eu.isas.peptideshaker.fileimport

Class PsmFirstHitRunnable

java.lang.Object

eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable

All Implemented Interfaces:

Runnable

public class PsmFirstHitRunnable
extends Object
implements Runnable

This class tries to find a best hit per search engine for each spectrum match.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description

PsmFirstHitRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, InputMap inputMap, 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
HashSet<Integer>	getCharges() Returns the different charges found.
double	getMaxPeptideErrorDa() Returns the maximal peptide mass error found in Da.
double	getMaxPeptideErrorPpm() Returns the maximal peptide mass error found in ppm.
double	getMaxTagErrorDa() Returns the maximal tag mass error found in Da.
double	getMaxTagErrorPpm() Returns the maximal tag mass error found in ppm.
int	getMissingProteins() Returns the number of PSMs where a protein was missing.
int	getnRetained() Returns the number of PSMs retained after filtering.
int	getPeptideIssue() Returns the number of PSMs which did not pass the import filters due to a peptide issue.
int	getPrecursorIssue() Returns the number of PSMs which did not pass the import filters due to a precursor issue.
int	getProteinIssue() Returns the number of PSMs which did not pass the import filters due to a protein issue.
int	getPsmsRejected() Returns the number of PSMs which did not pass the import filters.
void	run()

Methods inherited from class java.lang.Object

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

Constructor Detail

PsmFirstHitRunnable

public PsmFirstHitRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue,
                           com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                           com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                           com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                           InputMap inputMap,
                           HashMap<String,Integer> proteinCount,
                           com.compomics.util.waiting.WaitingHandler waitingHandler,
                           com.compomics.util.exceptions.ExceptionHandler exceptionHandler)

Constructor.

Parameters:

spectrumMatchQueue - The spectrum matches iterator to use.

identificationParameters - The identification parameters.

sequenceProvider - The protein sequence provider.

spectrumProvider - The spectrum provider.

inputMap - The input scores map.

proteinCount - The map of protein occurrence.

waitingHandler - The waiting handler to display feedback to the user.

exceptionHandler - The handler of exceptions.

Method Detail

run

public void run()

Specified by:

run in interface Runnable

getCharges

public HashSet<Integer> getCharges()

Returns the different charges found.

Returns:

the different charges found

getMaxPeptideErrorPpm

public double getMaxPeptideErrorPpm()

Returns the maximal peptide mass error found in ppm.

Returns:

the maximal peptide mass error found in ppm

getMaxPeptideErrorDa

public double getMaxPeptideErrorDa()

Returns the maximal peptide mass error found in Da.

Returns:

the maximal peptide mass error found in Da

getMaxTagErrorPpm

public double getMaxTagErrorPpm()

Returns the maximal tag mass error found in ppm.

Returns:

the maximal tag mass error found in ppm

getMaxTagErrorDa

public double getMaxTagErrorDa()

Returns the maximal tag mass error found in Da.

Returns:

the maximal tag mass error found in Da

getPsmsRejected

public int getPsmsRejected()

Returns the number of PSMs which did not pass the import filters.

Returns:

the number of PSMs which did not pass the import filters

getProteinIssue

public int getProteinIssue()

Returns the number of PSMs which did not pass the import filters due to a protein issue.

Returns:

the number of PSMs which did not pass the import filters due to a protein issue

getPeptideIssue

public int getPeptideIssue()

Returns the number of PSMs which did not pass the import filters due to a peptide issue.

Returns:

the number of PSMs which did not pass the import filters due to a peptide issue

getPrecursorIssue

public int getPrecursorIssue()

Returns the number of PSMs which did not pass the import filters due to a precursor issue.

Returns:

the number of PSMs which did not pass the import filters due to a precursor issue

getMissingProteins

public int getMissingProteins()

Returns the number of PSMs where a protein was missing.

Returns:

the number of PSMs where a protein was missing

getnRetained

public int getnRetained()

Returns the number of PSMs retained after filtering.

Returns:

the number of PSMs retained after filtering