This package contains pure data-holder classes which are mapped
to the database using Hibernate. In general, they are not much more
than structs with
to access the data.
The code in this package does not include any business logic, data validation,
error handling, database queries or Hibernate dependant code. It is the repsonsibility
of the business layer (the
net.sf.basedb.core package) to perform those tasks.
For each class in this package, there usually is a corresponding class
in the business layer, for example
Client applications do not get direct access to any of the classes
in this package. They must use classes from the bussiness layer package
- This class/package is not part of the Public API
- Except for the
BatchableDatainterface and classes implementing it.
Interface Summary Interface Description AnnotatableDataAn annotatable item is an item that can be annotated with name/value pairs. BatchableDataThis is a tagging interface only. ComponentDataTagging interface that we need all componenets to implement so that we are able to export them properly using generic code. DiskConsumableDataA diskconsumable item is an item that occupies a lot of diskspace and should be controlled by the quota system. ExtendableDataThis class is inherited by data classes that supports per-server additions of columns to the underlying database table. FileAttachableDataA fileattachable item is an item which can have a
Fileattached to it.
FileStoreEnabledDataItems implementing this interface can store data in files instead of in the database. IdentifiableDataAn identifiable item is an item which has an
LoggableDataTagging interface that should be implemented by all data classes that we want to log in the change history tables. NameableDataA nameable item is an item that has a
nameand, optionally, a
OwnableDataAn ownable item is an item which has an owner. RegisteredDataAdds the date an item was registered in the database. RemovableDataA removable item is an item that can be flagged as removed. ShareableDataA shareable item is an item which can be shared to other users, groups or projects. SubtypableDataA subtypable item is an item that can have a subtype. SystemDataA system item is an item which has an additional id in the form of string.
Class Summary Class Description AnnotatedData AnnotationDataThis class holds information about an annotation AnnotationSetDataThis class holds information about a set of annotations. AnnotationTypeCategoryDataThis data layer class holds information about annotation type categories. AnnotationTypeDataThis class holds information about an annotation type. AnyToAnyDataRepresents a link from one item to any other item. ArrayBatchDataThis class represents the making of a new batch of microarray slides of a particular design. ArrayDesignBlockDataThis holds information about a block in an arraydesign. ArrayDesignDataThis class holds information about an arrayDesign ArrayDesignPlateDataThis class connects the ArrayDesign with its plates and adding an index to that connection. ArraySlideDataThis class represents a phycsical microarray slide. BasicDataThis is the root superclass of all data classes. BioAssayDataThis class holds information about a bioassay. BioAssaySetDataThis class holds information about a bioassayset. BioMaterialDataThis class is the root class for biomaterials. BioMaterialEventDataThis class is used to register events for measured biomaterials. BioMaterialEventSourceDataData class for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay. BioPlateDataThis class holds information about a bioplate BioPlateEventDataThis class holds information about a bioplate event. BioPlateEventParticipantDataRegisters a plate as a participant in a bioplate event. BioPlateEventTypeDataEach bioplate event must have a type that defines what happened. BioPlateTypeDataThis class holds information about a biomaterial plate type. BioSourceDataThis represents a biosoruce which is the starting point of all biomaterials. BioWellDataThis class holds information about a bio well on a bio plate. BooleanParameterValueDataBoolean parameter value. ChangeHistoryDataRepresents the changes made in a single transaction. ChangeHistoryDetailDataRepresents a change (creation/update/deletion) made to a single entity in a transaction. ClientDataThis class holds information about a client. ClientDefaultSettingData ColoringDataHold coloring information. CommonData ContextDataThis class holds context information to help client applications with storing common settings for tables. ContextIndex DataCubeColumnDataThis class holds information about a single column in a data cube. DataCubeDataThis class holds information about a single data cube in a virtual database. DataCubeExtraValueDataThis class holds information about an extra value in a data cube. DataCubeFilterDataThis class holds information about a single filter in a data cube. DataCubeLayerDataThis class holds information about a single layer in a data cube. DataFileTypeDataThis class hols information about individual files attached to items that store data in files instead of in the database. DateParameterValueDataDate parameter value. DerivedBioAssayData DirectoryDataThis class holds information about directories. DiskUsageDataThis class holds information about a users and/or groups disk usage. DoubleParameterValueDataDouble parameter value. ExperimentDataHolds information about an experiment. ExtractDataThis represents an extract. ExtraValueDataThis represents the use of extra values that have been calculated for a bioassayset. ExtraValueTypeDataThis represents the definitiona of an extra value type that can be calculated by a plugin. FeatureDataThis class holds information about a regular feature. FileDataThis class holds information about a file. FileServerDataFile entries that are external files can be linked to a file server. FileSetDataThis class collects all files used to store data for an item that store data in files instead of in the database. FileSetMemberDataThis class hols information about individual files attached to items that store data in files instead of in the database. FileTypeIndex FloatParameterValueDataFloat parameter value. FormulaDataThis class holds information about a formula used in the analysis of raw data and bioassay sets. GlobalDefaultSettingData GroupDataThis class holds information about a group. GuiContextDataThis is a helper component for the
PluginDefinitionDataitem to store the contexts where a plugin can be used in a client application.
HardwareDataThis class holds information about a Hardware. HelpDataThis class holds information about an help item. IntegerParameterValueDataInteger parameter value. ItemKeyDataThis class holds information access privileges for users and groups. ItemListDataThis represents an arbitrary collection of items. ItemListSyncFilterDataSynchronization options for item lists. ItemParameterValueDataItem parameter value. ItemSubtypeDataItem subtypes can be used to classify items into sub-categories. ItemSubtypeFileTypeDataThis class hols information about which file types can be used together with item subtypes. JobAgentDataThis class holds information about a job agent. JobAgentSettingsDataThis class holds information about plugin settings for a particular job agent. JobDataThis class holds information about a job. KeyDataThis abstract class is the base class for the key classes which holds access privileges for users, groups, projects and roles. KitDataThis class holds information about a kit. LongParameterValueDataLong parameter value. MappingCoordinateThis class defines a mapping coordinate, which is a triplet of plate number, row and column. MeasuredBioMaterialDataThis class is the root class for measured biomaterials, ie biomaterials for where the quantity is tracked. MessageDataThis class holds information about messages. MimeTypeDataThis class holds information about mimetypes NewsDataThis class holds information about news items. OwnedData ParameterValueData<T>The base class for the different types of parameter values. PasswordDataThis class holds the password for a user. PermissionTemplateDataA permission template with permissions to users, groups and projects. PhysicalBioAssayDataThis class holds information about a physical bioassay (eg. a hybridization or similar). PlateCoordinateThis class defines a plate coordinate, which is row and column on a plate. PlateDataThis class holds information about a plate. PlateEventDataThis class holds information about a plate event. PlateEventTypeDataThis class holds information about a plate event type. PlateGeometryDataThis class holds information about a plate geometry. PlateMappingDataThis class holds information about a plate mapping. PlateTypeDataThis class holds information about a plate type. PlatformDataThis class hols information about experimental platforms. PlatformFileTypeDataThis class hols information about which file types are used on which experimental platforms and variants. PlatformVariantDataThis class hols information about variants of experimental platforms. PluginConfigurationDataThis data class is used to configure a plugin. PluginDefinitionDataThis class represent an installed plugin. PluginPermission PluginTypeDataThis class represent an interface that a plugin can implement. ProjectDataThis class holds information about a project. ProjectKeyDataThis class holds information access privileges for projects. PropertyFilterDataThis class holds context information to help client applications with storing common settings for tables. ProtocolData QuantityDataThis class holds information quantities. QuotaDataThis file holds information about a qouta. QuotaIndexThis is a helper class for the
QuotaDataitem to help with the Hibernate mapping between quota and quota type/location/max bytes.
QuotaTypeDataThis class holds information about different QuotaTypes. RawBioAssayDataThis class holds information about a raw bioassay, which is the raw data extracted from a scan. RawDataRepresents the measurements for single raw data spot. ReporterClonePropertyDataThis class holds information about cloned reporter properties. ReporterCloneTemplateDataA template for holding information about reporter properties that are/should be cloned in the dynamic database. ReporterDataThis class represents the idea of clone, oligo or some other reporter for a gene. ReporterListDataThis class holds information about a reporter list. ReporterListScoreDataThis class holds information about the score of a reporter in a reporter list. ReporterTypeDataThis class holds reporter type information. RoleDataThis class holds information about a role. RoleKeyDataThis class holds information access privileges for roles. RootRawBioAssayDataThis class holds the link between experiments and raw bioassays including an annotation set that is representing the experimental factor values. SampleDataThis represents a sample. SchemaVersionDataThis class holds information about the current schema version of the database. SessionDataThis class holds information about a session. SettingData SharedData SoftwareDataThis class holds information about a software. StringParameterValueDataString parameter value. TagDataThis represents a tag that is used to mark an extract so that it can be tracked on physical bioassays. TextParameterValueDataText parameter value. TimestampParameterValueDataDate+time parameter value. TransformationDataThis class holds information about a transformation. UnitDataThis class holds information units. UnitSymbolDataThis class holds information the symbol that are used with units. UserClientSettingData UserDataThis class holds information about a user. UserDefaultSettingData UserDeviceDataThis class holds information about a verified user device. VersionedParameterThe key to a plugin configuration parameter. VirtualDbDataThis class holds information about a virtual database in the dynamic part of Base. WellDataThis class holds information about a well on a plate.
Annotation Types Summary Annotation Type Description LoggableWithoutValuesGetter methods that are annotated with this annotation should not have their old/new values logged in the change history log. NotLoggableGetter methods that are annotated with this annotation should not trigger a log entry even if their values have changed. PropertyPathProtectedGetter methods that are annotated with this annotation should can not use Metadata.getPropertyPath to retreive their values.