Read command-line options¶

class lemon::Options : public App¶

The Options class is used to read command line arguments.

A majority of Lemon workflows begin with the parsing of various command- line arguments. This class helps the user parse the most common arguments such as the directory containing the Hadoop sequence files, the number of cores to use for a given search or a preselected set of entries. Users can add their own options with the add_options member function.

Public Functions

Options()¶

Default constructor to initialize a custom Options class

This constructor is intended for users who wish to add their own custom options. The work_dir, ncpu, and entries options are added automatically and additional options can be added with the add_option function.

Options(int argc, const char *const argv[])¶

Constructor for an Options class which does not use custom options

This constructor is indended for users who do not wish to add custom options. The work_dir, ncpu, and entries options are added automatically and the arguments are parsed immediately.

Parameters

argc: The number of arguments plus their values plus one. Typically obtained from the main function.
argv: The arguments and their values. Typically obtained from the main function.

template<typename T> CLI::Option *add_option(std::string option_name, T &variable, std::string description = "") noexcept¶

Adds an option to the current workflow

Parameters

option_name: The name of the option on the command line
variable: The location used to store the variable
description: The description of the new option

void parse_command_line(int argc, const char *const argv[])¶

Parse the command-line arguments and update containers

Use this function to read options and update the custom contains if needed. Once the options are parsed, this function will throw an error.

Parameters

argc: The number of arguments plus their values plus one. Typically obtained from the main function.
argv: The arguments and their values. Typically obtained from the main function.

const std::string &work_dir() const¶: Directory containing the MMTF or Hadoop files.

size_t ncpu() const¶: Number of CPUs used to run independent jobs.

const std::string &entries() const¶: Index to preselect entries. Eg a search on RCSB.

const std::string &skip_entries() const¶: Index to skip entries.