public class PhosphoRS extends Object
Modifier and Type | Field and Description |
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static int |
MAX_DEPTH
The maximal depth to use per window.
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static int |
MIN_DEPTH
The minimal depth to use per window.
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static double |
WINDOW_SIZE
The window size in m/z.
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Constructor and Description |
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PhosphoRS() |
Modifier and Type | Method and Description |
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static String |
getModificationProfileKey(int[] sites)
Returns a key as concatenated string for the given sites.
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static HashMap<Integer,Double> |
getSequenceProbabilities(Peptide peptide,
ArrayList<Modification> modifications,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters modificationSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
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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, Spectrum spectrum, SequenceProvider sequenceProvider, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, boolean accountNeutralLosses, SequenceMatchingParameters sequenceMatchingPreferences, SequenceMatchingParameters modificationSequenceMatchingPreferences, 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)spectrum
- the corresponding spectrumsequenceProvider
- a provider for the protein sequencesannotationSettings
- the global annotation settingsspecificAnnotationSettings
- the annotation settings 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 mappingmodificationSequenceMatchingPreferences
- the sequence matching
preferences for modification to peptide mappingspectrumAnnotator
- the peptide spectrum annotator to use for
spectrum annotation, can be nullpublic static String getModificationProfileKey(int[] sites)
sites
- the sitesCopyright © 2018. All rights reserved.