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.
-
ClassDescriptionAn annotatable item is an item that can be annotated with name/value pairs.This class extends the
CommonData
class and implements theAnnotatableData
interface.This class holds information about an annotationThis class holds information about a set of annotations.This data layer class holds information about annotation type categories.This class holds information about an annotation type.Represents a link from one item to any other item.This class represents the making of a new batch of microarray slides of a particular design.This holds information about a block in an arraydesign.This class holds information about an arrayDesignThis class connects the ArrayDesign with its plates and adding an index to that connection.This class represents a phycsical microarray slide.This is the root superclass of all data classes.This is a tagging interface only.This class holds information about a bioassay.This class holds information about a bioassayset.This class is the root class for biomaterials.This class is used to register events for measured biomaterials.Data class for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay.This class holds information about a bioplateThis class holds information about a bioplate event.Registers a plate as a participant in a bioplate event.Each bioplate event must have a type that defines what happened.This class holds information about a biomaterial plate type.This represents a biosoruce which is the starting point of all biomaterials.This class holds information about a bio well on a bio plate.Boolean parameter value.Represents the changes made in a single transaction.Represents a change (creation/update/deletion) made to a single entity in a transaction.This class holds information about a client.Hold coloring information.This is a convenience class that extends theSharedData
class and implements theNameableData
andRemovableData
interfaces.Tagging interface that we need all componenets to implement so that we are able to export them properly using generic code.This class holds context information to help client applications with storing common settings for tables.This class holds information about a single column in a data cube.This class holds information about a single data cube in a virtual database.This class holds information about an extra value in a data cube.This class holds information about a single filter in a data cube.This class holds information about a single layer in a data cube.This class hols information about individual files attached to items that store data in files instead of in the database.Date parameter value.This class holds information about directories.A diskconsumable item is an item that occupies a lot of diskspace and should be controlled by the quota system.This class holds information about a users and/or groups disk usage.Double parameter value.Holds information about an experiment.This class is inherited by data classes that supports per-server additions of columns to the underlying database table.This represents an extract.This represents the use of extra values that have been calculated for a bioassayset.This represents the definitiona of an extra value type that can be calculated by a plugin.This class holds information about a regular feature.A fileattachable item is an item which can have aFile
attached to it.This class holds information about a file.File entries that are external files can be linked to a file server.This class collects all files used to store data for an item that store data in files instead of in the database.This class hols information about individual files attached to items that store data in files instead of in the database.Items implementing this interface can store data in files instead of in the database.This is a helper class for thePlatformData
item to help with the Hibernate mapping toPlatformFileTypeData
object.Float parameter value.This class holds information about a formula used in the analysis of raw data and bioassay sets.This class holds information about a group.This is a helper component for thePluginDefinitionData
item to store the contexts where a plugin can be used in a client application.This class holds information about a Hardware.This class holds information about an help item.An identifiable item is an item which has anid
and aversion
.Integer parameter value.This class holds information access privileges for users and groups.This represents an arbitrary collection of items.Synchronization options for item lists.Item parameter value.Item subtypes can be used to classify items into sub-categories.This class hols information about which file types can be used together with item subtypes.This class holds information about a job agent.This class holds information about plugin settings for a particular job agent.This class holds information about a job.This abstract class is the base class for the key classes which holds access privileges for users, groups, projects and roles.This class holds information about a kit.Tagging interface that should be implemented by all data classes that we want to log in the change history tables.Getter methods that are annotated with this annotation should not have their old/new values logged in the change history log.Long parameter value.This class defines a mapping coordinate, which is a triplet of plate number, row and column.This class is the root class for measured biomaterials, ie biomaterials for where the quantity is tracked.This class holds information about messages.This class holds information about mimetypesA nameable item is an item that has aname
and, optionally, adescription
.This class holds information about news items.Tagging interface for items that are unlikely to be linked via an AnyToAny link.Getter methods that are annotated with this annotation should not trigger a log entry even if their values have changed.An ownable item is an item which has an owner.This class extends theBasicData
class and implements theOwnableData
interface.The base class for the different types of parameter values.This class holds the password for a user.A permission template with permissions to users, groups and projects.This class holds information about a physical bioassay (eg. a hybridization or similar).This class defines a plate coordinate, which is row and column on a plate.This class holds information about a plate.This class holds information about a plate event.This class holds information about a plate event type.This class holds information about a plate geometry.This class holds information about a plate mapping.This class holds information about a plate type.This class hols information about experimental platforms.This class hols information about which file types are used on which experimental platforms and variants.This class hols information about variants of experimental platforms.This data class is used to configure a plugin.This class represent an installed plugin.This class represent an interface that a plugin can implement.This class holds information about a project.This class holds information access privileges for projects.This class holds context information to help client applications with storing common settings for tables.Getter methods that are annotated with this annotation should can not use Metadata.getPropertyPath to retreive their values.This class holds information quantities.This file holds information about a qouta.This is a helper class for theQuotaData
item to help with the Hibernate mapping between quota and quota type/location/max bytes.This class holds information about different QuotaTypes.This class holds information about a raw bioassay, which is the raw data extracted from a scan.Represents the measurements for single raw data spot.Adds the date an item was registered in the database.A removable item is an item that can be flagged as removed.This class holds information about cloned reporter properties.A template for holding information about reporter properties that are/should be cloned in the dynamic database.This class represents the idea of clone, oligo or some other reporter for a gene.This class holds information about a reporter list.This class holds information about the score of a reporter in a reporter list.This class holds reporter type information.This class holds information about a role.This class holds information access privileges for roles.This class holds the link between experiments and raw bioassays including an annotation set that is representing the experimental factor values.This represents a sample.This class holds information about the current schema version of the database.This class holds information about a session.A shareable item is an item which can be shared to other users, groups or projects.This class extends theOwnedData
class and implements theShareableData
interface.This class holds information about a software.String parameter value.A subtypable item is an item that can have a subtype.A system item is an item which has an additional id in the form of string.This represents a tag that is used to mark an extract so that it can be tracked on physical bioassays.Text parameter value.Date+time parameter value.This class holds information about a transformation.This class holds information units.This class holds information the symbol that are used with units.This class holds information about a user.This class holds information about a verified user device.The key to a plugin configuration parameter.This class holds information about a virtual database in the dynamic part of Base.This class holds information about a well on a plate.