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,
AnnotationPreferences annotationPreferences,
SpecificAnnotationPreferences specificAnnotationPreferences,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
MathContext mathContext)
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, AnnotationPreferences annotationPreferences, SpecificAnnotationPreferences specificAnnotationPreferences, boolean accountNeutralLosses, SequenceMatchingPreferences sequenceMatchingPreferences, SequenceMatchingPreferences ptmSequenceMatchingPreferences, PeptideSpectrumAnnotator spectrumAnnotator, MathContext mathContext) throws IOException, InterruptedException, ClassNotFoundException, SQLException, org.apache.commons.math.MathException
peptide
- the peptide of interestptms
- the PTMs to score, for instance different phosphorylations
(the PTMs are considered as indistinguishable, i.e. of same mass)spectrum
- the corresponding spectrumannotationPreferences
- the global annotation preferencesspecificAnnotationPreferences
- the annotation preferences specific
to this peptide and spectrumaccountNeutralLosses
- a boolean indicating whether or not the
calculation shall account for neutral losses.sequenceMatchingPreferences
- the sequence matching preferences for
peptide to protein mappingptmSequenceMatchingPreferences
- the sequence matching preferences
for PTM to peptide mappingspectrumAnnotator
- the peptide spectrum annotator to use for
spectrum annotation, can be nullmathContext
- the math context to use for calculationIOException
- exception thrown whenever an error occurred
while reading or writing a fileInterruptedException
- exception thrown whenever a
threading issue occurred while scoring the PTMClassNotFoundException
- exception thrown whenever an
error occurred while deserializing an object from the protein tree (the
protein sequence index)SQLException
- exception thrown whenever an error occurred
while interacting with the protein treeorg.apache.commons.math.MathException
- exception thrown whenever a
math error occurred while computing the score.Copyright © 2015. All rights reserved.