Package com.compomics.cli.modifications

Class ModificationsCLIInputBean

java.lang.Object
com.compomics.cli.modifications.ModificationsCLIInputBean
public class ModificationsCLIInputBean extends Object
This class parses the parameters from an ModificationsCLI.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Details

    • ModificationsCLIInputBean

      public ModificationsCLIInputBean(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.

  • Method Details

    • 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

    • getFileIn

      public File getFileIn()
      Returns the file provided as input.
      Returns:
      the file provided as input

    • getFileOut

      public File getFileOut()
      Returns the file provided as output.
      Returns:
      the file provided as output

    • isList

      public boolean isList()
      Returns a boolean indicating whether the list of implemented enzymes should be printed.
      Returns:
      a boolean indicating whether the list of implemented enzymes should be printed

    • getModificationToRemove

      public String getModificationToRemove()
      Returns the name of the modification to remove.
      Returns:
      the name of the modification to remove

    • getModificationToAdd

      public Modification getModificationToAdd()
      Returns the modification to add.
      Returns:
      the modification to add