RNPxlModificationsGenerator.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
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#ifndef OPENMS_ANALYSIS_RNPXL_RNPXLMODIFICATIONSGENERATOR_H
#define OPENMS_ANALYSIS_RNPXL_RNPXLMODIFICATIONSGENERATOR_H

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <vector>
#include <map>
#include <set>
#include <iostream>

namespace OpenMS
{  
  class AASequence;

  struct OPENMS_DLLAPI RNPxlModificationMassesResult
  {
    std::map<String, double> mod_masses; // empirical formula -> mass
    std::map<String, std::set<String> > mod_combinations; // empirical formula -> nucleotide formula(s) (formulas if modifications lead to ambiguities)
    std::map<Size, String> mod_formula_idx;
  };

  class OPENMS_DLLAPI RNPxlModificationsGenerator
  {
    public:
      static RNPxlModificationMassesResult initModificationMassesRNA(StringList target_nucleotides, StringList mappings, StringList restrictions, 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);
    };
}

#endif // OPENMS_ANALYSIS_RNPXL_RNPXLMODIFICATIONSGENERATOR_H