configIO.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_QSAR_CONFIGIO_H
#define BALL_QSAR_CONFIGIO_H

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

#include <istream>
#include <set>

namespace BALL
{
  namespace QSAR
  {
    struct BALL_EXPORT InputConfiguration
    {
      InputConfiguration();
      
      String sd_file;
      std::multiset<int> activities;
      std::set<String> activity_names;
      bool read_sd_descriptors;
      bool center_data;
      bool center_y;
      String output;
      double validation_fraction;
      bool separate_activity_file;
      bool within_section;
      vector<String> csv_file;
      vector<int> csv_no_response;
      vector<bool> csv_desc_labels;
      vector<bool> csv_compound_labels;
      vector<String> csv_separator;
      bool nonnumeric_class_names;
      bool done;
    };
    
    struct BALL_EXPORT InputPartitioningConfiguration
    {
      InputPartitioningConfiguration(); 
      
      String input_file;
      double validation_fraction;
      int no_folds;
      bool even_split;
      int ID;
      bool done;
    };
    
    struct BALL_EXPORT ModelConfiguration
    {
      ModelConfiguration();
      
      bool done;
      String data_file;
      String output;
      String descriptor_source_model;
      vector<double> model_parameters;
      int model_no; 
      int kernel_type;
      double kernel_par1;
      double kernel_par2;
      int k_fold;
      bool optimize_model_parameters;
      double grid_search_stepwidth;
      int grid_search_steps;
      int grid_search_recursions;
      bool within_section;
      bool no_training;
    };
    
    struct BALL_EXPORT FeatureSelectionConfiguration
    {
      FeatureSelectionConfiguration();
      
      String model;
      String data_file;
      int feat_type;
      String output;
      int k_fold;
      bool within_section;
      String statistic_name;
      String selection_name;
      int statistic;
      bool remove_correlated;
      double cor_threshold;
      bool opt_model_after_fs;
      bool opt_kernel_after_fs;
      double quality_increase_cutoff;
      bool opt;
      bool done;
      int grid_search_steps;
      int grid_search_recursions;
      double grid_search_stepwidth;
      int opt_k_fold;
    };
    
    struct BALL_EXPORT ValidationConfiguration
    {
      ValidationConfiguration();
      
      String model;
      String data;
      String validation_data;
      int val_type;
      String output;
      int k_folds;
      int bootstrap_samples;
      int no_of_permutation_tests;
      int statistic;
      String statistic_name;
      vector<String> external_predictions;
      bool for_visualization_only;
      bool done;
    };
    
    struct BALL_EXPORT PredictionConfiguration
    {
      PredictionConfiguration();
      
      String model;
      String data;
      String output;
      int statistic;
      String statistic_name;
      bool print_expected;
      bool done;
    };
    
    
    class BALL_EXPORT ConfigIO
    {
      public:
        
        static void putbackLine(std::istream* input,String& line);
        
        static ModelConfiguration readModelConfiguration(std::istream* input);
    
        static FeatureSelectionConfiguration readFeatureSelectionConfiguration(std::istream* input);
    
        static InputConfiguration readInputConfiguration(std::istream* input);
    
        static InputPartitioningConfiguration readInputPartitioningConfiguration(std::istream* input);
        
        static ValidationConfiguration readValidationConfiguration(std::istream* input);
        
        static PredictionConfiguration readPredictionConfiguration(std::istream* input);    
    };
  }
}


#endif // BALL_QSAR_CONFIGIO_H