com.compomics.util.experiment.identification.scoring

Class PsmScores

java.lang.Object

com.compomics.util.experiment.identification.scoring.PsmScores

public class PsmScores
extends java.lang.Object

This class contains different ways of scoring a match.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
PsmScores()

Method Summary

Methods

Modifier and Type	Method and Description
static double	getAScorePeptideScore(Peptide peptide, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses) Returns a PSM score like the peptide score calculated for the A-score.
static java.util.HashMap<java.lang.Integer,MSnSpectrum>	getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance) Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used.
static java.util.HashMap<java.lang.Integer,MSnSpectrum>	getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance, int depthMax) Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used.

Methods inherited from class java.lang.Object

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

Constructor Detail

PsmScores

public PsmScores()

Method Detail

getAScorePeptideScore

public static double getAScorePeptideScore(Peptide peptide,
                           MSnSpectrum spectrum,
                           java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                           NeutralLossesMap neutralLosses,
                           java.util.ArrayList<java.lang.Integer> charges,
                           int precursorCharge,
                           double mzTolerance,
                           boolean accountNeutralLosses)
                                    throws java.io.IOException,
                                           java.lang.IllegalArgumentException,
                                           java.lang.InterruptedException

Returns a PSM score like the peptide score calculated for the A-score.

Parameters:

peptide - The peptide of interest

spectrum - The corresponding spectrum

iontypes - The fragment ions to look for

neutralLosses - The neutral losses to look for

charges - The fragment ions charges to look for

precursorCharge - The precursor charge

mzTolerance - The m/z tolerance to use

accountNeutralLosses - a boolean indicating whether or not the calculation shall account for neutral losses.

Returns:

a map containing the best or two best PTM location(s) and the corresponding A-score

Throws:

java.io.IOException - exception thrown whenever an error occurred while reading a protein sequence

java.lang.IllegalArgumentException - exception thrown whenever an error occurred while reading a protein sequence

java.lang.InterruptedException - exception thrown whenever an error occurred while reading a protein sequence

getReducedSpectra

public static java.util.HashMap<java.lang.Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum,
                                                                 double mzTolerance)

Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. (see A-score paper for more details).

Parameters:

baseSpectrum - the base spectrum

mzTolerance - the m/z tolerance

Returns:

a map containing the spectra filtered indexed by peak depth.

getReducedSpectra

public static java.util.HashMap<java.lang.Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum,
                                                                 double mzTolerance,
                                                                 int depthMax)

Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. (see A-score paper for more details).

Parameters:

baseSpectrum - the base spectrum

mzTolerance - the m/z tolerance

depthMax - the depth to look into (10 for A-score). If -1 the maximal depth will be used

Returns:

a map containing the spectra filtered indexed by peak depth.