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java.lang.Objectcom.compomics.util.experiment.identification.ptm.ptmscores.AScore
public class AScore
This class estimates the A-score as described in http://www.ncbi.nlm.nih.gov/pubmed/16964243 Note: Here the window size is adapted to mz tolerance and the score is not restricted to phosphorylation.
Constructor Summary | |
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AScore()
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Method Summary | |
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static HashMap<ArrayList<Integer>,Double> |
getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location without accounting for neutral losses. |
static HashMap<ArrayList<Integer>,Double> |
getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location accounting for neutral losses. |
static HashMap<ArrayList<Integer>,Double> |
getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the A-score for the best PTM location. |
static HashMap<Double,ArrayList<Integer>> |
getPeptideScoreToPositionMap(HashMap<Integer,HashMap<Integer,Double>> positionToScoreMap)
Estimates the peptide score for every modification localization and returns a map score -> localization. |
static HashMap<Integer,HashMap<Integer,Double>> |
getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
ArrayList<Integer> possibleSites,
MSnSpectrum spectrum,
HashMap<Integer,MSnSpectrum> spectrumMap,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap scoringLossesMap,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
SpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization -> score. |
static HashMap<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. |
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*m/z 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 AScore()
Method Detail |
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public static HashMap<ArrayList<Integer>,Double> getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, ArrayList<Integer> charges, int precursorCharge, double mzTolerance) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
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 use
IOException
- exception thrown whenever an error occurred while
reading a protein sequence
IllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequence
InterruptedException
- exception thrown whenever an error occurred
while reading a protein sequence
FileNotFoundException
ClassNotFoundException
public static HashMap<ArrayList<Integer>,Double> getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
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 use
IOException
- exception thrown whenever an error occurred while
reading a protein sequence
IllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequence
InterruptedException
- exception thrown whenever an error occurred
while reading a protein sequence
FileNotFoundException
ClassNotFoundException
public static HashMap<ArrayList<Integer>,Double> getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
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.
IOException
- exception thrown whenever an error occurred while
reading a protein sequence
IllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequence
InterruptedException
- exception thrown whenever an error occurred
while reading a protein sequence
FileNotFoundException
ClassNotFoundException
public static HashMap<Double,ArrayList<Integer>> getPeptideScoreToPositionMap(HashMap<Integer,HashMap<Integer,Double>> positionToScoreMap)
positionToScoreMap
- the position to score map
public static HashMap<Integer,HashMap<Integer,Double>> getPositionToScoreMap(Peptide peptide, Peptide noModPeptide, ArrayList<Integer> possibleSites, MSnSpectrum spectrum, HashMap<Integer,MSnSpectrum> spectrumMap, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap scoringLossesMap, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, SpectrumAnnotator spectrumAnnotator, PTM refPTM)
peptide
- noModPeptide
- spectrum
- iontypes
- spectrumMap
- scoringLossesMap
- charges
- precursorCharge
- mzTolerance
- spectrumAnnotator
- possibleSites
- refPTM
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public static HashMap<Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance)
baseSpectrum
- the base spectrummzTolerance
- the m/z tolerance
public 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 used
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