OpenPepXLAlgorithm.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    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.
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// $Maintainer: Eugen Netz $
// $Authors: Timo Sachsenberg, Eugen Netz $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>
 
namespace OpenMS
{
 
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
 
  class OPENMS_DLLAPI OpenPepXLAlgorithm :
   public DefaultParamHandler, public ProgressLogger
  {
public:
 
    enum ExitCodes
    {
      EXECUTION_OK,
      ILLEGAL_PARAMETERS,
      UNEXPECTED_RESULT,
      INCOMPATIBLE_INPUT_DATA
    };
 
    OpenPepXLAlgorithm();
 
    ~OpenPepXLAlgorithm() override;
 
    ExitCodes run(PeakMap& unprocessed_spectra, ConsensusMap& cfeatures, std::vector<FASTAFile::FASTAEntry>& fasta_db, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, OPXLDataStructs::PreprocessedPairSpectra& preprocessed_pair_spectra, std::vector< std::pair<Size, Size> >& spectrum_pairs, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms, PeakMap& spectra);
 
private:
    void updateMembers_() override;
 
    static OPXLDataStructs::PreprocessedPairSpectra preprocessPairs_(const PeakMap& spectra, const std::vector< std::pair<Size, Size> >& spectrum_pairs, const double cross_link_mass_iso_shift, double fragment_mass_tolerance, double fragment_mass_tolerance_xlinks, bool fragment_mass_tolerance_unit_ppm, bool deisotope);
 
    String decoy_string_;
    bool decoy_prefix_;
 
    Int min_precursor_charge_;
    Int max_precursor_charge_;
    double precursor_mass_tolerance_;
    bool precursor_mass_tolerance_unit_ppm_;
    IntList precursor_correction_steps_;
 
    double fragment_mass_tolerance_;
    double fragment_mass_tolerance_xlinks_;
    bool fragment_mass_tolerance_unit_ppm_;
 
    StringList cross_link_residue1_;
    StringList cross_link_residue2_;
    double cross_link_mass_light_;
    double cross_link_mass_iso_shift_;
    DoubleList cross_link_mass_mono_link_;
    String cross_link_name_;
 
    StringList fixedModNames_;
    StringList varModNames_;
    Size max_variable_mods_per_peptide_;
    Size peptide_min_size_;
    Size missed_cleavages_;
    String enzyme_name_;
 
    Int number_top_hits_;
    String deisotope_mode_;
 
    String add_y_ions_;
    String add_b_ions_;
    String add_x_ions_;
    String add_a_ions_;
    String add_c_ions_;
    String add_z_ions_;
    String add_losses_;
  };
}