net.sf.basedb.core
Class Hybridization

java.lang.Object
  net.sf.basedb.core.BasicItem<D>
      net.sf.basedb.core.OwnedItem<D>
          net.sf.basedb.core.SharedItem<D>
              net.sf.basedb.core.CommonItem<D>
                  net.sf.basedb.core.AnnotatedItem<HybridizationData>
                      net.sf.basedb.core.Hybridization

All Implemented Interfaces:

AccessControlled, Annotatable, Identifiable, Nameable, Ownable, Registered, Removable, Shareable

public class Hybridization
extends AnnotatedItem<HybridizationData>
implements Registered

A hybridization is a representation of the process of hybridizing one or more LabeledExtract:s on an ArraySlide.

Version:

2.0

Author:

Enell, Nicklas

Last modified

$Date$

Field Summary

private BioPlateEventParticipant	bioPlateEventParticipant
private BioMaterialEvent	creationEvent
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

Hybridization(HybridizationData hybridizationData)

Method Summary

long	countScans() Counts all scans that have been created from this hybridization.
Set<Annotatable>	getAnnotatableParents() Get the labeled extracts and array slide.
Set<Annotatable>	getAnnotatableParents(int arrayNum) Get the labeled extracts, possible on a specific array, and the array slide.
ArraySlide	getArraySlide() Get the ArraySlide this hyridization is using.
static Hybridization	getById(DbControl dc, int id) Get a Hybridization item when you know the id.
BioMaterialEvent	getCreationEvent() Get the event that represents the creation of this hybridization.
Date	getEntryDate() Get the date that the item was registered in the database.
ItemQuery<LabeledExtract>	getLabeledExtracts(int arrayNum) Get a query that returns labeled extracts connected to this hybridization.
static Hybridization	getNew(DbControl dc) Create a new Hybridization item.
static Hybridization	getNew(DbControl dc, BioPlateEventParticipant master) Create a new Hybridization item as part of a master bioplate event.
int	getNumArrays() Get the number of arrays that on the slide.
Protocol	getProtocol() Get the protocol from the creation event.
static ItemQuery<Hybridization>	getQuery() Get a query that returns hybridizations.
ItemQuery<Scan>	getScans() Get a query that returns all scans created from this hybridization.
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get all: Scan:s created from this hybridization
boolean	isUsed() Check that: No Scan:s use the hybridization
Scan	newScan() Create a new Scan from this hybridization.
(package private) void	onBeforeCommit(Transactional.Action action) Make sure the creation event is created at the same time this item is created and that source biomaterials get their used quantities back if this item is deleted.
void	setArraySlide(ArraySlide arraySlide) Set the ArraySlide this hybridization is using.
(package private) void	setBioPlateEventParticipant(BioPlateEventParticipant bioPlateEventParticipant)
void	setNumArrays(int numArrays) Set the number of arrays on a single slide.

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

getAnnotationSet, isAnnotated, removeAnnotations, toTransferable

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

getDescription, getName, isRemoved, setDescription, setName, setRemoved, toTransferable

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

getItemKey, getProjectKey, initPermissions, isShared, setItemKey, setProjectKey, toTransferable

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

getOwner, isOwner, setOwner, takeOwnership, toTransferable

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

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onRollback, setDbControl, setProjectDefaults, toString, toTransferable, validate

Methods inherited from class java.lang.Object

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

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

getId, getVersion

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

checkPermission, getPermissions, hasPermission

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

getOwner, isOwner, setOwner, takeOwnership

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.HYBRIDIZATION, getType()

creationEvent

private BioMaterialEvent creationEvent

bioPlateEventParticipant

private BioPlateEventParticipant bioPlateEventParticipant

Constructor Detail

Hybridization

Hybridization(HybridizationData hybridizationData)

Method Detail

getNew

public static Hybridization getNew(DbControl dc)
                            throws BaseException

Create a new Hybridization item.

Parameters:

dc - The DbControl which will be used for permission checking and database access

Returns:

The new Hybridization item

Throws:

BaseException - If there is an error

getNew

public static Hybridization getNew(DbControl dc,
                                   BioPlateEventParticipant master)
                            throws BaseException

Create a new Hybridization item as part of a master bioplate event.

Parameters:

dc - The DbControl which will be used for permission checking and database access

master - The master bioplate event participant or null

Returns:

The new Hybridization item

Throws:

BaseException - If there is an error

Since:

2.17

getById

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

Get a Hybridization 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 Hybridization 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<Hybridization> getQuery()

Get a query that returns hybridizations.

Returns:

An ItemQuery object

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 labeled extracts and array slide. Note that this method will include all labeled extracts, even on multi-array hybridizations.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

See Also:

getAnnotatableParents(int)

getProtocol

public Protocol getProtocol()

Get the protocol from the creation event.

Specified by:

getProtocol in interface Annotatable

Overrides:

getProtocol in class AnnotatedItem<HybridizationData>

Returns:

Always null

Since:

2.2

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

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• No Scan:s use the hybridization

Overrides:

isUsed in class BasicItem<HybridizationData>

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:

• Scan:s created from this hybridization

  Overrides:

  getUsingItems in class BasicItem<HybridizationData>

  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)

onBeforeCommit

void onBeforeCommit(Transactional.Action action)
              throws BaseException

Make sure the creation event is created at the same time this item is created and that source biomaterials get their used quantities back if this item is deleted. All events are deleted by cascade mapping in Hibernate.

Overrides:

onBeforeCommit in class SharedItem<HybridizationData>

Throws:

BaseException - If there is another error

See Also:

Transactional, Core API overview - Transaction handling, Coding rules and guidelines for item classes

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents(int arrayNum)
                                       throws BaseException

Get the labeled extracts, possible on a specific array, and the array slide.

Parameters:

arrayNum - If > 0 only include the labeled extracts which has been linked with BioMaterialEvent.setSourceGroup(MeasuredBioMaterial, int). If <= 0 include all labeled extracts.

Throws:

BaseException

getCreationEvent

public BioMaterialEvent getCreationEvent()
                                  throws PermissionDeniedException,
                                         BaseException

Get the event that represents the creation of this hybridization. Use this event to add source labeled extracts, a protocol, etc.

Returns:

A BioMaterialEvent data.

Throws:

PermissionDeniedException - If the logged in user don't have read permissions

BaseException - If there is another error.

setBioPlateEventParticipant

void setBioPlateEventParticipant(BioPlateEventParticipant bioPlateEventParticipant)

getArraySlide

public ArraySlide getArraySlide()
                         throws PermissionDeniedException,
                                BaseException

Get the ArraySlide this hyridization is using. A single slide can only be used on one hybridization.

Returns:

The ArraySlide item

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission to the array slide

BaseException - If there is another error.

setArraySlide

public void setArraySlide(ArraySlide arraySlide)
                   throws PermissionDeniedException

Set the ArraySlide this hybridization is using.

Parameters:

arraySlide - The array slide, or null

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the hybridization or use permission for the array slide

BaseException - If there is another error.

getNumArrays

public int getNumArrays()

Get the number of arrays that on the slide. The default value is 1.

Since:

2.6

setNumArrays

public void setNumArrays(int numArrays)

Set the number of arrays on a single slide. The value should be between 1 and the number of arrays specified by the connected array design. The latter requiremed is not checked.

Parameters:

numArrays - A value > 0

Throws:

NumberOutOfRangeException - If the value is <=0

Since:

2.6

getLabeledExtracts

public ItemQuery<LabeledExtract> getLabeledExtracts(int arrayNum)

Get a query that returns labeled extracts connected to this hybridization.

Parameters:

arrayNum - If > 0 only labeled extracts on the specific sub-array are returned by the query, if <= 0, all labeled extracts are returned

Returns:

An ItemQuery object

Since:

2.6

newScan

public Scan newScan()
             throws PermissionDeniedException,
                    BaseException

Create a new Scan from this hybridization.

Returns:

The new Scan item

Throws:

PermissionDeniedException - If the logged in user doesn't have use permission for the hybridzation

BaseException - If there is another error

getScans

public ItemQuery<Scan> getScans()

Get a query that returns all scans created from this hybridization.

Returns:

An ItemQuery object

countScans

public long countScans()
                throws BaseException

Counts all scans that have been created from this hybridization. The count includes scans that the logged in user doesn't have access to.

Returns:

The number of scans

Throws:

BaseException - If the scans could not be counted.