SequestOutfile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Martin Langwisch $
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#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;

  class OPENMS_DLLAPI SequestOutfile
  {
public:
    SequestOutfile();

    SequestOutfile(const SequestOutfile & sequest_outfile);

    virtual ~SequestOutfile();

    SequestOutfile & operator=(const SequestOutfile & sequest_outfile);

    bool operator==(const SequestOutfile & sequest_outfile) const;

    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);

    bool getColumns(const String & line, std::vector<String> & substrings, Size number_of_columns, Size reference_column);

    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);

    void getACAndACType(String line, String & accession, String & accession_type);

    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