public class AAIntensityRankScore extends Object
Modifier and Type | Field and Description |
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static int |
nBins
The number of bins for the spectrum intensities.
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Constructor and Description |
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AAIntensityRankScore() |
Modifier and Type | Method and Description |
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static double |
getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance)
Scores the match between the given peptide and spectrum using the
intensity rank of the matched peaks.
|
static double |
getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using the
intensity rank of the matched peaks.
|
public static final int nBins
public static double getScore(Peptide peptide, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int identificationCharge, double mzTolerance)
peptide
- the peptide of interestspectrum
- the spectrum of interestiontypes
- the fragment ions to annotateneutralLosses
- the neutral losses to annotatecharges
- the fragment charges to look foridentificationCharge
- the precursor chargemzTolerance
- the ms2 m/z tolerancepublic static double getScore(Peptide peptide, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int identificationCharge, double mzTolerance, PeptideSpectrumAnnotator peptideSpectrumAnnotator)
peptide
- the peptide of interestspectrum
- the spectrum of interestiontypes
- the fragment ions to annotateneutralLosses
- the neutral losses to annotatecharges
- the fragment charges to look foridentificationCharge
- the precursor chargemzTolerance
- the ms2 m/z tolerancepeptideSpectrumAnnotator
- an external annotator (if null an
internal will be used)Copyright © 2014. All rights reserved.