GetPenaltyTermModule.hpp

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#pragma once
#include "yaml-cpp/yaml.h"
#include "CLI/API/plugin.hpp"
 
namespace M3{
 
  class GetPenaltyTermModule: public IModuleBase{
 
    public:
      virtual ~GetPenaltyTermModule();
 
      MaCh3ArgumentParser* get_parser() override;
 
      int Run() override;
 
    private:
      void ReadCovFile(const std::string& inputFile,
                       std::vector <double>& Prior,
                       std::vector <bool>& isFlat,
                       std::vector<std::string>& ParamNames,
                       std::vector<std::vector<double>>& invCovMatrix,
                       int& nParams);
 
      void LoadSettings(YAML::Node& Settings,
                        std::vector<std::string>& SetsNames,
                        std::vector<std::string>& FancyTitle,
                        std::vector<std::vector<bool>>& isRelevantParam,
                        const std::vector<std::string>& ParamNames,
                        const int nParams);
 
      void GetPenaltyTerm(const std::string& inputFile, const std::string& configFile);
 
  };
}