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#include <fstream>
#include <BALL/QSAR/registry.h>
#include <BALL/QSAR/configIO.h>
using namespace BALL::QSAR;
using namespace BALL;
void startInputReading(std::ifstream& in, String data_path, QSARData* q, String* data_filename)
{
InputConfiguration conf = ConfigIO::readInputConfiguration(&in);
if(conf.done) return; // stop processing this section
bool created_data_object=0;
if(q==NULL || data_filename==NULL || conf.output!=*data_filename)
{
if(q==NULL)
{
q = new QSARData;
created_data_object=1;
}
if(data_filename) *data_filename = conf.output;
}
if(data_path!="")
{
q->setDataFolder(data_path.c_str());
}
if(conf.sd_file!="") // read sd-file (and csv-table)
{
if(!conf.separate_activity_file)
{
q->readSDFile(conf.sd_file.c_str(),conf.activities,conf.read_sd_descriptors,0);
}
else
{
q->readSDFile(conf.sd_file.c_str());
}
unsigned int no_csv = conf.csv_file.size();
for(unsigned int i=0; i<no_csv; i++)
{
q->readCSVFile(conf.csv_file[i].c_str(),0,conf.csv_desc_labels[i],conf.csv_compound_labels[i],conf.csv_separator[i].c_str(),1,conf.nonnumeric_class_names);
}
}
else // read csv-table only
{
if(conf.csv_file.size()==0 || conf.csv_file[0]=="")
{
std::cout<<"Error: sd-file and/or csv-table must be specified within config-file!"<< std::endl;
return;
}
q->readCSVFile(conf.csv_file[0].c_str(),conf.csv_no_response[0],conf.csv_desc_labels[0],conf.csv_compound_labels[0],conf.csv_separator[0].c_str(),0,conf.nonnumeric_class_names);
}
// now obsolete
if(conf.validation_fraction>0)
{
std::cout<<"conf.validation_fraction is obsolete. Use InputPartitioner(-section) instead!"<<std::endl;
}
if(conf.center_data)
{
q->centerData(conf.center_y);
}
q->saveToFile(conf.output);
if(created_data_object) delete q;
}
#ifndef EXT_MAIN
int main(int argc, char* argv[])
{
if(argc<2)
{
cout<<"Please specify configuration file!"<<endl;
return 0;
}
ifstream in(argv[1]);
if(!in)
{
cout<<"Configuration file '"<<argv[1]<<"' not found!"<<endl;
return 0;
}
String line;
for(int i=0;!in.eof();i++) // read ALL InputReader section
{
for(int j=0;!in.eof();j++) // skip everthing until the beginning of the next InputReader-section
{
getline(in,line);
if(!line.hasPrefix("[InputReader]")) continue;
else break;
}
if(!line.hasPrefix("[InputReader]")) break; // there are no (more) input-sections!
ConfigIO::putbackLine(&in,line);
startInputReading(in,argv[0], NULL, NULL);
}
}
#endif
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