AASequence.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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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch, Timo Sachsenberg $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CHEMISTRY/Residue.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>

#include <vector>
#include <iosfwd>
#include <map>

namespace OpenMS
{

  class OPENMS_DLLAPI AASequence
  {
public:

    class Iterator;

    class OPENMS_DLLAPI ConstIterator
    {
public:

      // TODO Iterator constructor for ConstIterator

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

      ConstIterator()
      {
      }

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

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

      ConstIterator(const AASequence::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 vector_ == rhs.vector_ && position_ == rhs.position_;
      }

      bool operator!=(const ConstIterator& rhs) const
      {
        return vector_ != rhs.vector_ || position_ != rhs.position_;
      }

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

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


protected:

      // pointer to the AASequence vector
      const std::vector<const Residue*>* vector_;

      // position in the AASequence vector
      difference_type position_;
    };


    class OPENMS_DLLAPI Iterator
    {
public:

      friend class AASequence::ConstIterator;

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

      Iterator()
      {
      }

      Iterator(std::vector<const Residue*>* 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 vector_ == rhs.vector_ && position_ == rhs.position_;
      }

      bool operator!=(const Iterator& rhs) const
      {
        return vector_ != rhs.vector_ || position_ != rhs.position_;
      }

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

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


protected:

      // pointer to the AASequence vector
      std::vector<const Residue*>* vector_;

      // position in the AASequence vector
      difference_type position_;
    };


    AASequence();

    AASequence(const AASequence&) = default;

    AASequence(AASequence&&) noexcept = default;

    virtual ~AASequence();

    AASequence& operator=(const AASequence&) = default;

    AASequence& operator=(AASequence&&) = default; // TODO: add noexcept (gcc 4.8 bug)

    bool empty() const;


    String toString() const;

    String toUnmodifiedString() const;

    String toUniModString() const;

    String toBracketString(bool integer_mass = true,
                           bool mass_delta = false,
                           const std::vector<String> & fixed_modifications = std::vector<String>()) const;

    void setModification(Size index, const String& modification);

    void setModification(Size index, const Residue* modification);

    void setModification(Size index, const ResidueModification* modification);

    void setModification(Size index, const ResidueModification& modification);

    void setModificationByDiffMonoMass(Size index, double diffMonoMass);

    void setNTerminalModification(const String& modification);

    void setNTerminalModification(const ResidueModification* modification);

    void setNTerminalModification(const ResidueModification& mod);

    void setNTerminalModificationByDiffMonoMass(double diffMonoMass, bool protein_term);

    const String& getNTerminalModificationName() const;

    const ResidueModification* getNTerminalModification() const;

    void setCTerminalModification(const String& modification);

    void setCTerminalModification(const ResidueModification* modification);

    void setCTerminalModification(const ResidueModification& mod);

    void setCTerminalModificationByDiffMonoMass(double diffMonoMass, bool protein_term);

    const String& getCTerminalModificationName() const;

    const ResidueModification* getCTerminalModification() const;

    const Residue& getResidue(Size index) const;

    EmpiricalFormula getFormula(Residue::ResidueType type = Residue::Full, Int charge = 0) const;

    double getAverageWeight(Residue::ResidueType type = Residue::Full, Int charge = 0) const;

    double getMonoWeight(Residue::ResidueType type = Residue::Full, Int charge = 0) const;

    double getMZ(Int charge, Residue::ResidueType type = Residue::Full) const;

    const Residue& operator[](Size index) const;

    AASequence operator+(const AASequence& peptide) const;

    AASequence& operator+=(const AASequence&);

    AASequence operator+(const Residue* residue) const;

    AASequence& operator+=(const Residue*);

    Size size() const;

    AASequence getPrefix(Size index) const;

    AASequence getSuffix(Size index) const;

    AASequence getSubsequence(Size index, UInt number) const;

    void getAAFrequencies(std::map<String, Size>& frequency_table) const;


    bool has(const Residue& residue) const;

    bool hasSubsequence(const AASequence& peptide) const;

    bool hasPrefix(const AASequence& peptide) const;

    bool hasSuffix(const AASequence& peptide) const;

    bool hasNTerminalModification() const;

    bool hasCTerminalModification() const;

    bool isModified() const;

    bool operator==(const AASequence& rhs) const;

    bool operator<(const AASequence& rhs) const;

    bool operator!=(const AASequence& rhs) const;

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

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

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

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

    friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const AASequence& peptide);

    friend OPENMS_DLLAPI std::istream& operator>>(std::istream& is, const AASequence& peptide);

    static AASequence fromString(const String& s,
                                 bool permissive = true);

    static AASequence fromString(const char* s,
                                 bool permissive = true);

  protected:

    std::vector<const Residue*> peptide_;

    const ResidueModification* n_term_mod_;

    const ResidueModification* c_term_mod_;

    static String::ConstIterator parseModRoundBrackets_(const String::ConstIterator str_it,
                                                        const String& str,
                                                        AASequence& aas,
                                                        const ResidueModification::TermSpecificity& specificity);

    static String::ConstIterator parseModSquareBrackets_(const String::ConstIterator str_it,
                                                         const String& str,
                                                         AASequence& aas,
                                                         const ResidueModification::TermSpecificity& specificity);

    static void parseString_(const String& peptide, AASequence& aas,
                             bool permissive = true);
  };

  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const AASequence& peptide);

  OPENMS_DLLAPI std::istream& operator>>(std::istream& os, const AASequence& peptide);

} // namespace OpenMS