realigneralgo.cc

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#include "realigneralgo.h"

#include <unistd.h>
#include <ctime>
#include <iostream>
#include <cstdlib>
#include <cstddef> // definierar bl.a. size_t
// #include <boost/timer.hpp>

#include "AlAlgs.hpp"
#include "dna_alphabet_n_x.hpp"
#include "MalWrapper.hpp"


// include the realigner
#include "Realigner_h.hpp"
using namespace std;
// using boost::timer;

typedef al::dna_alphabet_n_x alphabet;

typedef MAlWrapper<alphabet> LayAlCont;

void RealignerAlgo::start() 
{
  bool debug_update = false;
  bool debug_alignment = false;
  bool draw = false;
  int type = 1;

  // important parameters
  int bandSize = 8;
  double a_koeff = 0.5;

  // create a realigner

  al::Realigner<LayAlCont, alphabet> rea;  

  // initialize the realigner with bandSize, a_koeff an other things

  rea.init_div(bandSize, debug_update, debug_alignment, type, draw, a_koeff);


  // construct and initialize the wrapper with the mal object

  LayAlCont la(getMAl());

  // read alignment from stdin (doesn't work with MalWrapper)
  //  al::read_layout_alignment<al::dna_alphabet>(la, cin);

  // register the wrapped mal object in the realigner

  std::pair<bool, bool> set_la_ok = rea.set_la(la);

//   ofstream ut("alignment.my");
//   // write alignment to stdout
//   al::write_layout_alignment<al::dna_alphabet>(la, ut);
//   cerr << "Written file!" << endl;

  // do the actual realigning

//   timer t0;

  if (set_la_ok.first) {
//     t0.restart();
    rea.realign_loop();
    
//     cerr << "realign_loop(): " << t0.elapsed() << "seconds" << endl;
    
  }
  
}

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