text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2018.
  //
  // 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: Timo Sachsenberg $
  // $Authors: Martin Langwisch $
  // --------------------------------------------------------------------------
  
  #pragma once
  
  #include <OpenMS/CONCEPT/Exception.h>
  #include <OpenMS/DATASTRUCTURES/String.h>
  #include <OpenMS/METADATA/PeptideIdentification.h>
  
  #include <map>
  #include <vector>
  #include <cmath>
  
  namespace OpenMS
  {
    class ProteinIdentification;
    class DateTime;
  
    /**
    @brief Representation of a Sequest output file
  
    This class serves to read in a Sequest outfile. The information can be
    retrieved via the load function.
  
    @todo Handle Modifications (Andreas)
        @todo Complete rewrite of the parser (and those of InsPecT and PepNovo), the code is bullshit... (Andreas)
  
    @ingroup FileIO
  */
    class OPENMS_DLLAPI SequestOutfile
    {
  public:
      /// Constructor
      SequestOutfile();
  
      /// copy constructor
      SequestOutfile(const SequestOutfile & sequest_outfile);
  
      /// destructor
      virtual ~SequestOutfile();
  
      /// assignment operator
      SequestOutfile & operator=(const SequestOutfile & sequest_outfile);
  
      /// equality operator
      bool operator==(const SequestOutfile & sequest_outfile) const;
  
      /**
         @brief loads data from a Sequest outfile
  
         @param result_filename the file to be loaded
         @param peptide_identifications the identifications
         @param protein_identification the protein identifications
         @param p_value_threshold the significance level (for the peptide hit scores)
         @param pvalues a list with the pvalues of the peptides (pvalues computed with peptide prophet)
         @param database the database used for the search
         @param ignore_proteins_per_peptide this is a hack to deal with files that use a suffix like "+1" in column "Reference", but do not actually list extra protein references in subsequent lines
  
         @throw Exception::FileNotFound is thrown if the given result file could not be found
         @throw Exception::ParseError is thrown if the given result file could not be parsed
         @throw Exception::IllegalArgument
  
         This class serves to read in a Sequest outfile. The information can be
         retrieved via the load function.
     */
      void load(const String & result_filename, std::vector<PeptideIdentification> & peptide_identifications, ProteinIdentification & protein_identification, const double p_value_threshold, std::vector<double> & pvalues, const String & database = "", const bool ignore_proteins_per_peptide = false);
  
  // /// retrieve the p-values from the out files
  //          void getPValuesFromOutFiles(vector< pair < String, vector< double > > >& filenames_and_pvalues) throw (Exception::FileNotFound&, Exception::ParseError);
  
      /// retrieve columns from a Sequest outfile line
      bool getColumns(const String & line, std::vector<String> & substrings, Size number_of_columns, Size reference_column);
  
      /** retrieve sequences from a FASTA database
              @param database_filename
              @param ac_position_map
              @param sequences
              @param found
              @param not_found
              @throw Exception::FileNotFound is thrown if the database file could not be found
      */
      void getSequences(const String & database_filename, const std::map<String, Size> & ac_position_map, std::vector<String> & sequences, std::vector<std::pair<String, Size> > & found, std::map<String, Size> & not_found);
  
      /// retrieve the accession type and accession number from a protein description line
      /// (e.g. from FASTA line: >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus], get ac:AAD44166.1 ac type: GenBank)
      void getACAndACType(String line, String & accession, String & accession_type);
  
      /** read the header of an out file and retrieve various information
  
              @throw Exception::FileNotFound is thrown if the results file could not be found
              @throw Exception::ParseError is thrown if the results file could not be parsed
      */
      void readOutHeader(const String & result_filename, DateTime & datetime, double & precursor_mz_value, Int & charge, Size & precursor_mass_type, Size & ion_mass_type, Size & displayed_peptides, String & sequest, String & sequest_version, String & database_type, Int & number_column, Int & rank_sp_column, Int & id_column, Int & mh_column, Int & delta_cn_column, Int & xcorr_column, Int & sp_column, Int & sf_column, Int & ions_column, Int & reference_column, Int & peptide_column, Int & score_column, Size & number_of_columns);
  
  private:
  
      static double const_weights_[];
      static double xcorr_weights_[];
      static double delta_cn_weights_[];
      static double rank_sp_weights_[];
      static double delta_mass_weights_[];
      static Size max_pep_lens_[];
      static Size num_frags_[];
    };
  
  } //namespace OpenMS
  
  