public class PsmScorer extends Object
| Constructor and Description |
|---|
PsmScorer(com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)
Constructor.
|
| Modifier and Type | Method and Description |
|---|---|
void |
estimateIntermediateScoreProbabilities(com.compomics.util.experiment.identification.Identification identification,
InputMap inputMap,
com.compomics.util.parameters.tools.ProcessingParameters processingPreferences,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Estimates the probabilities associated to the intermediate PSM scores.
|
void |
estimateIntermediateScores(com.compomics.util.experiment.identification.Identification identification,
InputMap inputMap,
com.compomics.util.parameters.tools.ProcessingParameters processingParameters,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
Scores the PSMs contained in an identification object.
|
ArrayList<Integer> |
estimateIntermediateScores(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
InputMap inputMap,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator peptideSpectrumAnnotator,
com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore hyperScore,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Scores the PSMs contained in an identification object.
|
void |
scorePsms(com.compomics.util.experiment.identification.Identification identification,
InputMap inputMap,
com.compomics.util.parameters.tools.ProcessingParameters processingPreferences,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Attaches a score to the PSMs.
|
public PsmScorer(com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)
fastaParameters - The fasta parsing parameters.sequenceProvider - The sequence provider.spectrumProvider - The spectrum provider.public void estimateIntermediateScores(com.compomics.util.experiment.identification.Identification identification,
InputMap inputMap,
com.compomics.util.parameters.tools.ProcessingParameters processingParameters,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
throws InterruptedException,
TimeoutException
identification - the object containing the identification matchesinputMap - the input map scoresprocessingParameters - the processing preferencesidentificationParameters - identification parameters usedwaitingHandler - the handler displaying feedback to the userexceptionHandler - a handler for exceptionsInterruptedException - exception thrown if a thread is
interruptedTimeoutException - exception thrown if the
process times outpublic ArrayList<Integer> estimateIntermediateScores(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, InputMap inputMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator peptideSpectrumAnnotator, com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore hyperScore, com.compomics.util.waiting.WaitingHandler waitingHandler)
identification - the object containing the identification matchesspectrumMatch - a spectrum match containing the peptides and
spectrum to scoreinputMap - the input map scoresidentificationParameters - identification parameters usedpeptideSpectrumAnnotator - the spectrum annotator to usehyperScore - the object to use to compute the hyperscorewaitingHandler - the handler displaying feedback to the userpublic void estimateIntermediateScoreProbabilities(com.compomics.util.experiment.identification.Identification identification,
InputMap inputMap,
com.compomics.util.parameters.tools.ProcessingParameters processingPreferences,
com.compomics.util.waiting.WaitingHandler waitingHandler)
identification - the object containing the identification matchesinputMap - the input map scoresprocessingPreferences - the processing preferenceswaitingHandler - the handler displaying feedback to the userpublic void scorePsms(com.compomics.util.experiment.identification.Identification identification,
InputMap inputMap,
com.compomics.util.parameters.tools.ProcessingParameters processingPreferences,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.waiting.WaitingHandler waitingHandler)
identification - the object containing the identification matchesinputMap - the input map scoresprocessingPreferences - the processing preferencesidentificationParameters - the identification parameterswaitingHandler - the handler displaying feedback to the userCopyright © 2021. All rights reserved.