Package net.sf.basedb.core

This package contains the core business logic of BASE.

Interface Summary

Interface	Description
AbsoluteProgressReporter	This is interface is an extension to the ProgressReporter interface.
AccessControlled	This interface should be implemented by a class representing items which requires the logged in user to have permission to access them.
Annotatable	This interface is implemented by all items which can be annotated.
AnnotatableProxy	This interface is implemented by items that can be used to hold annotations that are intended for other items.
Batcher	The basic interface which all batchers must implement.
ClonableReporterQuery	An interface that indicates that a query may be used together with cloned reporter information.
Controlled	This is the base tagging interface for items that needs special attention by the DbControl object when DbControl.commit() is called.
DiskConsumable	This interface is implemented by items that can use a lot of disk space.
FileAttachable	A FileAttachable item is an item that can have a File attached to it.
FileStoreEnabled	This interface is implemented by items that can use files instead of the database for storing data.
Identifiable	An Identifiable item is an item which has an id a type and a version.
Listable	Tagging interface for items that can be put in an ItemList.
Metadata.PropertyPath<C,V>	Contract for getting the value of a specific property for an item.
Nameable	A Nameable item is an item that has a name and description.
Ownable	An Ownable item is an item which has a User as its owner.
ProgressReporter	Certain methods in BASE can report their progress back to the calling client application if they are giving an object that implements this interface.
QueryExecutor.Cancelable	Interface to be implemented by classes that knows how to cancel a query.
QueryRuntimeFilter	Represents a filter that is applied to a query just before it is executed in order to limit the result.
Registered	Items that implements this interface has their registration date stored in the database.
Removable	A Removable item is an item that can be flagged as removed.
Shareable	An Shareable item is an item which can be shared to other User:s, Group:s and Project:s.
Subtypable	A subtypable item is an item that can have a subtype.
SystemItem	A SystemItem is an item which has an additional systemwide unique id in the form of string.
Transactional	This interface is a tagging interface for items that wants to be notified before a transaction is committed or after it has been completed or rollbacked.
TransactionalAction	Interface that define hooks for callbacks during transaction commit and rollback.
UsableDataFileType	Utility interface for collecting information about data file requirements when used on a certain platform/variant or item subtype.
Validatable	This interface is a tagging interface for items that needs case 2 validation.

Class Summary

Class	Description
AbstractBatcher	This is an abstract class for batchers that are connected to a single DbControl object.
AbstractEntityQuery	An abstract implementation of the EntityQuery interface.
AbstractHqlQuery	An abstract implementation of the HqlQuery interface.
AbstractQuery	An abstract implementation of the Query interface.
AbstractResultList<I>	This is a list of the result from a query.
AbstractSqlQuery	An abstract implementation of the SqlQuery interface.
AnnotatedItem	This is a helper class for items that need to implement the Annotatable interface.
Annotation	This class represents an annotation.
Annotation.QueryRuntimeFilterImpl
AnnotationBatcher	Batcher implementation for adding, updating and removing multiple annotations to a large number of items in a single transaction while keeping the memory usage as low as possible.
AnnotationBatcher.CurrentAnnotationInfo	Holds information about an annotation for the current item.
AnnotationBatcher.InsertBatcher	Batcher implementation for inserting into tables.
AnnotationBatcher.UpdateBatcher	Batcher implementation for updating and deleting from tables.
AnnotationBetweenRestriction	Restricts a query using annotation values between a low and high value.
AnnotationInRestriction	Restricts a query using annotation values that exists in a set of given values.
AnnotationRestriction	Base class for creating restrictions based on annotations.
AnnotationRestriction.Options	Options that specify which annotations to consider when searching.
AnnotationSet	An annotation set is the container for all annotations on an item.
AnnotationSet.ProjectSpecificAnnotationsRestriction	Restriction for matching project-specific annotations against the currently active project.
AnnotationSet.QueryRuntimeFilterImpl
AnnotationSimpleRestriction	Restricts a query using annotation values with a simple expression: annotation operator value.
AnnotationType	Objects of this class defines an annotation type.
AnnotationType.RemoveInheritedAnnotationsAction
AnnotationTypeCategory	Objects of this class defines an annotation type category.
AnyToAny	An any-to-any link is a named, directed link from one item to another item.
AnyToAny.FastLinkLoader<S extends BasicItem,T extends BasicItem>	Helper class for faster loading of any-to-any links between items.
Application	This class represents the BASE application and is the starting point for all client applications.
Application.DbCleaner
Application.Pinger	A Pinger is an object that is used to protect another object from timing out by automatically pinging it.
Application.SessionControlCacheCleaner
Application.StartupOptions	Startup optins when starting the BASE application.
ArrayBatch	This class represents the making of a new batch of microarray slides of a particular design.
ArrayDesign	An array design is a description of the design of a microarray slide.
ArrayDesignBlock
ArrayDesignPlate
ArraySlide	This class represents a physical microarray slide.
AuthenticationContext	Gives authentication implementations limited access to the database.
BasicBatcher<D extends BatchableData>	This is an abstract class for batching functionallity.
BasicChildItem	An abstract base class for all items which are child items to a BasicItem parent item.
BasicItem	This is the root superclass of all item classes.
BatchedPropertyInfo	Holds information about a batchable property.
BatchUtil	Utility class for batching information.
BioAssay	Represents the current intensities of raw data after some transformation has been applied to it.
BioAssaySet	A bioassayset represents the current intensities of the raw data after some Transformation has been applied to it.
BioMaterial	This is the base class for for the three types of biomaterials: BioSource, Sample and Extract.
BioMaterialEvent	This class represents an event in the life of a MeasuredBioMaterial.
BioMaterialEventSource	Class for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay.
BioMaterialEventSource.BioMaterialEventSourceTransformer
BioPlate	This class is represents physical bio-plates.
BioPlateEvent	A bioplate event represents something that happened simultaneously to the biomaterial on one or more bioplates.
BioPlateEventParticipant	Holds information about a bioplate that is participating in a bioplate event.
BioPlateEventType	The type of a bioplate event defines what happened in the event.
BioPlateType	This class represents the type of a bio-plate.
BioSource	This class represent biosource items.
BioWell	A biowell is located on a BioPlate and contains a MeasuredBioMaterial.
BlockInfo	A BlockInfo object is used to represent the uniqe identifiers of an ArrayDesignBlock.
BooleanParameterType	This class represent a parameter type that is a boolean.
ChangeHistory
ChangeHistory.TransactionInfo	Holds information about a single transaction.
ChildItem	An abstract base class for all items which are child items to a Shareable parent item.
Client	This class represents a registered client application.
ClientDefaultSetting	This class is used to represent a setting for specific client application.
ClonableProperty	Represents a reporter property that can be cloned to a per-experiment table in the dynamic database.
Coloring	This class keeps coloring information for items which can be colored when values are displayed in a client application.
CommonItem
Config	Use this class to access the configuration settings for BASE.
ContextKey
DataCube	A data cube is the main unit for an experiment to store analysed data.
DataCube.RawMappingQuery	Select data from Dynamic#RawParents table.
DataCubeColumn	Represents the column coordinate in a data cube.
DataCubeExtraValue	Represents a set of extra value in a data cube.
DataCubeFilter	This represents a filter in a datacube.
DataCubeLayer	This represents the layer coordinate in a data cube.
DataFileType	This class is used to represent types of files that are used to hold data instead of importing the data into into the database.
DataQuery<I extends BasicData>	An implementation of the Query interface that returns data objects.
DataResultIterator<I extends BasicData>	Return the results of a DataQuery as an iterator.
DateParameterType	This class represent a parameter type that is a date.
DateUtil	Utility methods that will make it easier to handle date values.
DbControl	A DbControl object is the main object used for communicating with the database.
DbControl.SaveIf
DbControl.State	Main purpose is to write a warning to the log file in case some user code that created a DbControl instance never called the close() method before the DbControl became uncreachable.
DerivedBioAssay
DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction	Whenever we modify the parent items to a derived bioassay, we must make sure that the physical bioassays for all child items are synchronized with the same changes.
Directory	This is used to represent directory items.
DiskUsage	This class is used to represent the disk usage of DiskConsumable items.
DiskUsageStatistics	Get disk usage statistics for the BASE server.
DoubleParameterType	This class represent a parameter type that is a double.
DropDynamicTableAction	Transactional action that can drop a table from the dynamic database after a successful commit and/or rollback.
DynamicExtraValueQuery	Represents a query for extra values in the dynamic database.
DynamicJoin	Represents a join between two virtual tables in a dynamic query: leftTable JOIN rightTable ON columns.
DynamicPositionQuery	Represents a query for position information against the dynamic database.
DynamicPositionQueryJoiners	This class collects AutoJoiner:s for DynamicPositionQuery queries.
DynamicPositionQueryJoiners.ExtraValueJoiner	Joiner for extra values.
DynamicPositionQueryJoiners.ReporterJoiner	Joiner for reporters
DynamicPositionQueryJoiners.ReporterListJoiner	Auto joiner for reporter lists.
DynamicQuery	Represents a query against the dynamic database.
DynamicRawDataQuery	Represents a query for raw data in a "dynamic" way.
DynamicRawDataQuery.RawBioAssayJoiner	Auto joiner for raw bioassays.
DynamicRawDataQuery.ReporterJoiner	Auto joiner for reporters.
DynamicRawDataQuery.ReporterListJoiner	Auto joiner for reporter lists.
DynamicReporterQuery	Represents a query for reporter data in a "dynamic" way.
DynamicReporterQuery.MasterReporterJoiner	Auto joiner for master reporter table.
DynamicReporterQuery.ReporterListJoiner	Auto joiner for reporter lists.
DynamicRestriction	Creates a restriction that compares a dynamic column with a constant value: tableAlias.column = value or queryRootAlias.column = value
DynamicResultIterator	An iterator view of the result of an AbstractSqlQuery.
DynamicSpotQuery	Represents a query for spot information in the dynamic database.
DynamicSpotQueryJoiners	This class collects AutoJoiner:s for DynamicSpotQuery queries.
DynamicSpotQueryJoiners.ExtraValueJoiner	Joiner for extra values.
DynamicSpotQueryJoiners.RawDataJoiner	Joiner for raw data.
DynamicSpotQueryJoiners.ReporterJoiner	Joiner for reporters
DynamicSpotQueryJoiners.ReporterListJoiner	Joiner for reporter lists.
Experiment	An experiment is the starting point of the analysis in BASE.
ExtendedProperties	This class is used for reading XML files with information about extended properties.
ExtendedProperty	Holds information about an extended property for a class.
ExtendedPropertyAccessor	This class is used to interface with Hibernate for extended properties.
ExtendedPropertyAccessor.GetterSetter	This class implements the Hibernate Getter and Setter interfaces.
ExtendedPropertyLinker	Used to create links from extended property values.
Extract	This class is used to represent extract items.
ExtraValue	Represents extra values attached to a BioAssaySet.
ExtraValueExpression	Represents the value of an extra value in a dynamic query: alias.value.
ExtraValueJoin	Represents a join to an extra value in a dynamic query: leftTable JOIN extraValueTable ON ...
ExtraValueType	Defines extra values that can be calculated by plugins or some other application and inserted as part of a BioAssaySet.
FastAnnotationLoader<T>	Implements an API for simple and fast loading of annotation values optimized for situations when a single annotation is needed for many (=thousands) of items.
FastAnnotationLoader.FastAnnotation<T>	Holds information about a single annotation value.
FastAnnotationLoader.FastIterator<T>	Iterator implementation that splits the query into multiple calls depending on the max number of parameters that can be used in a query.
Feature	This is a utility class for Features.
FeatureBatcher	Batcher class for Features or AffyFeatures.
FeatureCoordinate	Represents the coordinate of a feature on an array design.
File	This class is used to represent individual file items and information about them.
FileParameterType	This class represent a parameter type that is a file.
FileServer	This class represents a file server that is used to store external files.
FileSet	A file set is the container for files that have been attach to an item to hold data instead of importing it to the database.
FileSet.QueryRuntimeFilterImpl
FileSetMember	This class represents a file that is member of a file set.
FileSetMember.QueryRuntimeFilterImpl
FileStoreUtil	Utility class working with FileStoreEnabled items.
FilterBatcher	Batcher class for filtered bioassaysets.
FloatParameterType	This class represent a parameter type that is a float.
Formula	This class represents a formula.
GlobalDefaultSetting	This class is used to represent a global default setting.
Group	This class is used to represent groups.
Group.QueryRuntimeFilterImpl	A runtime filter implementation that limits a query to only return groups where the logged in user is a member unless the logged in user has generic read permission.
GroupPermissions	This class is used to specify permissions to share an item to groups.
Hardware	This class is used to represent individual hardware items and information about them.
HasAnnotationRestriction	Restricts a query by the presence of absence of an annotation.
Help	This class is used to represent a help text for a client application.
HibernateUtil	This class collects most of the functionality we need for using Hibernate.
HibernateUtil.DelayedFilterDef
HibernateUtil.FilterConfigurator	Helper class for defining filters at runtime.
HqlQueryJoiners	This class collects AutoJoiner:s for HqlQuery queries.
HqlQueryJoiners.AnnotationJoiner	Joiner for annotations.
HqlQueryJoiners.ReporterListJoiner	Joiner for reporter lists.
Install	This class contains static methods used to install items into an empty database.
Install.ItemSubtypeFT
Install.PlatformFT
IntegerParameterType	This class represent a parameter type that is an integer.
IntegerUtil	Utility methods that will make it easier to implement data validation for integer attributes.
IntensityFormula	Holds information about the formulas used to calculate intensities from a raw data spot.
InternalJobQueue	A simple implementation of a job queue that executes jobs in order of priority and longest waiting time.
InternalJobQueue.JobQueueKeyring	Our own keyring containing the permissions we need to execute the jobs.
Item.DefinedPermissions	Helper class to make it easier to set up the defined permissions.
ItemContext	This item is a helper class for client applications when they need to store information about the current context for plugins that needs to find out the current context of the running client application.
ItemContext.PropertyFilterPair	Holds a pair of filter.
ItemContext.QueryRestrictions
ItemContext.RowRestrictions
ItemKey	This class is used to get information about which users and groups a Shareable item has been shared to.
ItemList	This class represents a list of items.
ItemList.DelayedAdditionManager	Handles items that should be added as members to the list, but since they were created in the same transaction doesn't have any ID until later in the commit phase.
ItemParameterType<T extends BasicItem>	This class represent a parameter type that is an object derived from BasicData.
ItemProxy
ItemQuery<I extends BasicItem>	An implementation of the Query interface that returns item objects.
ItemResultIterator<I extends BasicItem>	Return the results of an ItemQuery as an iterator.
ItemResultList<I extends BasicItem>	Return the results of an ItemQuery as a list.
ItemSubtype	Item subtypes can be used to classify items into sub-categories.
ItemSubtypeFileType	This class represents a specific DataFileType that is associated with an item subtype.
Job	This class represents the execution of a job.
Job.ProgressReporterImpl	Implements the ProgressReporter interface and stores the percentage completed for the current job.
Job.SignalKeyring	Our own keyring containing the permissions signal handlers may need to update job status, eq.
JobAgent	This class represents a job agent, which is a program running in another virtual machine on the same or a different server.
JobAgentSettings	This class contains a job agent's settings for a specific plugin.
Key	This is the base class for keys.
Keyring	Objects of this class holds information about a user's access permissions, group and role membership.
Kit	This class is used to represent a kit of reagents and other stuff used in the lab process.
LogControl	Gives information about the current transaction and gives log implementations limited access to the database.
LogUtil	Utility class for LOG4J logging.
LongParameterType	This class represent a parameter type that is a long.
MappingBatcher	Batcher class for inserting parent mapping information in the dynamic database.
MeanRawDataPropertyExpression	An expression representing the mean value of property of a raw data spot.
MeasuredBioMaterial	This class is the base class for measured biomaterial items.
MeasuredBioMaterial.RemainingQuantityAction	Transaction handler for updating the remaining quantity of a biomaterial based on the sum of the used quantity in this transaction.
Message	This class represents a message.
Message.QueryRuntimeFilterImpl	A runtime filter implementation that limits a query to only return messages for the currently logged in user unless the logged in user has generic read permission.
Metadata<C>	Utility methods for retreiving metadata about items.
Metadata.BasicData2ItemPropertyPath<C extends BasicData,V extends BasicItem>	Property path implementation that converts a BasicData object to a BasicItem.
Metadata.BasicItem2DataPropertyPath<C extends BasicItem,V extends BasicData>	Property path implementation that converts a BasicItem to a BasicData object.
Metadata.CollectionPropertyPath<C>	Property path implementation which wraps a collection inside an unmodifiable collection.
Metadata.CombinedPropertyPath<C,V>	Property path implementation that combines a list of property paths to create a long chain.
Metadata.ComponentPropertyPath<C,V>	Property path implementation which gets a value from a component.
Metadata.DateCopyPropertyPath	Property path implementation clones a Date.
Metadata.EntityPropertyPath<C,V>	Property path implementation which gets a value from an entity.
Metadata.EvictPropertyPath<C>	Property path implementation that evicts the selected item from the Hibernate first-level cache.
Metadata.IdentifierPropertyPath	Property path implementation which gets the id from an entity.
Metadata.MapPropertyPath	Property path implementation which wraps a map inside an unmodifiable map.
Metadata.NoopPropertyPath<C>	Property path implementation that does nothing.
Metadata.ReporterScore2DataPropertyPath	Property path implementation that converts a ReporterScore to a ReporterListScoreData object.
Migration	Class for migrating a database to PostgreSQL.
MimeType	This class is used to represent mime types.
MultiPermissions	This is a helper class that is very useful when you have a collection of Shareable items and want to modify some permissions on all of them without affecting the rest of the permissions.
NameableUtil	Utility methods that will make it easier to implement the Nameable interface, including data validation.
News	This class represents news items.
News.QueryRuntimeFilterImpl
OwnableUtil	Utility methods that will make it easier to implement the Ownable interface, including data validation.
OwnedItem	This class inherits from the BasicItem class and implements the Ownable interface.
ParameterInfo	Get information about a plugin configuration or parameter.
ParameterType<T>	This is the base class for all parameter types.
ParameterValuesImpl	An implementation of the ParameterValues interface that lets a plugin write the job's configuration.
PasswordParameterType	This class represent a parameter type that is a password (or any other type of masked string).
Path	This class is used represent the path to a Directory or File item.
PathParameterType	This class represent a parameter type that is a path to either a directory or a file.
PermissionTemplate	A permission template with permissions to users, groups and projects.
PhysicalBioAssay	A physical bioassay is a representation of the process of performing an experiment one or more Extract:s.
Plate	This class is represents physical plates.
PlateEvent	This class represents an event in the life of a Plate.
PlateEventType	This class is used together with the PlateType class to define event types for plates.
PlateGeometry	This class defines a plate geometry, which is the number of rows and columns of wells on a Plate.
PlateMapping	This class represents a mapping from one plate geometry to another.
PlateType	This class represents plate types, which is a name, description, geometry and a list of event types.
Platform	This class is used to represent an experimental platform in BASE.
PlatformFileType	This class represents a specific DataFileType that is part of a platform.
PlatformVariant	Represents variants of a Platform.
PluginConfiguration	This class is used to configure a plugin.
PluginConfigurationRequest	Configures a plugin or job.
PluginDefinition	A plugin definition represents the executable plugin.
PluginExecutionRequest	Executes a job.
PluginParameter<T>	Contains information about a single parameter that the plugin needs for a request.
PluginPermission
PluginRequest<P extends Plugin>	Configures or executes a plugin.
PluginResponse	Get the response from a configuration step or execution of a plugin.
PluginSessionControl	This is a special session control implementation that is used for executing plugins that prevents them from logging in or out.
PluginType
PositionBatcher	Batcher class for per-position data in the dynamic database.
PositionExtraValueBatcher<I>	Batcher class for per-position extra values.
PredefinedQuery	This class is used for reading XML files with information about predefined queries.
Presets	This is a generic class for handling named presets consisting of multiple key/value pairs.
Presets.Preset	Represents a single preset.
Project	This class is used to represent projects.
Project.QueryRuntimeFilterImpl	A runtime filter implementation that limits a query to only return projects where the logged in user is a member or owner unless the logged in user has generic read permission.
ProjectKey	This class is used to get information about which projects a Shareable item has been shared to.
ProjectPermissions	This class is used to specify permissions to share an item to projects.
ProjectSpecificAnnotationsManager	Internal class for keeping the "override_id" column in the "Annotations" table synchronized when annotations are creted and deleted.
ProjectSpecificAnnotationsManager.AnnotationInfo	Holds some information about the annotation that has been created.
PropertyFilter	Used to store filter settings in the current context.
Protocol	This class is used to represent individual protocol items and information about them.
Quantity	This class is used to represent a quantity for specifying units to annotations.
QueryExecutor	Utility class for executing SQL and Hibernate queries.
QueryExecutor.CancelableSession	Cancels the query running in a Hibernate session.
QueryExecutor.CancelableStatelessSession	Cancels a query running in a stateless Hibernate session.
QueryExecutor.CancelableStatement	Cancels a statement by calling Statement.cancel().
QueryExecutor.FutureItem<T>
QueryExecutor.FutureResultSet	A callable implementation the calls PreparedStatement.executeQuery()
QueryExecutor.FutureScrollIterator<T>	Calls Query.scroll(ScrollMode) and returns the result as a ScrollIterator.
QueryExecutor.FutureUpdate	A callable implementation the calls PreparedStatement.executeUpdate()
QueryRuntimeFilterFactory	This is a factory class for QueryRuntimeFilter implementations.
QueryRuntimeFilterFactory.AnnotatableFilter	A required filter for Annotatable items.
QueryRuntimeFilterFactory.BasicFilter	An optional default filter for BasicItem:s that are not Ownable or Shareable.
QueryRuntimeFilterFactory.ChainedFilter	Chains one or more filters into a single filter.
QueryRuntimeFilterFactory.ChildFilter	An optional filter that can be used by BasicItem:s to replace the QueryRuntimeFilterFactory.BasicFilter.
QueryRuntimeFilterFactory.DenyAllFilter	A required filter for all items, which checks if the logged in user has been "granted" the Permission.DENIED permission for a specific item type.
QueryRuntimeFilterFactory.OwnableFilter	An optional default filter for Ownable items that are not Shareable.
QueryRuntimeFilterFactory.RemovableFilter	A required filter for Removable items.
QueryRuntimeFilterFactory.ShareableFilter	An optional default filter for Shareable items.
QueryRuntimeFilterManager	This class manages the enabling/disabling of QueryRuntimeFilter:s.
Quota	This class is used to represent disk quota settings for users and groups.
Quota.QueryRuntimeFilterImpl	A runtime filter implementation that limits a query to only return the quota assigned to the logged in user unless the logged in user has generic read permission.
QuotaType	This class represents the different types a quota can have.
RawBioAssay	A rawbioassay represents the raw data generated from a single DerivedBioAssay.
RawBioAssayPropertyExpression	An expression representing the property of a raw bioassay.
RawDataBatcher	Batcher class for raw data.
RawDataBatcher.FeatureInfo
RawDataBatcher.FeatureProxy
RawDataBatcher.ReporterProxy
RawDataProperty	Holds information about an extended property for raw data.
RawDataPropertyExpression	An expression representing the property of a raw data spot.
RawDataType	This class holds information about a raw data type.
RawDataTypes	This class is used for reading the XML configuration file with information about raw data types.
RawDataTypes.NameComparator	Comparator implementation that sorts raw data types according to their name.
RawDataUtil	Utiltity class for getting and setting non-public properties of raw data objects.
RealJoin	Represents a join from one virtual table in the dynamic database to a table in the regular database or between two tables in the regular database.
RealTable	This class defines constants that are used to specify a table in the regular (non-dynamic) database while doing analysis with dynamic queries.
Reporter	This is an utilitiy class for reporters.
ReporterBatcher	Batcher class for reporters.
ReporterCloneBatcher	Batcher implementation that is used to handle cloned reporter information in the dynamic database.
ReporterCloneTemplate	A reporter clone template is a definition of which reporter properties/annotations that should be cloned to a per-experiment table in the dynamic database.
ReporterList
ReporterListJoin	Represents a join to a reporter list in a dynamic query: leftTable JOIN ReporterListScores ON ...
ReporterPropertyExpression	An expression representing the property of a reporter.
ReporterScore	Get information about the reporters and their score in a reporter list.
ReporterScoreQuery	This is a temporary solution to query against the reporter list's score.
ReporterScoreResultIterator	This is a temporary solution for returning reporter list scores as an iterator.
ReporterType	This class holds reporter type information.
RequestInformation	Get information about the parameters the plugin needs for a particular request.
Role	This class is used to represent roles.
Role.QueryRuntimeFilterImpl	A runtime filter implementation that limits a query to only return roles where the logged in user is a member unless the logged in user has generic read permission.
RoleKey	This class is used to represent a role key.
RootRawBioAssay	Represents the use of a raw bioassay in an experiment.
Sample	This class is used to represent sample items.
ScrollIterator<E>	This is an iterator view of the result from a query using the Hibernate ScrollableResults object.
ServiceSessionControl	A special session control implementation used for services.
ServiceSessionControl.FlushSessionAction	Flushes the given session before the transaction is committed.
ServiceSessionControl.ServicesKeyring	Our own keyring containing the only permission: Permission.ACT_AS_ANOTHER_USER.
ServicesUtil	Utility class for the "services" extension point.
Session	A session represents the time between login and logout for a single user.
Session.QueryRuntimeFilterImpl	A runtime filter implementation that limits a query to only return sessions for the currently logged in user unless the logged in user has generic read permission.
SessionControl	This class handles user sessions.
SessionControl.ClientInfo
SessionControl.LoginInfo	Internal class to hold information about the logged in user.
SessionControl.SettingInfo	Internal class to hold information about a setting
SessionControl.UnverifiedDeviceInfo	Class for storing temporary device information for a user that has been authenticated but before a device has been verified.
Setting	This is the base class for all setting items.
ShareableUtil	Utility methods that will make it easier to implement the Shareable interface, including data validation.
SharedItem	This class inherits from the OwnedItem class and implements the Shareable interface.
SimpleAbsoluteProgressReporter	This is a simple implementation of the AbsoluteProgressReporter interface, which simply remembers that last values.
SimpleProgressReporter	This is a simple implementation of the ProgressReporter interface, which simply remembers that last values.
Software	This class is used to represent individual software items and information about them.
SpecialQuery<C>	A special HQL query implementation that can return almost any kind of object.
SpotBatcher	Batcher class for per-spot intensity values for bioassaysets.
SpotExtraValueBatcher<I>	Batcher class for per-spot extra values.
StringParameterType	This class represent a parameter type that is a string.
StringUtil	Utility methods that will make it easier to implement data validation for string attributes.
SyncFilter	Holds information about a synchronization filter used by an item list.
SystemItems	This class is used to map the system id of all SystemData items to the numerical internal id in the current installation.
Tag	This class represents a tag.
TimestampParameterType	This class represent a parameter type that is a timestamp.
Transformation	A transformation represents an analysis step for an Experiment.
Trashcan	This class contains functionality to manage items that have been marked for deletion.
Trashcan.CircularRefInfo	Helper class for holding information about a single item, other items using it and other information that is relevant for resolving circular references.
Unit	This class is used to represent a specific unit that can be used with annotations.
UnmodifiableResultList<T>
Update	This class contains static methods used to update items already in the database.
Update.DropColumnChange	Action that drops a column in a table.
Update.SchemaChange	Action that need to make some change to the database schem after the main transaction in Update.adjustExistingItems(ProgressReporter, int, String, String) has finished.
User	This class is used to represent a user in BASE.
User.QueryRuntimeFilterImpl	A runtime filter implementation that limits a query to only return users which are members of at least one group where the logged in user is also a member unless the logged in user has generic read permission.
UserClientSetting	This class is used to represent a setting valid for a specific user using a specific client application.
UserDefaultSetting	This class is used to represent a setting valid for a specific user using any client application.
UserDevice	A user device represents a verified device a user may use for accessing BASE.
UserDevice.QueryRuntimeFilterImpl	A runtime filter implementation that limits a query to only return devices for the currently logged in user unless the logged in user has generic read permission.
UserPermissions	This class is used to specify permissions to share an item to users.
Values	Utility class to handle the conversion between data objects and item objects.
Version	Get information about the BASE version.
VirtualColumn	This class is used to define columns in the virtual tables in the dynamic part of the database that are storing analysed data.
VirtualDb	A virtual database represents the set of tables in the dynamic database used by a single experiment to store it's analysed data.
Well	A well is located on a Plate and contains a ReporterData.

Enum Summary

Enum	Description
Annotation.Source	The annotation source.
AnnotationBatcher.Change	A flag indicating what type of change that was made to an annotation as a result of calling AnnotationBatcher.setValues(AnnotationType, List, Unit, boolean)
BioMaterialEvent.Type	The type of the event.
BioWell.LockMode	The lock mode for a well is determined by the plate's bio plate type.
ExtraValue.CoordinateType	Defines which coordinates in the data cube the extra values are attached to.
FeatureIdentificationMethod	This enumeration defines constants that are used to specify which method to use for identifying features on an array design.
Formula.AverageMethod	The average method used for the values of this formula.
Formula.Parser	The parser used to parse the formula.
Formula.Type	The type of formula indicats in which situations it can be used.
Include	This enumeration defines constants that are used to specify which items to include in a query.
IntensityTransform	Gives information in what way spot intensities has been transformed before they were stored in the database.
Item	This class defines constants for various items in BASE.
ItemContext.SortDirection	Enumeration used to specify the sort direction.
ItemList.SynchronizeOption	Options for synchronizing an existing item list with a current settings in an ItemContext.
Job.ExecutionTime	A rough estimate of the execution time of a job.
Job.Status	The status of a job.
Job.Type	The type of job.
Location	This enumeration defines constants that are used to specify different file storage locations.
Operator
Path.Type	An enum that describes what type the path is
Permission	This enumeration defined constants for permissions.
ReporterCloneBatcher.CloneSource	Specifies which source table to use for finding out which reporters that are part of the current experiment.
SyncFilter.SourceItemTransform
Transactional.Action	Enumeration constants used to tell the item what is going on in the core.
Type	This class defines constants for supported value types in BASE.
VirtualTable	This enumeration defines constants that are used to specify different virtual tables in the dynamic part of the database used for analysis.

Exception Summary

Exception	Description
AccountExpiredException	This exception is thrown if you try to log in with an account that has expired.
AlreadyLoggedInException	This exception is thrown if you try to log in but are already logged in.
BaseException	This is the base class for exceptions in BASE.
ConfigurationException	This exception is thrown by the Config class if there is a problem with finding or loading the configuration settings.
ConnectionClosedException	This exception is thrown when trying to use a DbControl object that has been closed.
DatabaseException	Exceptions of this type are thrown when there is an error from the database.
DateFormatException	This exception is thrown when parsing a string into a date failed.
DetachedItemException	This exception is thrown when trying to use an item that has been detached from the DbControl that manages it.
DeviceNotVerifiedException	This exception can be thrown when a user is trying to login from a device that has not been verified.
DisallowedValueException	Exception that is thrown when a value is not found among a set of allowed values, for example, when setting an annotation value.
InvalidAnnotationException
InvalidDataException	Exceptions of this type are thrown when invalid data is encountered.
InvalidPasswordException	Exceptions of this type are thrown when user tries to log in, but the password is incorrect.
InvalidPathException	This exception is thrown when BASE is trying to parse a path which is invalid.
InvalidRelationException	Exceptions of this type are thrown when a ValidationAction has detected that a file related to the main file is invalid.
InvalidUseOfNullException	This exception is thrown when an object field or a parameter that mustn't be null is set to null.
ItemAlreadyExistsException	This exception is thrown when trying to save an object and another object with the same ID already exists.
ItemInUseException	This exception is thrown when trying delete an item that is used (reference to) by some other item or items.
ItemModifiedException	This exception is thrown when trying to save an item to the database that has been updated (or deleted) by another process in the meantime.
ItemNotFoundException	This exception is thrown when trying to load an item from the database that does not exist.
LoginException	Exceptions of this type are thrown when the BASE server uses an external authentication plug-in and it is not clear if the login or password is causing the failure.
NotLoggedInException	This exception is thrown if you try to perform a function that requires a user to be logged in without beeing logged in.
NumberOutOfRangeException	This exception is thrown when an item's field or a parameter that only accepts numeric values within a certain range are passed a value outside that range.
ParameterException	This exception is thrown by classes that uses the parameter system, ParameterType and ParameterValueData.
PermissionDeniedException	This exception is thrown when trying to load or manipulate an item in the database and you don't have the required permission.
QuotaException	This exception is thrown to signal that the user's quota has been exceeded and that an DiskConsumable item cannot be saved.
StringTooLongException	This exception is thrown when an item's field or a parameter which must be shorter than a specified length exceeds that length.
UnsavedItemException	This exception is thrown when trying to use an item that has not been saved to the database in places where this is required.
UnsupportedFileFormatException	Thrown when an import plug-in is forced to use a file that is not of the correct format.

Annotation Types Summary

Annotation Type	Description
SubtypableRelatedItems	Annotation that can be used by Subtypable items to tell about related items.
SupportsPushAnnotations	Annotation (java) that can be used by Subtypable items to enable/disable support for pushing annotations (BASE) to parent items.