org.proteios.core
Class MeasuredBioMaterial<D extends MeasuredBioMaterialData>

java.lang.Object
  org.proteios.core.BasicItem<D>
      org.proteios.core.OwnedItem<D>
          org.proteios.core.SharedItem<D>
              org.proteios.core.CommonItem<D>
                  org.proteios.core.AnnotatedItem<D>
                      org.proteios.core.BioMaterial<D>
                          org.proteios.core.MeasuredBioMaterial<D>

All Implemented Interfaces:

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

Direct Known Subclasses:

Extract, LabeledExtract, MeasuredArea, Sample

public abstract class MeasuredBioMaterial<D extends MeasuredBioMaterialData>
extends BioMaterial<D>

This class is the base class for measured biomaterial items. A measured item is an item which can have original and remaining quantities associated with them.

The core keeps track of the remaining quantity whenever an item is used to create other items. As it is, an item can be used when creating another item of the same type (pooling) or when creating an item of the appropriate subtype, ie. Sample -> Extract -> LabeledExtract.

It is also possible to add a note using a BioMaterialEvent saying that the quantity has been changed and why.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2009-04-09 08:48:11 +0200 (Thu, 09 Apr 2009) $

Field Summary

Fields inherited from class org.proteios.core.BioMaterial

MAX_EXTERNAL_ID_LENGTH, MAX_STORAGE_LOCATION_LENGTH

Fields inherited from interface org.proteios.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Method Summary

Float	getConcentrationInGramsPerLiter() Get the concentration (in mg protein / ml) of the biomaterial.
CreationEvent	getCreationEvent() Get the event that represents the creation of this biomaterial.
ItemQuery<BioMaterialEvent>	getEventQuery()
Set<BioMaterialEvent>	getEvents() Get the events that have used this biomaterial.
Float	getOriginalQuantityInMicroLiters() Get the original quantity of the biomaterial measured in microliters.
Float	getRemainingQuantityInMicroLiters() Get the remaining quantity of the biomaterial measured in microliters.
boolean	isPooled() Check if this biomaterial was created by pooling or not.
boolean	isUsed() Check that: no pooled biomaterial has been created from this item
void	setConcentrationInGramsPerLiter(Float concentration) Set the concentration (in mg protein / ml) of the biomaterial.
void	setCreationEvent(CreationEvent creationEvent)
void	setOriginalQuantityInMicroLiters(Float originalQuantity) Set the original quantity of the biomaterial measured in microliters.
void	setPooled(boolean pooled) Specify if this biomaterial was created by pooling or not.
void	setRemainingQuantityInMicroLiters(Float remainingQuantity) Set the remaining quantity of the biomaterial measured in microliters.

Methods inherited from class org.proteios.core.BioMaterial

addFile, getExternalId, getFiles, getStorageLocation, setExternalId, setFiles, setStorageLocation

Methods inherited from class org.proteios.core.CommonItem

getDescription, getName, isRemoved, setDescription, setName, setRemoved

Methods inherited from class org.proteios.core.SharedItem

getItemKey, getProjectKey, isShared, setItemKey, setProjectKey

Methods inherited from class org.proteios.core.OwnedItem

getOwner, setOwner

Methods inherited from class org.proteios.core.BasicItem

checkPermission, equals, getDbControl, getId, getPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.proteios.core.Identifiable

getId, getType, getVersion

Methods inherited from interface org.proteios.core.AccessControlled

checkPermission, hasPermission

Methods inherited from interface org.proteios.core.Ownable

getOwner, setOwner

Method Detail

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• no pooled biomaterial has been created from this item

Specified by:

isUsed in class BasicItem<D extends MeasuredBioMaterialData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getCreationEvent

public CreationEvent getCreationEvent()
                               throws PermissionDeniedException,
                                      BaseException

Get the event that represents the creation of this biomaterial. Return null if no creation event registered.

Returns:

A CreationEvent data.

Throws:

PermissionDeniedException

BaseException

setCreationEvent

public void setCreationEvent(CreationEvent creationEvent)

getConcentrationInGramsPerLiter

public Float getConcentrationInGramsPerLiter()

Get the concentration (in mg protein / ml) of the biomaterial.

Returns:

A Float holding concentration, or null if not known

setConcentrationInGramsPerLiter

public void setConcentrationInGramsPerLiter(Float concentration)

Set the concentration (in mg protein / ml) of the biomaterial.

Parameters:

concentration - A Float holding concentration, or null if not known

getOriginalQuantityInMicroLiters

public Float getOriginalQuantityInMicroLiters()

Get the original quantity of the biomaterial measured in microliters.

Returns:

A Float holding the original quantity, or null if not known

setOriginalQuantityInMicroLiters

public void setOriginalQuantityInMicroLiters(Float originalQuantity)
                                      throws PermissionDeniedException,
                                             InvalidDataException,
                                             BaseException

Set the original quantity of the biomaterial measured in microliters. If the remaining quantity is null, it's value is also set to the same as the original value.

Parameters:

originalQuantity - The new value for the original quantity, or null if not known

Throws:

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

InvalidDataException - If the original quantity is below zero

BaseException

getRemainingQuantityInMicroLiters

public Float getRemainingQuantityInMicroLiters()

Get the remaining quantity of the biomaterial measured in microliters. The remaining quantity cannot be modified directly. It is calculated based on the events for this biomaterial.

Returns:

A Float holding the remaining quantity or null if not known

setRemainingQuantityInMicroLiters

public void setRemainingQuantityInMicroLiters(Float remainingQuantity)
                                       throws PermissionDeniedException,
                                              InvalidDataException,
                                              BaseException

Set the remaining quantity of the biomaterial measured in microliters.

Parameters:

remainingQuantity - The new value for the remaining quantity, or null if not known

Throws:

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

InvalidDataException - If the remaining quantity is below zero

BaseException

isPooled

public boolean isPooled()

Check if this biomaterial was created by pooling or not.

setPooled

public void setPooled(boolean pooled)
               throws PermissionDeniedException,
                      BaseException

Specify if this biomaterial was created by pooling or not.

Throws:

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

BaseException - If there is another error

See Also:

BioMaterialEvent.getSources()

getEvents

public Set<BioMaterialEvent> getEvents()

Get the events that have used this biomaterial.

getEventQuery

public ItemQuery<BioMaterialEvent> getEventQuery()

Returns:

a Query for all events that used this extract