RNPxlModificationsGenerator.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <vector>
#include <map>
#include <set>
#include <iostream>
 
namespace OpenMS
{  
  class AASequence;
 
  struct OPENMS_DLLAPI RNPxlModificationMassesResult
  {
    std::map<String, double> mod_masses; 
    std::map<String, std::set<String> > mod_combinations; 
  };
 
  class OPENMS_DLLAPI RNPxlModificationsGenerator
  {
    public:
      static RNPxlModificationMassesResult initModificationMassesRNA(StringList target_nucleotides,
                                                                     StringList nt_groups,
                                                                     std::set<char> can_xl,
                                                                     StringList mappings,
                                                                     StringList modifications,
                                                                     String sequence_restriction,
                                                                     bool cysteine_adduct,
                                                                     Int max_length = 4);
    private:
      static bool notInSeq(String res_seq, String query);
      static void generateTargetSequences(const String& res_seq, Size param_pos, const std::map<char, std::vector<char> >& map_source2target, StringList& target_sequences);
    };
}