org.proteios.core
Class PeakList

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<PeakListData>
                      org.proteios.core.PeakList

All Implemented Interfaces:

Comparable<PeakList>, AccessControlled, Annotatable, Identifiable, Nameable, Ownable, Removable, Shareable

public class PeakList
extends AnnotatedItem<PeakListData>
implements Comparable<PeakList>

This class represent peaklist items. A peaklist has information about the peaks in an experiment.

Version:

2.0

Author:

Olle

Last modified

$Date: 2006-06-01 12:33:12Z $

Field Summary

static int	MAX_COMBINATIONMETHOD_LENGTH The maximum length of the combinationMethod string that can be stored in the database.
static int	MAX_DESCRIPTION_LENGTH The maximum length of the description string that can be stored in the database.
static Item	TYPE The type of item represented by this class.

Fields inherited from interface org.proteios.core.Nameable

MAX_NAME_LENGTH

Method Summary

void	addPeak(Peak peak)
Float	calculateTotalIntensity() Count the total intensity of all peaks in this peaklist
int	compareTo(PeakList p)
Float	findBasePeakIntensity() Find the most intense peak in this peaklist and return the intensity
List<Acquisition>	getAcquisitionList() Get the Acquisition acquisitionList.
ItemQuery<Acquisition>	getAcquisitionsQuery() Get a query that returns all Acquisition items created from this peaklist.
Set<Annotatable>	getAnnotatableParents() Always null.
Float	getBasePeakIntensity() Get the base peak intensity.
static PeakList	getById(DbControl dc, int id) Get a PeakList item when you know the id.
String	getCombinationMethod() Get the combination method of this PeakList.
String	getDescription() Get the description of this PeakList.
int	getMsLevel() Get the msLevel
Float	getMzRangeStart() Get the start of the mzRange.
Float	getMzRangeStop() Get the stop of the mzRange.
List<Peak>	getPeakArrayList() Get the Peak peakArrayList.
PeakListSet	getPeakListSet() Get the PeakListSet this peakList is created from.
ItemQuery<Peak>	getPeaksQuery() Get a query that returns all Peak items created from this peaklist.
List<Precursor>	getPrecursorList() Get the Precursor precursorList.
ItemQuery<Precursor>	getPrecursorsQuery() Get a query that returns all Precursor items created from this peaklist.
static ItemQuery<PeakList>	getQuery() Get a query that returns peaklist items.
int	getSpectrumId() Get the spectrumId
InstrumentConfiguration	getSpectrumInstrument() Get the InstrumentConfiguration spectrumInstrument.
Float	getTimeInMinutes() Get the time in minutes.
Float	getTotalIntensity() Get the total peak intensity.
Item	getType() Get the type of item represented by the object.
boolean	isIntensityDoublePrecision() Get the intensityDoublePrecision flag
boolean	isMonoisotopic() Get the monoisotopic flag
boolean	isMzDoublePrecision() Get the mzDoublePrecision flag
boolean	isUsed() Check that: no item has been created from this peaklist
void	setAcquisitionList(List<Acquisition> acquisitionList) Set the Acquisition acquisitionList.
void	setBasePeakIntensity(Float basePeakIntensity) Set the base peak intensity
void	setCombinationMethod(String combinationMethod) Set the combination method for this PeakList item.
void	setDescription(String description) Set the description for this PeakList item.
void	setIntensityDoublePrecision(boolean doublePrecision) Set the intensityDoublePrecision flag
void	setMonoisotopic(boolean monoisotopic) Set the monoisotopic flag
void	setMsLevel(int msLevel) Set the msLevel.
void	setMzDoublePrecision(boolean doublePrecision) Set the mzDoublePrecision flag
void	setMzRangeStart(Float mzRangeStart) Set the start of the mzRange
void	setMzRangeStop(Float mzRangeStop) Set the stop of the mzRange
void	setPeakArrayList(List<Peak> peakArrayList) Set the Peak peakArrayList.
void	setPeakListSet(PeakListSet peakListSet) Set the PeakListSet this peakList is created from.
void	setPrecursorList(List<Precursor> precursorList) Set the Precursor precursorList.
void	setSpectrumId(int spectrumId) Set the spectrumId.
void	setSpectrumInstrument(InstrumentConfiguration spectrumInstrument) Set the InstrumentConfiguration spectrumInstrument.
void	setTimeInMinutes(Float timeInMinutes) Set the time in minutes
void	setTotalIntensity(Float totalIntensity) Set the total intensity

Methods inherited from class org.proteios.core.CommonItem

getName, isRemoved, 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, getVersion

Methods inherited from interface org.proteios.core.AccessControlled

checkPermission, hasPermission

Methods inherited from interface org.proteios.core.Ownable

getOwner, setOwner

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.PROTEIOS_PEAKLIST, getType()

MAX_COMBINATIONMETHOD_LENGTH

public static final int MAX_COMBINATIONMETHOD_LENGTH

The maximum length of the combinationMethod string that can be stored in the database.

See Also:

setCombinationMethod(String), Constant Field Values

MAX_DESCRIPTION_LENGTH

public static final int MAX_DESCRIPTION_LENGTH

The maximum length of the description string that can be stored in the database.

See Also:

setDescription(String), Constant Field Values

Method Detail

compareTo

public int compareTo(PeakList p)

Specified by:

compareTo in interface Comparable<PeakList>

getById

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

Get a PeakList 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 PeakList item

Throws:

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

BaseException - If there is another error

getQuery

public static ItemQuery<PeakList> getQuery()

Get a query that returns peaklist 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

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 peaklist

Specified by:

isUsed in class BasicItem<PeakListData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getPeakListSet

public PeakListSet getPeakListSet()
                           throws BaseException

Get the PeakListSet this peakList is created from.

Returns:

The PeakListSet item or null if not known

Throws:

BaseException - If there is another error

setPeakListSet

public void setPeakListSet(PeakListSet peakListSet)
                    throws BaseException

Set the PeakListSet this peakList is created from.

Parameters:

peakListSet - The new PeakListSet item

Throws:

BaseException - If there is another error

getCombinationMethod

public String getCombinationMethod()

Get the combination method of this PeakList.

Returns:

the combination method of this peak list

setCombinationMethod

public void setCombinationMethod(String combinationMethod)
                          throws InvalidDataException

Set the combination method for this PeakList item. The value may be null but must not be longer than the value specified by the MAX_COMBINATIONMETHOD_LENGTH constant.

Parameters:

combinationMethod - The new combination method for this item

Throws:

InvalidDataException - If the combinationMethod is longer than MAX_COMBINATIONMETHOD_LENGTH

getDescription

public String getDescription()

Get the description of this PeakList.

Specified by:

getDescription in interface Nameable

Overrides:

getDescription in class CommonItem<PeakListData>

Returns:

the description of this peak list

setDescription

public void setDescription(String description)
                    throws InvalidDataException

Set the description for this PeakList item. The value may be null but must not be longer than the value specified by the MAX_DESCRIPTION_LENGTH constant.

Specified by:

setDescription in interface Nameable

Overrides:

setDescription in class CommonItem<PeakListData>

Parameters:

description - The new description for this item

Throws:

InvalidDataException - If the description is longer than MAX_DESCRIPTION_LENGTH

isMzDoublePrecision

public boolean isMzDoublePrecision()

Get the mzDoublePrecision flag

Returns:

the mzDoublePrecision flag

setMzDoublePrecision

public void setMzDoublePrecision(boolean doublePrecision)

Set the mzDoublePrecision flag

Parameters:

doublePrecision - The mzDoublePrecision flag

isIntensityDoublePrecision

public boolean isIntensityDoublePrecision()

Get the intensityDoublePrecision flag

Returns:

the intensityDoublePrecision flag

setIntensityDoublePrecision

public void setIntensityDoublePrecision(boolean doublePrecision)

Set the intensityDoublePrecision flag

Parameters:

doublePrecision - The intensityDoublePrecision flag

isMonoisotopic

public boolean isMonoisotopic()

Get the monoisotopic flag

Returns:

the monoisotopic flag

setMonoisotopic

public void setMonoisotopic(boolean monoisotopic)

Set the monoisotopic flag

Parameters:

monoisotopic - The monoisotopic flag

getMsLevel

public int getMsLevel()

Get the msLevel

Returns:

the msLevel value

setMsLevel

public void setMsLevel(int msLevel)
                throws InvalidDataException

Set the msLevel.

Parameters:

msLevel - The msLevel value

Throws:

InvalidDataException - If the msLevel is lower than zero

getTotalIntensity

public Float getTotalIntensity()

Get the total peak intensity. Try to calculate and set it if it was not given TODO: Commit to database and perform checks

Returns:

A Float holding the totalIntensity

calculateTotalIntensity

public Float calculateTotalIntensity()

Count the total intensity of all peaks in this peaklist

Returns:

A Float holding the totalIntensity

setTotalIntensity

public void setTotalIntensity(Float totalIntensity)
                       throws InvalidDataException,
                              BaseException

Set the total intensity

Parameters:

totalIntensity - The totalIntensity value

Throws:

InvalidDataException - If totalIntensity is below zero

BaseException

getBasePeakIntensity

public Float getBasePeakIntensity()

Get the base peak intensity.

Returns:

A Float holding the base peak intensity

setBasePeakIntensity

public void setBasePeakIntensity(Float basePeakIntensity)
                          throws InvalidDataException,
                                 BaseException

Set the base peak intensity

Parameters:

basePeakIntensity - The basePeakIntensity value

Throws:

InvalidDataException - If basePeakIntensity is below zero

BaseException

findBasePeakIntensity

public Float findBasePeakIntensity()

Find the most intense peak in this peaklist and return the intensity

Returns:

A Float holding the intensity

getMzRangeStart

public Float getMzRangeStart()

Get the start of the mzRange.

Returns:

A Float holding the mzRangeStart

setMzRangeStart

public void setMzRangeStart(Float mzRangeStart)
                     throws InvalidDataException,
                            BaseException

Set the start of the mzRange

Parameters:

mzRangeStart - The msRangeStart value

Throws:

InvalidDataException - If mzRangeStart is below zero

BaseException

getMzRangeStop

public Float getMzRangeStop()

Get the stop of the mzRange.

Returns:

A Float holding the mzRangeStop

setMzRangeStop

public void setMzRangeStop(Float mzRangeStop)
                    throws InvalidDataException,
                           BaseException

Set the stop of the mzRange

Parameters:

mzRangeStop - The msRangeStop value

Throws:

InvalidDataException - If mzRangeStop is below zero

BaseException

getSpectrumId

public int getSpectrumId()

Get the spectrumId

Returns:

the spectrumId value

setSpectrumId

public void setSpectrumId(int spectrumId)

Set the spectrumId.

Parameters:

spectrumId - The spectrumId value

getSpectrumInstrument

public InstrumentConfiguration getSpectrumInstrument()
                                              throws BaseException

Get the InstrumentConfiguration spectrumInstrument.

Returns:

An InstrumentConfiguration object

Throws:

BaseException - If there is another error

setSpectrumInstrument

public void setSpectrumInstrument(InstrumentConfiguration spectrumInstrument)
                           throws InvalidDataException

Set the InstrumentConfiguration spectrumInstrument.

Parameters:

spectrumInstrument - The new InstrumentConfiguration item

Throws:

InvalidDataException - If spectrumInstrument is null

BaseException - If there is another error

getTimeInMinutes

public Float getTimeInMinutes()

Get the time in minutes.

Returns:

A Float holding the timeInMinutes

setTimeInMinutes

public void setTimeInMinutes(Float timeInMinutes)
                      throws InvalidDataException,
                             BaseException

Set the time in minutes

Parameters:

timeInMinutes - The timeInMinutes value

Throws:

InvalidDataException - If timeInMinutes is below zero

BaseException

getAcquisitionList

public List<Acquisition> getAcquisitionList()
                                     throws ItemNotFoundException,
                                            BaseException

Get the Acquisition acquisitionList.

Returns:

An Acquisition list object

Throws:

BaseException - If there is another error

ItemNotFoundException

setAcquisitionList

public void setAcquisitionList(List<Acquisition> acquisitionList)
                        throws InvalidDataException

Set the Acquisition acquisitionList.

Parameters:

acquisitionList - The new Acquisition list item

Throws:

BaseException - If there is another error

InvalidDataException

getAcquisitionsQuery

public ItemQuery<Acquisition> getAcquisitionsQuery()

Get a query that returns all Acquisition items created from this peaklist.

Returns:

An ItemQuery object

getPrecursorList

public List<Precursor> getPrecursorList()
                                 throws ItemNotFoundException,
                                        BaseException

Get the Precursor precursorList.

Returns:

A Precursor list object

Throws:

BaseException - If there is another error

ItemNotFoundException

setPrecursorList

public void setPrecursorList(List<Precursor> precursorList)
                      throws InvalidDataException

Set the Precursor precursorList.

Parameters:

precursorList - The new Precursor list item

Throws:

BaseException - If there is another error

InvalidDataException

getPrecursorsQuery

public ItemQuery<Precursor> getPrecursorsQuery()

Get a query that returns all Precursor items created from this peaklist.

Returns:

An ItemQuery object

getPeakArrayList

public List<Peak> getPeakArrayList()
                            throws ItemNotFoundException,
                                   BaseException

Get the Peak peakArrayList.

Returns:

A Peak list object

Throws:

BaseException - If there is another error

ItemNotFoundException

setPeakArrayList

public void setPeakArrayList(List<Peak> peakArrayList)
                      throws InvalidDataException

Set the Peak peakArrayList.

Parameters:

peakArrayList - The new Peak list item

Throws:

BaseException - If there is another error

InvalidDataException

addPeak

public void addPeak(Peak peak)

getPeaksQuery

public ItemQuery<Peak> getPeaksQuery()

Get a query that returns all Peak items created from this peaklist.

Returns:

An ItemQuery object