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 2002-2012.
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
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#ifndef OPENMS_CHEMISTRY_AASEQUENCE_H
#define OPENMS_CHEMISTRY_AASEQUENCE_H

#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 <iostream>

namespace OpenMS
{
  class ResidueDB;
  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 & rhs);

    AASequence(const String & rhs);

    AASequence(const char * rhs);

    virtual ~AASequence();

    AASequence & operator=(const AASequence & rhs);

    bool empty() const;


    String toString() const;

    String toUnmodifiedString() const;

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

    void setNTerminalModification(const String & modification);

    const String & getNTerminalModification() const;

    void setCTerminalModification(const String & modification);

    const String & getCTerminalModification() const;

    bool setStringSequence(const String & sequence);

    const Residue & getResidue(SignedSize index) const;

    const Residue & getResidue(Size index) const;

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

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

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

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

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

    AASequence operator+(const AASequence & peptide) const;

    AASequence operator+(const String & peptide) const;

    AASequence operator+(const char * rhs) const;

    AASequence operator+(const Residue * residue) const;

    AASequence & operator+=(const AASequence &);

    AASequence & operator+=(const String &);

    AASequence & operator+=(const char * rhs);

    AASequence & operator+=(const Residue * residue);

    Size size() const;

    AASequence getPrefix(Size index) const;

    AASequence getSuffix(Size index) const;

    AASequence getSubsequence(Size index, UInt number) const;

    Size getNumberOf(const String & residue) const;

    void getAAFrequencies(Map<String, Size> & frequency_table) const;


    bool isValid() const;

    bool has(const Residue & residue) const;

    bool has(const String & name) const;

    bool hasSubsequence(const AASequence & peptide) const;

    bool hasSubsequence(const String & peptide) const;

    bool hasPrefix(const AASequence & peptide) const;

    bool hasPrefix(const String & peptide) const;

    bool hasSuffix(const AASequence & peptide) const;

    bool hasSuffix(const String & peptide) const;

    bool hasNTerminalModification() const;

    bool hasCTerminalModification() const;

    // returns true if any of the residues is modified
    bool isModified() const;

    bool isModified(Size index) const;

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

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

    bool operator==(const char * rhs) const;

    bool operator<(const AASequence & rhs) const;

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

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

    bool operator!=(const char * 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);

protected:

    std::vector<const Residue *> peptide_;

    String sequence_string_;

    void parseString_(std::vector<const Residue *> & sequence, const String & peptide);

    ResidueDB * getResidueDB_() const;

    bool valid_;

    const ResidueModification * n_term_mod_;

    const ResidueModification * c_term_mod_;
  };

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

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

} // namespace OpenMS

#endif