com.compomics.util.experiment.identification.ptm.ptmscores

Class AScore

java.lang.Object

com.compomics.util.experiment.identification.ptm.ptmscores.AScore

public class AScore
extends java.lang.Object

This class estimates the A-score as described in http://www.ncbi.nlm.nih.gov/pubmed/16964243 Note: Here the window size is adapted to mz tolerance and the score is not restricted to phosphorylation.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
AScore()

Method Summary

Methods

Modifier and Type	Method and Description
static java.util.HashMap<java.lang.Integer,java.lang.Double>	getAScore(Peptide peptide, java.util.ArrayList<PTM> ptms, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance, AminoAcidPattern.MatchingType matchingType) Returns the A-score for the best PTM location without accounting for neutral losses.
static java.util.HashMap<java.lang.Integer,java.lang.Double>	getAScore(Peptide peptide, java.util.ArrayList<PTM> ptms, 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, AminoAcidPattern.MatchingType matchingType) Returns the A-score for the best PTM location accounting for neutral losses.
static java.util.HashMap<java.lang.Integer,java.lang.Double>	getAScore(Peptide peptide, java.util.ArrayList<PTM> ptms, 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, AminoAcidPattern.MatchingType matchingType) Returns the A-score for the best PTM location.
static java.util.HashMap<java.lang.Double,java.util.ArrayList<java.lang.Integer>>	getPeptideScoreToPositionMap(java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.Double>> positionToScoreMap) Estimates the peptide score for every modification localization and returns a map score -> localization.
static java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.Double>>	getPositionToScoreMap(Peptide peptide, Peptide noModPeptide, java.util.ArrayList<java.lang.Integer> possibleSites, MSnSpectrum spectrum, java.util.HashMap<java.lang.Integer,MSnSpectrum> spectrumMap, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap scoringLossesMap, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance, PeptideSpectrumAnnotator spectrumAnnotator, PTM refPTM) Returns a map PTM localization -> 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*m/z 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*m/z 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

AScore

public AScore()

Method Detail

getAScore

public static java.util.HashMap<java.lang.Integer,java.lang.Double> getAScore(Peptide peptide,
                                                              java.util.ArrayList<PTM> ptms,
                                                              MSnSpectrum spectrum,
                                                              java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                                              java.util.ArrayList<java.lang.Integer> charges,
                                                              int precursorCharge,
                                                              double mzTolerance,
                                                              AminoAcidPattern.MatchingType matchingType)
                                                                       throws java.io.IOException,
                                                                              java.lang.IllegalArgumentException,
                                                                              java.lang.InterruptedException,
                                                                              java.io.FileNotFoundException,
                                                                              java.lang.ClassNotFoundException,
                                                                              java.sql.SQLException

Returns the A-score for the best PTM location without accounting for neutral losses. In case the two best locations score the same they are both given with the score of 0. Note that PTMs found on peptides must be loaded in the PTM factory.

Parameters:

peptide - The peptide of interest

ptms - The PTMs to score, for instance different phosphorylations. These PTMs are considered as indistinguishable, i.e. of same mass.

spectrum - The corresponding spectrum

iontypes - The fragment ions to look for

charges - The fragment ions charges to look for

precursorCharge - The precursor charge

mzTolerance - The m/z tolerance to use

matchingType - the amino acid matching type to use to map PTMs on peptides

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

java.io.FileNotFoundException

java.lang.ClassNotFoundException

java.sql.SQLException

getAScore

public static java.util.HashMap<java.lang.Integer,java.lang.Double> getAScore(Peptide peptide,
                                                              java.util.ArrayList<PTM> ptms,
                                                              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,
                                                              AminoAcidPattern.MatchingType matchingType)
                                                                       throws java.io.IOException,
                                                                              java.lang.IllegalArgumentException,
                                                                              java.lang.InterruptedException,
                                                                              java.io.FileNotFoundException,
                                                                              java.lang.ClassNotFoundException,
                                                                              java.sql.SQLException

Returns the A-score for the best PTM location accounting for neutral losses. In case the two best locations score the same they are both given with the score of 0. Note that PTMs found on peptides must be loaded in the PTM factory.

Parameters:

peptide - The peptide of interest

ptms - The PTMs to score, for instance different phosphorylations. These PTMs are considered as indistinguishable, i.e. of same mass.

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

matchingType - the amino acid matching type to use to map PTMs on peptides

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

java.io.FileNotFoundException

java.lang.ClassNotFoundException

java.sql.SQLException

getAScore

public static java.util.HashMap<java.lang.Integer,java.lang.Double> getAScore(Peptide peptide,
                                                              java.util.ArrayList<PTM> ptms,
                                                              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,
                                                              AminoAcidPattern.MatchingType matchingType)
                                                                       throws java.io.IOException,
                                                                              java.lang.IllegalArgumentException,
                                                                              java.lang.InterruptedException,
                                                                              java.io.FileNotFoundException,
                                                                              java.lang.ClassNotFoundException,
                                                                              java.sql.SQLException

Returns the A-score for the best PTM location. In case the two best locations score the same they are both given with the score of 0. 0 is the first amino acid. Note that PTMs found on peptides must be loaded in the PTM factory.

Parameters:

peptide - The peptide of interest

ptms - The PTMs to score, for instance different phosphorylations. These PTMs are considered as indistinguishable, i.e. of same mass.

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 MS2 m/z tolerance to use

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

matchingType - the amino acid matching type to use to map PTMs on peptides

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

java.io.FileNotFoundException

java.lang.ClassNotFoundException

java.sql.SQLException

getPeptideScoreToPositionMap

public static java.util.HashMap<java.lang.Double,java.util.ArrayList<java.lang.Integer>> getPeptideScoreToPositionMap(java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.Double>> positionToScoreMap)

Estimates the peptide score for every modification localization and returns a map score -> localization.

Parameters:

positionToScoreMap - the position to score map

Returns:

a score to position map

getPositionToScoreMap

public static java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.Double>> getPositionToScoreMap(Peptide peptide,
                                                                                                               Peptide noModPeptide,
                                                                                                               java.util.ArrayList<java.lang.Integer> possibleSites,
                                                                                                               MSnSpectrum spectrum,
                                                                                                               java.util.HashMap<java.lang.Integer,MSnSpectrum> spectrumMap,
                                                                                                               java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                                                                                               NeutralLossesMap scoringLossesMap,
                                                                                                               java.util.ArrayList<java.lang.Integer> charges,
                                                                                                               int precursorCharge,
                                                                                                               double mzTolerance,
                                                                                                               PeptideSpectrumAnnotator spectrumAnnotator,
                                                                                                               PTM refPTM)

Returns a map PTM localization -> score.

Parameters:

peptide -

noModPeptide -

spectrum -

iontypes -

spectrumMap -

scoringLossesMap -

charges -

precursorCharge -

mzTolerance -

spectrumAnnotator -

possibleSites -

refPTM -

Returns:

a map PTM localization -> score

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*m/z 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*m/z 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.