removealgo.cc

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#include "removealgo.h"

void RemoveAlgo::start()
{
  if ( getMAl()->get_num_seq() == 0 ) {
    cerr<<"Nothing to be done here! "<<endl;
    return;
  }

  //This can be done much more efficiently, removing stuff 
  //directly in the db instead. Oh, well...

  int num(0);
  for( size_t i = 0; i < getMAl()->get_num_seq(); i++ ) {
    for( size_t j = 0; j < getMAl()->get_len(i); j++ ) {
      if ( getMAl()->is_DNP(i, j) ) {
        num++;
        getMAl()->set_DNP(i, j, false);
      }
    }
  }
  cerr<<num<<" DNPs removed"<<endl;
}

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