eu.isas.peptideshaker.stirred

Class Stirred

java.lang.Object

eu.isas.peptideshaker.stirred.Stirred

public class Stirred
extends Object

This class imports the results of a search engine from SearchGUI in the utilities model.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
String	SOFTWARE_NAME The name of the software to annotate in the mzIdentML file.
String	SOFTWARE_URL The URL of the software to annotate in the mzIdentML file.
String	SOFTWARE_VERSION The version of the software to annotate in the mzIdentML file.

Constructor Summary

Constructors

Constructor and Description

Stirred(File inputFile, File spectrumFile, File fastaFile, File ouputFolder, File identificationParametersFile, File tempFolder, com.compomics.software.log.CliLogger cliLogger, int nThreads, int timeOutDays, String contactFirstName, String contactLastName, String contactAddress, String contactEmail, String contactOrganizationName, String contactOrganizationAddress, String contactOrganizationEmail) Constructor.

Method Summary

Modifier and Type	Method and Description
void	process(File searchEngineResultsFile, File fastaFile, File ouputFile, com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex fmIndex, com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary, com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters) Runs the stirred process.
void	run() Runs the stirred process.

Methods inherited from class java.lang.Object

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

Field Detail

SOFTWARE_NAME

public final String SOFTWARE_NAME

The name of the software to annotate in the mzIdentML file.

See Also:

Constant Field Values

SOFTWARE_VERSION

public final String SOFTWARE_VERSION

The version of the software to annotate in the mzIdentML file.

SOFTWARE_URL

public final String SOFTWARE_URL

The URL of the software to annotate in the mzIdentML file.

See Also:

Constant Field Values

Constructor Detail

Stirred

public Stirred(File inputFile,
               File spectrumFile,
               File fastaFile,
               File ouputFolder,
               File identificationParametersFile,
               File tempFolder,
               com.compomics.software.log.CliLogger cliLogger,
               int nThreads,
               int timeOutDays,
               String contactFirstName,
               String contactLastName,
               String contactAddress,
               String contactEmail,
               String contactOrganizationName,
               String contactOrganizationAddress,
               String contactOrganizationEmail)

Constructor.

Parameters:

inputFile - The input file.

spectrumFile - The spectrum file.

fastaFile - The fasta file.

ouputFolder - The output folder.

identificationParametersFile - The identification parameters file.

tempFolder - The temp folder to use for temp files.

cliLogger - The temp folder to use for temp files.

nThreads - The number of threads to use.

timeOutDays - Timeout time in days.

contactFirstName - The first name of the contact to annotate in the mzIdentML file.

contactLastName - The last name of the contact to annotate in the mzIdentML file.

contactAddress - The address of the contact to annotate in the mzIdentML file.

contactEmail - The email of the contact to annotate in the mzIdentML file.

contactOrganizationName - The name of the organization of the contact to annotate in the mzIdentML file.

contactOrganizationAddress - The address of the organization of the contact to annotate in the mzIdentML file.

contactOrganizationEmail - The email of the organization of the contact to annotate in the mzIdentML file.

Method Detail

run

public void run()
         throws InterruptedException,
                TimeoutException,
                IOException

Runs the stirred process.

Throws:

InterruptedException - Exception thrown if a thread is interrupted.

TimeoutException - Exception thrown if the process times out.

IOException - Exception thrown if an error occurred while reading or writing a file.

process

public void process(File searchEngineResultsFile,
                    File fastaFile,
                    File ouputFile,
                    com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex fmIndex,
                    com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary,
                    com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler,
                    com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
             throws InterruptedException,
                    TimeoutException,
                    IOException

Runs the stirred process.

Parameters:

searchEngineResultsFile - The search engine results file.

fastaFile - The fasta file.

ouputFile - The output file.

fmIndex - The FM index of the fasta file.

fastaSummary - The summary information on the fasta file.

msFileHandler - The mass spectrometry file handler to use.

identificationParameters - The identification parameters.

Throws:

InterruptedException - Exception thrown if a thread is interrupted.

TimeoutException - Exception thrown if the process times out.

IOException - Exception thrown if an error occurred while reading or writing a file.