Package com.compomics.cli.identification_parameters

Class AbstractIdentificationParametersCli

java.lang.Object
com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
All Implemented Interfaces:
Callable
Direct Known Subclasses:
IdentificationParametersCLI
public abstract class AbstractIdentificationParametersCli extends Object implements Callable
This class serves as a base for the implementation of IdentificationParametersCLI in specific tools. To make an IdentificationParametersCLI extend this class and call initiate in the constructor of your class.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Details

    • AbstractIdentificationParametersCli

      public AbstractIdentificationParametersCli()

  • Method Details

    • initiate

      public void initiate(String[] args)
      Initiates the IdentificationParametersCli.
      Parameters:
      args - the command line arguments

    • call

      public Object call()
      Specified by:
      call in interface Callable

    • printModifications

      public void printModifications()
      Prints the available modifications.

    • printEnzymes

      public void printEnzymes()
      Prints the available enzymes.

    • createOptionsCLI

      protected abstract void createOptionsCLI(org.apache.commons.cli.Options options)
      Provides the options left to the user.
      Parameters:
      options - the options object where the options will be added

    • getOptionsAsString

      protected abstract String getOptionsAsString()
      Returns the options left to the user as a string.
      Returns:
      the options left to the user as a string

    • getHeader

      public static String getHeader()
      IdentificationParametersCLI header message when printing the usage.
      Returns:
      the header message as a string