net.sf.basedb.core.PlateGeometry

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

public class PlateGeometry
extends BasicItem
implements Nameable, Removable, Registered

This class defines a plate geometry, which is the number of rows and columns of wells on a Plate. The number of rows and columns must be specified when the item is created, and the values can't be changed after that.

A PlateMapping is a way to specify how one geometry can be transformed to another. It holds information for how to map all source wells to destination wells. For example it can map four 96-well plates to one 384-well plate.

Version:: 2.0
Author:: Nicklas
See Also:: Plate, PlateMapping
Last modified: $Date: 2017-05-22 14:35:27 +0200 (må, 22 maj 2017) $

Field Summary

Fields

Modifier and Type Field Description

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

PlateGeometry(PlateGeometryData plateGeometryData)

Method Summary

Modifier and Type	Method	Description
`static PlateGeometry`	`getById(DbControl dc, int id)`	Get a `PlateGeometry` item when you know the id.
`int`	`getColumns()`	Get the number of columns in this geometry.
`(package private) PlateGeometryData`	`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`	`getName()`	Get the name of the item.
`static PlateGeometry`	`getNew(DbControl dc, int rows, int columns)`	Create a new `PlateGeometry` item.
`ItemQuery<PlateType>`	`getPlateTypes()`	Get a query returning all plate types using this geometry.
`static ItemQuery<PlateGeometry>`	`getQuery()`	Get a query configured to retrieve plate geometries.
`User`	`getRemovedBy()`	Get the user that flagged this item for removal.
`int`	`getRows()`	Get the number of rows in this geometry.
`Item`	`getType()`	Get the type of item represented by the object.
`Set<ItemProxy>`	`getUsingItems()`	Get all: `PlateType`:s of this geometry `PlateMapping`:s using this geometry `BioPlate`:s using this geometry
`boolean`	`isRemoved()`	Check if the removed flag is set for this item.
`boolean`	`isUsed()`	Check if: A `PlateType` with this geometry exists A `PlateMapping` to/from this geometry exists A `BioPlate` that uses this geometry exists
`PlateType`	`newPlateType()`	Create a new `PlateType` of this geometry.
`private void`	`setColumns(int columns)`	The number of columns cannot be changed, used at object creation only.
`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`	`setName(String name)`	Set the name of the item.
`void`	`setRemoved(boolean removed)`	Set the removed flag for this item.
`private void`	`setRows(int rows)`	The number of rows cannot be changed, used at object creation only.

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.PLATEGEOMETRY, getType()
Constructor Details
- PlateGeometry
  
  PlateGeometry(PlateGeometryData plateGeometryData)
Method Details
- getNew
  
  public static PlateGeometry getNew(DbControl dc, int rows, int columns) throws InvalidDataException, BaseException
  
  Create a new PlateGeometry item.
  
  Parameters:
  
  dc - The DbControl which will be used for permission checking and database access
  
  rows - The number of rows
  
  columns - The number of columns
  
  Returns:
  
  The new PlateGeometry item
  
  Throws:
  
  InvalidDataException - If the number of rows or columns is less than or equal to zero
  
  BaseException - If there is an error
- getById
  
  public static PlateGeometry getById(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
  
  Get a PlateGeometry item 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 PlateGeometry 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 item
  
  BaseException - If there is another error
- getQuery
  
  public static ItemQuery<PlateGeometry> getQuery()
  
  Get a query configured to retrieve plate geometries.
  
  Returns:
  
  An ItemQuery object
- getData
  
  PlateGeometryData 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:
  
  A PlateType with this geometry exists
  A PlateMapping to/from this geometry exists
  A BioPlate that uses this geometry 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:
  
  PlateType:s of this geometry
  PlateMapping:s using this geometry
  BioPlate:s using this geometry
  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)
- getRows
  
  public int getRows()
  
  Get the number of rows in this geometry.
  
  Returns:
  
  The number of rows
- setRows
  
  private void setRows(int rows) throws InvalidDataException
  
  The number of rows cannot be changed, used at object creation only.
  
  Throws:
  
  InvalidDataException - If the row count is less than 1
- getColumns
  
  public int getColumns()
  
  Get the number of columns in this geometry.
  
  Returns:
  
  The number of columns
- setColumns
  
  private void setColumns(int columns) throws InvalidDataException
  
  The number of columns cannot be changed, used at object creation only.
  
  Throws:
  
  InvalidDataException - If the column count is less than 1
- newPlateType
  
  public PlateType newPlateType() throws PermissionDeniedException, BaseException
  
  Create a new PlateType of this geometry.
  
  Returns:
  
  The new plate type
  
  Throws:
  
  PermissionDeniedException - If the logged in user doesn't have use permission for this plate geometry
  
  BaseException - If there is another error
- getPlateTypes
  
  public ItemQuery<PlateType> getPlateTypes()
  
  Get a query returning all plate types using this geometry.
  
  Returns:
  
  An ItemQuery

Class PlateGeometry

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

Constructor Details

PlateGeometry

Method Details

getNew

getById

getQuery

getData

getType

getName

setName

getDescription

setDescription

isRemoved

setRemoved

getRemovedBy

getEntryDate

setEntryDate

isUsed

getUsingItems

getRows

setRows

getColumns

setColumns

newPlateType

getPlateTypes