DnaStr.h

// Copyright (c) 2003, The Institute for Genomic Research (TIGR), Rockville,
// Maryland, U.S.A.  All rights reserved.
#ifndef DNASTR_H
#define DNASTR_H

#include <string>
#include <dsu.h>
#include <strstream>
#include <stdexcept>
#include <assert.h>

class DnaStr {
 public:
  DnaStr(const string& str, dsu::Strand_t strnd) : _str(str), _strnd(strnd) { }

  const string& getStr() const { return _str; }

  double gcPcnt(int = 1, int = -1) const;

  dsu::Strand_t getStrnd() const { return _strnd; }

  const char operator[](int idx) const
#if _RUNTIME_DEBUG < 3
    {
    assert(idx >= 1 && (idx-1) < (signed)_str.length());
    return _strnd==dsu::eNeg ? dsu::comp(_str[ idx-1]) : _str[idx-1];
  }
#else
  ;
#endif

  inline unsigned length() const { return _str.length(); }

  inline bool isStart(const char [3]) const;

  inline bool isStart(int)const;

  inline bool isStop(const char [3]) const;

  inline bool isStop(int bp) const; 

  friend std::ostream& operator<<(std::ostream& os, const DnaStr& str) {
                for(unsigned i = 0; i < str._str.length(); ++i)
                        os<<str[i];
                return os;
  }

#if _RUNTIME_DEBUG >= 1
  void printCodon(int start) const {
    if(_strnd == dsu::ePos)
      std::cout<<operator[](start)<<operator[](start+1)<<operator[](start+2)<<std::endl;
    else
      std::cout<<operator[](start+2)<<operator[](start+1)<<operator[](start)<<std::endl;
  }
#endif
private:
  inline static bool isU(char);
  inline static bool isA(char);
  inline static bool isG(char);
  inline static bool isC(char);
  inline static bool isR(char);

 private:
  const string& _str;
  dsu::Strand_t _strnd;

};

#include "inline/DnaStr.hpp"

#endif // DNASTR_H