com.compomics.util.experiment.identification
Class AScore

java.lang.Object
  extended by com.compomics.util.experiment.identification.AScore

public class AScore
extends Object

This class scores PTM locations using the A-score.

Author:
Marc

Constructor Summary
AScore()
           
 
Method Summary
static HashMap<ArrayList<Integer>,Double> getAScore(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, HashMap<NeutralLoss,Integer> neutralLosses, ArrayList<Integer> charges, double mzTolerance)
          Returns the A-score for the best PTM location.
static HashMap<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.
 
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 HashMap<ArrayList<Integer>,Double> getAScore(Peptide peptide,
                                                           PTM ptm,
                                                           int nPTM,
                                                           MSnSpectrum spectrum,
                                                           ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
                                                           HashMap<NeutralLoss,Integer> neutralLosses,
                                                           ArrayList<Integer> charges,
                                                           double mzTolerance)
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 50.

Parameters:
peptide - The peptide of interest
ptm - The name of the PTM to score
nPTM - The number of occurrences where this PTM is expected on this peptide
spectrum - The corresponding spectrum
expectedFragmentIons - The fragment ions to look for
neutralLosses - The neutral losses to look for
charges - The fragment ions charges to look for
mzTolerance - The m/z tolerance to use
Returns:
a map containing the best or two best PTM location(s) and the corresponding A-score

getReducedSpectra

public static HashMap<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.


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