libball1.4-dev 1.4.1+20111206-3 / usr / include / BALL / QSAR / configIO.h

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/* configIO.h
 * 
 * Copyright (C) 2009 Marcel Schumann
 * 
 * This file is part of QuEasy -- A Toolbox for Automated QSAR Model
 * Construction and Validation.
 * QuEasy is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or (at
 * your option) any later version.
 * 
 * QuEasy is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, see <http://www.gnu.org/licenses/>.
 */

#ifndef CONFIG_IO_H
#define CONFIG_IO_H

#include <istream>
#include <BALL/DATATYPE/string.h>
#include <istream>
#include <set>
 
namespace BALL
{
	namespace QSAR
	{
		struct BALL_EXPORT InputConfiguration
		{
			InputConfiguration();
			
			String sd_file;
			std::multiset<int> activities;
			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;
			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 // CONFIG_IO_H

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