uk.ac.ebi.pride.utilities.data.core

Class SpectrumIdentificationProtocol

java.lang.Object

uk.ac.ebi.pride.utilities.data.core.ParamGroup

uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

uk.ac.ebi.pride.utilities.data.core.Protocol

uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

All Implemented Interfaces:

Serializable, MassSpecObject

public class SpectrumIdentificationProtocol
extends Protocol

The parameters and settings of a SpectrumIdentification analysis.

Author:

Yasset Perez-Riverol Date: 05/08/11 Time: 15:56

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
SpectrumIdentificationProtocol(Comparable id, String name, Software analysisSoftware, ParamGroup analysisParam, ParamGroup threshold, ParamGroup searchType, List<SearchModification> searchModifications, boolean enzymeIndependent, List<Enzyme> enzymes, List<MassTable> massTables, List<CvParam> fragmentTolerance, List<CvParam> parentTolerance, List<Filter> filters, DataBaseTranslation dataBaseTranslation)
SpectrumIdentificationProtocol(ParamGroup analysisParam, Comparable id, String name, Software analysisSoftware, ParamGroup threshold, ParamGroup searchType, List<SearchModification> searchModifications, boolean enzymeIndependent, List<Enzyme> enzymes, List<MassTable> massTables, List<CvParam> fragmentTolerance, List<CvParam> parentTolerance, List<Filter> filters, DataBaseTranslation dataBaseTranslation)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
DataBaseTranslation	getDataBaseTranslation()
List<Enzyme>	getEnzymes()
List<Filter>	getFilters()
List<CvParam>	getFragmentTolerance()
List<MassTable>	getMassTables()
List<CvParam>	getParentTolerance()
List<SearchModification>	getSearchModifications()
ParamGroup	getSearchType()
int	hashCode()
boolean	isEnzymeIndependent()
void	setDataBaseTranslation(DataBaseTranslation dataBaseTranslation)
void	setEnzymeIndependent(boolean enzymeIndependent)
void	setEnzymes(List<Enzyme> enzymes)
void	setFilters(List<Filter> filters)
void	setFragmentTolerance(List<CvParam> fragmentTolerance)
void	setMassTables(List<MassTable> massTables)
void	setParentTolerance(List<CvParam> parentTolerance)
void	setSearchModifications(List<SearchModification> searchModifications)
void	setSearchType(ParamGroup searchType)

Methods inherited from class uk.ac.ebi.pride.utilities.data.core.Protocol

getAnalysisParam, getAnalysisSoftware, getThreshold, setAnalysisParam, setAnalysisSoftware, setThreshold

Methods inherited from class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

getId, getName, setId, setName, toString

Methods inherited from class uk.ac.ebi.pride.utilities.data.core.ParamGroup

addCvParam, addCvParams, addUserParam, addUserParams, getCvParams, getUserParams, isEmpty, removeCvParam, removeCvParams, removeUserParam, removeUserParams, setCvParams, setUserParams

Methods inherited from class java.lang.Object

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

Constructor Detail

SpectrumIdentificationProtocol

public SpectrumIdentificationProtocol(Comparable id,
                              String name,
                              Software analysisSoftware,
                              ParamGroup analysisParam,
                              ParamGroup threshold,
                              ParamGroup searchType,
                              List<SearchModification> searchModifications,
                              boolean enzymeIndependent,
                              List<Enzyme> enzymes,
                              List<MassTable> massTables,
                              List<CvParam> fragmentTolerance,
                              List<CvParam> parentTolerance,
                              List<Filter> filters,
                              DataBaseTranslation dataBaseTranslation)

SpectrumIdentificationProtocol

public SpectrumIdentificationProtocol(ParamGroup analysisParam,
                              Comparable id,
                              String name,
                              Software analysisSoftware,
                              ParamGroup threshold,
                              ParamGroup searchType,
                              List<SearchModification> searchModifications,
                              boolean enzymeIndependent,
                              List<Enzyme> enzymes,
                              List<MassTable> massTables,
                              List<CvParam> fragmentTolerance,
                              List<CvParam> parentTolerance,
                              List<Filter> filters,
                              DataBaseTranslation dataBaseTranslation)

Method Detail

getSearchType

public ParamGroup getSearchType()

setSearchType

public void setSearchType(ParamGroup searchType)

getSearchModifications

public List<SearchModification> getSearchModifications()

setSearchModifications

public void setSearchModifications(List<SearchModification> searchModifications)

isEnzymeIndependent

public boolean isEnzymeIndependent()

setEnzymeIndependent

public void setEnzymeIndependent(boolean enzymeIndependent)

getEnzymes

public List<Enzyme> getEnzymes()

setEnzymes

public void setEnzymes(List<Enzyme> enzymes)

getMassTables

public List<MassTable> getMassTables()

setMassTables

public void setMassTables(List<MassTable> massTables)

getFragmentTolerance

public List<CvParam> getFragmentTolerance()

setFragmentTolerance

public void setFragmentTolerance(List<CvParam> fragmentTolerance)

getParentTolerance

public List<CvParam> getParentTolerance()

setParentTolerance

public void setParentTolerance(List<CvParam> parentTolerance)

getFilters

public List<Filter> getFilters()

setFilters

public void setFilters(List<Filter> filters)

getDataBaseTranslation

public DataBaseTranslation getDataBaseTranslation()

setDataBaseTranslation

public void setDataBaseTranslation(DataBaseTranslation dataBaseTranslation)

equals

public boolean equals(Object o)

Overrides:

equals in class Protocol

hashCode

public int hashCode()

Overrides:

hashCode in class Protocol