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java.lang.Objectcom.compomics.util.experiment.identification.scoring.PsmScores
public class PsmScores
This class contains different ways of scoring a match.
Constructor Summary | |
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PsmScores()
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Method Summary | |
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static double |
getAScorePeptideScore(Peptide peptide,
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 a PSM score like the peptide score calculated for the A-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*mz 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*mz tolerance indexed by the depth used. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PsmScores()
Method Detail |
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public static double getAScorePeptideScore(Peptide peptide, 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
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.
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 sequencepublic static java.util.HashMap<java.lang.Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance)
baseSpectrum
- the base spectrummzTolerance
- the m/z tolerance
public 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 used
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