org.proteios.core
Class Peak

java.lang.Object
  org.proteios.core.BasicItem<PeakData>
      org.proteios.core.Peak

All Implemented Interfaces:

Comparable<Peak>, AccessControlled, Annotatable, Identifiable

public class Peak
extends BasicItem<PeakData>
implements Annotatable, Comparable<Peak>

This class represent peak items. A peak item has information about the peak in a 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.

Constructor Summary

Peak(PeakData peakData)

Method Summary

int	compareTo(Peak p)
static Peak	getById(DbControl dc, int id) Get a Peak item when you know the id.
Double	getIntensity() Get the intensity.
Double	getMassToChargeRatio() Get the massToChargeRatio.
PeakList	getPeakList() Get the PeakList this peak is created from.
static ItemQuery<Peak>	getQuery() Get a query that returns peak items.
Item	getType() Get the type of item represented by the object.
boolean	isUsed() Check that: no item has been created from this peak
void	setIntensity(Double intensity) Set the intensity
void	setMassToChargeRatio(Double massToChargeRatio) Set the massToChargeRatio
void	setPeakList(PeakList peakList) Set the PeakList this peak is created from.

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_PEAK, getType()

Constructor Detail

Peak

public Peak(PeakData peakData)

Method Detail

compareTo

public int compareTo(Peak p)

Specified by:

compareTo in interface Comparable<Peak>

getById

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

Get a Peak 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 Peak item

Throws:

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

BaseException - If there is another error

getQuery

public static ItemQuery<Peak> getQuery()

Get a query that returns peak 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.

Specified by:

getType in interface Identifiable

Returns:

A value indicating the type of item

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• no item has been created from this peak

Specified by:

isUsed in class BasicItem<PeakData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getMassToChargeRatio

public Double getMassToChargeRatio()

Get the massToChargeRatio.

Returns:

A Double holding the massToChargeRatio

setMassToChargeRatio

public void setMassToChargeRatio(Double massToChargeRatio)
                          throws InvalidDataException,
                                 BaseException

Set the massToChargeRatio

Parameters:

massToChargeRatio - The Double massToChargeRatio value

Throws:

InvalidDataException - If massToChargeRatio is below zero

BaseException

getIntensity

public Double getIntensity()

Get the intensity.

Returns:

A Double holding the intensity

setIntensity

public void setIntensity(Double intensity)
                  throws InvalidDataException,
                         BaseException

Set the intensity

Parameters:

intensity - The Double intensity value

Throws:

InvalidDataException - If intensity is below zero

BaseException

getPeakList

public PeakList getPeakList()
                     throws BaseException

Get the PeakList this peak 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 peak is created from.

Parameters:

peakList - The new PeakList item

Throws:

BaseException - If there is another error