2.17.2: 2011-06-17

Package net.sf.basedb.core.data

This package contains pure data-holder classes which are mapped to the database using Hibernate.

See:
          Description

Interface Summary
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.
SystemData A system item is an item which has an additional id in the form of string.
 

Class Summary
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.
BioMaterialListData This represents an arbitrary collection of biomaterials.
BioMaterialSourceEventData This class is needed to be able to map the inverse relation MeasuredBioMaterialData.getSourceEvents() and still be able to filter in the used quantity or the source group property.
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.
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.
FileTypeData This class hols information about the different filetyped
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.
HardwareTypeData This class holds information about a hardwaretype.
HelpData This class holds information about an help item.
HybridizationData This class holds information about an hybridization.
ImageData This class holds information about an image produced by scanning a hybridization.
IntegerParameterValueData Integer parameter value.
ItemKeyData This class holds information access privileges for users and groups.
ItemParameterValueData Item parameter value.
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.
LabelData This represents a labeling compund use to label extracts.
LabeledExtractData This represents a labeled extract.
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.
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  
ProtocolTypeData  
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.
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.
SampleData This represents a sample.
ScanData This class holds information about an scan.
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.
SoftwareTypeData This class holds information about a softwaretype.
SpotImagesData This class holds information about the settiings used to generate spot images for a raw bio assay.
StringParameterValueData String parameter value.
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.
UsedQuantity Hibernate will not save entries in the sources map BioMaterialEventData.getSources() where the element is null, so we have to use a composite element instead.
UserClientSettingData  
UserData This class holds information about a user.
UserDefaultSettingData  
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.
 

Package net.sf.basedb.core.data Description

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

This class/package is not part of the Public API
Except for the BatchableData interface and classes implementing it.


2.17.2: 2011-06-17