eu.isas.peptideshaker.processing

Class PsmProcessorRunnable

java.lang.Object

eu.isas.peptideshaker.processing.PsmProcessorRunnable

All Implemented Interfaces:

Runnable

public class PsmProcessorRunnable
extends Object
implements Runnable

This class processes PSMs.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description

PsmProcessorRunnable(ConcurrentLinkedQueue<Long> spectrumMatchKeysIterator, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, InputMap inputMap, 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, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Constructor.

Method Summary

Modifier and Type	Method and Description
void	run()

Methods inherited from class java.lang.Object

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

Constructor Detail

PsmProcessorRunnable

public PsmProcessorRunnable(ConcurrentLinkedQueue<Long> spectrumMatchKeysIterator,
                            com.compomics.util.experiment.identification.Identification identification,
                            com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                            InputMap inputMap,
                            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,
                            com.compomics.util.waiting.WaitingHandler waitingHandler,
                            com.compomics.util.exceptions.ExceptionHandler exceptionHandler)

Constructor.

Parameters:

spectrumMatchKeysIterator - Iterator for the spectrum match keys.

identification - The identification object.

identificationParameters - The identification parameters.

inputMap - The input map.

matchesValidator - The matches validator.

modificationLocalizationScorer - The post-translational modification localization scorer.

sequenceProvider - The protein sequences provider.

spectrumProvider - The spectrum provider.

modificationProvider - The modification provider to use.

proteinCount - The protein count.

waitingHandler - The waiting handler.

exceptionHandler - The exception handler.

Method Detail

run

public void run()

Specified by:

run in interface Runnable