome.services.blitz.gateway.services.GatewayFactory: Return the thumbnail service.
getTie(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI
getTime() - Method in class pojos.TimeAnnotationData: Returns the time value.
getTimelineService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getTimepoint(int) - Method in interface ome.api.RawPixelsStore
getTimepoint(Integer) - Method in class ome.io.nio.DeltaVision
getTimepoint(Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getTimepoint(Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
getTimepoint(Integer) - Method in class ome.io.nio.RomioPixelBuffer
getTimepoint(int) - Method in class ome.services.RawPixelsBean
getTimePoint() - Method in class pojos.ROICoordinate: Returns the timepoint.
getTimepoint_async(AMD_RawPixelsStore_getTimepoint, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.DeltaVision
getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getTimepointDirect(Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
getTimepointOffset(int) - Method in interface ome.api.RawPixelsStore
getTimepointOffset(Integer) - Method in class ome.io.nio.DeltaVision
getTimepointOffset(Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getTimepointOffset(Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
getTimepointOffset(Integer) - Method in class ome.io.nio.RomioPixelBuffer
getTimepointOffset(int) - Method in class ome.services.RawPixelsBean
getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getTimepointSize() - Method in interface ome.api.RawPixelsStore
getTimepointSize() - Method in class ome.io.nio.DeltaVision
getTimepointSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getTimepointSize() - Method in interface ome.io.nio.PixelBuffer: Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
getTimepointSize() - Method in class ome.io.nio.RomioPixelBuffer
getTimepointSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
getTimepointSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService: Get the timepoint size of the current image.
getTimepointSize() - Method in class ome.services.RawPixelsBean
getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getTimestampAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getTimestampAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTimestampAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTimestampAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTimestampAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTopicManager() - Method in class ome.services.blitz.util.BlitzConfiguration
getTotalDeletedCount() - Method in class ome.services.delete.DeleteState: Return the total number of ids which were deleted.
getTotalFoundCount() - Method in class ome.services.delete.DeleteState: Return the total number of ids loaded into this instance.
getTotalSize() - Method in interface ome.api.RawPixelsStore
getTotalSize() - Method in class ome.io.nio.DeltaVision
getTotalSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getTotalSize() - Method in interface ome.io.nio.PixelBuffer: Retrieves the in memory size of the entire pixel buffer.
getTotalSize() - Method in class ome.io.nio.RomioPixelBuffer
getTotalSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
getTotalSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService: Get the total size of the current image.
getTotalSize() - Method in class ome.services.RawPixelsBean
getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getTransactionAttribute(Method, Class) - Method in class ome.services.sharing.ShareRestrictionTransactionAttributeSource
getTransactionAttribute(Method, Class) - Method in class ome.tools.spring.ForceTransactionAttributeSource
getTransform() - Method in class pojos.ShapeData: Returns the transformation.
getTransmittance() - Method in class pojos.FilterData: Returns the cut out tolerance value or -1.
getType(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
getType() - Method in class pojos.DetectorData: Returns the type of the detector.
getType() - Method in class pojos.FilterData: Returns the type.
getType() - Method in class pojos.LightSourceData: Returns the type of light.
getTypesService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getTypesService() - Method in class ome.system.ServiceFactory
getUnique() - Method in class omero.sys.ParametersI
getUntied(Identity) - Method in class ome.services.blitz.util.ServantHolder
getUpdated() - Method in class pojos.DataObject: Returns the updated time of the object.
getUpdateEvent(Current) - Method in class omero.model.DetailsI
getUpdateService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getUpdateService() - Method in class ome.system.ServiceFactory
getUpgradeUrl() - Method in class ome.system.UpgradeCheck
getUpperLimit() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the constant level for bit-planes > planeSelected w.r.t the higher-order bits.
getUsageFraction() - Method in interface ome.api.IRepositoryInfo: This method returns a double of the used space divided by the free space.
getUsageFraction() - Method in class ome.logic.RepositoryInfoImpl
getUsageFraction_async(AMD_IRepositoryInfo_getUsageFraction, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
getUsedSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo: This method returns the total space in bytes for this file system including nested subdirectories.
getUsedSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl
getUsedSpaceInKilobytes_async(AMD_IRepositoryInfo_getUsedSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
getUserAttribute(String) - Method in class ome.security.auth.LdapConfig
getUserFilter() - Method in class ome.security.auth.LdapConfig
getUserGroupId() - Method in class ome.system.Roles
getUserGroupName() - Method in class ome.system.Roles
getUserId() - Method in class ome.services.ThumbnailCtx: Retrieves the current user ID to use for queries.
getUserImages(Parameters) - Method in interface ome.api.IContainer: Retrieve a user's images.
getUserImages(Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
getUserImages_async(AMD_IContainer_getUserImages, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
getUserName() - Method in class pojos.ExperimenterData: Returns the last name of the experimenter.
getUserPasswordHash(Long) - Method in class ome.security.auth.PasswordUtil
getUserRoles(Experimenter) - Method in interface ome.api.local.LocalAdmin: Finds the group names for all groups for which the given Experimenter is a member.
getUserRoles(Experimenter) - Method in class ome.logic.AdminImpl
getUserRoles() - Method in interface ome.services.sessions.SessionContext
getUserRoles() - Method in class ome.services.sessions.SessionContextImpl
getUserRoles(String) - Method in interface ome.services.sessions.SessionManager
getUserRoles(String) - Method in class ome.services.sessions.SessionManagerImpl
getUserScripts_async(AMD_IScript_getUserScripts, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI
getUuid() - Method in class ome.services.db.DatabaseIdentity
getUuid() - Method in class ome.services.scripts.ScriptRepoHelper: Uuid of this repository.
getUuid() - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
getValue() - Method in class pojos.BooleanAnnotationData: Returns the text of this annotation.
getVersion() - Method in interface ome.api.IConfig: Provides the release version.
getVersion() - Method in class ome.logic.ConfigImpl: see IConfig.getVersion()
getVersion() - Method in class pojos.DataObject: Returns the version of the object if the object is immutable, false otherwise.
getVersion_async(AMD_IConfig_getVersion, Current) - Method in class ome.services.blitz.impl.ConfigI
getVisibility() - Method in class ome.system.Preference
getVoltage() - Method in class pojos.DetectorData: Returns the voltage of the detector.
getWavelength() - Method in exception omeis.providers.re.quantum.QuantizationException: Returns the index of the wavelength that couldn't be rendered.
getWellOriginX() - Method in class pojos.PlateData: Returns the x-coordinate in 2D-space of the well.
getWellOriginY() - Method in class pojos.PlateData: Returns the y-coordinate in 2D-space of the well.
getWellSamples() - Method in class pojos.WellData: Returns the well samples linked to the well.
getWellType() - Method in class pojos.WellData: Returns a human readable identifier for the screening status e.g. empty, positive control, etc.
getWidth() - Method in class pojos.MaskData: Returns the width of the mask.
getWidth() - Method in class pojos.RectangleData: Returns the width untransformed rectangle.
getWindowEnd() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the upper bound of the input interval.
getWindowStart() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the lower bound of the input interval.
getWorkingDistance() - Method in class pojos.ObjectiveData: Returns the working distance.
getX() - Method in class omeis.providers.re.data.PlaneDef: Returns the index of the plane in the set identified by this object.
getX() - Method in class pojos.EllipseData: Returns the x-coordinate of the center of the ellipse.
getX() - Method in class pojos.MaskData: Returns the x-coordinate of the top-left corner of the mask.
getX() - Method in class pojos.PointData: Returns the x-coordinate of the shape.
getX() - Method in class pojos.RectangleData: Returns the x-coordinate of the top-left corner of an untransformed rectangle.
getX() - Method in class pojos.TextData: Returns the x-coordinate text field.
getX1() - Method in class pojos.LineData: Returns the x-coordinate of the starting point of an untransformed line.
getX2() - Method in class pojos.LineData: Returns the x-coordinate of the end point of an untransformed line.
getXEnd() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the x-coordinate of the pEnd point.
getXMLAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getXMLAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getXMLAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getXMLAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getXMLAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getXStart() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the x-coordinate of the pStart point.
getY() - Method in class omeis.providers.re.data.PlaneDef: Returns the index of the plane in the set identified by this object.
getY() - Method in class pojos.EllipseData: Returns the y-coordinate of the center of the ellipse.
getY() - Method in class pojos.MaskData: Returns the y-coordinate of the top-left corner of the mask.
getY() - Method in class pojos.PointData: Returns the y coordinate of the shape.
getY() - Method in class pojos.RectangleData: Returns the y-coordinate of the top-left corner of an untransformed rectangle.
getY() - Method in class pojos.TextData: Returns the y-coordinate text field.
getY1() - Method in class pojos.LineData: Returns the y-coordinate of the starting point of an untransformed line.
getY2() - Method in class pojos.LineData: Returns the y-coordinate of the end point of an untransformed line.
getYEnd() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-coordinate of the pEnd point.
getYStart() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-coordinate of the pStart point.
getZ() - Method in class omeis.providers.re.data.PlaneDef: Returns the index of the plane in the set identified by this object.
getZ() - Method in class pojos.ShapeData: Returns the z-section.
getZoom() - Method in class pojos.DetectorData: Returns the offset of the detector.
getZSection() - Method in class pojos.ROICoordinate: Returns the z-section.
GlobalMulticaster - Class in ome.services.messages: Global ApplicationEventMulticaster which can be used to integrate parent and child OmeroContext instances.
GlobalMulticaster() - Constructor for class ome.services.messages.GlobalMulticaster: Keeps track of which instance this is.
granted(int, int) - Method in class omero.model.PermissionsI
GREEN_INDEX - Static variable in class omeis.providers.re.ColorsFactory: Index of the red component of a color.
group - Variable in class ome.system.Principal
GROUP_EXPERIMENTER_MAP - Static variable in class pojos.ExperimenterData: Identifies the Experimenter#GROUPEXPERIMENTERMAP field.
GROUP_EXPERIMENTER_MAP - Static variable in class pojos.GroupData: Identifies the ExperimenterGroup#GROUPEXPERIMENTERMAP field.
GroupAttributeMapper - Class in ome.security.auth
GroupAttributeMapper(LdapConfig) - Constructor for class ome.security.auth.GroupAttributeMapper
GroupData - Class in pojos: The data that makes up an OME Group along with the various members of the Group
GroupData() - Constructor for class pojos.GroupData: Creates a new instance.
GroupData(ExperimenterGroup) - Constructor for class pojos.GroupData: Creates a new instance.
groupPermissions - Variable in class ome.system.SimpleEventContext
groupProxy(Long) - Method in interface ome.api.local.LocalAdmin: returns a possibly uninitialized proxy for the given group id.
groupProxy(String) - Method in interface ome.api.local.LocalAdmin: returns a possibly uninitialized proxy for the given group name.
groupProxy(Long) - Method in class ome.logic.AdminImpl
groupProxy(String) - Method in class ome.logic.AdminImpl
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.AttributeNewUserGroupBean
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in interface ome.security.auth.NewUserGroupBean
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.QueryNewUserGroupBean
grp(RLong) - Method in class omero.sys.ParametersI: Sets the value of the group parameter.
GUEST - Static variable in class ome.system.Login: CopyOfLogin constant which has username and password values set to null and other values set to their default.
GUEST - Static variable in class pojos.GroupData: Identifies the Guest group.
guests - Variable in class ome.services.sharing.data.ShareData
guests - Variable in class ome.services.sharing.data.ShareItem

H

Handle - Class in ome.util.mem: Provides the basic machinery to share the same logical state across objects with different identities.
Handle(Copiable) - Constructor for class ome.util.mem.Handle: Subclasses use this constructor to specify the Body instance this handle will be paired up with.
handle - Variable in class omero.grid.DeleteCallbackI: Proxy passed to this instance on creation.
handle(int, int) - Method in interface omero.model.SmartShape.PointCallback
handleException(Throwable, String) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities: Helper method to handle exceptions thrown by the connection library.
handleException(Throwable) - Method in class ome.services.blitz.impl.ServiceFactoryI
handleException(Throwable, OmeroContext) - Method in class omero.util.IceMapper
handleInput(Class<?>, Object) - Method in class omero.util.IceMapper
handleLsid(IObject) - Method in class ome.services.blitz.impl.OmeroMetadata
handleOutput(Class, Object) - Method in class omero.util.IceMapper
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.ConfigRedirector
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.NullRedirector: Does nothing.
handleRingShutdown(Redirector.Context, String) - Method in interface ome.services.blitz.redirect.Redirector: Gives the Redirector a chance to remove the current Ring when it is being shutdown.
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.ScaleRedirector: Nothing needs to be done on shutdown, since the Ring implementation will properly disable the Node table queried during the next call to Redirector.getProxyOrNull(Context, String, Glacier2.SessionControlPrx, Ice.Current)
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
hasAlias(String) - Method in class ome.system.Preference
hasDectector() - Method in class pojos.ChannelAcquisitionData: Returns true if there is a detector for that channel, false otherwise.
hasEmissionData(LogicalChannel) - Static method in class omeis.providers.re.ColorsFactory: Returns true if the channel has emission metadata, false otherwise.
hasFilter() - Method in class pojos.ChannelAcquisitionData: Returns true if there is a filter set linked to the channel false otherwise.
hash - Variable in class ome.security.auth.ConfigurablePasswordProvider: Hash implementation to use for encoding passwords to check and changed passwords.
hashCode() - Method in class ome.tools.FileSystem: Public hashcode implementation based on String hash() return
hashCode(Object) - Method in class ome.tools.hibernate.ArrayStringType
hashCode(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
hashCode(Object) - Method in class ome.tools.hibernate.PermissionsType
hashCode() - Method in class ome.util.math.geom2D.Line: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class ome.util.math.geom2D.PlanePoint: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class ome.util.math.geom2D.Segment: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class omeis.providers.re.data.PlaneDef: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class pojos.ROICoordinate: Calculate the hashCode for the data, The hashcode is generated by bitshifting z by ZTBITSPLIT bits and adding t.
hasIris() - Method in class pojos.ObjectiveData: Returns a boolean flag if the value has been set, null otherwise.
hasLightPath() - Method in class pojos.ChannelAcquisitionData: Returns true if there is a light path described for that channel, false otherwise.
hasMetadata(long) - Method in class ome.services.ThumbnailCtx: Whether or not thumbnail metadata is available for a given Pixels ID.
hasNext() - Method in interface ome.api.Search: Returns true if another call to Search.next() is valid.
hasNext() - Method in class ome.services.delete.BaseDeleteSpec.SubSpecIterator
hasNext() - Method in class ome.services.fulltext.EventLogLoader: Tests for available objects.
hasNext() - Method in class ome.services.SearchBean
hasNext_async(AMD_Search_hasNext, Current) - Method in class ome.services.blitz.impl.SearchI
hasntSeen(Object) - Method in class omero.util.IceMapper
hasOpticalAxisAveraged() - Method in class pojos.OTFData: Returns a boolean flag if the value has been set
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
hasPrivilegedToken(IObject) - Method in class ome.security.basic.BasicSecuritySystem: See {@link TokenHolder#hasPrivilegedToken(IObject)
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
hasPump() - Method in class pojos.LightSourceData: Returns true if the light source is a laser with a pump, false otherwise.
hasReplacement(Object) - Method in class ome.tools.hibernate.UpdateFilter
hasSession() - Method in class ome.system.SessionInitializer
hasSettings(long) - Method in class ome.services.ThumbnailCtx: Whether or not settings are available for a given Pixels ID.
hasShapes - Variable in class ome.services.roi.GeomTool
hasSubtypes(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: returns true if this offset points to a field which is an embedded component.
header - Variable in class ome.io.nio.DeltaVision
help(String[]) - Static method in class prefs: Returns a help string array.
helper - Variable in class ome.services.blitz.impl.ScriptI
Helper - Class in ome.services.blitz.measurements: Parallel type hierarchy to Column to facilitate (and speed-up) working with columns without adding methods to the slice definitions.
Helper() - Constructor for class ome.services.blitz.measurements.Helper
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 Hiberante array.
HibernateUtils() - Constructor for class ome.tools.hibernate.HibernateUtils
Hidden - Annotation Type in ome.annotations: annotation which specifies that a method parameter (e.g. a password) must be hidden from logging output.
Hierarchy - Class in ome.services.query: single-point of entry for walking of OME container hierarchies.
Hierarchy() - Constructor for class ome.services.query.Hierarchy
HierarchyTransformations - Class in ome.tools
HierarchyTransformations() - Constructor for class ome.tools.HierarchyTransformations
HqlQuery - Class in ome.services.search: Delegate to IQuery.findAllByQuery(String, Parameters).
HqlQuery(SearchValues, String, Parameters) - Constructor for class ome.services.search.HqlQuery
HTM - Static variable in class pojos.FileAnnotationData: Identifies the HTM file formats.
HTML - Static variable in class pojos.FileAnnotationData: Identifies the HTML file formats.

I

IAdmin - Interface in ome.api: Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.
IAnalysis - Interface in ome.api: Provides access to the model objects involved in analysis.
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.ShareData
ice_staticId() - Static method in class ome.services.sharing.data.ShareItem
IceMapper - Class in omero.util: Responsible for the mapping of ome.* types to omero.* types and back again.
IceMapper() - Constructor for class omero.util.IceMapper
IceMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.IceMapper
IceMapper.ReturnMapping - Interface in omero.util
IceMethodInvoker - Class in ome.services.blitz.util: Method-cache primed either with an ServiceInterface instance or with a Class with generic type ServiceInterface.
IceMethodInvoker(ServiceInterface, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker: Create an IceMethodInvoker instance using the Class of the passed argument to call IceMethodInvoker#IceMethodInvoker(Class).
IceMethodInvoker(Class<S>, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker: Creates an IceMethodInvoker instance by using reflection on the Class argument.
IConfig - Interface in ome.api: Access to server configuration.
IContainer - Interface in ome.api: Provides methods for dealing with the core "Pojos" of OME.
id - Variable in class ome.services.delete.BaseDeleteSpec: The id of the root type which will be deleted.
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
idCount(long) - Method in class ome.services.sharing.data.ShareMap
IDelete - Interface in ome.api: Provides simplifed methods for deleting instances from the database.
IdentityMapContext - Class in omeis.providers.re.codomain: An empty context for the identity map.
IdentityMapContext() - Constructor for class omeis.providers.re.codomain.IdentityMapContext
idEqual(IObject, IObject) - Static method in class ome.tools.hibernate.HibernateUtils: returns true under the following circumstatnces: both arguments are null, or both arguments are identical (==), or both arguments have the same id value(equals)
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(SimpleJdbcOperations) - 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) if the user is unknown, otherwise a Boolean.FALSE.
ILdap - Interface in ome.api: Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.
IllegalArgumentException - Exception in omero
IllegalArgumentException(String) - Constructor for exception omero.IllegalArgumentException
IMAGE - Static variable in class pojos.PixelsData: Identifies the Pixels#IMAGE field.
IMAGE_LINKS - Static variable in class pojos.DatasetData: Identifies the Dataset#IMAGELINKS field.
IMAGE_QUERY - Static variable in class ome.services.delete.DeleteBean: Loads an Image graph including: Pixels, Channel, LogicalChannel, StatsInfo, PlaneInfo, Thumbnails, file maps, OriginalFiles, and Settings
ImageAcquisitionData - Class in pojos: Object hosting the acquisition metadata.
ImageAcquisitionData(Image) - Constructor for class pojos.ImageAcquisitionData: Creates a new instance.
ImageData - Class in pojos: The data that makes up an OME Image along with links to its Pixels, enclosing Datasets, and the Experimenter that owns this Image.
ImageData() - Constructor for class pojos.ImageData: Creates a new instance.
ImageData(Image) - Constructor for class pojos.ImageData: Creates a new instance.
ImageService - Interface in ome.services.blitz.gateway.services
ImageServiceImpl - Class in ome.services.blitz.gateway.services.impl
ImageServiceImpl(GatewayFactory) - Constructor for class ome.services.blitz.gateway.services.impl.ImageServiceImpl: Instantiate the imageService with the serviceFactory.
IMetadata - Interface in ome.api: Provides method to interact with acquisition metadata and annotations.
ImportProcessor - Class in ome.services.procs
ImportProcessor() - Constructor for class ome.services.procs.ImportProcessor
in(String[]) - Method in class ome.io.nio.PixelData: Returns whether or not the pixel data type is is one of the elements in an array.
in(PixelsType, String[]) - Static method in class omeis.providers.re.data.PlaneFactory: A static helper method to check if a type is one of the elements in an array.
include(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: returns true if this offset points to a field which may contain an IObject instance
increment() - Method in class ome.services.sessions.SessionContext.Count: Increment the current reference count and return the new value atomically.
increment(int) - Method in class ome.services.sessions.stats.LongCounter
index(String, String[]) - Static method in class ome.tools.hibernate.HibernateUtils
indexAllEvents() - Static method in class ome.services.fulltext.Main
indexByClass(Set<String>) - Static method in class ome.services.fulltext.Main
indexer - Variable in class ome.services.fulltext.FullTextThread
indexFullDb() - Static method in class ome.services.fulltext.Main
indexObject(IObject) - Method in interface ome.api.IUpdate: Initiates full-text indexing for the given object.
indexObject(IObject) - Method in class ome.logic.UpdateImpl
indexObject_async(AMD_IUpdate_indexObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
init(ObjectAdapter, String) - Method in class ome.services.blitz.fire.Ring: Typically called from within BlitzConfiguration after the communicator and adapter have been properly setup.
init() - 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.
initFile(String) - Method in class ome.services.formats.OmeroReader
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()
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(Session) - Method in class ome.services.blitz.impl.OmeroMetadata
initialize(String[], String[], Class[], Map<String, Object>) - Method in class ome.services.blitz.measurements.MeasurementStore
initialize(String[], String[], Class[], Map<String, Object>) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
initialize(long, String, Map<String, String>) - Method in class ome.services.delete.AnnotationDeleteSpec
initialize(long, String, Map<String, String>) - Method in class ome.services.delete.BaseDeleteSpec
initialize(long, String, Map<String, String>) - Method in class ome.services.delete.DeleteEntry: Called during DeleteSpec.initialize(long, String, Map) to give the entry a chance to modify its #op based on the options and to initialize subspecs.
initialize(long, String, Map<String, String>) - Method in interface ome.services.delete.DeleteSpec: Called as each delete command is started.
initialize() - Method in class ome.services.fulltext.PersistentEventLogLoader: Called when the configuration database does not contain a valid current_id.
initializeRedirect(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector: Set the new redirect value if null, or if the uuid is null or empty, then the existing redirect will be removed.
initializeUserAttributes(MethodInvocation, ServiceFactory, Principal, boolean) - 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
InMemoryPlanarPixelBuffer - Class in ome.io.nio: Class implementation of the PixelBuffer interface for in memory planar pixel data.
InMemoryPlanarPixelBuffer(Pixels, byte[][][][]) - Constructor for class ome.io.nio.InMemoryPlanarPixelBuffer: Constructs an in memory pixel buffer based on a defined dimensionality.
INNER_JOIN - Static variable in class ome.services.query.Query: imported constant for ease of use
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
insert - Variable in class ome.services.fulltext.PersistentEventLogLoader: String use with parameters 'name', and 'value' to insert a new current id
insertStatement - Static variable in class ome.services.util.DBEnumCheck
INSIGHT_PUBLISHED_NS - Static variable in class pojos.BooleanAnnotationData: The name space used to indicate that the tag is used a tag set.
INSIGHT_RATING_NS - Static variable in class pojos.RatingAnnotationData: The name space used to identify the archived annotation linked to a set of pixels.
INSIGHT_TAGSET_NS - Static variable in class pojos.TagAnnotationData: The name space used to indicate that the tag is used a tag set.
instantiate(String, EntityMode, Serializable) - Method in class ome.security.basic.OmeroInterceptor: default logic, but we may want to use them eventually for dependency-injection.
INSTITUTION - Static variable in class pojos.ExperimenterData: Identifies the Experimenter#INSTITUTION field.
InstrumentData - Class in pojos: Hosts the instrument used to capture an image.
InstrumentData(Instrument) - Constructor for class pojos.InstrumentData: Creates a new instance.
INT - Static variable in class ome.io.nio.PixelData: Identifies the type used to store pixel values.
INT - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
INT16 - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the INT16 data type used to store pixel values, as per OME spec.
INT16_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
INT32 - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the INT32 data type used to store pixel values, as per OME spec.
INT32_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
INT8 - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the INT8 data type used to store pixel values, as per OME spec.
INT8_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
INT_16 - Static variable in class omerojava.util.PixelTypes: Identifies the type used to store pixel values.
INT_32 - Static variable in class omerojava.util.PixelTypes: Identifies the type used to store pixel values.
INT_8 - Static variable in class omerojava.util.PixelTypes: Identifies the type used to store pixel values.
IntConverter - Class in omerojava.util: Packs a sequence of bytes representing a signed (2's complement) big-endian integer into an integer value of appropriate integer value.
IntConverter() - Constructor for class omerojava.util.IntConverter
InteractiveProcessorI - Class in omero.grid: Processor implementation which delegates to an omero.grid.Processor servant.
InteractiveProcessorI(Principal, SessionManager, Executor, ProcessorPrx, Job, long, SessionControlPrx, ParamsHelper) - Constructor for class omero.grid.InteractiveProcessorI
interceptor - Variable in class ome.security.basic.BasicSecuritySystem
internalDelete(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl
internalMerge(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl: Note if we use anything other than merge here, functionality from ome.tools.hibernate.MergeEventListener needs to be moved to UpdateFilter or to another event listener.
InternalMessage - Class in ome.util.messages: Message which can be published via OmeroContext.publishEvent(ApplicationEvent) or OmeroContext.publishMessage(InternalMessage).
InternalMessage(Object) - Constructor for class ome.util.messages.InternalMessage: Sole constructor which takes the "source" of this EventObject.
internalSave(IObject, ReloadFilter, Session) - Method in class ome.logic.UpdateImpl: Note if we use anything other than merge here, functionality from ome.tools.hibernate.MergeEventListener needs to be moved to UpdateFilter or to another event listener.
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
intersects(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
intersects(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
intersects(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
intersects(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
intervalEnd - Variable in class omeis.providers.re.codomain.CodomainMapContext: The upper bound of the codomain interval.
intervalStart - Variable in class omeis.providers.re.codomain.CodomainMapContext: The lower bound of the codomain interval.
InThreadThrottlingStrategy - Class in ome.services.throttling: Throttling implementation which uses the calling server Thread for execution.
InThreadThrottlingStrategy(CurrentDetails) - Constructor for class ome.services.throttling.InThreadThrottlingStrategy
invalidateConnection(long, Experimenter) - Method in interface ome.api.IShare: Makes the connection invalid for share for specifiec user.
invalidateConnection(long, Experimenter) - Method in class ome.services.sharing.ShareBean
invalidateConnection_async(AMD_IShare_invalidateConnection, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
invalidateCurrentEventContext() - Method in class ome.security.basic.CurrentDetails: It suffices to set the Details to a new instance to make this context unusable.
invalidateEventContext() - Method in class ome.security.basic.BasicSecuritySystem
invalidateEventContext() - Method in interface ome.security.SecuritySystem: 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 prepairing this Thread for execution and subsequently reseting it.
invoke(MethodInvocation) - Method in class ome.security.basic.NullEventHandler
invoke(MethodInvocation) - Method in class ome.services.blitz.fire.AopContextInitializer
invoke(Object, Current, IceMapper, Object...) - Method in class ome.services.blitz.util.IceMethodInvoker: Calls the method named in Current.operation with the arguments provided mapped via the IceMapper instance.
invoke(MethodInvocation) - Method in class ome.services.util.ServiceHandler
invoke(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor
invoke(MethodInvocation) - Method in class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler: delegates to HibernateInterceptor or manages sessions internally, based on the type of service.
invoker - Variable in class ome.services.blitz.impl.AbstractAmdServant: If a service is provided, then an invoker will be created to cache all of its methods.
IObjectClassQuery - Class in ome.services.query: simple query subclass which uses the Parameters.CLASS parameter value to create a Criteria and then adds Expression instances based on all other parameter names.
IObjectClassQuery(Parameters) - Constructor for class ome.services.query.IObjectClassQuery
IPixels - Interface in ome.api: Metadata gateway for the RenderingEngine and clients.
iPixels - Variable in class ome.services.projection.ProjectionBean: Reference to the service used to retrieve the pixels metadata.
IProcessManager - Interface in ome.services.procs: Manages asynchronous processing logic for all Job instances created
IProjection - Interface in ome.api: Provides methods for performing projections of Pixels sets.
IQuery - Interface in ome.api: Provides methods for directly querying object graphs.
iQuery - Variable in class ome.logic.AbstractLevel2Service
iQuery - Variable in class ome.services.AbstractStatefulBean
IRenderingSettings - Interface in ome.api: Provides method to apply rendering settings to a collection of images.
IRepositoryInfo - Interface in ome.api: Provides methods for obtaining information for server repository disk space allocation.
IResults - Interface in ome.api: Provides methods for storing, quering, and retrieving analysis results.
IResults.PixelSet - Class in ome.api
IResults.PixelSet() - Constructor for class ome.api.IResults.PixelSet
IResults.Result - Interface in ome.api
is_adminorpi - Static variable in class ome.tools.hibernate.SecurityFilter
is_nonprivate - Static variable in class ome.tools.hibernate.SecurityFilter
is_share - Static variable in class ome.tools.hibernate.SecurityFilter
isAccepted(boolean, String, String, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI: Callback method called by the remote processor instance.
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(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
isActive(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService: Is the channel active.
isActive() - Method in interface ome.services.procs.Process
isActive() - Method in class ome.services.procs.ProcessSkeleton
isActive(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
isActive(int) - Method in interface omeis.providers.re.RenderingEngine: Returns true if the channel is mapped, false otherwise.
isActive() - Method in class pojos.ExperimenterData: Returns true if the experimenter is active, false otherwise.
isActive_async(AMD_RenderingEngine_isActive, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
isAdmin - Variable in class ome.system.SimpleEventContext
isAllowLeadingWildcard() - Method in interface ome.api.Search: Returns the current leading-wildcard setting.
isAllowLeadingWildcard() - Method in class ome.services.SearchBean
isAllowLeadingWildcard_async(AMD_Search_isAllowLeadingWildcard, Current) - Method in class ome.services.blitz.impl.SearchI
isAlphalessRendering() - Method in class omeis.providers.re.Optimizations: Returns true if the alphaless rendering optimization is enabled, and false if it is not.
isArchived() - Method in class pojos.ImageData: Returns true if the image has been archived, false otherwise.
isAutoCloseEnabled() - Method in class ome.tools.hibernate.CurrentSessionContext
IScale - Interface in ome.api: Provides methods for performing scaling (change of the image size through interpolation or other means) on BufferedImages.
isCaseSensitive() - Method in interface ome.api.Search: Returns the current case sensitivity setting.
isCaseSensitive() - Method in class ome.services.SearchBean
isCaseSensitive_async(AMD_Search_isCaseSensitive, Current) - Method in class ome.services.blitz.impl.SearchI
isClientObject() - Method in class pojos.ShapeData: Is the object one that has been created client side.
isClientSide() - Method in class pojos.ROIData: Returns true if the object a client-side object, false otherwise.
IsConstant() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the type of bit-planes mapping.
isCurrentUserAdmin() - Method in class ome.services.sessions.SessionContextImpl
isCurrentUserAdmin() - Method in interface ome.system.EventContext
isCurrentUserAdmin() - Method in class ome.system.SimpleEventContext
isDb() - Method in class ome.system.Preference
isDetectorSettingsDirty() - Method in class pojos.ChannelAcquisitionData: Returns true if the detector settings has been updated, false otherwise.
isDirectory() - Method in class pojos.FileData: Returns true if the file is a directory, false otherwise.
isDirty() - Method in class pojos.DataObject: Returns true if setter value has modified the value of the stored IObject, false otherwise.
isDisabled(String) - Method in class ome.security.basic.BasicSecuritySystem
isDisabled(String) - Method in class ome.security.basic.CurrentDetails
isDisabled(String) - Method in interface ome.security.SecuritySystem: checks if the listed id is disabled for the current Thread.
isDisabled(String) - Method in class ome.security.SecuritySystemHolder
isDisabled(String) - Method in class ome.security.sharing.SharingSecuritySystem
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
isEndTime() - Method in class omero.sys.ParametersI: Returns true if the map contains the end time parameter, false otherwise.
ISession - Interface in ome.api: Start here: Session creation service for OMERO.
isExceptionThrown() - Method in class ome.system.UpgradeCheck
isExperimenter() - Method in class omero.sys.ParametersI: Returns true if the filter contains and ownerId parameter, false otherwise.
isFloat() - Method in interface ome.api.RawPixelsStore
isFloat() - Method in class ome.io.nio.DeltaVision
isFloat() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
isFloat() - Method in interface ome.io.nio.PixelBuffer: Returns whether or not the pixel buffer has floating point pixels.
isFloat - Variable in class ome.io.nio.PixelData: If the data is floating point.
isFloat() - Method in class ome.io.nio.PixelData: Returns whether or not the data is floating point.
isFloat() - Method in class ome.io.nio.RomioPixelBuffer
isFloat(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
isFloat(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService: Are the bytes in the image floats.
isFloat() - Method in class ome.services.RawPixelsBean
isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
isFontBold() - Method in class pojos.ShapeSettingsData: Returns true if it is bold, false otherwise.
isFontItalic() - Method in class pojos.ShapeSettingsData: Returns true if it is italic, false otherwise.
isForce() - Method in class ome.services.delete.DeleteOpts
isGranted(Permissions.Role, Permissions.Right) - Static method in class ome.tools.hibernate.SecurityFilter
isGraphCritical() - Method in class ome.security.basic.BasicSecuritySystem
isGraphCritical() - Method in class ome.security.basic.CurrentDetails
isGraphCritical() - Method in interface ome.security.SecuritySystem: Determines if the current security context has the possibility of corrupting consistent graphs.
isGraphCritical() - Method in class ome.security.SecuritySystemHolder
isGraphCritical() - Method in class ome.security.sharing.SharingSecuritySystem
isGroup() - Method in class omero.sys.ParametersI: Returns true if the filter contains an groupId, false otherwise.
isGroupRead(Current) - Method in class omero.model.PermissionsI
isGroupRead() - Method in class pojos.PermissionData: Returns true if the group has read access, false otherwise.
isGroupWrite(Current) - Method in class omero.model.PermissionsI
isGroupWrite() - Method in class pojos.PermissionData: Returns true if the group has write access, false otherwise.
isHard() - Method in class ome.services.messages.stats.AbstractStatsMessage
IShare - Interface in ome.api: Provides method for sharing - collaboration process for images, datasets, projects.
isHidden() - Method in class pojos.FileData: Returns true if the file is hidden, false otherwise.
isImagingEnvironmentDirty() - Method in class pojos.ImageAcquisitionData: Returns true if the StageLabel has been updated, false otherwise.
isImmutable(Object) - Method in class omero.util.IceMapper
isInRepo(long) - Method in class ome.services.scripts.ScriptRepoHelper
isInRepo(SimpleJdbcOperations, long) - Method in class ome.services.scripts.ScriptRepoHelper
isInSystemGroup(Long) - Method in class ome.security.SystemTypes
isInSystemGroup(Details) - Method in class ome.security.SystemTypes
isInUserGroup(Long) - Method in class ome.security.SystemTypes
isInUserGroup(Details) - Method in class ome.security.SystemTypes
isKeep() - Method in class ome.services.delete.DeleteEntry
isLifetime() - Method in class pojos.ImageData: Returns true if the image is a lifetime image, false otherwise.
isLightSourceSettingsDirty() - Method in class pojos.ChannelAcquisitionData: Returns true if the light source settings has been updated, false otherwise.
isLoaded() - Method in class pojos.DataObject: Returns true if the object is loaded, false otherwise.
isMergedBatches() - Method in interface ome.api.Search: Returns the current merged-batches setting.
isMergedBatches() - Method in class ome.services.SearchBean
isMergedBatches_async(AMD_Search_isMergedBatches, Current) - Method in class ome.services.blitz.impl.SearchI
isModified() - Method in class ome.services.AbstractStatefulBean
isMovieFile() - Method in class pojos.FileAnnotationData: Returns true if it is a movie file.
isMutable() - Method in class ome.tools.hibernate.ArrayStringType
isMutable() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
isMutable() - Method in class ome.tools.hibernate.PermissionsType
isNative() - Method in class ome.io.nio.DeltaVisionHeader: Returns true if the DeltaVision file is of native endianness.
isNoiseReduction() - Method in class omeis.providers.re.metadata.StatsFactory: Returns true if the flag is on, false otherwise.
isNull() - Method in class ome.services.delete.DeleteEntry
isNullablePrimitive(Class<?>) - Static method in class omero.util.IceMapper
isObjectiveSettingsDirty() - Method in class pojos.ImageAcquisitionData: Returns true if the objective settings has been updated, false otherwise.
isolatedJdbc - Variable in class ome.security.basic.EventHandler
isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.BasicSecuritySystem: tests whether or not the current user is either the owner of this entity, or the superivsor of this entity, for example as root or as group owner.
isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.CurrentDetails
isPagination() - Method in class omero.sys.ParametersI: Returns true if the filter contains a limit OR a offset, false otherwise.
isPixelsTypeSigned() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
isPixelsTypeSigned() - Method in class omeis.providers.re.Renderer: Returns true if the pixels type is signed, false otherwise.
isPixelsTypeSigned() - Method in interface omeis.providers.re.RenderingEngine: Returns true if the pixels type is signed, false otherwise.
isPixelsTypeSigned_async(AMD_RenderingEngine_isPixelsTypeSigned, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
isPrefs() - Method in class ome.system.Preference
isPrimaryColorEnabled() - Method in class omeis.providers.re.Optimizations: Returns true if the primary color optimization is enabled, and false if it is not.
isPrimitive(Class<?>) - Method in class omero.util.IceMapper
isReadOnly() - Method in class ome.services.sessions.SessionContextImpl
isReadOnly() - Method in interface ome.system.EventContext
isReadOnly - Variable in class ome.system.SimpleEventContext
isReadOnly() - Method in class ome.system.SimpleEventContext
isReadOnly() - Method in class pojos.ShapeData: Is the object a read-only object.
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 , 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
isReturnUnloaded() - Method in interface ome.api.Search: Returns the current return-unloaded setting.
isReturnUnloaded() - Method in class ome.services.SearchBean
isReturnUnloaded_async(AMD_Search_isReturnUnloaded, Current) - Method in class ome.services.blitz.impl.SearchI
isRootUser(Experimenter) - Method in class ome.system.Roles
isSame(long) - Method in class omerojava.util.DataSink: Returns true if a data source has already been created for the specified pixels set, false otherwise.
isSecure() - Method in class omero.client: Specifies whether or not this client was created via a call to client.createClient(boolean) with a boolean of false.
isSet(Permissions.Flag) - Static method in class ome.tools.hibernate.SecurityFilter
isSigned() - Method in interface ome.api.RawPixelsStore
isSigned() - Method in class ome.io.nio.DeltaVision
isSigned() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
isSigned() - Method in interface ome.io.nio.PixelBuffer: Returns whether or not the pixel buffer has signed pixels.
isSigned - Variable in class ome.io.nio.PixelData: If the data is signed.
isSigned() - Method in class ome.io.nio.PixelData: Returns whether or not the data is signed.
isSigned() - Method in class ome.io.nio.RomioPixelBuffer
isSigned(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
isSigned(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService: Are the bytes in the image signed.
isSigned() - Method in class ome.services.RawPixelsBean
isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
isSingleton() - Method in class ome.security.basic.EventListenersFactoryBean: being a singleton implies that this FactoryBean will only ever create one instance.
isSoft() - Method in class ome.services.delete.DeleteEntry
isStageLabelDirty() - Method in class pojos.ImageAcquisitionData: Returns true if the position has been updated, false otherwise.
isStartTime() - Method in class omero.sys.ParametersI: Returns true if the map contains the start time parameter, false otherwise.
isSystemGroup(ExperimenterGroup) - Method in class ome.system.Roles
isSystemType(Class<? extends IObject>) - Method in class ome.security.basic.BasicSecuritySystem: classes which cannot be created by regular users.
isSystemType(Class<? extends IObject>) - Method in interface ome.security.SecuritySystem: checks if instances of the given type are "System-Types".
isSystemType(Class<? extends IObject>) - Method in class ome.security.SecuritySystemHolder
isSystemType(Class<? extends IObject>) - Method in class ome.security.sharing.SharingSecuritySystem
isSystemType(Class<?>) - Method in class ome.security.SystemTypes: classes which cannot be created by regular users.
isThisType(String, boolean) - Method in class ome.services.formats.OmeroReader
isThisType(RandomAccessInputStream) - Method in class ome.services.formats.OmeroReader
isThreadSafe() - Method in class ome.services.messages.AbstractSessionMessage
isThreadSafe() - Method in class ome.util.messages.InternalMessage: Returns true if this message can safely be passed to another Thread.
isThumbnailCached(long) - Method in class ome.services.ThumbnailCtx: Checks to see if a thumbnail is in the on disk cache or not.
isTransient(Object) - Method in class ome.security.basic.OmeroInterceptor
isTypeSigned(PixelsType) - Static method in class omeis.providers.re.data.PlaneFactory: A static helper method to retrieve pixel byte signage.
isUnloaded(Object) - Static method in class ome.tools.hibernate.HibernateUtils
isUpgradeNeeded() - Method in class ome.system.UpgradeCheck
isUseProjections() - Method in interface ome.api.Search: Returns the current use-projection setting.
isUseProjections() - Method in class ome.services.SearchBean
isUseProjections_async(AMD_Search_isUseProjections, Current) - Method in class ome.services.blitz.impl.SearchI
isUserGroup(ExperimenterGroup) - Method in class ome.system.Roles
isUserRead(Current) - Method in class omero.model.PermissionsI
isUserRead() - Method in class pojos.PermissionData: Returns true if the user has read access, false otherwise.
isUserWrite(Current) - Method in class omero.model.PermissionsI
isUserWrite() - Method in class pojos.PermissionData: Returns true if the user has write access, false otherwise.
isVoid(Current) - Method in class ome.services.blitz.util.IceMethodInvoker: Checks for a void return type, which is needed to know what type of ice_response() method to invoke.
isVoid - Variable in class ome.services.throttling.Task
isVoid() - Method in class omero.util.IceMapper: Returns true only if the current mapping is the IceMapper.VOID mapping.
isWorldRead(Current) - Method in class omero.model.PermissionsI
isWorldRead() - Method in class pojos.PermissionData: Returns true if the world has read access, false otherwise.
isWorldWrite(Current) - Method in class omero.model.PermissionsI
isWorldWrite() - Method in class pojos.PermissionData: Returns true if the world has write access, false otherwise.
isWrapperArray(Class<?>) - Static method in class omero.util.IceMapper
isXYPlanar() - Method in class omeis.providers.re.data.Plane2D: Returns true if the plane is an XY-plane, false otherwise.
iterate() - Method in class ome.services.scripts.ScriptRepoHelper
iterator() - Method in class ome.services.fulltext.EventLogLoader
iterator() - Method in class ome.services.messages.ShapeChangeMessage
ITypes - Interface in ome.api: Access to reflective type information.
IUpdate - Interface in ome.api: Provides methods for directly updating object graphs.
iUpdate - Variable in class ome.logic.AbstractLevel2Service
iUpdate - Variable in class ome.services.AbstractStatefulBean

J

JavaImageScalingService - Class in ome.logic: Provides methods for scaling buffered images using Java Image Scaling .
JavaImageScalingService() - Constructor for class ome.logic.JavaImageScalingService
javaType - Variable in class ome.io.nio.PixelData: The pixels type as it would be represented in Java.
javaType() - Method in class ome.io.nio.PixelData: Returns the Java type that has the same byte width of the pixel data.
javaType - Variable in class omeis.providers.re.data.Plane2D: The Java type that we're using for pixel value retrieval
jdbc - Variable in class ome.logic.AdminImpl
jdbc - Variable in class ome.services.blitz.impl.RoiI
jdbc - Variable in class ome.services.roi.GeomTool
jdbcOps - Variable in class ome.services.util.Executor.Impl
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
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 interface ome.api.JobHandle: Returns true if the Job has thrown an error.
jobError() - Method in class ome.services.JobBean
jobError_async(AMD_JobHandle_jobError, Current) - Method in class ome.services.blitz.impl.JobHandleI
jobFinished() - Method in interface ome.api.JobHandle
jobFinished() - Method in class ome.services.JobBean
jobFinished_async(AMD_JobHandle_jobFinished, Current) - Method in class ome.services.blitz.impl.JobHandleI
JobHandle - Interface in ome.api: Allows submission of asynchronous jobs.
JobHandleI - Class in ome.services.blitz.impl: Implementation of the JobHandle service.
JobHandleI(JobHandle, BlitzExecutor) - Constructor for class ome.services.blitz.impl.JobHandleI
jobMessage() - Method in interface ome.api.JobHandle
jobMessage() - Method in class ome.services.JobBean
jobMessage_async(AMD_JobHandle_jobMessage, Current) - Method in class ome.services.blitz.impl.JobHandleI
jobRunning() - Method in interface ome.api.JobHandle: Returns true if the Job is running, i.e. has an attached Process.
jobRunning() - Method in class ome.services.JobBean
jobRunning_async(AMD_JobHandle_jobRunning, Current) - Method in class ome.services.blitz.impl.JobHandleI
jobStatus() - Method in interface ome.api.JobHandle
jobStatus() - Method in class ome.services.JobBean
jobStatus_async(AMD_JobHandle_jobStatus, Current) - Method in class ome.services.blitz.impl.JobHandleI
join(QueryBuilder, String, String, String, String) - Method in class ome.services.delete.BaseDeleteSpec: Used to generate a join statement on the QueryBuilder making use of {@link ExtendedMetadata#getRelationship(String, String).
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
join(String...) - Static method in class prefs: Joins all the String arguments given into a single String (joined with " "), and returns that String as the first element of a new array.
joinChildren(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
joinParents(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
joinSession(String) - Method in class omero.client: Uses the given session uuid as name and password to rejoin a running session.

K

keepAlive(Current) - Method in class ome.services.blitz.gateway.OmeroGateway: Keep service alive.
keepAlive() - Method in class ome.services.blitz.gateway.services.GatewayFactory
keepAlive() - Method in interface ome.services.blitz.gateway.services.GatewayService: Keep service alive.
keepAlive(ServiceInterfacePrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI: Currently ignoring the individual proxies
keepAllAlive(ServiceInterfacePrx[], Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
key(String) - Method in class ome.security.auth.AttributeSet
key - Variable in class ome.services.fulltext.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.delete.DeleteSpecFactory: Returns the keys of all specs in the current factory.
keys() - Method in class ome.services.sharing.BlobShareStore
keys() - Method in class ome.services.sharing.FreezeShareStore
keys() - Method in class ome.services.sharing.ShareStore
keys(String[]) - Static method in class prefs: Returns Preferences.keys()
keySet() - Method in class ome.services.query.Definitions
kill(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
killSession() - Method in class omero.client: Calls ISession.closeSession(omero.model.Session) until the returned reference count is greater than zero.
knownManagers() - Method in class ome.services.blitz.fire.Ring

L

LASER - Static variable in class pojos.LightSourceData: Indicates that the light source is a laser.
lastEventLog() - Method in class ome.services.fulltext.EventLogLoader
lastModified() - Method in class pojos.FileData: Returns when the file was last modified.
LASTNAME - Static variable in class pojos.ExperimenterData: Identifies the Experimenter#LASTNAME field.
lastPlane() - Method in class pojos.ROIData: Returns the last plane that the ROI ends on.
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
LdapI - Class in ome.services.blitz.impl: Implementation of the ILdap service.
LdapI(ILdap, BlitzExecutor) - Constructor for class ome.services.blitz.impl.LdapI
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, SimpleJdbcOperations) - Constructor for class ome.logic.LdapImpl
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
ldapUtil - Variable in class ome.logic.AdminImpl
ldapUtil - Variable in class ome.security.auth.LdapPasswordProvider
leaderOfGroups - Variable in class ome.system.SimpleEventContext
leadingWildcard - Variable in class ome.services.search.SearchValues
leaves() - Method in class omero.sys.ParametersI: Sets the leaf parameter to true.
LEFT_JOIN - Static variable in class ome.services.query.Query: imported constant for ease of use
length() - Method in class ome.services.scripts.RepoFile.FsFile
length() - Method in class ome.services.scripts.RepoFile
length - Variable in class ome.util.mem.ReadOnlyByteArray: The length of the slice.
length - Variable in class omerojava.util.ReadOnlyByteArray: The length of the slice.
LEVEL_FIVE - Static variable in class pojos.RatingAnnotationData: Indicates the object is rated with five stars.
LEVEL_FOUR - Static variable in class pojos.RatingAnnotationData: Indicates the object is rated with four stars.
LEVEL_ONE - Static variable in class pojos.RatingAnnotationData: Indicates the object is rated with one star.
LEVEL_THREE - Static variable in class pojos.RatingAnnotationData: Indicates the object is rated with three stars.
LEVEL_TWO - Static variable in class pojos.RatingAnnotationData: Indicates the object is rated with two stars.
LEVEL_ZERO - Static variable in class pojos.RatingAnnotationData: Indicates the object is not rated.
lies(PlanePoint) - Method in class ome.util.math.geom2D.Line: Tells whether the specified point lies on this line.
lies(PlanePoint, boolean) - Method in class ome.util.math.geom2D.Line: Tells whether the specified point lies on this line and within the specified orientation.
lies(double, double) - Method in class ome.util.math.geom2D.Segment: Tells whether a specified point lies on this line.
LIGHT_EMITTING_DIODE - Static variable in class pojos.LightSourceData: Indicates that the light source is a light emitting diode.
LightPathData - Class in pojos: Object hosting a light path.
LightPathData(LightPath) - Constructor for class pojos.LightPathData: Creates a new instance.
LightSourceData - Class in pojos: Object hosting a light source: filament, arc, laser or light emiting diode
LightSourceData(LightSource) - Constructor for class pojos.LightSourceData: Creates a new instance.
Line - Class in ome.util.math.geom2D: An orientated line in the Euclidean space R².
Line(PlanePoint, PlanePoint) - Constructor for class ome.util.math.geom2D.Line: Creates a new object to represent the line passing through the o and p points.
Line(PlanePoint, PlanePoint, PlanePoint) - Constructor for class ome.util.math.geom2D.Line: Creates a new object to represent the line passing through o and having direction pq.
LINE_CAP_BUTT - Static variable in class pojos.ShapeSettingsData: The Butt descriptor.
LINE_CAP_ROUND - Static variable in class pojos.ShapeSettingsData: The Round descriptor.
LINE_CAP_SQUARE - Static variable in class pojos.ShapeSettingsData: The Square descriptor.
LINEAR - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a linear map for the quantization process.
LineData - Class in pojos: Represents a line in the Euclidean space R².
LineData(Shape) - Constructor for class pojos.LineData: Creates a new instance.
LineData() - Constructor for class pojos.LineData: Create a new instance of LineData, creating a new LineI Object.
LineData(double, double, double, double) - Constructor for class pojos.LineData: Create a new instance of the LineData,
link(ILink[], Parameters) - Method in interface ome.api.IContainer: Convenience method for creating links.
link(ILink[], Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
link_async(AMD_IContainer_link, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
linkGroupAndUser(ExperimenterGroup, Experimenter, boolean) - Method in class ome.security.auth.SimpleRoleProvider
list(List<Obj>) - Method in class ome.services.sharing.ShareBean
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.BOOLEAN - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$BOOLEAN" hibernate.column name="fieldName" sql-type="bool[]"
ListAsSQLArrayUserType.BOOLEAN() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
ListAsSQLArrayUserType.DATE - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$DATE" hibernate.column name="fieldName" sql-type="timestamp[]"
ListAsSQLArrayUserType.DATE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
ListAsSQLArrayUserType.DOUBLE - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$DOUBLE" hibernate.column name="fieldName" sql-type="float8[]"
ListAsSQLArrayUserType.DOUBLE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
ListAsSQLArrayUserType.ENUM<E extends Enum<E>> - Class in ome.tools.hibernate: Warning, this one is special.
ListAsSQLArrayUserType.ENUM(E[]) - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
ListAsSQLArrayUserType.FLOAT - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$FLOAT" hibernate.column name="fieldName" sql-type="real[]"
ListAsSQLArrayUserType.FLOAT() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
ListAsSQLArrayUserType.INTEGER - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$INTEGER" hibernate.column name="fieldName" sql-type="int[]"
ListAsSQLArrayUserType.INTEGER() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
ListAsSQLArrayUserType.STRING - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING" hibernate.column name="fieldName" sql-type="text[]"
ListAsSQLArrayUserType.STRING() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
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
ListAsSQLArrayUserType.STRING2() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
LISTOBJECTARRAY_TO_RTYPESEQSEQ - Static variable in class omero.util.IceMapper
ln(double, double, double, double) - Method in class ome.services.roi.GeomTool
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, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
load() - Method in interface omeis.providers.re.RenderingEngine: Creates a instance of the rendering engine.
load(String[]) - Static method in class prefs: Loads a profile from Properties files, or properly formatted System.in input if no files are given.
load_async(AMD_RenderingEngine_load, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
load_nowarn(String[]) - Static method in class prefs: Performs the same actions as prefs.load(String[]) but does not throw prefs.CONFLICT if a key already exists.
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.
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 interface ome.api.IMetadata: Loads the specified annotations.
loadAnnotation(Set<Long>) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadAnnotation_async(AMD_IMetadata_loadAnnotation, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Loads all the annotations of given types, that have been attached to the specified rootNodes for the specified annotatorIds.
loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadAnnotations_async(AMD_IMetadata_loadAnnotations, String, List<Long>, List<String>, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
loadAnnotationsUsedNotOwned(Class, long) - Method in interface ome.api.IMetadata: Loads the annotations of a given type used by the specified user but not owned by the user.
loadAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadAnnotationsUsedNotOwned_async(AMD_IMetadata_loadAnnotationsUsedNotOwned, String, long, Current) - Method in class ome.services.blitz.impl.MetadataI
loadChannelAcquisitionData(Set<Long>) - Method in interface ome.api.IMetadata: Loads the logical channels and the acquisition metadata related to them.
loadChannelAcquisitionData(Set<Long>) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadChannelAcquisitionData_async(AMD_IMetadata_loadChannelAcquisitionData, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
loadContainerHierarchy(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer: Retrieves hierarchy trees rooted by a given node (unless orphan is specified -- See below) This method also retrieves the Experimenters linked to the objects in the tree.
loadContainerHierarchy(Class, Set, Parameters) - Method in class ome.logic.PojosImpl: Implemented as speficied by the IContainer I/F
loadContainerHierarchy_async(AMD_IContainer_loadContainerHierarchy, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
loaded - Variable in class ome.services.blitz.fire.SessionManagerI
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.fulltext.FullTextIndexer
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 interface ome.api.IMetadata: Loads the instrument and its components i.e. detectors, objectives, etc.
loadInstrument(long) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadInstrument_async(AMD_IMetadata_loadInstrument, long, Current) - Method in class ome.services.blitz.impl.MetadataI
loadMeasuredRois(Session, long, long) - Method in class ome.services.blitz.impl.RoiI
loadMembers(ShareData) - Method in class ome.services.sharing.ShareBean
loadRenderingDef(long) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
loadRenderingDef(long) - Method in interface omeis.providers.re.RenderingEngine: Loads a specific set of rendering settings that does not necessarily have to be linked to the given Pixels set.
loadRenderingDef_async(AMD_RenderingEngine_loadRenderingDef, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
loadRndSettings(long) - Method in interface ome.api.IPixels: Loads a specific set of rendering settings with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
loadRndSettings(long) - Method in class ome.logic.PixelsImpl: Implemented as specified by the IPixels I/F.
loadRndSettings_async(AMD_IPixels_loadRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI
loadScripts(ServiceFactory, Parameters) - Method in class ome.services.scripts.ScriptFinder: Load all scripts that match the name, sha1, and format for script
loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata: Loads the annotations of a given type.
loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadSpecifiedAnnotations_async(AMD_IMetadata_loadSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
loadTagContent(Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Loads the Tag Set if the id is specified otherwise loads all the Tag Set.
loadTagContent(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadTagContent_async(AMD_IMetadata_loadTagContent, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
loadTagSets(Parameters) - Method in interface ome.api.IMetadata: Loads all the tag Sets.
loadTagSets(Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadTagSets_async(AMD_IMetadata_loadTagSets, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
LocalAdmin - Interface in ome.api.local: Provides local (internal) extensions for administration
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
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(String) - Method in class ome.security.basic.OmeroInterceptor
log - Variable in class ome.services.blitz.impl.AbstractAmdServant
log - Variable in class ome.services.blitz.redirect.AbstractRedirector
log - Static variable in class ome.services.delete.DeleteBean
log(String) - Method in class ome.services.delete.DeleteEntry: Similar to DeleteEntry.toString() but used to
log - Variable in class ome.services.roi.GeomTool
log - Variable in class ome.services.roi.PixelData
log - Variable in class ome.services.scripts.ScriptFinder
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 - Variable in class ome.services.throttling.AbstractThrottlingStrategy
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.DropBoxDirectoryCheck
log - Static variable in class ome.services.util.NamespaceCheck
log - Static variable in class ome.services.util.ServerVersionCheck
log(String) - Method in class ome.tools.hibernate.EventMethodInterceptor
LOGARITHMIC - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a logarithmic map for the quantization process.
LogarithmicMap - Class in omeis.providers.re.quantum: This class implements the QuantumMap interface.
LogarithmicMap() - Constructor for class omeis.providers.re.quantum.LogarithmicMap
logger() - Method in class ome.services.fulltext.BridgeHelper
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(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
Login - Class in ome.system: Provides simplified handling of login properties when creating a ServiceFactory.
Login(String, String) - Constructor for class ome.system.Login: standard constructor which leaves OMERO_GROUP and OMERO_EVENT null.
Login(String, String, String, String) - Constructor for class ome.system.Login: extended constructor.
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
logs - Variable in class ome.services.messages.ShapeChangeMessage
LONG - Static variable in class ome.io.nio.PixelData: Identifies the type used to store pixel values.
LONG - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
LongAnnotationData - Class in pojos: Wraps a long annotation.
LongAnnotationData(long) - Constructor for class pojos.LongAnnotationData: Creates a new instance.
LongAnnotationData() - Constructor for class pojos.LongAnnotationData: Creates a new instance.
LongAnnotationData(LongAnnotation) - Constructor for class pojos.LongAnnotationData: Creates a new instance.
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(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
lookup(String, ApplicationContext) - Method in class ome.system.OmeroContext.Locator: uses ContextSingletonBeanFactoryLocator.createDefinition(java.lang.String, java.lang.String) and ContextSingletonBeanFactoryLocator.initializeDefinition(org.springframework.beans.factory.BeanFactory) to create a new context from a given definition.
lookupClusterNodes() - Method in class ome.services.blitz.fire.Registry.Impl
lookupClusterNodes() - Method in interface ome.services.blitz.fire.Registry: Returns all found cluster nodes or null if something goes wrong during lookup (null QueryPrx for example)
lookupExperimenter(String) - Method in interface ome.api.IAdmin: look up an Experimenter and all related groups by name.
lookupExperimenter(String) - Method in class ome.logic.AdminImpl
lookupExperimenter_async(AMD_IAdmin_lookupExperimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI
lookupExperimenters() - Method in interface ome.api.IAdmin: Looks up all experimenters present and all related groups.
lookupExperimenters() - Method in class ome.logic.AdminImpl
lookupExperimenters_async(AMD_IAdmin_lookupExperimenters, Current) - Method in class ome.services.blitz.impl.AdminI
lookupGroup(String) - Method in interface ome.api.IAdmin: look up an ExperimenterGroup and all contained users by name.
lookupGroup(String) - Method in class ome.logic.AdminImpl
lookupGroup_async(AMD_IAdmin_lookupGroup, String, Current) - Method in class ome.services.blitz.impl.AdminI
lookupGroups() - Method in interface ome.api.IAdmin: Looks up all groups present and all related experimenters.
lookupGroups() - Method in class ome.logic.AdminImpl
lookupGroups_async(AMD_IAdmin_lookupGroups, Current) - Method in class ome.services.blitz.impl.AdminI
lookupLdapAuthExperimenter(long) - Method in interface ome.api.IAdmin: Looks up experimenters who uses LDAP authentication (has set dn on password table).
lookupLdapAuthExperimenter(long) - Method in class ome.logic.AdminImpl
lookupLdapAuthExperimenter(Long) - Method in class ome.logic.LdapImpl
lookupLdapAuthExperimenter_async(AMD_IAdmin_lookupLdapAuthExperimenter, long, Current) - Method in class ome.services.blitz.impl.AdminI
lookupLdapAuthExperimenters() - Method in interface ome.api.IAdmin: Looks up all id of experimenters who uses LDAP authentication (has set dn on password table).
lookupLdapAuthExperimenters() - Method in class ome.logic.AdminImpl
lookupLdapAuthExperimenters() - Method in class ome.logic.LdapImpl
lookupLdapAuthExperimenters_async(AMD_IAdmin_lookupLdapAuthExperimenters, Current) - Method in class ome.services.blitz.impl.AdminI
lookupMonitorServers() - Method in class ome.services.blitz.fire.Registry.Impl
lookupMonitorServers() - Method in interface ome.services.blitz.fire.Registry
lookupPixels(long) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
lookupPixels(long) - Method in interface omeis.providers.re.RenderingEngine: Loads the Pixels set this Rendering Engine is for.
lookupPixels_async(AMD_RenderingEngine_lookupPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
lookupProcessors() - Method in class ome.services.blitz.fire.Registry.Impl
lookupProcessors() - Method in interface ome.services.blitz.fire.Registry
lookupRenderingDef(long) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
lookupRenderingDef(long) - Method in interface omeis.providers.re.RenderingEngine: Loads the rendering settings associated to the specified pixels set.
lookupRenderingDef_async(AMD_RenderingEngine_lookupRenderingDef, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
lookupRepositories() - Method in class ome.services.blitz.fire.Registry.Impl
lookupRepositories() - Method in interface ome.services.blitz.fire.Registry
lookupTables() - Method in class ome.services.blitz.fire.Registry.Impl
lookupTables() - Method in interface ome.services.blitz.fire.Registry
loop(int, long) - Method in class omero.grid.DeleteCallbackI: Calls DeleteCallbackI.block(long) "loops" number of times with the "ms" argument.
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

M

mailSender - Variable in class ome.logic.AdminImpl
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(String[]) - Static method in class ome.services.blitz.Entry: Entry point to the server.
main(String[]) - Static method in class ome.services.blitz.Status: Uses the passed args to create an Communicator.
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.tools.FileSystem
main(String[]) - Static method in class omero.util.TempFileManager: Command-line interface to the global TempFileManager instance ( #manger).
main(String[]) - Static method in class prefs: Entry point to the prefs command line too.
makeAndLaunchHandle(Identity, DeleteCommand...) - Method in class ome.services.blitz.impl.DeleteI
makeAndRun(Identity, DeleteCommand...) - Method in class ome.services.blitz.impl.DeleteI
makeNew(int) - Method in class ome.util.mem.CopiableArray: Creates a new array of the speficied size.
makeNew(Pixels, ImageService) - Static method in class omerojava.util.DataSink: Factory method to create a new DataSink to handle access to the metadata associated with the specified pixels set.
MANAGED_CONTEXT - Static variable in class ome.system.OmeroContext: identifier for an OmeroContext configured in classpath*:beanRefContext.xml for use by server-side processes.
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: responsible for guaranteeing that external info is not modified by any users, including rot.
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
managedPermissions(boolean, IObject, Details, Details, Details, boolean) - Method in class ome.security.basic.OmeroInterceptor: responsible for properly copying user-requested permissions taking into account the Flag#LOCKED status.
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
managerOrNull() - Method in class ome.services.blitz.fire.TopicManager.Impl
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
map() - Method in class omero.sys.ParametersI: Deprecated.
map(Filterable[]) - Method in class omero.util.IceMapper
mapFromAttributes(Attributes) - Method in class ome.security.auth.GroupAttributeMapper
mapFromContext(Object) - Method in class ome.security.auth.PersonContextMapper
mapReturnValue(IceMapper, Object) - Method in class ome.services.blitz.impl.RoiI.RoiResultMapReturnMapper
mapReturnValue(IceMapper, Object) - Method in class ome.services.blitz.impl.RoiI.RoiResultReturnMapper
mapReturnValue(Object) - Method in class omero.util.IceMapper: Convert the given Object via the set IceMapper.ReturnMapping.
mapReturnValue(IceMapper, Object) - Method in interface omero.util.IceMapper.ReturnMapping
mapServerToClient(byte[], int, int, String) - Static method in class omerojava.util.DataSink
mapServerToClient(byte[], int, int, String, boolean) - Static method in class omerojava.util.DataSink
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.
MaskData - Class in pojos: Represents an Mask in the Euclidean space R².
MaskData(Shape) - Constructor for class pojos.MaskData: Creates a new instance.
MaskData() - Constructor for class pojos.MaskData: Creates a new instance of MaskData.
MaskData(double, double, double, double, byte[]) - Constructor for class pojos.MaskData: Creates a new instance of the MaskData.
matches(Class, Class) - Static method in class ome.services.blitz.util.ApiConsistencyCheck: Defines what Class types match.
matches(File) - Method in class ome.services.scripts.RepoFile
MAX - Static variable in class omeis.providers.re.quantum.QuantumStrategy: Maximum value (255) allowed for the upper bound of the codomain interval.
MAX_CHANNELS - Static variable in class omeis.providers.re.Renderer: The maximum number of channels.
maximum - Variable in class ome.io.nio.PixelData: The maximum pixel value for the pixels type of the pixel data.
MAXIMUM_INTENSITY - Static variable in interface ome.api.IProjection: Maximum intensity projection (MIP)
maxUserTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl
maxUserTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl
MEAN_INTENSITY - Static variable in interface ome.api.IProjection: Mean intensity projection
MEASUREMENT_NS - Static variable in class pojos.FileAnnotationData: The name space used to indicate that the FileAnnotation is a Measurement file.
MeasurementStore - Class in ome.services.blitz.measurements: Parser API implementation for storing result measurements from SPW companion files as ROIs and OMERO.tables.
MeasurementStore(LocalUpdate, TablePrx) - Constructor for class ome.services.blitz.measurements.MeasurementStore
memberOfGroups - Variable in class ome.system.SimpleEventContext
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. in particular in load/re-loading certain types to make use by clients easier.
MergeEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.MergeEventListener: main constructor.
message - Variable in exception ome.services.delete.DeleteException
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
MessageException - Exception in ome.util.messages: Message which wraps a Throwable instance since OmeroContext.publishEvent(org.springframework.context.ApplicationEvent) cannot throw a checked exception.
MessageException(String, Throwable) - Constructor for exception ome.util.messages.MessageException: Create an instance.
meta - Variable in class ome.services.roi.PixelData
metadata - Variable in class ome.logic.AbstractLevel2Service
MetadataI - Class in ome.services.blitz.impl: Implementation of the IMetadata service.
MetadataI(IMetadata, BlitzExecutor) - Constructor for class ome.services.blitz.impl.MetadataI: Creates a new instance.
MetadataImpl - Class in ome.logic: Implement the IMetadata I/F.
MetadataImpl() - Constructor for class ome.logic.MetadataImpl
MetadataStoreI - Class in ome.services.blitz.impl
MetadataStoreI(BlitzExecutor, PopulateRoiJob) - Constructor for class ome.services.blitz.impl.MetadataStoreI
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
METHODOLOGY_STRINGS - Static variable in interface ome.api.IProjection: Methodology strings
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
MIDDLENAME - Static variable in class pojos.ExperimenterData: Identifies the Experimenter#MIDDLENAME field.
MIN - Static variable in class omeis.providers.re.quantum.QuantumStrategy: Minimum value (0) allowed for the lower bound of the codomain interval.
minimum - Variable in class ome.io.nio.PixelData: The minimum pixel value for the pixels type of the pixel data.
MODEL_GREYSCALE - Static variable in class omeis.providers.re.Renderer: Identifies the type used to store model values.
MODEL_HSB - Static variable in class omeis.providers.re.Renderer: Identifies the type used to store model values.
MODEL_RGB - Static variable in class omeis.providers.re.Renderer: Identifies the type used to store model values.
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.fulltext.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.fulltext.AllEventsLogLoader
more() - Method in class ome.services.fulltext.EventLogLoader: Should return an estimate of how many more EventLog instances are available for processing.
more() - Method in class ome.services.fulltext.PersistentEventLogLoader
moveToCommonSpace(IObject...) - Method in interface ome.api.IAdmin: Moves the given objects into the "user" group to make them visible and linkable from all security contexts.
moveToCommonSpace(IObject...) - Method in class ome.logic.AdminImpl
moveToCommonSpace_async(AMD_IAdmin_moveToCommonSpace, List<IObject>, Current) - Method in class ome.services.blitz.impl.AdminI
MOVIE_MPEG_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is an MPEG file.
MOVIE_NS - Static variable in class pojos.FileAnnotationData: The name space used to indicate that the FileAnnotation is a movie.
MOVIE_QT_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is an QT file.
MOVIE_WMV_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is an WMV file.
MS_EXCEL - Static variable in class pojos.FileAnnotationData: Identifies the Excel file formats.
MS_POWER_POINT - Static variable in class pojos.FileAnnotationData: Identifies the Power point file formats.
MS_POWER_POINT_SHOW - Static variable in class pojos.FileAnnotationData: Identifies the Power point file formats.
MS_POWER_POINT_X - Static variable in class pojos.FileAnnotationData: Identifies the Power point file formats.
MS_WORD - Static variable in class pojos.FileAnnotationData: Identifies the Word file formats.
MS_WORD_X - Static variable in class pojos.FileAnnotationData: Identifies the Word file formats.
multicastEvent(ApplicationEvent) - Method in class ome.services.messages.GlobalMulticaster: Multicast only if this instance was the first created.
MultiImageData - Class in pojos: Handle image file composed of multiples files e.g. lei.
MultiImageData(OriginalFile) - Constructor for class pojos.MultiImageData: Creates a new instance.
mutex - Variable in class ome.system.SessionInitializer
MySeqGenerator - Class in ome.tools.hibernate: http://www.hibernate.org/296.html
MySeqGenerator() - Constructor for class ome.tools.hibernate.MySeqGenerator

N

name - Variable in class ome.services.query.QueryParameterDef: name of this parameter.
name - Variable in class ome.services.scripts.RepoFile.FsFile
name - Variable in class ome.system.Principal
NAME - Static variable in class pojos.DatasetData: Identifies the Dataset#NAME field.
NAME - Static variable in class pojos.GroupData: Identifies the ExperimenterGroup#NAME field.
NAME - Static variable in class pojos.ImageData: Identifies the Image#NAME field.
NAME - Static variable in class pojos.PlateData: Identifies the Plate#NAME field.
NAME - Static variable in class pojos.ProjectData: Identifies the Project#NAME field.
NAME - Static variable in class pojos.ScreenData: Identifies the Screen#NAME field.
nameById(long) - Method in interface ome.security.auth.RoleProvider
nameById(long) - Method in class ome.security.auth.SimpleRoleProvider
NamespaceCheck - Class in ome.services.util: Hook run by the context.
NamespaceCheck(Executor, String, Roles) - Constructor for class ome.services.util.NamespaceCheck
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.
newBlueColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new Blue Color object.
newEvent(long, EventType, TokenHolder) - Method in class ome.security.basic.CurrentDetails
newGreenColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new Green Color object.
newGreyColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new Grey Color object.
newlyEnabledFilters - Variable in class ome.services.query.Query: the set of filters that is being or has been enabled for this Query.
newRedColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new Red Color object.
newTable(long, String, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
newTransientDetails(IObject) - Method in class ome.security.basic.BasicSecuritySystem
newTransientDetails(IObject) - Method in class ome.security.basic.OmeroInterceptor
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.
newWhiteColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new White Color object.
next() - Method in interface ome.api.Search: Returns the next entity from the current query.
next() - Method in class ome.services.delete.BaseDeleteSpec.SubSpecIterator
next() - Method in class ome.services.fulltext.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.SearchBean
next_async(AMD_Search_next, Current) - Method in class ome.services.blitz.impl.SearchI
nextEventLog(long) - Method in class ome.services.fulltext.EventLogLoader: Returns the EventLog with the next id after the given argument or null if none exists.
noAcquisitionData() - Method in class omero.sys.ParametersI: Sets the acquisition data parameter to false.
nodeProxyQuery(Redirector.Context, String, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
NOISE_REDUCTION - Static variable in class omeis.providers.re.quantum.QuantumFactory: Default value.
noLeaves() - Method in class omero.sys.ParametersI: Sets the leaf parameter to false.
noOrphan() - Method in class omero.sys.ParametersI: Sets the orphan parameter to false.
noPage() - Method in class omero.sys.ParametersI: Nulls both the Filter.limit and Filter.offset values.
norm(String) - Static method in class ome.services.scripts.RepoFile: Somewhat complicated method to turn any path into a unique like path rooted at "/".
norm() - Method in class ome.util.math.geom2D.PlanePoint: Calculates the Euclidian norm of this vector.
normalize() - Method in class ome.util.math.geom2D.PlanePoint: Calculates the unit vector of this vector, provided this is not the null vector.
not() - Method in interface ome.api.Search: Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the intersection of the two calls.
not() - Method in class ome.services.SearchBean
not_async(AMD_Search_not, Current) - Method in class ome.services.blitz.impl.SearchI
notAnnotatedBy(Details) - Method in interface ome.api.Search: Restricts entities by who has not annotated them with an Annotation matching the other filters.
notAnnotatedBy - Variable in class ome.services.search.SearchValues
notAnnotatedBy(Details) - Method in class ome.services.SearchBean
notAnnotatedBy_async(AMD_Search_notAnnotatedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
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
notifyRemoveAll(Ehcache) - Method in class ome.services.sessions.state.CacheListener
NotNull - Annotation Type in ome.annotations: annotation used for determining the types of a Set
notNull(String[]) - Static method in class prefs: Returns an empty array if the argument is null.
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(Details) - Method in interface ome.api.Search: Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.
notOwnedBy - Variable in class ome.services.search.SearchValues
notOwnedBy(Details) - Method in class ome.services.SearchBean
notOwnedBy_async(AMD_Search_notOwnedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
noUnique() - Method in class omero.sys.ParametersI
NS_COMMENT - Static variable in class ome.services.sharing.ShareBean
NS_ENABLED - Static variable in class ome.services.sharing.ShareBean
NS_IMPORTER_ARCHIVED - Static variable in interface ome.api.IMetadata: The name space indicating that the Boolean annotation indicated if an archived image is imported with the image.
NS_INSIGHT_RATING - Static variable in interface ome.api.IMetadata: The name space indicating that the Long annotation is a rating annotation i.e. an integer in the interval [0, 5].
NS_INSIGHT_TAG_SET - Static variable in interface ome.api.IMetadata: The name space indicating that the tag is used a tag set.
nsExcludes - Static variable in class ome.services.delete.AnnotationDeleteSpec: Collection of namespace values (defined as AnnotationDeleteSpec.nsIncludes) which will be omitted from deletes by default.
NSEXPERIMENTERPHOTO - Static variable in class ome.logic.AdminImpl
nsIncludes - Static variable in class ome.services.delete.AnnotationDeleteSpec: Collection of namespace values (or LIKE values if they contain '%' or '?')
NULL_PLANE_SIZE - Static variable in class ome.io.nio.PixelsService: Null plane size constant.
NULL_RENDERER - Static variable in class ome.services.RenderingBean
nullDetails() - Method in class pojos.DataObject: Returns true if the details are null otherwise false otherwise.
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
nullPlane - Static variable in class ome.io.nio.PixelsService: Null plane byte array.
NullQuerySource - Class in ome.services.query: always returns null for any id.
NullQuerySource() - Constructor for class ome.services.query.NullQuerySource
NullRedirector - Class in ome.services.blitz.redirect: Redirector implementation to effectively disable redirects.
NullRedirector() - Constructor for class ome.services.blitz.redirect.NullRedirector
nullSafe(Integer) - Method in class pojos.DataObject
nullSafe(RInt) - Method in class pojos.DataObject
nullSafe(Long) - Method in class pojos.DataObject
nullSafe(Double) - Method in class pojos.DataObject
nullSafe(Float) - Method in class pojos.DataObject
nullSafe(RFloat) - Method in class pojos.DataObject
nullSafe(RDouble) - Method in class pojos.DataObject
nullSafeGet(ResultSet, String[], Object) - Method in class ome.tools.hibernate.ArrayStringType
nullSafeGet(ResultSet, String[], Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
nullSafeGet(ResultSet, String[], Object) - Method in class ome.tools.hibernate.PermissionsType
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.ArrayStringType
nullSafeSet(PreparedStatement, Object, int) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
nullSafeSet(PreparedStatement, Object, int) - Method in class ome.tools.hibernate.PermissionsType
NullSessionStats - Class in ome.services.sessions.stats: Implementation of SimpleStats 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.

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
OBJECT_TO_RTYPE - Static variable in class omero.util.IceMapper
OBJECTARRAY_TO_RTYPESEQ - Static variable in class omero.util.IceMapper
ObjectFactories - Static variable in class ome.services.roi.RoiTypes
ObjectFactories - Static variable in class omero.rtypes
ObjectiveData - Class in pojos: Hosts an objective used to capture an image.
ObjectiveData(Objective) - Constructor for class pojos.ObjectiveData: Creates a new instance.
objectList - Variable in class ome.services.sharing.data.ShareData
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
ObjHolder.Patcher - Class in ome.services.sharing.data
ObjHolder.Patcher() - Constructor for class ome.services.sharing.data.ObjHolder.Patcher
ObjPrx - Interface in ome.services.sharing.data
ObjPrxHelper - Class in ome.services.sharing.data
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
obtainProxy(String, Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
OCTETSTREAM - Static variable in class omero.grid.ParamsHelper
offset - Variable in class ome.util.mem.ReadOnlyByteArray: Marks the start of the slice.
offset - Variable in class omerojava.util.ReadOnlyByteArray: Marks the start of the slice.
ome.annotations - package ome.annotations: Runtime source annotation package for the OMERO server This includes classes that annotate source code and check metadata at runtime for server API calls.
ome.api - package ome.api: Contains the central verbs of the Omero System.
ome.api.local - package ome.api.local: Non-client service API for OMERO This includes interfaces for the local administration of the OMERO server.
ome.formats - package ome.formats
ome.formats.importer.util - package ome.formats.importer.util
ome.io.nio - package ome.io.nio: New Input/Output handling for the OMERO server This includes interfaces/classes for the input and output handling of data within the OMERO server.
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 This includes classes that provide security for the execution and usage of the OMERO server on a JBoss platform.
ome.security.auth - package ome.security.auth
ome.security.basic - package ome.security.basic: Basic OMERO security contextual classes Basic classes that provide security context objects necessary to secure the implementation of the OMERO server on a JBoss platform.
ome.security.sharing - package ome.security.sharing
ome.services - package ome.services: Base services package for OMERO API services This includes classes that implement OMERO API services described as interfaces in the OMERO Common component.
ome.services.blitz - package ome.services.blitz
ome.services.blitz.fire - package ome.services.blitz.fire
ome.services.blitz.gateway - package ome.services.blitz.gateway
ome.services.blitz.gateway.services - package ome.services.blitz.gateway.services
ome.services.blitz.gateway.services.impl - package ome.services.blitz.gateway.services.impl
ome.services.blitz.gateway.services.util - package ome.services.blitz.gateway.services.util
ome.services.blitz.impl - package ome.services.blitz.impl
ome.services.blitz.measurements - package ome.services.blitz.measurements
ome.services.blitz.redirect - package ome.services.blitz.redirect
ome.services.blitz.util - package ome.services.blitz.util
ome.services.db - package ome.services.db
ome.services.delete - package ome.services.delete: Implementations of the ome.api.IDelete service.
ome.services.formats - package ome.services.formats
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.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.procs - package ome.services.procs: Internal process and process management This includes interfaces and classes that provide thread process management for internal processes critical to the operation of the OMERO server.
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.roi - package ome.services.roi
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.api.IShare support infrastructure.
ome.services.sharing.data - package ome.services.sharing.data
ome.services.throttling - package ome.services.throttling
ome.services.util - package ome.services.util: Helper classes to support OMERO service beans Instead of abstract classes, IOC methods and dependency injection is used to provide service interception for the Service (binary) bean classes.
ome.system - package ome.system: Provides the necessary container structure for the entire Omero system.
ome.tools - package ome.tools: OMERO Server Utility and Spring/Hibernate Tools Classes/Interfaces that implement File, Hibernate, Spring, Annotation, Hierarchy, etc. method mechanics for the OMERO server Related Documentation For more information, please see: TODO
ome.tools.hibernate - package ome.tools.hibernate: Hibernate specific tools for the OMERO Server Classes/Interfaces that implement Hibernate method mechanics for the OMERO server Related Documentation For more information, please see: TODO
ome.tools.lsid - package ome.tools.lsid: Life Science Identifier (LSID) tools Classes/Interfaces that manage conversions and creation of LSID unique identifiers Related Documentation For more information, please see: TODO
ome.tools.spring - package ome.tools.spring: OMERO Server tools specific to Spring Classes/Interfaces that implement AOP, Post-processing injection, session flushing, and factory management.
ome.util.math.geom2D - package ome.util.math.geom2D: Plane geometry data structures for OMERO This includes a several implementations of various two dimensional simple geometry classes to represent these structures within the OMERO system.
ome.util.mem - package ome.util.mem: Dynamic object instance and state management for OMERO This includes various implementations of copy and clonable operations.
ome.util.messages - package ome.util.messages: Messages package for specialized exception handling for OMERO.
omeis.providers.re - package omeis.providers.re: Red-Green-Blue (RGB) data structures and Image Rendering Service This package provides basic data structures to represent an RGB pixel set and provide a service for the rendering of this pixel set.
omeis.providers.re.codomain - package omeis.providers.re.codomain: Provides codomain pixel set data structures for Maps and Contexts.
omeis.providers.re.data - package omeis.providers.re.data: Provides classes needed to define XY planes within a dynamic 3D context.
omeis.providers.re.metadata - package omeis.providers.re.metadata
omeis.providers.re.quantum - package omeis.providers.re.quantum
OMENAME - Static variable in class pojos.ExperimenterData: Identifies the Experimenter#OMENAME field.
omero - package omero
omero.grid - package omero.grid
omero.model - package omero.model
omero.sys - package omero.sys
omero.util - package omero.util
OMERO_EVENT - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
OMERO_GROUP - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
OMERO_HOST - Static variable in class ome.system.Server: Java property name for use in configuration of the client connection.
OMERO_PASS - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
OMERO_PORT - Static variable in class ome.system.Server: Java property name for use in configuration of the client connection.
OMERO_USER - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
omeroClass(String, boolean) - Static method in class omero.util.IceMapper
OmeroContext - Class in ome.system: Provides static access for the creation of singleton and non-singleton application contexts.
OmeroContext(String) - Constructor for class ome.system.OmeroContext
OmeroContext(String[]) - Constructor for class ome.system.OmeroContext
OmeroContext(String[], boolean) - Constructor for class ome.system.OmeroContext
OmeroContext(String[], ApplicationContext) - Constructor for class ome.system.OmeroContext
OmeroContext(String[], boolean, ApplicationContext) - Constructor for class ome.system.OmeroContext
OmeroContext.Locator - Class in ome.system: provides access to the protected methods of ContextSingletonBeanFactoryLocator which cannot be used externally.
OmeroContext.Locator() - Constructor for class ome.system.OmeroContext.Locator
OmeroGateway - Class in ome.services.blitz.gateway
OmeroGateway(BlitzExecutor) - Constructor for class ome.services.blitz.gateway.OmeroGateway
OmeroInterceptor - Class in ome.security.basic: implements Interceptor for controlling various aspects of the Hibernate runtime.
OmeroInterceptor(Roles, SystemTypes, ExtendedMetadata, CurrentDetails, TokenHolder, SessionStats) - Constructor for class ome.security.basic.OmeroInterceptor
omerojava.util - package omerojava.util
OmeroMeasurementStore - Interface in ome.services.blitz.measurements: Sub-interface of MeasurementStore with extended life-cycle methods for handling exceptions during saving the measurements to multiple stores.
OmeroMetadata - Class in ome.services.blitz.impl: An implementation for MetadataStore and MetadataRetrieve that knows how to read and write the OMERO object model.
OmeroMetadata(DatabaseIdentity) - Constructor for class ome.services.blitz.impl.OmeroMetadata
OMEROMetadataStore - Class in ome.formats: An OMERO metadata store.
OMEROMetadataStore() - Constructor for class ome.formats.OMEROMetadataStore: Empty constructor for testing purposes.
OMEROMetadataStore(ServiceFactory) - Constructor for class ome.formats.OMEROMetadataStore: Creates a new instance.
OmeroOriginalFileMetadataProvider - Class in ome.services: OMERO implementation of an original file metadata provider, uses IQuery.
OmeroOriginalFileMetadataProvider(IQuery) - Constructor for class ome.services.OmeroOriginalFileMetadataProvider: Constructor.
OmeroReader - Class in ome.services.formats: Implementation of IFormatReader for use in export.
OmeroReader(RawPixelsStore, Pixels) - Constructor for class ome.services.formats.OmeroReader
OmeroReader(RawPixelsStorePrx, Pixels) - Constructor for class ome.services.formats.OmeroReader
onApplicationEvent(LoginAttemptMessage) - Method in class ome.security.auth.LoginAttemptListener
onApplicationEvent(EventLogMessage) - Method in class ome.security.basic.BasicSecuritySystem
onApplicationEvent(ApplicationEvent) - Method in class ome.services.blitz.fire.SessionManagerI
onApplicationEvent(ApplicationEvent) - Method in class ome.services.blitz.fire.TopicManager.Impl
onApplicationEvent(ApplicationEvent) - Method in class ome.services.blitz.util.CheckAllJobs
onApplicationEvent(ApplicationEvent) - Method in class ome.services.fulltext.EventLogLoader
onApplicationEvent(ApplicationEvent) - Method in class ome.services.roi.GeomTool
onApplicationEvent(ApplicationEvent) - Method in class ome.services.scheduler.SchedulerFactoryBean
onApplicationEvent(ApplicationEvent) - Method in interface ome.services.sessions.SessionManager
onApplicationEvent(ApplicationEvent) - Method in class ome.services.sessions.SessionManagerImpl
onApplicationEvent(ApplicationEvent) - Method in class ome.services.throttling.AbstractThrottlingStrategy
onApplicationEvent(ApplicationEvent) - Method in class ome.services.util.DropBoxDirectoryCheck
onApplicationEvent(ContextRefreshedEvent) - Method in class ome.services.util.NamespaceCheck
onApplicationEvent(ApplicationEvent) - Method in class ome.services.util.ServiceHandler
onApplicationEvent(ApplicationEvent) - 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).
onBoundaries(double, double) - Method in class ome.util.math.geom2D.EllipseArea: Implemented as specified by the PlaneArea I/F.
onBoundaries(double, double) - Method in interface ome.util.math.geom2D.PlaneArea: Controls if a specified point is on the boundary of the PlaneArea.
onBoundaries(double, double) - Method in class ome.util.math.geom2D.RectangleArea: Implemented as specified by the PlaneArea I/F.
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
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
onFlushDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: callsback to BasicSecuritySystem.checkManagedDetails(IObject, Details) for properly setting Details.
onHearbeat(Runnable) - Method in class omero.client
onLoad(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: default logic.
onlyAnnotatedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search: Restricts entities by the time in which any annotation (which matches the other filters) was added them.
onlyAnnotatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
onlyAnnotatedBetween_async(AMD_Search_onlyAnnotatedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
onlyAnnotatedBy(Details) - Method in interface ome.api.Search: Restricts entities by who has annotated them with an Annotation matching the other filters.
onlyAnnotatedBy(Details) - Method in class ome.services.SearchBean
onlyAnnotatedBy_async(AMD_Search_onlyAnnotatedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
onlyAnnotatedWith(Class...) - Method in interface ome.api.Search: Restricts entities to having an Annotation of all the given types.
onlyAnnotatedWith - Variable in class ome.services.search.SearchValues
onlyAnnotatedWith(Class...) - Method in class ome.services.SearchBean
onlyAnnotatedWith_async(AMD_Search_onlyAnnotatedWith, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
onlyCreatedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search: Restricts the time between which an entity may have been created.
onlyCreatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
onlyCreatedBetween_async(AMD_Search_onlyCreatedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
onlyIds(Long...) - Method in interface ome.api.Search: Restricts the set of ids which will be checked.
onlyIds - Variable in class ome.services.search.SearchValues
onlyIds(Long...) - Method in class ome.services.SearchBean
onlyIds_async(AMD_Search_onlyIds, List<Long>, Current) - Method in class ome.services.blitz.impl.SearchI
onlyModifiedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search: Restricts the time between which an entity may have last been modified.
onlyModifiedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
onlyModifiedBetween_async(AMD_Search_onlyModifiedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
onlyOwnedBy(Details) - Method in interface ome.api.Search: Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.
onlyOwnedBy(Details) - Method in class ome.services.SearchBean
onlyOwnedBy_async(AMD_Search_onlyOwnedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
onlyPermissionsChanged(Details, Details) - Static method in class ome.tools.hibernate.HibernateUtils
onlyType(Class<T>) - Method in interface ome.api.Search: Restricts the search to a single type.
onlyType(Class<T>) - Method in class ome.services.SearchBean
onlyType_async(AMD_Search_onlyType, String, Current) - Method in class ome.services.blitz.impl.SearchI
onlyTypes(Class<T>...) - Method in interface ome.api.Search: Restricts searches to a set of types.
onlyTypes - Variable in class ome.services.search.SearchValues
onlyTypes(Class<T>...) - Method in class ome.services.SearchBean
onlyTypes_async(AMD_Search_onlyTypes, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
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() - Method in class ome.system.OmeroContext
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: callsback to BasicSecuritySystem.newTransientDetails(IObject) for properly setting Details
onSaveOrUpdate(SaveOrUpdateEvent) - Method in class ome.security.basic.SaveEventListener
onSessionClosed(Runnable) - Method in class omero.client
onSetOmeroContext(OmeroContext) - Method in class ome.services.blitz.impl.AbstractAmdServant: To be overridden by subclasses.
onSetOmeroContext(OmeroContext) - Method in class ome.services.blitz.impl.MetadataStoreI
onShutdown(Runnable) - Method in class omero.client
onWindowChange() - Method in class omeis.providers.re.quantum.BinaryMaskQuantizer
onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_8_16_bit: The input window size changed, rebuild the LUT.
onWindowChange() - Method in class omeis.providers.re.quantum.QuantumStrategy: Notifies when the input interval has changed or the mapping strategy has changed.
openBytes(int, byte[], int, int, int, int) - Method in class ome.services.formats.OmeroReader
openTable(OriginalFile, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
Optimizations - Class in omeis.providers.re: A container for any potential optimizations that the renderer can enable based on the data and rendering settings it has been fed.
Optimizations() - Constructor for class omeis.providers.re.Optimizations
optional - Variable in class ome.services.query.QueryParameterDef: whether or not this QueryParameter can be omitted or its value null.
options - Variable in class ome.services.delete.BaseDeleteSpec: Options passed to the #initialize(long, Map) method, which may be used during #delete(Session, int) to alter behavior.
optlock - Variable in class ome.services.sharing.data.ShareData
or() - Method in interface ome.api.Search: Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the union of the two calls.
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.
or_async(AMD_Search_or, Current) - Method in class ome.services.blitz.impl.SearchI
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
origin - Variable in class ome.util.math.geom2D.Line: The origin point of the line.
OriginalFileMetadataProvider - Interface in ome.io.nio: Denotes an object which can provide metadata about original files and their formats.
OriginalFilesService - Class in ome.io.nio: Raw file service which provides access to FileBuffers.
OriginalFilesService(String) - Constructor for class ome.io.nio.OriginalFilesService: Constructor
originX1 - Variable in class ome.util.math.geom2D.Segment: The origin of the segment's first element.
originX2 - Variable in class ome.util.math.geom2D.Segment: The origin of the segment's first element.
orphan() - Method in class omero.sys.ParametersI: Sets the orphan parameter to true.
osf - Variable in class ome.logic.AdminImpl
OTFData - Class in pojos: Hosts an OTF.
OTFData(OTF) - Constructor for class pojos.OTFData: Creates a new instance.
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
overrideKeep() - Method in class ome.services.delete.AnnotationDeleteSpec: Returns true to prevent skipping of the entire subspec if there were any "excludes" passed in with the options.
overrideKeep() - Method in class ome.services.delete.BaseDeleteSpec: Always returns false.
overrideKeep() - Method in interface ome.services.delete.DeleteSpec: For some DeleteSpec type/option combinations, a "KEEP" setting may need to be overridden.
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
ownerCount(long) - Method in class ome.services.sharing.data.ShareMap
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 PojoOptions#isExperimenter() and PojoOptions#isGroup() booleans to see if a filter should be turned on.

P

pack(ReadOnlyByteArray, int, int) - Method in class omerojava.util.DoubleConverter: Implemented as specified by BytesConverter
pack(ReadOnlyByteArray, int, int) - Method in class omerojava.util.FloatConverter: Implemented as specified by BytesConverter
pack(ReadOnlyByteArray, int, int) - Method in class omerojava.util.IntConverter: Implemented as specified by BytesConverter
pack(ReadOnlyByteArray, int, int) - Method in class omerojava.util.UintConverter: Implemented as specified by BytesConverter
page(int, int) - Method in class omero.sys.ParametersI: Sets both the Filter.limit and Filter.offset values by wrapping the arguments in RInt and passing the values to ParametersI.page(RInt, RInt)
page(RInt, RInt) - Method in class omero.sys.ParametersI: Creates a Filter if necessary and sets both Filter.limit and Filter.offset.
param(String, Object) - Method in class ome.tools.hibernate.QueryBuilder
ParametersI - Class in omero.sys: Helper subclass of Parameters for simplifying method parameter creation.
ParametersI() - Constructor for class omero.sys.ParametersI: Default constructor creates the ParametersI.map() instance to prevent later NullPointerExceptions.
ParametersI(Map<String, RType>) - Constructor for class omero.sys.ParametersI: Uses (and does not copy) the given Map as the named parameter store in this instance.
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
params(Current) - Method in class omero.grid.InteractiveProcessorI
ParamsHelper - Class in omero.grid
ParamsHelper(ParamsHelper.Acquirer, Executor, Principal) - Constructor for class omero.grid.ParamsHelper
ParamsHelper.Acquirer - Interface in omero.grid: Interface added in order to allow ParamHelper instances to use methods from SharedResourcesI.
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: 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
parseAndSetInt(InitializationData, String, int) - Method in class omero.client
parseAwtPath(String) - Static method in class omero.model.SmartShape.Util
parseData(Map) - Method in interface ome.api.IResults: server-side parsing of data maps
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 org.hibernate.Critieria instance.
parsePoints(String) - Static method in class omero.model.SmartShape.Util
parsePointsToIntegerList(String) - Method in class pojos.ShapeData: Parses the points list from the string to a list of integer objects.
parsePointsToPath(String, boolean) - Static method in class omero.model.SmartShape.Util
parsePointsToPoint2DList(String) - Method in class pojos.ShapeData: Parses the points list from the string to a list of point2d objects.
parsers - Variable in class ome.services.fulltext.FullTextBridge
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(Details, Long, Long, boolean, boolean, boolean) - Method in class ome.tools.hibernate.SecurityFilter: tests that the Details argument passes the security test that this filter defines.
passivate() - Method in interface ome.api.StatefulServiceInterface: Perform whatever passivation is possible or throw an exception.
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
passivate_async(AMD_StatefulServiceInterface_passivate, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
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.
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
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(SimpleJdbcOperations) - Constructor for class ome.security.auth.PasswordUtil
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.Patcher
patch(Object) - Method in class ome.services.sharing.data.ShareDataHolder.Patcher
patch(Object) - Method in class ome.services.sharing.data.ShareItemHolder.Patcher
path(String) - Method in class ome.services.delete.DeleteEntry
path - Variable in class ome.services.scripts.RepoFile.FsFile
PDF - Static variable in class pojos.FileAnnotationData: Identifies the PDF file formats.
PdfParser - Class in ome.services.fulltext: FileParser for "application/pdf" files using PDFBox.
PdfParser() - Constructor for class ome.services.fulltext.PdfParser
PermissionData - Class in pojos: Simple data object to wrap a Permissions instance.
PermissionData() - Constructor for class pojos.PermissionData: Creates a new instance.
PermissionData(Permissions) - Constructor for class pojos.PermissionData: Creates a new instance.
permissions(Class<T>) - Method in class ome.logic.TypesImpl
permissionsClause(EventContext, QueryBuilder) - Static method in class ome.services.delete.DeleteState: Appends a clause to the QueryBuilder based on the current user.
PermissionsI - Class in omero.model: Blitz wrapper around the Permissions class.
PermissionsI() - Constructor for class omero.model.PermissionsI
PermissionsI(String) - Constructor for class omero.model.PermissionsI
PermissionsType - Class in ome.tools.hibernate
PermissionsType() - Constructor for class ome.tools.hibernate.PermissionsType
PermissionsVerifierI - Class in ome.services.blitz.fire
PermissionsVerifierI(Ring, SessionManager) - Constructor for class ome.services.blitz.fire.PermissionsVerifierI
PermitAll - Annotation Type in ome.annotations: Security annotation which allows a method to be called by all users regardless of their status.
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.fulltext: EventLogLoader implementation which keeps tracks of the last EventLog instance, and always provides the next unindexed instance.
PersistentEventLogLoader() - Constructor for class ome.services.fulltext.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
PgArrayHelper - Class in ome.services.db: Strategy class for setting array values in the database.
PgArrayHelper(SimpleJdbcOperations) - Constructor for class ome.services.db.PgArrayHelper
PHOTOMETRIC_MONOCHROME - Static variable in class omeis.providers.re.Renderer: Identifies the type used to store photometric interpretation values.
pid() - Method in class omero.util.TempFileManager: Returns some representation of the current process's id
PIXEL_TYPE_2BYTE_COMPLEX - Static variable in class ome.io.nio.DeltaVisionHeader: Pixels are of type 4 byte, complex, composed of two 2 byte signed integers.
PIXEL_TYPE_4BYTE_COMPLEX - Static variable in class ome.io.nio.DeltaVisionHeader: Pixels are of type 8 byte, complex, composed of two 4 byte floating-point numbers.
PIXEL_TYPE_BYTE - Static variable in class ome.io.nio.DeltaVisionHeader: Pixels are of type 1 byte, unsigned integer.
PIXEL_TYPE_FLOAT - Static variable in class ome.io.nio.DeltaVisionHeader: Pixels are of type 4 byte, floating-point.
PIXEL_TYPE_SIGNED_SHORT - Static variable in class ome.io.nio.DeltaVisionHeader: Pixels are of type 2 byte, unsigned integer.
PIXEL_TYPE_UNSIGNED_SHORT - Static variable in class ome.io.nio.DeltaVisionHeader: Pixels are of type 2 byte, signed integer.
PixelBuffer - Interface in ome.io.nio: This interface declares the I/O responsibilities of a buffer, file or otherwise, that contains a 5-dimensional Pixel array (XYZCT).
PixelData - Class in ome.io.nio: Represents a block of pixel data.
PixelData(PixelsType, ByteBuffer) - Constructor for class ome.io.nio.PixelData: Default constructor.
PixelData - Class in ome.services.roi: Strategy for loading and optionally caching pixel data.
PixelData(PixelsService, IPixels) - Constructor for class ome.services.roi.PixelData
pixelMap - Static variable in class omerojava.util.PixelTypes: Set the pixels Map containing the byte size of the map.
PIXELS - Static variable in class pojos.ImageData: Identifies the Image#PIXELS field.
PIXELS_PATH - Static variable in class ome.io.nio.AbstractFileSystemService
PixelsCache - Class in omerojava.util: Caches Plane2D data, within a given pixels set, that have been rendered.
PixelsCache(int, int) - Constructor for class omerojava.util.PixelsCache: Creates a new instance.
pixelsData - Variable in class ome.logic.RenderingSettingsImpl: Reference to the service used to retrieve the pixels data.
PixelsData - Class in pojos: The data that makes up an OME Pixels object along with a back pointer to the Image that owns this Pixels.
PixelsData() - Constructor for class pojos.PixelsData: Creates a new instance.
PixelsData(Pixels) - Constructor for class pojos.PixelsData: Creates a new instance.
PixelsI - Class in ome.services.blitz.impl: Implementation of the IPixels service.
PixelsI(IPixels, BlitzExecutor) - Constructor for class ome.services.blitz.impl.PixelsI
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 - Class in ome.io.nio
PixelsService(String) - Constructor for class ome.io.nio.PixelsService: Constructor.
pixelsService - Variable in class ome.services.projection.ProjectionBean: Reference to the service used to retrieve the pixels data.
pixelsType - Variable in class ome.io.nio.PixelData: Type of the pixel data.
PixelTypes - Class in omerojava.util
PixelTypes() - Constructor for class omerojava.util.PixelTypes
Plane1D - Class in omerojava.util
Plane1D(ReadOnlyByteArray, int, int, int, BytesConverter) - Constructor for class omerojava.util.Plane1D: Creates a new intance.
Plane2D - Class in omeis.providers.re.data
Plane2D(PlaneDef, Pixels, PixelData) - Constructor for class omeis.providers.re.data.Plane2D: Constructor that sub-classes must call.
Plane2D - Class in omerojava.util: Holds structure used to mapped the raw pixels data.
Plane2D(ReadOnlyByteArray, int, int, int, BytesConverter) - Constructor for class omerojava.util.Plane2D: Creates a new intance.
PlaneArea - Interface in ome.util.math.geom2D: Interface that all areas of the Euclidean space R² must implement.
planeDef - Variable in class omeis.providers.re.data.Plane2D: The type of plane.
PlaneDef - Class in omeis.providers.re.data: Identifies a 2D-plane in the XYZ moving frame of the 3D stack.
PlaneDef(int, int) - Constructor for class omeis.providers.re.data.PlaneDef: Creates a new instance.
PlaneFactory - Class in omeis.providers.re.data: Encapsulates access to the image raw data.
PlaneFactory() - Constructor for class omeis.providers.re.data.PlaneFactory
PlanePoint - Class in ome.util.math.geom2D: Represents a point in the Euclidean space R².
PlanePoint(double, double) - Constructor for class ome.util.math.geom2D.PlanePoint: Creates a new instance.
planes - Variable in class ome.services.formats.OmeroReader
PlaneSlicingContext - Class in omeis.providers.re.codomain: We consider that the image is composed of eight 1-bit planes ranging from bit-plane 0 for the least significant bit to bit-plane 7 for the most significant bit.
PlaneSlicingContext(int, int, boolean) - Constructor for class omeis.providers.re.codomain.PlaneSlicingContext: Creates a new instance.
PLATE_LINKS - Static variable in class pojos.ScreenData: Identifies the Screen#PLATELINKS field.
PlateAcquisitionData - Class in pojos: The data that makes up an OME PlateAcquisition.
PlateAcquisitionData() - Constructor for class pojos.PlateAcquisitionData: Creates a new instance.
PlateAcquisitionData(PlateAcquisition) - Constructor for class pojos.PlateAcquisitionData: Creates a new instance.
PlateData - Class in pojos: The data that makes up an OME Plate along with links to its contained Well and enclosing Screen as well as the Experimenter that owns this Plate.
PlateData() - Constructor for class pojos.PlateData: Creates a new instance.
PlateData(Plate) - Constructor for class pojos.PlateData: Creates a new instance.
PLATEIMAGES_QUERY - Static variable in class ome.services.delete.DeleteBean
PointData - Class in pojos: Represents a point in the Euclidean space R².
PointData(Shape) - Constructor for class pojos.PointData: Creates a new instance.
PointData() - Constructor for class pojos.PointData: Create a new instance of PointData, creating a new pointI Object.
PointData(double, double) - Constructor for class pojos.PointData: Create a new instance of the PointData,
points(double, double, double, double) - Static method in class omero.model.SmartShape.Util: Returns the four corner points of a rectangle
pointsByBoundingBox(Shape, Rectangle2D, SmartShape.PointCallback) - Static method in class omero.model.SmartShape.Util
pointsToPath(List<Point>, boolean) - Static method in class omero.model.SmartShape.Util
pojos - package pojos
pojos.util - package pojos.util
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
poll(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
PolygonData - Class in pojos: Represents an Polygon shape in the Euclidean space R².
PolygonData(Shape) - Constructor for class pojos.PolygonData: Creates a new instance.
PolygonData() - Constructor for class pojos.PolygonData: Creates a new instance of PolygonData.
PolygonData(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Constructor for class pojos.PolygonData: Creates a new instance of the PolygonData, set the points in the polygon.
PolylineData - Class in pojos: Represents an Polyline shape in the Euclidean space R².
PolylineData(Shape) - Constructor for class pojos.PolylineData: Creates a new instance.
PolylineData() - Constructor for class pojos.PolylineData: Creates a new instance of polyline, creating a new PolylineI Object.
PolylineData(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Constructor for class pojos.PolylineData: Create a new instance of the PolylineData, set the points in the polyline.
POLYNOMIAL - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a polynomial map for the quantization process.
PolynomialMap - Class in omeis.providers.re.quantum: This class implements the QuantumMap interface.
PolynomialMap() - Constructor for class omeis.providers.re.quantum.PolynomialMap
pop(DeleteOpts) - Method in class ome.services.delete.DeleteEntry
pop() - Method in class ome.services.delete.DeleteOpts
pop(DeleteOpts) - Method in class ome.services.delete.DeleteStep
pop(List<IObject>) - Method in class ome.services.SearchBean: Wrapper method which should be called on all results for the user.
pop(String[]) - Static method in class prefs: Creates a new subarray from the argument, effectively popping off the first element.
popRoi - Variable in class ome.services.blitz.impl.MetadataStoreI
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.
populateMinMax_async(AMD_MetadataStore_populateMinMax, double[][][], Current) - Method in class ome.services.blitz.impl.MetadataStoreI
PopulateRoiJob - Class in ome.services.roi: Start-up task which guarantees that lib/python/populateroi.py is added as a script to the server.
PopulateRoiJob(Roles, String, Executor) - Constructor for class ome.services.roi.PopulateRoiJob
PopulateRoiJob(Roles, String, Executor, File) - Constructor for class ome.services.roi.PopulateRoiJob
PopulateRoiJob(Roles, Principal, Executor, File) - Constructor for class ome.services.roi.PopulateRoiJob
postFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor
postProcess(ListableBeanFactory) - Method in class ome.services.delete.BaseDeleteSpec
postProcess(ListableBeanFactory) - Method in class ome.services.delete.DeleteEntry: Load the spec which has the same name as this entry, but do not load the spec if the name matches DeleteEntry.name.
postProcess(ListableBeanFactory) - Method in interface ome.services.delete.DeleteSpec: Gives all specs a chance to reference subspecs.
postProcess_async(AMD_MetadataStore_postProcess, Current) - Method in class ome.services.blitz.impl.MetadataStoreI: Called after some number of Passes the #savedPixels to a background processor for further work.
postProcessAfterInitialization(Object, String) - Method in class ome.services.blitz.util.ApiConsistencyCheck
postProcessBeforeInitialization(Object, String) - Method in class ome.services.blitz.util.ApiConsistencyCheck: No-op
preClose() - Method in class ome.services.blitz.gateway.OmeroGateway
preClose() - Method in class ome.services.blitz.impl.AbstractAmdServant
preClose() - Method in class ome.services.blitz.impl.ExporterI
preClose() - Method in class ome.services.blitz.impl.MetadataStoreI
preClose() - Method in class ome.services.blitz.impl.SharedResourcesI
Preference - Class in ome.system: Definition of a server configuration variable ("preference") along with its mutability, visibility, aliases and other important information.
Preference() - Constructor for class ome.system.Preference: By default, configures this instance for PropertyPlaceholderConfigurer.SYSTEM_PROPERTIES_MODE_OVERRIDE as well as ignoring unfound resources.
Preference(String, boolean, Preference.Visibility, String[]) - Constructor for class ome.system.Preference
Preference.Visibility - Enum in ome.system
PreferenceContext - Class in ome.system: Central configuration for OMERO properties from (in order): Any injected Properties instances Java System.getProperties() Any configured property files As of OMERO 4.2, server configurations are not stored in Java's Preferences API but in an IceGrid xml file under etc/grid of the server installation.
PreferenceContext() - Constructor for class ome.system.PreferenceContext: By default, configures this instance for PropertyPlaceholderConfigurer.SYSTEM_PROPERTIES_MODE_OVERRIDE as well as ignoring unfound resources.
preFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor
prefs - Class in <Unnamed>: Command-line (and static) utility for working with the omero.prefs Preferences node in order to store Java properties-file like values on a user basis.
prefs() - Constructor for class prefs
prepare(Set<Long>) - Method in interface ome.api.RawPixelsStore: Prepares the stateful service with a cache of loaded Pixels objects.
prepare(Set<Long>) - Method in class ome.services.RawPixelsBean
prepare_async(AMD_RawPixelsStore_prepare, List<Long>, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
preparePassword(String) - Method in class ome.security.auth.PasswordUtil
prepareReload() - Method in class ome.services.sessions.SessionManagerImpl
prepareReload() - Method in interface ome.services.sessions.state.SessionCache.StaleCacheListener: Called once before all the reload methods are called to push out the current state to database and trigger any exceptions as the current user.
previewImageDelete(long, boolean) - Method in interface ome.api.IDelete: Returns all entities which would be deleted by a call to IDelete.deleteImage(long, boolean).
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.
previewImageDelete_async(AMD_IDelete_previewImageDelete, long, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI
primaryColorEnabled - Variable in class omeis.providers.re.Optimizations: The channel bindings are only "primary" colors.
PRIMITIVE - Static variable in class omero.util.IceMapper
PRIMITIVE_FILTERABLE_COLLECTION_MAP - Static variable in class omero.util.IceMapper
PRIMITIVE_MAP - Static variable in class omero.util.IceMapper
principal - Variable in class ome.services.blitz.fire.Ring
principal() - Method in class ome.services.blitz.fire.Ring
principal() - Method in interface ome.services.blitz.redirect.Redirector.Context: Principal instance which can be used for internal calls the Executor.
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.
Principal - Class in ome.system: implementation of Principal.
Principal(String) - Constructor for class ome.system.Principal: Creates a Principal with null group and event type.
Principal(String, String, String) - Constructor for class ome.system.Principal
principal - Variable in class ome.system.SessionInitializer: Principal given by the user
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
print(String) - Method in class ome.services.blitz.util.CommonsLoggingAdapter
print(String[]) - Static method in class prefs: Prints the arg array and returns an empty array (for exit purposes)
printDebug(String[]) - Static method in class prefs: Delegates to prefs.printErr(String[]) iff prefs.DEBUG is true.
printErr(String[]) - Static method in class prefs: Prints the arg array and returns the input array (for exit purposes)
printErrorText(Throwable) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities: Utility method to print the error message
process(long) - Method in class ome.services.procs.ImportProcessor
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
process - Variable in class omero.grid.ProcessCallbackI: Proxy passed to this instance on creation.
ProcessCallback - Interface in ome.services.procs
ProcessCallbackI - Class in omero.grid
ProcessCallbackI(client, ProcessPrx) - Constructor for class omero.grid.ProcessCallbackI
ProcessCallbackI(client, ProcessPrx, boolean) - Constructor for class omero.grid.ProcessCallbackI
ProcessCallbackI(ObjectAdapter, ProcessPrx) - Constructor for class omero.grid.ProcessCallbackI
ProcessCallbackI(ObjectAdapter, ProcessPrx, boolean) - Constructor for class omero.grid.ProcessCallbackI
ProcessCallbackI.Action - Enum in omero.grid
processCancelled(Process) - Method in class ome.services.JobBean
processCancelled(Process) - Method in interface ome.services.procs.ProcessCallback
processCancelled(boolean, Current) - Method in class omero.grid.ProcessCallbackI
processFinished(Process) - Method in class ome.services.JobBean
processFinished(Process) - Method in interface ome.services.procs.ProcessCallback
processFinished(int, Current) - Method in class omero.grid.ProcessCallbackI
processKilled(boolean, Current) - Method in class omero.grid.ProcessCallbackI
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().
ProcessManager.Work(SecuritySystem, Processor...) - Constructor for class ome.services.procs.ProcessManager.Work
processor() - Method in interface ome.services.procs.Process
Processor - Interface in ome.services.procs
processor() - Method in class ome.services.procs.ProcessSkeleton
ProcessorCallbackI - Class in ome.services.blitz.impl: Callback used to lookup active processors via IceStorm.
ProcessorCallbackI(ServiceFactoryI) - Constructor for class ome.services.blitz.impl.ProcessorCallbackI: Simplified constructor used to see if any usermode processor is active for either the current group or the current user.
ProcessorCallbackI(ServiceFactoryI, ResultHolder<String>, Job) - Constructor for class ome.services.blitz.impl.ProcessorCallbackI: Primary constructor.
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
procMap - Variable in class ome.services.procs.ProcessManager.Work: Map of all active processes.
PROJECT_LINKS - Static variable in class pojos.DatasetData: Identifies the Dataset#PROJECTLINKS field.
ProjectData - Class in pojos: The data that makes up an OME Project along with links to its contained Datasets and the Experimenter that owns this Project.
ProjectData() - Constructor for class pojos.ProjectData: Creates a new instance.
ProjectData(Project) - Constructor for class pojos.ProjectData: Creates a new instance.
projection(String, Parameters) - Method in interface ome.api.IQuery: Return a list of Java Object instances (not IObject instances).
projection(String, Parameters) - Method in class ome.logic.QueryImpl
projection_async(AMD_IQuery_projection, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
ProjectionBean - Class in ome.services.projection: Implements projection functionality for Pixels sets as declared in IProjection.
ProjectionBean() - Constructor for class ome.services.projection.ProjectionBean
ProjectionI - Class in ome.services.blitz.impl: Implementation of the IProjection service.
ProjectionI(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ProjectionI
projectPixels(long, PixelsType, int, int, int, List<Integer>, int, int, int, String) - Method in interface ome.api.IProjection: Performs a projection through selected optical sections and optical sections for a given set of time points of a Pixels set.
projectPixels(long, PixelsType, int, int, int, List<Integer>, int, int, int, String) - Method in class ome.services.projection.ProjectionBean
projectPixels_async(AMD_IProjection_projectPixels, long, PixelsType, ProjectionType, int, int, List<Integer>, int, int, int, String, Current) - Method in class ome.services.blitz.impl.ProjectionI
projectStack(long, PixelsType, int, int, int, int, int, int) - Method in interface ome.api.IProjection: Performs a projection through the optical sections of a particular wavelength at a given time point of a Pixels set.
projectStack(long, PixelsType, int, int, int, int, int, int) - Method in class ome.services.projection.ProjectionBean
projectStack_async(AMD_IProjection_projectStack, long, PixelsType, ProjectionType, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.ProjectionI
ProjectWithImageNameBridge - Class in ome.services.fulltext.bridges: Example custom FieldBridge implementation which parses all Image names from a Project and inserts them into the index for that Project.
ProjectWithImageNameBridge() - Constructor for class ome.services.fulltext.bridges.ProjectWithImageNameBridge
propagateHiddenValues(IObject, IObject) - Method in class ome.security.basic.MergeEventListener
proxy() - Method in class ome.services.blitz.impl.ServiceFactoryI
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 null to ProxyCleanupFilter.ProxyCleanupFilter(CurrentDetails) such that all restricted objects will be unloaded.
ProxyCleanupFilter(CurrentDetails) - Constructor for class ome.tools.hibernate.ProxyCleanupFilter: Constructor take a CurrentDetails object in order to check the security restrictions on certain objects.
ProxyCleanupFilter.Interceptor - Class in ome.tools.hibernate: wraps a filter for each invocation
ProxyCleanupFilter.Interceptor() - Constructor for class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
proxyForSession(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
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
pt(double, double) - Method in class ome.services.roi.GeomTool
publisher - Variable in class ome.services.fulltext.BridgeHelper
publisher - Variable in class ome.services.sessions.stats.CounterFactory
publisherOrNull(String) - Method in class ome.services.blitz.fire.TopicManager.Impl
publishEvent(ApplicationEvent) - Method in class ome.system.OmeroContext
publishMessage(InternalMessage) - Method in class ome.system.OmeroContext: Convenience method around OmeroContext.publishEvent(org.springframework.context.ApplicationEvent) which catches all MessageException and unwraps the contained Throwable instance and rethrows.
purgeNode(String) - Method in class ome.services.blitz.fire.Ring
push(DeleteOpts, EventContext) - Method in class ome.services.delete.DeleteEntry
push(DeleteOpts.Op, boolean, EventContext) - Method in class ome.services.delete.DeleteOpts: Adds the given operation to the current list if the user has permissions to do so.
push(DeleteOpts) - Method in class ome.services.delete.DeleteStep
put(String, String) - Method in class ome.security.auth.AttributeSet
put(Identity, Object) - Method in class ome.services.blitz.util.ServantHolder
put(Callback) - Method in class ome.services.throttling.Queue
putSession(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache: Puts a session blindly into the context.
PYTHONSCRIPT - Static variable in class omero.grid.ParamsHelper: The text representation of the format in a python script.

Q

qDef - Variable in class omeis.providers.re.quantum.QuantumStrategy: Reference to a quantumDef object.
Quantization_8_16_bit - Class in omeis.providers.re.quantum: Quantization process.
Quantization_8_16_bit(QuantumDef, PixelsType) - Constructor for class omeis.providers.re.quantum.Quantization_8_16_bit: Creates a new strategy.
QuantizationException - Exception in omeis.providers.re.quantum: This exception is thrown during the quantization process if something goes wrong.
QuantizationException() - Constructor for exception omeis.providers.re.quantum.QuantizationException: Creates a new exception.
QuantizationException(String) - Constructor for exception omeis.providers.re.quantum.QuantizationException: Constructs a new exception with the specified detail message.
QuantizationException(Throwable) - Constructor for exception omeis.providers.re.quantum.QuantizationException: Constructs a new exception with the specified cause.
QuantizationException(String, Throwable) - Constructor for exception omeis.providers.re.quantum.QuantizationException: Constructs a new exception with the specified detail message and cause.
quantize(double) - Method in class omeis.providers.re.quantum.BinaryMaskQuantizer: Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.Quantization_8_16_bit: Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.QuantumStrategy: Maps a value from [windowStart, windowEnd] to a value in the codomain interval.
QuantumFactory - Class in omeis.providers.re.quantum: Factory to create objects to carry out quantization for a given context.
QuantumFactory(List<Family>) - Constructor for class omeis.providers.re.quantum.QuantumFactory: Default constructor.
QuantumMap - Interface in omeis.providers.re.quantum: Provides methods to map value.
QuantumStrategy - Class in omeis.providers.re.quantum: Subclasses Work on explicit pixel types.
QuantumStrategy(QuantumDef, PixelsType) - Constructor for class omeis.providers.re.quantum.QuantumStrategy: Creates a new instance.
query() - Method in class ome.services.fulltext.AllEntitiesPseudoLogLoader
query() - Method in class ome.services.fulltext.AllEventsLogLoader
query() - Method in class ome.services.fulltext.EventLogLoader
query - Variable in class ome.services.fulltext.PersistentEventLogLoader: Query used with parameter 'name' to lookup configuration value
query() - Method in class ome.services.fulltext.PersistentEventLogLoader
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
queryBackupIds(Session, int, DeleteEntry, QueryBuilder) - Method in class ome.services.delete.AnnotationDeleteSpec
queryBackupIds(Session, int, DeleteEntry, QueryBuilder) - Method in class ome.services.delete.BaseDeleteSpec
queryBackupIds(Session, int, DeleteEntry, QueryBuilder) - Method in interface ome.services.delete.DeleteSpec: If a given path is deleted before its sub-path, this points to a one-to-one relationship.
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(int) - Constructor for class ome.tools.hibernate.QueryBuilder
QueryConstraints - Class in ome.services.delete: AdminAction which queries all datasets and annotations belonging to the given Image
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.
QueryI - Class in ome.services.blitz.impl: Implementation of the IQuery service.
QueryI(IQuery, BlitzExecutor) - Constructor for class ome.services.blitz.impl.QueryI
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 etc/omero.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.
queryResults(Class, Set, String[], boolean[], int, int) - Method in interface ome.api.IResults: querying for IResults
queryResultsPrimitive(String, int[], String[], boolean[], int, int) - Method in interface ome.api.IResults
queryService - Variable in class ome.services.fulltext.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.
Queue - Class in ome.services.throttling: Manages AMD-based method dispatches from blitz
Queue(OmeroContext) - Constructor for class ome.services.throttling.Queue
QUEUED - Static variable in interface ome.api.JobHandle
queueDelete_async(AMD_IDelete_queueDelete, DeleteCommand[], Current) - Method in class ome.services.blitz.impl.DeleteI

R

R_BAND - Static variable in class omeis.providers.re.RGBBuffer: Index of the red band in the image's data buffer.
random(int) - Method in class ome.services.roi.GeomTool
randomize(Random) - Method in class omero.model.SmartEllipseI
randomize(Random) - Method in class omero.model.SmartLineI
randomize(Random) - Method in class omero.model.SmartMaskI
randomize(Random) - Method in class omero.model.SmartPathI
randomize(Random) - Method in class omero.model.SmartPointI
randomize(Random) - Method in class omero.model.SmartPolygonI
randomize(Random) - Method in class omero.model.SmartPolylineI
randomize(Random) - Method in class omero.model.SmartRectI
randomize(Random) - Method in interface omero.model.SmartShape: Initializes this shape with completely random data.
randomize(Random) - Method in class omero.model.SmartTextI
rarray(RType...) - Static method in class omero.rtypes
rarray(Collection<RType>) - Static method in class omero.rtypes
RatingAnnotationData - Class in pojos: Annotation used to rate an object.
RatingAnnotationData() - Constructor for class pojos.RatingAnnotationData: Creates a new instance of value LEVEL_ZERO.
RatingAnnotationData(int) - Constructor for class pojos.RatingAnnotationData: Creates a new instance.
RatingAnnotationData(LongAnnotation) - Constructor for class pojos.RatingAnnotationData: Creates a new instance.
RawFileBean - Class in ome.services: Raw file gateway which provides access to the OMERO file repository.
RawFileBean() - Constructor for class ome.services.RawFileBean: default constructor
RawFileBean(boolean) - Constructor for class ome.services.RawFileBean: overriden to allow Spring to set boolean
RawFileStore - Interface in ome.api: Raw file gateway which provides access to the OMERO file repository.
RawFileStoreI - Class in ome.services.blitz.impl: Implementation of the RawFileStore service.
RawFileStoreI(RawFileStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawFileStoreI
RawFileStoreService - Interface in ome.services.blitz.gateway.services
RawFileStoreServiceImpl - Class in ome.services.blitz.gateway.services.impl
RawFileStoreServiceImpl(RawFileStorePrx) - Constructor for class ome.services.blitz.gateway.services.impl.RawFileStoreServiceImpl: Create the ImageService passing the gateway.
RawPixelsBean - Class in ome.services: Implementation of the RawPixelsStore stateful service.
RawPixelsBean() - Constructor for class ome.services.RawPixelsBean: default constructor
RawPixelsBean(boolean) - Constructor for class ome.services.RawPixelsBean: overriden to allow Spring to set boolean
RawPixelsStore - Interface in ome.api: Binary data provider.
RawPixelsStoreI - Class in ome.services.blitz.impl: Implementation of the RawPixelsStore service.
RawPixelsStoreI(RawPixelsStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawPixelsStoreI
RawPixelsStoreService - Interface in ome.services.blitz.gateway.services
RawPixelsStoreServiceImpl - Class in ome.services.blitz.gateway.services.impl
RawPixelsStoreServiceImpl(RawPixelsStorePrx) - Constructor for class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl: Create the ImageService passing the gateway.
rbool(boolean) - Static method in class omero.rtypes
rclass(String) - Static method in class omero.rtypes
rdouble(double) - Static method in class omero.rtypes
read(long, int) - Method in interface ome.api.RawFileStore: Delegates to FileBuffer
read(ByteBuffer) - Method in class ome.io.nio.FileBuffer: Delegates to FileChannel
read(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer: Delegates to FileChannel
read(long, long, int) - Method in class ome.services.blitz.gateway.services.impl.RawFileStoreServiceImpl
read(long, long, int) - Method in interface ome.services.blitz.gateway.services.RawFileStoreService: Read from the file in the rawFileStore.
read(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
read_async(AMD_Exporter_read, long, int, Current) - Method in class ome.services.blitz.impl.ExporterI
read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
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
readerClass - Static variable in class ome.services.util.DBEnumCheck
readOnly - Variable in class ome.security.basic.EventHandler
readOnly - Variable in class ome.services.sessions.SessionManagerImpl
READONLY_FLAG - Static variable in class pojos.ShapeData: Flag stating that the ROI is read only.
ReadOnlyByteArray - Class in ome.util.mem: A read-only slice of a given array.
ReadOnlyByteArray(byte[], int, int) - Constructor for class ome.util.mem.ReadOnlyByteArray: Creates a read-only slice of base.
ReadOnlyByteArray - Class in omerojava.util: A read-only slice of a given array.
ReadOnlyByteArray(byte[], int, int) - Constructor for class omerojava.util.ReadOnlyByteArray: Creates a read-only slice of base.
reapSession(String) - Method in class ome.services.blitz.fire.SessionManagerI: Destroys all the ServiceFactoryI instances based on the given sessionId.
recreate(Connection, String, Comparator, Map) - Static method in class ome.services.sharing.data.ShareItems
recreate(Connection, String, Comparator) - Static method in class ome.services.sharing.data.ShareItems
recreate(Connection, String, Comparator, Map) - Static method in class ome.services.sharing.data.ShareMap
recreate(Connection, String, Comparator) - Static method in class ome.services.sharing.data.ShareMap
rect(double, double, double, double) - Method in class ome.services.roi.GeomTool
RectangleArea - Class in ome.util.math.geom2D: Represents a rectangle in the Euclidean space R².
RectangleArea() - Constructor for class ome.util.math.geom2D.RectangleArea: Constructs a new RectangleAreaAdapter whose top-left corner is (0, 0) and whose width and height are both zero.
RectangleArea(int, int, int, int) - Constructor for class ome.util.math.geom2D.RectangleArea: Constructs a new RectangleAreaAdapter whose top-left corner is specified as (x, y) and whose width and height are specified by the arguments of the same name.
RectangleData - Class in pojos: Represents a rectangle in the Euclidean space R².
RectangleData(Shape) - Constructor for class pojos.RectangleData: Creates a new instance.
RectangleData() - Constructor for class pojos.RectangleData: Creates a new instance with a default rectangle.
RectangleData(double, double, double, double) - Constructor for class pojos.RectangleData: Creates a new instance of the RectangleData.
RED_INDEX - Static variable in class omeis.providers.re.ColorsFactory: Index of the red component of a color.
Redirector - Interface in ome.services.blitz.redirect: Strategy interface for helping a Ring instance decide whether to redirect SessionPrx creation to another SessionManagerI instance.
Redirector.Context - Interface in ome.services.blitz.redirect: Interface implemented by Ring instances to allow passing in the context necessary for making strategy decisions.
refresh(T) - Method in interface ome.api.IQuery: refreshes an entire IObject graph, recursive loading all data for the managed instances in the graph from the database.
refresh(T) - Method in class ome.logic.QueryImpl
refresh_async(AMD_IQuery_refresh, IObject, Current) - Method in class ome.services.blitz.impl.QueryI
refreshAll() - Method in class ome.system.OmeroContext: refreshes all the nested OmeroContexts within this instance.
refreshAllIfNecessary() - Method in class ome.system.OmeroContext: Calls #refreshAll() if {@link #isRunning()} throws an {@link IllegalStateException}.
register(String, ObjectPrx, boolean) - Method in class ome.services.blitz.fire.TopicManager.Impl
register(String, ObjectPrx, boolean) - Method in interface ome.services.blitz.fire.TopicManager: Enforces no security constraints.
register(Communicator) - Method in class ome.services.roi.RoiTypes.ObjectFactory
register(Communicator) - Method in class omero.rtypes.ObjectFactory
registerAll(Ehcache, CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
registerCallback(ProcessCallbackPrx, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
registerCallback(ProcessCallback) - Method in interface ome.services.procs.Process
registerCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton
registerObjectFactory(Map<String, ObjectFactory>) - Method in class ome.services.blitz.util.BlitzConfiguration: Registers both the code generated ObjectFactory for all the omero.model.* classes as well as all the classes which the server would like to receive from clients.
registerServant(Identity, Object) - Method in class ome.services.blitz.impl.ServiceFactoryI: Registers the servant with the adapter (or throws an exception if one is already registered) as well as configures the servant in any post-Spring way necessary, based on the type of the servant.
RegisterServantMessage - Class in ome.services.blitz.util: InternalMessage raised when a servant should be registered for clean.
RegisterServantMessage(Object, Object, Current) - Constructor for class ome.services.blitz.util.RegisterServantMessage
RegisterServiceCleanupMessage - Class in ome.services.messages: Published when some resource must be cleaned up after method execution.
RegisterServiceCleanupMessage(Object, Object) - Constructor for class ome.services.messages.RegisterServiceCleanupMessage
registerTrigger(String, Trigger) - Method in class ome.services.scheduler.SchedulerFactoryBean: Registers a JobDetailAwareTrigger.
Registry - Interface in ome.services.blitz.fire: Helper class which makes the RegistryPrx available within OmeroBlitz.
registry - Variable in class ome.services.blitz.fire.SessionManagerI
Registry.Impl - Class in ome.services.blitz.fire
Registry.Impl(Communicator) - Constructor for class ome.services.blitz.fire.Registry.Impl
reindex(T) - Method in class ome.services.fulltext.BridgeHelper: Publishes a ReindexMessage which will get processed asynchronously.
reindexAll(List<T>) - Method in class ome.services.fulltext.BridgeHelper: 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
release(DeleteStep) - Method in class ome.services.delete.DeleteState
releaseLock(String) - Method in class ome.services.blitz.util.ServantHolder: Releases the given lock if found, otherwise throws an InternalException
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(SessionContext) - Method in interface ome.services.sessions.state.SessionCache.StaleCacheListener: Method called for every active session in the cache.
ReloadFilter - Class in ome.tools.hibernate: UpdateFilter subclass specialized for use with the Session.save(Object) (as opposed to Session.merge(Object)) method.
ReloadFilter(Session) - Constructor for class ome.tools.hibernate.ReloadFilter
ReloadingRefreshEventListener - Class in ome.tools.hibernate: responsible for responding to RefreshEvent. in particular in reloading the unloaded entities.
ReloadingRefreshEventListener() - Constructor for class ome.tools.hibernate.ReloadingRefreshEventListener
remove() - Method in interface ome.api.Search: Unsupported operation.
remove(Identity) - Method in class ome.services.blitz.util.ServantHolder
remove() - Method in class ome.services.delete.BaseDeleteSpec.SubSpecIterator
remove() - Method in class ome.services.fulltext.EventBacklog: Removes and returns the next EventLog instance or null if none is present.
remove() - Method in class ome.services.fulltext.EventLogLoader
remove() - Method in class ome.services.SearchBean
remove() - Method in class omeis.providers.re.codomain.CodomainChain: Removes all CodomainMapContexts except the identity and resets the interval.
remove(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain: Removes a map context from the chain.
remove(Resources.Entry) - Method in class omero.util.Resources
remove_async(AMD_Search_remove, Current) - Method in class ome.services.blitz.impl.SearchI
remove_path(File) - Static method in class omero.util.TempFileManager: Calls TempFileManager.removePath(File) on TempFileManager.manager.
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: Implemented as specified by the RenderingEngine interface.
removeCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine: Removes the specified context from the chain.
removeCodomainMap_async(AMD_RenderingEngine_removeCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
removeDisabled(String) - Method in class ome.security.basic.CurrentDetails
removeFiles(List<Long>) - Method in class ome.io.nio.OriginalFilesService: Removes files from data repository based on a parameterized List of Long file ids
removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in interface ome.api.IAdmin: removes the given users from the owner list for this group.
removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in class ome.logic.AdminImpl
removeGroupOwners_async(AMD_IAdmin_removeGroupOwners, ExperimenterGroup, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.AdminI
removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.api.IAdmin: removes a user from the given groups.
removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
removeGroups_async(AMD_IAdmin_removeGroups, Experimenter, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
removeGuest(long, String) - Method in interface ome.api.IShare: Removes guest email address from share.
removeGuest(long, String) - Method in class ome.services.sharing.ShareBean
removeGuest_async(AMD_IShare_removeGuest, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
removeGuests(long, String...) - Method in interface ome.api.IShare: Removes guest email addresses from the share.
removeGuests(long, String...) - Method in class ome.services.sharing.ShareBean
removeGuests_async(AMD_IShare_removeGuests, long, List<String>, Current) - Method in class ome.services.blitz.impl.ShareI
removeMissingFilesFromDb(SimpleJdbcOperations, Session, List<OriginalFile>) - Method in class ome.services.scripts.ScriptRepoHelper: Given the current files on disk, ScriptRepoHelper.unregister(Long, Session) all files which have been removed from disk.
removeNamespace(String) - Method in class pojos.ROIData: Removes the namespace from the ROI.
removeObject(long, T) - Method in interface ome.api.IShare: Removes existing item from the share.
removeObject(Identity) - Method in class ome.services.blitz.fire.Registry.Impl
removeObject(Identity) - Method in interface ome.services.blitz.fire.Registry
removeObject(long, T) - Method in class ome.services.sharing.ShareBean
removeObject_async(AMD_IShare_removeObject, long, IObject, Current) - Method in class ome.services.blitz.impl.ShareI
removeObjects(long, T...) - Method in interface ome.api.IShare: Remove existing items from the share.
removeObjects(long, T...) - Method in class ome.services.sharing.ShareBean
removeObjects_async(AMD_IShare_removeObjects, long, List<IObject>, Current) - Method in class ome.services.blitz.impl.ShareI
removeObjectSafely(Identity) - Method in class ome.services.blitz.fire.Registry.Impl
removeObjectSafely(Identity) - Method in interface ome.services.blitz.fire.Registry
removePath(File) - Method in class omero.util.TempFileManager: If the given file is under TempFileManager.dir, then it is deleted whether file or folder.
removePixels(List<Long>) - Method in class ome.io.nio.PixelsService: Removes files from data repository based on a parameterized List of Long pixels ids
removeProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
removeSession(String) - Method in class ome.services.sessions.state.SessionCache
removeSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache
removeShapeData(ShapeData) - Method in class pojos.ROIData: Removes the ShapeData object from ROIData.
removeThumbnails(List<Long>) - Method in class ome.io.nio.ThumbnailService: Removes files from data repository based on a parameterized List of Long thumbnail ids
removeUnusedFiles() - Method in interface ome.api.IRepositoryInfo: Removes all files from the server that do not have an OriginalFile complement in the database, all the Pixels that do not have a complement in the database and all the Thumbnail's that do not have a complement in the database.
removeUnusedFiles() - Method in class ome.logic.RepositoryInfoImpl
removeUnusedFiles_async(AMD_IRepositoryInfo_removeUnusedFiles, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
removeUser(long, Experimenter) - Method in interface ome.api.IShare: Removes experimenter from share
removeUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean
removeUser_async(AMD_IShare_removeUser, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
removeUsers(long, List<Experimenter>) - Method in interface ome.api.IShare: Removes experimenters from share
removeUsers(long, List<Experimenter>) - Method in class ome.services.sharing.ShareBean
removeUsers_async(AMD_IShare_removeUsers, long, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.ShareI
removingOnly() - Method in class ome.services.fulltext.EventBacklog: Check the current state of the EventBacklog.
render(PlaneDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
render(PlaneDef) - Method in class omeis.providers.re.Renderer: Renders the data selected by pd according to the current rendering settings.
render(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine: Renders the data selected by pd according to the current rendering settings.
render_async(AMD_RenderingEngine_render, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
renderAsPackedInt(Long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
renderAsPackedInt(Long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService: Render as a packedInt
renderAsPackedInt(PlaneDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderAsPackedInt(PlaneDef, PixelBuffer) - Method in class omeis.providers.re.Renderer: Renders the data selected by pd according to the current rendering settings.
renderAsPackedInt(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine: Renders the data selected by pd according to the current rendering settings.
renderAsPackedInt_async(AMD_RenderingEngine_renderAsPackedInt, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
renderAsPackedIntAsRGBA(long, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
renderAsPackedIntAsRGBA(long, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService: Render image as Buffered image.
renderAsPackedIntAsRGBA(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
renderAsPackedIntAsRGBA(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
renderAsPackedIntAsRGBA(long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService: Render image as Buffered image.
renderAsPackedIntAsRGBA(PlaneDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderAsPackedIntAsRGBA(PlaneDef, PixelBuffer) - Method in class omeis.providers.re.Renderer: Renders the data selected by pd according to the current rendering settings.
renderAsPackedIntAsRGBA(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine: Renders the data selected by pd according to the current rendering settings.
renderAsPackedIntAsRGBA_async(AMD_RenderingEngine_renderAsPackedIntAsRGBA, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
renderCompressed(PlaneDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderCompressed(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine: Renders the data selected by pd according to the current rendering settings and compresses the resulting RGBA composite image.
renderCompressed_async(AMD_RenderingEngine_renderCompressed, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
Renderer - Class in omeis.providers.re: Transforms raw image data into an RGB image that can be displayed on screen.
Renderer(QuantumFactory, List<RenderingModel>, Pixels, RenderingDef, PixelBuffer) - Constructor for class omeis.providers.re.Renderer: Creates a new instance to render the specified pixels set and get this new instance ready for rendering.
RENDERING_DEF_QUERY_PREFIX - Static variable in class ome.logic.PixelsImpl: Standard rendering definition HQL query prefix
RenderingBean - Class in ome.services: Provides the RenderingEngine service.
RenderingBean(PixelsService, LocalCompress, OriginalFileMetadataProvider, Executor, SecuritySystem) - Constructor for class ome.services.RenderingBean: Compression service Bean injector.
RenderingEngine - Interface in omeis.providers.re: Defines a service to render a given pixels set.
RenderingEngineI - Class in ome.services.blitz.impl: Implementation of the RenderingEngine service.
RenderingEngineI(RenderingEngine, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingEngineI
RenderingService - Interface in ome.services.blitz.gateway.services
RenderingServiceImpl - Class in ome.services.blitz.gateway.services.impl
RenderingServiceImpl(RenderingEnginePrx) - Constructor for class ome.services.blitz.gateway.services.impl.RenderingServiceImpl: Create the ImageService passing the gateway.
RenderingSettingsI - Class in ome.services.blitz.impl: Implementation of the IRenderingSettings service.
RenderingSettingsI(IRenderingSettings, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingSettingsI
RenderingSettingsImpl - Class in ome.logic: Implementation of the IRenderingSettings I/F.
RenderingSettingsImpl() - Constructor for class ome.logic.RenderingSettingsImpl
RenderingStats - Class in omeis.providers.re: Exposes methods to time the various steps in the rendering process and provides a stats report.
RenderingStats(Renderer, PlaneDef) - Constructor for class omeis.providers.re.RenderingStats: Creates a new instance.
RenderingTask - Interface in omeis.providers.re: This interface represents a rendering operation task.
renderProjectedAsPackedInt(int, int, int, int, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderProjectedAsPackedInt(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine: Performs a projection through selected optical sections of a particular timepoint with the currently active channels and renders the data for display.
renderProjectedAsPackedInt_async(AMD_RenderingEngine_renderProjectedAsPackedInt, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
renderProjectedCompressed(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 interface omeis.providers.re.RenderingEngine: Performs a projection through selected optical sections of a particular timepoint with the currently active channels, renders the data for display and compresses the resulting RGBA composite image.
renderProjectedCompressed_async(AMD_RenderingEngine_renderProjectedCompressed, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
ReorderedPixelData - Class in ome.io.nio: Represents a block of pixel data that needs to be re-ordered in accordance with a DeltaVision file.
ReorderedPixelData(PixelsType, ByteBuffer, int) - Constructor for class ome.io.nio.ReorderedPixelData: Default constructor.
replace(Object, Object, Object) - Method in class ome.tools.hibernate.ArrayStringType
replace(Object, Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
replace(Object, Object, Object) - Method in class ome.tools.hibernate.PermissionsType
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 RepoFile.FsFile 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.
report(Current) - Method in class ome.services.blitz.impl.DeleteHandleI
reportForgottenPassword(String, String) - Method in interface ome.api.IAdmin: Can be used after repeated AuthenticationException instances are thrown, to request that an email with a temporary password be sent.
reportForgottenPassword(String, String) - Method in class ome.logic.AdminImpl
reportForgottenPassword_async(AMD_IAdmin_reportForgottenPassword, String, String, Current) - Method in class ome.services.blitz.impl.AdminI
repositories(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
RepositoryInfoI - Class in ome.services.blitz.impl: Implementation of the IRepositoryInfo service.
RepositoryInfoI(IRepositoryInfo, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RepositoryInfoI
RepositoryInfoImpl - Class in ome.logic: Class implementation of the IRepositoryInfo service interface.
RepositoryInfoImpl() - Constructor for class ome.logic.RepositoryInfoImpl
RepositoryTask - Class in ome.tools: Class implementation of various mechanised tasks, database queries, file I/O, etc.
RepositoryTask(SimpleJdbcOperations) - Constructor for class ome.tools.RepositoryTask: Constructor
reps - Variable in class ome.services.fulltext.FullTextIndexer
requestHeartBeats() - Method in class ome.services.blitz.fire.SessionManagerI: Destroys all the ServiceFactoryI instances based on the given sessionId.
REQUEUED - Static variable in interface ome.api.JobHandle
requiresCompanion(String) - Static method in class ome.services.util.DBEnumCheck
resetCacheSize(int) - Method in class omerojava.util.PixelsCache: Resets the size of the cache.
resetCallGroup() - Method in class ome.security.basic.CurrentDetails
resetCallGroup() - Method in class ome.services.util.Executor.Impl
resetCallGroup() - Method in interface ome.services.util.Executor: Delegates to CurrentDetails.resetCallGroup().
resetDefaults(RenderingDef, Pixels) - Method in interface ome.api.IRenderingSettings: Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.
resetDefaults() - Method in interface ome.api.Search: Resets all settings (non-query state) to the original default values, as if the instance had just be created.
resetDefaults() - Method in interface ome.api.ThumbnailStore: Resets the rendering definition for the active pixels set to its default settings.
resetDefaults(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
resetDefaults() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
resetDefaults() - Method in class ome.services.SearchBean
resetDefaults() - Method in class ome.services.ThumbnailBean
resetDefaults() - Method in interface omeis.providers.re.RenderingEngine: Resets the default settings i.e. the default values internal to the Rendering engine.
resetDefaults_async(AMD_RenderingEngine_resetDefaults, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
resetDefaults_async(AMD_IRenderingSettings_resetDefaults, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaults_async(AMD_Search_resetDefaults, Current) - Method in class ome.services.blitz.impl.SearchI
resetDefaults_async(AMD_ThumbnailStore_resetDefaults, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets the rendering settings of a given group of containers based on the owner's (essentially a copy).
resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsByOwnerInSet_async(AMD_IRenderingSettings_resetDefaultsByOwnerInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaultsForPixels(long) - Method in interface ome.api.IRenderingSettings: Resets a Pixels' default rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsForPixels_async(AMD_IRenderingSettings_resetDefaultsForPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaultsInDataset(long) - Method in interface ome.api.IRenderingSettings: Resets a dataset's rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInDataset_async(AMD_IRenderingSettings_resetDefaultsInDataset, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaultsInImage(long) - Method in interface ome.api.IRenderingSettings: Resets an image's default rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInImage(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInImage_async(AMD_IRenderingSettings_resetDefaultsInImage, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaultsInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets a rendering settings back to one or many containers that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInSet_async(AMD_IRenderingSettings_resetDefaultsInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaultsNoSave(RenderingDef, Pixels) - Method in interface ome.api.IRenderingSettings: Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.
resetDefaultsNoSave(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
resetDefaultsNoSave() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
resetDefaultsNoSave() - Method in interface omeis.providers.re.RenderingEngine: Resets the default settings i.e. the default values internal to the Rendering engine.
resetDefaultsNoSave_async(AMD_RenderingEngine_resetDefaultsNoSave, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
resetDefaultsNoSave_async(AMD_IRenderingSettings_resetDefaultsNoSave, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDetails(IObject, Object[], Object[], int) - Method in class ome.security.basic.OmeroInterceptor: asks BasicSecuritySystem to create a new managed Details based on the previous state of this entity.
resetEnumerations(Class<T>) - Method in interface ome.api.ITypes
resetEnumerations(Class<T>) - Method in class ome.logic.TypesImpl
resetEnumerations_async(AMD_ITypes_resetEnumerations, String, Current) - Method in class ome.services.blitz.impl.TypesI
resetMinMaxInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets a the channel windows for one or many containers back to their global minimum and global maximum for the channel.
resetMinMaxInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetMinMaxInSet_async(AMD_IRenderingSettings_resetMinMaxInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetReadFilter(Session) - Method in interface ome.api.local.LocalShare
resetReadFilter(Session) - Method in class ome.services.sharing.ShareBean
resolveAlias(String) - Method in class ome.system.PreferenceContext
resolveConfigFile(String) - Method in class ome.services.blitz.util.BlitzConfiguration: Resolve the given config file to a concrete location, possibly throwing an exception if stored in a jar.
resource - Variable in class ome.services.messages.RegisterServiceCleanupMessage
Resources - Class in omero.util: Container class for storing resources which should be cleaned up on close and periodically checked.
Resources() - Constructor for class omero.util.Resources: As Resources.Resources(int) but specifies a 60 second sleep period between task execution.
Resources(int) - Constructor for class omero.util.Resources: As Resources#Resources(int, ExecutorService) but uses a Executors.newSingleThreadExecutor().
Resources(int, ScheduledExecutorService) - Constructor for class omero.util.Resources
Resources.Entry - Interface in omero.util: Interface to be implemented by any object which wants to be managed by the Resources class.
response - Variable in class ome.services.throttling.Task
response(Object, OmeroContext) - Method in class ome.services.throttling.Task: Calls the response method
responseRunning(List<Long>, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI: Callback method which should not be called for this instance.
restartIfNeeded() - Method in class ome.services.scheduler.SchedulerFactoryBean: Similar to the SchedulerFactoryBean.isRunning() method, but properly handles the situation where the Scheduler has been completely shutdown and therefore must be replaced.
RESUBMITTED - Static variable in interface ome.api.JobHandle
ResultHolder<U> - Class in ome.services.blitz.util
ResultHolder(long) - Constructor for class ome.services.blitz.util.ResultHolder
results() - Method in interface ome.api.Search: Returns up to batch size number of results along with the related query metadata.
results() - Method in class ome.services.SearchBean
results_async(AMD_Search_results, Current) - Method in class ome.services.blitz.impl.SearchI
retrieveAllRndSettings(long, long) - Method in interface ome.api.IPixels: Retrieves all the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
retrieveAllRndSettings(long, long) - Method in class ome.logic.PixelsImpl: Implemented as specified by the IPixels I/F.
retrieveAllRndSettings_async(AMD_IPixels_retrieveAllRndSettings, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI
retrieveCollection(IObject, String, Parameters) - Method in interface ome.api.IContainer: Retrieves a collection with all members initialized ("loaded").
retrieveCollection(IObject, String, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
retrieveCollection_async(AMD_IContainer_retrieveCollection, IObject, String, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
retrievePixDescription(long) - Method in interface ome.api.IPixels: Retrieves the pixels metadata with the following objects pre-linked: pixels.pixelsType pixels.pixelsDimensions pixels.channels pixels.channnels.statsInfo pixels.channnels.colorComponent pixels.channnels.logicalChannel pixels.channnels.logicalChannel.photometricInterpretation
retrievePixDescription(long) - Method in class ome.logic.PixelsImpl
retrievePixDescription_async(AMD_IPixels_retrievePixDescription, long, Current) - Method in class ome.services.blitz.impl.PixelsI
retrieveResult(int, List) - Method in interface ome.api.IResults: retrieving data for PixelSet
retrieveResultPrimitive(int, String[]) - Method in interface ome.api.IResults
retrieveResultsBulk(int[], List[]) - Method in interface ome.api.IResults
retrieveResultsBulkPrimitive(int[], String[][]) - Method in interface ome.api.IResults
retrieveRndSettings(long) - Method in interface ome.api.IPixels: Retrieves the rendering settings for a given pixels set and the currently logged in user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
retrieveRndSettings(long) - Method in class ome.logic.PixelsImpl: Implemented as specified by the IPixels I/F.
retrieveRndSettings_async(AMD_IPixels_retrieveRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI
retrieveRndSettingsFor(long, long) - Method in interface ome.api.IPixels: Retrieves the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
retrieveRndSettingsFor(long, long) - Method in class ome.logic.PixelsImpl: Implemented as specified by the IPixels I/F.
retrieveRndSettingsFor_async(AMD_IPixels_retrieveRndSettingsFor, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI
returnedClass() - Method in class ome.tools.hibernate.ArrayStringType
returnedClass() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
returnedClass() - Method in class ome.tools.hibernate.PermissionsType
returnSeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
returnUnloaded - Variable in class ome.services.search.SearchValues
reverse(Object) - Method in class omero.util.IceMapper
reverse(Collection) - Method in class omero.util.IceMapper: Copied from ModelMapper.findCollection(Collection) This could be unified in that a method findCollection(Collection, Map) was added with ModelMapper calling findCollection(source,model2target) and #reverseCollection(Collection) calling findCollection(source,target2model).
reverse(Collection, Class) - Method in class omero.util.IceMapper: Creates a collection assignable to the given type.
reverse(Map) - Method in class omero.util.IceMapper
reverse(ModelBased) - Method in class omero.util.IceMapper: Copied from ReverseModelMapper#map(ModelBased)
reverseArray(List, Class) - Method in class omero.util.IceMapper: Supports the separate case of reversing for arrays.
ReverseIntensityContext - Class in omeis.providers.re.codomain: The empty context of the reverse intensity map.
ReverseIntensityContext() - Constructor for class omeis.providers.re.codomain.ReverseIntensityContext
RevisionDate - Annotation Type in ome.annotations: annotation used for tracking source code changes.
RevisionNumber - Annotation Type in ome.annotations: annotation used for tracking source code changes.
rfloat(float) - Static method in class omero.rtypes
RGBAIntBuffer - Class in omeis.providers.re: Holds the data of an RGBA image.
RGBAIntBuffer(int, int) - Constructor for class omeis.providers.re.RGBAIntBuffer: Creates a new 4-band packed integer buffer.
RGBBuffer - Class in omeis.providers.re: Holds the data of an RGB image.
RGBBuffer() - Constructor for class omeis.providers.re.RGBBuffer: Simple constructor to avoid memory allocations.
RGBBuffer(int, int) - Constructor for class omeis.providers.re.RGBBuffer: Creates a new 3-band buffer.
RGBIntBuffer - Class in omeis.providers.re: Holds the data of an RGB image.
RGBIntBuffer(int, int) - Constructor for class omeis.providers.re.RGBIntBuffer: Creates a new 3-band packed integer buffer.
Ring - Class in ome.services.blitz.fire: Distributed ring of BlitzConfiguration objects which manages lookups of sessions and other resources from all the blitzes which take part in the cluster.
Ring(String, Executor, SessionCache) - Constructor for class ome.services.blitz.fire.Ring
Ring(String, Executor, SessionCache, Redirector) - Constructor for class ome.services.blitz.fire.Ring
ring - Variable in class ome.services.blitz.fire.SessionManagerI
rint(int) - Static method in class omero.rtypes
rinternal(Internal) - Static method in class omero.rtypes
rlist(RType...) - Static method in class omero.rtypes
rlist(Collection<RType>) - Static method in class omero.rtypes
rlong(long) - Static method in class omero.rtypes
rmap() - Static method in class omero.rtypes
rmap(Map<String, RType>) - Static method in class omero.rtypes
rmap(String, RType) - Static method in class omero.rtypes
robject(IObject) - Static method in class omero.rtypes
ROIComponent - Class in pojos.util: Component hosting the ROI.
ROIComponent(long) - Constructor for class pojos.util.ROIComponent: Instantiate the ROIComponent.
ROICoordinate - Class in pojos: Defines a plane.
ROICoordinate() - Constructor for class pojos.ROICoordinate: Creates a default instance.
ROICoordinate(int, int) - Constructor for class pojos.ROICoordinate: Creates a new instance.
ROIData - Class in pojos: Converts the ROI object.
ROIData(Roi) - Constructor for class pojos.ROIData: Creates a new instance.
ROIData() - Constructor for class pojos.ROIData: Create a new instance of an ROIData object.
RoiI - Class in ome.services.blitz.impl: implementation of the IRoi service interface.
RoiI(BlitzExecutor, GeomTool, SimpleJdbcOperations) - Constructor for class ome.services.blitz.impl.RoiI
RoiI.RoiResultMapper - Class in ome.services.blitz.impl
RoiI.RoiResultMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultMapper
RoiI.RoiResultMapReturnMapper - Class in ome.services.blitz.impl
RoiI.RoiResultMapReturnMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultMapReturnMapper
RoiI.RoiResultReturnMapper - Class in ome.services.blitz.impl
RoiI.RoiResultReturnMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultReturnMapper
RoiTypes - Class in ome.services.roi: Intelligent server-side representations of the Roi and Shape types.
RoiTypes() - Constructor for class ome.services.roi.RoiTypes
RoiTypes.ObjectFactory - Class in ome.services.roi
RoiTypes.ObjectFactory(String) - Constructor for class ome.services.roi.RoiTypes.ObjectFactory
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.BasicSecuritySystem
roles - Variable in class ome.services.sessions.SessionManagerImpl
Roles - Class in ome.system: encapsulates the naming scheme for critical system groups and accounts.
Roles() - Constructor for class ome.system.Roles: default constructor which assigns hard-coded values to all roles
Roles(long, String, long, String, long, String) - Constructor for class ome.system.Roles: constructor which allows full specification of all roles
RolesAllowed - Annotation Type in ome.annotations: Security annotation which specifies a list of user roles which will be permitted to execute this method.
rollback(DeleteStep) - Method in class ome.services.delete.DeleteState
rollback(EventLog) - Method in class ome.services.fulltext.EventLogLoader
RomioPixelBuffer - Class in ome.io.nio: Class implementation of the PixelBuffer interface for standard "proprietary" ROMIO/OMEIS data format.
RomioPixelBuffer(String, Pixels) - Constructor for class ome.io.nio.RomioPixelBuffer
ROOT - Static variable in class prefs: "omero.prefs", the value of the root Preferences node used for all configuration work.
ROOT_DEFAULT - Static variable in class ome.io.nio.AbstractFileSystemService
ROUTED_FROM - Static variable in class ome.services.blitz.redirect.AbstractRedirector
Router - Class in ome.services.blitz: Wrapper around a call to 'glacier2router' to permit Java control over the process.
Router() - Constructor for class ome.services.blitz.Router
rset(RType...) - Static method in class omero.rtypes
rset(Collection<RType>) - Static method in class omero.rtypes
rstring(String) - Static method in class omero.rtypes
RTF - Static variable in class pojos.FileAnnotationData: Identifies the RTF file formats.
rtime(long) - Static method in class omero.rtypes
rtime(Date) - Static method in class omero.rtypes
rtime_max() - Static method in class omero.rtypes
rtime_min() - Static method in class omero.rtypes
rtime_str(String) - Static method in class omero.rtypes
rtype() - Method in class omero.rtypes.ObjectFactory
rtype(Object) - Static method in class omero.rtypes: Attempts to dispatch to the other omero.rtypes.* static methods to create a proper RType subclass by checking the type of the input.
RTYPEDICT - Static variable in class omero.util.IceMapper
RTypeMapper - Class in omero.util: Extension of IceMapper which guarantees that RCollection and RMap instances are properly created.
RTypeMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.RTypeMapper
rtypes - Class in omero: Abstract class similar to Arrays or Collections which is responsible for creating RTypes from static factory methods.
rtypes() - Constructor for class omero.rtypes
rtypes.Conversion - Interface in omero: SPI-style interface which helps the omero server to properly convert omero.RType objects into Java-native objects for use in Hibernate.
rtypes.ObjectFactory - Class in omero
rtypes.ObjectFactory(String) - Constructor for class omero.rtypes.ObjectFactory
run() - Method in class ome.services.blitz.DbCreate
run() - Method in class ome.services.blitz.impl.DeleteHandleI: NB: only executes if DeleteHandleI.state is State#CREATED.
run() - Method in class ome.services.blitz.Status
run() - Method in class ome.services.blitz.util.CheckAllJobs
run() - Method in interface ome.services.procs.IProcessManager: Runs the processing phase as root.
run(OmeroContext) - Method in class ome.services.throttling.Adapter
run(OmeroContext) - Method in class ome.services.throttling.Callback
run(OmeroContext) - Method in class ome.services.throttling.Callback2
run() - Method in class ome.services.throttling.Slot
run(OmeroContext) - Method in class ome.services.throttling.Task
run() - Method in class ome.services.util.DropBoxDirectoryCheck: Synchronizes the ${omero.data.dir}/DropBox directory by creating a directory for any user who does not have one.
run() - Method in class ome.services.util.ExecutionThread: Initializes the Session for this Thread if necessary, then calls ExecutionThread.doRun().
run() - Method in class ome.system.UpgradeCheck: If the UpgradeCheck.url has been set to null or the empty string, then no upgrade check will be performed (silently).
runAsAdmin() - Method in interface ome.security.AdminAction: executes with special privilegs within the SecuritySystem.
runAsAdmin(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(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 class ome.security.SecuritySystemHolder
runAsAdmin(AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
runAsAdmin() - Method in class ome.services.delete.QueryConstraints
runnableCall(Current, Task) - Method in class ome.services.blitz.impl.AbstractAmdServant
runnableCall(Current, Task) - Method in interface ome.services.blitz.util.BlitzExecutor
runnableCall(Current, Task) - Method in class ome.services.throttling.InThreadThrottlingStrategy
runnableCall(Current, Task) - Method in class ome.services.throttling.SerialThrottlingStrategy
RUNNING - Static variable in interface ome.api.JobHandle
runningProcess(long) - Method in interface ome.services.procs.IProcessManager: Returns a running Process for the id or null.
runningProcess(long) - Method in class ome.services.procs.ProcessManager
runScript_async(AMD_IScript_runScript, long, Map<String, RType>, RInt, Current) - Method in class ome.services.blitz.impl.ScriptI
runTopLevel(Session, List<Long>) - Method in class ome.services.delete.AnnotationDeleteSpec
runTopLevel(Session, List<Long>) - Method in class ome.services.delete.BaseDeleteSpec
runTopLevel(Session, List<Long>) - Method in interface ome.services.delete.DeleteSpec: Workaround for the removal of DeleteSpec#delete when refactoring to DeleteState.

S

safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.blitz.impl.AbstractAmdServant
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in interface ome.services.blitz.util.BlitzExecutor
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.throttling.InThreadThrottlingStrategy
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.throttling.SerialThrottlingStrategy
sanityCheckPixels(Pixels, Pixels) - Method in interface ome.api.IRenderingSettings: Checks if the specified sets of pixels are compatible.
sanityCheckPixels(Pixels, Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
sanityCheckPixels_async(AMD_IRenderingSettings_sanityCheckPixels, Pixels, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
sanityCheckRepository() - Method in interface ome.api.IRepositoryInfo: Checks that image data repository has not exceeded 95% disk space use level.
sanityCheckRepository() - Method in class ome.logic.RepositoryInfoImpl
sanityCheckRepository_async(AMD_IRepositoryInfo_sanityCheckRepository, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
save() - Method in interface ome.api.RawFileStore: Saves the OriginalFile associated with the service if it has been modified.
save() - Method in class ome.services.blitz.measurements.MeasurementStore
save() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
save() - Method in class ome.services.RawFileBean
save_async(AMD_RawFileStore_save, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
SAVE_EVENT - Static variable in class ome.security.basic.SaveEventListener
saveAndReturnArray(IObject[]) - Method in interface ome.api.IUpdate
saveAndReturnArray(IObject[]) - Method in class ome.logic.UpdateImpl
saveAndReturnArray(List<IObject>, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
saveAndReturnArray(List<IObject>) - Method in interface ome.services.blitz.gateway.services.DataService: Save and return the array.
saveAndReturnArray(List<IObject>) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
saveAndReturnArray_async(AMD_IUpdate_saveAndReturnArray, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
saveAndReturnIds(IObject[]) - Method in interface ome.api.IUpdate: Logic differs from other methods.
saveAndReturnIds(IObject[]) - Method in class ome.logic.UpdateImpl
saveAndReturnIds_async(AMD_IUpdate_saveAndReturnIds, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
saveAndReturnObject(T) - Method in interface ome.api.IUpdate
saveAndReturnObject(IObject) - Method in class ome.logic.UpdateImpl
saveAndReturnObject(IObject, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
saveAndReturnObject(IObject) - Method in interface ome.services.blitz.gateway.services.DataService: Save and return the Object.
saveAndReturnObject(IObject) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
saveAndReturnObject_async(AMD_IUpdate_saveAndReturnObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
saveArray(IObject[]) - Method in interface ome.api.IUpdate
saveArray(IObject[]) - Method in class ome.logic.UpdateImpl
saveArray(List<IObject>, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
saveArray(List<IObject>) - Method in interface ome.services.blitz.gateway.services.DataService: Save the array.
saveArray(List<IObject>) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
saveArray_async(AMD_IUpdate_saveArray, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
saveCollection(Collection<IObject>) - Method in interface ome.api.IUpdate
saveCollection(Collection) - Method in class ome.logic.UpdateImpl
saveCollection_async(AMD_IUpdate_saveCollection, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
saveCurrentSettings() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
saveCurrentSettings() - Method in interface omeis.providers.re.RenderingEngine: Saves the current rendering settings in the database.
saveCurrentSettings_async(AMD_RenderingEngine_saveCurrentSettings, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
savedPlates - Variable in class ome.services.blitz.impl.MetadataStoreI
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 interface ome.api.IUpdate
saveObject(IObject) - Method in class ome.logic.UpdateImpl
saveObject(IObject, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
saveObject(IObject) - Method in interface ome.services.blitz.gateway.services.DataService: Save the object to the db .
saveObject(IObject) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
saveObject_async(AMD_IUpdate_saveObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
savePath(long, String) - Method in class ome.services.roi.GeomTool
savepoint(DeleteStep) - Method in class ome.services.delete.DeleteState
saveRndSettings(RenderingDef) - Method in interface ome.api.IPixels: Saves the specified rendering settings.
saveRndSettings(RenderingDef) - Method in class ome.logic.PixelsImpl
saveRndSettings_async(AMD_IPixels_saveRndSettings, RenderingDef, Current) - Method in class ome.services.blitz.impl.PixelsI
saveToDB() - Method in class ome.formats.OMEROMetadataStore: Saves the current object graph to the database.
saveToDB_async(AMD_MetadataStore_saveToDB, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
scalar(double) - Method in class ome.util.math.geom2D.PlanePoint: Multiplies this vector by the specified scalar.
scale(double) - Method in class ome.util.math.geom2D.EllipseArea: Implemented as specified by the PlaneArea I/F.
scale(double) - Method in interface ome.util.math.geom2D.PlaneArea: Resets the bounding Rectangle of the planeArea according to the specified scaling factor.
scale(double) - Method in class ome.util.math.geom2D.RectangleArea: Implemented as specified by the PlaneArea I/F.
scaleBufferedImage(BufferedImage, float, float) - Method in interface ome.api.IScale: Scales a buffered image using defined X and Y axis scale factors.
scaleBufferedImage(BufferedImage, float, float) - Method in class ome.logic.AWTScaleService
scaleBufferedImage(BufferedImage, float, float) - Method in class ome.logic.JavaImageScalingService
ScaleRedirector - Class in ome.services.blitz.redirect: Planned implementation (NYI): will use the "Node.scale" column to randomly choose a target.
ScaleRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ScaleRedirector
SchedulerFactoryBean - Class in ome.services.scheduler: Produces a SchedulerFactoryBean() - Constructor for class ome.services.scheduler.SchedulerFactoryBean
SCORE - Static variable in interface ome.api.Search: String constant used to look up the score value of Lucene queries returned by this interface.
SCREEN_LINKS - Static variable in class pojos.PlateData: Identifies the Plate#SCREENLINKS field.
ScreenData - Class in pojos: The data that makes up an OME Screen along with links to its contained Plates and the Experimenter that owns this Screen.
ScreenData() - Constructor for class pojos.ScreenData: Creates a new instance.
ScreenData(Screen) - Constructor for class pojos.ScreenData: Creates a new instance.
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.
SCRIPT_REPO - Static variable in class ome.services.scripts.ScriptRepoHelper: Id used by all script repositories.
ScriptFinder - Class in ome.services.scripts: Looks up an official script based on path for internal use.
ScriptFinder(Roles, String, Executor, File) - Constructor for class ome.services.scripts.ScriptFinder
ScriptFinder(Roles, Principal, Executor, File) - Constructor for class ome.services.scripts.ScriptFinder
ScriptI - Class in ome.services.blitz.impl: implementation of the IScript service interface.
ScriptI(BlitzExecutor, ScriptRepoHelper) - Constructor for class ome.services.blitz.impl.ScriptI
ScriptProcess - Class in ome.services.procs.scripts
ScriptProcess(Processor) - Constructor for class ome.services.procs.scripts.ScriptProcess
ScriptProcessI - Class in ome.services.blitz.impl
ScriptProcessI(ServiceFactoryI, Current, InteractiveProcessorPrx, InteractiveProcessorI, ProcessPrx) - Constructor for class ome.services.blitz.impl.ScriptProcessI
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
ScriptRepoHelper(File, Executor, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
ScriptRepoHelper(String, File, Executor, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
scripts - Variable in class ome.services.blitz.impl.ScriptI
Search - Interface in ome.api: Central search interface, allowing Web2.0 style queries.
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 interface ome.api.ILdap: Searchs all Experimenter list on LDAP for attribute objectClass = person.
searchAll() - Method in class ome.logic.LdapImpl
searchAll_async(AMD_ILdap_searchAll, Current) - Method in class ome.services.blitz.impl.LdapI
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 interface ome.api.ILdap: Searchs all Experimenter in LDAP for specyfied attribute
searchByAttribute(String, String, String) - Method in class ome.logic.LdapImpl
searchByAttribute_async(AMD_ILdap_searchByAttribute, String, String, String, Current) - Method in class ome.services.blitz.impl.LdapI
searchByAttributes(String, String[], String[]) - Method in interface ome.api.ILdap: Searchs all Experimenter in LDAP for specyfied attributes.
searchByAttributes(String, String[], String[]) - Method in class ome.logic.LdapImpl
searchByAttributes_async(AMD_ILdap_searchByAttributes, String, List<String>, List<String>, Current) - Method in class ome.services.blitz.impl.LdapI
searchByDN(String) - Method in interface ome.api.ILdap: Searchs one Experimenter in LDAP for specyfied Distinguished Name - String
searchByDN(String) - Method in class ome.logic.LdapImpl
searchByDN_async(AMD_ILdap_searchByDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
searchDnInGroups(String, String) - Method in interface ome.api.ILdap: Searchs Distinguished Name - String in groups
searchDnInGroups(String, String) - Method in class ome.logic.LdapImpl
searchDnInGroups_async(AMD_ILdap_searchDnInGroups, String, String, Current) - Method in class ome.services.blitz.impl.LdapI
SearchI - Class in ome.services.blitz.impl: Implementation of the Search service.
SearchI(Search, BlitzExecutor) - Constructor for class ome.services.blitz.impl.SearchI
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(IObject, SecureAction).
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 - Class in ome.tools.hibernate: overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.
SecurityFilter() - Constructor for class ome.tools.hibernate.SecurityFilter: default constructor which calls all the necessary setters for this FactoryBean.
SecurityFilter(Roles) - Constructor for class ome.tools.hibernate.SecurityFilter
SecuritySystem - Interface in ome.security: central security interface.
securitySystem - Variable in class ome.services.blitz.fire.SessionManagerI
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
Segment - Class in ome.util.math.geom2D: A segment in the Euclidean space R².
Segment(double, double, double, double) - Constructor for class ome.util.math.geom2D.Segment: Creates a new instance.
select(String...) - Method in class ome.tools.hibernate.QueryBuilder
SelfConfigurableService - Interface in ome.system
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) - Static method in class ome.security.basic.BasicSecuritySystem: Simpilifed factory method which generates all the security primitives internally.
selfConfigure() - Method in class ome.services.AbstractStatefulBean
selfConfigure() - Method in interface ome.system.SelfConfigurableService
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
SerialThrottlingStrategy - Class in ome.services.throttling: Throttling implementation which only allows a single invocation to be run at any given time.
SerialThrottlingStrategy(OmeroContext) - Constructor for class ome.services.throttling.SerialThrottlingStrategy
ServantHolder - Class in ome.services.blitz.util: Manager for all active servants in a single ServiceFactoryI.
ServantHolder() - Constructor for class ome.services.blitz.util.ServantHolder
Server - Class in ome.system: Provides simplified handling of server properties when creating a ServiceFactory.
Server(String) - Constructor for class ome.system.Server: standard constructor which users Server.DEFAULT_PORT.
Server(String, int) - Constructor for class ome.system.Server: extended constructor.
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.blitz.impl.AbstractAmdServant: If there is no undering ome.* service, then this value can be null.
service - Variable in class ome.services.util.Executor.Impl
ServiceFactory - Class in ome.system: Entry point for all client calls.
ServiceFactory() - Constructor for class ome.system.ServiceFactory: default constructor which obtains the global static client context from OmeroContext.
ServiceFactory(Login) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new (non-static) client context, passing in the Properties representation of the Login for configuration.
ServiceFactory(Server) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new (non-static) client context, passing in the Properties representation of the Server for configuration.
ServiceFactory(Server, Login) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new (non-static) client context, passing in the Properties representation of both the Server and the Login for configuration.
ServiceFactory(Properties) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new client context, passing in the provided properties for configuration.
ServiceFactory(OmeroContext) - Constructor for class ome.system.ServiceFactory: constructor which uses the provided OmeroContext for all loookups.
ServiceFactory(String) - Constructor for class ome.system.ServiceFactory: constructor which finds the global static OmeroContext with the given name.
ServiceFactoryAware - Interface in ome.services.blitz.util: Servant which is aware of the ServiceFactoryI-instance which it belongs to and will have it injected on instantiation.
ServiceFactoryI - Class in ome.services.blitz.impl: Responsible for maintaining all servants for a single session.
ServiceFactoryI(Current, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, List<HardWiredInterceptor>, TopicManager, Registry) - Constructor for class ome.services.blitz.impl.ServiceFactoryI
ServiceFactoryI(boolean, Current, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, List<HardWiredInterceptor>, TopicManager, Registry) - Constructor for class ome.services.blitz.impl.ServiceFactoryI
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
ServiceInterface - Interface in ome.api: Marker interface representing an OMERO API Interface.
ServiceUtilities - Class in ome.services.blitz.gateway.services.util
ServiceUtilities() - Constructor for class ome.services.blitz.gateway.services.util.ServiceUtilities
sess() - Method in class omero.client: Helper method to access session id
session - Variable in class ome.system.SessionInitializer
SessionBean - Class in ome.services.sessions: Implementation of ISession.
SessionBean(SessionManager, Executor, CurrentDetails) - 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 clear the blocked SessionCache#needsUpdate state, which prevents all further calls from happening.
SessionCallback - Interface in ome.services.sessions
SessionCallback.SimpleCloseCallback - Class in ome.services.sessions: Assumes that only close() will be called.
SessionCallback.SimpleCloseCallback() - Constructor for class ome.services.sessions.SessionCallback.SimpleCloseCallback
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.
SessionContext.Count(String) - Constructor for class ome.services.sessions.SessionContext.Count
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, 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) - 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 DataSource and a SessionFactory.
SessionI - Class in ome.services.blitz.impl: Implementation of the ISession service.
SessionI(ISession, BlitzExecutor) - Constructor for class ome.services.blitz.impl.SessionI
sessionId(String, String) - Static method in class ome.services.blitz.impl.ServiceFactoryI: Definition of session ids: "session-/"
sessionId() - Method in class ome.services.blitz.impl.ServiceFactoryI: Returns the Identity for this instance as defined by ServiceFactoryI.sessionId(String, String)
sessionInit() - Method in class ome.services.util.ExecutionThread
SessionInitializer - Class in ome.system: Manages the creation of a single Session created via the injected ISession service.
SessionInitializer() - Constructor for class ome.system.SessionInitializer
sessionManager - Variable in class ome.logic.UpdateImpl
sessionManager - Variable in class ome.security.basic.BasicSecuritySystem
sessionManager - Variable in class ome.services.blitz.fire.SessionManagerI
SessionManager - Interface in ome.services.sessions: Responsible for holding onto Session instances for optimized login.
sessionManager - Variable in class ome.services.sharing.ShareBean
SessionManagerI - Class in ome.services.blitz.fire: Central login logic for all OMERO.blitz clients.
SessionManagerI(Ring, ObjectAdapter, SecuritySystem, SessionManager, Executor, TopicManager, Registry) - Constructor for class ome.services.blitz.fire.SessionManagerI
SessionManagerImpl - Class in ome.services.sessions: Is for ISession a cache and will be kept there in sync?
SessionManagerImpl() - Constructor for class ome.services.sessions.SessionManagerImpl
sessions - Variable in class ome.system.SessionInitializer
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
sessionToClientIds - Variable in class ome.services.blitz.fire.SessionManagerI: An internal mapping to all ServiceFactoryI instances for a given session since there is no method on ObjectAdapter to retrieve all servants.
set(U) - Method in class ome.services.blitz.util.ResultHolder
set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper: Method to be implemented by all bridges.
set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.ProjectWithImageNameBridge: 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.FullTextBridge: Default implementation of the #set(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float) method which calls #set_file(String, IObject, Document, Store, org.apache.lucene.document.Field.Index, Float) #set_annotations(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float), #set_details(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float), and finally #set_custom(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float).
set(Share, long, List<T>, List<Long>, List<String>, boolean) - Method in class ome.services.sharing.ShareStore
set(int, byte) - Method in class ome.util.mem.ByteArray: Writes value into the element at the index position within this slice.
set(int, byte[]) - Method in class ome.util.mem.ByteArray: Copies the values in buf into this slice, starting from index.
set(int, int, InputStream) - Method in class ome.util.mem.ByteArray: Writes up to maxLength bytes from the supplied stream into this slice, starting from index.
set(Copiable, int) - Method in class ome.util.mem.CopiableArray: Replaces the element at the specified position with the specified Copiable.
set(int, int, boolean) - Method in class omero.model.PermissionsI
set(String[]) - Static method in class prefs: Takes an array of length 2, using args[0] as the key and args[1] as the value to be set.
set_annotations(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge: 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: Loops over each field bridge class and calls its FieldBridge#set(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float) method.
set_details(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge: 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: Uses #parse(OriginalFile) to get a Reader for the given file which is then passed to #add(Document, String, Reader, Float) using the field name "file".
setActive(long, boolean) - Method in interface ome.api.IShare
setActive(long, int, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
setActive(Long, int, boolean) - Method in interface ome.services.blitz.gateway.services.ImageService: Set the active channels in the pixels.
setActive(Long, int, boolean) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl
setActive(Long, int, boolean) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
setActive(Long, int, boolean) - Method in interface ome.services.blitz.gateway.services.RenderingService: Set the active channels in the pixels.
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
setActive(int, boolean) - Method in class omeis.providers.re.Renderer: Makes a particular channel active or inactive.
setActive(int, boolean) - Method in interface omeis.providers.re.RenderingEngine: Maps the specified channel if true, unmaps the channel otherwise.
setActive_async(AMD_RenderingEngine_setActive, int, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setActive_async(AMD_IShare_setActive, long, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
setAgent(String) - Method in class omero.client: Sets the user agent string for this client.
setAirPressure(double) - Method in class pojos.ImageAcquisitionData: Sets the air pressure.
setAliases(String[]) - Method in class ome.system.Preference: Setter injector
setAllowedBlockTime(long) - Method in class ome.services.sessions.state.SessionCache: Inject time in milliseconds to allow blocking
setAllowLeadingWildcard(boolean) - Method in interface ome.api.Search: Permits full-text queries with a leading query if true.
setAllowLeadingWildcard(boolean) - Method in class ome.services.SearchBean
setAllowLeadingWildcard_async(AMD_Search_setAllowLeadingWildcard, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
setAllPixels(List<PixelsData>) - Method in class pojos.ImageData: Sets the set of pixels related to this image.
setAlpha(Integer) - Method in class pojos.WellData: Sets the alpha component of the color associated to the well.
setAlphalessRendering(boolean) - Method in class omeis.providers.re.Optimizations: Enable or disable the alphaless rendering optimization.
setAnalyzer(Class<? extends Analyzer>) - Method in class ome.logic.QueryImpl
setAnalyzer(Class<? extends Analyzer>) - Method in class ome.services.SearchBean: Injector used by Spring.
setAnnotations(Set) - Method in class pojos.DatasetData: Sets the annotations related to this dataset.
setAnnotations(Set) - Method in class pojos.ImageData: Sets the image's annotations.
setApplicationContext(ApplicationContext) - Method in class ome.logic.AdminImpl
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.services.blitz.fire.SessionManagerI
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.impl.AbstractAmdServant: Creates an IceMethodInvoker for this instance if AbstractAmdServant.service is non-null.
setApplicationContext(ApplicationContext) - Method in class ome.services.delete.DeleteSpecFactory
setApplicationContext(ApplicationContext) - Method in class ome.services.fulltext.FileParser
setApplicationContext(ApplicationContext) - Method in class ome.services.procs.ImportProcessor
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 cyclical dependency SF->ACLVoter->BlobStore->SF we have to lazy-load the session factory via the context.
setApplicationContext(ApplicationContext) - Method in class ome.services.throttling.AbstractThrottlingStrategy
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
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.BridgeHelper
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.CounterFactory
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.LongCounter
setBatchSize(int) - Method in interface ome.api.Search: Sets the maximum number of results that will be returned by one call to Search.results().
setBatchSize(int) - Method in class ome.services.fulltext.EventLogLoader: Set the number of EventLog instances will be loaded in a single run.
setBatchSize(int) - Method in class ome.services.SearchBean
setBatchSize_async(AMD_Search_setBatchSize, int, Current) - Method in class ome.services.blitz.impl.SearchI
setBeanFactory(BeanFactory) - Method in class ome.services.messages.GlobalMulticaster
setBeanName(String) - Method in class ome.services.delete.BaseDeleteSpec
setBeanName(String) - Method in class ome.system.Preference: Setter injector
setBit(byte[], int, int) - Method in class pojos.MaskData: Sets the bit value in a byte array at position bit to be the value value.
setBlue(Integer) - Method in class pojos.WellData: Sets the blue component of the color associated to the well.
setBlueValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer: Sets the Blue value for a particular pixel index.
setBlueValue(int, int) - Method in class omeis.providers.re.RGBBuffer: Sets the Blue value for a particular pixel index.
setBlueValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer: Sets the Blue value for a particular pixel index.
setBounds(int, int, int, int) - Method in class ome.util.math.geom2D.EllipseArea: Implemented as specified in the PlaneArea I/F.
setBounds(int, int, int, int) - Method in interface ome.util.math.geom2D.PlaneArea: Sets the bounding Rectangle of the planeArea to the specified x, y, width, and height.
setBounds(int, int, int, int) - Method in class ome.util.math.geom2D.RectangleArea: Implemented as specified by the PlaneArea I/F.
setC(int) - Method in class pojos.ShapeData: Set the channel
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
setCallback(ClientCallbackPrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
setCallGroup(Long) - Method in class ome.security.basic.CurrentDetails
setCallGroup(long) - Method in class ome.services.util.Executor.Impl
setCallGroup(long) - Method in interface ome.services.util.Executor: Delegates to CurrentDetails.setCallGroup(Long) to permit thread-specific setting of the group.
setCaseSentivice(boolean) - Method in interface ome.api.Search: Sets the case sensitivity on all queries where case-sensitivity is supported.
setCaseSentivice(boolean) - Method in class ome.services.SearchBean
setCaseSentivice_async(AMD_Search_setCaseSentivice, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
setChannelGlobalMinMax(long, int, double, double) - Method in interface ome.api.IPixels: Sets the channel global (all 2D optical sections corresponding to a particular channel) minimum and maximum for a Pixels set.
setChannelGlobalMinMax(long, int, double, double) - Method in class ome.logic.PixelsImpl
setChannelGlobalMinMax_async(AMD_IPixels_setChannelGlobalMinMax, long, int, double, double, Current) - Method in class ome.services.blitz.impl.PixelsI
setChannelWindow(Long, int, double, double) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
setChannelWindow(Long, int, double, double) - Method in interface ome.services.blitz.gateway.services.RenderingService: Set the channel min, max.
setChannelWindow(int, double, double) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setChannelWindow(int, double, double) - Method in class omeis.providers.re.Renderer: Sets the pixels intensity interval for the specified channel.
setChannelWindow(int, double, double) - Method in interface omeis.providers.re.RenderingEngine: Returns the pixels intensity interval.
setChannelWindow_async(AMD_RenderingEngine_setChannelWindow, int, double, double, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setClasses(Set<String>) - Method in class ome.services.fulltext.AllEntitiesPseudoLogLoader
setClientEndpoints(String, int) - Method in class ome.services.blitz.Router
setClientObject(boolean) - Method in class pojos.ShapeData: Set the object to be a client side object.
setClientSide(boolean) - Method in class pojos.ROIData: Sets the flag indicating if the object is a client-side object or not.
setCo2Percent(double) - Method in class pojos.ImageAcquisitionData: Sets the co2 level.
setCodomain(int, int) - Method in class omeis.providers.re.codomain.CodomainMapContext: Sets the codomain interval.
setCodomainInterval(int, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setCodomainInterval(int, int) - Method in class omeis.providers.re.Renderer: Sets the codomain interval i.e. a sub-interval of [0, 255].
setCodomainInterval(int, int) - Method in interface omeis.providers.re.RenderingEngine: Sets the sub-interval of the device space i.e. a discrete sub-interval of [0, 255]
setCodomainInterval_async(AMD_RenderingEngine_setCodomainInterval, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setComponents(List<ImageData>) - Method in class pojos.MultiImageData: Sets the images composing the file.
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.
setCompressionLevel(float) - Method in interface omeis.providers.re.RenderingEngine: Sets the current compression level for the service.
setCompressionLevel_async(AMD_RenderingEngine_setCompressionLevel, float, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setCompressionService(LocalCompress) - Method in class ome.services.ThumbnailBean: Compression service Bean injector.
setConfigValue(String, String) - Method in interface ome.api.IConfig: set a configuration value in the backend store.
setConfigValue(String, String) - Method in class ome.logic.ConfigImpl: see IConfig.setConfigValue(String, String)
setConfigValue_async(AMD_IConfig_setConfigValue, String, String, Current) - Method in class ome.services.blitz.impl.ConfigI
setConfigValueIfEquals(String, String, String) - Method in interface ome.api.IConfig: Calls IConfig.setConfigValue(String, String) if and only if the configuration property is currently equal to the test argument.
setConfigValueIfEquals(String, String, String) - Method in class ome.logic.ConfigImpl: see IConfig.setConfigValueIfEquals(String, String, String)
setConfigValueIfEquals_async(AMD_IConfig_setConfigValueIfEquals, String, String, String, Current) - Method in class ome.services.blitz.impl.ConfigI
setConstant(boolean) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Sets the type of mapping.
setContent(Object) - Method in class pojos.AnnotationData: Sets the annotation value.
setContent(Object) - Method in class pojos.BooleanAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.DoubleAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.FileAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.LongAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.RatingAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.TagAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.TermAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.TextualAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.TimeAnnotationData: Sets the time annotation.
setContext(Map<String, String>) - Method in class ome.security.basic.CurrentDetails
setContext(CodomainMapContext) - Method in interface omeis.providers.re.codomain.CodomainMap: Sets the parameters used to write the equation of the specified codomain transformation.
setContrastMethod(ContrastMethod) - Method in class pojos.ChannelData: Sets the contrast method value.
setCoordinates(int, int, int, int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Sets the coordinates of the points used to determine the equations of the lines.
setCorrectionCollar(double) - Method in class pojos.ImageAcquisitionData: Sets the correction of the objective.
setCounterFactory(CounterFactory) - Method in class ome.services.sessions.SessionManagerImpl
setCreationEvent(Event, Current) - Method in class omero.model.DetailsI
setCredentials(String) - Method in class ome.system.SessionInitializer
setCriteria(Criteria) - Method in class ome.services.query.Query: provide this Query instance with a Criteria to be used for retrieving data.
setCurrentDetails(CurrentDetails) - Method in class ome.logic.ConfigImpl: PreferenceContext setter for dependency injection.
setCurrentDetails(CurrentDetails) - Method in class ome.services.delete.BaseDeleteSpec
setCurrentDetails(CurrentDetails) - Method in class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
setCurrentId(long) - Method in class ome.services.fulltext.PersistentEventLogLoader
setDatabaseIdentity(DatabaseIdentity) - Method in class ome.logic.ConfigImpl
setDatadir(String) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for data repository directory
setDataObjects(Set<DataObject>) - Method in class pojos.TagAnnotationData: Sets the collection of data objects related to that tag.
setDatasets(Set) - Method in class pojos.ImageData: Sets the datasets containing the image.
setDatasets(Set<DatasetData>) - Method in class pojos.ProjectData: Sets the datasets contained in this project.
setDataValue(double) - Method in class pojos.DoubleAnnotationData: Sets the rating value.
setDataValue(long) - Method in class pojos.LongAnnotationData: Sets the rating value.
setDb(boolean) - Method in class ome.system.Preference: Setter injector
setDebug(boolean) - Method in class ome.tools.hibernate.EventMethodInterceptor
setDebugAll(boolean) - Method in class ome.security.basic.EventListenersFactoryBean: for setter injection
setDefaultGroup(Experimenter, ExperimenterGroup) - Method in interface ome.api.IAdmin: sets the default group for a given user.
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
setDefaultGroup_async(AMD_IAdmin_setDefaultGroup, Experimenter, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
setDefaultPixels(PixelsData) - Method in class pojos.ImageData: Sets the default set of pixels.
setDefaultSample(int) - Method in class pojos.PlateData: Sets the default sample.
setDefaultT(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
setDefaultT(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService: Set the default timepoint of the image.
setDefaultT(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setDefaultT(int) - Method in class omeis.providers.re.Renderer: Sets the default timepoint index.
setDefaultT(int) - Method in interface omeis.providers.re.RenderingEngine: Sets the default timepoint index.
setDefaultT_async(AMD_RenderingEngine_setDefaultT, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setDefaultTimeToIdle(long) - Method in class ome.services.sessions.SessionManagerImpl
setDefaultTimeToLive(long) - Method in class ome.services.sessions.SessionManagerImpl
setDefaultZ(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl
setDefaultZ(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService: Set the default Z section of the image.
setDefaultZ(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setDefaultZ(int) - Method in class omeis.providers.re.Renderer: Sets the index of the default focal section.
setDefaultZ(int) - Method in interface omeis.providers.re.RenderingEngine: Sets the index of the default focal section.
setDefaultZ_async(AMD_RenderingEngine_setDefaultZ, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setDelete(String) - Method in class ome.services.fulltext.PersistentEventLogLoader
setDescription(long, String) - Method in interface ome.api.IShare
setDescription(long, String) - Method in class ome.services.sharing.ShareBean
setDescription(String) - Method in class pojos.DatasetData: Sets the description of the dataset.
setDescription(String) - Method in class pojos.FileAnnotationData: Sets the description of the annotation.
setDescription(String) - Method in class pojos.FileData: Sets the description.
setDescription(String) - Method in class pojos.GroupData: Sets the name of the group.
setDescription(String) - Method in class pojos.ImageData: Sets the description of the image.
setDescription(String) - Method in class pojos.PlateAcquisitionData: Sets the name of the acquisition.
setDescription(String) - Method in class pojos.PlateData: Sets the description of the plate.
setDescription(String) - Method in class pojos.ProjectData: Sets the description of the project.
setDescription(String) - Method in class pojos.ScreenData: Sets the description of the screen.
setDescription_async(AMD_IShare_setDescription, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
setDetach(boolean, Current) - Method in class omero.grid.InteractiveProcessorI
setDetectorSettingBinning(Binning) - Method in class pojos.ChannelAcquisitionData: Sets the detector's binning.
setDetectorSettingOffset(double) - Method in class pojos.ChannelAcquisitionData: Sets the detector's setting offset.
setDetectorSettingsGain(double) - Method in class pojos.ChannelAcquisitionData: Sets the detector setting's gain.
setDetectorSettingsReadOutRate(double) - Method in class pojos.ChannelAcquisitionData: Sets the detector setting's read out rate.
setDetectorSettingsVoltage(double) - Method in class pojos.ChannelAcquisitionData: Sets the detector setting's voltage.
setDirty(boolean) - Method in class pojos.DataObject: Sets to true if the value has been modified, otherwise.
setDirty(boolean) - Method in class pojos.ShapeData: Has the figure been changed from the server side version.
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 interface ome.api.ILdap: Searchs all Experimenter in LDAP for objectClass = person
setDN(Long, String) - Method in class ome.logic.LdapImpl
setDN_async(AMD_ILdap_setDN, RLong, String, Current) - Method in class ome.services.blitz.impl.LdapI
setDriver(String) - Method in class ome.tools.DbUpdateTask
setEmail(String) - Method in class pojos.ExperimenterData: Sets the e-mail of the experimenter.
setEmissionWavelength(int) - Method in class pojos.ChannelData: Sets the emission wavelength.
setExcitationWavelength(int) - Method in class pojos.ChannelData: Sets the excitation wavelength.
setExcludes(String[]) - Method in class ome.services.fulltext.EventLogLoader: Spring injector
setExecutor(Executor) - Method in class ome.logic.UpdateImpl
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
setExperimenters(Set<ExperimenterData>) - Method in class pojos.GroupData: Sets the experimenters contained in this group.
setExpiration(long, Timestamp) - Method in interface ome.api.IShare
setExpiration(long, Timestamp) - Method in class ome.services.sharing.ShareBean
setExpiration_async(AMD_IShare_setExpiration, long, RTime, Current) - Method in class ome.services.blitz.impl.ShareI
setExtendedMetadata(ExtendedMetadata) - Method in class ome.logic.AbstractLevel2Service
setExtendedMetadata(ExtendedMetadata) - Method in class ome.services.delete.AnnotationDeleteSpec: Performs sanity checks on the annotation entries found in ExtendedMetadata.
setExtendedMetadata(ExtendedMetadata) - Method in class ome.services.delete.BaseDeleteSpec
setExtent(double, double) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the maximum range of the input window.
setExternalDescription(String) - Method in class pojos.WellData: Sets the external description of the well.
setExternalIdentifier(String) - Method in class pojos.PlateData: Sets the external identifier.
setExternalInfo(ExternalInfo, Current) - Method in class omero.model.DetailsI
setFileId(long) - Method in interface ome.api.RawFileStore: This method manages the state of the service.
setFileId(long) - Method in class ome.services.RawFileBean
setFileId_async(AMD_RawFileStore_setFileId, long, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
setFileParam(long, String, String) - Method in class ome.services.db.PgArrayHelper: Appends "{key, value}" onto the original file "params" field or replaces the value if already present.
setFileParams(long, Map<String, String>) - Method in class ome.services.db.PgArrayHelper: Resets the entire original file "params" field.
setFileService(OriginalFilesService) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for ROMIO file service
setFillColor(Color) - Method in class pojos.ShapeSettingsData: Set the fill colour.
setFillRule(String) - Method in class pojos.ShapeSettingsData: Set the fill rule.
setFirstName(String) - Method in class pojos.ExperimenterData: Sets the first name of the experimenter.
setFluor(String) - Method in class pojos.ChannelData: Sets the fluor.
setFontFamily(String) - Method in class pojos.ShapeSettingsData: Returns the stroke.
setFontSize(int) - Method in class pojos.ShapeSettingsData: Set the size of the font.
setFontStyle(String) - Method in class pojos.ShapeSettingsData: Set the style of the font.
setFontWeight(String) - Method in class pojos.ShapeSettingsData: Set the weight of the font.
setFullTextBridge(FullTextBridge) - Method in class ome.logic.UpdateImpl
setGreen(Integer) - Method in class pojos.WellData: Sets the green component of the color associated to the well.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer: Sets the Green value for a particular pixel index.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBBuffer: Sets the Green value for a particular pixel index.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer: Sets the Green value for a particular pixel index.
setGroup(ExperimenterGroup, Current) - Method in class omero.model.DetailsI
setGroupOwner(ExperimenterGroup, Experimenter) - Method in interface ome.api.IAdmin: adds the user to the owner list for this group.
setGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl
setGroupOwner_async(AMD_IAdmin_setGroupOwner, ExperimenterGroup, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
setGroupRead(boolean, Current) - Method in class omero.model.PermissionsI
setGroupRead(boolean) - Method in class pojos.PermissionData: Sets to true if the group has read access, false otherwise.
setGroups(List<GroupData>) - Method in class pojos.ExperimenterData: Sets the groups the experimenter is a member of.
setGroupWrite(boolean, Current) - Method in class omero.model.PermissionsI
setGroupWrite(boolean) - Method in class pojos.PermissionData: Sets to true if the group has write access, false otherwise.
setHeight(double) - Method in class pojos.MaskData: Sets the height of an untransformed mask.
setHeight(double) - Method in class pojos.RectangleData: Sets the height of an untransformed rectangle.
setHumidity(double) - Method in class pojos.ImageAcquisitionData: Sets the humidity.
setIContainer(IContainer) - Method in class ome.logic.MetadataImpl: IContainer bean injector.
setId(long) - Method in class pojos.DataObject: Sets the database id.
setIdOnly() - Method in class ome.services.SearchBean
setIllumination(Illumination) - Method in class pojos.ChannelData: Sets the illumination value.
setImage(ImageData) - Method in class pojos.PixelsData: Sets the image linked to this pixels' set.
setImage(Image) - Method in class pojos.ROIData: Sets the imageId for the ROI.
setImage(ImageData) - Method in class pojos.WellSampleData: Sets the image linked to this well sample.
setImages(Set<ImageData>) - Method in class pojos.DatasetData: Sets the images contained in this dataset.
setInput(String, String, Object) - Method in interface ome.api.ISession: Places an entry in the given session's input environment.
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
setInput(String, RType) - Method in class omero.client: Sets an item in the "input" shared (session) memory under the given name.
setInput_async(AMD_ISession_setInput, String, String, RType, Current) - Method in class ome.services.blitz.impl.SessionI
setInsert(String) - Method in class ome.services.fulltext.PersistentEventLogLoader
setInstitution(String) - Method in class pojos.ExperimenterData: Sets the institution where the experimenter works.
setInterval(int, int) - Method in class omeis.providers.re.codomain.CodomainChain: Sets the codomain interval.
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
setJdbcTemplate(SimpleJdbcOperations) - Method in class ome.logic.ConfigImpl: SimpleJdbcTemplate setter for dependency injection.
setKey(String) - Method in class ome.services.fulltext.PersistentEventLogLoader
setKeyStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
setKeyStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
setKeywords(String) - Method in class pojos.WorkflowData: Sets the keywords of the workflow.
setKeywords(List<String>) - Method in class pojos.WorkflowData: Sets the keywords of the workflow.
setLabelName(String) - Method in class pojos.ImageAcquisitionData: Sets the name of the stage label.
setLastName(String) - Method in class pojos.ExperimenterData: Sets the last name of the experimenter.
setLigthSettingsAttenuation(double) - Method in class pojos.ChannelAcquisitionData: Sets the attenuation of the light settings.
setLigthSettingsWavelength(int) - Method in class pojos.ChannelAcquisitionData: Returns the wavelength of the light source.
setLimits(int, int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Set the limits.
setLineCap(int) - Method in class pojos.ShapeSettingsData: Set the line cap.
setLowerLimit(int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Sets the value (in [intervalStart, intervalEnd]) used to set the level of the bit-plane < bit-plane selected.
setMap(QuantumMap) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the quantum map.
setMapping(Family, double, boolean) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the selected family, the curve coefficient and the noise reduction flag.
setMask(byte[]) - Method in class pojos.MaskData: Sets the mask image.
setMask(BufferedImage) - Method in class pojos.MaskData: Sets the mask from the bufferedImage.
setMaxClauseCount(Integer) - Method in class ome.services.SearchBean: Injector used by Spring.
setMedium(Medium) - Method in class pojos.ImageAcquisitionData: Sets the medium of the objective.
setMergedBatches(boolean) - Method in interface ome.api.Search: Set whether or not results from two separate queries can be returned in the same call to Search.results().
setMergedBatches(boolean) - Method in class ome.services.SearchBean
setMergedBatches_async(AMD_Search_setMergedBatches, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
setMessage(String) - Method in interface ome.api.JobHandle: Sets the job's message string, and returns the previous value.
setMessage(String, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
setMessage(String) - Method in class ome.services.JobBean
setMessage_async(AMD_JobHandle_setMessage, String, Current) - Method in class ome.services.blitz.impl.JobHandleI
setMethodHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
setMethodSecurity(MethodSecurity) - Method in class ome.security.basic.BasicSecurityWiring: Setter injection.
setMiddleName(String) - Method in class pojos.ExperimenterData: Sets the middle name of the experimenter.
setMode(AcquisitionMode) - Method in class pojos.ChannelData: Sets the acquisition mode value.
setModel(RenderingModel) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setModel(RenderingModel) - Method in class omeis.providers.re.Renderer: Specifies the model that dictates how transformed raw data has to be mapped onto a color space.
setModel(RenderingModel) - Method in interface omeis.providers.re.RenderingEngine: Specifies the model that dictates how transformed raw data has to be mapped onto a color space.
setModel_async(AMD_RenderingEngine_setModel, RenderingModel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setMutable(boolean) - Method in class ome.system.Preference: Setter injector
setName(String) - Method in class pojos.ChannelData: Sets the name of the logical channel.
setName(String) - Method in class pojos.DatasetData: Sets the name of the dataset.
setName(String) - Method in class pojos.GroupData: Sets the name of the group.
setName(String) - Method in class pojos.ImageData: Sets the name of the image.
setName(String) - Method in class pojos.PlateAcquisitionData: Sets the name of the acquisition.
setName(String) - Method in class pojos.PlateData: Sets the name of the plate.
setName(String) - Method in class pojos.ProjectData: Sets the name of the project.
setName(String) - Method in class pojos.ScreenData: Sets the name of the screen.
setNameSpace(String) - Method in class pojos.AnnotationData: Sets the name space of the underlying Annotation instance.
setNameSpace(String) - Method in class pojos.TermAnnotationData: Returns the namespace of the term.
setNamespace(String) - Method in class pojos.WorkflowData: Sets the namespace of the workflow.
setNamespaceKeywords(String, String[]) - Method in class pojos.ROIData: Sets the namespace and keywords.
setNamespaceMap(Map<String, List<String>>) - Method in class pojos.ROIData: Sets the namespaces and keywords of the ROI from the map.
setNDFilter(double) - Method in class pojos.ChannelData: Sets the ND filter.
setObjectsReadHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
setObjectsWrittenHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
setOrder(ByteOrder) - Method in class ome.io.nio.PixelData: Set the byte order of the backing buffer.
setOrder(ByteOrder) - Method in class ome.io.nio.ReorderedPixelData: Set the byte order of the backing buffer.
setOriginalFilesService(OriginalFilesService) - Method in class ome.services.RawFileBean: I/O service (OriginalFilesService) Bean injector.
setOriginalSettingsForPixels(long) - Method in interface ome.api.IRenderingSettings: Resets an Pixels' default rendering settings back to channel global minimum and maximum.
setOriginalSettingsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsForPixels_async(AMD_IRenderingSettings_setOriginalSettingsForPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
setOriginalSettingsInDataset(long) - Method in interface ome.api.IRenderingSettings: Resets a dataset's rendering settings back to channel global minimum and maximum.
setOriginalSettingsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsInDataset_async(AMD_IRenderingSettings_setOriginalSettingsInDataset, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
setOriginalSettingsInImage(long) - Method in interface ome.api.IRenderingSettings: Resets an image's default rendering settings back to channel global minimum and maximum.
setOriginalSettingsInImage(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsInImage_async(AMD_IRenderingSettings_setOriginalSettingsInImage, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
setOriginalSettingsInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets a rendering settings back to channel global minimum and maximum for the specified containers.
setOriginalSettingsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsInSet_async(AMD_IRenderingSettings_setOriginalSettingsInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
setOutput(String, String, Object) - Method in interface ome.api.ISession: Places an entry in the given session's output environment.
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
setOutput(String, RType) - Method in class omero.client: Sets an item in the "output" shared (session) memory under the given name.
setOutput_async(AMD_ISession_setOutput, String, String, RType, Current) - Method in class ome.services.blitz.impl.SessionI
setOverlays(Map<byte[], Integer>) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setOverlays(Map<byte[], Integer>) - Method in class omeis.providers.re.Renderer: Sets a map of overlays to be rendered.
setOverlays(Map<byte[], Integer>) - Method in interface omeis.providers.re.RenderingEngine: Informs the rendering engine that it should render a set of overlays on each rendered frame.
setOverlays_async(AMD_RenderingEngine_setOverlays, RLong, RLong, Map<Long, Integer>, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setOwner(Experimenter, Current) - Method in class omero.model.DetailsI
setParameterValues(Properties) - Method in class ome.tools.hibernate.PermissionsType
setParentFilePath(String, int) - Method in class pojos.ImageData: Sets the path to the file hosting the image.
setPathToFile(String) - Method in class pojos.ImageData: Sets the path to the file.
setPerm1(long, Current) - Method in class omero.model.PermissionsI
setPerm1(Long) - Method in class omero.model.PermissionsI
setPermissions(Permissions, Current) - Method in class omero.model.DetailsI
setPermissionsVerifier(String, int) - Method in class ome.services.blitz.Router
setPinholeSize(double) - Method in class pojos.ChannelData: Sets the pinhole size.
setPixelDataService(PixelsService) - Method in class ome.services.ThumbnailBean: Pixels 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 interface ome.api.RawPixelsStore: Initializes the stateful service for a given Pixels set.
setPixelsId(long) - Method in interface ome.api.ThumbnailStore: This method manages the state of the service; it must be invoked before using any other methods.
setPixelsId(long) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl: Lookup the pixels for the renderingEngine for pixelsId
setPixelsId(long, boolean) - Method in class ome.services.RawPixelsBean
setPixelsId(long) - Method in class ome.services.ThumbnailBean
setPixelsId_async(AMD_RawPixelsStore_setPixelsId, long, boolean, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
setPixelsId_async(AMD_ThumbnailStore_setPixelsId, long, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
setPixelSizeX(double) - Method in class pojos.PixelsData: Sets the dimension of a pixel along the X-axis, dimension is in microns.
setPixelSizeY(double) - Method in class pojos.PixelsData: Sets the dimension of a pixel along the Y-axis, dimension is in microns.
setPixelSizeZ(double) - Method in class pojos.PixelsData: Sets the dimension of a pixel along the Z-axis, dimension is in microns.
setPixelsMetadata(IPixels) - Method in class ome.logic.RenderingSettingsImpl: Sets injector.
setPixelsMetadata(IPixels) - Method in class ome.services.RawPixelsBean
setPixelsParam(long, String, String) - Method in class ome.services.db.PgArrayHelper: Appends "{key, value}" onto the original file "params" field or replaces the value if already present.
setPixelsParams(long, Map<String, String>) - Method in class ome.services.db.PgArrayHelper: Resets the entire original file "params" field.
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.
setPixelValue(int, double) - Method in class ome.io.nio.PixelData: Sets the pixel intensity value of the pixel at a given offset within the backing buffer.
setPixelValueDirect(int, double) - Method in class ome.io.nio.PixelData: Sets the pixel intensity value of the pixel at a given offset within the backing buffer.
setPlane(byte[], int, int, int) - Method in interface ome.api.RawPixelsStore
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision: not implemented
setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision: not implemented
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Sets a particular 2D image plane in this pixel buffer.
setPlane(byte[], Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Sets a particular 2D image plane in this pixel buffer.
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
setPlane(long, byte[], int, int, int) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl
setPlane(long, byte[], int, int, int) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService: set the plane at z, c, t to the bytes of buf.
setPlane(byte[], int, int, int) - Method in class ome.services.RawPixelsBean
setPlane_async(AMD_RawPixelsStore_setPlane, byte[], int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
setPlanes(int, int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Sets the value of the selected planes i.e. the previous plane and the selected one.
setPlateAcquisition(Set<PlateAcquisitionData>) - Method in class pojos.PlateData: Sets the plate acquisition linked to the plate.
setPlates(Set<PlateData>) - Method in class pojos.ScreenData: Sets the plates contained in this screen.
setPockelCell(int) - Method in class pojos.ChannelData: Sets the pockel cell.
setPoints(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Method in class pojos.PolygonData: Sets the points in the polygon.
setPoints(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Method in class pojos.PolylineData: Sets the points in the polyline.
setPositionX(double) - Method in class pojos.ImageAcquisitionData: Sets the x-position.
setPositionY(double) - Method in class pojos.ImageAcquisitionData: Sets the y-position.
setPositionZ(double) - Method in class pojos.ImageAcquisitionData: Sets the z-position.
setPreferenceContext(PreferenceContext) - Method in class ome.logic.ConfigImpl: PreferenceContext setter for dependency injection.
setPreferences(List<Preference>) - Method in class ome.system.PreferenceContext
setPrefs(boolean) - Method in class ome.system.Preference
setPrimaryColorEnabled(boolean) - Method in class omeis.providers.re.Optimizations: Enable or disable the primary color optimization.
setPrincipal(Principal) - Method in class ome.system.SessionInitializer
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.
setProjects(Set<ProjectData>) - Method in class pojos.DatasetData: Sets the projects containing the dataset.
setProperty(String, String) - Method in class ome.system.PreferenceContext: With ticket:2214, preferences are no longer mutable.
setProtocolDescription(String) - Method in class pojos.ScreenData: Sets the description of the protocol.
setProtocolIdentifier(String) - Method in class pojos.ScreenData: Sets the identifier of the protocol.
setProxy(ObjectPrx) - Method in class ome.services.blitz.util.RegisterServantMessage
setQuantizationMap(int, Family, double, boolean) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setQuantizationMap(Family, double, boolean) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the selected family, the curve coefficient and the noise reduction flag and rebuilds the look-up table.
setQuantizationMap(int, Family, double, boolean) - Method in class omeis.providers.re.Renderer: Sets the mapping strategy for the specified channel.
setQuantizationMap(int, Family, double, boolean) - Method in interface omeis.providers.re.RenderingEngine: Sets the quantization map, one per channel.
setQuantizationMap_async(AMD_RenderingEngine_setQuantizationMap, int, Family, double, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setQuantumStrategy(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setQuantumStrategy(int) - Method in class omeis.providers.re.Renderer: Sets the bit resolution.
setQuantumStrategy(int) - Method in interface omeis.providers.re.RenderingEngine: Sets the quantization strategy.
setQuantumStrategy_async(AMD_RenderingEngine_setQuantumStrategy, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setQuery(String) - Method in class ome.services.fulltext.PersistentEventLogLoader
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(LocalQuery) - Method in class ome.services.AbstractStatefulBean: Query service Bean injector.
setQueryService(IQuery) - Method in class ome.services.fulltext.EventLogLoader: Spring injector
setQueryService(IQuery) - Method in class ome.services.procs.ProcessorSkeleton
setRadiusX(double) - Method in class pojos.EllipseData: Sets the radius along the X-axis.
setRadiusY(double) - Method in class pojos.EllipseData: Sets the radius along the Y-axis.
setRating(int) - Method in class pojos.RatingAnnotationData: Sets the rating value.
setReadOnly(boolean) - Method in class ome.services.sessions.SessionManagerImpl
setReadOnly(boolean) - Method in class pojos.ShapeData: Set the Shape object to be readOnly
setReagentSetDescripion(String) - Method in class pojos.ScreenData: Sets the identifier of the reagent.
setReagentSetIdentifier(String) - Method in class pojos.ScreenData: Sets the identifier of the reagent.
setRed(Integer) - Method in class pojos.WellData: Sets the red component of the color associated to the well.
setRedValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer: Sets the Red value for a particular pixel index.
setRedValue(int, int) - Method in class omeis.providers.re.RGBBuffer: Sets the Red value for a particular pixel index.
setRedValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer: Sets the Red value for a particular pixel index.
setReference(OriginalFile) - Method in class pojos.ImageData: Sets the reference to the file to register.
setRefPlateId(long) - Method in class pojos.PlateAcquisitionData: Sets the id of the plate this plate acquisition is for.
setRefractiveIndex(double) - Method in class pojos.ImageAcquisitionData: Sets the refractive index of the objective.
setRegion(int, long, byte[]) - Method in interface ome.api.RawPixelsStore
setRegion(Integer, Long, byte[]) - Method in class ome.io.nio.DeltaVision: not implemented
setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.nio.DeltaVision: not implemented
setRegion(Integer, Long, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setRegion(Integer, Long, byte[]) - Method in interface ome.io.nio.PixelBuffer: Sets a region in this pixel buffer.
setRegion(Integer, Long, ByteBuffer) - Method in interface ome.io.nio.PixelBuffer: Sets a region in this pixel buffer.
setRegion(Integer, Long, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.nio.RomioPixelBuffer
setRegion(int, long, byte[]) - Method in class ome.services.RawPixelsBean
setRegion_async(AMD_RawPixelsStore_setRegion, int, long, byte[], Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
setRegisteredFile(OriginalFile) - Method in class pojos.FileData: Sets the registered file.
setRegisteredFile(Image) - Method in class pojos.ImageData: Sets the registered file.
setRegistry(Registry) - Method in class ome.services.blitz.fire.Ring: Sets the Registry for this instance.
setRenderingDefId(long) - Method in interface ome.api.ThumbnailStore: This method manages the state of the service; it should be invoked directly after setPixelsId.
setRenderingDefId(long, long) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl
setRenderingDefId(long, long) - Method in interface ome.services.blitz.gateway.services.ThumbnailService: Set the rendering def from the default to another.
setRenderingDefId(long) - Method in class ome.services.ThumbnailBean
setRenderingDefId_async(AMD_ThumbnailStore_setRenderingDefId, long, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
setRepetitions(int) - Method in class ome.services.fulltext.FullTextIndexer: Spring injector.
setRepositoryPath(String) - Method in class pojos.FileData: Sets the path to the parent.
setReturnUnloaded(boolean) - Method in interface ome.api.Search: Determines if all results should be returned as unloaded objects.
setReturnUnloaded(boolean) - Method in class ome.services.SearchBean
setReturnUnloaded_async(AMD_Search_setReturnUnloaded, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
setRGBA(int, int, int, int, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setRGBA(int, int, int, int, int) - Method in class omeis.providers.re.Renderer: Sets the color associated to the specified channel.
setRGBA(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine: Sets the four components composing the color associated to the specified channel.
setRGBA_async(AMD_RenderingEngine_setRGBA, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setROICoordinate(ROICoordinate) - Method in class pojos.ShapeData: Set the ROICoordinate for the ShapeData
setRoles(Roles) - Method in class ome.services.sessions.SessionManagerImpl
setRow(byte[], int, int, int, int) - Method in interface ome.api.RawPixelsStore
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision: not implemented
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Sets a particular row or scanline in this pixel buffer.
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
setRow(byte[], int, int, int, int) - Method in class ome.services.RawPixelsBean
setRow_async(AMD_RawPixelsStore_setRow, byte[], int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
setScaleService(IScale) - Method in class ome.services.ThumbnailBean: Scale service Bean injector.
setScreens(Set<ScreenData>) - Method in class pojos.PlateData: Sets the screens containing the plate.
setSecurityContext(IObject, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
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
setSecuritySystem(SecuritySystem) - Method in class ome.services.blitz.impl.TimelineI
setSequence(short) - Method in class ome.io.nio.DeltaVision: Sets the sequence of the file.
setSequence(short) - Method in class ome.io.nio.DeltaVisionHeader: Sets the sequence of the file.
setServerEndpoints(String, int) - Method in class ome.services.blitz.Router
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.gateway.OmeroGateway: Initialize the service factory which creates the gateway and services and links the different services together.
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.DeleteI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.ExporterI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.MetadataStoreI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RawFileStoreI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RenderingEngineI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RoiI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.ScriptI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.SharedResourcesI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.TimelineI
setServiceFactory(ServiceFactoryI) - Method in interface ome.services.blitz.util.ServiceFactoryAware
setSession(Session) - Method in class ome.system.ServiceFactory
setSession(Session) - Method in class ome.system.SessionInitializer
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.
setSessionHandler(SessionHandler) - Method in class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
setSessionManager(SessionManager) - Method in class ome.logic.UpdateImpl
setSessionManager(SessionManager) - Method in class ome.security.basic.BasicMethodSecurity
setSessionManager(SessionManager) - Method in class ome.services.blitz.impl.TimelineI
setSessionManager(String, int) - Method in class ome.services.blitz.Router
setSessionService(ISession) - Method in class ome.system.SessionInitializer
setSettingsService(IRenderingSettings) - Method in class ome.services.ThumbnailBean: Rendering settings service Bean injector.
setShapeSettings(Shape) - Method in class pojos.ShapeData: Set the settings associated to the shape.
setShareId(Long) - Method in interface ome.api.local.LocalShare
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
setShareId(Long) - Method in class ome.services.sharing.ShareBean: Not in the public interface (since it allows setting to -1 which makes everything readable, but used internally similar to a LocalShare interface.
setSimpleJdbcOperations(SimpleJdbcOperations) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for JDBC operations
setSizeC(int) - Method in class pojos.PixelsData: Sets the number of channels.
setSizeT(int) - Method in class pojos.PixelsData: Sets the number of time-points.
setSizeX(int) - Method in class pojos.PixelsData: Sets the number of pixels along the X-axis.
setSizeY(int) - Method in class pojos.PixelsData: Sets the number of pixels along the Y-axis.
setSizeZ(int) - Method in class pojos.PixelsData: Sets the number of pixels along the Z-axis.
setSqldir(File) - Method in class ome.tools.DbUpdateTask
setStack(byte[], int, int, int) - Method in interface ome.api.RawPixelsStore
setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision: not implemented
setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.DeltaVision: not implemented
setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setStack(ByteBuffer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
setStack(byte[], Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
setStack(byte[], int, int, int) - Method in class ome.services.RawPixelsBean
setStack_async(AMD_RawPixelsStore_setStack, byte[], int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
setStaleCacheListener(SessionCache.StaleCacheListener) - Method in class ome.services.sessions.state.SessionCache
setStatus(String) - Method in interface ome.api.JobHandle: Updates the JobStatus for the current job.
setStatus(String) - Method in class ome.services.JobBean
setStatus(String) - Method in class pojos.PlateData: Sets the status.
setStatus_async(AMD_JobHandle_setStatus, String, Current) - Method in class ome.services.blitz.impl.JobHandleI
setStatusAndMessage(String, String) - Method in interface ome.api.JobHandle: Like JobHandle.setStatus(String) but also sets the message.
setStatusAndMessage(String, String) - Method in class ome.services.JobBean
setStatusAndMessage_async(AMD_JobHandle_setStatusAndMessage, String, RString, Current) - Method in class ome.services.blitz.impl.JobHandleI
setStrokeColor(Color) - Method in class pojos.ShapeSettingsData: Set the stroke colour.
setStrokeDashArray(double[]) - Method in class pojos.ShapeSettingsData: Set the stroke dashes.
setStrokeWidth(double) - Method in class pojos.ShapeSettingsData: Set the stroke width.
setT(int) - Method in class pojos.ShapeData: Set the timepoint.
setTagDescription(String) - Method in class pojos.TagAnnotationData: Sets the description of the tag.
setTagDescriptions(List<TextualAnnotationData>) - Method in class pojos.TagAnnotationData: Sets the tag's descriptions.
setTags(Set<TagAnnotationData>) - Method in class pojos.TagAnnotationData: Sets the collection of tags.
setTagValue(String) - Method in class pojos.TagAnnotationData: Sets the value of the tag.
setTemperature(double) - Method in class pojos.ImageAcquisitionData: Sets the temperature.
setTemplate(SimpleJdbcTemplate) - Method in class ome.services.fulltext.PersistentEventLogLoader
setTerm(String) - Method in class pojos.TermAnnotationData: Sets the term.
setText(String) - Method in class pojos.EllipseData: Sets the text of the shape.
setText(String) - Method in class pojos.LineData: Sets the text of the shape.
setText(String) - Method in class pojos.MaskData: Sets the text of the shape.
setText(String) - Method in class pojos.PointData: Sets the text of the shape.
setText(String) - Method in class pojos.PolygonData: Sets the text of the shape.
setText(String) - Method in class pojos.PolylineData: Sets the text of the shape.
setText(String) - Method in class pojos.RectangleData: Sets the text of the shape.
setText(String) - Method in class pojos.TextData: Sets the text of the shape.
setText(String) - Method in class pojos.TextualAnnotationData: Sets the text.
setThumbnailService(ThumbnailService) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for ROMIO thumbnail service
setTie(TieBase) - Method in class ome.services.blitz.impl.RawFileStoreI
setTie(TieBase) - Method in interface ome.services.blitz.util.TieAware
setTimeout(int) - Method in class ome.services.blitz.Router
setTimepoint(byte[], int) - Method in interface ome.api.RawPixelsStore
setTimepoint(ByteBuffer, Integer) - Method in class ome.io.nio.DeltaVision: not implemented
setTimepoint(byte[], Integer) - Method in class ome.io.nio.DeltaVision: not implemented
setTimepoint(ByteBuffer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setTimepoint(byte[], Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setTimepoint(ByteBuffer, Integer) - Method in interface ome.io.nio.PixelBuffer: Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
setTimepoint(byte[], Integer) - Method in interface ome.io.nio.PixelBuffer: Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
setTimepoint(ByteBuffer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
setTimepoint(byte[], Integer) - Method in class ome.io.nio.RomioPixelBuffer
setTimepoint(byte[], int) - Method in class ome.services.RawPixelsBean
setTimepoint_async(AMD_RawPixelsStore_setTimepoint, byte[], int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
settings - Variable in class pojos.ShapeData: The representation of the shape.
SETTINGSID_QUERY - Static variable in class ome.services.delete.DeleteBean
setToken(GraphHolder) - Method in class ome.security.basic.TokenHolder
setTransform(String) - Method in class pojos.ShapeData: Sets the Affine transform of the shape.
setTrustStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
setTrustStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
setTypes(ITypes) - Method in class ome.services.fulltext.PersistentEventLogLoader
setTypesService(ITypes) - Method in class ome.services.JobBean: Types service Bean injector.
setTypesService(ITypes) - Method in class ome.services.procs.ProcessorSkeleton
setUp() - Method in class ome.formats.importer.util.TinyImportFixture: checks for the necessary fields and initializes the ImportLibrary
setUpdate(String) - Method in class ome.services.fulltext.PersistentEventLogLoader
setUpdateEvent(Event, Current) - Method in class omero.model.DetailsI
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
setUpperLimit(int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Sets the value (in [intervalStart, intervalEnd]) used to set the level of the bit-plane > bit-plane selected.
setUseProjections(boolean) - Method in interface ome.api.Search: Determines if Lucene queries should not hit the database.
setUseProjections(boolean) - Method in class ome.services.SearchBean
setUseProjections_async(AMD_Search_setUseProjections, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
setUserId(long) - Method in class ome.services.ThumbnailCtx: Sets the user ID to use for queries.
setUserRead(boolean, Current) - Method in class omero.model.PermissionsI
setUserRead(boolean) - Method in class pojos.PermissionData: Sets to true if the user has read access, false otherwise.
setUserWrite(boolean, Current) - Method in class omero.model.PermissionsI
setUserWrite(boolean) - Method in class pojos.PermissionData: Sets to true if the user has write access, false otherwise.
setUuid(String) - Method in class ome.services.sessions.SessionManagerImpl
setValue(boolean) - Method in class pojos.BooleanAnnotationData: Returns the text.
setValue(IObject) - Method in class pojos.DataObject: Sets the IObject.
setVersion(int) - Method in class pojos.DataObject: Sets the version of the object if it is immutable.
setVisibility(Preference.Visibility) - Method in class ome.system.Preference: Setter injector
setWavelength(int) - Method in exception omeis.providers.re.quantum.QuantizationException: Sets the index of the wavelength that couldn't be rendered.
setWellSamples(List<WellSampleData>) - Method in class pojos.WellData: Sets the well samples linked to the well.
setWellType(String) - Method in class pojos.WellData: Sets a human readable identifier for the screening status e.g. empty, positive control, etc.
setWidth(double) - Method in class pojos.MaskData: Sets the width of an untransformed mask.
setWidth(double) - Method in class pojos.RectangleData: Sets width of an untransformed rectangle.
setWindow(double, double) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the input window interval.
setWorldRead(boolean, Current) - Method in class omero.model.PermissionsI
setWorldRead(boolean) - Method in class pojos.PermissionData: Sets to true if the world has read access, false otherwise.
setWorldWrite(boolean, Current) - Method in class omero.model.PermissionsI
setWorldWrite(boolean) - Method in class pojos.PermissionData: Sets to true if the world has write access, false otherwise.
setX(int) - Method in class omeis.providers.re.data.PlaneDef: Selects a plane in the set identified by this object.
setX(double) - Method in class pojos.EllipseData: Sets the x-coordinate of the center of the ellipse.
setX(double) - Method in class pojos.MaskData: Sets the x-coordinate top-left corner of an untransformed mask.
setX(double) - Method in class pojos.PointData: set the x-coordinate of the shape.
setX(double) - Method in class pojos.RectangleData: Sets the x-coordinate of the top-left corner of an untransformed rectangle.
setX(double) - Method in class pojos.TextData: Sets the x-coordinate of the text field.
setX1(double) - Method in class pojos.LineData: Set the x-coordinate of the starting point of an untransformed line.
setX2(double) - Method in class pojos.LineData: Set the x-coordinate of the end point of an untransformed line.
setXEnd(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Sets the x-coodinate of the pEnd point.
setXStart(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Sets the x-coodinate of the pStart point.
setY(int) - Method in class omeis.providers.re.data.PlaneDef: Selects a plane in the set identified by this object.
setY(double) - Method in class pojos.EllipseData: Sets the y-coordinate of the center of the ellipse.
setY(double) - Method in class pojos.MaskData: Sets the y-coordinate top-left corner of an untransformed mask.
setY(double) - Method in class pojos.PointData: set the y-coordinate of the shape.
setY(double) - Method in class pojos.RectangleData: Sets the y-coordinate of the top-left corner of an untransformed rectangle.
setY(double) - Method in class pojos.TextData: Sets the y-coordinate of the text field.
setY1(double) - Method in class pojos.LineData: Set the y-coordinate of the starting point of an untransformed line.
setY2(double) - Method in class pojos.LineData: Set the y-coordinate of the end point of an untransformed line.
setYEnd(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Sets the y-coodinate of the pEnd point.
setYStart(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Sets the y-coodinate of the pStart point.
setZ(int) - Method in class omeis.providers.re.data.PlaneDef: Selects a plane in the set identified by this object.
setZ(int) - Method in class pojos.ShapeData: Set the z-section.
sf - Variable in class ome.logic.AdminImpl
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.blitz.impl.MetadataStoreI
sf - Variable in class ome.services.delete.DeleteBean
sha1() - Method in class ome.services.scripts.RepoFile.FsFile
sha1() - Method in class ome.services.scripts.RepoFile
sha1(File) - Method in class omero.client: Calculates the local sha1 for a file.
shape() - Method in class ome.services.roi.RoiTypes.ObjectFactory
ShapeChangeMessage - Class in ome.services.messages: Published on any modification to a Shape.
ShapeChangeMessage(Object, List<EventLog>) - Constructor for class ome.services.messages.ShapeChangeMessage
ShapeData - Class in pojos: Hosts a shape.
ShapeData(Shape, boolean) - Constructor for class pojos.ShapeData: Creates a new instance.
ShapeData(Shape) - Constructor for class pojos.ShapeData: Creates a new instance.
ShapeSettingsData - Class in pojos: Stores the settings related to a given shape.
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. i.e.
ShareBean(LocalAdmin, SessionManager, ShareStore, Executor) - Constructor for class ome.services.sharing.ShareBean
shareCount(long) - Method in class ome.services.sharing.data.ShareItems
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
ShareDataHolder.Patcher - Class in ome.services.sharing.data
ShareDataHolder.Patcher() - Constructor for class ome.services.sharing.data.ShareDataHolder.Patcher
ShareDataPrx - Interface in ome.services.sharing.data
ShareDataPrxHelper - Class in ome.services.sharing.data
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
sharedResources(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
SharedResourcesI - Class in ome.services.blitz.impl: Implementation of the SharedResources interface.
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper) - Constructor for class ome.services.blitz.impl.SharedResourcesI
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper, long) - Constructor for class ome.services.blitz.impl.SharedResourcesI
ShareI - Class in ome.services.blitz.impl: Implementation of the IShare service.
ShareI(IShare, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ShareI
shareId - Variable in class ome.system.SimpleEventContext
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
ShareItemHolder.Patcher - Class in ome.services.sharing.data
ShareItemHolder.Patcher() - Constructor for class ome.services.sharing.data.ShareItemHolder.Patcher
ShareItemPrx - Interface in ome.services.sharing.data
ShareItemPrxHelper - Class in ome.services.sharing.data
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
ShareItems - Class in ome.services.sharing.data
ShareItems(Connection, String, boolean, Comparator, Map) - Constructor for class ome.services.sharing.data.ShareItems
ShareItems(Connection, String, boolean, Comparator) - Constructor for class ome.services.sharing.data.ShareItems
ShareItems(Connection, String, boolean) - Constructor for class ome.services.sharing.data.ShareItems
ShareItems(Connection, String) - Constructor for class ome.services.sharing.data.ShareItems
ShareMap - Class in ome.services.sharing.data
ShareMap(Connection, String, boolean, Comparator, Map) - Constructor for class ome.services.sharing.data.ShareMap
ShareMap(Connection, String, boolean, Comparator) - Constructor for class ome.services.sharing.data.ShareMap
ShareMap(Connection, String, boolean) - Constructor for class ome.services.sharing.data.ShareMap
ShareMap(Connection, String) - Constructor for class ome.services.sharing.data.ShareMap
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) - Constructor for class ome.security.sharing.SharingACLVoter
SharingSecuritySystem - Class in ome.security.sharing: central security interface.
SharingSecuritySystem() - Constructor for class ome.security.sharing.SharingSecuritySystem
SHORT - Static variable in class ome.io.nio.PixelData: Identifies the type used to store pixel values.
SHORT - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
shouldBeOmitted(String) - Static method in class ome.services.util.DBEnumCheck
shutdown(boolean) - Method in class ome.services.blitz.Entry: Calls OmeroContext.closeAll() to recursively close all OMERO.blitz resources in the reverse order that they were created.
shutdown(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
shutdown(Communicator) - Method in class ome.services.blitz.Router: Uses the administrative interface for the Glacier2 router to call AdminPrx.shutdown().
ShutdownSafeEhcacheManagerFactoryBean - Class in ome.tools.spring: Workaround for the Spring/EHCache shutdown sequence.
ShutdownSafeEhcacheManagerFactoryBean() - Constructor for class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean
signed - Variable in class omeis.providers.re.data.Plane2D: The sign of the type
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
SimpleEventContext - Class in ome.system: simple, non-thread-safe, serializable EventContext
SimpleEventContext() - Constructor for class ome.system.SimpleEventContext: Constructor for subclasses
SimpleEventContext(EventContext) - Constructor for class ome.system.SimpleEventContext: copy constructor.
simpleJdbc - Variable in class ome.security.basic.EventHandler
SimpleLuceneOptions - Class in ome.services.fulltext: Implementation of LuceneOptions which takes an existing instance and possible overrides for each of the values.
SimpleLuceneOptions(LuceneOptions, Float) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
SimpleLuceneOptions(LuceneOptions, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
SimpleLuceneOptions(LuceneOptions, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
SimpleLuceneOptions(LuceneOptions, Float, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
SimpleRoleProvider - Class in ome.security.auth: Implements RoleProvider.
SimpleRoleProvider(SecuritySystem, SessionFactory) - 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
size() - Method in interface ome.api.RawFileStore: Returns the size of the file on disk (not as stored in the database since that value will only be updated on RawFileStore.save().
size() - Method in class ome.io.nio.FileBuffer
size() - Method in class ome.io.nio.PixelData: Returns the pixel count of this block of pixel data.
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.services.scheduler.ThreadPool
size() - Method in class ome.tools.FileSystem: This method is used to get the used space of a File or FileSystem in bytes
size() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: the total number of fields for this entity.
size() - Method in class omero.util.Resources
size_async(AMD_RawFileStore_size, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
sizeC - Variable in class ome.services.formats.OmeroReader
sizeImages() - Method in class ome.services.blitz.impl.OmeroMetadata
sizeT - Variable in class ome.services.formats.OmeroReader
sizeX - Variable in class ome.services.formats.OmeroReader
sizeX - Variable in class omeis.providers.re.data.Plane2D: Number of pixels along the X-axis.
sizeY - Variable in class ome.services.formats.OmeroReader
sizeY - Variable in class omeis.providers.re.data.Plane2D: Number of pixels along the Y-axis.
sizeZ - Variable in class ome.services.formats.OmeroReader
skip() - Method in class ome.services.delete.DeleteEntry: A KEEP setting is a way of putting a KEEP suggestion to vote.
skipFrom() - Method in class ome.tools.hibernate.QueryBuilder
skipWhere() - Method in class ome.tools.hibernate.QueryBuilder
slice - Variable in class omeis.providers.re.data.Plane2D: The slice we're working with
Slot - Class in ome.services.throttling: Worker which consumes from the Queue.
Slot(Queue) - Constructor for class ome.services.throttling.Slot
sm - Variable in class ome.services.blitz.impl.TimelineI
SmartEllipseI - Class in omero.model
SmartEllipseI() - Constructor for class omero.model.SmartEllipseI
SmartLineI - Class in omero.model
SmartLineI() - Constructor for class omero.model.SmartLineI
SmartMaskI - Class in omero.model
SmartMaskI() - Constructor for class omero.model.SmartMaskI
SmartPathI - Class in omero.model
SmartPathI() - Constructor for class omero.model.SmartPathI
SmartPointI - Class in omero.model
SmartPointI() - Constructor for class omero.model.SmartPointI
SmartPolygonI - Class in omero.model
SmartPolygonI() - Constructor for class omero.model.SmartPolygonI
SmartPolylineI - Class in omero.model
SmartPolylineI() - Constructor for class omero.model.SmartPolylineI
SmartRectI - Class in omero.model
SmartRectI() - Constructor for class omero.model.SmartRectI
SmartShape - Interface in omero.model: Orthogonal interface hierarchy of types for working with the Shape hierarchy.
SmartShape.PointCallback - Interface in omero.model: Callback interface passed every point which is within the area of this shape.
SmartShape.Util - Class in omero.model: Utility class used as a mixin by all of the SmartShape implementations.
SmartShape.Util() - Constructor for class omero.model.SmartShape.Util
SmartTextI - Class in omero.model: THIS CLASS IS CURRENTLY BROKEN.
SmartTextI() - Constructor for class omero.model.SmartTextI
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
sources - Variable in class ome.services.query.QueryFactory: sources available for lookups.
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.BOOLEAN(List<Boolean>) - Constructor for class ome.tools.hibernate.SqlArray.BOOLEAN
SqlArray.DATE - Class in ome.tools.hibernate
SqlArray.DATE(List<Date>) - Constructor for class ome.tools.hibernate.SqlArray.DATE
SqlArray.DOUBLE - Class in ome.tools.hibernate
SqlArray.DOUBLE(List<Double>) - Constructor for class ome.tools.hibernate.SqlArray.DOUBLE
SqlArray.FLOAT - Class in ome.tools.hibernate
SqlArray.FLOAT(List<Float>) - Constructor for class ome.tools.hibernate.SqlArray.FLOAT
SqlArray.INTEGER - Class in ome.tools.hibernate
SqlArray.INTEGER(List<Integer>) - Constructor for class ome.tools.hibernate.SqlArray.INTEGER
SqlArray.STRING - Class in ome.tools.hibernate
SqlArray.STRING(List<String>) - Constructor for class ome.tools.hibernate.SqlArray.STRING
SqlArray.STRING2 - Class in ome.tools.hibernate
SqlArray.STRING2(List<String[]>) - Constructor for class ome.tools.hibernate.SqlArray.STRING2
sqlTypes() - Method in class ome.tools.hibernate.ArrayStringType
sqlTypes() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
sqlTypes() - Method in class ome.tools.hibernate.PermissionsType
ss - Variable in class ome.services.blitz.impl.TimelineI
stackAsString(Throwable) - Static method in class omero.util.IceMapper
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.blitz.Entry: Obtains the named OmeroContext, creating it if necessary, and then delegates to _CommunicatorOperationsNC.waitForShutdown() until either it is externally shutdown, or until a signal is caught.
start() - Method in class ome.services.blitz.Router
start() - Method in class ome.services.fulltext.FullTextThread: Called by Spring on creation.
start() - Method in class ome.services.util.DBEnumCheck
start() - Method in class ome.services.util.DBPatchCheck
start() - Method in class ome.services.util.ServerVersionCheck: Prints simple banner with OMERO version.
Start() - Method in class omerojava.util.GatewayHeartbeat: Start the heartbeat thread.
startIO(int) - Method in class omeis.providers.re.RenderingStats: Notifies the start of pixels data retrieval for the specified wavelength (channel).
startMalloc() - Method in class omeis.providers.re.RenderingStats: Notifies the start of the allocation of an RGB memory buffer for the rendering process.
startProcess(ServiceFactory, long) - Method in class ome.services.procs.ProcessManager.Work
startRendering() - Method in class omeis.providers.re.RenderingStats: Notifies the start of the trasnformation of the raw pixels data.
startTime(RTime) - Method in class omero.sys.ParametersI: Sets the value of the start time parameter.
StatefulServiceInterface - Interface in ome.api: OMERO API Interface with stateful semantics.
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
StatsFactory - Class in omeis.providers.re.metadata: Computes two types of statistics: The PixelsStats and the location stats.
StatsFactory() - Constructor for class omeis.providers.re.metadata.StatsFactory
status() - Method in class ome.services.blitz.Entry
Status - Class in ome.services.blitz: Status check for OMERO.blitz.
Status(String[]) - Constructor for class ome.services.blitz.Status
STDIN - Static variable in class prefs: Storing the standard in as a Properties instance as early as possible to prevent lost data.
steps(Session, DeleteHandleI.Report) - Method in class ome.services.blitz.impl.DeleteHandleI
stop() - Method in class ome.services.fulltext.FullTextThread: Called by Spring on destruction.
stop() - Method in class ome.services.util.ServerVersionCheck: Prints simple banner with "Stopping OMERO"
stop() - Method in class omeis.providers.re.RenderingStats: Notifies this object that the rendering process has finished.
stop(Current) - Method in class omero.grid.InteractiveProcessorI: Cancels the current process, nulls the value, and returns immediately if detach is false.
Stop() - Method in class omerojava.util.GatewayHeartbeat: Stop the the OmeroJava service and kill the heartbeat thread.
store(int, Class, int, IResults.Result) - Method in interface ome.api.IResults: storing results.
store - Variable in class ome.services.blitz.impl.MetadataStoreI
store - Variable in class ome.services.sharing.ShareBean
store(Object, Object) - Method in class omero.util.IceMapper
storeMultiBulk(int, Class[], int[], IResults.Result[]) - Method in interface ome.api.IResults
storeMultiBulkPrimitive(int, String[], int[], Map[]) - Method in interface ome.api.IResults
storePrimitive(int, String, int, Map) - Method in interface ome.api.IResults
storeShareData(long, ShareData) - Method in class ome.services.sharing.ShareBean
storeSingleBulk(int, Class, int, IResults.Result[]) - Method in interface ome.api.IResults
storeSingleBulkPrimitive(int, Class, int, Map[]) - Method in interface ome.api.IResults
STRING - Static variable in class ome.services.query.StringQuery: parameter name for the definition of the HQL string.
STRING_TO_RSTRING - Static variable in class omero.util.IceMapper
stringFromSvnString(String) - Static method in class ome.system.Version: Parses the given String to remove the leading "$", keyword name, and colons.
StringQuery - Class in ome.services.query: simple HQL query.
StringQuery(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
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
StringUtils - Class in ome.tools
StringUtils() - Constructor for class ome.tools.StringUtils
submit(Job) - Method in interface ome.api.JobHandle: Submits a Job and returns its database id.
submit(Job) - Method in class ome.services.JobBean
submit(Callable<T>) - Method in class ome.services.util.Executor.Impl
submit(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_async(AMD_JobHandle_submit, Job, Current) - Method in class ome.services.blitz.impl.JobHandleI
SUBMITTED - Static variable in interface ome.api.JobHandle
subscribe(String, ObjectPrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
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 - Variable in class ome.services.messages.LoginAttemptMessage
sum(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the sum of this vector with the specified argument.
SUM_INTENSITY - Static variable in interface ome.api.IProjection: Sum intensity projection
superspec - Variable in class ome.services.delete.BaseDeleteSpec: Path of the superspec.
SVN_DATE_FORMAT - Static variable in class ome.system.Version: Date format used by Subversions "Date" keyword.
synchronizeJobs() - Method in class ome.services.blitz.util.CheckAllJobs
synchronizeLoginCache() - Method in interface ome.api.IAdmin: uses JMX to refresh the login cache if supported.
synchronizeLoginCache() - Method in class ome.logic.AdminImpl
synchronizeLoginCache_async(AMD_IAdmin_synchronizeLoginCache, Current) - Method in class ome.services.blitz.impl.AdminI
synchronizeShapeGeometries(List<Long>) - Method in class ome.services.roi.GeomTool
synchronizeShapeGeometry(long) - Method in class ome.services.roi.GeomTool
sys(String[]) - Static method in class prefs: Replaces the user Preferences instance with the system Preferences and continues dispatching.
SYSTEM - Static variable in class pojos.GroupData: Identifies the System group.
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

t - Variable in exception ome.util.messages.MessageException
TagAnnotationData - Class in pojos: A tag annotation can either be related to an image or a tag but not to both at the same time.
TagAnnotationData(String, boolean) - Constructor for class pojos.TagAnnotationData: Creates a new instance.
TagAnnotationData(String) - Constructor for class pojos.TagAnnotationData: Creates a new instance.
TagAnnotationData(String, String) - Constructor for class pojos.TagAnnotationData: Creates a new instance.
TagAnnotationData(String, String, boolean) - Constructor for class pojos.TagAnnotationData: Creates a new instance.
TagAnnotationData(TagAnnotation) - Constructor for class pojos.TagAnnotationData: Creates a new instance.
TagAnnotationData(TagAnnotation, List<CommentAnnotation>) - Constructor for class pojos.TagAnnotationData: Creates a new instance.
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
take() - Method in class ome.services.throttling.Queue
target2model - Variable in class omero.util.IceMapper
Task - Class in ome.services.throttling: Simple base task which contains logic for routing calls reflectively to ice_response and ice_exception of any AMD callback.
Task(Object, Current, boolean) - Constructor for class ome.services.throttling.Task
tearDown() - Method in class ome.formats.importer.util.TinyImportFixture
TempFileManager - Class in omero.util: Creates temporary files and folders and makes a best effort to remove them on exit (or sooner).
TempFileManager() - Constructor for class omero.util.TempFileManager: Default constructor, passes "omero" to TempFileManager.TempFileManager(String)
TempFileManager(String) - Constructor for class omero.util.TempFileManager: Initializes a TempFileManager instance with a userDir containing the given prefix value.
template - Variable in class ome.services.fulltext.PersistentEventLogLoader
templateMessage - Variable in class ome.logic.AdminImpl
TermAnnotationData - Class in pojos: Define a Term Annotation.
TermAnnotationData(String) - Constructor for class pojos.TermAnnotationData: Creates a new instance.
TermAnnotationData(TermAnnotation) - Constructor for class pojos.TermAnnotationData: Creates a new instance.
test(String[]) - Static method in class prefs: Simple test framework, callable from the command line via "java prefs test"
TEXT - Static variable in class pojos.FileAnnotationData: Identifies the Text file formats.
TextData - Class in pojos: Represents a Text in the Euclidean space R².
TextData(Shape) - Constructor for class pojos.TextData: Creates a new instance of Text data from an existing shape.
TextData() - Constructor for class pojos.TextData: Creates a new instance of TextData, creating a new TextI Object.
TextData(String, double, double) - Constructor for class pojos.TextData: Creates a new instance of the TextData, sets the centre and major, minor axes.
TextualAnnotationData - Class in pojos: Basic textual annotation used to add comments to a given object.
TextualAnnotationData() - Constructor for class pojos.TextualAnnotationData: Creates a new instance.
TextualAnnotationData(String) - Constructor for class pojos.TextualAnnotationData: Creates a new instance.
TextualAnnotationData(CommentAnnotation) - Constructor for class pojos.TextualAnnotationData: Creates a new instance.
ThreadPool - Class in ome.services.scheduler: Produces a ThreadPool(int, int, long) - Constructor for class ome.services.scheduler.ThreadPool
threadSafe - Variable in class ome.util.messages.InternalMessage
ThrottlingStrategy - Interface in ome.services.throttling: Strategy interface for controlling the execution of blitz methods.
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
throwIfInitialized(Object) - Method in class ome.services.blitz.util.BlitzConfiguration: If this configuration is finished and BlitzConfiguration.communicator is not-null, throw a IllegalStateException
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
throwUsage() - Method in class ome.tools.hibernate.QueryBuilder
ThumbnailBean - Class in ome.services: Provides methods for directly querying object graphs.
ThumbnailBean() - Constructor for class ome.services.ThumbnailBean: default constructor
ThumbnailBean(boolean) - Constructor for class ome.services.ThumbnailBean: overriden to allow Spring to set boolean
ThumbnailCtx - Class in ome.services
ThumbnailCtx(IQuery, IUpdate, IPixels, IRenderingSettings, ThumbnailService, SecuritySystem, long) - Constructor for class ome.services.ThumbnailCtx: Default constructor.
thumbnailExists(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Checks if a thumbnail of a particular size exists for a pixels set.
thumbnailExists(Integer, Integer) - Method in class ome.services.ThumbnailBean
thumbnailExists_async(AMD_ThumbnailStore_thumbnailExists, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
THUMBNAILS_PATH - Static variable in class ome.io.nio.AbstractFileSystemService
ThumbnailService - Class in ome.io.nio
ThumbnailService(String) - Constructor for class ome.io.nio.ThumbnailService: Constructor
ThumbnailService - Interface in ome.services.blitz.gateway.services
ThumbnailServiceImpl - Class in ome.services.blitz.gateway.services.impl
ThumbnailServiceImpl(ThumbnailStorePrx) - Constructor for class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl: Create the ThumbnailService passing the gateway.
ThumbnailStore - Interface in ome.api: Provides methods for dealing with thumbnails.
ThumbnailStoreI - Class in ome.services.blitz.impl: Implementation of the ThumbnailStore service.
ThumbnailStoreI(ThumbnailStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ThumbnailStoreI
TieAware - Interface in ome.services.blitz.util: Servant which is aware of the TieBase-instance which it belongs to and will have it injected on instantiation.
TimeAnnotationData - Class in pojos: Basic time annotation.
TimeAnnotationData() - Constructor for class pojos.TimeAnnotationData: Creates a default instance.
TimeAnnotationData(TimestampAnnotation) - Constructor for class pojos.TimeAnnotationData: Creates a new instance.
TimelineI - Class in ome.services.blitz.impl: implementation of the ITimeline service interface.
TimelineI(BlitzExecutor) - Constructor for class ome.services.blitz.impl.TimelineI
timeOfEvent(Event) - Method in class pojos.DataObject
TinyImportFixture - Class in ome.formats.importer.util: test fixture which uses a hard-coded file ("tinyTest.d3d.dv") from the classpath, and adds them to a new UUID-named dataset.
TinyImportFixture(ServiceFactory) - Constructor for class ome.formats.importer.util.TinyImportFixture
tmpdir() - Method in class omero.util.TempFileManager: Returns a platform-specific user-writable temporary directory.
to - Variable in class ome.services.blitz.util.ConvertToBlitzExceptionMessage
toBufferedImage(Pixels, int[]) - Static method in class omerojava.util.GatewayUtils: Convert the raw integer(4byte colour data) to a bufferedImage, for pixels object pixels.
toJavaType(RInt) - Method in class ome.services.blitz.impl.MetadataStoreI: Transforms an OMERO RType into the corresponding Java type.
toJavaType(RLong) - Method in class ome.services.blitz.impl.MetadataStoreI: Transforms an OMERO RType into the corresponding Java type.
toJavaType(RBool) - Method in class ome.services.blitz.impl.MetadataStoreI: Transforms an OMERO RType into the corresponding Java type.
toJavaType(RFloat) - Method in class ome.services.blitz.impl.MetadataStoreI: Transforms an OMERO RType into the corresponding Java type.
toJavaType(RDouble) - Method in class ome.services.blitz.impl.MetadataStoreI: Transforms an OMERO RType into the corresponding Java type.
toJavaType(RString) - Method in class ome.services.blitz.impl.MetadataStoreI: Transforms an OMERO RType into the corresponding Java type.
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: Returns a LowercaseAlphaNumericTokenizer
toNumber(double) - Static method in class pojos.ShapeData: Returns a double array as a number attribute value.
topicManager - Variable in class ome.services.blitz.fire.SessionManagerI
TopicManager - Interface in ome.services.blitz.fire: Local dispatcher to TopicManager
TopicManager.Impl - Class in ome.services.blitz.fire
TopicManager.Impl(Communicator) - Constructor for class ome.services.blitz.fire.TopicManager.Impl
TopicManager.TopicMessage - Class in ome.services.blitz.fire
TopicManager.TopicMessage(Object, String, ObjectPrxHelperBase, String, Object...) - Constructor for class ome.services.blitz.fire.TopicManager.TopicMessage
topicOrNull(String) - Method in class ome.services.blitz.fire.TopicManager.Impl
toPoints(Point2D.Double[]) - Static method in class pojos.ShapeData: Returns a Point2D.Double array as a Points attribute value. as specified in http://www.w3.org/TR/SVGMobile12/shapes.html#PointsBNF
toRType(Object) - Method in class omero.util.IceMapper
toString() - Method in class ome.io.nio.AbstractBuffer
toString() - Method in class ome.services.blitz.impl.ServiceFactoryI
toString() - Method in class ome.services.delete.BaseDeleteSpec
toString() - Method in class ome.services.delete.DeleteEntry
toString() - Method in exception ome.services.delete.DeleteException
toString() - Method in class ome.services.delete.DeleteState
toString() - Method in class ome.services.scripts.RepoFile.FsFile
toString() - Method in class ome.services.scripts.RepoFile
toString() - Method in class ome.services.throttling.Task
toString() - Method in class ome.system.Principal: returns only the name of the instance because that is the expected behavior of Principal implementations
toString() - Method in class ome.tools.FileSystem: Public toString implementation
toString() - Method in class ome.tools.hibernate.QueryBuilder
toString() - Method in class ome.tools.hibernate.SqlArray
toString() - Method in class omeis.providers.re.codomain.CodomainChain: Overrides the toString method.
toString() - Method in class omeis.providers.re.data.PlaneDef: Overrides generic toString method to provide a specific string representation of this object.
toString() - Method in class pojos.DataObject: Overridden to return the name of the class and the object id.
toString() - Method in class pojos.ROICoordinate: Returns the string of the coordinates.
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.
totalSharedItems() - Method in class ome.services.sharing.BlobShareStore
totalSharedItems() - Method in class ome.services.sharing.FreezeShareStore
totalSharedItems() - Method in class ome.services.sharing.ShareStore
totalShares() - Method in class ome.services.sharing.BlobShareStore
totalShares() - Method in class ome.services.sharing.FreezeShareStore
totalShares() - Method in class ome.services.sharing.ShareStore
trace(String, String) - Method in class ome.services.blitz.util.CommonsLoggingAdapter
transform(int) - Method in class omeis.providers.re.codomain.CodomainChain: Applies the transformation.
transform(int) - Method in interface omeis.providers.re.codomain.CodomainMap: Performs the transformation.
transform(int, double) - Method in class omeis.providers.re.quantum.ExponentialMap: Implemented as specified in QuantumMap.
transform(double, double) - Method in class omeis.providers.re.quantum.ExponentialMap: Implemented as specified in QuantumMap.
transform(float, double) - Method in class omeis.providers.re.quantum.ExponentialMap: Implemented as specified in QuantumMap.
transform(int, double) - Method in class omeis.providers.re.quantum.LogarithmicMap: Implemented as specified in QuantumMap.
transform(double, double) - Method in class omeis.providers.re.quantum.LogarithmicMap: Implemented as specified in QuantumMap.
transform(float, double) - Method in class omeis.providers.re.quantum.LogarithmicMap: Implemented as specified in QuantumMap.
transform(int, double) - Method in class omeis.providers.re.quantum.PolynomialMap: Implemented as specified in QuantumMap.
transform(double, double) - Method in class omeis.providers.re.quantum.PolynomialMap: Implemented as specified in QuantumMap.
transform(float, double) - Method in class omeis.providers.re.quantum.PolynomialMap: Implemented as specified in QuantumMap.
transform(int, double) - Method in interface omeis.providers.re.quantum.QuantumMap: Maps the specified value.
transform(double, double) - Method in interface omeis.providers.re.quantum.QuantumMap: Maps the specified value.
transform(float, double) - Method in interface omeis.providers.re.quantum.QuantumMap: Maps the specified value.
translateException(Throwable) - Method in class ome.services.util.BeanHelper
truncate(long) - Method in interface ome.api.RawFileStore: Limits the size of a file to the given length.
truncate(long) - Method in class ome.io.nio.FileBuffer
truncate(long) - Method in class ome.services.RawFileBean
truncate_async(AMD_RawFileStore_truncate, long, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
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.Patcher
type() - Method in class ome.services.sharing.data.ShareDataHolder.Patcher
type - Variable in class ome.services.sharing.data.ShareItem
type() - Method in class ome.services.sharing.data.ShareItemHolder.Patcher
type - Variable in class ome.system.Principal
type - Variable in class omeis.providers.re.quantum.QuantumStrategy: The type of pixels this strategy is for.
type() - Method in interface omero.rtypes.Conversion: Specifies the type that can be expected from the rtypes.Conversion.convert(IceMapper) method.
typeCount(String) - Method in class ome.services.sharing.data.ShareItems
types - Variable in class ome.services.fulltext.PersistentEventLogLoader
TypesI - Class in ome.services.blitz.impl: Implementation of the ITypes service.
TypesI(ITypes, BlitzExecutor) - Constructor for class ome.services.blitz.impl.TypesI
TypesImpl - Class in ome.logic: implementation of the ITypes service interface.
TypesImpl() - Constructor for class ome.logic.TypesImpl

U

UINT16 - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the UINT16 data type used to store pixel values, as per OME spec.
UINT16_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
UINT32 - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the UINT32 data type used to store pixel values, as per OME spec.
UINT32_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
UINT8 - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the UINT8 data type used to store pixel values, as per OME spec.
UINT8_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
UINT_16 - Static variable in class omerojava.util.PixelTypes: Identifies the type used to store pixel values.
UINT_32 - Static variable in class omerojava.util.PixelTypes: Identifies the type used to store pixel values.
UINT_8 - Static variable in class omerojava.util.PixelTypes: Identifies the type used to store pixel values.
UintConverter - Class in omerojava.util: Packs a sequence of bytes representing an unsigned big-endian integer into an integer value of appropriate integer type.
UintConverter() - Constructor for class omerojava.util.UintConverter
umask - Variable in class ome.system.SimpleEventContext
uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper
uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ObjPrxHelper
uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
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() - Method in class omero.sys.ParametersI
unique_alias(String) - Method in class ome.tools.hibernate.QueryBuilder: Obtain a unique alias to be used in the SQL.
UNKNOWN - Static variable in class pojos.FileAnnotationData: Indicates that the format is not recognized.
unlink(ILink[], Parameters) - Method in interface ome.api.IContainer: Removes links between OmeroDataObjects e.g Project-Dataset, Dataset-Image Note that the objects themselves aren't deleted, only the Link objects.
unlink(ILink[], Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
unlink_async(AMD_IContainer_unlink, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
unload(Current) - Method in class omero.model.DetailsI
unload(Current) - Method in class omero.model.PermissionsI
UnloadedCollectionException - Exception in omero
UnloadedCollectionException(String) - Constructor for exception omero.UnloadedCollectionException
UnloadedEntityException - Exception in omero
UnloadedEntityException(String) - Constructor for exception omero.UnloadedEntityException
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.
UNMAPPED - Static variable in class omero.util.IceMapper: Specifies a return type which should not be parsed.
unordered() - Method in interface ome.api.Search: Removes the current stack of order statements.
unordered() - Method in class ome.services.SearchBean
unordered_async(AMD_Search_unordered, Current) - Method in class ome.services.blitz.impl.SearchI
unregister(String, ObjectPrx) - Method in class ome.services.blitz.fire.TopicManager.Impl
unregister(String, ObjectPrx) - Method in interface ome.services.blitz.fire.TopicManager
unregister(Long, Session) - Method in class ome.services.scripts.ScriptRepoHelper: Unregisters a given file from the script repository by setting its Repo uuid to null.
unregisterCallback(ProcessCallbackPrx, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
unregisterCallback(ProcessCallback) - Method in interface ome.services.procs.Process
unregisterCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton
unregisterServant(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI: Reverts all the additions made by #registerServant(ServantInterface, Ice.Current, Ice.Identity) Now called by SessionManagerI in response to an UnregisterServantMessage
UnregisterServantMessage - Class in ome.services.blitz.util: InternalMessage raised when a servant should be removed from the adapter.
UnregisterServantMessage(Object, Current) - Constructor for class ome.services.blitz.util.UnregisterServantMessage
unsetGroupOwner(ExperimenterGroup, Experimenter) - Method in interface ome.api.IAdmin: removes the user from the owner list for this group.
unsetGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl
unsetGroupOwner_async(AMD_IAdmin_unsetGroupOwner, ExperimenterGroup, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
update - Variable in class ome.services.fulltext.PersistentEventLogLoader: String used with parameters 'value' and 'name' to change the current id
update(RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper
update(Session) - Method in interface ome.services.sessions.SessionManager: See ISession#updateSession(Session) for the logic that's implemented here.
update(Session, boolean) - Method in interface ome.services.sessions.SessionManager: Same as SessionManager.update(Session) but some security checks can be overriden.
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(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain: Updates a map context in the chain.
UPDATE_EVENT - Static variable in class ome.security.basic.UpdateEventListener
updateCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
updateCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine: Updates the specified context.
updateCodomainMap_async(AMD_RenderingEngine_updateCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
updateDataObject(T, Parameters) - Method in interface ome.api.IContainer: Updates a data object.
updateDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
updateDataObject_async(AMD_IContainer_updateDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
updateDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer: convenience method to save network calls.
updateDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
updateDataObjects_async(AMD_IContainer_updateDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
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 interface ome.api.ITypes: updates enumeration value specified by object
updateEnumeration(T) - Method in class ome.logic.TypesImpl
updateEnumeration_async(AMD_ITypes_updateEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
updateEnumerations(List<T>) - Method in interface ome.api.ITypes: updates enumeration value specified by object
updateEnumerations(List<T>) - Method in class ome.logic.TypesImpl
updateEnumerations_async(AMD_ITypes_updateEnumerations, List<IObject>, Current) - Method in class ome.services.blitz.impl.TypesI
updateEvent(UserGroupUpdateEvent) - Method in class ome.services.sessions.state.SessionCache: Marks a new update request in SessionCache.lastUpdateRequest.
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. controls access to individual db rows..
updateExperimenter(Experimenter) - Method in interface ome.api.IAdmin: Updates an experimenter if admin or owner of group.
updateExperimenter(Experimenter) - Method in class ome.logic.AdminImpl
updateExperimenter_async(AMD_IAdmin_updateExperimenter, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
updateExperimenterWithPassword(Experimenter, String) - Method in interface ome.api.IAdmin: Updates an experimenter if admin or owner of group.
updateExperimenterWithPassword(Experimenter, String) - Method in class ome.logic.AdminImpl
updateExperimenterWithPassword_async(AMD_IAdmin_updateExperimenterWithPassword, Experimenter, RString, Current) - Method in class ome.services.blitz.impl.AdminI
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 interface ome.api.IAdmin: Updates an experimenter group if admin or owner of group.
updateGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
updateGroup_async(AMD_IAdmin_updateGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
UpdateI - Class in ome.services.blitz.impl: Implementation of the IUpdate service.
UpdateI(IUpdate, BlitzExecutor) - Constructor for class ome.services.blitz.impl.UpdateI
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 privilegs within the SecuritySystem.
updateObject(T...) - Method in class ome.tools.hibernate.SecureMerge
updateObjects_async(AMD_MetadataStore_updateObjects, IObjectContainer[], Current) - Method in class ome.services.blitz.impl.MetadataStoreI
updatePixels(Pixels, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
updatePixels(Pixels) - Method in interface ome.services.blitz.gateway.services.DataService: Update the pixels object in the server.
updatePixels(Pixels) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl
updateQuantumManager() - Method in class omeis.providers.re.Renderer: Updates the QuantumManager and configures it according to the current quantum definition.
updateReadFilter(Session) - Method in class ome.security.basic.BasicSecuritySystem
updateReferences(Map<String, String[]>) - Method in class ome.formats.OMEROMetadataStore: Updates our object graph references.
updateReferences_async(AMD_MetadataStore_updateReferences, Map<String, String[]>, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
updateSelf(Experimenter) - Method in interface ome.api.IAdmin: Allows a user to update his/her own information.
updateSelf(Experimenter) - Method in class ome.logic.AdminImpl
updateSelf_async(AMD_IAdmin_updateSelf, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
updateSession(Session) - Method in class ome.services.sessions.SessionBean
UpgradeCheck - Class in ome.system: Contacts a given URL which should be an OME server which will return either an empty String or a URL which points to a needed upgrade.
UpgradeCheck(String, String, String) - Constructor for class ome.system.UpgradeCheck: Calls UpgradeCheck.UpgradeCheck(String, String, String, int) using UpgradeCheck.DEFAULT_TIMEOUT
UpgradeCheck(String, String, String, int) - Constructor for class ome.system.UpgradeCheck: Main constructor.
upload(File) - Method in class omero.client
upload(File, OriginalFile) - Method in class omero.client
upload(File, OriginalFile, Integer) - Method in class omero.client: Utility method to upload a file to the server
UploadMask - Class in pojos.util: Uploaded for masks.
UploadMask(long) - Constructor for class pojos.util.UploadMask: Creates a new instance.
uploadMask_async(AMD_IRoi_uploadMask, long, int, int, byte[], Current) - Method in class ome.services.blitz.impl.RoiI
uploadMyUserPhoto(String, String, byte[]) - Method in interface ome.api.IAdmin: Uploads a photo for the user which will be displayed on his/her profile.
uploadMyUserPhoto(String, String, byte[]) - Method in class ome.logic.AdminImpl
uploadMyUserPhoto_async(AMD_IAdmin_uploadMyUserPhoto, String, String, byte[], Current) - Method in class ome.services.blitz.impl.AdminI
uploadOfficialScript_async(AMD_IScript_uploadOfficialScript, String, String, Current) - Method in class ome.services.blitz.impl.ScriptI
uploadPlane(long, int, int, int, byte[], Current) - Method in class ome.services.blitz.gateway.OmeroGateway
uploadPlane(long, int, int, int, byte[]) - Method in interface ome.services.blitz.gateway.services.ImageService: Upload the plane to the server, on pixels id with channel and the time, + z section. the data is the client 2d data values.
uploadPlane(long, int, int, int, byte[]) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl: Upload the plane to the server, on pixels id with channel and the time, + z section. the data is the client 2d data values.
uploadScript_async(AMD_IScript_uploadScript, String, String, Current) - Method in class ome.services.blitz.impl.ScriptI: Upload script to the server.
usage() - Static method in class ome.services.fulltext.Main
usage(String[]) - Static method in class prefs: Returns a usage string array.
used() - Method in class ome.tools.FileSystem: This method is used to get the used space of a File or FileSystem in kilobytes
useProjections - Variable in class ome.services.search.SearchValues
user - Variable in class ome.services.messages.LoginAttemptMessage
USER - Static variable in class pojos.GroupData: Identifies the User group.
userGroups(String) - Method in class ome.security.auth.PasswordUtil
UserGroupUpdateEvent - Class in ome.services.sessions.events: InteralMessage 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
username() - Method in class omero.util.TempFileManager: Returns the current OS-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.services.blitz.fire.Ring: UUID for this cluster node.
uuid() - Method in class ome.services.blitz.fire.Ring
uuid() - Method in interface ome.services.blitz.redirect.Redirector.Context: The UUID for the local node which will be used as the redirect lookup string for this Redirector.Context.
uuid - Variable in class ome.services.roi.GeomTool

V

valid(String) - Method in class ome.services.db.DatabaseIdentity
Validate - Annotation Type in ome.annotations: annotation used for determining the types of a Set
validatePassword(String, String) - Method in class ome.logic.LdapImpl: Validates password for base.
validateScript_async(AMD_IScript_validateScript, Job, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI
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.IdMapHolder
value - Variable in class ome.services.sharing.data.LongSeqHolder
value - Variable in class ome.services.sharing.data.ObjHolder
value - Variable in class ome.services.sharing.data.ObjPrxHolder
value - Variable in class ome.services.sharing.data.ObjSeqHolder
value - Variable in class ome.services.sharing.data.ShareDataHolder
value - Variable in class ome.services.sharing.data.ShareDataPrxHolder
value - Variable in class ome.services.sharing.data.ShareItemHolder
value - Variable in class ome.services.sharing.data.ShareItemPrxHolder
value - Variable in class ome.services.sharing.data.StringSeqHolder
valueMapper - Variable in class omeis.providers.re.quantum.QuantumStrategy: Reference to the value mapper.
valueOf(String) - Static method in enum ome.services.delete.DeleteOpts.Op: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.system.Preference.Visibility: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum omero.grid.ProcessCallbackI.Action: Returns the enum constant of this type with the specified name.
values() - Static method in enum ome.services.delete.DeleteOpts.Op: 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.system.Preference.Visibility: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum omero.grid.ProcessCallbackI.Action: Returns an array containing the constants of this enum type, in the order they are declared.
vec(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the vector associated to this point and the specified argument.
vec(double, double) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the vector associated to this point and the specified argument.
verbose - Variable in class ome.tools.hibernate.EventMethodInterceptor
Version - Class in ome.system: static utililty for checking Omero classes for revision number and date.
Version() - Constructor for class ome.system.Version
VERSION_REGEX - Static variable in interface ome.api.IConfig: Defines how the omero.version Preference will be parsed into the form: Major.minor.patch for IConfig.getVersion()
VOID - Static variable in class omero.util.IceMapper

W

waitForLock - Variable in class ome.services.fulltext.FullTextThread
waitForUpdate() - Method in class ome.services.sessions.state.SessionCache: If SessionCache.lastUpdateRun is older than SessionCache.lastUpdateRequest, then wait until the next background thread updates lastUpdateRequest.
WAITING - Static variable in interface ome.api.JobHandle
walk() - Method in class ome.services.delete.BaseDeleteSpec
walk() - Method in interface ome.services.delete.DeleteSpec: Returns an iterator over all subspecs and their subspecs, depth-first.
warning(String) - Method in class ome.services.blitz.util.CommonsLoggingAdapter
WellData - Class in pojos: The data that makes up an OME Well and the Experimenter that owns this Well.
WellData() - Constructor for class pojos.WellData: Creates a new instance.
WellData(Well) - Constructor for class pojos.WellData: Creates a new instance.
WELLS - Static variable in class pojos.PlateData: Identifies the Plate#WELLS field.
WellSampleData - Class in pojos: The data that makes up an OME WellSample along with links to its images and the Experimenter that owns this WellSample.
WellSampleData() - Constructor for class pojos.WellSampleData: Creates a new instance.
WellSampleData(WellSample) - Constructor for class pojos.WellSampleData: Creates a new instance.
where() - Method in class ome.tools.hibernate.QueryBuilder: Marks the end of all fetches by adding a "where" clause to the string.
work - Variable in class ome.services.util.ExecutionThread
WorkflowData - Class in pojos: The data that makes up an OME worflow object.
WorkflowData(Namespace) - Constructor for class pojos.WorkflowData: Creates a new instance.
WorkflowData(String, List<String>) - Constructor for class pojos.WorkflowData: Creates a new instance.
WorkflowData(String, String) - Constructor for class pojos.WorkflowData: Creates a new instance.
WorkflowData() - Constructor for class pojos.WorkflowData: Creates a new instance.
wrap(String, IObject) - Method in class ome.services.fulltext.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 interface ome.api.RawFileStore: Delegates to FileBuffer
write(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer: Delegates to FileChannel
write(ByteBuffer) - Method in class ome.io.nio.FileBuffer: Delegates to FileChannel
write(long, byte[], long, int) - Method in class ome.services.blitz.gateway.services.impl.RawFileStoreServiceImpl
write(long, byte[], long, int) - Method in interface ome.services.blitz.gateway.services.RawFileStoreService: Write the contents of the buffer to the the file starting from position and for length bytes.
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
write_async(AMD_RawFileStore_write, byte[], long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
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
WZT_SEQUENCE - Static variable in class ome.io.nio.DeltaVisionHeader: The most common sequence of images acquired from a microscope.

X

x1 - Variable in class ome.util.math.geom2D.PlanePoint: The first element.
x2 - Variable in class ome.util.math.geom2D.PlanePoint: The second element.
XML - Static variable in class pojos.FileAnnotationData: Identifies the XML file formats.
XY - Static variable in class omeis.providers.re.data.PlaneDef: Flag to identify an XY-plane.
XZ - Static variable in class omeis.providers.re.data.PlaneDef: Flag to identify an XZ-plane.

Z

zero() - Method in class omeis.providers.re.RGBAIntBuffer
zero() - Method in class omeis.providers.re.RGBBuffer: Zeros out (sets every pixel offset to zero) each band.
zero() - Method in class omeis.providers.re.RGBIntBuffer
ZTW_SEQUENCE - Static variable in class ome.io.nio.DeltaVisionHeader: A common sequence of processed images.
ZWT_SEQUENCE - Static variable in class ome.io.nio.DeltaVisionHeader: A new image sequence, as of DeltaVision version 2.10.
ZY - Static variable in class omeis.providers.re.data.PlaneDef: Flag to identify an YZ-plane.

_

__createDelegateD() - Method in class ome.services.sharing.data.ObjPrxHelper
__createDelegateD() - Method in class ome.services.sharing.data.ShareDataPrxHelper
__createDelegateD() - Method in class ome.services.sharing.data.ShareItemPrxHelper
__createDelegateM() - Method in class ome.services.sharing.data.ObjPrxHelper
__createDelegateM() - Method in class ome.services.sharing.data.ShareDataPrxHelper
__createDelegateM() - Method in class ome.services.sharing.data.ShareItemPrxHelper
__del__() - Method in class omero.client: Calls closeSession() and ignores any exceptions.
__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.ShareData
__ids - Static variable in class ome.services.sharing.data.ShareItem
__read(BasicStream, boolean) - Method in class ome.services.sharing.data.Obj
__read(InputStream, boolean) - Method in class ome.services.sharing.data.Obj
__read(BasicStream) - Static method in class ome.services.sharing.data.ObjPrxHelper
__read(BasicStream, boolean) - Method in class ome.services.sharing.data.ShareData
__read(InputStream, boolean) - Method in class ome.services.sharing.data.ShareData
__read(BasicStream) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
__read(BasicStream, boolean) - Method in class ome.services.sharing.data.ShareItem
__read(InputStream, boolean) - Method in class ome.services.sharing.data.ShareItem
__read(BasicStream) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
__redirect(long, _RawFileStoreTie, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
__write(BasicStream) - Method in class ome.services.sharing.data.Obj
__write(OutputStream) - Method in class ome.services.sharing.data.Obj
__write(BasicStream, ObjPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper
__write(BasicStream) - Method in class ome.services.sharing.data.ShareData
__write(OutputStream) - Method in class ome.services.sharing.data.ShareData
__write(BasicStream, ShareDataPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
__write(BasicStream) - Method in class ome.services.sharing.data.ShareItem
__write(OutputStream) - Method in class ome.services.sharing.data.ShareItem
__write(BasicStream, ShareItemPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
_addGraph(ShareData, ShareBean.Graph) - Method in class ome.services.sharing.ShareBean
_driver - Variable in class ome.tools.DbUpdateTask
_ObjDel - Interface in ome.services.sharing.data
_ObjDelD - Class in ome.services.sharing.data
_ObjDelD() - Constructor for class ome.services.sharing.data._ObjDelD
_ObjDelM - Class in ome.services.sharing.data
_ObjDelM() - Constructor for class ome.services.sharing.data._ObjDelM
_ShareDataDel - Interface in ome.services.sharing.data
_ShareDataDelD - Class in ome.services.sharing.data
_ShareDataDelD() - Constructor for class ome.services.sharing.data._ShareDataDelD
_ShareDataDelM - Class in ome.services.sharing.data
_ShareDataDelM() - Constructor for class ome.services.sharing.data._ShareDataDelM
_ShareItemDel - Interface in ome.services.sharing.data
_ShareItemDelD - Class in ome.services.sharing.data
_ShareItemDelD() - Constructor for class ome.services.sharing.data._ShareItemDelD
_ShareItemDelM - Class in ome.services.sharing.data
_ShareItemDelM() - Constructor for class ome.services.sharing.data._ShareItemDelM
_wait(Current) - Method in class ome.services.blitz.impl.ScriptProcessI

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