Package org.proteios.core

This package contains the core business logic of Proteios 2.

See:
Description

Interface Summary

AbortableJobQueueInterface	An interface for a job queue class that allows abortion of jobs.
AbortableJobQueueReadOnlyInterface	An interface for a job queue class that allows abortion of jobs, restricted to methods that do not modify the job queue when called.
AbortablePluginInterface	This interface defines methods to notify the plugin if the job command is aborted.
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.
Batcher	The basic interface which all batchers must implement.
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.
Identifiable	An Identifiable item is an item which has an id a type and a version.
ManageableJobQueueInterface	An interface for a job queue class that allows external requests for adding jobs.
ManageableJobQueueReadOnlyInterface	An interface for a job queue class, restricted to methods that do not modify the job queue when called.
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 Proteios can report their progress back to the calling client application if they are giving an object that implements this interface.
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.
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.
UpdateToSchemaVersionInterface	This interface describes methods used to perform incremental update from previous schema version to the version the class corresponds to.
Validatable	This interface is a tagging interface for items that needs case 2 validation.

Class Summary

AbstractBatcher	This is an abstract class for batchers that are connected to a single DbControl object.
AbstractUpdateToSchemaVersion	This abstract class contains methods to perform incremental update and adjustment of existing database items from a previous schema version to the version corresponding to this class.
Acquisition	This class represent acquisition items.
AliasKeyManager
AnnotatedItem<D extends AnnotatedData>	This is a helper class for items that need to implement the Annotatable interface.
Annotation	This class represents an annotation.
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.
AnnotationSet	An annotation set is the container for all annotations on an item.
AnnotationSimpleRestriction	Restricts a query using annotation values with a simple expression: annotation operator value.
AnnotationType	Objects of this class defines an annotation type.
Annotator	Use this class whenever you want to add or list annotations of an Annotatable item.
Application	This class represents the Proteios application and is the starting point for all client applications.
Base64Coder
BasicBatcher<D extends BatchableData>	This is an abstract class for batching functionallity.
BasicItem<D extends BasicData>	This is the root superclass of all item classes.
BatchedPropertyInfo	Holds information about a batchable property.
BioMaterial<D extends BioMaterialData>	This is the base class for for the four types of biomaterials: BioSource, Sample, Extract and LabeledExtract.
BioMaterialEvent<D extends BioMaterialEventData>	This class represents an event in the life of a MeasuredBioMaterial.
BioSource	This class represent biosource items.
BooleanParameterType	This class represent a parameter type that is a boolean.
ClassMetadataExposed	Exposes only get methods of the meta data.
Client	This class represents a registered client application.
CommonItem<D extends CommonData>
Config	Use this class to access the configuration settings for Proteios.
CreationEvent	This class is used for creation events like pooling of biomaterials
DataProcessingStep	This class represent data processing steps items.
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.
DefaultAttributeFilter	A filter for basic item attributes.
DigestParameter	This class represent spectrumsearch.
Directory	This is used to represent directory items.
DiskUsage	This class is used to represent the disk usage of DiskConsumable items.
DoubleParameterType	This class represent a parameter type that is a double.
DynamicResultIterator	An iterator view of the result of an AbstractSqlQuery.
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.
Extract	This class is used to represent extract items.
Feature	Represents information about features from an LC-MS run, as picked by a feature extraction algorithm.
File	This class is used to represent individual file items and information about them.
FileAttributeFilter	A filter for file item attributes.
FileNode	FileNode's are used to connect files in projects.
FileParameterType	This class represent a parameter type that is a file.
FileType	This class is used to represent the type of File items in Proteios.
FloatParameterType	This class represent a parameter type that is a float.
GelElectrophoresis	This class represent gel electrophoresis items.
GelImageAnalysisEvent	This class represent GelImageAnalysisEvent items.
GelScanEvent	This class represent GelScanEvent items.
GlobalDefaultSetting	This class is used to represent a global default setting.
Group	This class is used to represent groups.
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.
HardwareConfiguration	This class represent hardware configuration items.
HardwareType	This class is used to represent the type of Hardware items in Proteios.
HibernateUtil	This class collects most of the functionality we need for using Hibernate.
Hit
HitsFilterForGelBasedProjects	A filter for basic item attributes.
HitsFilterForNonGelBasedProjects	A filter for basic item attributes.
Install	This class contains static methods used to install items into an empty database.
InstrumentConfiguration<D extends InstrumentConfigurationData>	This is the base class for for the two types of instrumentconfigurations: HardwareConfiguration and SoftwareConfiguration.
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.
IPG	This class represent IPG (Immobilized pH Gradient) items.
ItemFactory	Used to create persistent item instances
ItemKey	This class is used to get information about which users and groups a Shareable item has been shared to.
ItemParameterType<T extends BasicItem>	This class represent a parameter type that is an object derived from BasicData.
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.
Job	This class represents the execution of a job.
JobQueueManager	This class manages instances of job queue classes.
JobQueueScheduler	This class schedules instances of job queue classes.
Key<D extends KeyData>	This is the base class for keys.
Label	This class represents a labelling compund.
LabeledExtract	This class is used to represent labeled extract items.
LiquidChromatography	This class represent LiquidChromatography items.
LongParameterType	This class represent a parameter type that is a long.
LsidElement
LsidElement.SequenceRetriever	This class will retrieve the data from a given LSID.
MascotParameterSetStorage	This class represents MascotParameterSetStorage.
MeasuredArea	This class represent measured areas.
MeasuredBioMaterial<D extends MeasuredBioMaterialData>	This class is the base class for measured biomaterial items.
Message	This class represents a message.
Metadata<C>	Utility methods for retreiving metadata about items.
MimeType	This class is used to represent mime types.
MinimalAttributeFilter	A minimal filter for basic item attributes.
MinimalAttributeFilter2	A minimal filter for basic item attributes.
Modification<D extends ModificationData>	This is the base class for for the two types of Modifications: ObservedModification and SearchModification.
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.
ObservedModification	This class represent observedModifications.
OMSSAParameterSetStorage	This class represents OMSSAParameterSetStorage.
OwnableUtil	Utility methods that will make it easier to implement the Ownable interface, including data validation.
OwnedItem<D extends OwnedData>	This class inherits from the BasicItem class and implements the Ownable interface.
ParameterType<T>	This is the base class for all parameter types.
Path	This class is used represent the path to a Directory or File item.
Peak	This class represent peak items.
PeakBatcher
PeakList	This class represent peaklist items.
PeakListBatcher
PeakListSet	This class represent peaklistset items.
Peptide	This class represent peptide.
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.
PluginResponse	Get the response from a configuration step or execution of a plugin.
PluginType
PolyPeptide<D extends PolyPeptideData>	This is the base class for for the two types of polypeptide: Protein and Peptide.
Precursor	This class represent precursor items.
PreferencesFile	Manages user preferences data stored in user preference file.
Project	This class is used to represent projects.
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.
PropertiesFileHandler
PropertyFilter	Used to store filter settings in the current context.
Protein	This class represent proteins.
Protocol	This class is used to represent individual protocol items and information about them.
ProtocolType	This class is used to represent the type of the Protocol items in Proteios.
QueryFactory	Used to query for items.
Quota	This class is used to represent disk quota settings for users and groups.
QuotaType	This class represents the different types a quota can have.
RealTable	This class defines constants that are used to specify a table in the regular (non-dynamic) database while doing analysis with dynamic queries.
RequestInformation	Get information about the parameters the plugin needs for a particular request.
Role	This class is used to represent roles.
RoleKey	This class is used to represent a role key.
Sample	This class is used to represent sample items.
SchemaVersion	This class contains methods to get and set the schema version data in the database.
SearchDatabase	This class represent spectrumsearch.
SearchModification	This class represent searchModifications.
SearchResult	This class represent spectrumsearch.
SeparationEvent	This represents a SeparationEvent.
SeparationMethod<D extends SeparationMethodData>	This class is the root class for separation methods.
Session	A session represents the time between login and logout for a single user.
SessionControl	This class handles user sessions.
Setting<D extends SettingData>	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<D extends SharedData>	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.
SoftwareConfiguration	This class represent software configuration items.
SoftwareType	This class is used to represent the type of Software items in Proteios.
SpectrumSearch	This class represent spectrumsearch.
StainingEvent	This class represent StainingEvent items.
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.
SystemItems	This class is used to map the system id of all SystemData items to the numerical internal id in the current installation.
Update	This class contains methods used to update items already in the database.
UpdateEvent	This class represent UpdateEvent items.
UpdatesFactory	This class is a factory of incremental update classes.
UpdateToSchemaVersion10	Following tables are removed from schema 9-10 Plates, PlateEvents, PlateEventTypes, PlateGeometries, PlateMappings PlateParents, PlateTypes, PropertyFilters ContextSettings, Contexts, Experiments, FileMaps, Wells
UpdateToSchemaVersion2
UpdateToSchemaVersion3
UpdateToSchemaVersion4	This class contains methods used to perform incremental update from database schema version 3 to 4.
UpdateToSchemaVersion5	This class contains methods used to perform incremental update from database schema version 4 to 5.
UpdateToSchemaVersion6	This class contains methods used to perform incremental update from database schema version 5 to 6.
UpdateToSchemaVersion7	This class contains methods used to perform incremental update from database schema version 6 to 7.
UpdateToSchemaVersion8	This class contains methods used to perform incremental update from database schema version 7 to 8.
UpdateToSchemaVersion9	This class is a template for a class that contains methods used to perform incremental update from one schema version to the next.
UpdateToSchemaVersionTmpl	This class is a template for a class that contains methods used to perform incremental update from one schema version to the next.
User	This class is used to represent a user in Proteios.
UserPermissions	This class is used to specify permissions to share an item to users.
XTandemParameterSetStorage	This class represents XTandemParameterSetStorage.

Enum Summary

File.Action	A fileaction describes if a file should be moved to secondary storage or brought back from it.
Include	This enumeration defines constants that are used to specify which items to include in a query.
Item	This class defines constants for various items in Proteios.
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.
SearchModification.TerminalSpecificity	This enum is used to verify terminal specificities.
SortOrder
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 Proteios.

Exception Summary

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 Proteios.
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.
DetachedItemException	This exception is thrown when trying to use an item that has been detached from the DbControl that manages it.
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 Proteios is trying to parse a path which 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.
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.

Package org.proteios.core Description

This package contains the core business logic of Proteios 2.