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 2002-2020.
//
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
#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/Residue.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
 
#include <vector>
#include <iosfwd>
 
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);
 
    // sets the (potentially modified) residue
    void setModification(Size index, const Residue* modification) { peptide_[index] = modification; }
 
    void setNTerminalModification(const String& modification);
 
    void setNTerminalModification(const ResidueModification* modification);
 
    const String& getNTerminalModificationName() const;
 
    const ResidueModification* getNTerminalModification() const;
 
    void setCTerminalModification(const String& modification);
 
    void setCTerminalModification(const ResidueModification* modification);
 
    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;
 
    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(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