net.sf.basedb.core.ExtraValueType

All Implemented Interfaces:: AccessControlled, Identifiable, Nameable, Registered, Removable

public class ExtraValueType
extends BasicItem
implements Nameable, Removable, Registered

Defines extra values that can be calculated by plugins or some other application and inserted as part of a BioAssaySet. All extra value types must have a unique external id that is used for identification.

Currently only extra values of Type.INT, Type.FLOAT and Type.STRING are supported.

Version:: 2.0
Author:: Nicklas
See Also:: ExtraValue, BioAssaySet.getSpotExtraValueBatcher(Class, ExtraValueType, Job), BioAssaySet.getPositionExtraValueBatcher(Class, ExtraValueType, Job)
Last modified: $Date: 2017-05-22 14:35:27 +0200 (må, 22 maj 2017) $

Field Summary

Fields
Modifier and Type	Field	Description
`private Coloring`	`coloring`
`static int`	`MAX_EXTERNAL_ID_LENGTH`	The maximum length of the external id variable that can be stored in the database.
`static Item`	`TYPE`	The type of item represented by this class.

Fields inherited from interface net.sf.basedb.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

Constructors

Constructor Description

ExtraValueType(ExtraValueTypeData data)
Creates a new extra value type item.

Method Summary

Modifier and Type	Method	Description
`Formula.AverageMethod`	`getAverageMethod()`	Get the average method for this extra value type.
`static ExtraValueType`	`getByExternalId(DbControl dc, String externalId)`	Get a `ExtraValueType` when you know the external id.
`static ExtraValueType`	`getById(DbControl dc, int id)`	Get an `ExtraValueType` object when you know the id.
`Coloring`	`getColoring()`	Get coloring information for this extra value.
`(package private) ExtraValueTypeData`	`getData()`	Get the `BasicData` object that holds all data for this item.
`String`	`getDescription()`	Get the description for the item.
`Date`	`getEntryDate()`	Get the date that the item was registered in the database.
`String`	`getExternalId()`	Get the external id for this `ExtraValueType` item.
`String`	`getName()`	Get the name of the item.
`static ExtraValueType`	`getNew(DbControl dc, String externalId, Type valueType)`	Create a new `ExtraValue` item.
`static ItemQuery<ExtraValueType>`	`getQuery()`	Get a query configured to retrieve extra value types.
`User`	`getRemovedBy()`	Get the user that flagged this item for removal.
`Item`	`getType()`	Get the type of item represented by the object.
`Set<ItemProxy>`	`getUsingItems()`	Get all: `ExtraValue`:s of this type
`Type`	`getValueType()`	Get the value type for this extra value type.
`boolean`	`isRemoved()`	Check if the removed flag is set for this item.
`boolean`	`isUsed()`	Check if: Any `ExtraValue`:s of this type exists
`void`	`setAverageMethod(Formula.AverageMethod averageMethod)`	Set the average method of the extra value type..
`void`	`setDescription(String description)`	Set the description for the item.
`void`	`setEntryDate(Date entryDate)`	Set the date the entry was registered in the database.
`void`	`setExternalId(String externalId)`	Set the external id for this `Client` item.
`void`	`setName(String name)`	Set the name of the item.
`void`	`setRemoved(boolean removed)`	Set the removed flag for this item.
`private void`	`setValueType(Type valueType)`	Set the value type for this extra value type.

Methods inherited from class net.sf.basedb.core.BasicItem

addAnnotatableParents, addUsingItems, addUsingItems, breakCircularReferences, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, initPermissions, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onBeforeCommit, onRollback, setDbControl, setProjectDefaults, toString, validate

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.AccessControlled

checkPermission, getPermissions, hasPermission

Methods inherited from interface net.sf.basedb.core.Identifiable

getId, getVersion

Field Details
- TYPE
  
  public static final Item TYPE
  
  The type of item represented by this class.
  
  See Also:
  
  Item.EXTRAVALUETYPE, getType()
- MAX_EXTERNAL_ID_LENGTH
  
  public static final int MAX_EXTERNAL_ID_LENGTH
  
  The maximum length of the external id variable that can be stored in the database. Check the length against this value before calling the setExternalId(String) method to avoid exceptions.
  
  See Also:
  
  Constant Field Values
- coloring
  
  private Coloring coloring
Constructor Details
- ExtraValueType
  
  ExtraValueType(ExtraValueTypeData data)
  
  Creates a new extra value type item.
  
  Parameters:
  
  data - The data
Method Details
- getNew
  
  public static ExtraValueType getNew(DbControl dc, String externalId, Type valueType) throws BaseException
  
  Create a new ExtraValue item. Currently only extra values of Type.INT, Type.FLOAT and Type.STRING are supported.
  
  Parameters:
  
  dc - The DbControl which will be used for permission checking and database access
  
  externalId - A unique string identifying the extra value type
  
  valueType - The Type of the extra value
  
  Returns:
  
  The new ExtraValue item
  
  Throws:
  
  BaseException - If there is an error
- getById
  
  public static ExtraValueType getById(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
  
  Get an ExtraValueType object when you know the id.
  
  Parameters:
  
  dc - The DbControl which will be used for permission checking and database access.
  
  id - The id of the item to load
  
  Returns:
  
  The ExtraValueType item
  
  Throws:
  
  ItemNotFoundException - If an item with the specified id is not found
  
  PermissionDeniedException - If the logged in user doesn't have Permission.READ permission to the items
  
  BaseException - If there is an error
- getByExternalId
  
  public static ExtraValueType getByExternalId(DbControl dc, String externalId) throws ItemNotFoundException, PermissionDeniedException, BaseException
  
  Get a ExtraValueType when you know the external id.
  
  Parameters:
  
  dc - The DbControl which will be used for database access.
  
  externalId - The external id of the extra value type to load
  
  Returns:
  
  The ExtraValueType item
  
  Throws:
  
  ItemNotFoundException - If an item with the specified id is not found
  
  PermissionDeniedException - If the logged in user doesn't have read permission to the item
  
  BaseException - If there is another error
- getQuery
  
  public static ItemQuery<ExtraValueType> getQuery()
  
  Get a query configured to retrieve extra value types.
  
  Returns:
  
  An ItemQuery object
- getData
  
  ExtraValueTypeData getData()
  
  Description copied from class: BasicItem
  
  Get the BasicData object that holds all data for this item.
  
  Specified by:
  
  getData in class BasicItem
- getType
  
  public Item getType()
  
  Description copied from interface: Identifiable
  
  Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.
  
  Specified by:
  
  getType in interface Identifiable
  
  Returns:
  
  A value indicating the type of item
- getName
  
  public String getName()
  
  Description copied from interface: Nameable
  
  Get the name of the item.
  
  Specified by:
  
  getName in interface Nameable
  
  Returns:
  
  A String with the name of the item
- setName
  
  public void setName(String name) throws PermissionDeniedException, InvalidDataException
  
  Description copied from interface: Nameable
  
  Set the name of the item. The name cannot be null and mustn't be longer than the value specified by the Nameable.MAX_NAME_LENGTH constant.
  
  Specified by:
  
  setName in interface Nameable
  
  Parameters:
  
  name - The new name for the item
  
  Throws:
  
  PermissionDeniedException - If the logged in user doesn't have write permission
  
  InvalidDataException - If the name is null or longer than specified by the Nameable.MAX_NAME_LENGTH constant
- getDescription
  
  public String getDescription()
  
  Description copied from interface: Nameable
  
  Get the description for the item.
  
  Specified by:
  
  getDescription in interface Nameable
  
  Returns:
  
  A String with a description of the item
- setDescription
  
  public void setDescription(String description) throws PermissionDeniedException, InvalidDataException
  
  Description copied from interface: Nameable
  
  Set the description for the item. The description can be null but mustn't be longer than the value specified by the Nameable.MAX_DESCRIPTION_LENGTH constant.
  
  Specified by:
  
  setDescription in interface Nameable
  
  Parameters:
  
  description - The new description for the item
  
  Throws:
  
  PermissionDeniedException - If the logged in user doesn't have write permission
  
  InvalidDataException - If the description longer than specified by the Nameable.MAX_DESCRIPTION_LENGTH constant
- isRemoved
  
  public boolean isRemoved()
  
  Description copied from interface: Removable
  
  Check if the removed flag is set for this item.
  
  Specified by:
  
  isRemoved in interface Removable
  
  Returns:
  
  TRUE if the item is flagged as removed, FALSE otherwise
- setRemoved
  
  public void setRemoved(boolean removed) throws PermissionDeniedException
  
  Description copied from interface: Removable
  
  Set the removed flag for this item.
  
  Specified by:
  
  setRemoved in interface Removable
  
  Parameters:
  
  removed - TRUE if the item should be flagged as removed, FALSE otherwise
  
  Throws:
  
  PermissionDeniedException - If the logged in user doesn't have Permission.DELETE permission for setting the flag to TRUE or Permission.WRITE permission for setting the flag to FALSE
- getRemovedBy
  
  public User getRemovedBy() throws PermissionDeniedException, ItemNotFoundException
  
  Description copied from interface: Removable
  
  Get the user that flagged this item for removal.
  
  Specified by:
  
  getRemovedBy in interface Removable
  
  Returns:
  
  A User object, or null if this item has not been flagged
  
  Throws:
  
  PermissionDeniedException - If the logged in user doesn't have Permission.READ permission for the user
  
  ItemNotFoundException - If the user that removed this item can't be found
- getEntryDate
  
  public Date getEntryDate()
  
  Description copied from interface: Registered
  
  Get the date that the item was registered in the database.
  
  Specified by:
  
  getEntryDate in interface Registered
  
  Returns:
  
  A date or null if this is not known
- setEntryDate
  
  public void setEntryDate(Date entryDate)
  
  Description copied from interface: Registered
  
  Set the date the entry was registered in the database. Implementations should only allow this property to be set before the item is first stored in the database. The intention of this method is to facilitate export/import of data between server.
  
  Specified by:
  
  setEntryDate in interface Registered
  
  Parameters:
  
  entryDate - A date or null to use today's date
- isUsed
  
  public boolean isUsed() throws BaseException
  Check if:
  
  Any ExtraValue:s of this type exists
  Overrides:
  
  isUsed in class BasicItem
  
  Returns:
  
  TRUE if this item is used, FALSE otherwise
  
  Throws:
  
  BaseException - If not able to tell if item is used or not.
  
  See Also:
  
  BasicItem.getUsingItems()
- getUsingItems
  
  public Set<ItemProxy> getUsingItems()
  Get all:
  
  ExtraValue:s of this type
  Overrides:
  
  getUsingItems in class BasicItem
  
  Returns:
  
  A set containing proxies for the items, or an empty set if no items are using this item
  
  Since:
  
  2.2
  
  See Also:
  
  BasicItem.addUsingItems(Set, Item, org.hibernate.query.Query)
- getValueType
  
  public Type getValueType()
  
  Get the value type for this extra value type. It can't be change once the object has been created.
- setValueType
  
  private void setValueType(Type valueType) throws InvalidDataException
  
  Set the value type for this extra value type. Null is not allowed and it must be one of the supported value types.
  
  Throws:
  
  InvalidDataException
  
  See Also:
  
  VirtualColumn.extraValue(Type)
- getExternalId
  
  public String getExternalId()
  
  Get the external id for this ExtraValueType item.
  
  Returns:
  
  A string with the external id of this item
- setExternalId
  
  public void setExternalId(String externalId) throws PermissionDeniedException, InvalidDataException
  
  Set the external id for this Client item. The value cannot be null and must not be longer than the value specified by the MAX_EXTERNAL_ID_LENGTH constant.
  
  Parameters:
  
  externalId - The new external id for this item
  
  Throws:
  
  PermissionDeniedException - If the logged in user doesn't have write permission
  
  InvalidDataException - If the new value is null or longer than MAX_EXTERNAL_ID_LENGTH
- getColoring
  
  public Coloring getColoring()
  
  Get coloring information for this extra value.
  
  Returns:
  
  A Coloring object
- getAverageMethod
  
  public Formula.AverageMethod getAverageMethod()
  
  Get the average method for this extra value type.
  
  Returns:
  
  A Formula.AverageMethod object
  
  Since:
  
  2.4
- setAverageMethod
  
  public void setAverageMethod(Formula.AverageMethod averageMethod) throws PermissionDeniedException, InvalidDataException
  
  Set the average method of the extra value type..
  
  Parameters:
  
  averageMethod - A Formula.AverageMethod object, null is not allowed
  
  Throws:
  
  PermissionDeniedException - If the logged in user doesn't have write permission
  
  InvalidDataException - If the averageMethod is null
  
  Since:
  
  2.4

Class ExtraValueType

Field Summary

Fields inherited from interface net.sf.basedb.core.Nameable

Constructor Summary

Method Summary

Methods inherited from class net.sf.basedb.core.BasicItem

Methods inherited from class java.lang.Object

Methods inherited from interface net.sf.basedb.core.AccessControlled

Methods inherited from interface net.sf.basedb.core.Identifiable

Field Details

TYPE

MAX_EXTERNAL_ID_LENGTH

coloring

Constructor Details

ExtraValueType

Method Details

getNew

getById

getByExternalId

getQuery

getData

getType

getName

setName

getDescription

setDescription

isRemoved

setRemoved

getRemovedBy

getEntryDate

setEntryDate

isUsed

getUsingItems

getValueType

setValueType

getExternalId

setExternalId

getColoring

getAverageMethod

setAverageMethod