OpenPepXLLFAlgorithm.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 2002-2022.
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// $Maintainer: Eugen Netz $
// $Authors: Eugen Netz $
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#pragma once

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>

namespace OpenMS
{

  //-------------------------------------------------------------
  //Doxygen docu
  //-------------------------------------------------------------

  class OPENMS_DLLAPI OpenPepXLLFAlgorithm :
   public DefaultParamHandler, public ProgressLogger
  {
public:

    enum ExitCodes
    {
      EXECUTION_OK,
      ILLEGAL_PARAMETERS,
      UNEXPECTED_RESULT,
      INCOMPATIBLE_INPUT_DATA
    };

    OpenPepXLLFAlgorithm();

    ~OpenPepXLLFAlgorithm() override;

    ExitCodes run(PeakMap& unprocessed_spectra, std::vector<FASTAFile::FASTAEntry>& fasta_db, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms, PeakMap& spectra);

private:
    void updateMembers_() override;

    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_;
    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_;
    bool use_sequence_tags_;
    Size sequence_tag_min_length_;

    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_;
  };
}