org.proteios.core
Class SearchResult

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<SearchResultData>
                      org.proteios.core.SearchResult

All Implemented Interfaces:

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

public class SearchResult
extends AnnotatedItem<SearchResultData>
implements Comparable<SearchResult>

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_SCORETYPE_LENGTH The maximum length of the scoreType string that can be stored in the database.
static int	MAX_SPECTRUMSTRINGID_LENGTH
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	addPolyPeptide(PolyPeptide pp) Add a PolyPeptide to the collection.
void	addReferencedResult(SearchResult referencedResult) Add a result to the list of referenced results.
int	compareTo(SearchResult o)
Set<Annotatable>	getAnnotatableParents() Always null.
Float	getExpectationValue()
int	getIndex()
int	getInputSpectrumId()
PeakList	getPeakList() Get the PeakList this SearchResult is associated with.
Set<Peptide>	getPeptides() Get the Peptide polypeptides.
Set<PolyPeptide>	getPolyPeptides()
Set<Protein>	getProteins() Get the Peptide polypeptides.
static ItemQuery<SearchResult>	getQuery() Get a query that returns spectrumsearchset items.
List<SearchResult>	getReferencedResults() Get the SearchResult referenced results.
Float	getScore()
String	getScoreType() Get the input filename of this SearchResult.
SpectrumSearch	getSpectrumSearch() Get the SpectrumSearch this SearchResult is associated with.
String	getSpectrumStringId()
Item	getType() Get the type of item represented by the object.
boolean	isUsed() Check that: no item has been created from this peaklistset
void	setExpectationValue(Float eValue)
void	setIndex(int index)
void	setInputSpectrumId(int inputSpectrumId)
void	setPeakList(PeakList peakList) Set the PeakList this SearchResult is associated with.
void	setPolyPeptides(Set<PolyPeptide> polyPeptides) Set the PolyPeptide polypeptides
void	setReferencedResults(List<SearchResult> referencedResults) Set the SearchResult referenced results.
void	setScore(Float score)
void	setScoreType(String scoreType) Set the scoreType for this SearchResult item.
void	setSpectrumSearch(SpectrumSearch spectrumSearch) Set the SpectrumSearch this SearchResult is associated with.
void	setSpectrumStringId(String spectrumStringId) Set the spectrumStringId for this SearchResult item.

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_SEARCHRESULT, getType()

MAX_SCORETYPE_LENGTH

public static final int MAX_SCORETYPE_LENGTH

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

See Also:

setScoreType(String), Constant Field Values

MAX_SPECTRUMSTRINGID_LENGTH

public static final int MAX_SPECTRUMSTRINGID_LENGTH

See Also:

Constant Field Values

Method Detail

compareTo

public int compareTo(SearchResult o)

Specified by:

compareTo in interface Comparable<SearchResult>

getQuery

public static ItemQuery<SearchResult> 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.

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 peaklistset

Specified by:

isUsed in class BasicItem<SearchResultData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getPeakList

public PeakList getPeakList()
                     throws BaseException

Get the PeakList this SearchResult is associated with.

Returns:

The PeakList item or null if not known

Throws:

BaseException - If there is another error

setPeakList

public void setPeakList(PeakList peakList)
                 throws BaseException

Set the PeakList this SearchResult is associated with.

Parameters:

peakList - The new PeakList item

Throws:

BaseException - If there is another error

getSpectrumSearch

public SpectrumSearch getSpectrumSearch()
                                 throws BaseException

Get the SpectrumSearch this SearchResult is associated with.

Returns:

The SpectrumSearch item or null if not known

Throws:

BaseException - If there is another error

setSpectrumSearch

public void setSpectrumSearch(SpectrumSearch spectrumSearch)
                       throws BaseException

Set the SpectrumSearch this SearchResult is associated with.

Parameters:

spectrumSearch - The new SpectrumSearch item

Throws:

BaseException - If there is another error

getIndex

public int getIndex()

Returns:

Returns the index used for sorting.

setIndex

public void setIndex(int index)

Parameters:

index - The index for sorting.

getInputSpectrumId

public int getInputSpectrumId()

Returns:

Returns the inputSpectrumId.

setInputSpectrumId

public void setInputSpectrumId(int inputSpectrumId)

Parameters:

inputSpectrumId - The inputSpectrumId to set.

getScore

public Float getScore()

Returns:

Returns the score.

setScore

public void setScore(Float score)

Parameters:

score - The primary score.

getExpectationValue

public Float getExpectationValue()

Returns:

Returns the expectation value.

setExpectationValue

public void setExpectationValue(Float eValue)

Parameters:

eValue - The primary expectation value.

getScoreType

public String getScoreType()

Get the input filename of this SearchResult.

Returns:

the filename

setScoreType

public void setScoreType(String scoreType)
                  throws InvalidDataException

Set the scoreType for this SearchResult item. The value may be null but must not be longer than the value specified by the MAX_SCORETYPE_LENGTH constant.

Parameters:

scoreType - The new scoreType for this item

Throws:

InvalidDataException - If the scoreType is longer than MAX_SCORETYPE_LENGTH

getSpectrumStringId

public String getSpectrumStringId()

Returns:

Returns the spectrumStringId.

setSpectrumStringId

public void setSpectrumStringId(String spectrumStringId)
                         throws InvalidDataException

Set the spectrumStringId for this SearchResult item. The value may be null but must not be longer than the value specified by the

Parameters:

spectrumStringId - The spectrumStringId to set.

Throws:

InvalidDataException - If the spectrumStringId is longer than MAX_SPECTRUMSTRINGID_LENGTH

getReferencedResults

public List<SearchResult> getReferencedResults()
                                        throws ItemNotFoundException,
                                               BaseException

Get the SearchResult referenced results.

Returns:

A SearchResult list object

Throws:

BaseException - If there is another error

ItemNotFoundException

setReferencedResults

public void setReferencedResults(List<SearchResult> referencedResults)
                          throws InvalidDataException

Set the SearchResult referenced results.

Parameters:

referencedResults - The new SearchResult list item

Throws:

BaseException - If there is another error

InvalidDataException

addReferencedResult

public void addReferencedResult(SearchResult referencedResult)

Add a result to the list of referenced results.

getPolyPeptides

public Set<PolyPeptide> getPolyPeptides()
                                 throws ItemNotFoundException,
                                        BaseException

Throws:

ItemNotFoundException

BaseException

setPolyPeptides

public void setPolyPeptides(Set<PolyPeptide> polyPeptides)
                     throws InvalidDataException

Set the PolyPeptide polypeptides

Parameters:

polyPeptides - The new PolyPeptide set item

Throws:

BaseException - If there is another error

InvalidDataException

addPolyPeptide

public void addPolyPeptide(PolyPeptide pp)

Add a PolyPeptide to the collection. Backward reference is set

Parameters:

pp - the PolyPeptide to set

getPeptides

public Set<Peptide> getPeptides()
                         throws ItemNotFoundException,
                                BaseException

Get the Peptide polypeptides. Only returns peptides from the polypeptide collection

Returns:

A Peptide set object

Throws:

BaseException - If there is another error

ItemNotFoundException

getProteins

public Set<Protein> getProteins()
                         throws ItemNotFoundException,
                                BaseException

Get the Peptide polypeptides. Only returns peptides from the polypeptide collection

Returns:

A Peptide set object

Throws:

BaseException - If there is another error

ItemNotFoundException