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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/commandlineParser.h>
#include <BALL/QSAR/registry.h>
#include <BALL/QSAR/featureSelection.h>
#include <BALL/QSAR/configIO.h>
#include <fstream>
#include "version.h"
using namespace BALL::QSAR;
using namespace BALL;
using namespace std;
void startInputPartitioning(InputPartitioningConfiguration& conf, QSARData* q, String* data_filename);
void startInputPartitioning(ifstream& in, QSARData* q, String* data_filename)
{
InputPartitioningConfiguration conf = ConfigIO::readInputPartitioningConfiguration(&in);
if(conf.done) return; // stop processing this section
startInputPartitioning(conf,q,data_filename);
}
void startInputPartitioning(InputPartitioningConfiguration& conf, QSARData* q, String* data_filename)
{
bool created_data_object=0;
if(q==NULL || data_filename==NULL || conf.input_file!=*data_filename)
{
if(q==NULL)
{
q = new QSARData;
created_data_object=1;
}
q->readFromFile(conf.input_file);
if(data_filename) *data_filename = conf.input_file;
}
// -- create prefix for output-files ---
String output_prefix = conf.input_file;
size_t index = output_prefix.find_first_of(".");
if(index != string::npos)
{
output_prefix=output_prefix.substr(0,index);
}
if(conf.ID>0)
{
output_prefix+="_"+String(conf.ID);
}
// -----------
for(int fold_id=0; fold_id<conf.no_folds; fold_id++)
{
vector<QSARData*> sets;
if(conf.even_split)
{
sets = q->evenSplit(conf.no_folds,fold_id);
}
else
{
sets = q->generateExternalSet(conf.validation_fraction); // length==2
}
if(q->isDataCentered())
{
bool center_y = q->isResponseCentered();
sets[0]->centerData(center_y); // train-partition
sets[1]->centerData(center_y); // test-partition
}
String train_name = output_prefix+"_TRAIN"+String(fold_id)+".dat";
String test_name = output_prefix+"_TEST"+String(fold_id)+".dat";
sets[0]->saveToFile(train_name);
sets[1]->saveToFile(test_name);
}
if(created_data_object) delete q;
}
#ifndef EXT_MAIN
int main(int argc, char* argv[])
{
CommandlineParser par("InputPartitioner","split QSAR data set ", VERSION, String(__DATE__), "QuEasy (QSAR)");
par.registerMandatoryInputFile("i", "input data-file");
par.registerMandatoryOutputFile("o", "output dat-file");
par.registerMandatoryIntegerParameter("n", "number of partitions");
String man = "InputPartitioner partitions a given QSAR data set into n partitions with evenly distributed response values.\nThus, this tool can be useful as part of a nested validation pipeline.\nInput is a data file as generated by InputReader.\nOutput will be written to n files postfixed '_TRAIN<i>.dat' and '_TEST<i>.dat', where <i> is the ID of the resp. partition. For each of these partitions, the training set contains only those compounds that were not selected for the resp. test set.";
par.setToolManual(man);
par.setSupportedFormats("i","dat");
par.setSupportedFormats("o","dat");
par.parse(argc,argv);
InputPartitioningConfiguration conf;
conf.input_file = par.get("i");
conf.no_folds = par.get("n").toInt();
startInputPartitioning(conf,0,0);
}
#endif
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