public class AScore extends Object
Constructor and Description |
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AScore() |
Modifier and Type | Method and Description |
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static HashMap<Integer,Double> |
getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location without accounting for
neutral losses.
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static HashMap<Integer,Double> |
getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location.
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static HashMap<Integer,Double> |
getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the A-score for the best PTM location.
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static HashMap<Integer,Double> |
getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
Integer rounding)
Returns the A-score for the best PTM location.
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static HashMap<Integer,Double> |
getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location accounting for neutral
losses.
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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.
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static HashMap<Integer,HashMap<Integer,Double>> |
getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
ArrayList<Integer> possibleSites,
MSnSpectrum spectrum,
HashMap<Integer,MSnSpectrum> spectrumMap,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap scoringLossesMap,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
PeptideSpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization > 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*m/z 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*m/z tolerance indexed by the depth used.
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public static HashMap<Integer,Double> getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,HashSet<Integer>> iontypes, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
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 usesequenceMatchingPreferences
- the sequence matching preferencesIOException
- 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 sequenceFileNotFoundException
- if a FileNotFoundException occursClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occurspublic static HashMap<Integer,Double> getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,HashSet<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
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 usesequenceMatchingPreferences
- the sequence matching preferencesIOException
- 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 sequenceFileNotFoundException
- if a FileNotFoundException occursClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occurspublic static HashMap<Integer,Double> getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,HashSet<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
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 MS2 m/z tolerance to useaccountNeutralLosses
- a boolean indicating whether or not the
calculation shall account for neutral losses.sequenceMatchingPreferences
- the sequence matching preferencesIOException
- 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 sequenceFileNotFoundException
- if a FileNotFoundException occursClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occurspublic static HashMap<Integer,Double> getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,HashSet<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses, SequenceMatchingPreferences sequenceMatchingPreferences, PeptideSpectrumAnnotator spectrumAnnotator) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
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 MS2 m/z tolerance to useaccountNeutralLosses
- a boolean indicating whether or not the
calculation shall account for neutral losses.sequenceMatchingPreferences
- the sequence matching preferencesspectrumAnnotator
- a spectrum annotator to annotate the spectraIOException
- 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 sequenceFileNotFoundException
- if a FileNotFoundException occursClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occurspublic static HashMap<Integer,Double> getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,HashSet<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses, SequenceMatchingPreferences sequenceMatchingPreferences, PeptideSpectrumAnnotator spectrumAnnotator, Integer rounding) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
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 MS2 m/z tolerance to useaccountNeutralLosses
- a boolean indicating whether or not the
calculation shall account for neutral losses.sequenceMatchingPreferences
- the sequence matching preferencesspectrumAnnotator
- a spectrum annotator to annotate the spectrarounding
- decimal to which the score should be floored, ignored if
nullIOException
- 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 sequenceFileNotFoundException
- if a FileNotFoundException occursClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occurspublic static HashMap<Double,ArrayList<Integer>> getPeptideScoreToPositionMap(HashMap<Integer,HashMap<Integer,Double>> positionToScoreMap)
positionToScoreMap
- the position to score mappublic static HashMap<Integer,HashMap<Integer,Double>> getPositionToScoreMap(Peptide peptide, Peptide noModPeptide, ArrayList<Integer> possibleSites, MSnSpectrum spectrum, HashMap<Integer,MSnSpectrum> spectrumMap, HashMap<Ion.IonType,HashSet<Integer>> iontypes, NeutralLossesMap scoringLossesMap, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, PeptideSpectrumAnnotator spectrumAnnotator, PTM refPTM)
peptide
- the peptide of interestnoModPeptide
- the peptide without the variable modification of
interestrefPTM
- the PTM of interestiontypes
- the ion types to look for in the spectrumscoringLossesMap
- the neutral losses to look for in the spectrumcharges
- the fragment ion charges to look for in the spectrumprecursorCharge
- the precursor charge to look for in the spectrummzTolerance
- the fragment ion m/z tolerance for spectrum annotationspectrumAnnotator
- the spectrum annotator which should be used to
annotate the spectrumspectrum
- the spectrum of interestspectrumMap
- the map of the extracted spectra: depth > extracted
spectrumpossibleSites
- the possible modification sitespublic 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 © 2015. All rights reserved.