Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors

Deprecated Interfaces

Interface and Description
ome.api.IShare
loci.ome.io.services.OMEReaderWriterService As of release 5.3.0

Deprecated Classes

Class and Description
ome.services.fulltext.BridgeHelper
omero.cmd.graphs.DiskUsageI will be removed in OMERO 5.4, use DiskUsage2 instead
ome.services.fulltext.FullTextAnalyzer
ome.services.fulltext.FullTextBridge
ome.services.fulltext.FullTextIndexer
ome.services.fulltext.FullTextThread
omero.cmd.graphs.IgnoreTypePolicy experimental: may be wholly removed in next major version
loci.ome.io.OMECredentials As of release 5.3.0
ome.formats.OMEROImportFixture to be moved to components/blitz/test/
loci.ome.io.OmeroReader As of release 5.3.0
ome.services.fulltext.ParserSession
ome.services.fulltext.PersistentEventLogLoader
ome.services.fulltext.bridges.ProjectWithImageNameBridge
omeis.providers.re.codomain.ReverseIntensityContext This class will be renamed to InverseIntensityContext (or similar) in future versions
ome.services.fulltext.SimpleLuceneOptions
ome.services.fulltext.bridges.TablesBridge
ome.formats.importer.util.TinyImportFixture
ome.formats.importer.Version As of release 5.3.2

Deprecated Fields

Field and Description
omeis.providers.re.data.PlaneFactory.BIT
omeis.providers.re.data.PlaneFactory.DOUBLE_TYPE
omeis.providers.re.quantum.QuantumFactory.EXPONENTIAL
omeis.providers.re.data.PlaneFactory.FLOAT_TYPE
ome.util.actions.PostgresSqlAction.insertFormatSql
omeis.providers.re.data.PlaneFactory.INT16
omeis.providers.re.data.PlaneFactory.INT32
omeis.providers.re.data.PlaneFactory.INT8
omeis.providers.re.quantum.QuantumFactory.LINEAR
omeis.providers.re.quantum.QuantumFactory.LOGARITHMIC
omeis.providers.re.Renderer.PHOTOMETRIC_MONOCHROME
omeis.providers.re.quantum.QuantumFactory.POLYNOMIAL
ome.formats.importer.ImportConfig.targetClass
ome.formats.importer.ImportConfig.targetId
omeis.providers.re.data.PlaneFactory.UINT16
omeis.providers.re.data.PlaneFactory.UINT32
omeis.providers.re.data.PlaneFactory.UINT8
ome.formats.importer.ImportConfig.useFullPath

Deprecated Methods

Method and Description
omeis.providers.re.RenderingEngine.addCodomainMap(CodomainMapContext)
ome.services.RenderingBean.addCodomainMap(CodomainMapContext)
ome.parameters.Parameters.cache() experimental: may be wholly removed in next major version
omero.sys.ParametersI.cache() experimental: may be wholly removed in next major version
ome.model.internal.Permissions.copyRestrictions()
ome.model.internal.Permissions.copyRestrictions(boolean[], String[])
ome.logic.LdapImpl.createUserFromLdap(String, String)
omero.gateway.model.ROIData.firstPlane() Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
ome.logic.PixelsImpl.getAllEnumerations(Class<T>)
ome.formats.OMEROMetadataStoreClient.getDefaultGroupLevel()
ome.logic.PixelsImpl.getEnumeration(Class<T>, String)
ome.services.scheduler.ThreadPool.getExecutor()
ome.io.nio.PixelsService.getPixelBuffer(Pixels) In the future callers should use the more descriptive PixelsService.getPixelBuffer(Pixels, boolean).
omero.gateway.model.ROIData.getPlaneCount() Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
omero.gateway.model.ROIData.getShapesInRange(ROICoordinate, ROICoordinate) Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
ome.services.graphs.GraphPathBean.getSimpleProperties(String) instead use GraphPathBean.getSimpleProperties(String, boolean) setting isNested to false
ome.logic.RepositoryInfoImpl.getUsageFraction()
ome.logic.RepositoryInfoImpl.getUsedSpaceInKilobytes()
ome.formats.importer.ImportConfig.getUserFullPath()
ome.formats.importer.util.IniFileLoader.getUserFullPath()
ome.formats.importer.ImportLibrary.importImage(ImportContainer, int, int, int) now used by tests only
ome.util.SqlAction.insertFormat(String)
ome.util.actions.PostgresSqlAction.insertFormat(String)
ome.services.blitz.impl.ProcessorCallbackI.isAccepted(boolean, String, String, Current)
omero.gateway.model.ROIData.lastPlane() Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
ome.logic.LdapImpl.loadLdapGroups(String, DistinguishedName)
ome.security.basic.OmeroInterceptor.managedExternalInfo(boolean, IObject, Details, Details, Details)
ome.services.blitz.repo.PublicRepositoryI.persistLogFile(OriginalFile, Current)
ome.services.blitz.repo.PublicRepositoryI.pixels(String, Current)
omeis.providers.re.RenderingEngine.removeCodomainMap(CodomainMapContext)
ome.services.RenderingBean.removeCodomainMap(CodomainMapContext)
ome.api.IAdmin.reportForgottenPassword(String, String)
ome.model.internal.Permissions.setDisallow(boolean[], int, boolean)
ome.api.ILdap.setDN(Long, String) As of release 5.1, relevant model objects have the "ldap" property added to their state.
ome.logic.LdapImpl.setDN(Long, String)
ome.services.RenderingBean.setOverlays(Map<byte[], Integer>) As of release 5.1.0, replaced by PlaneDef.setShapeIds(List).
ome.services.graphs.GraphTraversal.setOwnsAll() An ugly expedient hack that requires review and may be removed without notice.
ome.formats.importer.ImportConfig.setUserFullPath(boolean)
ome.formats.importer.util.IniFileLoader.setUserFullPath(boolean)
omeis.providers.re.RenderingEngine.updateCodomainMap(CodomainMapContext)
ome.services.RenderingBean.updateCodomainMap(CodomainMapContext)

Deprecated Constructors

Constructor and Description
ome.io.nio.AbstractFileSystemService(String)
ome.services.blitz.repo.AbstractRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, PublicRepositoryI)
ome.services.blitz.repo.AbstractRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI)
ome.security.basic.BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService)
ome.model.units.ElectricPotential()
ome.security.basic.EventHandler(SqlAction, BasicSecuritySystem, SessionFactory, TransactionAttributeSource)
ome.model.units.Frequency()
omero.cmd.HandleI(int)
ome.services.blitz.repo.InternalRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI)
ome.services.blitz.repo.LegacyRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, PublicRepositoryI)
ome.services.blitz.repo.LegacyRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI)
ome.model.units.Length()
ome.model.internal.NamedValue()
ome.io.nio.OriginalFilesService(String)
ome.services.pixeldata.PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int)
ome.services.pixeldata.PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics)
ome.services.pixeldata.PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics, ReadOnlyStatus)
ome.services.pixeldata.PixelDataThread(SessionManager, Executor, PixelDataHandler, String)
ome.services.pixeldata.PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int)
ome.services.pixeldata.PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int, Metrics)
ome.io.nio.PixelsService(String, boolean, long, FilePathResolver, BackOff, TileSizes, IQuery)
ome.io.nio.PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes, IQuery)
ome.io.nio.PixelsService(String, FilePathResolver)
ome.io.nio.PixelsService(String, long, FilePathResolver, BackOff, TileSizes, IQuery)
ome.model.units.Power()
ome.model.units.Pressure()
ome.services.scripts.ScriptRepoHelper(Executor, String, Roles)
ome.services.scripts.ScriptRepoHelper(File, Executor, String, Principal, Roles)
ome.services.scripts.ScriptRepoHelper(File, Executor, String, Principal, Roles, ReadOnlyStatus)
ome.services.scripts.ScriptRepoHelper(String, File, Executor, String, Principal, Roles)
ome.services.blitz.repo.ScriptRepositoryI(ObjectAdapter, Registry, Executor, Principal, ScriptRepoHelper, PublicRepositoryI, Set<String>)
ome.model.units.Temperature()
ome.io.nio.ThumbnailService(String)
ome.model.units.Time()