// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// This software is released under a three-clause BSD license:
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_RNPXL_MODIFIEDPEPTIDEGENERATOR_H
#define OPENMS_ANALYSIS_RNPXL_MODIFIEDPEPTIDEGENERATOR_H

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <vector>
#include <map>
#include <set>

namespace OpenMS
{
  class OPENMS_DLLAPI ModifiedPeptideGenerator
  {
   /*
    * @brief Modifications can be generated and applied to AASequences. 
    */

  public
:
    // Applies fixed modifications to a single peptide
    static void applyFixedModifications(const std::vector<ResidueModification>::const_iterator& fixed_mods_begin, const std::vector<ResidueModification>::const_iterator& fixed_mods_end, AASequence& peptide);

    // Applies variable modifications to a single peptide. If keep_original is set the original (e.g. unmodified version) is also returned
    static void applyVariableModifications(const std::vector<ResidueModification>::const_iterator& var_mods_begin, const std::vector<ResidueModification>::const_iterator& var_mods_end, const AASequence& peptide, Size max_variable_mods_per_peptide, std::vector<AASequence>& all_modified_peptides, bool keep_original=true);

  protected:
    // Recursively generate all combinatoric placements at compatible sites
    static void recurseAndGenerateVariableModifiedPeptides_(const std::vector<int>& subset_indices, const std::map<int, std::vector<ResidueModification> >& map_compatibility, int depth, const AASequence& current_peptide, std::vector<AASequence>& modified_peptides);

    // Fast implementation of modification placement. No combinatoric placement is needed in this case - just every site is modified once by each compatible modification. Already modified residues are skipped
    static void applyAtMostOneVariableModification_(const std::vector<ResidueModification>::const_iterator& var_mods_begin, const std::vector<ResidueModification>::const_iterator& var_mods_end, const AASequence& peptide, std::vector<AASequence>& all_modified_peptides, bool keep_original=true);

  };
}

#endif

