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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
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
BALL::QSAR::ConfigIO
Definition configIO.h:136
BALL::QSAR::ConfigIO::readInputPartitioningConfiguration
static InputPartitioningConfiguration readInputPartitioningConfiguration(std::istream *input)
BALL::QSAR::ConfigIO::readModelConfiguration
static ModelConfiguration readModelConfiguration(std::istream *input)
BALL::QSAR::ConfigIO::readPredictionConfiguration
static PredictionConfiguration readPredictionConfiguration(std::istream *input)
BALL::QSAR::ConfigIO::putbackLine
static void putbackLine(std::istream *input, String &line)
BALL::QSAR::ConfigIO::readInputConfiguration
static InputConfiguration readInputConfiguration(std::istream *input)
BALL::QSAR::ConfigIO::readFeatureSelectionConfiguration
static FeatureSelectionConfiguration readFeatureSelectionConfiguration(std::istream *input)
BALL::QSAR::ConfigIO::readValidationConfiguration
static ValidationConfiguration readValidationConfiguration(std::istream *input)
BALL::String
Definition string.h:57
BALL::QSAR
Definition allModel.h:17
BALL
Definition constants.h:13
string.h
BALL::QSAR::FeatureSelectionConfiguration
Definition configIO.h:77
BALL::QSAR::FeatureSelectionConfiguration::data_file
String data_file
Definition configIO.h:81
BALL::QSAR::FeatureSelectionConfiguration::opt_model_after_fs
bool opt_model_after_fs
Definition configIO.h:91
BALL::QSAR::FeatureSelectionConfiguration::opt
bool opt
Definition configIO.h:94
BALL::QSAR::FeatureSelectionConfiguration::opt_k_fold
int opt_k_fold
Definition configIO.h:99
BALL::QSAR::FeatureSelectionConfiguration::grid_search_stepwidth
double grid_search_stepwidth
Definition configIO.h:98
BALL::QSAR::FeatureSelectionConfiguration::remove_correlated
bool remove_correlated
Definition configIO.h:89
BALL::QSAR::FeatureSelectionConfiguration::model
String model
Definition configIO.h:80
BALL::QSAR::FeatureSelectionConfiguration::selection_name
String selection_name
Definition configIO.h:87
BALL::QSAR::FeatureSelectionConfiguration::grid_search_recursions
int grid_search_recursions
Definition configIO.h:97
BALL::QSAR::FeatureSelectionConfiguration::k_fold
int k_fold
Definition configIO.h:84
BALL::QSAR::FeatureSelectionConfiguration::statistic
int statistic
Definition configIO.h:88
BALL::QSAR::FeatureSelectionConfiguration::within_section
bool within_section
Definition configIO.h:85
BALL::QSAR::FeatureSelectionConfiguration::opt_kernel_after_fs
bool opt_kernel_after_fs
Definition configIO.h:92
BALL::QSAR::FeatureSelectionConfiguration::done
bool done
Definition configIO.h:95
BALL::QSAR::FeatureSelectionConfiguration::feat_type
int feat_type
Definition configIO.h:82
BALL::QSAR::FeatureSelectionConfiguration::FeatureSelectionConfiguration
FeatureSelectionConfiguration()
BALL::QSAR::FeatureSelectionConfiguration::quality_increase_cutoff
double quality_increase_cutoff
Definition configIO.h:93
BALL::QSAR::FeatureSelectionConfiguration::statistic_name
String statistic_name
Definition configIO.h:86
BALL::QSAR::FeatureSelectionConfiguration::grid_search_steps
int grid_search_steps
Definition configIO.h:96
BALL::QSAR::FeatureSelectionConfiguration::cor_threshold
double cor_threshold
Definition configIO.h:90
BALL::QSAR::FeatureSelectionConfiguration::output
String output
Definition configIO.h:83
BALL::QSAR::InputConfiguration
Definition configIO.h:20
BALL::QSAR::InputConfiguration::done
bool done
Definition configIO.h:39
BALL::QSAR::InputConfiguration::csv_file
vector< String > csv_file
Definition configIO.h:33
BALL::QSAR::InputConfiguration::within_section
bool within_section
Definition configIO.h:32
BALL::QSAR::InputConfiguration::activities
std::multiset< int > activities
Definition configIO.h:24
BALL::QSAR::InputConfiguration::center_data
bool center_data
Definition configIO.h:27
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::InputConfiguration::activity_names
std::set< String > activity_names
Definition configIO.h:25
BALL::QSAR::InputConfiguration::csv_compound_labels
vector< bool > csv_compound_labels
Definition configIO.h:36
BALL::QSAR::InputConfiguration::InputConfiguration
InputConfiguration()
BALL::QSAR::InputConfiguration::output
String output
Definition configIO.h:29
BALL::QSAR::InputConfiguration::validation_fraction
double validation_fraction
Definition configIO.h:30
BALL::QSAR::InputConfiguration::center_y
bool center_y
Definition configIO.h:28
BALL::QSAR::InputConfiguration::separate_activity_file
bool separate_activity_file
Definition configIO.h:31
BALL::QSAR::InputConfiguration::csv_separator
vector< String > csv_separator
Definition configIO.h:37
BALL::QSAR::InputConfiguration::csv_desc_labels
vector< bool > csv_desc_labels
Definition configIO.h:35
BALL::QSAR::InputConfiguration::nonnumeric_class_names
bool nonnumeric_class_names
Definition configIO.h:38
BALL::QSAR::InputConfiguration::read_sd_descriptors
bool read_sd_descriptors
Definition configIO.h:26
BALL::QSAR::InputPartitioningConfiguration
Definition configIO.h:43
BALL::QSAR::InputPartitioningConfiguration::InputPartitioningConfiguration
InputPartitioningConfiguration()
BALL::QSAR::InputPartitioningConfiguration::input_file
String input_file
Definition configIO.h:46
BALL::QSAR::InputPartitioningConfiguration::validation_fraction
double validation_fraction
Definition configIO.h:47
BALL::QSAR::InputPartitioningConfiguration::ID
int ID
Definition configIO.h:50
BALL::QSAR::InputPartitioningConfiguration::no_folds
int no_folds
Definition configIO.h:48
BALL::QSAR::InputPartitioningConfiguration::even_split
bool even_split
Definition configIO.h:49
BALL::QSAR::InputPartitioningConfiguration::done
bool done
Definition configIO.h:51
BALL::QSAR::ModelConfiguration
Definition configIO.h:55
BALL::QSAR::ModelConfiguration::kernel_type
int kernel_type
Definition configIO.h:64
BALL::QSAR::ModelConfiguration::done
bool done
Definition configIO.h:58
BALL::QSAR::ModelConfiguration::kernel_par2
double kernel_par2
Definition configIO.h:66
BALL::QSAR::ModelConfiguration::output
String output
Definition configIO.h:60
BALL::QSAR::ModelConfiguration::descriptor_source_model
String descriptor_source_model
Definition configIO.h:61
BALL::QSAR::ModelConfiguration::within_section
bool within_section
Definition configIO.h:72
BALL::QSAR::ModelConfiguration::grid_search_recursions
int grid_search_recursions
Definition configIO.h:71
BALL::QSAR::ModelConfiguration::grid_search_stepwidth
double grid_search_stepwidth
Definition configIO.h:69
BALL::QSAR::ModelConfiguration::data_file
String data_file
Definition configIO.h:59
BALL::QSAR::ModelConfiguration::optimize_model_parameters
bool optimize_model_parameters
Definition configIO.h:68
BALL::QSAR::ModelConfiguration::ModelConfiguration
ModelConfiguration()
BALL::QSAR::ModelConfiguration::kernel_par1
double kernel_par1
Definition configIO.h:65
BALL::QSAR::ModelConfiguration::k_fold
int k_fold
Definition configIO.h:67
BALL::QSAR::ModelConfiguration::model_parameters
vector< double > model_parameters
Definition configIO.h:62
BALL::QSAR::ModelConfiguration::grid_search_steps
int grid_search_steps
Definition configIO.h:70
BALL::QSAR::ModelConfiguration::no_training
bool no_training
Definition configIO.h:73
BALL::QSAR::ModelConfiguration::model_no
int model_no
Definition configIO.h:63
BALL::QSAR::PredictionConfiguration
Definition configIO.h:122
BALL::QSAR::PredictionConfiguration::model
String model
Definition configIO.h:125
BALL::QSAR::PredictionConfiguration::data
String data
Definition configIO.h:126
BALL::QSAR::PredictionConfiguration::PredictionConfiguration
PredictionConfiguration()
BALL::QSAR::PredictionConfiguration::done
bool done
Definition configIO.h:131
BALL::QSAR::PredictionConfiguration::print_expected
bool print_expected
Definition configIO.h:130
BALL::QSAR::PredictionConfiguration::output
String output
Definition configIO.h:127
BALL::QSAR::PredictionConfiguration::statistic
int statistic
Definition configIO.h:128
BALL::QSAR::PredictionConfiguration::statistic_name
String statistic_name
Definition configIO.h:129
BALL::QSAR::ValidationConfiguration
Definition configIO.h:103
BALL::QSAR::ValidationConfiguration::done
bool done
Definition configIO.h:118
BALL::QSAR::ValidationConfiguration::for_visualization_only
bool for_visualization_only
Definition configIO.h:117
BALL::QSAR::ValidationConfiguration::validation_data
String validation_data
Definition configIO.h:108
BALL::QSAR::ValidationConfiguration::statistic
int statistic
Definition configIO.h:114
BALL::QSAR::ValidationConfiguration::no_of_permutation_tests
int no_of_permutation_tests
Definition configIO.h:113
BALL::QSAR::ValidationConfiguration::output
String output
Definition configIO.h:110
BALL::QSAR::ValidationConfiguration::k_folds
int k_folds
Definition configIO.h:111
BALL::QSAR::ValidationConfiguration::model
String model
Definition configIO.h:106
BALL::QSAR::ValidationConfiguration::ValidationConfiguration
ValidationConfiguration()
BALL::QSAR::ValidationConfiguration::statistic_name
String statistic_name
Definition configIO.h:115
BALL::QSAR::ValidationConfiguration::val_type
int val_type
Definition configIO.h:109
BALL::QSAR::ValidationConfiguration::bootstrap_samples
int bootstrap_samples
Definition configIO.h:112
BALL::QSAR::ValidationConfiguration::data
String data
Definition configIO.h:107
BALL::QSAR::ValidationConfiguration::external_predictions
vector< String > external_predictions
Definition configIO.h:116