packed_string.cpp

/*

    SeedHam is a program to learn DNA binding motifs from SELEX datasets.
    Copyright (C) 2016, 2017  Jarkko Toivonen

    SeedHam is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.

    SeedHam is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License along
    with this program; if not, write to the Free Software Foundation, Inc.,
    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

*/
#include "packed_string.hpp"

#include <cassert>

packed_string::packed_string(const std::string& s) : bits(0), k(0) 
{
  k = s.length();
  assert(k <= max_len);
  bits = dna_to_number<big_int>(s);
}

int 
packed_string::length() const
{
  return k;
}

char
packed_string::operator[](size_t i) const 
{
  assert(i < k);
  return (bits >> (2*(k-i-1))) & 3;
}

packed_string::my_wrapper
packed_string::operator[](size_t i)
{
  assert(i < k);
  return my_wrapper(bits, 2*(k-i-1));
}

packed_string&
packed_string::erase(int pos, int dummy_count)
{
  assert(pos < k);
  big_int suffix_mask = 1;
  suffix_mask = (suffix_mask << (2*(k-pos-1))) - 1;
  big_int prefix_mask = ~suffix_mask;
  bits = ((bits >> 2) & prefix_mask) | (bits & suffix_mask);
  --k;
  return *this;
}

packed_string&
packed_string::insert(int pos, int dummy_count, char ch)
{
  assert(pos <= k);
  big_int suffix_mask = 1;
  suffix_mask = (suffix_mask << (2*(k-pos))) - 1;
  big_int prefix_mask = ~suffix_mask;
  big_int c = ch & 3;
  c <<= (2*(k-pos));
  bits = ((bits & prefix_mask) << 2) | c | (bits & suffix_mask);
  ++k;
  assert(k <= max_len);

  return *this;
}