source: plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc @ 1014

// $Id: qQN.cc 1014 2009-03-30 16:40:55Z jari $

/*
  Copyright (C) 2009 Jari Häkkinen

  This file is part of the Normalizers plug-in package for BASE
  (net.sf.based.normalizers). The package is available at
  http://baseplugins.thep.lu.se/ BASE main site is
  http://base.thep.lu.se/

  This is free software; you can redistribute it and/or modify it
  under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 3 of the License, or
  (at your option) any later version.

  The software is distributed in the hope that it will be useful, but
  WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program. If not, see <http://www.gnu.org/licenses/>.
*/

#include <config.h> // this header file is created by configure

#include <yat/normalizer/ColumnNormalizer.h>
#include <yat/normalizer/qQuantileNormalizer.h>

#include <yat/utility/CommandLine.h>
#include <yat/utility/Matrix.h>
#include <yat/utility/OptionArg.h>
#include <yat/utility/OptionHelp.h>
#include <yat/utility/OptionSwitch.h>

#include <cstdlib>
#include <fstream>
#include <iostream>

using namespace theplu::yat;

int main(int argc, char* argv[])
{  
  using namespace normalizer;
  using namespace utility;

  CommandLine cmd;
  OptionArg<std::string> dir(cmd, "assay-data", "assay annotation file");
  OptionHelp help(cmd);
  help.synopsis()=(std::string("See ") +
                   "http://baseplugins.thep.lu.se/net.sf.basedb.normalizers " +
                   "for\ndetails on this program\n");
  OptionSwitch version(cmd, "version", "output version and exit");
  std::stringstream copyright;
  copyright << cmd.program_name() << VERSION << '\n'
            << "Copyright (C) 2009 Jari Häkkinen\n\n"
            << "This is free software see the source for copying "
            << "conditions. There is NO\nwarranty; not even for "
            << "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n";
  try {
    cmd.parse(argc, argv);
  }
  catch (cmd_error& e) {
    if (version.present()) {
      std::cout << copyright.str();
      return EXIT_SUCCESS;
    }
    std::cout << e.what() << std::endl;
    return EXIT_FAILURE;
  }  
  if (version.present()) {
    std::cout << copyright.str();
    return EXIT_SUCCESS;
  }

  Matrix m(std::cin,'\t');
  Matrix result(m.rows(),m.columns());
  qQuantileNormalizer qqn(m.begin_column(0), m.end_column(0),100);
  ColumnNormalizer<qQuantileNormalizer> cn(qqn);
  cn(m,result);
  std::cout << result << std::endl;

  return EXIT_SUCCESS;
}