public class PsmScores extends Object
Constructor and Description |
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PsmScores() |
Modifier and Type | Method and Description |
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static double |
getAScorePeptideScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns a PSM score like the peptide score calculated for the A-score.
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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.
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static HashMap<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.
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public static double getAScorePeptideScore(Peptide peptide, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses) throws IOException, IllegalArgumentException, InterruptedException
peptide
- The peptide of interestspectrum
- 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.IOException
- exception thrown whenever an error occurred while
reading a protein sequenceIllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequenceInterruptedException
- exception thrown whenever an error occurred
while reading a protein sequencepublic static HashMap<Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance)
baseSpectrum
- the base spectrummzTolerance
- the m/z tolerancepublic static HashMap<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.