public class AScore
extends java.lang.Object
Constructor and Description |
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AScore() |
Modifier and Type | Method and Description |
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static java.util.HashMap<java.util.ArrayList<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)
Returns the A-score for the best PTM location without accounting for
neutral losses.
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static java.util.HashMap<java.util.ArrayList<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)
Returns the A-score for the best PTM location accounting for neutral
losses.
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static java.util.HashMap<java.util.ArrayList<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)
Returns the A-score for the best PTM location.
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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.
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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,
SpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization -> score.
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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.
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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.
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public static java.util.HashMap<java.util.ArrayList<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) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException, java.io.FileNotFoundException, java.lang.ClassNotFoundException, java.sql.SQLException
peptide
- The peptide of interestptms
- The PTMs to score, for instance different phosphorylations.
These PTMs are considered as indistinguishable, i.e. of same mass.spectrum
- The corresponding spectrumiontypes
- The fragment ions to look forcharges
- The fragment ions charges to look forprecursorCharge
- The precursor chargemzTolerance
- The m/z tolerance to usejava.io.IOException
- exception thrown whenever an error occurred while
reading a protein sequencejava.lang.IllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequencejava.lang.InterruptedException
- exception thrown whenever an error occurred
while reading a protein sequencejava.io.FileNotFoundException
java.lang.ClassNotFoundException
java.sql.SQLException
public static java.util.HashMap<java.util.ArrayList<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) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException, java.io.FileNotFoundException, java.lang.ClassNotFoundException, java.sql.SQLException
peptide
- The peptide of interestptms
- The PTMs to score, for instance different phosphorylations.
These PTMs are considered as indistinguishable, i.e. of same mass.spectrum
- The corresponding spectrumiontypes
- The fragment ions to look forneutralLosses
- The neutral losses to look forcharges
- The fragment ions charges to look forprecursorCharge
- The precursor chargemzTolerance
- The m/z tolerance to usejava.io.IOException
- exception thrown whenever an error occurred while
reading a protein sequencejava.lang.IllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequencejava.lang.InterruptedException
- exception thrown whenever an error occurred
while reading a protein sequencejava.io.FileNotFoundException
java.lang.ClassNotFoundException
java.sql.SQLException
public static java.util.HashMap<java.util.ArrayList<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) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException, java.io.FileNotFoundException, java.lang.ClassNotFoundException, java.sql.SQLException
peptide
- The peptide of interestptms
- The PTMs to score, for instance different phosphorylations.
These PTMs are considered as indistinguishable, i.e. of same mass.spectrum
- The corresponding spectrumiontypes
- The fragment ions to look forneutralLosses
- The neutral losses to look forcharges
- The fragment ions charges to look forprecursorCharge
- The precursor chargemzTolerance
- The m/z tolerance to useaccountNeutralLosses
- a boolean indicating whether or not the
calculation shall account for neutral losses.java.io.IOException
- exception thrown whenever an error occurred while
reading a protein sequencejava.lang.IllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequencejava.lang.InterruptedException
- exception thrown whenever an error occurred
while reading a protein sequencejava.io.FileNotFoundException
java.lang.ClassNotFoundException
java.sql.SQLException
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)
positionToScoreMap
- the position to score mappublic 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, SpectrumAnnotator spectrumAnnotator, PTM refPTM)
peptide
- noModPeptide
- spectrum
- iontypes
- spectrumMap
- scoringLossesMap
- charges
- precursorCharge
- mzTolerance
- spectrumAnnotator
- possibleSites
- refPTM
- public static java.util.HashMap<java.lang.Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance)
baseSpectrum
- the base spectrummzTolerance
- the m/z tolerancepublic static java.util.HashMap<java.lang.Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance, int depthMax)
baseSpectrum
- the base spectrummzTolerance
- the m/z tolerancedepthMax
- the depth to look into (10 for A-score). If -1 the
maximal depth will be usedCopyright © 2013. All Rights Reserved.