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.
