Uses of Class
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Package | Description |
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com.compomics.util.experiment.identification.modification.scores |
PTM scores.
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com.compomics.util.experiment.identification.psm_scoring |
Main PSM scoring class.
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com.compomics.util.experiment.identification.psm_scoring.psm_scores |
Main PTM scoring classes.
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com.compomics.util.experiment.io.identification.writers |
Writer for identification results.
|
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Uses of PeptideSpectrumAnnotator in com.compomics.util.experiment.identification.modification.scores
Methods in com.compomics.util.experiment.identification.modification.scores with parameters of type PeptideSpectrumAnnotator Modifier and Type Method Description static HashMap<Integer,Double>
PhosphoRS. 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. -
Uses of PeptideSpectrumAnnotator in com.compomics.util.experiment.identification.psm_scoring
Methods in com.compomics.util.experiment.identification.psm_scoring with parameters of type PeptideSpectrumAnnotator Modifier and Type Method Description double
PsmScoresEstimator. getDecreasingScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)
Scores the match between the given peptide and spectrum using the given score.double
PsmScoresEstimator. getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)
Scores the match between the given peptide and spectrum using the given score.double
PsmScoresEstimator. getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, PsmScore psmScore)
Scores the match between the given peptide and spectrum using the given score. -
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 Description double
HyperScore. getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the hyperscore.double
SnrScore. getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the score. -
Uses of PeptideSpectrumAnnotator in com.compomics.util.experiment.io.identification.writers
Methods in com.compomics.util.experiment.io.identification.writers with parameters of type PeptideSpectrumAnnotator Modifier and Type Method Description void
SimpleMzIdentMLExporter. addSpectrum(String spectrumFile, String spectrumTitle, ArrayList<PeptideAssumption> peptideAssumptions, ArrayList<TreeMap<Double,HashMap<Integer,Double>>> modificationLocalizationScores, PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Adds a peptide-spectrum match to the file.