Package org.proteios.core.data

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

See:
Description

Interface Summary

AnnotatableData	An annotatable item is an item that can be annotated with name/value pairs.
BatchableData	This is a tagging interface only.
CreationInterface
DiskConsumableData	A diskconsumable item is an item that occupies a lot of diskspace and should be controlled by the quota system.
ExtendableData	This class is inherited by data classes that supports per-server additions of columns to the underlying database table.
FileAttachableData	A fileattachable item is an item which can have a File attached to it.
IdentifiableData	An identifiable item is an item which has an id and a version.
NameableData	A nameable item is an item that has a name and, optionally, a description.
OwnableData	An ownable item is an item which has an owner.
RemovableData	A removable item is an item that can be flagged as removed.
ShareableData	A shareable item is an item which can be shared to other users, groups or projects.
SystemData	A system item is an item which has an additional id in the form of string.

Class Summary

AcquisitionData	This represents an acquisition.
AnnotatedData	This class extends the CommonData class and implements the AnnotatableData interface.
AnnotationData	This class holds information about an annotation
AnnotationSetData	This class holds information about a set of annotations.
AnnotationTypeData	This class holds information about an annotation type.
BasicData	This is the root superclass of all data classes.
BioMaterialData	This class is the root class for biomaterials.
BioMaterialEventData	This class is used to register events for measured biomaterials.
BioSourceData	This represents a biosoruce which is the starting point of all biomaterials.
BooleanParameterValueData	Boolean parameter value.
ClientData	This class holds information about a client.
ClientDefaultSettingData
CommonData	This is a convenience class that extends the SharedData class and implements the NameableData and RemovableData interfaces.
CreationEventData	This class is used for creation events like pooling of biomaterials.
DataProcessingStepData	This represents a data processing step of a peak list set.
DateParameterValueData	Date parameter value.
DigestParameterData	This represents a digestion parameter.
DirectoryData	This class holds information about directories.
DiskUsageData	This class holds information about a users and/or groups disk usage.
DoubleParameterValueData	Double parameter value.
ExtractData	This represents an extract.
FeatureData	Represents information about features from an LC-MS run.
FileData	This class holds information about a file.
FileParameterValueData	File parameter value.
FileTypeData	This class hols information about the different filetyped
FloatParameterValueData	Float parameter value.
GelElectrophoresisData	This represents a gel object which is generated by a separation event.
GelImageAnalysisEventData	This represents a GelImageAnalysisEventData which is a starting point of a MeasuredItem.
GelScanEventData	This class represent GelScanEvent items.
GlobalDefaultSettingData
GroupData	This class holds information about a group.
GuiContextData	This is a helper component for the PluginDefinitionData item to store the contexts where a plugin can be used in a client application.
HardwareConfigurationData	This represents a hardwareconfiguration which is a starting point of an instrumentconfiguration.
HardwareData	This class holds information about a Hardware.
HardwareTypeData	This class holds information about a hardwaretype.
HitData	Represents information about a spot and it's identification.
InputSpectraData	This represents a file with spectra or peaklists used for a spectrum search.
InstrumentConfigurationData	This class is the root class for instrumentconfigurations.
IntegerParameterValueData	Integer parameter value.
IPGData	This represents an IPG (Immobilized pH Gradient) which is a starting point of a separationmethod.
ItemKeyData	This class holds information access privileges for users and groups.
ItemParameterValueData	Item parameter value.
JobData	This class holds information about a job.
KeyData	This abstract class is the base class for the key classes which holds access privileges for users, groups, projects and roles.
LabelData	This represents a labeling compund use to label extracts.
LabeledExtractData	This represents a labeled extract.
LiquidChromatographyData	This represents Liquid Chromatography, which is a separation event without a separation method.
LongParameterValueData	Long parameter value.
MappingCoordinate	This class defines a mapping coordinate, which is a triplet of plate number, row and column.
MascotParameterSetStorageData	This represents the top element of a protein identification search.
MeasuredAreaData	This represents a measured area.
MeasuredBioMaterialData	This class is the root class for measured biomaterials, ie biomaterials for where the quantity is tracked.
MessageData	This class holds information about messages.
MimeTypeData	This class holds information about mimetypes
ModificationData	This class is the root class for modifications.
NewsData	This class holds information about news items.
ObservedModificationData	This represents a ObservedModification of a Modification
OMSSAParameterSetStorageData	This represents the top element of a protein identification search.
OwnedData	This class extends the BasicData class and implements the OwnableData interface.
ParameterValueData<T>	The base class for the different types of parameter values.
PasswordData	This class holds the password for a user.
PeakData	This represents a peak.
PeakListData	This represents a peaklist which is a starting point of a peak.
PeakListSetData	This represents a peaklistset which is a starting point of a peaklist.
PeptideData	This represents a peptide
PluginConfigurationData	This data class is used to configure a plugin.
PluginDefinitionData	This class represent an installed plugin.
PluginTypeData	This class represent an interface that a plugin can implement.
PolyPeptideData	This class is the root class for biomaterials.
PrecursorData	This represents a precursor.
ProjectData	This class holds information about a project.
ProjectKeyData	This class holds information access privileges for projects.
PropertyFilterData	This class holds context information to help client applications with storing common settings for tables.
ProteinData	This represents a Protein (ParentMolecule for of a PolyPeptide
ProtocolData
ProtocolTypeData
QuotaData	This file holds information about a qouta.
QuotaIndex	This is a helper class for the QuotaData item to help with the Hibernate mapping between quota and quota type/location/max bytes.
QuotaTypeData	This class holds information about different QuotaTypes.
RoleData	This class holds information about a role.
RoleKeyData	This class holds information access privileges for roles.
SampleData	This represents a sample.
SchemaVersionData	This class holds information about the current schema version of the database.
SearchDatabaseData	This class hold information about a database used for a SpectrumSearch.
SearchModificationData	This represents a SearchModification of a Modification
SearchResultData	This class represents a search result.
SeparationEventData	This represents a SeparationEvent.
SeparationMethodData	This class is the root class for separation methods.
SessionData	This class holds information about a session.
SettingData
SharedData	This class extends the OwnedData class and implements the ShareableData interface.
SoftwareConfigurationData	This represents a softwareconfiguration which is a starting point of an instrumentconfiguration.
SoftwareData	This class holds information about a software.
SoftwareTypeData	This class holds information about a softwaretype.
SpectrumSearchData	This represents the top element of a protein identification search.
StainingEventData	This represents a StainingEventData which is a starting point of a MeasuredItem.
StringParameterValueData	String parameter value.
TextParameterValueData	Text parameter value.
UpdateEventData	This represents an UpdateEventData which is a change of a MeasuredItem.
UsedQuantity	Hibernate will not save entries in the sources map BioMaterialEventData.getSources() where the element is null, so we have to use a composite element instead.
UserClientSettingData
UserData	This class holds information about a user.
UserDefaultSettingData
XTandemParameterSetStorageData	This represents the top element of a protein identification search.

Package org.proteios.core.data Description

This package contains pure data-holder classes which are mapped to the database using Hibernate. In general, they are not much more than structs with get and set methods to access the data.

The code in this package does not include any business logic, data validation, error handling, database queries or Hibernate dependant code. It is the repsonsibility of the business layer (the org.proteios.core package) to perform those tasks. For each class in this package, there usually is a corresponding class in the business layer, for example org.proteios.core.data.UserData and org.proteios.core.User.

Client applications do not get direct access to any of the classes in this package. They must use classes from the bussiness layer package org.proteios.core.

See also

• An overview of the database schema and data layer API
• Coding rules and guidelines for the data layer