NASequence.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Samuel Wein $
// $Authors: Samuel Wein, Timo Sachsenberg, Hendrik Weisser $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CHEMISTRY/Ribonucleotide.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <iosfwd>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI NASequence
  {
  public:
    enum NASFragmentType
    {                //< NB: Not all fragments types are valid for all residue types, this class should probably get split
      Full = 0,      
      Internal,      
      FivePrime,     
      ThreePrime,    
      AIon,          
      BIon,          
      CIon,          
      XIon,          
      YIon,          
      ZIon,          
      Precursor,     
      BIonMinusH20,  
      YIonMinusH20,  
      BIonMinusNH3,  
      YIonMinusNH3,  
      NonIdentified, 
      Unannotated,   
      WIon,          
      AminusB,       
      DIon,          
      SizeOfNASFragmentType
    };

    using ConstRibonucleotidePtr = const Ribonucleotide*;

    class Iterator;

    class OPENMS_DLLAPI ConstIterator
    {
    public:
      typedef Ribonucleotide value_type;
      typedef const value_type& const_reference;
      typedef value_type& reference;
      typedef const value_type* const_pointer;
      typedef std::vector<const value_type*>::difference_type difference_type;
      typedef const value_type* pointer;
      typedef std::random_access_iterator_tag iterator_category;

      ConstIterator() = default;

      ConstIterator(const std::vector<const Ribonucleotide*>* vec_ptr, difference_type position)
      {
        vector_ = vec_ptr;
        position_ = position;
      }

      ConstIterator(const ConstIterator& rhs) : vector_(rhs.vector_), position_(rhs.position_)
      {
      }

      ConstIterator(const NASequence::Iterator& rhs) : vector_(rhs.vector_), position_(rhs.position_)
      {
      }

      virtual ~ConstIterator()
      {
      }


      ConstIterator& operator=(const ConstIterator& rhs)
      {
        if (this != &rhs)
        {
          position_ = rhs.position_;
          vector_ = rhs.vector_;
        }
        return *this;
      }

      const_reference operator*() const
      {
        return *(*vector_)[position_];
      }

      const_pointer operator->() const
      {
        return (*vector_)[position_];
      }

      const ConstIterator operator+(difference_type diff) const
      {
        return ConstIterator(vector_, position_ + diff);
      }

      difference_type operator-(ConstIterator rhs) const
      {
        return position_ - rhs.position_;
      }

      const ConstIterator operator-(difference_type diff) const
      {
        return ConstIterator(vector_, position_ - diff);
      }

      bool operator==(const ConstIterator& rhs) const
      {
        return (std::tie(vector_, position_) == std::tie(rhs.vector_, rhs.position_));
      }

      bool operator!=(const ConstIterator& rhs) const
      {
        return !(operator==(rhs));
      }

      ConstIterator& operator++()
      {
        ++position_;
        return *this;
      }

      ConstIterator& operator--()
      {
        --position_;
        return *this;
      }


    protected:
      // pointer to the vector
      const std::vector<const Ribonucleotide*>* vector_;

      // position in the vector
      difference_type position_;
    };


    class OPENMS_DLLAPI Iterator
    {
    public:
      friend class NASequence::ConstIterator;

      typedef Ribonucleotide value_type;
      typedef const value_type& const_reference;
      typedef value_type& reference;
      typedef const value_type* const_pointer;
      typedef const value_type* pointer;
      typedef std::vector<const value_type*>::difference_type difference_type;

      Iterator() = default;

      Iterator(std::vector<const Ribonucleotide*>* vec_ptr, difference_type position)
      {
        vector_ = vec_ptr;
        position_ = position;
      }

      Iterator(const Iterator& rhs) : vector_(rhs.vector_), position_(rhs.position_)
      {
      }

      virtual ~Iterator()
      {
      }


      Iterator& operator=(const Iterator& rhs)
      {
        if (this != &rhs)
        {
          position_ = rhs.position_;
          vector_ = rhs.vector_;
        }
        return *this;
      }

      const_reference operator*() const
      {
        return *(*vector_)[position_];
      }

      const_pointer operator->() const
      {
        return (*vector_)[position_];
      }

      pointer operator->()
      {
        return (*vector_)[position_];
      }

      const Iterator operator+(difference_type diff) const
      {
        return Iterator(vector_, position_ + diff);
      }

      difference_type operator-(Iterator rhs) const
      {
        return position_ - rhs.position_;
      }

      const Iterator operator-(difference_type diff) const
      {
        return Iterator(vector_, position_ - diff);
      }

      bool operator==(const Iterator& rhs) const
      {
        return (std::tie(vector_, position_) == std::tie(rhs.vector_, rhs.position_));
      }

      bool operator!=(const Iterator& rhs) const
      {
        return !this->operator==(rhs);
      }

      Iterator& operator++()
      {
        ++position_;
        return *this;
      }

      Iterator& operator--()
      {
        --position_;
        return *this;
      }


    protected:
      std::vector<const Ribonucleotide*>* vector_;

      // position in the vector
      difference_type position_;
    };

  public:
    /*
     * Default constructors and assignment operators.
     */
    NASequence() = default;                               
    NASequence(const NASequence&) = default;              
    NASequence(NASequence&&) = default;                   
    NASequence& operator=(const NASequence&) & = default; 
    NASequence& operator=(NASequence&&) & = default;      

    NASequence(std::vector<const Ribonucleotide*> s, const RibonucleotideChainEnd* five_prime, const RibonucleotideChainEnd* three_prime);

    virtual ~NASequence() = default; 

    bool operator==(const NASequence& rhs) const; 
    bool operator!=(const NASequence& rhs) const; 
    bool operator<(const NASequence& rhs) const;  

    void setSequence(const std::vector<const Ribonucleotide*>& seq);

    const std::vector<const Ribonucleotide*>& getSequence() const
    {
      return seq_;
    }

    std::vector<const Ribonucleotide*>& getSequence()
    {
      return seq_;
    }

    void set(size_t index, const Ribonucleotide* r);

    const Ribonucleotide* get(size_t index)
    {
      return seq_[index];
    }

    inline const Ribonucleotide*& operator[](size_t index)
    {
      return seq_[index];
    }

    inline const Ribonucleotide* const& operator[](size_t index) const
    {
      return seq_[index];
    }

    bool empty() const;
    size_t size() const;
    void clear();

    bool hasFivePrimeMod() const;
    void setFivePrimeMod(const RibonucleotideChainEnd* r);
    const RibonucleotideChainEnd* getFivePrimeMod() const;
    bool hasThreePrimeMod() const;
    void setThreePrimeMod(const RibonucleotideChainEnd* r);
    const RibonucleotideChainEnd* getThreePrimeMod() const;

    inline Iterator begin()
    {
      return Iterator(&seq_, 0);
    }

    inline ConstIterator begin() const
    {
      return ConstIterator(&seq_, 0);
    }

    inline Iterator end()
    {
      return Iterator(&seq_, (Int)seq_.size());
    }

    inline ConstIterator end() const
    {
      return ConstIterator(&seq_, (Int)seq_.size());
    }

    inline ConstIterator cbegin() const
    {
      return ConstIterator(&seq_, 0);
    }

    inline ConstIterator cend() const
    {
      return ConstIterator(&seq_, (Int)seq_.size());
    }


    double getMonoWeight(NASFragmentType type = Full, Int charge = 0) const;

    double getAverageWeight(NASFragmentType type = Full, Int charge = 0) const;

    EmpiricalFormula getFormula(NASFragmentType type = Full, Int charge = 0) const;

    NASequence getPrefix(Size length) const;

    NASequence getSuffix(Size length) const;

    NASequence getSubsequence(Size start = 0, Size length = Size(-1)) const;

    static NASequence fromString(const String& s);

    friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const NASequence& seq);

    static NASequence fromString(const char* s);

    std::string toString() const;

  private:
    // TODO: query RNA / DNA depending on type
    static void parseString_(const String& s, NASequence& nas);

    // TODO: query RNA / DNA depending on type
    static String::ConstIterator parseMod_(const String::ConstIterator str_it, const String& str, NASequence& nas);

    std::vector<const Ribonucleotide*> seq_;

    const RibonucleotideChainEnd* five_prime_ = nullptr;
    const RibonucleotideChainEnd* three_prime_ = nullptr;
  };

} // namespace OpenMS