text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2015.
  //
  // This software is released under a three-clause BSD license:
  //  * Redistributions of source code must retain the above copyright
  //    notice, this list of conditions and the following disclaimer.
  //  * Redistributions in binary form must reproduce the above copyright
  //    notice, this list of conditions and the following disclaimer in the
  //    documentation and/or other materials provided with the distribution.
  //  * Neither the name of any author or any participating institution
  //    may be used to endorse or promote products derived from this software
  //    without specific prior written permission.
  // For a full list of authors, refer to the file AUTHORS.
  // --------------------------------------------------------------------------
  // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
  // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
  // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
  // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
  // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
  // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
  // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
  // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  //
  // --------------------------------------------------------------------------
  // $Maintainer: Clemens Groepl $
  // $Authors: $
  // --------------------------------------------------------------------------
  
  #include <OpenMS/config.h>
  #include <OpenMS/APPLICATIONS/TOPPBase.h>
  #include <OpenMS/CONCEPT/FuzzyStringComparator.h>
  #include <OpenMS/DATASTRUCTURES/ListUtils.h>
  
  using namespace OpenMS;
  using namespace std;
  
  //-------------------------------------------------------------
  //Doxygen docu
  //-------------------------------------------------------------
  
  /**
      @page UTILS_FuzzyDiff FuzzyDiff
  
      @brief Compares two files, tolerating numeric differences.
  
      In the diff output, \"position\" refers to the characters in the string, whereas \"column\" is meant for the text editor.
  
      Only one of 'ratio' or 'absdiff' has to be satisfied.  Use \"absdiff\" to deal with cases like \"zero vs. epsilon\".
  
      <B>The command line parameters of this tool are:</B>
      @verbinclude UTILS_FuzzyDiff.cli
      <B>INI file documentation of this tool:</B>
      @htmlinclude UTILS_FuzzyDiff.html
  */
  
  // We do not want this class to show up in the docu:
  /// @cond TOPPCLASSES
  
  class TOPPFuzzyDiff :
    public TOPPBase
  {
  public:
    TOPPFuzzyDiff() :
      TOPPBase("FuzzyDiff", "Compares two files, tolerating numeric differences.", false)
    {
    }
  
  protected:
  
    void registerOptionsAndFlags_()
    {
      addEmptyLine_();
      registerInputFile_("in1", "<file>", "", "first input file", true, false);
      registerInputFile_("in2", "<file>", "", "second input file", true, false);
      addEmptyLine_();
  
      registerDoubleOption_("ratio", "<double>", 1, "acceptable relative error. Only one of 'ratio' or 'absdiff' has to be satisfied.  Use \"absdiff\" to deal with cases like \"zero vs. epsilon\".", false, false);
      setMinFloat_("ratio", 1);
      registerDoubleOption_("absdiff", "<double>", 0, "acceptable absolute difference. Only one of 'ratio' or 'absdiff' has to be satisfied. ", false, false);
      setMinFloat_("absdiff", 0);
      addEmptyLine_();
  
      registerStringList_("whitelist", "<string list>", ListUtils::create<String>("<?xml-stylesheet"), "Lines containing one of these strings are skipped", false, true);
  
      registerIntOption_("verbose", "<int>", 2, "set verbose level:\n"
                                                "0 = very quiet mode (absolutely no output)\n"
                                                "1 = quiet mode (no output unless differences detected)\n"
                                                "2 = default (include summary at end)\n"
                                                "3 = continue after errors\n",
                         false, false
                         );
      setMinInt_("verbose", 0);
      setMaxInt_("verbose", 3);
      registerIntOption_("tab_width", "<int>", 8, "tabulator width, used for calculation of column numbers", false, false);
      setMinInt_("tab_width", 1);
      registerIntOption_("first_column", "<int>", 1, "number of first column, used for calculation of column numbers", false, false);
      setMinInt_("first_column", 0);
    }
  
    ExitCodes main_(int, const char **)
    {
  
      //-------------------------------------------------------------
      // parameter handling
      //-------------------------------------------------------------
  
      String in1 = getStringOption_("in1");
      String in2 = getStringOption_("in2");
      double acceptable_ratio = getDoubleOption_("ratio");
      double acceptable_absdiff = getDoubleOption_("absdiff");
      StringList whitelist = getStringList_("whitelist");
      int verbose_level = getIntOption_("verbose");
      int tab_width = getIntOption_("tab_width");
      int first_column = getIntOption_("first_column");
  
      // This is for debugging the parsing of whitelist_ from cmdline or ini file.  Converting StringList back to String is intentional.
      writeDebug_(String("whitelist: ") + String(whitelist) + " (size: " + whitelist.size() + ")", 1);
  
      OpenMS::FuzzyStringComparator fsc;
  
      fsc.setAcceptableRelative(acceptable_ratio);
      fsc.setAcceptableAbsolute(acceptable_absdiff);
      fsc.setWhitelist(whitelist);
      fsc.setVerboseLevel(verbose_level);
      fsc.setTabWidth(tab_width);
      fsc.setFirstColumn(first_column);
  
      if (fsc.compareFiles(in1, in2))
      {
        return EXECUTION_OK;
      }
      else
      {
        // TODO think about better exit codes.
        return PARSE_ERROR;
      }
    }
  
  };
  
  int main(int argc, const char ** argv)
  {
    TOPPFuzzyDiff tool;
    return tool.main(argc, argv);
  }
  
  /// @endcond
  