public class PhosphoRS extends Object
Modifier and Type | Field and Description |
---|---|
static int |
MAX_DEPTH
The maximal depth to use per window.
|
static int |
MIN_DEPTH
The minimal depth to use per window.
|
static double |
WINDOW_SIZE
The window size in m/z.
|
Constructor and Description |
---|
PhosphoRS()
Empty default constructor
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
getSequenceProbabilities(Peptide peptide,
ArrayList<Modification> modifications,
ModificationParameters modificationParameters,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationParameters,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceMatchingParameters modificationSequenceMatchingParameters,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
|
public static final double WINDOW_SIZE
public static final int MAX_DEPTH
public static final int MIN_DEPTH
public static HashMap<Integer,Double> getSequenceProbabilities(Peptide peptide, ArrayList<Modification> modifications, ModificationParameters modificationParameters, Spectrum spectrum, SequenceProvider sequenceProvider, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationSettings, boolean accountNeutralLosses, SequenceMatchingParameters sequenceMatchingParameters, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator spectrumAnnotator)
peptide
- the peptide of interestmodifications
- the modifications to score, for instance different
phosphorylations (the modifications are considered as indistinguishable,
i.e. of same mass)modificationParameters
- the modification parametersspectrum
- the corresponding spectrumsequenceProvider
- a provider for the protein sequencesannotationParameters
- the global annotation parametersspecificAnnotationSettings
- the annotation settings specific to
this peptide and spectrumaccountNeutralLosses
- a boolean indicating whether or not the
calculation shall account for neutral losses.sequenceMatchingParameters
- the sequence matching preferences for
peptide to protein mappingmodificationSequenceMatchingParameters
- the sequence matching
preferences for modification to peptide mappingspectrumAnnotator
- the peptide spectrum annotator to use for
spectrum annotation, can be nullCopyright © 2021. All rights reserved.