Package eu.isas.searchgui.cmd

Class FastaCLIInputBean

java.lang.Object
eu.isas.searchgui.cmd.FastaCLIInputBean
public class FastaCLIInputBean extends Object
This class contains the information necessary for running the FastaCLI.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Details

    • FastaCLIInputBean

      public FastaCLIInputBean(org.apache.commons.cli.CommandLine aLine)
      Constructor.
      Parameters:
      aLine - the command line given to the tool

  • Method Details

    • getPathSettingsCLIInputBean

      public PathSettingsCLIInputBean getPathSettingsCLIInputBean()
      Returns the path settings provided by the user.
      Returns:
      the path settings provided by the user

    • getInputFile

      public File getInputFile()
      Returns the input file.
      Returns:
      the input file

    • isDecoy

      public boolean isDecoy()
      Indicates whether decoy sequences shall be added.
      Returns:
      a boolean indicating whether whether decoy sequences shall be added

    • getDecoySuffix

      public String getDecoySuffix()
      Returns the tag added after adding decoy sequences to a FASTA file.
      Returns:
      the decoy suffix tag

    • isValidStartup

      public static boolean isValidStartup(org.apache.commons.cli.CommandLine aLine)
      Verifies the command line start parameters.
      Parameters:
      aLine - the command line to validate
      Returns:
      true if the startup was valid