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 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * 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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// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// $Maintainer: Samuel Wein $
// $Authors: Samuel Wein, Timo Sachsenberg, Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CHEMISTRY/Ribonucleotide.h>
 
#include <vector>
#include <iosfwd>
 
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;
  };
 
}