eu.isas.peptideshaker.processing

Class PsmProcessor

java.lang.Object

eu.isas.peptideshaker.processing.PsmProcessor

public class PsmProcessor
extends Object

Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
PsmProcessor(com.compomics.util.experiment.identification.Identification identification) Constructor.

Method Summary

Modifier and Type

Method and Description

void

processPsms(InputMap inputMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, MatchesValidator matchesValidator, ModificationLocalizationScorer modificationLocalizationScorer, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, HashMap<String,Integer> proteinCount, int nThreads, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PsmProcessor

public PsmProcessor(com.compomics.util.experiment.identification.Identification identification)

Constructor.

Parameters:

identification - the identification

Method Detail

processPsms

public void processPsms(InputMap inputMap,
                        com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                        MatchesValidator matchesValidator,
                        ModificationLocalizationScorer modificationLocalizationScorer,
                        com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                        com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                        com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
                        HashMap<String,Integer> proteinCount,
                        int nThreads,
                        com.compomics.util.waiting.WaitingHandler waitingHandler,
                        com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
                 throws InterruptedException,
                        TimeoutException

Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.

Parameters:

inputMap - The input map.

identificationParameters - The identification parameters.

matchesValidator - The matches validator.

modificationLocalizationScorer - Post-translational modifications scorer.

sequenceProvider - Protein sequence provider.

spectrumProvider - The spectrum provider.

modificationProvider - The modification provider to use.

proteinCount - Map of the protein occurrence.

nThreads - The number of threads to use.

waitingHandler - Waiting handler to display progress and allow canceling the import.

exceptionHandler - The handler of exceptions.

Throws:

InterruptedException - Exception thrown if a thread is interrupted.

TimeoutException - Exception thrown if the process timed out.