Package eu.isas.peptideshaker.cmd

Class StirredOptionsBean

java.lang.Object
eu.isas.peptideshaker.cmd.StirredOptionsBean
public class StirredOptionsBean extends Object
This class parses the parameters from an ModificationsCLI.
Author:
Marc Vaudel, Harald Barsnes

  • Field Details

    • inputFile

      public final File inputFile
      The input file.

    • spectrumFile

      public File spectrumFile
      The spectrum file.

    • fastaFile

      public File fastaFile
      The fasta file.

    • identificationParametersFile

      public File identificationParametersFile
      The identification parameters file.

    • tempFolder

      public final File tempFolder
      The temp folder to use for temp files.

    • logFile

      public final File logFile
      The log file.

    • nThreads

      public int nThreads
      The number of threads to use.

    • timeOutDays

      public int timeOutDays
      The timeout time in days.

    • outputFolder

      public final File outputFolder
      The output folder.

    • contactFirstName

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

    • contactLastName

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

    • contactAddress

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

    • contactEmail

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

    • contactOrganizationName

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

    • contactOrganizationAddress

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

    • contactOrganizationEmail

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

  • Constructor Details

    • StirredOptionsBean

      public StirredOptionsBean(org.apache.commons.cli.CommandLine aLine) throws IOException
      Parses all the arguments from a command line.
      Parameters:
      aLine - the command line
      Throws:
      IOException - if an error occurs while reading or writing a file.