public class PhosphoRS extends Object
Modifier and Type | Field and Description |
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static int |
maxDepth
The maximal depth to use per window (8 in the original paper).
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Constructor and Description |
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PhosphoRS() |
Modifier and Type | Method and Description |
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static HashMap<Integer,Double> |
getSequenceProbabilities(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 PhosphoRS sequence probabilities for the PTM possible
locations.
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static HashMap<Integer,Double> |
getSequenceProbabilities(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 PhosphoRS sequence probabilities for the PTM possible
locations.
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public static final int maxDepth
public static HashMap<Integer,Double> getSequenceProbabilities(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 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
ClassNotFoundException
SQLException
public static HashMap<Integer,Double> getSequenceProbabilities(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 m/z tolerance to useaccountNeutralLosses
- a boolean indicating whether or not the
calculation shall account for neutral losses.sequenceMatchingPreferences
- the sequence matching preferencesspectrumAnnotator
- the peptide spectrum annotator to use for spectrum annotation, can be 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
ClassNotFoundException
SQLException
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