validate_profile.cpp

/**
   This is the program for validation of SAXS profiles.
 */
#include <IMP/Model.h>
#include <IMP/atom/pdb.h>

#include <IMP/saxs/Profile.h>

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

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

#if defined(_WIN32) || defined(_WIN64)
// Simple basename implementation on platforms that don't have libgen.h
const char *basename(const char *path)
{
  int i;
  for (i = path ? strlen(path) : 0; i > 0; --i) {
    if (path[i] == '/' || path[i] == '\\') {
      return &path[i + 1];
    }
  }
  return path;
}
#else
#include <libgen.h>
#endif

namespace {
std::string trim_extension(const std::string file_name) {
  if(file_name[file_name.size()-4] == '.')
    return file_name.substr(0, file_name.size() - 4);
  return file_name;
}
}

int main(int argc, char **argv)
{
  // output arguments
  for (int i = 0; i < argc; i++) std::cerr << argv[i] << " ";
  std::cerr << std::endl;
  float max_q = 0.0;
  po::options_description desc("Usage: <profile_file1> <profile_file2> ...");
  desc.add_options()
    ("help", "Any number of input profiles is supported. \
Each profile is read and written back, with simulated error added if necessary")
    ("max_q,q", po::value<float>(&max_q)->default_value(0.0),
     "maximal q value")
    ("input-files", po::value< std::vector<std::string> >(),
     "input PDB and profile files")
    ;
  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;
  }

  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;
      // write back
      std::string profile_name =
        trim_extension(basename(const_cast<char *>(files[i].c_str())));
      std::string file_name = profile_name + "_v.dat";
      profile->write_SAXS_file(file_name, max_q);
      std::cout << "Profile written to file " << file_name << std::endl;
    }
  }
  return 0;
}