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CommandLineReader.h

#ifndef COMMANDLINEREADER_H
#define COMMANDLINEREADER_H

#include <string>
#include <vector>

class CommandLineReader
{
 public:

  CommandLineReader( const std::string& p_command_line );

  CommandLineReader( void );

  virtual ~CommandLineReader(){};
  
  void initialize( void );

  void parseLine( const std::string& p_command_line );

  const std::string getUsage( void ) const;

  const std::string& getOutputFileName( void ) const;

  const std::vector<std::string>& getLibraryFileNames( void ) const;

  const std::vector<std::string>& getFrozenLibraryNames( void ) const;

  float getFractionGoodHitThreshold( void ) const;

  int   getMaximumIteration( void ) const;

  std::string getPropertyAnalysisFileName( void ) const;

  std::vector<std::string> getLibraryDefinitionFileName( void ) const;

  bool getIsCutWhenZeroGoodness( void ) const;

  bool getDoScaleWithSize( void  ) const;

  float getScaleWithSizeParam( void ) const;

  std::string getEnumerationStrategy( void ) const { return m_EnumerationStrategy; }

  int getNumberPartition( void ) const { return m_NumberPartition; }

  void setFirstFractionToKeep( float p_first_fraction_to_keep );

  float getFirstFractionToKeep( void ) const;

 protected:
 private:

  // Output file name.
  std::string m_OutputFileName;

  // Fraction (between 0 and 1) of the enumerated compounds that must satisfy the goodness criteria before the optimization stops.
  float m_FractionGoodHitThreshold;

  // Maximum number of iteration to reach.
  int m_MaximumIteration;

  // File name containing the combining instruction.
  std::vector<std::string> m_LibraryDefinitionFileNames;

  // Boolean set to true when all the fragments with a zero goodness counter are cut.
  bool m_IsCutWhenZeroGoodness;

  // Fraction of fragment to keep is scaled. Larger library are pruned faster.
  bool m_DoScaleWithSize;
  
  // Parameter when scaling with size.
  float m_ScaleWithSizeParam;

  // Enumeration strategy: 'part' stands for partitioning, 'full' stands for full enumeration.
  std::string m_EnumerationStrategy;

  // Number of partitions used with the 'part' Enumeration strategy.
  int m_NumberPartition;

  // First fraction of each library to keep in GoodHit algorithm. A value of 0.75 means that 25% worst fragments from each dimension is thrown after the first iteration
  float m_FirstFractionToKeep;
};

#endif
A value of 0.75 means that 25% worst fragments from each dimension is thrown after the first iteration
  float m_FirstFractionToKeep;
};

#endif

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