commandlineParser.h

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#ifndef BALL_FORMAT_COMMANDLINEPARSER_H
#define BALL_FORMAT_COMMANDLINEPARSER_H

#ifndef BALL_DATATYPE_OPTIONS_H
# include <BALL/DATATYPE/options.h>
#endif

#ifndef BALL_DATATYPE_STRING_H
# include <BALL/DATATYPE/string.h>
#endif

#ifndef BALL_FORMAT_PARAMFILE_H
# include <BALL/FORMAT/paramFile.h>
#endif

#include <map>
#include <set>

namespace BALL
{
  class BALL_EXPORT CommandlineParser
  {
    public:
      CommandlineParser(String tool_name, String tool_description, String tool_version, String build_date, String category="");

      void setToolManual(const String& manual);

      static const String NOT_FOUND;
      static const list<String> EMTPY_LIST;

      // - CLI switch
      // - description
      // - parameter type
      // - required
      // - default value
      // - hidden in galaxy
      void registerParameter(String name, String description, ParameterType type, bool mandatory = false, String default_value = "", bool hidden = false);

      void registerFlag(String name, String description, bool default_gui_value = false, bool hidden = false);

      void registerAdvancedParameters(Options& options);

      // exclude parameter from showing in help mode e.g. galaxy specific multi-output parameter
      void setParameterAsAdvanced(String name);

      void setParameterRestrictions(String par_name, double min_value, double max_value);

      void setParameterRestrictions(String par_name, list<String>& allowed_values);

      void setOutputFormatSource(String output_parname, String input_parname);

      void setSupportedFormats(String par_name, String supported_formats);

      void parse(int argc, char* argv[]);

      void copyAdvancedParametersToOptions(Options& options);

      const String& get(String name);

      bool has(String name);

      const list<String>& getList(String name);

      void printHelp(const std::set<String>& parameter_names = std::set<String>(), bool show_manual = true);

      void printToolInfo();

      const String& getStartTime();

      const String& getStartCommand();

    private:

      void replaceEscapedCharacters_(String& parameter_value);

      void checkAndRegisterParameter(String name, String description, ParameterType type, bool mandatory = false, String default_value = "", bool perform_check = true, bool hidden=false);

      void checkAndRegisterFlag(String name, String description, bool default_gui_value = false, bool perform_check = true, bool hidden=false);


      void validateRegisteredFilesHaveFormats();

      void checkParameterName(const String& name, const bool perform_check = true);

      std::set<String> reserved_params_;

      std::list<std::pair<String, String> > escaped_chars_;
      std::map<String, list<String> > parameter_map_;
      std::map<String, ParameterDescription> registered_parameters_;

      std::map<String, ParameterDescription> registered_flags_;
      typedef std::map<String, ParameterDescription>::iterator MapIterator;
      std::list<MapIterator> original_parameter_order_;
      std::list<MapIterator> original_flag_order_;
      Size max_parname_length_;
      Size max_flagname_length_;
      String tool_name_;
      String tool_description_;
      String tool_version_;
      String build_date_;
      String hostname_;
      String start_time_;
      String tool_manual_;
      String start_command_;
      String tool_category_;
  };
}

#endif // BALL_FORMAT_COMMANDLINEPARSER_H