BALL  1.5.0
configIO.h
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1 // -*- Mode: C++; tab-width: 2; -*-
2 // vi: set ts=2:
3 //
4 
5 #ifndef BALL_QSAR_CONFIGIO_H
6 #define BALL_QSAR_CONFIGIO_H
7 
8 #ifndef BALL_DATATYPE_STRING_H
9 #include <BALL/DATATYPE/string.h>
10 #endif
11 
12 #include <istream>
13 #include <set>
14 
15 namespace BALL
16 {
17  namespace QSAR
18  {
20  {
22 
24  std::multiset<int> activities;
25  std::set<String> activity_names;
28  bool center_y;
33  vector<String> csv_file;
34  vector<int> csv_no_response;
35  vector<bool> csv_desc_labels;
36  vector<bool> csv_compound_labels;
37  vector<String> csv_separator;
39  bool done;
40  };
41 
43  {
45 
48  int no_folds;
49  bool even_split;
50  int ID;
51  bool done;
52  };
53 
55  {
57 
58  bool done;
62  vector<double> model_parameters;
63  int model_no;
65  double kernel_par1;
66  double kernel_par2;
67  int k_fold;
74  };
75 
77  {
79 
82  int feat_type;
84  int k_fold;
88  int statistic;
90  double cor_threshold;
94  bool opt;
95  bool done;
100  };
101 
103  {
105 
109  int val_type;
111  int k_folds;
116  vector<String> external_predictions;
118  bool done;
119  };
120 
122  {
124 
131  bool done;
132  };
133 
134 
136  {
137  public:
138 
139  static void putbackLine(std::istream* input,String& line);
140 
141  static ModelConfiguration readModelConfiguration(std::istream* input);
142 
143  static FeatureSelectionConfiguration readFeatureSelectionConfiguration(std::istream* input);
144 
145  static InputConfiguration readInputConfiguration(std::istream* input);
146 
147  static InputPartitioningConfiguration readInputPartitioningConfiguration(std::istream* input);
148 
149  static ValidationConfiguration readValidationConfiguration(std::istream* input);
150 
151  static PredictionConfiguration readPredictionConfiguration(std::istream* input);
152  };
153  }
154 }
155 
156 
157 #endif // BALL_QSAR_CONFIGIO_H
BALL::QSAR::ValidationConfiguration::statistic
int statistic
Definition: configIO.h:114
BALL::QSAR::InputPartitioningConfiguration::done
bool done
Definition: configIO.h:51
BALL::QSAR::FeatureSelectionConfiguration::opt_model_after_fs
bool opt_model_after_fs
Definition: configIO.h:91
BALL::QSAR::PredictionConfiguration::statistic
int statistic
Definition: configIO.h:128
BALL::QSAR::ModelConfiguration::data_file
String data_file
Definition: configIO.h:59
BALL::QSAR::FeatureSelectionConfiguration::statistic_name
String statistic_name
Definition: configIO.h:86
BALL::QSAR::FeatureSelectionConfiguration::quality_increase_cutoff
double quality_increase_cutoff
Definition: configIO.h:93
BALL::QSAR::PredictionConfiguration::print_expected
bool print_expected
Definition: configIO.h:130
BALL::QSAR::InputConfiguration::csv_separator
vector< String > csv_separator
Definition: configIO.h:37
BALL::QSAR::ModelConfiguration::kernel_type
int kernel_type
Definition: configIO.h:64
BALL::QSAR::ValidationConfiguration::validation_data
String validation_data
Definition: configIO.h:108
BALL::QSAR::ValidationConfiguration::bootstrap_samples
int bootstrap_samples
Definition: configIO.h:112
BALL::QSAR::FeatureSelectionConfiguration
Definition: configIO.h:76
BALL::QSAR::FeatureSelectionConfiguration::statistic
int statistic
Definition: configIO.h:88
BALL::QSAR::ModelConfiguration::model_no
int model_no
Definition: configIO.h:63
BALL::QSAR::ModelConfiguration::kernel_par1
double kernel_par1
Definition: configIO.h:65
BALL::QSAR::InputConfiguration::center_data
bool center_data
Definition: configIO.h:27
BALL::QSAR::InputPartitioningConfiguration::validation_fraction
double validation_fraction
Definition: configIO.h:47
BALL::QSAR::PredictionConfiguration
Definition: configIO.h:121
BALL::QSAR::InputPartitioningConfiguration::input_file
String input_file
Definition: configIO.h:46
BALL::QSAR::InputConfiguration::read_sd_descriptors
bool read_sd_descriptors
Definition: configIO.h:26
BALL::QSAR::InputConfiguration::csv_compound_labels
vector< bool > csv_compound_labels
Definition: configIO.h:36
BALL::QSAR::FeatureSelectionConfiguration::opt_k_fold
int opt_k_fold
Definition: configIO.h:99
BALL::QSAR::InputConfiguration::center_y
bool center_y
Definition: configIO.h:28
BALL::QSAR::ModelConfiguration
Definition: configIO.h:54
BALL::QSAR::ValidationConfiguration::for_visualization_only
bool for_visualization_only
Definition: configIO.h:117
BALL::QSAR::FeatureSelectionConfiguration::feat_type
int feat_type
Definition: configIO.h:82
BALL::String
Definition: string.h:56
BALL::QSAR::FeatureSelectionConfiguration::grid_search_steps
int grid_search_steps
Definition: configIO.h:96
BALL::QSAR::FeatureSelectionConfiguration::opt_kernel_after_fs
bool opt_kernel_after_fs
Definition: configIO.h:92
BALL::QSAR::ModelConfiguration::done
bool done
Definition: configIO.h:58
BALL
Definition: constants.h:12
BALL::QSAR::InputConfiguration
Definition: configIO.h:19
BALL::QSAR::FeatureSelectionConfiguration::selection_name
String selection_name
Definition: configIO.h:87
BALL::QSAR::InputPartitioningConfiguration::no_folds
int no_folds
Definition: configIO.h:48
BALL::QSAR::ValidationConfiguration::output
String output
Definition: configIO.h:110
BALL::QSAR::ValidationConfiguration::val_type
int val_type
Definition: configIO.h:109
BALL::QSAR::InputConfiguration::activity_names
std::set< String > activity_names
Definition: configIO.h:25
BALL::QSAR::FeatureSelectionConfiguration::cor_threshold
double cor_threshold
Definition: configIO.h:90
BALL::QSAR::ValidationConfiguration::external_predictions
vector< String > external_predictions
Definition: configIO.h:116
BALL::QSAR::PredictionConfiguration::done
bool done
Definition: configIO.h:131
BALL::QSAR::PredictionConfiguration::data
String data
Definition: configIO.h:126
BALL::QSAR::PredictionConfiguration::model
String model
Definition: configIO.h:125
BALL::QSAR::ConfigIO
Definition: configIO.h:135
BALL::QSAR::FeatureSelectionConfiguration::opt
bool opt
Definition: configIO.h:94
BALL::QSAR::InputConfiguration::nonnumeric_class_names
bool nonnumeric_class_names
Definition: configIO.h:38
BALL::QSAR::PredictionConfiguration::output
String output
Definition: configIO.h:127
BALL::QSAR::ValidationConfiguration::done
bool done
Definition: configIO.h:118
BALL::QSAR::ValidationConfiguration::k_folds
int k_folds
Definition: configIO.h:111
string.h
BALL::QSAR::ModelConfiguration::grid_search_stepwidth
double grid_search_stepwidth
Definition: configIO.h:69
BALL::QSAR::InputPartitioningConfiguration::even_split
bool even_split
Definition: configIO.h:49
BALL::QSAR::FeatureSelectionConfiguration::data_file
String data_file
Definition: configIO.h:81
BALL::QSAR::ModelConfiguration::kernel_par2
double kernel_par2
Definition: configIO.h:66
BALL::QSAR::InputConfiguration::separate_activity_file
bool separate_activity_file
Definition: configIO.h:31
BALL::QSAR::FeatureSelectionConfiguration::grid_search_stepwidth
double grid_search_stepwidth
Definition: configIO.h:98
BALL::QSAR::ModelConfiguration::grid_search_steps
int grid_search_steps
Definition: configIO.h:70
BALL::QSAR::PredictionConfiguration::statistic_name
String statistic_name
Definition: configIO.h:129
BALL::QSAR::FeatureSelectionConfiguration::remove_correlated
bool remove_correlated
Definition: configIO.h:89
BALL::QSAR::InputConfiguration::done
bool done
Definition: configIO.h:39
BALL::QSAR::InputConfiguration::activities
std::multiset< int > activities
Definition: configIO.h:24
BALL::QSAR::FeatureSelectionConfiguration::output
String output
Definition: configIO.h:83
BALL::QSAR::InputConfiguration::csv_file
vector< String > csv_file
Definition: configIO.h:33
BALL::QSAR::InputConfiguration::sd_file
String sd_file
Definition: configIO.h:23
BALL::QSAR::InputConfiguration::csv_no_response
vector< int > csv_no_response
Definition: configIO.h:34
BALL::QSAR::ModelConfiguration::descriptor_source_model
String descriptor_source_model
Definition: configIO.h:61
BALL::QSAR::ModelConfiguration::model_parameters
vector< double > model_parameters
Definition: configIO.h:62
BALL::QSAR::ModelConfiguration::optimize_model_parameters
bool optimize_model_parameters
Definition: configIO.h:68
BALL::QSAR::ModelConfiguration::output
String output
Definition: configIO.h:60
BALL::QSAR::FeatureSelectionConfiguration::k_fold
int k_fold
Definition: configIO.h:84
BALL::QSAR::ValidationConfiguration::statistic_name
String statistic_name
Definition: configIO.h:115
BALL::QSAR::ModelConfiguration::no_training
bool no_training
Definition: configIO.h:73
BALL::QSAR::InputConfiguration::csv_desc_labels
vector< bool > csv_desc_labels
Definition: configIO.h:35
BALL::QSAR::InputConfiguration::within_section
bool within_section
Definition: configIO.h:32
BALL::QSAR::InputConfiguration::output
String output
Definition: configIO.h:29
BALL::QSAR::ValidationConfiguration
Definition: configIO.h:102
BALL::QSAR::ValidationConfiguration::data
String data
Definition: configIO.h:107
BALL_EXPORT
#define BALL_EXPORT
Definition: COMMON/global.h:50
BALL::QSAR::ModelConfiguration::grid_search_recursions
int grid_search_recursions
Definition: configIO.h:71
BALL::QSAR::InputPartitioningConfiguration
Definition: configIO.h:42
BALL::QSAR::ModelConfiguration::within_section
bool within_section
Definition: configIO.h:72
BALL::QSAR::FeatureSelectionConfiguration::within_section
bool within_section
Definition: configIO.h:85
BALL::QSAR::FeatureSelectionConfiguration::done
bool done
Definition: configIO.h:95
BALL::QSAR::ValidationConfiguration::model
String model
Definition: configIO.h:106
BALL::QSAR::FeatureSelectionConfiguration::model
String model
Definition: configIO.h:80
BALL::QSAR::InputPartitioningConfiguration::ID
int ID
Definition: configIO.h:50
BALL::QSAR::InputConfiguration::validation_fraction
double validation_fraction
Definition: configIO.h:30
BALL::QSAR::ValidationConfiguration::no_of_permutation_tests
int no_of_permutation_tests
Definition: configIO.h:113
BALL::QSAR::ModelConfiguration::k_fold
int k_fold
Definition: configIO.h:67
BALL::QSAR::FeatureSelectionConfiguration::grid_search_recursions
int grid_search_recursions
Definition: configIO.h:97