eu.isas.peptideshaker.stirred.modules

Class StirRunnable

java.lang.Object

eu.isas.peptideshaker.stirred.modules.StirRunnable

All Implemented Interfaces:

Runnable

public class StirRunnable
extends Object
implements Runnable

This class scores the modification localization.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description

StirRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches, com.compomics.util.experiment.io.identification.IdfileReader idfileReader, com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter writer, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.software.log.CliLogger cliLogger) Constructor.

Method Summary

Modifier and Type	Method and Description
int	getnModificationIssues() Returns the number of peptides where the modification could not be parsed.
int	getnPeptides() Returns the total number of peptides processed.
void	run()

Methods inherited from class java.lang.Object

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

Constructor Detail

StirRunnable

public StirRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches,
                    com.compomics.util.experiment.io.identification.IdfileReader idfileReader,
                    com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter writer,
                    com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                    com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper,
                    com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                    com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                    com.compomics.software.log.CliLogger cliLogger)

Constructor.

Parameters:

spectrumMatches - The spectrum matches to process.

idfileReader - The id file reader.

writer - The mzIdentML writer.

identificationParameters - The identification parameters.

fastaMapper - The sequence mapper.

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

cliLogger - The logger for CLI feedback.

Method Detail

run

public void run()

Specified by:

run in interface Runnable

getnModificationIssues

public int getnModificationIssues()

Returns the number of peptides where the modification could not be parsed.

Returns:

The number of peptides where the modification could not be parsed.

getnPeptides

public int getnPeptides()

Returns the total number of peptides processed.

Returns:

The total number of peptides processed.