com.compomics.util.preferences

Class IdentificationParameters

java.lang.Object

com.compomics.util.preferences.IdentificationParameters

All Implemented Interfaces:

MarshallableParameter, Serializable

public class IdentificationParameters
extends Object
implements Serializable, MarshallableParameter

Generic class grouping the parameters used for protein identification.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface com.compomics.util.preferences.MarshallableParameter

MarshallableParameter.Type

Constructor Summary

Constructors

Constructor and Description
IdentificationParameters() Creates empty identification parameters.
IdentificationParameters(SearchParameters searchParameters) Creates default identification parameters from the given search parameters.
IdentificationParameters(String name, String description, SearchParameters searchParameters, AnnotationSettings annotationSettings, SequenceMatchingPreferences sequenceMatchingPreferences, GenePreferences genePreferences, PsmScoringPreferences psmScoringPreferences, PeptideAssumptionFilter peptideAssumptionFilter, PTMScoringPreferences ptmScoringPreferences, ProteinInferencePreferences proteinInferencePreferences, IdMatchValidationPreferences idValidationPreferences, FractionSettings fractionSettings) Constructor.

Method Summary

Modifier and Type	Method and Description
boolean	equals(IdentificationParameters otherIdentificationParameters) Returns true if the identification parameter objects have identical settings.
boolean	equalsExceptValidationPreferences(IdentificationParameters otherIdentificationParameters) Returns true if the identification parameter objects have identical settings except for the validation preferences.
AnnotationSettings	getAnnotationPreferences() Returns the annotation preferences used for identification.
static double	getDaTolerance(double ppmTolerance, double refMass) Returns the absolute tolerance in Dalton corresponding to the relative tolerance in ppm at the given reference mass.
Boolean	getDefaultDescription() Indicates whether the description is automatically generated.
String	getDescription() Returns the description of the parameters.
FractionSettings	getFractionSettings() Returns the fraction settings.
GenePreferences	getGenePreferences() Returns the gene preferences.
static IdentificationParameters	getIdentificationParameters(File identificationParametersFile) Loads the identification parameters from a file.
IdMatchValidationPreferences	getIdValidationPreferences() Returns the identification matches validation preferences.
String	getName() Returns the name of the parameters.
PeptideAssumptionFilter	getPeptideAssumptionFilter() Returns the filter used when importing PSMs.
static double	getPpmTolerance(double daltonTolerance, double refMass) Returns the relative tolerance in ppm corresponding to the absolute tolerance in Dalton at the given reference mass.
ProteinInferencePreferences	getProteinInferencePreferences() Returns the protein inference preferences.
PsmScoringPreferences	getPsmScoringPreferences() Returns the scoring preferences used when scoring PSMs.
PTMScoringPreferences	getPtmScoringPreferences() Returns the PTM localization scoring preferences.
SearchParameters	getSearchParameters() Returns the parameters used for the spectrum matching.
SequenceMatchingPreferences	getSequenceMatchingPreferences() Returns the sequence matching preferences.
MarshallableParameter.Type	getType() Returns the type of marshalled parameter from an unmarshalled object.
static void	saveIdentificationParameters(IdentificationParameters identificationParameters, File identificationParametersFile) Saves the identification parameters to a file.
void	setAnnotationSettings(AnnotationSettings annotationSettings) Sets the annotation preferences used for identification.
void	setDescription(String description, boolean automaticallyGenerated) Sets the description of the parameters.
void	setFractionSettings(FractionSettings fractionSettings) Sets the fraction settings.
void	setGenePreferences(GenePreferences genePreferences) Sets the gene preferences.
void	setIdFilter(PeptideAssumptionFilter peptideAssumptionFilter) Sets the filter used when importing PSMs.
void	setIdValidationPreferences(IdMatchValidationPreferences idValidationPreferences) Sets the identification matches validation preferences.
void	setName(String name) Sets the name of the parameters.
void	setParametersFromSearch(SearchParameters searchParameters) Sets identification parameters based on given search parameters.
void	setProteinInferencePreferences(ProteinInferencePreferences proteinInferencePreferences) Sets the protein inference preferences.
void	setPsmScoringPreferences(PsmScoringPreferences psmScoringPreferences) Sets the scoring preferences used when scoring PSMs.
void	setPtmScoringPreferences(PTMScoringPreferences ptmScoringPreferences) Sets the PTM localization scoring preferences.
void	setSearchParameters(SearchParameters searchParameters) Sets the parameters used for the spectrum matching.
void	setSequenceMatchingPreferences(SequenceMatchingPreferences sequenceMatchingPreferences) Sets the sequence matching preferences.
void	setType() Sets the parameters type.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IdentificationParameters

public IdentificationParameters()

Creates empty identification parameters.

IdentificationParameters

public IdentificationParameters(SearchParameters searchParameters)

Creates default identification parameters from the given search parameters.

Parameters:

searchParameters - the search parameters

IdentificationParameters

public IdentificationParameters(String name,
                                String description,
                                SearchParameters searchParameters,
                                AnnotationSettings annotationSettings,
                                SequenceMatchingPreferences sequenceMatchingPreferences,
                                GenePreferences genePreferences,
                                PsmScoringPreferences psmScoringPreferences,
                                PeptideAssumptionFilter peptideAssumptionFilter,
                                PTMScoringPreferences ptmScoringPreferences,
                                ProteinInferencePreferences proteinInferencePreferences,
                                IdMatchValidationPreferences idValidationPreferences,
                                FractionSettings fractionSettings)

Constructor.

Parameters:

name - the name of the parameters

description - the description

searchParameters - the search parameters

annotationSettings - the annotation preferences

sequenceMatchingPreferences - the sequence matching preferences

genePreferences - the gene preferences

psmScoringPreferences - the PSM scoring preferences

peptideAssumptionFilter - the peptide assumption filters

ptmScoringPreferences - the PTM localization scoring preferences

proteinInferencePreferences - the protein inference preferences

idValidationPreferences - the matches validation preferences

fractionSettings - the fraction settings

Method Detail

getSearchParameters

public SearchParameters getSearchParameters()

Returns the parameters used for the spectrum matching.

Returns:

the parameters used for the spectrum matching

setSearchParameters

public void setSearchParameters(SearchParameters searchParameters)

Sets the parameters used for the spectrum matching.

Parameters:

searchParameters - the parameters used for the spectrum matching

getPpmTolerance

public static double getPpmTolerance(double daltonTolerance,
                                     double refMass)

Returns the relative tolerance in ppm corresponding to the absolute tolerance in Dalton at the given reference mass.

Parameters:

daltonTolerance - the absolute tolerance in Dalton

refMass - the reference mass in Dalton

Returns:

the relative tolerance in ppm

getDaTolerance

public static double getDaTolerance(double ppmTolerance,
                                    double refMass)

Returns the absolute tolerance in Dalton corresponding to the relative tolerance in ppm at the given reference mass.

Parameters:

ppmTolerance - the absolute tolerance in ppm

refMass - the reference mass in Dalton

Returns:

the relative tolerance in ppm

getAnnotationPreferences

public AnnotationSettings getAnnotationPreferences()

Returns the annotation preferences used for identification.

Returns:

the annotation preferences used for identification

setAnnotationSettings

public void setAnnotationSettings(AnnotationSettings annotationSettings)

Sets the annotation preferences used for identification.

Parameters:

annotationSettings - the annotation preferences used for identification

getPeptideAssumptionFilter

public PeptideAssumptionFilter getPeptideAssumptionFilter()

Returns the filter used when importing PSMs.

Returns:

the filter used when importing PSMs

setIdFilter

public void setIdFilter(PeptideAssumptionFilter peptideAssumptionFilter)

Sets the filter used when importing PSMs.

Parameters:

peptideAssumptionFilter - the filter used when importing PSMs

getPsmScoringPreferences

public PsmScoringPreferences getPsmScoringPreferences()

Returns the scoring preferences used when scoring PSMs.

Returns:

the scoring preferences used when scoring PSMs

setPsmScoringPreferences

public void setPsmScoringPreferences(PsmScoringPreferences psmScoringPreferences)

Sets the scoring preferences used when scoring PSMs.

Parameters:

psmScoringPreferences - the scoring preferences used when scoring PSMs

getPtmScoringPreferences

public PTMScoringPreferences getPtmScoringPreferences()

Returns the PTM localization scoring preferences.

Returns:

the PTM localization scoring preferences

setPtmScoringPreferences

public void setPtmScoringPreferences(PTMScoringPreferences ptmScoringPreferences)

Sets the PTM localization scoring preferences.

Parameters:

ptmScoringPreferences - the PTM localization scoring preferences

getSequenceMatchingPreferences

public SequenceMatchingPreferences getSequenceMatchingPreferences()

Returns the sequence matching preferences.

Returns:

the sequence matching preferences

setSequenceMatchingPreferences

public void setSequenceMatchingPreferences(SequenceMatchingPreferences sequenceMatchingPreferences)

Sets the sequence matching preferences.

Parameters:

sequenceMatchingPreferences - the sequence matching preferences

getIdValidationPreferences

public IdMatchValidationPreferences getIdValidationPreferences()

Returns the identification matches validation preferences.

Returns:

the identification matches validation preferences

setIdValidationPreferences

public void setIdValidationPreferences(IdMatchValidationPreferences idValidationPreferences)

Sets the identification matches validation preferences.

Parameters:

idValidationPreferences - the identification matches validation preferences

getProteinInferencePreferences

public ProteinInferencePreferences getProteinInferencePreferences()

Returns the protein inference preferences.

Returns:

the protein inference preferences

setProteinInferencePreferences

public void setProteinInferencePreferences(ProteinInferencePreferences proteinInferencePreferences)

Sets the protein inference preferences.

Parameters:

proteinInferencePreferences - the protein inference preferences

getGenePreferences

public GenePreferences getGenePreferences()

Returns the gene preferences.

Returns:

the gene preferences

setGenePreferences

public void setGenePreferences(GenePreferences genePreferences)

Sets the gene preferences.

Parameters:

genePreferences - the gene preferences

getFractionSettings

public FractionSettings getFractionSettings()

Returns the fraction settings.

Returns:

the fraction settings

setFractionSettings

public void setFractionSettings(FractionSettings fractionSettings)

Sets the fraction settings.

Parameters:

fractionSettings - the fraction settings

getIdentificationParameters

public static IdentificationParameters getIdentificationParameters(File identificationParametersFile)
                                                            throws IOException,
                                                                   ClassNotFoundException

Loads the identification parameters from a file. If the given file is a search parameters file, default identification parameters are inferred.

Parameters:

identificationParametersFile - the file

Returns:

the parameters

Throws:

IOException - if an IOException occurs

ClassNotFoundException - if a ClassNotFoundException occurs

saveIdentificationParameters

public static void saveIdentificationParameters(IdentificationParameters identificationParameters,
                                                File identificationParametersFile)
                                         throws IOException

Saves the identification parameters to a file.

Parameters:

identificationParameters - the identification parameters

identificationParametersFile - the file

Throws:

IOException - if an IOException occurs

getName

public String getName()

Returns the name of the parameters.

Returns:

the name of the parameters

setName

public void setName(String name)

Sets the name of the parameters.

Parameters:

name - the name of the parameters

getDescription

public String getDescription()

Returns the description of the parameters.

Returns:

the description of the parameters

getDefaultDescription

public Boolean getDefaultDescription()

Indicates whether the description is automatically generated.

Returns:

a boolean indicating whether the description is automatically generated

setDescription

public void setDescription(String description,
                           boolean automaticallyGenerated)

Sets the description of the parameters.

Parameters:

description - the description of the parameters

automaticallyGenerated - boolean indicating whether the description is automatically generated

setParametersFromSearch

public void setParametersFromSearch(SearchParameters searchParameters)

Sets identification parameters based on given search parameters.

Parameters:

searchParameters - the parameters used for the search

setType

public void setType()

Description copied from interface: MarshallableParameter

Sets the parameters type. The type must be set before writing a file but not in the constructor.

Specified by:

setType in interface MarshallableParameter

getType

public MarshallableParameter.Type getType()

Description copied from interface: MarshallableParameter

Returns the type of marshalled parameter from an unmarshalled object. The type must be written in the file but not set in the constructor. Null if not a MarshallableParameter.

Specified by:

getType in interface MarshallableParameter

Returns:

the type of marshalled parameter from an unmarshalled object

equals

public boolean equals(IdentificationParameters otherIdentificationParameters)

Returns true if the identification parameter objects have identical settings.

Parameters:

otherIdentificationParameters - the parameters to compare to

Returns:

true if the identification parameter objects have identical settings

equalsExceptValidationPreferences

public boolean equalsExceptValidationPreferences(IdentificationParameters otherIdentificationParameters)

Returns true if the identification parameter objects have identical settings except for the validation preferences.

Parameters:

otherIdentificationParameters - the parameters to compare to

Returns:

true if the identification parameter objects have identical settings except for the validation preferences