com.compomics.util.experiment.identification.psm_scoring

Enum PsmScores

java.lang.Object

java.lang.Enum<PsmScores>

com.compomics.util.experiment.identification.psm_scoring.PsmScores

All Implemented Interfaces:

Serializable, Comparable<PsmScores>

public enum PsmScores
extends Enum<PsmScores>

Enum listing the PSM scores implemented in compomics utilities.

Author:

Marc Vaudel

Enum Constant Summary

Enum Constants

Enum Constant and Description
aa_intensity The intensity sub-score as adapted from the DirecTag paper (http://www.ncbi.nlm.nih.gov/pubmed/18630943) per amino acid.
aa_ms2_mz_fidelity The m/z fidelity score as adapted from the DirecTag paper (http://www.ncbi.nlm.nih.gov/pubmed/18630943) per amino acid.
complementarity The complementarity score as adapted from the DirecTag paper (http://www.ncbi.nlm.nih.gov/pubmed/18630943).
intensity The intensity sub-score as adapted from the DirecTag paper (http://www.ncbi.nlm.nih.gov/pubmed/18630943).
ms2_mz_fidelity The m/z fidelity score as adapted from the DirecTag paper (http://www.ncbi.nlm.nih.gov/pubmed/18630943).
native_score The native score of the search engine.
precursor_accuracy The precursor accuracy.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	increasing Indicates whether the score increases with the quality of the match.
int	index The index of the score of interest.
String	name The name of the score.

Method Summary

Modifier and Type	Method and Description
static double	getDecreasingScore(Peptide peptide, Integer peptideCharge, MSnSpectrum spectrum, ShotgunProtocol shotgunProtocol, IdentificationParameters identificationParameters, SpecificAnnotationSettings specificAnnotationPreferences, int scoreIndex) Scores the match between the given peptide and spectrum using the given score.
static PsmScores	getScore(int scoreIndex) Returns the PSM score of the given index.
static double	getScore(Peptide peptide, Integer peptideCharge, MSnSpectrum spectrum, ShotgunProtocol shotgunProtocol, IdentificationParameters identificationParameters, SpecificAnnotationSettings specificAnnotationPreferences, int scoreIndex) Scores the match between the given peptide and spectrum using the given score.
static double	getScore(Peptide peptide, Integer peptideCharge, MSnSpectrum spectrum, ShotgunProtocol shotgunProtocol, IdentificationParameters identificationParameters, SpecificAnnotationSettings specificAnnotationPreferences, PsmScores psmScore) Scores the match between the given peptide and spectrum using the given score.
static PsmScores	valueOf(String name) Returns the enum constant of this type with the specified name.
static PsmScores[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

native_score

public static final PsmScores native_score

The native score of the search engine.

precursor_accuracy

public static final PsmScores precursor_accuracy

The precursor accuracy.

ms2_mz_fidelity

public static final PsmScores ms2_mz_fidelity

The m/z fidelity score as adapted from the DirecTag paper (http://www.ncbi.nlm.nih.gov/pubmed/18630943).

aa_ms2_mz_fidelity

public static final PsmScores aa_ms2_mz_fidelity

The m/z fidelity score as adapted from the DirecTag paper (http://www.ncbi.nlm.nih.gov/pubmed/18630943) per amino acid.

intensity

public static final PsmScores intensity

The intensity sub-score as adapted from the DirecTag paper (http://www.ncbi.nlm.nih.gov/pubmed/18630943).

aa_intensity

public static final PsmScores aa_intensity

The intensity sub-score as adapted from the DirecTag paper (http://www.ncbi.nlm.nih.gov/pubmed/18630943) per amino acid.

complementarity

public static final PsmScores complementarity

The complementarity score as adapted from the DirecTag paper (http://www.ncbi.nlm.nih.gov/pubmed/18630943).

Field Detail

name

public final String name

The name of the score.

index

public final int index

The index of the score of interest.

increasing

public final boolean increasing

Indicates whether the score increases with the quality of the match.

Method Detail

values

public static PsmScores[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (PsmScores c : PsmScores.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static PsmScores valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

getScore

public static PsmScores getScore(int scoreIndex)

Returns the PSM score of the given index. Null if not found.

Parameters:

scoreIndex - the index of the desired score

Returns:

the score of given index

getDecreasingScore

public static double getDecreasingScore(Peptide peptide,
                                        Integer peptideCharge,
                                        MSnSpectrum spectrum,
                                        ShotgunProtocol shotgunProtocol,
                                        IdentificationParameters identificationParameters,
                                        SpecificAnnotationSettings specificAnnotationPreferences,
                                        int scoreIndex)

Scores the match between the given peptide and spectrum using the given score. The score is forced to decrease with the quality of the match by taking the opposite value when relevant.

Parameters:

peptide - the peptide of interest

peptideCharge - the charge of the peptide

spectrum - the spectrum of interest

shotgunProtocol - information on the protocol used

identificationParameters - the identification parameters

specificAnnotationPreferences - the annotation preferences specific to this psm

scoreIndex - the index of the score to use

Returns:

the score of the match

getScore

public static double getScore(Peptide peptide,
                              Integer peptideCharge,
                              MSnSpectrum spectrum,
                              ShotgunProtocol shotgunProtocol,
                              IdentificationParameters identificationParameters,
                              SpecificAnnotationSettings specificAnnotationPreferences,
                              int scoreIndex)

Scores the match between the given peptide and spectrum using the given score.

Parameters:

peptide - the peptide of interest

peptideCharge - the charge of the peptide

spectrum - the spectrum of interest

shotgunProtocol - information on the protocol used

identificationParameters - the identification parameters

specificAnnotationPreferences - the annotation preferences specific to this psm

scoreIndex - the index of the score to use

Returns:

the score of the match

getScore

public static double getScore(Peptide peptide,
                              Integer peptideCharge,
                              MSnSpectrum spectrum,
                              ShotgunProtocol shotgunProtocol,
                              IdentificationParameters identificationParameters,
                              SpecificAnnotationSettings specificAnnotationPreferences,
                              PsmScores psmScore)

Scores the match between the given peptide and spectrum using the given score.

Parameters:

peptide - the peptide of interest

peptideCharge - the charge of the peptide

spectrum - the spectrum of interest

shotgunProtocol - information on the protocol used

identificationParameters - the identification parameters

specificAnnotationPreferences - the annotation preferences specific to this psm

psmScore - the score to use

Returns:

the score of the match