/**
   This is the program for validation of SAXS profiles.
 */
#include <IMP/saxs/Profile.h>
#include <IMP/saxs/ProfileFitter.h>

#include <fstream>
#include <vector>
#include <string>

#include <boost/lexical_cast.hpp>
#include <boost/program_options.hpp>
namespace po = boost::program_options;

int main(int argc, char **argv)
{
  // output arguments
  for (int i = 0; i < argc; i++) std::cerr << argv[i] << " ";
  std::cerr << std::endl;

  bool use_offset = false;

  po::options_description
    desc("Usage: <experimental_profile> <profile_file1> <profile_file2> ...");
  desc.add_options()
    ("help", "Any number of input profiles is supported. \
The chi value is computed relative to the first profile using its error column")
    ("input-files", po::value< std::vector<std::string> >(),
     "input PDB and profile files")
     ("offset,o", "use offset in fitting (default = false)")
    ;
  po::positional_options_description p;
  p.add("input-files", -1);
  po::variables_map vm;
  po::store(
      po::command_line_parser(argc,argv).options(desc).positional(p).run(), vm);
  po::notify(vm);

  std::vector<std::string> files, dat_files;
  if(vm.count("input-files")) {
    files = vm["input-files"].as< std::vector<std::string> >();
  }
  if(vm.count("help") || files.size() == 0) {
    std::cout << desc << "\n";
    return 0;
  }
  if(vm.count("offset")) use_offset=true;

  std::vector<IMP::saxs::Profile *> exp_profiles;
  for(unsigned int i=0; i<files.size(); i++) {
    // check if file exists
    std::ifstream in_file(files[i].c_str());
    if(!in_file) {
      std::cerr << "Can't open file " << files[i] << std::endl;
      exit(1);
    }

    IMP::saxs::Profile *profile = new IMP::saxs::Profile(files[i]);
    if(profile->size() == 0) {
      std::cerr << "can't parse input file " << files[i] << std::endl;
      return 1;
    } else {
      dat_files.push_back(files[i]);
      exp_profiles.push_back(profile);
      std::cout << "Profile read from file " << files[i] << " size = "
                << profile->size() << std::endl;
    }
  }

  IMP::saxs::Profile* exp_saxs_profile = exp_profiles[0];
  IMP::Pointer<IMP::saxs::ProfileFitter<IMP::saxs::ChiScore> >saxs_score =
    new IMP::saxs::ProfileFitter<IMP::saxs::ChiScore>(*exp_saxs_profile);
  for(unsigned int i=1; i<exp_profiles.size(); i++) {
    std::string fit_file = "fit" +
      std::string(boost::lexical_cast<std::string>(i)) + ".dat";
    float chi = saxs_score->compute_score(*exp_profiles[i], use_offset, "fit");
    std::cout << "File " << files[i] << " chi=" << chi << std::endl;
  }
  return 0;
}