org.proteios.core
Class GelElectrophoresis

java.lang.Object
  org.proteios.core.BasicItem<D>
      org.proteios.core.OwnedItem<D>
          org.proteios.core.SharedItem<D>
              org.proteios.core.SeparationMethod<GelElectrophoresisData>
                  org.proteios.core.GelElectrophoresis

All Implemented Interfaces:

AccessControlled, Identifiable, Ownable, Shareable

public class GelElectrophoresis
extends SeparationMethod<GelElectrophoresisData>

This class represent gel electrophoresis items. A gel electrophoresis has information about the separation method used in an experiment.

Version:

2.0

Author:

Olle

Last modified

$Date: 2006-09-19 12:33:12Z $

Field Summary

static Item

TYPE The type of item represented by this class.

Fields inherited from class org.proteios.core.SeparationMethod

MAX_EXTERNAL_ID_LENGTH

Method Summary

void	addGelScanEvent(GelScanEvent dp) Add a GelScanEvent
void	addStainingEvent(StainingEvent dp) Add a StainingEvent
Set<Annotatable>	getAnnotatableParents() Always null.
static GelElectrophoresis	getByExternalId(DbControl dc, String externalId) Get a GelElectrophoresis item when you know the external ID.
String	getDenaturatingAgent() Get the denaturatingAgent of this GelElectrophoresis.
Set<GelScanEvent>	getGelScanEvents()
Integer	getMassEndInKiloDaltons() Get the integer massEnd value.
Integer	getMassStartInKiloDaltons() Get the integer massStart value.
Integer	getPercentAcrylamide() Get the integer percentAcrylamide value.
String	getProteinAssay() Get the proteinAssay of this GelElectrophoresis.
static ItemQuery<GelElectrophoresis>	getQuery() Get a query that returns gelelectrophoresis items.
Integer	getSizeXInCentiMeters() Get the Integer sizeX value.
Integer	getSizeYInCentiMeters() Get the Integer sizeY value.
String	getSolubilizationBuffer() Get the solubilizationBuffer of this GelElectrophoresis.
Set<StainingEvent>	getStainingEvents()
Item	getType() Get the type of item represented by the object.
boolean	isUsed() Check that: no item has been created from this gelelectrophoresis
void	setDenaturatingAgent(String denaturatingAgent) Set the denaturatingAgent for this GelElectrophoresis item.
void	setMassEndInKiloDaltons(Integer massEnd) Set the integer massEnd value.
void	setMassStartInKiloDaltons(Integer massStart) Set the integer massStart value.
void	setPercentAcrylamide(Integer percentAcrylamide) Set the integer percentAcrylamide value.
void	setProteinAssay(String proteinAssay) Set the proteinAssay for this GelElectrophoresis item.
void	setSizeXInCentiMeters(Integer sizeX) Set the Integer sizeX value.
void	setSizeYInCentiMeters(Integer sizeY) Set the Integer sizeY value.
void	setSolubilizationBuffer(String solubilizationBuffer) Set the solubilizationBuffer for this GelElectrophoresis item.

Methods inherited from class org.proteios.core.SeparationMethod

getExternalId, getIdsForSeparationMethodsWithSeaprationEvent, getSeparationEvents, setExternalId

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.Ownable

getOwner, setOwner

Methods inherited from interface org.proteios.core.Identifiable

getId, getVersion

Methods inherited from interface org.proteios.core.AccessControlled

checkPermission, hasPermission

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.PROTEIOS_GELELECTROPHORESIS, getType()

Method Detail

getQuery

public static ItemQuery<GelElectrophoresis> getQuery()

Get a query that returns gelelectrophoresis items.

Returns:

An ItemQuery object.

getByExternalId

public static GelElectrophoresis getByExternalId(DbControl dc,
                                                 String externalId)
                                          throws ItemNotFoundException,
                                                 PermissionDeniedException,
                                                 BaseException

Get a GelElectrophoresis item when you know the external ID. The method with the same name inherited from the super class is used to retrieve the item, which is then casted to the right type.

Parameters:

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

externalId - The external id of the item to load

Returns:

The GelElectrophoresis item

Throws:

ItemNotFoundException - If an item with the specified ID is not found

PermissionDeniedException - If the logged in user doesn't have READ permission for the item

BaseException - If there is another error

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

Overrides:

getType in class SeparationMethod<GelElectrophoresisData>

Returns:

A value indicating the type of item

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Always null.

Throws:

BaseException

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• no item has been created from this gelelectrophoresis

Overrides:

isUsed in class SeparationMethod<GelElectrophoresisData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

addGelScanEvent

public void addGelScanEvent(GelScanEvent dp)

Add a GelScanEvent

Parameters:

dp - The GelScanEvent to add to the Set

getGelScanEvents

public Set<GelScanEvent> getGelScanEvents()
                                   throws ItemNotFoundException,
                                          BaseException

Returns:

Returns the gelScanEvents.

Throws:

ItemNotFoundException

BaseException

addStainingEvent

public void addStainingEvent(StainingEvent dp)

Add a StainingEvent

Parameters:

dp - The StainingEvent to add to the Set

getStainingEvents

public Set<StainingEvent> getStainingEvents()
                                     throws ItemNotFoundException,
                                            BaseException

Returns:

Returns the stainingEvents.

Throws:

ItemNotFoundException

BaseException

getDenaturatingAgent

public String getDenaturatingAgent()

Get the denaturatingAgent of this GelElectrophoresis.

Returns:

the String denaturatingAgent of this gel electrophoresis

setDenaturatingAgent

public void setDenaturatingAgent(String denaturatingAgent)

Set the denaturatingAgent for this GelElectrophoresis item.

Parameters:

denaturatingAgent - The new String denaturatingAgent for this item

getMassStartInKiloDaltons

public Integer getMassStartInKiloDaltons()

Get the integer massStart value.

Returns:

the integer massStart value

setMassStartInKiloDaltons

public void setMassStartInKiloDaltons(Integer massStart)
                               throws InvalidDataException

Set the integer massStart value.

Parameters:

massStart - The integer massStart value to set.

Throws:

InvalidDataException - If the massStart is lower than zero

getMassEndInKiloDaltons

public Integer getMassEndInKiloDaltons()

Get the integer massEnd value.

Returns:

the integer massEnd value

setMassEndInKiloDaltons

public void setMassEndInKiloDaltons(Integer massEnd)
                             throws InvalidDataException

Set the integer massEnd value.

Parameters:

massEnd - The integer massEnd value to set.

Throws:

InvalidDataException - If the massEnd is lower than zero

getPercentAcrylamide

public Integer getPercentAcrylamide()

Get the integer percentAcrylamide value.

Returns:

the integer percentAcrylamide value

setPercentAcrylamide

public void setPercentAcrylamide(Integer percentAcrylamide)
                          throws InvalidDataException

Set the integer percentAcrylamide value.

Parameters:

percentAcrylamide - The integer percentAcrylamide value to set.

Throws:

InvalidDataException - If the percentAcrylamide is lower than zero

getProteinAssay

public String getProteinAssay()

Get the proteinAssay of this GelElectrophoresis.

Returns:

the String proteinAssay of this gel electrophoresis

setProteinAssay

public void setProteinAssay(String proteinAssay)

Set the proteinAssay for this GelElectrophoresis item.

Parameters:

proteinAssay - The new String proteinAssay for this item

getSizeXInCentiMeters

public Integer getSizeXInCentiMeters()

Get the Integer sizeX value.

Returns:

the Integer sizeX value

setSizeXInCentiMeters

public void setSizeXInCentiMeters(Integer sizeX)

Set the Integer sizeX value.

Parameters:

sizeX - The Integer sizeX value to set.

getSizeYInCentiMeters

public Integer getSizeYInCentiMeters()

Get the Integer sizeY value.

Returns:

the Integer sizeY value

setSizeYInCentiMeters

public void setSizeYInCentiMeters(Integer sizeY)

Set the Integer sizeY value.

Parameters:

sizeY - The Integer sizeY value to set.

getSolubilizationBuffer

public String getSolubilizationBuffer()

Get the solubilizationBuffer of this GelElectrophoresis.

Returns:

the String solubilizationBuffer of this gel electrophoresis

setSolubilizationBuffer

public void setSolubilizationBuffer(String solubilizationBuffer)

Set the solubilizationBuffer for this GelElectrophoresis item.

Parameters:

solubilizationBuffer - The new String solubilizationBuffer for this item