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

A

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.
acquireLicense() - Method in interface ome.services.licenses.ILicense
Reserves a license for the current user.
acquireLicense() - Method in class ome.services.licenses.LicenseBean
See ILicense.acquireLicense()
acquireLicense() - Method in class ome.services.licenses.Store
 
acquireLicense_async(AMD_ILicense_acquireLicense, Current) - Method in class ome.services.licenses.LicenseI
 
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.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.gateway.OmeroGateway
 
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
 
add(Point) - Method in class pojos.util.MaskClass
Add the point to the Mask.
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
Add a Mask Shape to the appropriate ROIClass, creating one if neccessary.
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
Add a Mask Shape to the appropriate ROIClass, creating one if neccessary.
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
Add 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
Add 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.
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
 
asBytes() - Method in class pojos.util.MaskClass
Convert the mask data to a byte array.
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.
asMaskData(int, int, int) - Method in class pojos.util.MaskClass
Return the MaskClass as a MaskData object, and assign it to The coords provided.
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
 
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.
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.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
 
Cache<K extends ome.model.IObject,V extends Serializable> - Interface in ome.services.util.cache
 
cache - Variable in class ome.services.util.cache.DelegatingCache
 
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.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
 
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.
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
 
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
 
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(boolean, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
close(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
Deprecated. 
close() - Method in class ome.services.blitz.impl.SharedResourcesI
 
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.ProcessCallbackI
 
close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.gateway.OmeroGateway
 
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.
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.
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
Does the keyword exist in the workflow.
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 - Variable in class ome.services.licenses.TokenInfo
 
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<?>) - 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.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 interface ome.services.sessions.SessionContext
Decrement the current reference count and return the new value atomically.
decrement() - Method in class ome.services.sessions.SessionContextImpl
 
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 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.
DelegatingCache<K extends ome.model.IObject,V extends Serializable> - Class in ome.services.util.cache
Simple base Cache which delegates all methods to the Cache with which it is constructed.
DelegatingCache(Cache<K, V>) - Constructor for class ome.services.util.cache.DelegatingCache
 
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
 
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
 
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
 
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
 
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
 
DeleteI - Class in ome.services.blitz.impl
Implementation of the IDelete service.
DeleteI(IDelete, BlitzExecutor) - 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
 
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
 
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.
DiskCache<K extends ome.model.IObject,V extends Serializable> - Class in ome.services.util.cache
Disk cache which is keyed to a particular type.
DiskCache(LocalQuery, CacheManager, String, File, Class<K>) - Constructor for class ome.services.util.cache.DiskCache
 
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() - 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
Create a new instance of EllipseData, creating a new EllipseI Object.
EllipseData(double, double, double, double) - Constructor for class pojos.EllipseData
Create a new instance of the EllipseData, set the centre and major, minor axes.
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.
enterMethod(byte[], Principal) - Method in class ome.services.licenses.LicenseBean
See LicenseStore#enterValid(byte[])
enterMethod(byte[], Principal) - Method in interface ome.services.licenses.LicenseStore
Increments the number of currently active methods associated with a single license and prevents timeouts during the method call.
enterMethod(byte[], Principal) - Method in class ome.services.licenses.Store
 
entityIsDetached(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
 
entityIsTransient(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
 
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
 
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
 
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(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.
exitMethod(byte[], Principal) - Method in class ome.services.licenses.LicenseBean
See LicenseStore#exitMethod(byte[])
exitMethod(byte[], Principal) - Method in interface ome.services.licenses.LicenseStore
Decrements the number of active methods associated with a single license and timestamps the last use of the license.
exitMethod(byte[], Principal) - Method in class ome.services.licenses.Store
 
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 - Class in ome.tools.hibernate
extension of the model metadata provided by SessionFactory.
ExtendedMetadata() - Constructor for class ome.tools.hibernate.ExtendedMetadata
 

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
 
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
 
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
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.
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(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(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(long) - Method in interface ome.services.util.cache.Cache
 
get(long) - Method in class ome.services.util.cache.DelegatingCache
 
get(long) - Method in class ome.services.util.cache.DiskCache
 
get(long) - Method in class ome.services.util.cache.IdBackedCache
 
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 acquistion 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
 
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 class ome.tools.hibernate.ExtendedMetadata
Returns all the classes which implement IAnnotated
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
 
getAvailableLicenseCount() - Method in interface ome.services.licenses.ILicense
Returns the number of licenses which can currently be acquired.
getAvailableLicenseCount() - Method in class ome.services.licenses.LicenseBean
See ILicense.getAvailableLicenseCount()
getAvailableLicenseCount() - Method in class ome.services.licenses.Store
 
getAvailableLicenseCount_async(AMD_ILicense_getAvailableLicenseCount, Current) - Method in class ome.services.licenses.LicenseI
 
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
Set the bit value in a byte array at position bit to be the value value.
getBit(byte[], int) - Method in class pojos.util.MaskClass
Set 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.
getColour() - Method in class pojos.util.MaskClass
Return the colour of the mask.
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.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 class ome.tools.hibernate.ExtendedMetadata
Returns the query for obtaining the number of collection items to a particular instance.
getCreated() - Method in class pojos.DataObject
Returns the creation time of the object.
getCreationEvent(Current) - Method in class omero.model.DetailsI
 
getCurrent() - Method in class ome.services.blitz.util.RegisterServantMessage
 
getCurrent() - Method in class ome.services.blitz.util.UnregisterServantMessage
 
getCurrentEventContext() - Method in interface ome.api.StatefulServiceInterface
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.gateway.OmeroGateway
 
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
 
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.
getExecutor() - Method in class ome.services.blitz.impl.ServiceFactoryI
 
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.
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.
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 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.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
Get 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(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata
 
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
 
getKeys() - Method in interface ome.services.util.cache.Cache
 
getKeys() - Method in class ome.services.util.cache.DelegatingCache
 
getKeys() - Method in class ome.services.util.cache.DiskCache
 
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.
getLicenseTimeout() - Method in interface ome.services.licenses.ILicense
Returns the timeout per license as interpreted by the LicenseStore implementation.
getLicenseTimeout() - Method in class ome.services.licenses.LicenseBean
See ILicense.getLicenseTimeout()
getLicenseTimeout() - Method in class ome.services.licenses.Store
 
getLicenseTimeout_async(AMD_ILicense_getLicenseTimeout, Current) - Method in class ome.services.licenses.LicenseI
 
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 class 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.
getLockChecks(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata
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
Get 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.
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.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.licenses.LicenseWiring
 
getName() - Method in class ome.services.roi.PopulateRoiJob
 
getName() - Method in class ome.services.scripts.ScriptFinder
Subclasses should override to return the name of the file under scripts/ which should be uploaded.
getName() - Method in interface ome.services.sessions.SessionCallback
 
getName() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
 
getName() - Method in class ome.system.Login
simple getter for the user name passed into the constructor
getName() - Method in class ome.system.Preference
 
getName() - Method in class ome.system.Principal
 
getName() - Method in class pojos.ChannelData
Returns the name of the channel.
getName() - Method in class pojos.DatasetData
Returns the name of the dataset.
getName() - Method in class pojos.FileData
Returns the name of the file.
getName() - Method in class pojos.GroupData
Returns the name of the group.
getName() - Method in class pojos.ImageData
Returns the name of the image.
getName() - Method in class pojos.PlateAcquisitionData
Returns the name of the plate acquisition.
getName() - Method in class pojos.PlateData
Returns the name of the plate.
getName() - Method in class pojos.ProjectData
Returns the name of the project.
getName() - Method in class pojos.ScreenData
Returns the name of the screen.
getNameSpace() - Method in class pojos.AnnotationData
Retrieves the nameSpace of the underlying Annotation instance.
getNameSpace() - Method in class pojos.WorkflowData
Returns the namespace of this workflow.
getNamespaceKeywords(String) - Method in class pojos.ROIData
Get the keywords of the namespace on the ROI.
getNamespaceKeywords() - Method in class pojos.ROIData
Get the keywords of the ROI.
getNamespaces() - Method in class pojos.ROIData
Get 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.
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.
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
 
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() - Method in class pojos.FileData
Returns the (relative) path of the file.
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.
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
Get 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
 
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
Return all the roi in the component as a list.
getROI() - Method in class pojos.util.UploadMask
Get 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.licenses.LicenseBean
 
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
Get 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.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.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.
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.
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
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
 
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
 
getToken(byte[]) - Method in class ome.services.licenses.Store
 
getTopicManager() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getTotalLicenseCount() - Method in interface ome.services.licenses.ILicense
Returns the total number of licenses which the server has.
getTotalLicenseCount() - Method in class ome.services.licenses.LicenseBean
See ILicense.getTotalLicenseCount()
getTotalLicenseCount() - Method in class ome.services.licenses.Store
 
getTotalLicenseCount_async(AMD_ILicense_getTotalLicenseCount, Current) - Method in class ome.services.licenses.LicenseI
 
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() - Method in interface ome.services.util.cache.Cache
 
getType() - Method in class ome.services.util.cache.DelegatingCache
 
getType() - Method in class ome.services.util.cache.DiskCache
 
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 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 x-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 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(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
 
handleILicense(MethodInvocation, Principal) - Method in class ome.services.licenses.LicenseWiring
This method implements special handling for calls to ILicense.
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.
hasLicense(byte[]) - Method in class ome.services.licenses.LicenseBean
See LicenseStore.hasLicense(byte[])
hasLicense(byte[]) - Method in interface ome.services.licenses.LicenseStore
Checks for the validity of a token and that the Not responsible for timeouts.
hasLicense(byte[]) - Method in class ome.services.licenses.Store
 
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.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
 
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
 
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.sharing.data.Obj
 
id - Variable in class ome.services.sharing.data.ShareData
 
id - Variable in class ome.services.sharing.data.ShareItem
 
IdBackedCache<K extends ome.model.IObject,V extends Serializable> - Class in ome.services.util.cache
Wrapper which provides clean-up functionality.
IdBackedCache(LocalQuery, Cache<K, V>) - Constructor for class ome.services.util.cache.IdBackedCache
 
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.
ILicense - Interface in ome.services.licenses
(CLIENT) Provides methods for acquiring and releasing server licenses.
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.
increment() - Method in interface ome.services.sessions.SessionContext
Increment the current reference count and return the new value atomically.
increment() - Method in class ome.services.sessions.SessionContextImpl
 
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() - 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.
InstrumentData(List<IObject>) - 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
 
InvalidLicenseException - Exception in ome.services.licenses
(CLIENT) Exception thrown on a regular method call when the provided license token is rejected by the LicenseStore.
InvalidLicenseException(String) - Constructor for exception ome.services.licenses.InvalidLicenseException
 
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.licenses.LicenseWiring
Interceptor method which enforces the LicenseWiring policy.
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
Is the object a clientside object
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.
isFailedReacquisition() - Method in exception ome.services.licenses.LicenseTimeout
Returns Boolean.TRUE if a reacquisition was attempted and failed, Boolean.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.
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
 
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.
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.
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

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(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.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.
LicenseAPIException - Exception in ome.services.licenses
(CLIENT) Thrown by a properly functioning server only when the client has improperly used the licensing infrastructure (non-null LicensedPrincipal requirement).
LicenseAPIException(String) - Constructor for exception ome.services.licenses.LicenseAPIException
 
LicenseBean - Class in ome.services.licenses
Implementation of the ILicense service interface.
LicenseBean() - Constructor for class ome.services.licenses.LicenseBean
 
LicenseException - Exception in ome.services.licenses
(CLIENT) Abstract superclass of all License exceptions.
LicenseException(String) - Constructor for exception ome.services.licenses.LicenseException
 
LicenseExceptionListener - Class in ome.services.licenses
Listens for ConvertToBlitzExceptionMessage sent by IceMethodInvoker and converts LicenseException instances to omero.licenses.NoAvailableLicenseException et al.
LicenseExceptionListener() - Constructor for class ome.services.licenses.LicenseExceptionListener
 
LicenseI - Class in ome.services.licenses
Implementation of the ILicense service.
LicenseI(ILicense, BlitzExecutor) - Constructor for class ome.services.licenses.LicenseI
 
LicenseSessionListener - Class in ome.services.licenses
Listens for AbstractSessionMessages sent by ome.services.blitz.fire.SesssionManagerI and ServiceFactoryI and creates licenses when necessary for the user.
LicenseSessionListener() - Constructor for class ome.services.licenses.LicenseSessionListener
 
LicenseStore - Interface in ome.services.licenses
Provides local extensions of ILicense for validating license tokens and tracking license timeouts.
LicenseTimeout - Exception in ome.services.licenses
(CLIENT) Exception thrown on a regular method call when a previously valid license has timed out as interpreted by the LicenseStore.
LicenseTimeout(String) - Constructor for exception ome.services.licenses.LicenseTimeout
 
LicenseTimeout(String, boolean) - Constructor for exception ome.services.licenses.LicenseTimeout
 
LicenseWiring - Class in ome.services.licenses
Responsible for enforcing a generic licensing policy: All methods to ILicense are allowed.
LicenseWiring() - Constructor for class ome.services.licenses.LicenseWiring
 
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 - 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.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(AbstractSessionMessage) - Method in class ome.services.licenses.LicenseSessionListener
 
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.
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
 
logout() - Method in class ome.services.licenses.LicenseSessionListener
 
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
 
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.
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.
MaskClass - Class in pojos.util
 
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
Create a new instance of MaskData, creating a new MaskI Object.
MaskData(double, double, double, double, byte[]) - Constructor for class pojos.MaskData
Create 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() - 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
 
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.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.
NoAvailableLicensesException - Exception in ome.services.licenses
(CLIENT) Exception thrown on license acquisition when no licenses are available.
NoAvailableLicensesException(String) - Constructor for exception ome.services.licenses.NoAvailableLicensesException
 
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.
NSEXPERIMENTERPHOTO - Static variable in class ome.logic.AdminImpl
 
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
 

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.licenses - package ome.services.licenses
Contains an add-on service and interceptor for license administration.
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.services.util.cache - package ome.services.util.cache
OMERO utilities for caching.
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() - 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(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.licenses.LicenseExceptionListener
 
onApplicationEvent(ApplicationEvent) - Method in class ome.services.licenses.LicenseSessionListener
 
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(ApplicationEvent) - Method in class ome.services.util.ServiceHandler
 
onApplicationEvent(ApplicationEvent) - Method in class ome.tools.hibernate.ExtendedMetadata
Listener method which waits for a ContextRefreshedEvent and then extracts the SessionFactory from the ApplicationContext and pases it to ExtendedMetadata.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.
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
 
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
 
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
 
parsePointsToPath(String, boolean) - Static method in class omero.model.SmartShape.Util
 
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.gateway.OmeroGateway
 
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 - 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
 
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, SessionManager) - 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
Create a new instance of PolygonData, creating a new PolygonI Object.
PolygonData(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Constructor for class pojos.PolygonData
Create 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
Create 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(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_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.impl.AbstractAmdServant
 
preClose() - Method in class ome.services.blitz.impl.ExporterI
 
preClose() - Method in class ome.services.blitz.impl.MetadataStoreI
 
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
 
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
 
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
 
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
 
put(long, V) - Method in interface ome.services.util.cache.Cache
 
put(long, V) - Method in class ome.services.util.cache.DelegatingCache
 
put(long, V) - Method in class ome.services.util.cache.DiskCache
 
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
 
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
 

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.
reap() - Method in interface ome.services.util.cache.Cache
 
reap() - Method in class ome.services.util.cache.DelegatingCache
 
reap() - Method in class ome.services.util.cache.DiskCache
 
reap() - Method in class ome.services.util.cache.IdBackedCache
 
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
Create a new instance of RectangleData, creating a new EllipseI Object.
RectangleData(double, double, double, double) - Constructor for class pojos.RectangleData
Create a new instance of the RectangleData, set the x, y coord and Width and height.
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.
refCount() - Method in interface ome.services.sessions.SessionContext
Return the current number of references which this session is aware of.
refCount() - Method in class ome.services.sessions.SessionContextImpl
 
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
 
releaseLicense(byte[]) - Method in interface ome.services.licenses.ILicense
Frees a license for re-reservation via ILicense.acquireLicense().
releaseLicense(byte[]) - Method in class ome.services.licenses.LicenseBean
See ILicense.releaseLicense(byte[])
releaseLicense(byte[]) - Method in class ome.services.licenses.Store
 
releaseLicense_async(AMD_ILicense_releaseLicense, byte[], Current) - Method in class ome.services.licenses.LicenseI
 
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.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(long) - Method in interface ome.services.util.cache.Cache
 
remove(long) - Method in class ome.services.util.cache.DelegatingCache
 
remove(long) - Method in class ome.services.util.cache.DiskCache
 
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
Remove 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
Remove 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.
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
 
resetLicenses() - Method in interface ome.services.licenses.ILicense
Administrative method to clear all active licenses and possibly to re-initialize the LicenseStore.
resetLicenses() - Method in class ome.services.licenses.LicenseBean
See ILicense.resetLicenses()
resetLicenses() - Method in class ome.services.licenses.Store
 
resetLicenses_async(AMD_ILicense_resetLicenses, Current) - Method in class ome.services.licenses.LicenseI
 
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
 
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(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.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
 

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
 
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
 
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.
SessionContextImpl - Class in ome.services.sessions
 
SessionContextImpl(Session, List<Long>, List<Long>, List<String>, SessionStats) - Constructor for class ome.services.sessions.SessionContextImpl
 
SessionContextImpl(Session, List<Long>, List<Long>, List<String>, SessionStats, Roles) - 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.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.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.system.Preference
Setter injector
setBit(byte[], int, int) - Method in class pojos.MaskData
Set the bit value in a byte array at position bit to be the value value.
setBit(byte[], int, int) - Method in class pojos.util.MaskClass
Set 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
Is the object a clientside object
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.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
 
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.
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
set height of an untransformed mask.
setHeight(double) - Method in class pojos.RectangleData
set 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
Set 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
Set the keywords of the workflow.
setKeywords(List<String>) - Method in class pojos.WorkflowData
Set 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.
setLicenseCount(int) - Method in class ome.services.licenses.Store
 
setLicenseWiring(LicenseWiring) - Method in class ome.services.licenses.LicenseSessionListener
 
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
Set the mask image.
setMask(BufferedImage) - Method in class pojos.MaskData
Set 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.WorkflowData
Set the namespace of the workflow.
setNamespaceKeywords(String, String[]) - Method in class pojos.ROIData
Set the namespace keywords of the.
setNamespaceMap(Map<String, List<String>>) - Method in class pojos.ROIData
Set 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
Set the points in the polygon.
setPoints(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Method in class pojos.PolylineData
Set 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.
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
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
 
setSecuritySystem(SecuritySystem) - Method in class ome.services.licenses.LicenseSessionListener
 
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
 
setService(ILicense) - Method in class ome.services.licenses.LicenseSessionListener
 
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.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
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
 
setSessionManager(SessionManager) - Method in class ome.services.licenses.LicenseBean
 
setSessionManager(SessionManager) - Method in interface ome.services.licenses.LicenseStore
Starting with OmeroSessions, the LicenseStore needs to have access more to the SessionManager rather than the SecuritySystem since during session-creation, no user is logged in.
setSessionManager(SessionManager) - Method in class ome.services.licenses.Store
See {@link LicenseStore#setSessionManager(SessionManager)
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
 
setStaticSecuritySystem(SecuritySystem) - Method in class ome.services.licenses.LicenseBean
This injector does not synchronize or check for null as specified in the LicenseStore.setStaticSecuritySystem(SecuritySystem) method, but delegates to the LicenseBean.STORE instance which should implement that logic.
setStaticSecuritySystem(SecuritySystem) - Method in interface ome.services.licenses.LicenseStore
Injector which allows the central SecuritySystem instance to be injected in the store post-constructor (since the main instance may be constructed statically.
setStaticSecuritySystem(SecuritySystem) - Method in class ome.services.licenses.Store
See LicenseStore.setStaticSecuritySystem(SecuritySystem)
setStatus(String) - Method in interface ome.api.JobHandle
Updates the JobStatus for the current job.
setStatus(String) - Method in class ome.services.JobBean
 
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.
SETTINGS_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
Set 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.
setUsedLicenses(int) - Method in class ome.services.licenses.Store
 
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
set width of an untransformed mask.
setWidth(double) - Method in class pojos.RectangleData
set 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 centre of the ellipse.
setX(double) - Method in class pojos.MaskData
set 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
set the x-coordinate 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 centre of the ellipse.
setY(double) - Method in class pojos.MaskData
set 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
set the y-coordinate 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.tools.FileSystem
This method is used to get the used space of a File or FileSystem in bytes
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
 
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.
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 - Class in ome.services.licenses
Example LicenseStore implementation.
Store() - Constructor for class ome.services.licenses.Store
 
Store(int) - Constructor for class ome.services.licenses.Store
 
Store(int, int) - Constructor for class ome.services.licenses.Store
 
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.
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
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.
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.
time - Variable in class ome.services.licenses.TokenInfo
 
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
 
TokenInfo - Class in ome.services.licenses
Example struct of the information that can be stored for used license.
TokenInfo() - Constructor for class ome.services.licenses.TokenInfo
 
tokenStream(String, Reader) - Method in class ome.services.fulltext.FullTextAnalyzer
Returns a LowercaseAlphaNumericTokenizer
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
 
toRType(Object) - Method in class omero.util.IceMapper
 
toString() - Method in class ome.io.nio.AbstractBuffer
 
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.
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(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
 
UploadMask(long) - Constructor for class pojos.util.UploadMask
Instantiate the class.
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 - 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.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 - 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
 
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
 
WorkflowData(NamespaceI) - Constructor for class pojos.WorkflowData
Instantiate the class.
WorkflowData(String, List<String>) - Constructor for class pojos.WorkflowData
Instantiate the class.
WorkflowData(String, String) - Constructor for class pojos.WorkflowData
Instantiate the class.
WorkflowData() - Constructor for class pojos.WorkflowData
Instantiate the class.
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
 

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

OmeroJava Api

Version: Beta-4.2.0-r7571-b29

Copyright © 2009 The University of Dundee. All Rights Reserved.