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configIO.h
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1 /* configIO.h
2  *
3  * Copyright (C) 2009 Marcel Schumann
4  *
5  * This file is part of QuEasy -- A Toolbox for Automated QSAR Model
6  * Construction and Validation.
7  * QuEasy is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 3 of the License, or (at
10  * your option) any later version.
11  *
12  * QuEasy is distributed in the hope that it will be useful, but
13  * WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
15  * General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, see <http://www.gnu.org/licenses/>.
19  */
20 
21 #ifndef CONFIG_IO_H
22 #define CONFIG_IO_H
23 
24 #include <istream>
25 #include <BALL/DATATYPE/string.h>
26 #include <istream>
27 #include <set>
28 
29 namespace BALL
30 {
31  namespace QSAR
32  {
33  struct BALL_EXPORT InputConfiguration
34  {
35  InputConfiguration();
36 
37  String sd_file;
38  std::multiset<int> activities;
39  bool read_sd_descriptors;
40  bool center_data;
41  bool center_y;
42  String output;
43  double validation_fraction;
44  bool separate_activity_file;
45  bool within_section;
46  vector<String> csv_file;
47  vector<int> csv_no_response;
48  vector<bool> csv_desc_labels;
49  vector<bool> csv_compound_labels;
50  vector<String> csv_separator;
51  bool nonnumeric_class_names;
52  bool done;
53  };
54 
55  struct BALL_EXPORT InputPartitioningConfiguration
56  {
57  InputPartitioningConfiguration();
58 
59  String input_file;
60  double validation_fraction;
61  int no_folds;
62  int ID;
63  bool done;
64  };
65 
66  struct BALL_EXPORT ModelConfiguration
67  {
68  ModelConfiguration();
69 
70  bool done;
71  String data_file;
72  String output;
73  String descriptor_source_model;
74  vector<double> model_parameters;
75  int model_no;
76  int kernel_type;
77  double kernel_par1;
78  double kernel_par2;
79  int k_fold;
80  bool optimize_model_parameters;
81  double grid_search_stepwidth;
82  int grid_search_steps;
83  int grid_search_recursions;
84  bool within_section;
85  bool no_training;
86  };
87 
88  struct BALL_EXPORT FeatureSelectionConfiguration
89  {
90  FeatureSelectionConfiguration();
91 
92  String model;
93  String data_file;
94  int feat_type;
95  String output;
96  int k_fold;
97  bool within_section;
98  String statistic_name;
99  String selection_name;
100  int statistic;
101  bool remove_correlated;
102  double cor_threshold;
103  bool opt_model_after_fs;
104  bool opt_kernel_after_fs;
105  double quality_increase_cutoff;
106  bool opt;
107  bool done;
108  int grid_search_steps;
109  int grid_search_recursions;
110  double grid_search_stepwidth;
111  int opt_k_fold;
112  };
113 
114  struct BALL_EXPORT ValidationConfiguration
115  {
116  ValidationConfiguration();
117 
118  String model;
119  String data;
120  String validation_data;
121  int val_type;
122  String output;
123  int k_folds;
124  int bootstrap_samples;
125  int no_of_permutation_tests;
126  int statistic;
127  String statistic_name;
128  vector<String> external_predictions;
129  bool for_visualization_only;
130  bool done;
131  };
132 
133  struct BALL_EXPORT PredictionConfiguration
134  {
135  PredictionConfiguration();
136 
137  String model;
138  String data;
139  String output;
140  int statistic;
141  String statistic_name;
142  bool print_expected;
143  bool done;
144  };
145 
146 
147  class BALL_EXPORT ConfigIO
148  {
149  public:
150 
151  static void putbackLine(std::istream* input,String& line);
152 
153  static ModelConfiguration readModelConfiguration(std::istream* input);
154 
155  static FeatureSelectionConfiguration readFeatureSelectionConfiguration(std::istream* input);
156 
157  static InputConfiguration readInputConfiguration(std::istream* input);
158 
159  static InputPartitioningConfiguration readInputPartitioningConfiguration(std::istream* input);
160 
161  static ValidationConfiguration readValidationConfiguration(std::istream* input);
162 
163  static PredictionConfiguration readPredictionConfiguration(std::istream* input);
164  };
165  }
166 }
167 
168 
169 #endif // CONFIG_IO_H
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