Package 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 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 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 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 Details

  • Constructor Details

    • 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 Details

    • 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.