Package net.sf.basedb.core

Class Plate

java.lang.Object
net.sf.basedb.core.BasicItem
net.sf.basedb.core.OwnedItem
net.sf.basedb.core.SharedItem
net.sf.basedb.core.CommonItem
net.sf.basedb.core.AnnotatedItem
net.sf.basedb.core.Plate
All Implemented Interfaces:
AccessControlled, Annotatable, Identifiable, Nameable, Ownable, Registered, Removable, Shareable
public class Plate
extends AnnotatedItem
implements Registered
This class is represents physical plates. A plate must have a PlateType, which defines the geometry and possible events for the plate.

A plate consists of Well:s which are created at the same time the plate is created. The wells are organised into rows and columns as specified by the plate geometry.

A plate is either created directly or as the result of a PlateMapping operation from other plates. In the first case the wells must be linked to reporters before the plate is saved. In the latter case the linking is done automatically from the source plates.

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

  • Field Details

    • TYPE

      public static final Item TYPE
      The type of item represented by this class.
      See Also:
      Item.PLATE, getType()

    • MAX_BARCODE_LENGTH

      public static final int MAX_BARCODE_LENGTH
      The maximum length of the barcode that can be stored in the database. Check the length against this value before calling the setBarcode(String) method to avoid exceptions.
      See Also:
      Constant Field Values

  • Constructor Details

  • Method Details

    • getNew

      public static Plate getNew​(DbControl dc, PlateType plateType) throws BaseException
      Create a new Plate item.
      Parameters:
      dc - The DbControl which will be used for permission checking and database access
      plateType - The type of the new plate
      Returns:
      The new Plate item
      Throws:
      PermissionDeniedException - If the loggged in user doesn't have use permission for the plate type
      InvalidDataException - If the plate type is null
      BaseException - If there is another error

    • getById

      public static Plate getById​(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
      Get a Plate 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 Plate 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<Plate> getQuery()
      Get a query that returns plates.
      Returns:
      An ItemQuery object

    • getData

      PlateData getData()
      Description copied from class: BasicItem
      Get the BasicData object that holds all data for this item.
      Overrides:
      getData in class AnnotatedItem

    • 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

    • getAnnotatableParents

      public Set<Annotatable> getAnnotatableParents() throws BaseException
      Get the parent plates, if any.
      Specified by:
      getAnnotatableParents in interface Annotatable
      Returns:
      A set containing annotatable items, or null
      Throws:
      BaseException - If there is an error

    • 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: Wells are deleted automatically.
      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:
      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)

    • getPlateType

      public PlateType getPlateType() throws PermissionDeniedException, BaseException
      Get the PlateType of this plate.
      Returns:
      The PlateType item
      Throws:
      PermissionDeniedException - If the logged in user doesn't have Permission.READ permission for the plate type
      BaseException - If there is another error

    • setPlateType

      private void setPlateType​(PlateType plateType) throws PermissionDeniedException, InvalidDataException
      Set the plate type of this plate.
      Throws:
      PermissionDeniedException - If the logged in user doesn't have use permission for the plate type
      InvalidDataException - If the plate type is null

    • getPlateMapping

      public PlateMapping getPlateMapping() throws PermissionDeniedException, BaseException
      Get the PlateMapping used to create this plate.
      Returns:
      The PlateMapping item, or null if this plate was not created using a mapping
      Throws:
      PermissionDeniedException - If the logged in user doesn't have read permission to the plate mapping
      BaseException - If there is another error

    • getDestinationIndex

      public int getDestinationIndex()
      If the plate was created by a plate mapping, this is the index of this plate in the list of created plates. First plate have index 0.

    • getBarcode

      public String getBarcode()
      Get the barcode of this plate. The barcode is not used by the core and it is not required that it is unique.

    • setBarcode

      public void setBarcode​(String barcode) throws PermissionDeniedException, InvalidDataException
      Set the barcode for the plate. Null is allowed but the value can't be longer than the value specified by the MAX_BARCODE_LENGTH constant. Normally, this should be a unique value among all plates, but the core does not check this.
      Parameters:
      barcode - The new barcode for the plate
      Throws:
      PermissionDeniedException - If the logged in user doesn't have write permission
      InvalidDataException - If the value is too long

    • isDestroyed

      public boolean isDestroyed()
      Check if the plate has been destroyed. A destroyed plate can't be used by a PlateMapping to create new plates or to create ArrayDesign:s.

    • setDestroyed

      public void setDestroyed​(boolean destroyed) throws PermissionDeniedException
      Set the destroyed flag. A destroyed plate can't be used by a PlateMapping to create new plates or to create ArrayDesign:s.
      Parameters:
      destroyed - TRUE if the plate is destroyed, FALSE otherwise.
      Throws:
      PermissionDeniedException - If the logged in user doesn't have write permission on the item.

    • getParentPlates

      public ItemQuery<Plate> getParentPlates()
      Get a query returning the parent plates of this plate. A plate has parents if it was created by a PlateMapping.
      Returns:
      An ItemQuery object

    • getSourceIndex

      public int getSourceIndex​(Plate parent) throws InvalidDataException
      If this plate was created by a PlateMapping and the specified plate is a parent, get the index of the parent plate in the list of source plates used by the plate mapping. If the plate is not a parent, -1 is returned.
      Parameters:
      parent - The plate to get source index of, if it's a parent. Null is not allowed.
      Returns:
      The source index or -1 if the plate is not a parent plate
      Throws:
      InvalidDataException - If the parent is null

    • getChildPlates

      public ItemQuery<Plate> getChildPlates()
      Get a query returning the child plates of this plate.
      Returns:
      An ItemQuery object

    • getEvent

      public PlateEvent getEvent​(PlateEventType eventType) throws PermissionDeniedException, InvalidDataException, BaseException
      Get the event for the specified event type. If no event for that type exist a new one is created.
      Parameters:
      eventType - The event type to get or create the event for
      Returns:
      The PlateEvent item
      Throws:
      PermissionDeniedException - If the logged in user doesn't have read permission for an existing event or doesn't have write permission if a new event must be created
      InvalidDataException - If the event type is null or doesn't belong to the same PlateType as the plate
      BaseException - If there is another error
      See Also:
      hasEvent(PlateEventType), getEvents()

    • hasEvent

      public boolean hasEvent​(PlateEventType eventType)
      Check if an event for the specified event type has been created for this plate. A plate may only have one event of each type.
      Parameters:
      eventType - The event type to check
      Returns:
      TRUE if an event of the specified type exists, FALSE otherwise
      See Also:
      getEvent(PlateEventType), getEvents()

    • getEvents

      public ItemQuery<PlateEvent> getEvents()
      Get a query that returns all event types for this plate type.
      Returns:
      An ItemQuery object
      Throws:
      BaseException - If there is an error

    • getWell

      public Well getWell​(int row, int column) throws PermissionDeniedException, BaseException
      Get the well on the specified plate coordinate.
      Parameters:
      row - The row coordinate of the well. Starting at 0.
      column - The column coordinate of the well. Starting at 0.
      Returns:
      A Well item or null if the coordinates are outside the range specified by the geometry
      Throws:
      PermissionDeniedException - If the logged in user doesn't have read permission for the well
      BaseException - If there is another error

    • getWells

      public ItemQuery<Well> getWells()
      Get a query returning all wells for this plate.
      Returns:
      An ItemQuery object
      Throws:
      BaseException - If there is an error

    • getReporters

      public DataQuery<ReporterData> getReporters()
      Get a query that returns the reporters on this plate. The query is rooted at the wells, which means that:
      • All filters, sorting, etc. that works for getWells() can be used without modifications on this query.
      • The same reporter may be returned multiple times if it is present on several wells.
      • 'Null' values may be returned if there are wells without a reporter
      Returns:
      A DataQuery object
      Since:
      2.8