com.compomics.util.experiment.identification.filtering

Class PeptideAssumptionFilter

java.lang.Object

com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter

All Implemented Interfaces:

Serializable

public class PeptideAssumptionFilter
extends Object
implements Serializable

This class filters peptide assumptions based on various properties.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PeptideAssumptionFilter() Constructor with default settings.
PeptideAssumptionFilter(int minPepLength, int maxPepLength, double maxMzDeviation, boolean isPpm, boolean unknownPTM, Integer minMissedCleavages, Integer maxMissedCleavages, Integer minIsotopes, Integer maxIsotopes) Constructor for an Identification filter.

Method Summary

Modifier and Type	Method and Description
Integer	getMaxIsotopes() Returns the maximal number of isotopes allowed (inclusive).
Integer	getMaxMissedCleavages() Returns the maximum number of missed cleavages.
double	getMaxMzDeviation() Returns the maximal m/z deviation allowed.
int	getMaxPepLength() Returns the maximal peptide length allowed.
Integer	getMinIsotopes() Returns the minimal number of isotopes allowed (inclusive).
Integer	getMinMissedCleavages() Returns the minimum number of missed cleavages.
int	getMinPepLength() Returns the maximal peptide length allowed.
String	getShortDescription() Returns a short description of the parameters.
boolean	isIsPpm() Indicates whether the mass tolerance is in ppm (true) or Dalton (false).
boolean	isSameAs(PeptideAssumptionFilter anotherFilter) Indicates whether this filter is the same as another one.
boolean	removeUnknownPTMs() Returns a boolean indicating whether unknown PTMs shall be removed.
void	setFilterFromSearchParameters(SearchParameters searchParameters) Updates the filter based on the search parameters.
void	setIsPpm(boolean isPpm) Sets whether the mass tolerance is in ppm (true) or Dalton (false).
void	setMaxIsotopes(Integer maxIsotopes) Sets the maximal number of isotopes allowed (inclusive).
void	setMaxMissedCleavages(Integer maxMissedCleavages) Set the maximum number of missed cleavages.
void	setMaxMzDeviation(double maxMzDeviation) Sets the maximal m/z deviation allowed.
void	setMaxPepLength(int maxPepLength) Sets the maximal peptide length allowed.
void	setMinIsotopes(Integer minIsotopes) Sets the minimal number of isotopes allowed (inclusive).
void	setMinMissedCleavages(Integer minMissedCleavages) Set the minimum number of missed cleavages.
void	setMinPepLength(int minPepLength) Sets the maximal peptide length allowed.
void	setRemoveUnknownPTMs(boolean unknownPtm) Set whether unknown PTMs shall be removed.
boolean	validateModifications(Peptide peptide, SequenceMatchingPreferences sequenceMatchingPreferences, SequenceMatchingPreferences ptmSequenceMatchingPreferences, PtmSettings modificationProfile) Validates the modifications of a peptide.
boolean	validatePeptide(Peptide peptide, SequenceMatchingPreferences sequenceMatchingPreferences, Enzyme enzyme) Validates the peptide based on the peptide length, the share of X's in the sequence and the allowed number of missed cleavages.
boolean	validatePrecursor(PeptideAssumption assumption, String spectrumKey, SpectrumFactory spectrumFactory, SearchParameters searchParameters) Validates the mass deviation of a peptide assumption.
boolean	validateProteins(Peptide peptide, SequenceMatchingPreferences sequenceMatchingPreferences) Validates a peptide depending on its protein inference status.
boolean	validateProteins(Peptide peptide, SequenceMatchingPreferences sequenceMatchingPreferences, 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

PeptideAssumptionFilter

public PeptideAssumptionFilter()

Constructor with default settings.

PeptideAssumptionFilter

public PeptideAssumptionFilter(int minPepLength,
                               int maxPepLength,
                               double maxMzDeviation,
                               boolean isPpm,
                               boolean unknownPTM,
                               Integer minMissedCleavages,
                               Integer maxMissedCleavages,
                               Integer minIsotopes,
                               Integer maxIsotopes)

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)

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

minMissedCleavages - the minimum number of missed cleavages allowed (null for disabled)

maxMissedCleavages - the maximum number of missed cleavages allowed (null for disabled)

minIsotopes - the minimum number of isotopes allowed (null for disabled)

maxIsotopes - the maximum number of isotopes allowed (null for disabled)

Method Detail

setFilterFromSearchParameters

public void setFilterFromSearchParameters(SearchParameters searchParameters)

Updates the filter based on the search parameters.

Parameters:

searchParameters - the search parameters where to take the information from

validatePeptide

public boolean validatePeptide(Peptide peptide,
                               SequenceMatchingPreferences sequenceMatchingPreferences,
                               Enzyme enzyme)

Validates the peptide based on the peptide length, the share of X's in the sequence and the allowed number of missed cleavages.

Parameters:

peptide - the peptide to validate

sequenceMatchingPreferences - the sequence matching preferences containing the maximal share of X's allowed

enzyme - the enzyme

Returns:

a boolean indicating whether the peptide passed the test

validateProteins

public boolean validateProteins(Peptide peptide,
                                SequenceMatchingPreferences sequenceMatchingPreferences)
                         throws IOException,
                                SQLException,
                                ClassNotFoundException,
                                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

sequenceMatchingPreferences - the sequence matching preferences

Returns:

a boolean indicating whether the peptide passed the test

Throws:

IOException - if an IOException occurs

SQLException - if an SQLException occurs

ClassNotFoundException - if a ClassNotFoundException occurs

InterruptedException - if an InterruptedException occurs

validateProteins

public boolean validateProteins(Peptide peptide,
                                SequenceMatchingPreferences sequenceMatchingPreferences,
                                ProteinTree proteinTree)
                         throws IOException,
                                SQLException,
                                ClassNotFoundException,
                                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

sequenceMatchingPreferences - the sequence matching preferences

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

Returns:

a boolean indicating whether the peptide passed the test

Throws:

IOException - if an IOException occurs

SQLException - if an SQLException occurs

ClassNotFoundException - if a ClassNotFoundException occurs

InterruptedException - if an InterruptedException occurs

validateModifications

public boolean validateModifications(Peptide peptide,
                                     SequenceMatchingPreferences sequenceMatchingPreferences,
                                     SequenceMatchingPreferences ptmSequenceMatchingPreferences,
                                     PtmSettings modificationProfile)

Validates the modifications of a peptide.

Parameters:

peptide - the peptide of interest

sequenceMatchingPreferences - the sequence matching preferences for peptide to protein mapping

ptmSequenceMatchingPreferences - the sequence matching preferences for PTM to peptide mapping

modificationProfile - the modification profile of the identification

Returns:

a boolean indicating whether the peptide passed the test

validatePrecursor

public boolean validatePrecursor(PeptideAssumption assumption,
                                 String spectrumKey,
                                 SpectrumFactory spectrumFactory,
                                 SearchParameters searchParameters)
                          throws 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

searchParameters - the search parameters

Returns:

a boolean indicating whether the given assumption passes the filter

Throws:

IOException - if an error occurs while reading the spectrum

uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException - if an MzMLUnmarshallerException occurs reading while the spectrum

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)

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

getMinIsotopes

public Integer getMinIsotopes()

Returns the minimal number of isotopes allowed (inclusive).

Returns:

the minimal number of isotopes allowed

setMinIsotopes

public void setMinIsotopes(Integer minIsotopes)

Sets the minimal number of isotopes allowed (inclusive).

Parameters:

minIsotopes - the minimal number of isotopes allowed

getMaxIsotopes

public Integer getMaxIsotopes()

Returns the maximal number of isotopes allowed (inclusive).

Returns:

the maximal number of isotopes allowed

setMaxIsotopes

public void setMaxIsotopes(Integer maxIsotopes)

Sets the maximal number of isotopes allowed (inclusive).

Parameters:

maxIsotopes - the maximal number of isotopes allowed

isSameAs

public boolean isSameAs(PeptideAssumptionFilter 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

getShortDescription

public String getShortDescription()

Returns a short description of the parameters.

Returns:

a short description of the parameters

getMinMissedCleavages

public Integer getMinMissedCleavages()

Returns the minimum number of missed cleavages. Null means no limit.

Returns:

the minMissedCleavages

setMinMissedCleavages

public void setMinMissedCleavages(Integer minMissedCleavages)

Set the minimum number of missed cleavages. Null means no limit.

Parameters:

minMissedCleavages - the minMissedCleavages to set

getMaxMissedCleavages

public Integer getMaxMissedCleavages()

Returns the maximum number of missed cleavages. Null means no limit.

Returns:

the maxMissedCleavages

setMaxMissedCleavages

public void setMaxMissedCleavages(Integer maxMissedCleavages)

Set the maximum number of missed cleavages. Null means no limit.

Parameters:

maxMissedCleavages - the maxMissedCleavages to set