Struct ApplicationSettings¶

Defined in File ApplicationSettings.h

Struct Documentation¶

struct ApplicationSettings¶

Stores and handles program parameters passed from command line.

Public Functions

inline explicit ApplicationSettings(Parser &parser)¶

Initializes ApplicationSettings object.

Parameters: parser – instance of cli::Parser

virtual ~ApplicationSettings() = default¶

virtual void define_options()¶: Defines required and optional program options. The help option which displays a summary about available by default.

virtual void load_options()¶: Reads program options from parser.

virtual void process_options()¶: Transfrom raw options, e.g. converts strings to upper case.

virtual void validate() const¶: Check values against criteria.

inline virtual std::string usage() const¶

Return a string containing a full description of program parameters.

Returns: Full description of program options

inline virtual Parser &get_parser()¶

inline virtual const Parser &get_parser() const¶

void validate_report() const¶

void validate_report_sample_types() const¶

void validate_report_metadata() const¶

void validate_workflow() const¶

void validate_integrity() const¶

Public Members

std::string load_session¶

std::vector<std::string> report¶

std::vector<std::string> report_sample_types¶

std::vector<std::string> report_metadata¶

std::vector<std::string> workflow¶

std::vector<std::string> integrity¶

bool allow_inconsistent¶

bool verbose¶

bool disable_colors¶

bool disable_progressbar¶

std::string log_dir¶

std::string features_out_dir¶

std::string features_in_dir¶

std::vector<std::string> input_files¶

std::vector<std::string> parameters¶

std::string mzml_dir¶

std::string reports_out_dir¶

int nb_threads¶

Public Static Functions

static bool contains_option(const std::vector<std::string> &list, const std::string &option, std::string log_msg = "")¶

Check if an option is included in a list.

Parameters

list – list of strings
option – option name
log_msg – log message on success

static std::pair<std::string, std::string> get_key_value_from_option(const std::string &option)¶: Returns a pair key/value from one string “key1=value1”