org.proteios.core
Class Precursor

java.lang.Object
  org.proteios.core.BasicItem<PrecursorData>
      org.proteios.core.Precursor

All Implemented Interfaces:

AccessControlled, Identifiable

public class Precursor
extends BasicItem<PrecursorData>

This class represent precursor items. A precursor item has information about the precursor in a 2-D mass spectrometry experiment.

Version:

2.0

Author:

Olle

Last modified

$Date: 2006-06-02 12:33:12Z $

Field Summary

static Item

TYPE The type of item represented by this class.

Method Summary

InstrumentConfiguration	getActivation() Get the InstrumentConfiguration activation.
Set<Annotatable>	getAnnotatableParents() Always null.
AnnotationSet	getAnnotationSet()
static Precursor	getById(DbControl dc, int id) Get a Precursor item when you know the id.
int	getChargeState() Get the chargeState
Float	getIntensity() Get the precursor intensity.
InstrumentConfiguration	getIonSelection() Get the InstrumentConfiguration ionSelection.
Float	getMassToChargeRatio() Get the mass to charge ratio.
int	getMsLevel() Get the msLevel
PeakList	getPeakList() Get the PeakList this precursor is created from.
static ItemQuery<Precursor>	getQuery() Get a query that returns precursor items.
int	getSpectrumRef() Get the spectrumRef
Item	getType() Get the type of item represented by the object.
boolean	isAnnotated()
boolean	isUsed() Check that: no item has been created from this precursor
void	removeAnnotations()
void	setActivation(InstrumentConfiguration activation) Set the InstrumentConfiguration activation.
void	setChargeState(int chargeState) Set the chargeState.
void	setIntensity(Float intensity) Set the mass to charge ratio
void	setIonSelection(InstrumentConfiguration ionSelection) Set the InstrumentConfiguration ionSelection.
void	setMassToChargeRatio(Float massToChargeRatio) Set the mass to charge ratio
void	setMsLevel(int msLevel) Set the msLevel.
void	setPeakList(PeakList peakList) Set the PeakList this precursor is created from.
void	setSpectrumRef(int spectrumRef) Set the spectrumRef.

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

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.PROTEIOS_PRECURSOR, getType()

Method Detail

getById

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

Get a Precursor item when you know the id.

Parameters:

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

id - The id of the item to load

Returns:

The Precursor item

Throws:

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

BaseException - If there is another error

getQuery

public static ItemQuery<Precursor> getQuery()

Get a query that returns precursor items.

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.

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 precursor

Specified by:

isUsed in class BasicItem<PrecursorData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getActivation

public InstrumentConfiguration getActivation()
                                      throws BaseException

Get the InstrumentConfiguration activation.

Returns:

An InstrumentConfiguration object

Throws:

BaseException - If there is another error

setActivation

public void setActivation(InstrumentConfiguration activation)
                   throws InvalidDataException

Set the InstrumentConfiguration activation.

Parameters:

activation - The new InstrumentConfiguration item

Throws:

InvalidDataException - If activation is null

BaseException - If there is another error

getChargeState

public int getChargeState()

Get the chargeState

Returns:

the chargeState value

setChargeState

public void setChargeState(int chargeState)

Set the chargeState.

Parameters:

chargeState - The chargeState value

getIonSelection

public InstrumentConfiguration getIonSelection()
                                        throws BaseException

Get the InstrumentConfiguration ionSelection.

Returns:

An InstrumentConfiguration object

Throws:

BaseException - If there is another error

setIonSelection

public void setIonSelection(InstrumentConfiguration ionSelection)
                     throws InvalidDataException

Set the InstrumentConfiguration ionSelection.

Parameters:

ionSelection - The new InstrumentConfiguration item

Throws:

InvalidDataException - If ionSelection is null

BaseException - If there is another error

getMassToChargeRatio

public Float getMassToChargeRatio()

Get the mass to charge ratio.

Returns:

A Float holding the massToChargeRatio

setMassToChargeRatio

public void setMassToChargeRatio(Float massToChargeRatio)
                          throws InvalidDataException,
                                 BaseException

Set the mass to charge ratio

Parameters:

massToChargeRatio - The massToChargeRatio value

Throws:

InvalidDataException - If massToChargeRatio is below zero

BaseException

getIntensity

public Float getIntensity()

Get the precursor intensity.

Returns:

A Float holding the intensity

setIntensity

public void setIntensity(Float intensity)
                  throws InvalidDataException,
                         BaseException

Set the mass to charge ratio

Parameters:

intensity - The intensity value

Throws:

InvalidDataException - If intensity is below zero

BaseException

getMsLevel

public int getMsLevel()

Get the msLevel

Returns:

the msLevel value

setMsLevel

public void setMsLevel(int msLevel)

Set the msLevel.

Parameters:

msLevel - The msLevel value

getSpectrumRef

public int getSpectrumRef()

Get the spectrumRef

Returns:

the spectrumRef value

setSpectrumRef

public void setSpectrumRef(int spectrumRef)

Set the spectrumRef.

Parameters:

spectrumRef - The spectrumRef value

getPeakList

public PeakList getPeakList()
                     throws BaseException

Get the PeakList this precursor is created from.

Returns:

The PeakList item or null if not known

Throws:

BaseException - If there is another error

setPeakList

public void setPeakList(PeakList peakList)

Set the PeakList this precursor is created from.

Parameters:

peakList - The new PeakList item

Throws:

BaseException - If there is another error

getAnnotationSet

public AnnotationSet getAnnotationSet()
                               throws PermissionDeniedException,
                                      BaseException

Throws:

PermissionDeniedException

BaseException

isAnnotated

public boolean isAnnotated()

removeAnnotations

public void removeAnnotations()
                       throws PermissionDeniedException,
                              BaseException

Throws:

PermissionDeniedException

BaseException