org.proteios.core
Enum Item

java.lang.Object
  java.lang.Enum<Item>
      org.proteios.core.Item

All Implemented Interfaces:

Serializable, Comparable<Item>

public enum Item
extends Enum<Item>

This class defines constants for various items in Proteios.

Version:

2.0

Author:

Samuel

Last modified

$Date: 2010-04-20 14:02:33 +0200 (Tue, 20 Apr 2010) $

Enum Constant Summary

ANNOTATION
The item is an Annotation.

ANNOTATIONSET
The item is an AnnotationSet.

ANNOTATIONTYPE
The item is an AnnotationType.

BIOMATERIALEVENT
The item is a BioMaterialEvent.

BIOSOURCE
The item is a BioSource.

CLIENT
The item is an Client.

DIRECTORY
The item is a Directory.

DISKUSAGE
The item is a DiskUsage.

EXTRACT
The item is an Extract.

FILE
The item is a File.

FILETYPE
The item is a FileType.

GLOBALDEFAULTSETTING
The item is an GlobalDefaultSetting.

GROUP
The item is a Group.

HARDWARE
The item is a Hardware.

HARDWARECONFIGURATION
The item is a HardwareConfiguration

HARDWARETYPE
The item is a HardwareType.

ITEMKEY
The item is an ItemKey.

JOB
The item is a Job

LABEL
The item is a Label.

LABELEDEXTRACT
The item is a LabeledExtract.

MESSAGE
The item is a Message.

MIMETYPE
The item is a MimeType.

NEWS
The item is a News.

PLUGINCONFIGURATION
The item is a PluginConfiguration

PLUGINDEFINITION
The item is a PluginDefinition

PLUGINTYPE
The item is a PluginType

PROJECT
The item is a Project.

PROJECTKEY
The item is a ProjectKey.

PROTEIOS_ACQUISITION
The item is an Acquisition

PROTEIOS_BIOMATERIAL
The item is a BioMaterial.

PROTEIOS_CREATIONEVENT
The item is a CreationEvent

PROTEIOS_DATAPROCESSINGSTEP
The item is a DataProcessingStep

PROTEIOS_DIGESTPARAMETER
The item is an DigestParameter

PROTEIOS_FEATURE
The item is a MascotParameterSetStorage

PROTEIOS_GELELECTROPHORESIS
The item is a GelElectrophoresis

PROTEIOS_GELIMAGEANALYSISEVENT
The item is a GelImageAnalysisEvent

PROTEIOS_GELSCANEVENT
The item is a GelScanEvent

PROTEIOS_HIT
The item is a Hit

PROTEIOS_IPG
The item is an IPG

PROTEIOS_LIQUIDCHROMATOGRAPHY
The item is a LiquidChromatography

PROTEIOS_MASCOTPARAMETERSETSTORAGE
The item is a MascotParameterSetStorage

PROTEIOS_MEASUREDAREA
The item is a MeasuredArea

PROTEIOS_OBSERVEDMODIFICATION
The item is a ObservedModification

PROTEIOS_OFFSET
Not an item as such.

PROTEIOS_OMSSAPARAMETERSETSTORAGE
The item is an OMSSAParameterSetStorage

PROTEIOS_PEAK
The item is a Peak

PROTEIOS_PEAKLIST
The item is a PeakList

PROTEIOS_PEAKLISTSET
The item is a PeakListSet

PROTEIOS_PEPTIDE
The item is a Peptide

PROTEIOS_PRECURSOR
The item is a Precursor

PROTEIOS_PROTEIN
The item is a Protein

PROTEIOS_SEARCHDATABASE
The item is an SearchDatabase

PROTEIOS_SEARCHMODIFICATION
The item is a SearchModification

PROTEIOS_SEARCHRESULT
The item is a SearchResult

PROTEIOS_SEPARATIONEVENT
The item is a SeparationEvent

PROTEIOS_SEPARATIONMETHOD
The item is a SeparationMethod

PROTEIOS_SPECTRUMSEARCH
The item is an SpectrumSearch

PROTEIOS_STAININGEVENT
The item is a StainingEvent

PROTEIOS_UPDATEEVENT
The item is an UpdateEvent

PROTEIOS_XTANDEMPARAMETERSETSTORAGE
The item is an XTandemParameterSetStorage

PROTOCOL
The item is a Protocol.

PROTOCOLTYPE
The item is a ProtocolType.

QUOTA
The item is a Quota.

QUOTATYPE
The item is a QuotaType.

ROLE
The item is a Role.

ROLEKEY
The item is a RoleKey.

SAMPLE
The item is a Sample.

SESSION
The item is an Session.

SETTING
The item is an Setting.

SOFTWARE
The item is a Software.

SOFTWARECONFIGURATION
The item is a SoftwareConfiguration

SOFTWARETYPE
The item is a SoftwareType.

SYSTEM
Not an item as such.

USER
The item is a User.

Method Summary

static Item	fromClass(Class<?> anyClass) Get the Item object when you know either the item or data class.
static Item	fromDataClass(Class<? extends BasicData> dataClass) Get the Item object when you know the data class.
static Item	fromDataObject(BasicData data) Get the Item object when you have a data layer object.
static Item	fromItemClass(Class<? extends BasicItem> itemClass) Get the Item object when you know the item class.
static Item	fromValue(int value) Get the Item object when you know the integer code.
String	getAlias() Get the alias for this item, which is used in queries,
BasicItem	getById(DbControl dc, int id) Get the item of the type represented by this enumeration constant with the specified id.
Class<? extends BasicData>	getDataClass() Get the data object that is used to store information in the database for items of this type.
Set<Permission>	getDefinedPermissions() Get the permissions which are meaningful to assign to an item if this type.
Class<? extends BasicItem>	getItemClass() Get the class object that is used to handle items of this type.
int	getValue() Get the integer value that is used when storing an item to the database.
String	toString()
static Item	valueOf(String name) Returns the enum constant of this type with the specified name.
static Item[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

SYSTEM

public static final Item SYSTEM

Not an item as such. Used for setting system permissions to role keys.

See Also:

Install, SessionControl.hasSystemPermission(Permission)

USER

public static final Item USER

The item is a User.

GROUP

public static final Item GROUP

The item is a Group.

ROLE

public static final Item ROLE

The item is a Role.

PROJECT

public static final Item PROJECT

The item is a Project.

ITEMKEY

public static final Item ITEMKEY

The item is an ItemKey.

PROJECTKEY

public static final Item PROJECTKEY

The item is a ProjectKey.

ROLEKEY

public static final Item ROLEKEY

The item is a RoleKey.

CLIENT

public static final Item CLIENT

The item is an Client.

SESSION

public static final Item SESSION

The item is an Session.

SETTING

public static final Item SETTING

The item is an Setting.

GLOBALDEFAULTSETTING

public static final Item GLOBALDEFAULTSETTING

The item is an GlobalDefaultSetting.

QUOTA

public static final Item QUOTA

The item is a Quota.

QUOTATYPE

public static final Item QUOTATYPE

The item is a QuotaType.

DISKUSAGE

public static final Item DISKUSAGE

The item is a DiskUsage.

FILE

public static final Item FILE

The item is a File.

FILETYPE

public static final Item FILETYPE

The item is a FileType.

DIRECTORY

public static final Item DIRECTORY

The item is a Directory.

MIMETYPE

public static final Item MIMETYPE

The item is a MimeType.

PROTOCOL

public static final Item PROTOCOL

The item is a Protocol.

PROTOCOLTYPE

public static final Item PROTOCOLTYPE

The item is a ProtocolType.

HARDWARE

public static final Item HARDWARE

The item is a Hardware.

HARDWARETYPE

public static final Item HARDWARETYPE

The item is a HardwareType.

SOFTWARE

public static final Item SOFTWARE

The item is a Software.

SOFTWARETYPE

public static final Item SOFTWARETYPE

The item is a SoftwareType.

NEWS

public static final Item NEWS

The item is a News.

MESSAGE

public static final Item MESSAGE

The item is a Message.

ANNOTATIONSET

public static final Item ANNOTATIONSET

The item is an AnnotationSet.

ANNOTATION

public static final Item ANNOTATION

The item is an Annotation.

ANNOTATIONTYPE

public static final Item ANNOTATIONTYPE

The item is an AnnotationType.

BIOSOURCE

public static final Item BIOSOURCE

The item is a BioSource.

SAMPLE

public static final Item SAMPLE

The item is a Sample.

EXTRACT

public static final Item EXTRACT

The item is an Extract.

LABELEDEXTRACT

public static final Item LABELEDEXTRACT

The item is a LabeledExtract.

BIOMATERIALEVENT

public static final Item BIOMATERIALEVENT

The item is a BioMaterialEvent.

LABEL

public static final Item LABEL

The item is a Label.

PLUGINTYPE

public static final Item PLUGINTYPE

The item is a PluginType

PLUGINDEFINITION

public static final Item PLUGINDEFINITION

The item is a PluginDefinition

PLUGINCONFIGURATION

public static final Item PLUGINCONFIGURATION

The item is a PluginConfiguration

JOB

public static final Item JOB

The item is a Job

HARDWARECONFIGURATION

public static final Item HARDWARECONFIGURATION

The item is a HardwareConfiguration

SOFTWARECONFIGURATION

public static final Item SOFTWARECONFIGURATION

The item is a SoftwareConfiguration

PROTEIOS_OFFSET

public static final Item PROTEIOS_OFFSET

Not an item as such. Used as a convenient way to set an offset for the index value of Proteios constants.

PROTEIOS_PEAKLISTSET

public static final Item PROTEIOS_PEAKLISTSET

The item is a PeakListSet

PROTEIOS_PEAKLIST

public static final Item PROTEIOS_PEAKLIST

The item is a PeakList

PROTEIOS_DATAPROCESSINGSTEP

public static final Item PROTEIOS_DATAPROCESSINGSTEP

The item is a DataProcessingStep

PROTEIOS_PRECURSOR

public static final Item PROTEIOS_PRECURSOR

The item is a Precursor

PROTEIOS_PEAK

public static final Item PROTEIOS_PEAK

The item is a Peak

PROTEIOS_ACQUISITION

public static final Item PROTEIOS_ACQUISITION

The item is an Acquisition

PROTEIOS_SPECTRUMSEARCH

public static final Item PROTEIOS_SPECTRUMSEARCH

The item is an SpectrumSearch

PROTEIOS_DIGESTPARAMETER

public static final Item PROTEIOS_DIGESTPARAMETER

The item is an DigestParameter

PROTEIOS_SEARCHDATABASE

public static final Item PROTEIOS_SEARCHDATABASE

The item is an SearchDatabase

PROTEIOS_SEARCHRESULT

public static final Item PROTEIOS_SEARCHRESULT

The item is a SearchResult

PROTEIOS_PROTEIN

public static final Item PROTEIOS_PROTEIN

The item is a Protein

PROTEIOS_PEPTIDE

public static final Item PROTEIOS_PEPTIDE

The item is a Peptide

PROTEIOS_HIT

public static final Item PROTEIOS_HIT

The item is a Hit

PROTEIOS_MEASUREDAREA

public static final Item PROTEIOS_MEASUREDAREA

The item is a MeasuredArea

PROTEIOS_GELELECTROPHORESIS

public static final Item PROTEIOS_GELELECTROPHORESIS

The item is a GelElectrophoresis

PROTEIOS_IPG

public static final Item PROTEIOS_IPG

The item is an IPG

PROTEIOS_SEPARATIONMETHOD

public static final Item PROTEIOS_SEPARATIONMETHOD

The item is a SeparationMethod

PROTEIOS_GELIMAGEANALYSISEVENT

public static final Item PROTEIOS_GELIMAGEANALYSISEVENT

The item is a GelImageAnalysisEvent

PROTEIOS_GELSCANEVENT

public static final Item PROTEIOS_GELSCANEVENT

The item is a GelScanEvent

PROTEIOS_SEPARATIONEVENT

public static final Item PROTEIOS_SEPARATIONEVENT

The item is a SeparationEvent

PROTEIOS_STAININGEVENT

public static final Item PROTEIOS_STAININGEVENT

The item is a StainingEvent

PROTEIOS_OBSERVEDMODIFICATION

public static final Item PROTEIOS_OBSERVEDMODIFICATION

The item is a ObservedModification

PROTEIOS_SEARCHMODIFICATION

public static final Item PROTEIOS_SEARCHMODIFICATION

The item is a SearchModification

PROTEIOS_CREATIONEVENT

public static final Item PROTEIOS_CREATIONEVENT

The item is a CreationEvent

PROTEIOS_BIOMATERIAL

public static final Item PROTEIOS_BIOMATERIAL

The item is a BioMaterial. Was introduced when trying to display any biomaterial by clicking on it.

PROTEIOS_UPDATEEVENT

public static final Item PROTEIOS_UPDATEEVENT

The item is an UpdateEvent

PROTEIOS_LIQUIDCHROMATOGRAPHY

public static final Item PROTEIOS_LIQUIDCHROMATOGRAPHY

The item is a LiquidChromatography

PROTEIOS_XTANDEMPARAMETERSETSTORAGE

public static final Item PROTEIOS_XTANDEMPARAMETERSETSTORAGE

The item is an XTandemParameterSetStorage

PROTEIOS_OMSSAPARAMETERSETSTORAGE

public static final Item PROTEIOS_OMSSAPARAMETERSETSTORAGE

The item is an OMSSAParameterSetStorage

PROTEIOS_MASCOTPARAMETERSETSTORAGE

public static final Item PROTEIOS_MASCOTPARAMETERSETSTORAGE

The item is a MascotParameterSetStorage

PROTEIOS_FEATURE

public static final Item PROTEIOS_FEATURE

The item is a MascotParameterSetStorage

Method Detail

values

public static Item[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (Item c : Item.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static Item valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

toString

public String toString()

Overrides:

toString in class Enum<Item>

getValue

public int getValue()

Get the integer value that is used when storing an item to the database.

getAlias

public String getAlias()

Get the alias for this item, which is used in queries,

See Also:

Query.getRootAlias()

getItemClass

public Class<? extends BasicItem> getItemClass()

Get the class object that is used to handle items of this type.

getDataClass

public Class<? extends BasicData> getDataClass()

Get the data object that is used to store information in the database for items of this type.

getDefinedPermissions

public Set<Permission> getDefinedPermissions()

Get the permissions which are meaningful to assign to an item if this type. This is not used internally by the core, but is can be used by client applications to dynamically display a proper input form while assigning permissions.

Returns:

A Set containing the permissions

getById

public BasicItem getById(DbControl dc,
                         int id)
                  throws ItemNotFoundException,
                         PermissionDeniedException,
                         BaseException

Get the item of the type represented by this enumeration constant with the specified id. Ie. Item.SAMPLE.getById() is the same as Sample.getById.

Parameters:

dc - The DbControl object used for database access and permission checking

id - The id of the item

Returns:

An item of the type represented by this enumeration constant

Throws:

ItemNotFoundException - If an item with the specified id isn't found

PermissionDeniedException - If the logged in user hasn't read permission for the item

BaseException - If there is another error

fromValue

public static Item fromValue(int value)

Get the Item object when you know the integer code.

fromItemClass

public static Item fromItemClass(Class<? extends BasicItem> itemClass)

Get the Item object when you know the item class.

fromDataClass

public static Item fromDataClass(Class<? extends BasicData> dataClass)

Get the Item object when you know the data class.

fromClass

public static Item fromClass(Class<?> anyClass)

Get the Item object when you know either the item or data class.

Returns:

The Item object, or null if no matching item is found

fromDataObject

public static Item fromDataObject(BasicData data)

Get the Item object when you have a data layer object. This method takes Hibernate proxies into account.