net.sf.basedb.core
Class ArraySlide

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<ArraySlideData>
                      net.sf.basedb.core.ArraySlide

All Implemented Interfaces:

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

public class ArraySlide
extends AnnotatedItem<ArraySlideData>
implements Registered

This class represents a physical microarray slide.

Version:

2.0

Author:

Nicklas, Enell

Field Summary

static int	MAX_BARCODE_LENGTH The maximum length of the barcode 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

ArraySlide(ArraySlideData data)

Method Summary

static boolean	barcodeExists(DbControl dc, String barcode) Checks if a slide with the given barcode already exists in the database.
Set<Annotatable>	getAnnotatableParents() Get the array batch.
ArrayBatch	getArrayBatch() Get the ArrayBatch item to which this slide belongs.
String	getBarcode() Get the barcode of the slide.
int	getBatchIndex() Get the index of this slide in the batch.
static ArraySlide	getById(DbControl dc, int id) Get a ArraySlide object when you know the ID.
Date	getEntryDate() Get the date that the item was registered in the database.
Hybridization	getHybridization() Get the Hybridization item which was used on this slide.
static ArraySlide	getNew(DbControl dc, ArrayBatch arrayBatch) Create a new ArraySlide item.
static ItemQuery<ArraySlide>	getQuery() Get a ItemQuery object configured to retrieve array slides.
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get the hybridization that was used on this plate.
boolean	isDestroyed() Check if the slide is flagged as destroyed or not.
boolean	isUsed() Check if this item is used by some other item.
boolean	isUsedByOther(Hybridization hyb) Checks if this array design is used by a different hybridization than the given one.
private void	setArrayBatch(ArrayBatch arrayBatch) Set the ArrayBatch this arrayslide belongs to.
void	setBarcode(String barcode) Set the barcode for the slide.
void	setBatchIndex(int batchIndex) Set the index of this slide in the batch.
void	setDestroyed(boolean destroyed) Set if the slide should be flagged as destroyed.

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

getAnnotationSet, getProtocol, 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, onBeforeCommit, 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.ARRAYSLIDE, 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 method to avoid exceptions.

See Also:

Constant Field Values

Constructor Detail

ArraySlide

ArraySlide(ArraySlideData data)

Method Detail

getNew

public static ArraySlide getNew(DbControl dc,
                                ArrayBatch arrayBatch)
                         throws PermissionDeniedException,
                                BaseException

Create a new ArraySlide item.

Parameters:

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

arrayBatch - The ArrayBatch this slide belongs to

Returns:

The new ArraySlide item

Throws:

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

BaseException - If there is another error

getById

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

Get a ArraySlide 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 ArraySlide 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

barcodeExists

public static boolean barcodeExists(DbControl dc,
                                    String barcode)

Checks if a slide with the given barcode already exists in the database. The check is done on ALL slides, even on those not normally accessible by the logged in user.

Parameters:

dc - The DbControl to use for database access

barcode - The barcode to check

Returns:

TRUE if the barcode exists, FALSE if not or if the argument is NULL

Since:

2.7

getQuery

public static ItemQuery<ArraySlide> getQuery()

Get a ItemQuery object configured to retrieve array slides.

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 array batch.

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

isUsed

public boolean isUsed()
               throws BaseException

Description copied from class: BasicItem

Check if this item is used by some other item. With used we mean that another item is linking to this item in way that prevents this item from beeing deleted. Ie. if we tried to delete an item that is used, we would get a foreign key violation error from the database. If the subclass overrides this method it should propagate the call to the superclass, ie. super.isUsed(), unless it has decided that the item is used by some other means.

Overrides:

isUsed in class BasicItem<ArraySlideData>

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()
                             throws BaseException

Get the hybridization that was used on this plate.

Overrides:

getUsingItems in class BasicItem<ArraySlideData>

Returns:

A set containing proxies for the items, or an empty set if no items are using this item

Throws:

BaseException - If there is an error loading the items

Since:

2.2

See Also:

BasicItem.addUsingItems(Set, Item, org.hibernate.Query)

getBatchIndex

public int getBatchIndex()

Get the index of this slide in the batch.

Returns:

The index of the slide

setBatchIndex

public void setBatchIndex(int batchIndex)
                   throws PermissionDeniedException

Set the index of this slide in the batch.

Parameters:

batchIndex - The index of the slide in the batch

Throws:

PermissionDeniedException - This exception is thrown if the logged in user doesn't have write permission.

getBarcode

public String getBarcode()

Get the barcode of the slide.

Returns:

A string with the barcode sequence

setBarcode

public void setBarcode(String barcode)
                throws PermissionDeniedException,
                       InvalidDataException

Set the barcode for the slide. The value can be null and must not be longer than the value specified by the MAX_BARCODE_LENGTH constant.

Parameters:

barcode - The new barcode for the slide

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - This exception is thrown if the barcode is longer than MAX_BARCODE_LENGTH

isDestroyed

public boolean isDestroyed()

Check if the slide is flagged as destroyed or not. A destroyed slide may not be connected to a hybridization.

Returns:

TRUE if the slide is destroyed, FALSE otherwise

setDestroyed

public void setDestroyed(boolean destroyed)
                  throws PermissionDeniedException

Set if the slide should be flagged as destroyed. A destroyed slide may not be connected to a hybridization.

Parameters:

destroyed - true if the slide should be flagged as destroyed, false otherwise

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

getArrayBatch

public ArrayBatch getArrayBatch()
                         throws PermissionDeniedException,
                                BaseException

Get the ArrayBatch item to which this slide belongs.

Returns:

The ArrayBatch item

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the array batch

BaseException - If there is another error

setArrayBatch

private void setArrayBatch(ArrayBatch arrayBatch)
                    throws InvalidDataException,
                           PermissionDeniedException

Set the ArrayBatch this arrayslide belongs to.

Parameters:

arrayBatch - the arrayBatch to be set. Cannot be null.

Throws:

InvalidDataException - If the arrayBatch is null

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

getHybridization

public Hybridization getHybridization()
                               throws PermissionDeniedException,
                                      BaseException

Get the Hybridization item which was used on this slide. To set the hybridization use the Hybridization.setArraySlide(ArraySlide) method.

Returns:

The Hybridization item

Throws:

PermissionDeniedException - This exception is thrown if the logged in user doesn't have read permission to the item

BaseException - If there is another error

isUsedByOther

public boolean isUsedByOther(Hybridization hyb)

Checks if this array design is used by a different hybridization than the given one.

Parameters:

hyb - The hybridization to check, or null to check if the slide is used by any hybridization

Returns:

TRUE if the slide is used by a different hybridization, or FALSE if it is used by the given hybridization, or not used at all

Since:

2.8.3