OmeroJava API
| Package | Description |
|---|---|
| ome.logic |
The central repository of implementations which will be accessible through this server.
|
| 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.delete |
Implementations of the ome.api.IDelete service.
|
| ome.services.projection | |
| ome.services.sessions | |
| ome.services.sharing |
ome.api.IShare support infrastructure.
|
| Modifier and Type | Method and Description |
|---|---|
void |
AdminImpl.addGroupOwners(ExperimenterGroup group,
Experimenter... owner) |
void |
AdminImpl.addGroups(Experimenter user,
ExperimenterGroup... groups) |
java.lang.Long |
QueryImpl.aggByQuery(java.lang.String agg,
java.lang.String field,
java.lang.String query,
Parameters params) |
java.util.Map<java.lang.String,java.lang.Long> |
QueryImpl.aggMapByQuery(java.lang.String agg,
java.lang.String mapKey,
java.lang.String field,
java.lang.String query,
Parameters params) |
<T extends IEnum> |
TypesImpl.allEnumerations(java.lang.Class<T> k) |
java.util.Map<java.lang.Boolean,java.util.List<java.lang.Long>> |
RenderingSettingsImpl.applySettingsToDataset(long from,
long to)
Implemented as specified by the
IRenderingSettings I/F. |
boolean |
RenderingSettingsImpl.applySettingsToImage(long from,
long to)
Implemented as specified by the
IRenderingSettings I/F |
java.util.Map<java.lang.Boolean,java.util.List<java.lang.Long>> |
RenderingSettingsImpl.applySettingsToImages(long from,
java.util.List<java.lang.Long> nodeIds)
Implemented as specified by the
IRenderingSettings I/F |
boolean |
RenderingSettingsImpl.applySettingsToPixels(long from,
long to)
Implemented as specified by the
IRenderingSettings I/F |
java.util.Map<java.lang.Boolean,java.util.List<java.lang.Long>> |
RenderingSettingsImpl.applySettingsToProject(long from,
long to)
Implemented as specified by the
IRenderingSettings I/F. |
<T extends IObject> |
RenderingSettingsImpl.applySettingsToSet(long from,
java.lang.Class<T> klass,
java.util.Set<java.lang.Long> nodeIds)
Implemented as specified by the
IRenderingSettings I/F. |
boolean |
AdminImpl.canAnnotate(IObject obj) |
boolean |
AdminImpl.canUpdate(IObject obj) |
void |
AdminImpl.changeGroup(IObject iObject,
java.lang.String groupName) |
void |
AdminImpl.changeOwner(IObject iObject,
java.lang.String omeName) |
void |
AdminImpl.changePassword(java.lang.String newPassword) |
void |
AdminImpl.changePasswordWithOldPassword(java.lang.String oldPassword,
java.lang.String newPassword) |
void |
AdminImpl.changePermissions(IObject iObject,
Permissions perms)
the implementation of this method is somewhat tricky in that
Permissions changes must be allowed even when other updates are
not. |
void |
AdminImpl.changeUserPassword(java.lang.String user,
java.lang.String newPassword) |
boolean |
QueryImpl.checkProperty(java.lang.String type,
java.lang.String property) |
boolean |
QueryImpl.checkType(java.lang.String type) |
void |
QueryImpl.clear() |
Experimenter[] |
AdminImpl.containedExperimenters(long groupId) |
ExperimenterGroup[] |
AdminImpl.containedGroups(long experimenterId) |
boolean |
QueryImpl.contains(java.lang.Object obj) |
java.lang.Long |
PixelsImpl.copyAndResizeImage(long imageId,
java.lang.Integer sizeX,
java.lang.Integer sizeY,
java.lang.Integer sizeZ,
java.lang.Integer sizeT,
java.util.List<java.lang.Integer> channelList,
java.lang.String name,
boolean copyStats) |
java.lang.Long |
PixelsImpl.copyAndResizePixels(long pixelsId,
java.lang.Integer sizeX,
java.lang.Integer sizeY,
java.lang.Integer sizeZ,
java.lang.Integer sizeT,
java.util.List<java.lang.Integer> channelList,
java.lang.String methodology,
boolean copyStats) |
java.lang.Long |
MetadataImpl.countAnnotationsUsedNotOwned(java.lang.Class annotationType,
long userID) |
java.lang.Long |
MetadataImpl.countSpecifiedAnnotations(java.lang.Class type,
java.util.Set<java.lang.String> include,
java.util.Set<java.lang.String> exclude,
Parameters options) |
IObject |
PojosImpl.createDataObject(IObject arg0,
Parameters arg1) |
IObject[] |
PojosImpl.createDataObjects(IObject[] arg0,
Parameters arg1) |
<T extends IEnum> |
TypesImpl.createEnumeration(T newEnum) |
long |
AdminImpl.createExperimenter(Experimenter experimenter,
ExperimenterGroup defaultGroup,
ExperimenterGroup... otherGroups) |
long |
AdminImpl.createExperimenterWithPassword(Experimenter experimenter,
java.lang.String password,
ExperimenterGroup defaultGroup,
ExperimenterGroup... otherGroups) |
long |
AdminImpl.createGroup(ExperimenterGroup group) |
java.lang.Long |
PixelsImpl.createImage(int sizeX,
int sizeY,
int sizeZ,
int sizeT,
java.util.List<java.lang.Integer> channelList,
PixelsType pixelsType,
java.lang.String name,
java.lang.String description) |
long |
AdminImpl.createRestrictedSystemUser(Experimenter newSystemUser,
java.util.List<AdminPrivilege> privileges) |
long |
AdminImpl.createRestrictedSystemUserWithPassword(Experimenter newSystemUser,
java.util.List<AdminPrivilege> privileges,
java.lang.String password) |
long |
AdminImpl.createSystemUser(Experimenter newSystemUser) |
long |
AdminImpl.createUser(Experimenter newUser,
java.lang.String defaultGroup) |
Experimenter |
LdapImpl.createUser(java.lang.String username)
Creates an
Experimenter based on the supplied LDAP username. |
boolean |
LdapImpl.createUserFromLdap(java.lang.String username,
java.lang.String password)
Deprecated.
|
<T extends IEnum> |
TypesImpl.deleteEnumeration(T oEnum) |
void |
AdminImpl.deleteExperimenter(Experimenter user) |
void |
AdminImpl.deleteGroup(ExperimenterGroup group) |
void |
UpdateImpl.deleteObject(IObject row) |
java.util.List<Experimenter> |
LdapImpl.discover() |
java.util.List<ExperimenterGroup> |
LdapImpl.discoverGroups() |
void |
QueryImpl.evict(java.lang.Object obj) |
<T> T |
QueryImpl.execute(org.springframework.orm.hibernate3.HibernateCallback callback) |
<T> T |
QueryImpl.execute(Query<T> query) |
IObject |
QueryImpl.find(java.lang.Class klass,
long id) |
<T extends IObject> |
QueryImpl.findAll(java.lang.Class<T> klass,
Filter filter) |
<T extends IObject> |
QueryImpl.findAllByExample(T example,
Filter filter) |
<T extends IObject> |
QueryImpl.findAllByFullText(java.lang.Class<T> type,
java.lang.String query,
Parameters params) |
<T extends IObject> |
QueryImpl.findAllByQuery(java.lang.String queryName,
Parameters params) |
<T extends IObject> |
QueryImpl.findAllByString(java.lang.Class<T> klass,
java.lang.String fieldName,
java.lang.String value,
boolean caseSensitive,
Filter filter) |
<T extends IObject> |
QueryImpl.findByExample(T example) |
<T extends IObject> |
QueryImpl.findByQuery(java.lang.String queryName,
Parameters params) |
<T extends IObject> |
QueryImpl.findByString(java.lang.Class<T> klass,
java.lang.String fieldName,
java.lang.String value) |
java.util.Set |
PojosImpl.findContainerHierarchies(java.lang.Class rootNodeType,
java.util.Set imageIds,
Parameters options) |
java.lang.String |
LdapImpl.findDN(java.lang.String username) |
Experimenter |
LdapImpl.findExperimenter(java.lang.String username) |
ExperimenterGroup |
LdapImpl.findGroup(java.lang.String groupname) |
java.lang.String |
LdapImpl.findGroupDN(java.lang.String groupname) |
void |
UpdateImpl.flush() |
IObject |
QueryImpl.get(java.lang.Class klass,
long id) |
java.util.List<AdminPrivilege> |
AdminImpl.getAdminPrivileges(Experimenter user) |
java.util.List<Experimenter> |
AdminImpl.getAdminsWithPrivileges(java.util.List<AdminPrivilege> privileges) |
<T extends IObject> |
PixelsImpl.getAllEnumerations(java.lang.Class<T> klass)
Deprecated.
|
java.util.List<java.lang.Class<IAnnotated>> |
TypesImpl.getAnnotationTypes() |
int |
PixelsImpl.getBitDepth(PixelsType pixelsType) |
java.util.Map |
PojosImpl.getCollectionCount(java.lang.String type,
java.lang.String property,
java.util.Set ids,
Parameters options) |
java.util.Map<java.lang.String,java.lang.String> |
ConfigImpl.getConfigDefaults() |
<T extends IObject> |
TypesImpl.getContainerTypes() |
java.util.List<AdminPrivilege> |
AdminImpl.getCurrentAdminPrivileges() |
ExperimenterGroup |
AdminImpl.getDefaultGroup(long experimenterId) |
<T extends IEnum> |
TypesImpl.getEnumeration(java.lang.Class<T> k,
java.lang.String string) |
<T extends IObject> |
PixelsImpl.getEnumeration(java.lang.Class<T> klass,
java.lang.String value)
Deprecated.
|
<T extends IEnum> |
TypesImpl.getEnumerationsWithEntries() |
<T extends IEnum> |
TypesImpl.getEnumerationTypes() |
Experimenter |
AdminImpl.getExperimenter(long id) |
long |
RepositoryInfoImpl.getFreeSpaceInKilobytes() |
ExperimenterGroup |
AdminImpl.getGroup(long id) |
java.util.Set |
PojosImpl.getImages(java.lang.Class rootNodeType,
java.util.Set rootNodeIds,
Parameters options) |
java.util.Set |
PojosImpl.getImagesByOptions(Parameters options) |
java.util.Map<java.lang.Long,java.util.Map<java.lang.Boolean,java.util.List<java.lang.Long>>> |
PojosImpl.getImagesBySplitFilesets(java.util.Map<java.lang.Class<? extends IObject>,java.util.List<java.lang.Long>> included,
Parameters options) |
<T extends IObject> |
TypesImpl.getImportTypes() |
java.util.List<java.lang.Long> |
AdminImpl.getLeaderOfGroupIds(Experimenter e) |
java.util.List<java.lang.Long> |
AdminImpl.getMemberOfGroupIds(Experimenter e) |
<T extends IEnum> |
TypesImpl.getOriginalEnumerations() |
<T extends IObject> |
TypesImpl.getPojoTypes() |
RenderingDef |
RenderingSettingsImpl.getRenderingSettings(long pixelsId)
Implemented as specified by the
IRenderingSettings I/F |
<T extends IObject> |
TypesImpl.getResultTypes() |
boolean |
LdapImpl.getSetting() |
java.util.Map |
MetadataImpl.getTaggedObjectsCount(java.util.Set<java.lang.Long> tagIds,
Parameters options) |
double |
RepositoryInfoImpl.getUsageFraction()
Deprecated.
|
long |
RepositoryInfoImpl.getUsedSpaceInKilobytes()
Deprecated.
|
java.util.Set |
PojosImpl.getUserImages(Parameters options) |
java.util.List<java.lang.String> |
AdminImpl.getUserRoles(Experimenter e) |
ExperimenterGroup |
AdminImpl.groupProxy(java.lang.Long id) |
ExperimenterGroup |
AdminImpl.groupProxy(java.lang.String groupName) |
void |
UpdateImpl.indexObject(IObject row) |
void |
QueryImpl.initialize(java.lang.Object obj) |
ILink[] |
PojosImpl.link(ILink[] arg0,
Parameters arg1) |
<A extends Annotation> |
MetadataImpl.loadAnnotation(java.util.Set<java.lang.Long> annotationIds) |
<T extends IObject,A extends Annotation> |
MetadataImpl.loadAnnotations(java.lang.Class<T> rootNodeType,
java.util.Set<java.lang.Long> rootNodeIds,
java.util.Set<java.lang.String> annotationTypes,
java.util.Set<java.lang.Long> annotatorIds,
Parameters options) |
java.util.Set<IObject> |
MetadataImpl.loadAnnotationsUsedNotOwned(java.lang.Class annotationType,
long userID) |
java.util.Set |
MetadataImpl.loadChannelAcquisitionData(java.util.Set<java.lang.Long> ids) |
java.util.Set |
PojosImpl.loadContainerHierarchy(java.lang.Class rootNodeType,
java.util.Set rootNodeIds,
Parameters options) |
Instrument |
MetadataImpl.loadInstrument(long id) |
java.util.Map<java.lang.Long,java.util.Set<IObject>> |
MetadataImpl.loadLogFiles(java.lang.Class<? extends IObject> rootNodeType,
java.util.Set<java.lang.Long> ids) |
RenderingDef |
PixelsImpl.loadRndSettings(long renderingDefId) |
<A extends Annotation> |
MetadataImpl.loadSpecifiedAnnotations(java.lang.Class type,
java.util.Set<java.lang.String> include,
java.util.Set<java.lang.String> exclude,
Parameters options) |
<A extends Annotation> |
MetadataImpl.loadSpecifiedAnnotationsLinkedTo(java.lang.Class type,
java.util.Set<java.lang.String> include,
java.util.Set<java.lang.String> exclude,
java.lang.Class rootNodeType,
java.util.Set<java.lang.Long> rootNodeIds,
Parameters options) |
java.util.Map<java.lang.Long,java.util.Set<IObject>> |
MetadataImpl.loadTagContent(java.util.Set<java.lang.Long> tagIds,
Parameters options) |
java.util.Set<IObject> |
MetadataImpl.loadTagSets(Parameters options) |
Experimenter |
AdminImpl.lookupExperimenter(java.lang.String omeName) |
java.util.List<Experimenter> |
AdminImpl.lookupExperimenters() |
ExperimenterGroup |
AdminImpl.lookupGroup(java.lang.String groupName) |
java.util.List<ExperimenterGroup> |
AdminImpl.lookupGroups() |
java.lang.String |
AdminImpl.lookupLdapAuthExperimenter(long id) |
java.util.List<java.util.Map<java.lang.String,java.lang.Object>> |
AdminImpl.lookupLdapAuthExperimenters() |
void |
AdminImpl.moveToCommonSpace(IObject... iObjects) |
<T extends IObject> |
TypesImpl.permissions(java.lang.Class<T> k) |
java.util.List<java.lang.Object[]> |
QueryImpl.projection(java.lang.String query,
Parameters p) |
void |
AdminImpl.removeGroupOwners(ExperimenterGroup group,
Experimenter... owner) |
void |
AdminImpl.removeGroups(Experimenter user,
ExperimenterGroup... groups) |
void |
RepositoryInfoImpl.removeUnusedFiles() |
void |
RenderingSettingsImpl.resetDefaults(RenderingDef def,
Pixels pixels)
Implemented as specified by the
IRenderingSettings I/F |
<T extends IObject> |
RenderingSettingsImpl.resetDefaultsByOwnerInSet(java.lang.Class<T> klass,
java.util.Set<java.lang.Long> nodeIds)
Implemented as specified by the
IRenderingSettings I/F. |
void |
RenderingSettingsImpl.resetDefaultsForPixels(long to)
Implemented as specified by the
IRenderingSettings I/F. |
java.util.Set<java.lang.Long> |
RenderingSettingsImpl.resetDefaultsInDataset(long to)
Implemented as specified by the
IRenderingSettings I/F. |
void |
RenderingSettingsImpl.resetDefaultsInImage(long to)
Implemented as specified by the
IRenderingSettings I/F. |
<T extends IObject> |
RenderingSettingsImpl.resetDefaultsInSet(java.lang.Class<T> klass,
java.util.Set<java.lang.Long> nodeIds)
Implemented as specified by the
IRenderingSettings I/F. |
RenderingDef |
RenderingSettingsImpl.resetDefaultsNoSave(RenderingDef def,
Pixels pixels)
Implemented as specified by the
IRenderingSettings I/F |
<T extends IEnum> |
TypesImpl.resetEnumerations(java.lang.Class<T> klass) |
<T extends IObject> |
RenderingSettingsImpl.resetMinMaxInSet(java.lang.Class<T> klass,
java.util.Set<java.lang.Long> nodeIds)
Implemented as specified by the
IRenderingSettings I/F. |
java.util.List<IObject> |
PixelsImpl.retrieveAllRndSettings(long pixId,
long userId) |
java.util.Collection |
PojosImpl.retrieveCollection(IObject arg0,
java.lang.String arg1,
Parameters arg2) |
Pixels |
PixelsImpl.retrievePixDescription(long pixId) |
RenderingDef |
PixelsImpl.retrieveRndSettings(long pixId) |
RenderingDef |
PixelsImpl.retrieveRndSettingsFor(long pixId,
long userId) |
void |
RepositoryInfoImpl.sanityCheckRepository() |
IObject[] |
UpdateImpl.saveAndReturnArray(IObject[] graph) |
java.util.List<java.lang.Long> |
UpdateImpl.saveAndReturnIds(IObject[] graph) |
IObject |
UpdateImpl.saveAndReturnObject(IObject graph) |
void |
UpdateImpl.saveArray(IObject[] graph) |
void |
UpdateImpl.saveCollection(java.util.Collection graph) |
void |
UpdateImpl.saveObject(IObject graph) |
void |
PixelsImpl.saveRndSettings(RenderingDef rndSettings) |
java.util.List<Experimenter> |
LdapImpl.searchAll() |
java.util.List<Experimenter> |
LdapImpl.searchByAttribute(java.lang.String dns,
java.lang.String attr,
java.lang.String value) |
java.util.List<Experimenter> |
LdapImpl.searchByAttributes(java.lang.String dn,
java.lang.String[] attributes,
java.lang.String[] values) |
Experimenter |
LdapImpl.searchByDN(java.lang.String dns) |
java.util.List<java.lang.String> |
LdapImpl.searchDnInGroups(java.lang.String attr,
java.lang.String value) |
void |
AdminImpl.setAdminPrivileges(Experimenter user,
java.util.List<AdminPrivilege> privileges) |
void |
PixelsImpl.setChannelGlobalMinMax(long pixelsId,
int channelIndex,
double min,
double max) |
void |
ConfigImpl.setConfigValue(java.lang.String key,
java.lang.String value)
|
boolean |
ConfigImpl.setConfigValueIfEquals(java.lang.String key,
java.lang.String value,
java.lang.String test)
|
void |
AdminImpl.setDefaultGroup(Experimenter user,
ExperimenterGroup group) |
void |
LdapImpl.setDN(java.lang.Long experimenterID,
java.lang.String dn)
Deprecated.
|
void |
AdminImpl.setGroupOwner(ExperimenterGroup group,
Experimenter owner) |
void |
RenderingSettingsImpl.setOriginalSettingsForPixels(long to)
Implemented as specified by the
IRenderingSettings I/F. |
java.util.Set<java.lang.Long> |
RenderingSettingsImpl.setOriginalSettingsInDataset(long to)
Implemented as specified by the
IRenderingSettings I/F. |
void |
RenderingSettingsImpl.setOriginalSettingsInImage(long to)
Implemented as specified by the
IRenderingSettings I/F. |
<T extends IObject> |
RenderingSettingsImpl.setOriginalSettingsInSet(java.lang.Class<T> klass,
java.util.Set<java.lang.Long> nodeIds)
Implemented as specified by the
IRenderingSettings I/F. |
void |
AdminImpl.synchronizeLoginCache() |
void |
PojosImpl.unlink(ILink[] arg0,
Parameters arg1) |
void |
AdminImpl.unsetGroupOwner(ExperimenterGroup group,
Experimenter owner) |
IObject |
PojosImpl.updateDataObject(IObject arg0,
Parameters arg1) |
IObject[] |
PojosImpl.updateDataObjects(IObject[] arg0,
Parameters arg1) |
<T extends IEnum> |
TypesImpl.updateEnumeration(T oEnum) |
<T extends IEnum> |
TypesImpl.updateEnumerations(java.util.List<T> listEnum) |
void |
AdminImpl.updateExperimenter(Experimenter experimenter) |
void |
AdminImpl.updateExperimenterWithPassword(Experimenter experimenter,
java.lang.String password) |
void |
AdminImpl.updateGroup(ExperimenterGroup group) |
void |
AdminImpl.updateSelf(Experimenter e) |
long |
AdminImpl.uploadMyUserPhoto(java.lang.String filename,
java.lang.String mimetype,
byte[] data) |
Experimenter |
AdminImpl.userProxy(java.lang.Long id) |
Experimenter |
AdminImpl.userProxy(java.lang.String omeName) |
| Modifier and Type | Method and Description |
|---|---|
void |
JobBean.activate()
Does almost nothing.
|
void |
RawFileBean.activate() |
void |
RawPixelsBean.activate() |
void |
RenderingBean.activate() |
void |
SearchBean.activate() |
void |
ThumbnailBean.activate() |
int |
SearchBean.activeQueries() |
void |
RenderingBean.addCodomainMap(CodomainMapContext mapCtx)
Deprecated.
|
void |
RenderingBean.addCodomainMapToChannel(CodomainMapContext mapCtx,
int w)
Implemented as specified by the
RenderingEngine interface. |
void |
SearchBean.addOrderByAsc(java.lang.String path) |
void |
SearchBean.addOrderByDesc(java.lang.String path) |
void |
SearchBean.allTypes() |
void |
SearchBean.and() |
JobStatus |
JobBean.attach(long id) |
void |
SearchBean.byAnnotatedWith(Annotation... examples) |
void |
SearchBean.byFullText(java.lang.String query) |
void |
SearchBean.byGroupForTags(java.lang.String group) |
void |
SearchBean.byHqlQuery(java.lang.String query,
Parameters p) |
void |
SearchBean.byLuceneQueryBuilder(java.lang.String fields,
java.lang.String from,
java.lang.String to,
java.lang.String dateType,
java.lang.String query) |
void |
SearchBean.bySimilarTerms(java.lang.String... terms) |
void |
SearchBean.bySomeMustNone(java.lang.String[] some,
java.lang.String[] must,
java.lang.String[] none) |
void |
SearchBean.byTagForGroups(java.lang.String tag) |
void |
SearchBean.byUUID(java.lang.String[] uuids) |
byte[] |
RawPixelsBean.calculateMessageDigest() |
void |
JobBean.cancelJob() |
void |
SearchBean.clearQueries() |
void |
JobBean.close() |
void |
RawFileBean.close() |
void |
RawFileBeanReadOnly.close() |
void |
RawPixelsBean.close() |
void |
RawPixelsBeanReadOnly.close() |
void |
RenderingBean.close() |
void |
SearchBean.close() |
void |
ThumbnailBean.close() |
void |
ThumbnailBean.createThumbnail(java.lang.Integer sizeX,
java.lang.Integer sizeY) |
void |
ThumbnailBean.createThumbnails() |
void |
ThumbnailBean.createThumbnailsByLongestSideSet(java.lang.Integer size,
java.util.Set<java.lang.Long> pixelsIds) |
java.util.Map<java.lang.String,Annotation> |
SearchBean.currentMetadata() |
java.util.List<java.util.Map<java.lang.String,Annotation>> |
SearchBean.currentMetadataList() |
boolean |
RawFileBean.exists() |
<T extends IObject> |
SearchBean.fetchAlso(java.util.Map<T,java.lang.String> fetches) |
void |
SearchBean.fetchAlso(java.lang.String... fetches) |
void |
SearchBean.fetchAnnotations(java.lang.Class... classes) |
java.util.Map<java.lang.Integer,double[]> |
RawPixelsBean.findMinMax(int[] channels) |
java.util.List |
RenderingBean.getAvailableFamilies()
Implemented as specified by the
RenderingEngine interface. |
java.util.List |
RenderingBean.getAvailableModels()
Implemented as specified by the
RenderingEngine interface. |
int |
SearchBean.getBatchSize() |
int |
RawPixelsBean.getByteWidth() |
double |
RenderingBean.getChannelCurveCoefficient(int w)
Implemented as specified by the
RenderingEngine interface. |
Family |
RenderingBean.getChannelFamily(int w)
Implemented as specified by the
RenderingEngine interface. |
java.lang.String |
RenderingBean.getChannelLookupTable(int w) |
boolean |
RenderingBean.getChannelNoiseReduction(int w)
Implemented as specified by the
RenderingEngine interface. |
double[] |
RenderingBean.getChannelStats(int w)
Implemented as specified by the
RenderingEngine interface. |
double |
RenderingBean.getChannelWindowEnd(int w)
Implemented as specified by the
RenderingEngine interface. |
double |
RenderingBean.getChannelWindowStart(int w)
Implemented as specified by the
RenderingEngine interface. |
java.util.List<CodomainMapContext> |
RenderingBean.getCodomainMapContext(int w)
Implemented as specified by the
RenderingEngine interface. |
byte[] |
RawPixelsBean.getCol(int arg0,
int arg1,
int arg2,
int arg3) |
float |
RenderingBean.getCompressionLevel()
Implemented as specified by the
RenderingEngine interface. |
EventContext |
AbstractStatefulBean.getCurrentEventContext() |
EventContext |
RenderingBean.getCurrentEventContext()
Implemented as specified by the
RenderingEngine interface. |
int |
RenderingBean.getDefaultT()
Implemented as specified by the
RenderingEngine interface. |
int |
RenderingBean.getDefaultZ()
Implemented as specified by the
RenderingEngine interface. |
java.lang.Long |
RawFileBean.getFileId() |
java.util.Map<java.lang.Integer,int[]> |
RawPixelsBean.getHistogram(int[] channels,
int binCount,
boolean globalRange,
PlaneDef plane) |
byte[] |
RawPixelsBean.getHypercube(java.util.List<java.lang.Integer> offset,
java.util.List<java.lang.Integer> size,
java.util.List<java.lang.Integer> step) |
Job |
JobBean.getJob() |
RenderingModel |
RenderingBean.getModel()
Implemented as specified by the
RenderingEngine interface. |
Pixels |
RenderingBean.getPixels()
Implemented as specified by the
RenderingEngine interface. |
long |
RawPixelsBean.getPixelsId() |
java.lang.String |
RawPixelsBean.getPixelsPath() |
double |
RenderingBean.getPixelsTypeLowerBound(int w)
Implemented as specified by the
RenderingEngine interface. |
double |
RenderingBean.getPixelsTypeUpperBound(int w)
Implemented as specified by the
RenderingEngine interface. |
byte[] |
RawPixelsBean.getPlane(int arg0,
int arg1,
int arg2) |
long |
RawPixelsBean.getPlaneOffset(int arg0,
int arg1,
int arg2) |
byte[] |
RawPixelsBean.getPlaneRegion(int z,
int c,
int t,
int count,
int offset) |
long |
RawPixelsBean.getPlaneSize() |
QuantumDef |
RenderingBean.getQuantumDef()
Implemented as specified by the
RenderingEngine interface. |
byte[] |
RawPixelsBean.getRegion(int arg0,
long arg1) |
long |
RenderingBean.getRenderingDefId() |
long |
ThumbnailBean.getRenderingDefId() |
java.util.List<java.util.List<java.lang.Integer>> |
RawPixelsBean.getResolutionDescriptions() |
java.util.List<java.util.List<java.lang.Integer>> |
RenderingBean.getResolutionDescriptions() |
int |
RawPixelsBean.getResolutionLevel() |
int |
RenderingBean.getResolutionLevel() |
int |
RawPixelsBean.getResolutionLevels() |
int |
RenderingBean.getResolutionLevels() |
int[] |
RenderingBean.getRGBA(int w)
Implemented as specified by the
RenderingEngine interface. |
byte[] |
RawPixelsBean.getRow(int arg0,
int arg1,
int arg2,
int arg3) |
long |
RawPixelsBean.getRowOffset(int arg0,
int arg1,
int arg2,
int arg3) |
int |
RawPixelsBean.getRowSize() |
byte[] |
RawPixelsBean.getStack(int arg0,
int arg1) |
long |
RawPixelsBean.getStackOffset(int arg0,
int arg1) |
long |
RawPixelsBean.getStackSize() |
byte[] |
ThumbnailBean.getThumbnail(java.lang.Integer sizeX,
java.lang.Integer sizeY) |
byte[] |
ThumbnailBeanReadOnly.getThumbnail(java.lang.Integer sizeX,
java.lang.Integer sizeY) |
byte[] |
ThumbnailBean.getThumbnailByLongestSide(java.lang.Integer size) |
byte[] |
ThumbnailBeanReadOnly.getThumbnailByLongestSide(java.lang.Integer size) |
byte[] |
ThumbnailBean.getThumbnailByLongestSideDirect(java.lang.Integer size) |
java.util.Map<java.lang.Long,byte[]> |
ThumbnailBean.getThumbnailByLongestSideSet(java.lang.Integer size,
java.util.Set<java.lang.Long> pixelsIds) |
java.util.Map<java.lang.Long,byte[]> |
ThumbnailBeanReadOnly.getThumbnailByLongestSideSet(java.lang.Integer size,
java.util.Set<java.lang.Long> pixelsIds) |
byte[] |
ThumbnailBean.getThumbnailDirect(java.lang.Integer sizeX,
java.lang.Integer sizeY) |
byte[] |
ThumbnailBean.getThumbnailForSectionByLongestSideDirect(int theZ,
int theT,
java.lang.Integer size) |
byte[] |
ThumbnailBean.getThumbnailForSectionDirect(int theZ,
int theT,
java.lang.Integer sizeX,
java.lang.Integer sizeY) |
java.util.Map<java.lang.Long,byte[]> |
ThumbnailBean.getThumbnailSet(java.lang.Integer sizeX,
java.lang.Integer sizeY,
java.util.Set<java.lang.Long> pixelsIds) |
byte[] |
RawPixelsBean.getTile(int z,
int c,
int t,
int x,
int y,
int w,
int h) |
int[] |
RawPixelsBean.getTileSize() |
int[] |
RenderingBean.getTileSize() |
byte[] |
RawPixelsBean.getTimepoint(int arg0) |
long |
RawPixelsBean.getTimepointOffset(int arg0) |
long |
RawPixelsBean.getTimepointSize() |
long |
RawPixelsBean.getTotalSize() |
boolean |
SearchBean.hasNext() |
boolean |
RenderingBean.isActive(int w)
Implemented as specified by the
RenderingEngine interface. |
boolean |
SearchBean.isAllowLeadingWildcard() |
boolean |
SearchBean.isCaseSensitive() |
boolean |
RawPixelsBean.isFloat() |
boolean |
ThumbnailBean.isInProgress() |
boolean |
SearchBean.isMergedBatches() |
boolean |
RenderingBean.isPixelsTypeSigned()
Implemented as specified by the
RenderingEngine interface. |
boolean |
SearchBean.isReturnUnloaded() |
boolean |
RawPixelsBean.isSigned() |
boolean |
SearchBean.isUseProjections() |
boolean |
JobBean.jobError() |
java.sql.Timestamp |
JobBean.jobFinished() |
java.lang.String |
JobBean.jobMessage() |
boolean |
JobBean.jobRunning() |
JobStatus |
JobBean.jobStatus() |
void |
SearchBean.lastresultsAsWorkingGroup() |
void |
RenderingBean.load()
Implemented as specified by the
RenderingEngine interface. |
void |
RenderingBean.loadRenderingDef(long renderingDefId)
Implemented as specified by the
RenderingEngine interface. |
void |
RenderingBean.lookupPixels(long pixelsId)
Implemented as specified by the
RenderingEngine interface. |
boolean |
RenderingBean.lookupRenderingDef(long pixelsId)
Implemented as specified by the
RenderingEngine interface. |
IObject |
SearchBean.next() |
void |
SearchBean.not() |
void |
SearchBean.notAnnotatedBy(Details d) |
void |
SearchBean.notOwnedBy(Details d) |
void |
SearchBean.onlyAnnotatedBetween(java.sql.Timestamp start,
java.sql.Timestamp stop) |
void |
SearchBean.onlyAnnotatedBy(Details d) |
void |
SearchBean.onlyAnnotatedWith(java.lang.Class... classes) |
void |
SearchBean.onlyCreatedBetween(java.sql.Timestamp start,
java.sql.Timestamp stop) |
void |
SearchBean.onlyIds(java.lang.Long... ids) |
void |
SearchBean.onlyModifiedBetween(java.sql.Timestamp start,
java.sql.Timestamp stop) |
void |
SearchBean.onlyOwnedBy(Details d) |
<T extends IObject> |
SearchBean.onlyType(java.lang.Class<T> klass) |
<T extends IObject> |
SearchBean.onlyTypes(java.lang.Class<T>... classes) |
void |
SearchBean.or() |
void |
JobBean.passivate()
Does nothing.
|
void |
RawFileBean.passivate() |
void |
RawPixelsBean.passivate() |
void |
RenderingBean.passivate() |
void |
SearchBean.passivate() |
void |
ThumbnailBean.passivate() |
void |
RawPixelsBean.prepare(java.util.Set<java.lang.Long> pixelsIds) |
byte[] |
RawFileBean.read(long position,
int length) |
void |
SearchBean.remove() |
void |
RenderingBean.removeCodomainMap(CodomainMapContext mapCtx)
Deprecated.
|
void |
RenderingBean.removeCodomainMapFromChannel(CodomainMapContext mapCtx,
int w)
Implemented as specified by the
RenderingEngine interface. |
RGBBuffer |
RenderingBean.render(PlaneDef pd)
Implemented as specified by the
RenderingEngine interface. |
int[] |
RenderingBean.renderAsPackedInt(PlaneDef pd)
Implemented as specified by the
RenderingEngine interface. |
byte[] |
RenderingBean.renderCompressed(PlaneDef pd)
Implemented as specified by the
RenderingEngine interface. |
int[] |
RenderingBean.renderProjectedAsPackedInt(int algorithm,
int timepoint,
int stepping,
int start,
int end)
Implemented as specified by the
RenderingEngine interface. |
byte[] |
RenderingBean.renderProjectedCompressed(int algorithm,
int timepoint,
int stepping,
int start,
int end)
Implemented as specified by the
RenderingEngine interface. |
boolean |
RawPixelsBean.requiresPixelsPyramid() |
boolean |
RenderingBean.requiresPixelsPyramid() |
void |
SearchBean.resetDefaults() |
void |
ThumbnailBean.resetDefaults() |
long |
RenderingBean.resetDefaultSettings(boolean save)
Implemented as specified by the
RenderingEngine interface. |
<T extends IObject> |
SearchBean.results() |
OriginalFile |
RawFileBean.save() |
Pixels |
RawPixelsBean.save() |
long |
RenderingBean.saveAsNewSettings()
Implemented as specified by the
RenderingEngine interface. |
void |
RenderingBean.saveCurrentSettings()
Implemented as specified by the
RenderingEngine interface. |
void |
RenderingBean.setActive(int w,
boolean active)
Implemented as specified by the
RenderingEngine interface. |
void |
SearchBean.setAllowLeadingWildcard(boolean allowLeadingWildcard) |
void |
SearchBean.setBatchSize(int size) |
void |
SearchBean.setCaseSentivice(boolean caseSensitive) |
void |
RenderingBean.setChannelLookupTable(int w,
java.lang.String lookup) |
void |
RenderingBean.setChannelWindow(int w,
double start,
double end)
Implemented as specified by the
RenderingEngine interface. |
void |
RenderingBean.setCodomainInterval(int start,
int end)
Implemented as specified by the
RenderingEngine interface. |
void |
RenderingBean.setCompressionLevel(float percentage)
Implemented as specified by the
RenderingEngine interface. |
void |
RenderingBean.setDefaultT(int t)
Implemented as specified by the
RenderingEngine interface. |
void |
RenderingBean.setDefaultZ(int z)
Implemented as specified by the
RenderingEngine interface. |
void |
RawFileBean.setFileId(long fileId) |
void |
SearchBean.setIdOnly() |
void |
SearchBean.setMergedBatches(boolean merge) |
java.lang.String |
JobBean.setMessage(java.lang.String message) |
void |
RenderingBean.setModel(RenderingModel model)
Implemented as specified by the
RenderingEngine interface. |
void |
RenderingBean.setOverlays(java.util.Map<byte[],java.lang.Integer> overlays)
Deprecated.
As of release 5.1.0, replaced by
PlaneDef.setShapeIds(List). |
boolean |
ThumbnailBean.setPixelsId(long id) |
boolean |
ThumbnailBeanReadOnly.setPixelsId(long id) |
void |
RawPixelsBean.setPixelsId(long pixelsId,
boolean bypassOriginalFile) |
void |
RawPixelsBean.setPlane(byte[] arg0,
int arg1,
int arg2,
int arg3) |
void |
RenderingBean.setQuantizationMap(int w,
Family family,
double coefficient,
boolean noiseReduction)
Implemented as specified by the
RenderingEngine interface. |
void |
RenderingBean.setQuantumStrategy(int bitResolution)
Implemented as specified by the
RenderingEngine interface. |
void |
RawPixelsBean.setRegion(int arg0,
long arg1,
byte[] arg2) |
void |
ThumbnailBean.setRenderingDefId(long id) |
void |
RawPixelsBean.setResolutionLevel(int resolutionLevel) |
void |
RenderingBean.setResolutionLevel(int resolutionLevel) |
void |
SearchBean.setReturnUnloaded(boolean returnUnloaded) |
void |
RenderingBean.setRGBA(int w,
int red,
int green,
int blue,
int alpha)
Implemented as specified by the
RenderingEngine interface. |
void |
RawPixelsBean.setRow(byte[] arg0,
int arg1,
int arg2,
int arg3,
int arg4) |
void |
RawPixelsBean.setStack(byte[] arg0,
int arg1,
int arg2,
int arg3) |
java.lang.String |
JobBean.setStatus(java.lang.String status) |
java.lang.String |
JobBean.setStatusAndMessage(java.lang.String status,
java.lang.String message) |
void |
RawPixelsBean.setTile(byte[] data,
int z,
int c,
int t,
int x,
int y,
int w,
int h) |
void |
RawPixelsBean.setTimepoint(byte[] arg0,
int arg1) |
void |
SearchBean.setUseProjections(boolean useProjections) |
long |
RawFileBean.size() |
long |
JobBean.submit(Job newJob) |
boolean |
ThumbnailBean.thumbnailExists(java.lang.Integer sizeX,
java.lang.Integer sizeY) |
boolean |
RawFileBean.truncate(long length) |
void |
SearchBean.unordered() |
void |
RenderingBean.updateCodomainMap(CodomainMapContext mapCtx)
Deprecated.
|
void |
RenderingBean.updateSettings(RenderingDef settings)
Implemented as specified by the
RenderingEngine interface. |
void |
RawFileBean.write(byte[] buf,
long position,
int length) |
| Modifier and Type | Method and Description |
|---|---|
java.util.List<IObject> |
DeleteBean.checkImageDelete(long id,
boolean force) |
void |
DeleteBean.deleteChannels(long imageId) |
void |
DeleteBean.deleteImage(long id,
boolean force) |
void |
DeleteBean.deleteImages(java.util.Set<java.lang.Long> ids,
boolean force) |
void |
DeleteBean.deleteImagesByDataset(long datasetId,
boolean force) |
void |
DeleteBean.deletePlate(long plateId) |
void |
DeleteBean.deleteSettings(long imageId) |
java.util.List<IObject> |
DeleteBean.previewImageDelete(long id,
boolean force)
This uses
DeleteBean.IMAGE_QUERY to load all the subordinate metadata of the
Image which will be deleted. |
| Modifier and Type | Method and Description |
|---|---|
long |
ProjectionBean.projectPixels(long pixelsId,
PixelsType pixelsType,
int algorithm,
int tStart,
int tEnd,
java.util.List<java.lang.Integer> channels,
int stepping,
int zStart,
int zEnd,
java.lang.String name) |
byte[] |
ProjectionBean.projectStack(long pixelsId,
PixelsType pixelsType,
int algorithm,
int timepoint,
int channelIndex,
int stepping,
int start,
int end) |
| Modifier and Type | Method and Description |
|---|---|
int |
SessionBean.closeSession(Session session) |
Session |
SessionBean.createSession(Principal principal,
java.lang.String credentials) |
Session |
SessionBean.createSessionWithTimeout(Principal principal,
long milliseconds) |
Session |
SessionBean.createSessionWithTimeouts(Principal principal,
long timeToLiveMilliseconds,
long timeToIdleMilliseconds) |
Session |
SessionBean.createUserSession(long timeToLiveMs,
long timeToIdleMs,
java.lang.String defaultGroup) |
java.lang.Object |
SessionBean.getInput(java.lang.String session,
java.lang.String key) |
java.util.Set<java.lang.String> |
SessionBean.getInputKeys(java.lang.String session) |
java.util.Map<java.lang.String,java.lang.Object> |
SessionBean.getInputs(java.lang.String session) |
java.util.List<Session> |
SessionBean.getMyOpenAgentSessions(java.lang.String agent) |
java.util.List<Session> |
SessionBean.getMyOpenClientSessions() |
java.util.List<Session> |
SessionBean.getMyOpenSessions() |
java.lang.Object |
SessionBean.getOutput(java.lang.String session,
java.lang.String key) |
java.util.Set<java.lang.String> |
SessionBean.getOutputKeys(java.lang.String session) |
java.util.Map<java.lang.String,java.lang.Object> |
SessionBean.getOutputs(java.lang.String session) |
int |
SessionBean.getReferenceCount(java.lang.String sessionUuid) |
Session |
SessionBean.getSession(java.lang.String sessionUuid) |
void |
SessionBean.setInput(java.lang.String session,
java.lang.String key,
java.lang.Object object) |
void |
SessionBean.setOutput(java.lang.String session,
java.lang.String key,
java.lang.Object object) |
Session |
SessionBean.updateSession(Session session) |
| Modifier and Type | Method and Description |
|---|---|
void |
ShareBean.activate(long shareId) |
CommentAnnotation |
ShareBean.addComment(long shareId,
java.lang.String commentText) |
void |
ShareBean.addGuest(long shareId,
java.lang.String emailAddress) |
void |
ShareBean.addGuests(long shareId,
java.lang.String... emailAddresses) |
<T extends IObject> |
ShareBean.addObject(long shareId,
T object) |
<T extends IObject> |
ShareBean.addObjects(long shareId,
T... objects) |
CommentAnnotation |
ShareBean.addReply(long shareId,
java.lang.String comment,
CommentAnnotation replyTo) |
void |
ShareBean.addUser(long shareId,
Experimenter exp) |
void |
ShareBean.addUsers(long shareId,
Experimenter... exps) |
void |
ShareBean.closeShare(long shareId) |
<T extends IObject> |
ShareBean.createShare(java.lang.String description,
java.sql.Timestamp expiration,
java.util.List<T> items,
java.util.List<Experimenter> exps,
java.util.List<java.lang.String> guests,
boolean enabled) |
void |
ShareBean.deactivate() |
void |
ShareBean.deleteComment(Annotation comment) |
java.util.Map<java.lang.String,Experimenter> |
ShareBean.getActiveConnections(long shareId) |
java.util.Set<java.lang.String> |
ShareBean.getAllGuests(long shareId) |
java.util.Set<Experimenter> |
ShareBean.getAllMembers(long shareId) |
java.util.Set<java.lang.String> |
ShareBean.getAllUsers(long shareId) |
java.util.Map<java.lang.Long,java.lang.Long> |
ShareBean.getCommentCount(java.util.Set<java.lang.Long> ids) |
java.util.List<Annotation> |
ShareBean.getComments(long shareId) |
<T extends IObject> |
ShareBean.getContentMap(long shareId) |
<T extends IObject> |
ShareBean.getContents(long shareId) |
int |
ShareBean.getContentSize(long shareId) |
<T extends IObject> |
ShareBean.getContentSubList(long shareId,
int start,
int finish) |
java.util.List<Event> |
ShareBean.getEvents(long shareId,
Experimenter experimenter,
java.sql.Timestamp from,
java.sql.Timestamp to) |
java.util.Map<java.lang.Long,java.lang.Long> |
ShareBean.getMemberCount(java.util.Set<java.lang.Long> shareIds) |
java.util.Set<Session> |
ShareBean.getMemberShares(boolean active) |
java.util.Set<Session> |
ShareBean.getMemberSharesFor(Experimenter user,
boolean active) |
java.util.Set<Session> |
ShareBean.getOwnShares(boolean active) |
java.util.Map<java.lang.String,Experimenter> |
ShareBean.getPastConnections(long shareId) |
Share |
ShareBean.getShare(long sessionId) |
java.util.Set<Session> |
ShareBean.getSharesOwnedBy(Experimenter user,
boolean active) |
void |
ShareBean.invalidateConnection(long shareId,
Experimenter exp) |
void |
ShareBean.notifyMembersOfShare(long shareId,
java.lang.String subject,
java.lang.String message,
boolean html) |
void |
ShareBean.removeGuest(long shareId,
java.lang.String emailAddress) |
void |
ShareBean.removeGuests(long shareId,
java.lang.String... emailAddresses) |
<T extends IObject> |
ShareBean.removeObject(long shareId,
T object) |
<T extends IObject> |
ShareBean.removeObjects(long shareId,
T... objects) |
void |
ShareBean.removeUser(long shareId,
Experimenter exp) |
void |
ShareBean.removeUsers(long shareId,
java.util.List<Experimenter> exps) |
void |
ShareBean.setActive(long shareId,
boolean active) |
void |
ShareBean.setDescription(long shareId,
java.lang.String description) |
void |
ShareBean.setExpiration(long shareId,
java.sql.Timestamp expiration) |
OmeroJava API
Version: 5.4.6-ice35-b87
Copyright © 2018 The University of Dundee & Open Microscopy Environment. All Rights Reserved.