Uses of Class
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator

Packages that use PeptideSpectrumAnnotator

Package	Description
com.compomics.util.experiment.identification.psm_scoring.psm_scores	Main PTM scoring classes.
com.compomics.util.experiment.identification.ptm.ptmscores	PTM scores.

Uses of PeptideSpectrumAnnotator in com.compomics.util.experiment.identification.psm_scoring.psm_scores

Methods in com.compomics.util.experiment.identification.psm_scoring.psm_scores with parameters of type PeptideSpectrumAnnotator

Modifier and Type	Method and Description
static double	MS2MzFidelityScore.getScore(Peptide peptide, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator peptideSpectrumAnnotator) Scores the match between the given peptide and spectrum using an m/z fidelity score.
static double	IntensityRankScore.getScore(Peptide peptide, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator peptideSpectrumAnnotator) Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks.
static double	ComplementarityScore.getScore(Peptide peptide, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator peptideSpectrumAnnotator) Scores the match between the given peptide and spectrum using the complementarity of the matched peaks.
static double	AAMS2MzFidelityScore.getScore(Peptide peptide, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator peptideSpectrumAnnotator) Scores the match between the given peptide and spectrum using an m/z fidelity score.
static double	AAIntensityRankScore.getScore(Peptide peptide, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator peptideSpectrumAnnotator) Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks.

Uses of PeptideSpectrumAnnotator in com.compomics.util.experiment.identification.ptm.ptmscores

Methods in com.compomics.util.experiment.identification.ptm.ptmscores with parameters of type PeptideSpectrumAnnotator

Modifier and Type	Method and Description
static HashMap<Integer,Double>	AScore.getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, boolean accountNeutralLosses, SequenceMatchingPreferences sequenceMatchingPreferences, SequenceMatchingPreferences ptmSequenceMatchingPreferences, PeptideSpectrumAnnotator spectrumAnnotator) Returns the A-score for the best PTM location.
static HashMap<Integer,HashMap<Integer,Double>>	AScore.getPositionToScoreMap(Peptide peptide, Peptide noModPeptide, ArrayList<Integer> possibleSites, MSnSpectrum spectrum, HashMap<Integer,MSnSpectrum> spectrumMap, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator spectrumAnnotator, PTM refPTM) Returns a map PTM localization > score.
static HashMap<Integer,Double>	PhosphoRS.getSequenceProbabilities(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings, boolean accountNeutralLosses, SequenceMatchingPreferences sequenceMatchingPreferences, SequenceMatchingPreferences ptmSequenceMatchingPreferences, PeptideSpectrumAnnotator spectrumAnnotator) Returns the PhosphoRS sequence probabilities for the PTM possible locations.