com.compomics.util.preferences

Class IdFilter

java.lang.Object

com.compomics.util.preferences.IdFilter

All Implemented Interfaces:

java.io.Serializable

public class IdFilter
extends java.lang.Object
implements java.io.Serializable

This class achieves a pre-filtering of the identifications for PeptideShaker.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
IdFilter() Constructor with default settings.
IdFilter(int minPepLength, int maxPepLength, double mascotMaxEvalue, double omssaMaxEvalue, double xtandemMaxEvalue, double maxMzDeviation, boolean isPpm, boolean unknownPTM) Constructor for an Identification filter.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(IdFilter anotherFilter) Indicates whether this filter is the same as another one.
double	getMascotMaxEvalue() Returns the maximal Mascot e-value allowed.
double	getMaxMzDeviation() Returns the maximal m/z deviation allowed.
int	getMaxPepLength() Returns the maximal peptide length allowed.
int	getMinPepLength() Returns the maximal peptide length allowed.
double	getOmssaMaxEvalue() Returns the OMSSA maximal e-value allowed.
double	getXtandemMaxEvalue() Returns the maximal X!Tandem e-value allowed.
boolean	isIsPpm() Indicates whether the mass tolerance is in ppm (true) or Dalton (false).
boolean	removeUnknownPTMs() Returns a boolean indicating whether unknown PTMs shall be removed.
void	setIsPpm(boolean isPpm) Sets whether the mass tolerance is in ppm (true) or Dalton (false).
void	setMascotMaxEvalue(double mascotMaxEvalue) Sets the maximal Mascot e-value allowed.
void	setMaxMzDeviation(double maxMzDeviation) Sets the maximal m/z deviation allowed.
void	setMaxPepLength(int maxPepLength) Sets the maximal peptide length allowed.
void	setMinPepLength(int minPepLength) Sets the maximal peptide length allowed.
void	setOmssaMaxEvalue(double omssaMaxEvalue) Sets the OMSSA maximal e-value allowed.
void	setRemoveUnknownPTMs(boolean unknownPtm) Set whether unknown PTMs shall be removed.
void	setXtandemMaxEvalue(double xtandemMaxEvalue) Sets the OMSSA maximal e-value allowed.
boolean	validateModifications(Peptide peptide, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance, ModificationProfile modificationProfile) Validates the modifications of a peptide.
boolean	validatePeptideAssumption(PeptideAssumption assumption) Validates the peptide assumption based on the peptide length and maximal e-values allowed.
boolean	validatePrecursor(PeptideAssumption assumption, java.lang.String spectrumKey, SpectrumFactory spectrumFactory) Validates the mass deviation of a peptide assumption.
boolean	validateProteins(Peptide peptide, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance) Validates a peptide depending on its protein inference status.
boolean	validateProteins(Peptide peptide, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance, ProteinTree proteinTree) Validates a peptide depending on its protein inference status.

Methods inherited from class java.lang.Object

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

Constructor Detail

IdFilter

public IdFilter()

Constructor with default settings.

IdFilter

public IdFilter(int minPepLength,
        int maxPepLength,
        double mascotMaxEvalue,
        double omssaMaxEvalue,
        double xtandemMaxEvalue,
        double maxMzDeviation,
        boolean isPpm,
        boolean unknownPTM)

Constructor for an Identification filter.

Parameters:

minPepLength - The minimal peptide length allowed (0 or less for disabled)

maxPepLength - The maximal peptide length allowed (0 or less for disabled)

mascotMaxEvalue - The maximal Mascot e-value allowed (0 or less for disabled)

omssaMaxEvalue - The maximal OMSSA e-value allowed (0 or less for disabled)

xtandemMaxEvalue - The maximal X!Tandem e-value allowed (0 or less for disabled)

maxMzDeviation - The maximal m/z deviation allowed (0 or less for disabled)

isPpm - Boolean indicating the unit of the allowed m/z deviation (true: ppm, false: Da)

unknownPTM - Shall peptides presenting unknownPTMs be ignored

Method Detail

validatePeptideAssumption

public boolean validatePeptideAssumption(PeptideAssumption assumption)

Validates the peptide assumption based on the peptide length and maximal e-values allowed.

Parameters:

assumption - the assumption to validate

Returns:

a boolean indicating whether the assumption passed the test

validateProteins

public boolean validateProteins(Peptide peptide,
                       AminoAcidPattern.MatchingType matchingType,
                       java.lang.Double massTolerance)
                         throws java.io.IOException,
                                java.sql.SQLException,
                                java.lang.ClassNotFoundException,
                                java.lang.InterruptedException

Validates a peptide depending on its protein inference status. Maps the peptide to proteins in case it was not done before using the default protein tree of the sequence factory

Parameters:

peptide - the peptide

matchingType - the desired peptide to protein matching type

massTolerance - the ms2 mass tolerance

Returns:

a boolean indicating whether the peptide passed the test

Throws:

java.io.IOException

java.sql.SQLException

java.lang.ClassNotFoundException

java.lang.InterruptedException

validateProteins

public boolean validateProteins(Peptide peptide,
                       AminoAcidPattern.MatchingType matchingType,
                       java.lang.Double massTolerance,
                       ProteinTree proteinTree)
                         throws java.io.IOException,
                                java.sql.SQLException,
                                java.lang.ClassNotFoundException,
                                java.lang.InterruptedException

Validates a peptide depending on its protein inference status. Maps the peptide to proteins in case it was not done before

Parameters:

peptide - the peptide

matchingType - the desired peptide to protein matching type

massTolerance - the ms2 mass tolerance

proteinTree - the protein tree to use for peptide to protein mapping

Returns:

a boolean indicating whether the peptide passed the test

Throws:

java.io.IOException

java.sql.SQLException

java.lang.ClassNotFoundException

java.lang.InterruptedException

validateModifications

public boolean validateModifications(Peptide peptide,
                            AminoAcidPattern.MatchingType matchingType,
                            java.lang.Double massTolerance,
                            ModificationProfile modificationProfile)

Validates the modifications of a peptide.

Parameters:

peptide - the peptide of interest

matchingType - the peptide-protein matching type

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

modificationProfile - the modification profile of the identification

Returns:

a boolean indicating whether the peptide passed the test

validatePrecursor

public boolean validatePrecursor(PeptideAssumption assumption,
                        java.lang.String spectrumKey,
                        SpectrumFactory spectrumFactory)
                          throws java.io.IOException,
                                 uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException

Validates the mass deviation of a peptide assumption.

Parameters:

assumption - the considered peptide assumption

spectrumKey - the key of the spectrum used to get the precursor the precursor should be accessible via the spectrum factory

spectrumFactory - the spectrum factory

Returns:

a boolean indicating whether the given assumption passes the filter

Throws:

java.io.IOException

uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException

removeUnknownPTMs

public boolean removeUnknownPTMs()

Returns a boolean indicating whether unknown PTMs shall be removed.

Returns:

a boolean indicating whether unknown PTMs shall be removed

setRemoveUnknownPTMs

public void setRemoveUnknownPTMs(boolean unknownPtm)

Set whether unknown PTMs shall be removed.

Parameters:

unknownPtm - whether unknown PTMs shall be removed

isIsPpm

public boolean isIsPpm()

Indicates whether the mass tolerance is in ppm (true) or Dalton (false).

Returns:

a boolean indicating whether the mass tolerance is in ppm (true) or Dalton (false)

setIsPpm

public void setIsPpm(boolean isPpm)

Sets whether the mass tolerance is in ppm (true) or Dalton (false).

Parameters:

isPpm - a boolean indicating whether the mass tolerance is in ppm (true) or Dalton (false)

getMascotMaxEvalue

public double getMascotMaxEvalue()

Returns the maximal Mascot e-value allowed.

Returns:

the maximal Mascot e-value allowed

setMascotMaxEvalue

public void setMascotMaxEvalue(double mascotMaxEvalue)

Sets the maximal Mascot e-value allowed.

Parameters:

mascotMaxEvalue - the maximal Mascot e-value allowed

getMaxMzDeviation

public double getMaxMzDeviation()

Returns the maximal m/z deviation allowed.

Returns:

the maximal mass deviation allowed

setMaxMzDeviation

public void setMaxMzDeviation(double maxMzDeviation)

Sets the maximal m/z deviation allowed.

Parameters:

maxMzDeviation - the maximal mass deviation allowed

getMaxPepLength

public int getMaxPepLength()

Returns the maximal peptide length allowed.

Returns:

the maximal peptide length allowed

setMaxPepLength

public void setMaxPepLength(int maxPepLength)

Sets the maximal peptide length allowed.

Parameters:

maxPepLength - the maximal peptide length allowed

getMinPepLength

public int getMinPepLength()

Returns the maximal peptide length allowed.

Returns:

the maximal peptide length allowed

setMinPepLength

public void setMinPepLength(int minPepLength)

Sets the maximal peptide length allowed.

Parameters:

minPepLength - the maximal peptide length allowed

getOmssaMaxEvalue

public double getOmssaMaxEvalue()

Returns the OMSSA maximal e-value allowed.

Returns:

the OMSSA maximal e-value allowed

setOmssaMaxEvalue

public void setOmssaMaxEvalue(double omssaMaxEvalue)

Sets the OMSSA maximal e-value allowed.

Parameters:

omssaMaxEvalue - the OMSSA maximal e-value allowed

getXtandemMaxEvalue

public double getXtandemMaxEvalue()

Returns the maximal X!Tandem e-value allowed.

Returns:

the OMSSA maximal e-value allowed

setXtandemMaxEvalue

public void setXtandemMaxEvalue(double xtandemMaxEvalue)

Sets the OMSSA maximal e-value allowed.

Parameters:

xtandemMaxEvalue - the OMSSA maximal e-value allowed

equals

public boolean equals(IdFilter anotherFilter)

Indicates whether this filter is the same as another one.

Parameters:

anotherFilter - another filter

Returns:

a boolean indicating that the filters have the same parameters