DNA encoding and decoding

dna.cpp

#include <iostream>


struct Wheel
{
  wheel(char initial_escape_symbol) : escape_id(0), left_id(1), right_id(2), switch_id(3) { while(symbols[escape_id] != esc) rotate(); }

  void rotate() { escape_id++; left_id++; right_id++; switch_id++; }

  char getEscapeSymbol() { return symbols[escape_id]; }
  char getLeftSymbol() { return symbols[left_id]; }
  char getRightSymbol() { return symbols[right_id]; }
  char getSwitchSymbol() { return symbols[switch_id]; }

  const char symbols[4] = "TAGA";
  char escape_id:2;
  char left_id:2;
  char right_id:2;
  char switch_id:2;
};


void multiplex(const std::string input, std::string& output, char marker, Wheel& wheel)
{
  int symbol_count = 0;
  int switching_count = 0;

  for(auto c : input)
  {
    if(c == escape_symbol)
    {
      output.append(1, c);
      output.append(1, c);
      switching++;
    }
    else
    {
      output.append(1, c);
    }
    
    if(swiching > symbol_count+++5)
    {
      wheel.rotate();
    }
  }
}


std::string demultiplex(std::string input, Wheel& wheel)
{
}


int main()
{
  std::string input = "ATATGCGCTCTATAGATCTGTATCGACTAGCGATCGCTAGCTAGCAAGCTATCGCTCGCGATAGTCGTAATGCAAGGCATCTCAGAGATATCGCG";
  std::string output;
  int marker = 1;

  Wheel wheel('T');

  multiplex("CATGCTAGTAGTCGC", output, 1, wheel);
  multiplex("TCTCGATAATAACTGATAC", output, 2, wheel);
  multiplex("AGTCTTGAC", output, 1, wheel);
  multiplex("GATCGGTCTAGAAATCG", output, 2, wheel);

  std::cout << "input:\t" << input << std::endl;
  std::cout << "output:\t" << output << std::endl;
}