org.proteios.core.data
Class SpectrumSearchData

java.lang.Object
  org.proteios.core.data.BasicData
      org.proteios.core.data.OwnedData
          org.proteios.core.data.SharedData
              org.proteios.core.data.CommonData
                  org.proteios.core.data.AnnotatedData
                      org.proteios.core.data.SpectrumSearchData

All Implemented Interfaces:

AnnotatableData, IdentifiableData, NameableData, OwnableData, RemovableData, ShareableData

public class SpectrumSearchData
extends AnnotatedData

This represents the top element of a protein identification search.

Version:

2.0

Author:

Fredrik

See Also:

SpectrumSearch, SpectrumSearch overview

Last modified

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

Hibernate: class

table="`SpectrumSearches`" lazy="true"

Hibernate: subclass

discriminator-value="1"

Field Summary

static int

MAX_INPUTSPECTRUMFILENAME_LENGTH

Fields inherited from interface org.proteios.core.data.NameableData

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

SpectrumSearchData()

Method Summary

Date	getAnalysisTime()
Set<DigestParameterData>	getDigestParameters() Get the digestParameters.
InputSpectraData	getInputSpectra()
String	getInputSpectrumFileName()
PeakListSetData	getPeakListSet()
FileData	getResultFile() Get the result file that this spectrumsearch was generated from
Set<SearchDatabaseData>	getSearchDatabases() Get the searchDatabases.
SoftwareData	getSearchEngine() Get the software
Set<SearchModificationData>	getSearchModifications() Get the searchModifications.
SortedSet<SearchResultData>	getSearchResults()
void	setAnalysisTime(Date analysisTime)
void	setDigestParameters(Set<DigestParameterData> digestParameters) Set the searchDatabaes
void	setInputSpectra(InputSpectraData inputSpectra)
void	setInputSpectrumFileName(String inputSpectrumFileName)
void	setPeakListSet(PeakListSetData peakListSet)
void	setResultFile(FileData resultFile) Set the result file
void	setSearchDatabases(Set<SearchDatabaseData> searchDatabases) Set the searchDatabaes
void	setSearchEngine(SoftwareData searchEngine)
void	setSearchModifications(Set<SearchModificationData> searchModifications) Set the searchDatabases
void	setSearchResults(SortedSet<SearchResultData> searchResults)

Methods inherited from class org.proteios.core.data.AnnotatedData

getAnnotationSet, setAnnotationSet

Methods inherited from class org.proteios.core.data.CommonData

getDescription, getName, isRemoved, setDescription, setName, setRemoved

Methods inherited from class org.proteios.core.data.SharedData

getItemKey, getProjectKey, setItemKey, setProjectKey

Methods inherited from class org.proteios.core.data.OwnedData

getOwner, setOwner

Methods inherited from class org.proteios.core.data.BasicData

equals, getId, getVersion, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.proteios.core.data.IdentifiableData

getId, getVersion

Methods inherited from interface org.proteios.core.data.OwnableData

getOwner, setOwner

Field Detail

MAX_INPUTSPECTRUMFILENAME_LENGTH

public static final int MAX_INPUTSPECTRUMFILENAME_LENGTH

See Also:

Constant Field Values

Constructor Detail

SpectrumSearchData

public SpectrumSearchData()

Method Detail

getAnalysisTime

public Date getAnalysisTime()

Returns:

Returns the analysisTime.

Hibernate: property

column="`analysis_time`" type="timestamp" not-null="false"

setAnalysisTime

public void setAnalysisTime(Date analysisTime)

Parameters:

analysisTime - The analysisTime to set.

getResultFile

public FileData getResultFile()

Get the result file that this spectrumsearch was generated from

Returns:

the FileData

Hibernate: many-to-one

column="`resultFile`" not-null="false"

setResultFile

public void setResultFile(FileData resultFile)

Set the result file

Parameters:

resultFile - The results File this spectrumSearch was generated from

getInputSpectrumFileName

public String getInputSpectrumFileName()

Returns:

Returns the inputSpectrumFile.

Hibernate: property

column="`input_spectrum_filename`" type="string" length="255" not-null="false"

setInputSpectrumFileName

public void setInputSpectrumFileName(String inputSpectrumFileName)

Parameters:

inputSpectrumFileName - The inputSpectrumFile to set.

getDigestParameters

public Set<DigestParameterData> getDigestParameters()

Get the digestParameters.

Returns:

The DigestParameterData digestParameterList

Hibernate: set

table="`DigestParameters`" cascade="all" lazy="true" inverse="true"

Hibernate: collection-key

column="`spectrumSearchId`"

Hibernate: collection-one-to-many

class="org.proteios.core.data.DigestParameterData" not-null="false"

setDigestParameters

public void setDigestParameters(Set<DigestParameterData> digestParameters)

Set the searchDatabaes

Parameters:

digestParameters - The DigestParameterData digestParameters

getSearchEngine

public SoftwareData getSearchEngine()

Get the software

Returns:

The SoftwareData software

Hibernate: many-to-one

column="`software_id`" not-null="false" outer-join="false"

setSearchEngine

public void setSearchEngine(SoftwareData searchEngine)

Parameters:

searchEngine - The SoftwareData software used in this search

getSearchDatabases

public Set<SearchDatabaseData> getSearchDatabases()

Get the searchDatabases.

Returns:

The SearchDatabaseData searchDatabaseList

Hibernate: set

table="`SearchDatabases`" cascade="all" lazy="true" inverse="true"

Hibernate: collection-key

column="`spectrumSearchId`"

Hibernate: collection-one-to-many

class="org.proteios.core.data.SearchDatabaseData" not-null="false"

setSearchDatabases

public void setSearchDatabases(Set<SearchDatabaseData> searchDatabases)

Set the searchDatabaes

Parameters:

searchDatabases - The SearchDatabaseData searchDatabases

getPeakListSet

public PeakListSetData getPeakListSet()

Returns:

Returns the peakListSet if only one was used. Otherwise go through inputSpectra.

Hibernate: collection-many-to-one

column="`peakListSetId`"

setPeakListSet

public void setPeakListSet(PeakListSetData peakListSet)

Parameters:

peakListSet - The peakListSet to set.

getInputSpectra

public InputSpectraData getInputSpectra()

Returns:

Returns the inputSpectra.

Hibernate: collection-many-to-one

column="inputSpectra_id" not-null="false"

setInputSpectra

public void setInputSpectra(InputSpectraData inputSpectra)

Parameters:

inputSpectra - The inputSpectra to set.

getSearchResults

public SortedSet<SearchResultData> getSearchResults()

Returns:

Returns the searchResults.

Hibernate: set

table="`SearchResults`" sort="natural" cascade="all" lazy="true" inverse="true"

Hibernate: collection-key

column="`spectrumSearchId`"

Hibernate: collection-one-to-many

class="org.proteios.core.data.SearchResultData" not-null="false"

setSearchResults

public void setSearchResults(SortedSet<SearchResultData> searchResults)

Parameters:

searchResults - The searchResults to set.

getSearchModifications

public Set<SearchModificationData> getSearchModifications()

Get the searchModifications.

Returns:

The SearchModificationData searchModificationList

Hibernate: set

table="`Modifications`" cascade="all" lazy="true" inverse="true"

Hibernate: collection-key

column="`spectrumSearchId`"

Hibernate: collection-one-to-many

class="org.proteios.core.data.SearchModificationData" not-null="false"

setSearchModifications

public void setSearchModifications(Set<SearchModificationData> searchModifications)

Set the searchDatabases

Parameters:

searchModifications - The SearchModificationData searchModifications