BALL: configIO.h Source File

00001 /* configIO.h
00002  * 
00003  * Copyright (C) 2009 Marcel Schumann
00004  * 
00005  * This file is part of QuEasy -- A Toolbox for Automated QSAR Model
00006  * Construction and Validation.
00007  * QuEasy is free software; you can redistribute it and/or modify
00008  * it under the terms of the GNU General Public License as published by
00009  * the Free Software Foundation; either version 3 of the License, or (at
00010  * your option) any later version.
00011  * 
00012  * QuEasy is distributed in the hope that it will be useful, but
00013  * WITHOUT ANY WARRANTY; without even the implied warranty of
00014  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
00015  * General Public License for more details.
00016  * 
00017  * You should have received a copy of the GNU General Public License
00018  * along with this program; if not, see <http://www.gnu.org/licenses/>.
00019  */
00020 
00021 #ifndef CONFIG_IO_H
00022 #define CONFIG_IO_H
00023 
00024 #include <istream>
00025 #include <BALL/DATATYPE/string.h>
00026 #include <istream>
00027 #include <set>
00028  
00029 namespace BALL
00030 {
00031   namespace QSAR
00032   {
00033     struct BALL_EXPORT InputConfiguration
00034     {
00035       InputConfiguration();
00036       
00037       String sd_file;
00038       std::multiset<int> activities;
00039       bool read_sd_descriptors;
00040       bool center_data;
00041       bool center_y;
00042       String output;
00043       double validation_fraction;
00044       bool separate_activity_file;
00045       bool within_section;
00046       vector<String> csv_file;
00047       vector<int> csv_no_response;
00048       vector<bool> csv_desc_labels;
00049       vector<bool> csv_compound_labels;
00050       vector<String> csv_separator;
00051       bool nonnumeric_class_names;
00052       bool done;
00053     };
00054     
00055     struct BALL_EXPORT InputPartitioningConfiguration
00056     {
00057       InputPartitioningConfiguration(); 
00058       
00059       String input_file;
00060       double validation_fraction;
00061       int no_folds;
00062       int ID;
00063       bool done;
00064     };
00065     
00066     struct BALL_EXPORT ModelConfiguration
00067     {
00068       ModelConfiguration();
00069       
00070       bool done;
00071       String data_file;
00072       String output;
00073       String descriptor_source_model;
00074       vector<double> model_parameters;
00075       int model_no; 
00076       int kernel_type;
00077       double kernel_par1;
00078       double kernel_par2;
00079       int k_fold;
00080       bool optimize_model_parameters;
00081       double grid_search_stepwidth;
00082       int grid_search_steps;
00083       int grid_search_recursions;
00084       bool within_section;
00085       bool no_training;
00086     };
00087     
00088     struct BALL_EXPORT FeatureSelectionConfiguration
00089     {
00090       FeatureSelectionConfiguration();
00091       
00092       String model;
00093       String data_file;
00094       int feat_type;
00095       String output;
00096       int k_fold;
00097       bool within_section;
00098       String statistic_name;
00099       String selection_name;
00100       int statistic;
00101       bool remove_correlated;
00102       double cor_threshold;
00103       bool opt_model_after_fs;
00104       bool opt_kernel_after_fs;
00105       double quality_increase_cutoff;
00106       bool opt;
00107       bool done;
00108       int grid_search_steps;
00109       int grid_search_recursions;
00110       double grid_search_stepwidth;
00111       int opt_k_fold;
00112     };
00113     
00114     struct BALL_EXPORT ValidationConfiguration
00115     {
00116       ValidationConfiguration();
00117       
00118       String model;
00119       String data;
00120       String validation_data;
00121       int val_type;
00122       String output;
00123       int k_folds;
00124       int bootstrap_samples;
00125       int no_of_permutation_tests;
00126       int statistic;
00127       String statistic_name;
00128       vector<String> external_predictions;
00129       bool for_visualization_only;
00130       bool done;
00131     };
00132     
00133     struct BALL_EXPORT PredictionConfiguration
00134     {
00135       PredictionConfiguration();
00136       
00137       String model;
00138       String data;
00139       String output;
00140       int statistic;
00141       String statistic_name;
00142       bool print_expected;
00143       bool done;
00144     };
00145     
00146     
00147     class BALL_EXPORT ConfigIO
00148     {
00149       public:
00150         
00151         static void putbackLine(std::istream* input,String& line);
00152         
00153         static ModelConfiguration readModelConfiguration(std::istream* input);
00154     
00155         static FeatureSelectionConfiguration readFeatureSelectionConfiguration(std::istream* input);
00156     
00157         static InputConfiguration readInputConfiguration(std::istream* input);
00158     
00159         static InputPartitioningConfiguration readInputPartitioningConfiguration(std::istream* input);
00160         
00161         static ValidationConfiguration readValidationConfiguration(std::istream* input);
00162         
00163         static PredictionConfiguration readPredictionConfiguration(std::istream* input);    
00164     };
00165   }
00166 }
00167 
00168 
00169 #endif // CONFIG_IO_H