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
.
- 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 aFile
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 anid
and aversion
.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 aname
and, optionally, adescription
.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 theCommonData
class and implements theAnnotatableData
interface.AnnotationData This class holds information about an annotationAnnotationSetData 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 arrayDesignArrayDesignPlateData 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 bioplateBioPlateEventData 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 theSharedData
class and implements theNameableData
andRemovableData
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 thePlatformData
item to help with the Hibernate mapping toPlatformFileTypeData
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 thePluginDefinitionData
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 mimetypesNewsData This class holds information about news items.OwnedData This class extends theBasicData
class and implements theOwnableData
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 theQuotaData
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 theOwnedData
class and implements theShareableData
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.