org.proteios.core
Class SpectrumSearch

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<SpectrumSearchData>
                      org.proteios.core.SpectrumSearch

All Implemented Interfaces:

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

public class SpectrumSearch
extends AnnotatedItem<SpectrumSearchData>

This class represent spectrumsearch.

Version:

2.0

Author:

Fredrik

Last modified

$Date: 2009-04-09 08:48:11 +0200 (Thu, 09 Apr 2009) $

Field Summary

static int	MAX_INPUTSPECTRUMFILENAME_LENGTH The maximum length of the inputSpectrumFileName 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_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Method Summary

void	addDigestParameter(DigestParameter dp) Add a DigestParameter
void	addSearchDatabase(SearchDatabase db) Add a SearchDatabase
void	addSearchModification(SearchModification dp) Add a SearchModification
void	addSearchResult(SearchResult sr) Add a SearchResult and set the association back to this SpectrumSearch
Date	getAnalysisTime()
Set<Annotatable>	getAnnotatableParents() Always null.
Set<DigestParameter>	getDigestParameters()
String	getInputSpectrumFileName() Get the input filename of this SpectrumSearch.
PeakListSet	getPeakListSet() Get the PeakListSet this SpectrumSearch is associated with.
static ItemQuery<SpectrumSearch>	getQuery() Get a query that returns spectrumsearchset items.
File	getResultFile() Get the result file that this spectrumsearch was generated from
Set<SearchDatabase>	getSearchDatabases()
Software	getSearchEngine() Get the earch engine Software this SpectrumSearch is associated with.
Set<SearchModification>	getSearchModifications()
SortedSet<SearchResult>	getSearchResults()
Item	getType() Get the type of item represented by the object.
boolean	isUsed() Check that: no item has been created from this peaklistset
void	setAnalysisTime(Date date)
void	setDigestParameters(Set<DigestParameter> digestParameters) Set the DigestParameter digestParameters set.
void	setInputSpectrumFileName(String inputSpectrumFileName) Set the inputSpectrumFileName for this SpectrumSearch item.
void	setPeakListSet(PeakListSet peakListSet) Set the PeakListSet this SpectrumSearch is associated with.
void	setResultFile(File resultFile) Set the result file
void	setSearchDatabases(Set<SearchDatabase> searchDatabases) Set the SearchDatabase searchDatabases set.
void	setSearchEngine(Software software) Set the search engine Software this SpectrumSearch is associated with.
void	setSearchModifications(Set<SearchModification> searchModifications) Set the SearchModification searchModifications set.
void	setSearchResults(SortedSet<SearchResult> searchResults) Set the SearchResult searchResults 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_SPECTRUMSEARCH, getType()

MAX_INPUTSPECTRUMFILENAME_LENGTH

public static final int MAX_INPUTSPECTRUMFILENAME_LENGTH

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

See Also:

setInputSpectrumFileName(String), Constant Field Values

Method Detail

getQuery

public static ItemQuery<SpectrumSearch> getQuery()

Get a query that returns spectrumsearchset 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 peaklistset

Specified by:

isUsed in class BasicItem<SpectrumSearchData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getPeakListSet

public PeakListSet getPeakListSet()
                           throws BaseException

Get the PeakListSet this SpectrumSearch is associated with.

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 SpectrumSearch is associated with.

Parameters:

peakListSet - The new PeakListSet item

Throws:

BaseException - If there is another error

getSearchEngine

public Software getSearchEngine()
                         throws BaseException

Get the earch engine Software this SpectrumSearch is associated with.

Returns:

The Software item or null if not known

Throws:

BaseException - If there is another error

setSearchEngine

public void setSearchEngine(Software software)
                     throws BaseException

Set the search engine Software this SpectrumSearch is associated with.

Parameters:

software - The new Software item

Throws:

BaseException - If there is another error

addDigestParameter

public void addDigestParameter(DigestParameter dp)

Add a DigestParameter

Parameters:

dp - The DigestParameter to add to the Set

getDigestParameters

public Set<DigestParameter> getDigestParameters()
                                         throws ItemNotFoundException,
                                                BaseException

Returns:

Returns the digestParameters.

Throws:

ItemNotFoundException

BaseException

setDigestParameters

public void setDigestParameters(Set<DigestParameter> digestParameters)

Set the DigestParameter digestParameters set.

Parameters:

digestParameters - The new Set item.

Throws:

InvalidDataException - If dataProcessingStep is null

BaseException - If there is another error

getSearchDatabases

public Set<SearchDatabase> getSearchDatabases()
                                       throws ItemNotFoundException,
                                              BaseException

Returns:

Returns the searchDatabases.

Throws:

ItemNotFoundException

BaseException

setSearchDatabases

public void setSearchDatabases(Set<SearchDatabase> searchDatabases)

Set the SearchDatabase searchDatabases set.

Parameters:

searchDatabases - The new Set item.

Throws:

InvalidDataException - If dataProcessingStep is null

BaseException - If there is another error

addSearchResult

public void addSearchResult(SearchResult sr)
                     throws InvalidDataException

Add a SearchResult and set the association back to this SpectrumSearch

Parameters:

sr - The Search Result to add to the SortedSet

Throws:

InvalidDataException - if the search result could not be added (probable reason=duplicate indexes)

addSearchDatabase

public void addSearchDatabase(SearchDatabase db)

Add a SearchDatabase

Parameters:

db - The Search Database to add to the Set

getSearchResults

public SortedSet<SearchResult> getSearchResults()
                                         throws ItemNotFoundException,
                                                BaseException

Returns:

Returns the searchResults.

Throws:

ItemNotFoundException

BaseException

setSearchResults

public void setSearchResults(SortedSet<SearchResult> searchResults)

Set the SearchResult searchResults set.

Parameters:

searchResults - The new Set item.

Throws:

InvalidDataException - If searchResults is null

BaseException - If there is another error

getAnalysisTime

public Date getAnalysisTime()

Returns:

Returns the analysis date.

setAnalysisTime

public void setAnalysisTime(Date date)

Parameters:

date - The analysis time.

getResultFile

public File getResultFile()

Get the result file that this spectrumsearch was generated from

Returns:

the File

setResultFile

public void setResultFile(File resultFile)

Set the result file

Parameters:

resultFile - The results File this spectrumSearch was generated from

getInputSpectrumFileName

public String getInputSpectrumFileName()

Get the input filename of this SpectrumSearch.

Returns:

the filename

setInputSpectrumFileName

public void setInputSpectrumFileName(String inputSpectrumFileName)
                              throws InvalidDataException

Set the inputSpectrumFileName for this SpectrumSearch item. The value may be null but must not be longer than the value specified by the MAX_INPUTSPECTRUMFILENAME_LENGTH constant.

Parameters:

inputSpectrumFileName - The new inputSpectrumFileName for this item

Throws:

InvalidDataException - If the inputSpectrumFileName is longer than MAX_INPUTSPECTRUMFILENAME_LENGTH

addSearchModification

public void addSearchModification(SearchModification dp)

Add a SearchModification

Parameters:

dp - The SearchModification to add to the Set

getSearchModifications

public Set<SearchModification> getSearchModifications()
                                               throws ItemNotFoundException,
                                                      BaseException

Returns:

Returns the searchModifications.

Throws:

ItemNotFoundException

BaseException

setSearchModifications

public void setSearchModifications(Set<SearchModification> searchModifications)

Set the SearchModification searchModifications set.

Parameters:

searchModifications - The new Set item.

Throws:

InvalidDataException - If dataProcessingStep is null

BaseException - If there is another error