eu.isas.peptideshaker.fileimport

Class PsmImportRunnable

java.lang.Object

eu.isas.peptideshaker.fileimport.PsmImportRunnable

All Implemented Interfaces:

Runnable

public class PsmImportRunnable
extends Object
implements Runnable

Runnable for the import of PSMs.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static int	BATCH_SIZE Size of the batches to use when adding objects to the database.

Constructor Summary

Constructors

Constructor and Description

PsmImportRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.identification.IdfileReader fileReader, File idFile, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Constructor.

Method Summary

Modifier and Type	Method and Description
int	getModificationIssue() Returns the number of PSMs which did not pass the import filters due to a modification parsing issue.
long	getnPeptideAssumptionsTotal() Returns the total number of peptide assumptions parsed.
long	getnPSMs() Returns the number of PSMs processed.
int	getPeptideIssue() Returns the number of PSMs which did not pass the import filters due to a peptide issue.
HashMap<String,Integer>	getProteinCount() Returns the occurrence of each protein.
void	run()

Methods inherited from class java.lang.Object

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

Field Detail

BATCH_SIZE

public static final int BATCH_SIZE

Size of the batches to use when adding objects to the database.

See Also:

Constant Field Values

Constructor Detail

PsmImportRunnable

public PsmImportRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue,
                         com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                         com.compomics.util.experiment.io.identification.IdfileReader fileReader,
                         File idFile,
                         com.compomics.util.experiment.identification.Identification identification,
                         com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                         com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper,
                         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

fileReader - the reader of the file which the matches are imported from

idFile - the file which the matches are imported from

identification - the identification object where to store the matches

sequenceProvider - the protein sequence provider

fastaMapper - the FASTA mapper used to map peptides to proteins

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

getnPSMs

public long getnPSMs()

Returns the number of PSMs processed.

Returns:

the number of PSMs processed

getnPeptideAssumptionsTotal

public long getnPeptideAssumptionsTotal()

Returns the total number of peptide assumptions parsed.

Returns:

the total number of peptide assumptions parsed

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

getModificationIssue

public int getModificationIssue()

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

Returns:

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

getProteinCount

public HashMap<String,Integer> getProteinCount()

Returns the occurrence of each protein.

Returns:

the occurrence of each protein