OpenPepXLAlgorithm.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
 
namespace OpenMS
{
 
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
 
  class OPENMS_DLLAPI OpenPepXLAlgorithm :
   public DefaultParamHandler, public ProgressLogger
  {
public:
 
    enum class 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, PeptideIdentificationList& 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);
 
    std::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_;    
    std::string cross_link_name_;                  
 
    StringList fixedModNames_;                
    StringList varModNames_;                  
    Size max_variable_mods_per_peptide_;      
    Size peptide_min_size_;                   
    Size missed_cleavages_;                   
    std::string enzyme_name_;                      
 
    Int number_top_hits_;                     
    std::string deisotope_mode_;                   
 
    std::string add_y_ions_;   
    std::string add_b_ions_;   
    std::string add_x_ions_;   
    std::string add_a_ions_;   
    std::string add_c_ions_;   
    std::string add_z_ions_;   
    std::string add_losses_;   
  };
}