Package net.sf.basedb.core.data

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 get and set methods 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 net.sf.basedb.core.data.UserData and net.sf.basedb.core.User.

Client applications do not get direct access to any of the classes in this package. They must use classes from the bussiness layer package net.sf.basedb.core.

See also

• An overview of the database schema and data layer API
• Coding rules and guidelines for the data layer

This class/package is not part of the Public API

Except for the BatchableData interface and classes implementing it.

Interface Summary

Interface	Description
AnnotatableData	An annotatable item is an item that can be annotated with name/value pairs.
BatchableData	This is a tagging interface only.
ComponentData	Tagging interface that we need all componenets to implement so that we are able to export them properly using generic code.
DiskConsumableData	A diskconsumable item is an item that occupies a lot of diskspace and should be controlled by the quota system.
ExtendableData	This class is inherited by data classes that supports per-server additions of columns to the underlying database table.
FileAttachableData	A fileattachable item is an item which can have a File attached to it.
FileStoreEnabledData	Items implementing this interface can store data in files instead of in the database.
IdentifiableData	An identifiable item is an item which has an id and a version.
LoggableData	Tagging interface that should be implemented by all data classes that we want to log in the change history tables.
NameableData	A nameable item is an item that has a name and, optionally, a description.
OwnableData	An ownable item is an item which has an owner.
RegisteredData	Adds the date an item was registered in the database.
RemovableData	A removable item is an item that can be flagged as removed.
ShareableData	A shareable item is an item which can be shared to other users, groups or projects.
SubtypableData	A subtypable item is an item that can have a subtype.
SystemData	A system item is an item which has an additional id in the form of string.

Class Summary

Class	Description
AnnotatedData	This class extends the CommonData class and implements the AnnotatableData interface.
AnnotationData	This class holds information about an annotation
AnnotationSetData	This class holds information about a set of annotations.
AnnotationTypeCategoryData	This data layer class holds information about annotation type categories.
AnnotationTypeData	This class holds information about an annotation type.
AnyToAnyData	Represents a link from one item to any other item.
ArrayBatchData	This class represents the making of a new batch of microarray slides of a particular design.
ArrayDesignBlockData	This holds information about a block in an arraydesign.
ArrayDesignData	This class holds information about an arrayDesign
ArrayDesignPlateData	This class connects the ArrayDesign with its plates and adding an index to that connection.
ArraySlideData	This class represents a phycsical microarray slide.
BasicData	This is the root superclass of all data classes.
BioAssayData	This class holds information about a bioassay.
BioAssaySetData	This class holds information about a bioassayset.
BioMaterialData	This class is the root class for biomaterials.
BioMaterialEventData	This class is used to register events for measured biomaterials.
BioMaterialEventSourceData	Data class for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay.
BioPlateData	This class holds information about a bioplate
BioPlateEventData	This class holds information about a bioplate event.
BioPlateEventParticipantData	Registers a plate as a participant in a bioplate event.
BioPlateEventTypeData	Each bioplate event must have a type that defines what happened.
BioPlateTypeData	This class holds information about a biomaterial plate type.
BioSourceData	This represents a biosoruce which is the starting point of all biomaterials.
BioWellData	This class holds information about a bio well on a bio plate.
BooleanParameterValueData	Boolean parameter value.
ChangeHistoryData	Represents the changes made in a single transaction.
ChangeHistoryDetailData	Represents a change (creation/update/deletion) made to a single entity in a transaction.
ClientData	This class holds information about a client.
ClientDefaultSettingData
ColoringData	Hold coloring information.
CommonData	This is a convenience class that extends the SharedData class and implements the NameableData and RemovableData interfaces.
ContextData	This class holds context information to help client applications with storing common settings for tables.
ContextIndex
DataCubeColumnData	This class holds information about a single column in a data cube.
DataCubeData	This class holds information about a single data cube in a virtual database.
DataCubeExtraValueData	This class holds information about an extra value in a data cube.
DataCubeFilterData	This class holds information about a single filter in a data cube.
DataCubeLayerData	This class holds information about a single layer in a data cube.
DataFileTypeData	This class hols information about individual files attached to items that store data in files instead of in the database.
DateParameterValueData	Date parameter value.
DerivedBioAssayData
DirectoryData	This class holds information about directories.
DiskUsageData	This class holds information about a users and/or groups disk usage.
DoubleParameterValueData	Double parameter value.
ExperimentData	Holds information about an experiment.
ExtractData	This represents an extract.
ExtraValueData	This represents the use of extra values that have been calculated for a bioassayset.
ExtraValueTypeData	This represents the definitiona of an extra value type that can be calculated by a plugin.
FeatureData	This class holds information about a regular feature.
FileData	This class holds information about a file.
FileServerData	File entries that are external files can be linked to a file server.
FileSetData	This class collects all files used to store data for an item that store data in files instead of in the database.
FileSetMemberData	This class hols information about individual files attached to items that store data in files instead of in the database.
FileTypeIndex	This is a helper class for the PlatformData item to help with the Hibernate mapping to PlatformFileTypeData object.
FloatParameterValueData	Float parameter value.
FormulaData	This class holds information about a formula used in the analysis of raw data and bioassay sets.
GlobalDefaultSettingData
GroupData	This class holds information about a group.
GuiContextData	This is a helper component for the PluginDefinitionData item to store the contexts where a plugin can be used in a client application.
HardwareData	This class holds information about a Hardware.
HelpData	This class holds information about an help item.
IntegerParameterValueData	Integer parameter value.
ItemKeyData	This class holds information access privileges for users and groups.
ItemListData	This represents an arbitrary collection of items.
ItemListSyncFilterData	Synchronization options for item lists.
ItemParameterValueData	Item parameter value.
ItemSubtypeData	Item subtypes can be used to classify items into sub-categories.
ItemSubtypeFileTypeData	This class hols information about which file types can be used together with item subtypes.
JobAgentData	This class holds information about a job agent.
JobAgentSettingsData	This class holds information about plugin settings for a particular job agent.
JobData	This class holds information about a job.
KeyData	This abstract class is the base class for the key classes which holds access privileges for users, groups, projects and roles.
KitData	This class holds information about a kit.
LongParameterValueData	Long parameter value.
MappingCoordinate	This class defines a mapping coordinate, which is a triplet of plate number, row and column.
MeasuredBioMaterialData	This class is the root class for measured biomaterials, ie biomaterials for where the quantity is tracked.
MessageData	This class holds information about messages.
MimeTypeData	This class holds information about mimetypes
NewsData	This class holds information about news items.
OwnedData	This class extends the BasicData class and implements the OwnableData interface.
ParameterValueData<T>	The base class for the different types of parameter values.
PasswordData	This class holds the password for a user.
PermissionTemplateData	A permission template with permissions to users, groups and projects.
PhysicalBioAssayData	This class holds information about a physical bioassay (eg. a hybridization or similar).
PlateCoordinate	This class defines a plate coordinate, which is row and column on a plate.
PlateData	This class holds information about a plate.
PlateEventData	This class holds information about a plate event.
PlateEventTypeData	This class holds information about a plate event type.
PlateGeometryData	This class holds information about a plate geometry.
PlateMappingData	This class holds information about a plate mapping.
PlateTypeData	This class holds information about a plate type.
PlatformData	This class hols information about experimental platforms.
PlatformFileTypeData	This class hols information about which file types are used on which experimental platforms and variants.
PlatformVariantData	This class hols information about variants of experimental platforms.
PluginConfigurationData	This data class is used to configure a plugin.
PluginDefinitionData	This class represent an installed plugin.
PluginPermission
PluginTypeData	This class represent an interface that a plugin can implement.
ProjectData	This class holds information about a project.
ProjectKeyData	This class holds information access privileges for projects.
PropertyFilterData	This class holds context information to help client applications with storing common settings for tables.
ProtocolData
QuantityData	This class holds information quantities.
QuotaData	This file holds information about a qouta.
QuotaIndex	This is a helper class for the QuotaData item to help with the Hibernate mapping between quota and quota type/location/max bytes.
QuotaTypeData	This class holds information about different QuotaTypes.
RawBioAssayData	This class holds information about a raw bioassay, which is the raw data extracted from a scan.
RawData	Represents the measurements for single raw data spot.
ReporterClonePropertyData	This class holds information about cloned reporter properties.
ReporterCloneTemplateData	A template for holding information about reporter properties that are/should be cloned in the dynamic database.
ReporterData	This class represents the idea of clone, oligo or some other reporter for a gene.
ReporterListData	This class holds information about a reporter list.
ReporterListScoreData	This class holds information about the score of a reporter in a reporter list.
ReporterTypeData	This class holds reporter type information.
RoleData	This class holds information about a role.
RoleKeyData	This class holds information access privileges for roles.
RootRawBioAssayData	This class holds the link between experiments and raw bioassays including an annotation set that is representing the experimental factor values.
SampleData	This represents a sample.
SchemaVersionData	This class holds information about the current schema version of the database.
SessionData	This class holds information about a session.
SettingData
SharedData	This class extends the OwnedData class and implements the ShareableData interface.
SoftwareData	This class holds information about a software.
StringParameterValueData	String parameter value.
TagData	This represents a tag that is used to mark an extract so that it can be tracked on physical bioassays.
TextParameterValueData	Text parameter value.
TimestampParameterValueData	Date+time parameter value.
TransformationData	This class holds information about a transformation.
UnitData	This class holds information units.
UnitSymbolData	This class holds information the symbol that are used with units.
UserClientSettingData
UserData	This class holds information about a user.
UserDefaultSettingData
UserDeviceData	This class holds information about a verified user device.
VersionedParameter	The key to a plugin configuration parameter.
VirtualDbData	This class holds information about a virtual database in the dynamic part of Base.
WellData	This class holds information about a well on a plate.

Annotation Types Summary

Annotation Type	Description
LoggableWithoutValues	Getter methods that are annotated with this annotation should not have their old/new values logged in the change history log.
NotLoggable	Getter methods that are annotated with this annotation should not trigger a log entry even if their values have changed.
PropertyPathProtected	Getter methods that are annotated with this annotation should can not use Metadata.getPropertyPath to retreive their values.