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. |
SecondaryStorageController |
This interface defines the methods that needs to be implemented
by a class to be able to use it as a controller for seconday storage.
|
Shareable | |
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 | 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.
|
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.SecondaryStorageControllerTask | |
Application.SessionControlCacheCleaner | |
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 | |
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 | |
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 | |
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 . |
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.
|
InternalStorageController |
A simple implementation of a secondary storage controller which just moves
files to another directory.
|
InternalStorageController.StorageKeyring |
Our own keyring containing the permissions we need to move the files.
|
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.
|
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.
|
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 | |
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 | |
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 | |
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 | |
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.
|
SessionControl |
This class handles user sessions.
|
SessionControl.LoginInfo |
Internal class to hold information about the logged in user.
|
SessionControl.SettingInfo |
Internal class to hold information about a setting
|
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 | |
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.
|
SpotImage |
Holds the image information about a single spot image
in PNG format.
|
SpotImages |
Holds settings for creating small spot iamges from 1-3
image files and the raw data information for a single raw bioassay.
|
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.
|
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 | 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.
|
File.Action |
A fileaction describes if a file should be moved to secondary storage
or brought back from it.
|
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 | 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. |
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 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. |
This package contains the core business logic of BASE.