org.proteios.core
Class PeakListSet

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<PeakListSetData>
                      org.proteios.core.PeakListSet

All Implemented Interfaces:

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

public class PeakListSet
extends AnnotatedItem<PeakListSetData>

This class represent peaklistset items. A peaklistset has information about the peak lists in an experiment.

Version:

2.0

Author:

Olle

Last modified

$Date: 2006-05-31 12:33:12Z $

Field Summary

static Item

TYPE The type of item represented by this class.

Fields inherited from interface org.proteios.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Method Summary

void	addDataProcessingStep(DataProcessingStep dp) Add a DataProcessingStep
void	addPeakList(PeakList peakList)
List<HardwareConfiguration>	getAnalyzers() Get the HardwareConfiguration analyzers list.
Set<Annotatable>	getAnnotatableParents() Always null.
static PeakListSet	getById(DbControl dc, int id) Get a PeakListSet item when you know the id.
List<DataProcessingStep>	getDataProcessingStepList() Get the DataProcessingStep dataProcessingStepList.
HardwareConfiguration	getDetector() Get the HardwareConfiguration detector.
Hardware	getInstrument() Get the Hardware instrument.
HardwareConfiguration	getIonisationSource() Get the HardwareConfiguration ionisationSource.
InstrumentConfiguration	getOtherInstrumentInfo() Get the InstrumentConfiguration otherInstrumentInfo.
List<PeakList>	getPeakListArrayList() Get the PeakList peakListArrayList.
ItemQuery<PeakList>	getPeakListsQuery() Get a query that returns all PeakList items created from this peaklistset.
static ItemQuery<PeakListSet>	getQuery() Get a query that returns peaklistset items.
Sample	getSample() Get the Sample /** Get the Sample
File	getSourceFile() Get the File sourceFile.
Set<SpectrumSearch>	getSpectrumSearches()
Item	getType() Get the type of item represented by the object.
boolean	isUsed() Check if this item is used by some other item.
void	setAnalyzers(List<HardwareConfiguration> analyzers) Set the HardwareConfiguration analyzers.
void	setDataProcessingStepList(List<DataProcessingStep> dataProcessingStepList) Set the DataProcessingStep dataProcessingStepList.
void	setDetector(HardwareConfiguration detector) Set the HardwareConfiguration detector.
void	setInstrument(Hardware instrument) Set the Hardware instrument.
void	setIonisationSource(HardwareConfiguration ionisationSource) Set the HardwareConfiguration ionisationSource.
void	setOtherInstrumentInfo(InstrumentConfiguration otherInstrumentInfo) Set the InstrumentConfiguration otherInstrumentInfo.
void	setPeakListArrayList(List<PeakList> peakListArrayList) Set the PeakList peakListArrayList.
void	setSample(Sample sample) Set the Sample
void	setSourceFile(File sourceFile) Set the File sourceFile.
void	setSpectrumSearches(Set<SpectrumSearch> spectrumSearches) Set the SpectrumSearch spectrumSearches set.

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, 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_PEAKLISTSET, getType()

Method Detail

getById

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

Get a PeakListSet 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 PeakListSet item

Throws:

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

BaseException - If there is another error

getQuery

public static ItemQuery<PeakListSet> getQuery()

Get a query that returns peaklistset 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

getPeakListsQuery

public ItemQuery<PeakList> getPeakListsQuery()

Get a query that returns all PeakList items created from this peaklistset.

Returns:

An ItemQuery object

getSample

public Sample getSample()
                 throws BaseException

Get the Sample /** Get the Sample

Returns:

A Sample object

Throws:

BaseException - If there is another error

setSample

public void setSample(Sample sample)
               throws InvalidDataException

Set the Sample

Parameters:

sample - The new Sample item

Throws:

InvalidDataException - If the sample is null

BaseException - If there is another error

getOtherInstrumentInfo

public InstrumentConfiguration getOtherInstrumentInfo()
                                               throws BaseException

Get the InstrumentConfiguration otherInstrumentInfo.

Returns:

An InstrumentConfiguration object

Throws:

BaseException - If there is another error

setOtherInstrumentInfo

public void setOtherInstrumentInfo(InstrumentConfiguration otherInstrumentInfo)
                            throws InvalidDataException

Set the InstrumentConfiguration otherInstrumentInfo.

Parameters:

otherInstrumentInfo - The new InstrumentConfiguration item

Throws:

InvalidDataException - If the otherInstrumentInfo is null

BaseException - If there is another error

getAnalyzers

public List<HardwareConfiguration> getAnalyzers()
                                         throws ItemNotFoundException,
                                                BaseException

Get the HardwareConfiguration analyzers list.

Returns:

A HardwareConfiguration object

Throws:

BaseException - If there is another error

ItemNotFoundException

setAnalyzers

public void setAnalyzers(List<HardwareConfiguration> analyzers)
                  throws InvalidDataException

Set the HardwareConfiguration analyzers.

Parameters:

analyzers - The new HardwareConfiguration list item

Throws:

InvalidDataException - If analyzers hardware not equal to instrument hardware

BaseException - If there is another error

getDetector

public HardwareConfiguration getDetector()
                                  throws BaseException

Get the HardwareConfiguration detector.

Returns:

A HardwareConfiguration object

Throws:

BaseException - If there is another error

setDetector

public void setDetector(HardwareConfiguration detector)
                 throws InvalidDataException

Set the HardwareConfiguration detector.

Parameters:

detector - The new HardwareConfiguration item

Throws:

InvalidDataException - If detector hardware not equal to instrument hardware

BaseException - If there is another error

getInstrument

public Hardware getInstrument()
                       throws BaseException

Get the Hardware instrument.

Returns:

A Hardware object

Throws:

BaseException - If there is another error

setInstrument

public void setInstrument(Hardware instrument)
                   throws InvalidDataException

Set the Hardware instrument.

Parameters:

instrument - The new Hardware item

Throws:

InvalidDataException - If instrument is null

BaseException - If there is another error

getIonisationSource

public HardwareConfiguration getIonisationSource()
                                          throws BaseException

Get the HardwareConfiguration ionisationSource.

Returns:

A HardwareConfiguration object

Throws:

BaseException - If there is another error

setIonisationSource

public void setIonisationSource(HardwareConfiguration ionisationSource)
                         throws InvalidDataException

Set the HardwareConfiguration ionisationSource.

Parameters:

ionisationSource - The new HardwareConfiguration item

Throws:

InvalidDataException - If ionisationSource hardware not equal to instrument hardware

BaseException - If there is another error

getSourceFile

public File getSourceFile()
                   throws BaseException

Get the File sourceFile.

Returns:

A File object

Throws:

BaseException - If there is another error

setSourceFile

public void setSourceFile(File sourceFile)
                   throws InvalidDataException

Set the File sourceFile.

Parameters:

sourceFile - The new File item

Throws:

InvalidDataException - If sourceFile is null

BaseException - If there is another error

getDataProcessingStepList

public List<DataProcessingStep> getDataProcessingStepList()
                                                   throws ItemNotFoundException,
                                                          BaseException

Get the DataProcessingStep dataProcessingStepList.

Returns:

A DataProcessingStep list object

Throws:

BaseException - If there is another error

ItemNotFoundException

setDataProcessingStepList

public void setDataProcessingStepList(List<DataProcessingStep> dataProcessingStepList)
                               throws InvalidDataException

Set the DataProcessingStep dataProcessingStepList.

Parameters:

dataProcessingStepList - The new DataProcessingStep list item

Throws:

BaseException - If there is another error

InvalidDataException

addDataProcessingStep

public void addDataProcessingStep(DataProcessingStep dp)

Add a DataProcessingStep

Parameters:

dp - The DataProcessingStep to add to the List

getSpectrumSearches

public Set<SpectrumSearch> getSpectrumSearches()
                                        throws ItemNotFoundException,
                                               BaseException

Returns:

Returns the spectrumSearches.

Throws:

ItemNotFoundException

BaseException

setSpectrumSearches

public void setSpectrumSearches(Set<SpectrumSearch> spectrumSearches)

Set the SpectrumSearch spectrumSearches set.

Parameters:

spectrumSearches - The new Set item.

Throws:

InvalidDataException - If dataProcessingStep is null

BaseException - If there is another error

getPeakListArrayList

public List<PeakList> getPeakListArrayList()
                                    throws ItemNotFoundException,
                                           BaseException

Get the PeakList peakListArrayList. It is a set in the database, but will be returned as a sorted list in ascending spectrumId order

Returns:

A PeakList list object

Throws:

BaseException - If there is another error

ItemNotFoundException

setPeakListArrayList

public void setPeakListArrayList(List<PeakList> peakListArrayList)
                          throws InvalidDataException

Set the PeakList peakListArrayList. Observe that it is a set in the database

Parameters:

peakListArrayList - The new PeakList list item

Throws:

BaseException - If there is another error

InvalidDataException

addPeakList

public void addPeakList(PeakList peakList)

isUsed

public boolean isUsed()
               throws BaseException

Description copied from class: BasicItem

Check if this item is used by some other item. With used we mean that another item is linking to this item in way that prevents this item from beeing deleted. Ie. if we tried to delete an item that is used, we would get a foreign key violation error from the database.

Specified by:

isUsed in class BasicItem<PeakListSetData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException