stateCounter.cc

/*

  Copyright (C) 2003-2009 Kevin Thornton, krthornt[]@[]uci.edu

  Remove the brackets to email me.

  This file is part of libsequence.

  libsequence 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 3 of the License, or
  (at your option) any later version.

  libsequence 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
  long with libsequence.  If not, see <http://www.gnu.org/licenses/>.

*/

#include <Sequence/stateCounter.hpp>
#include <cctype>

namespace Sequence
{
  stateCounter::stateCounter( char gapchar):a(0),g(0),c(0),
                                            t(0),zero(0),one(0),gap(0),n(0),ndna(false),_gap(gapchar)
  {}

  void stateCounter::operator()(const char &ch)
  {
    if (ch == _gap)
      {
        ++gap;
      }
    else
      {
        char _ch = char(toupper(ch));
        switch(_ch)
          {
          case 'A':
            ++a;
            break;
          case 'G':
            ++g;
            break;
          case 'C':
            ++c;
            break;
          case 'T':
            ++t;
            break;
          case '0':
            ++zero;
            break;
          case '1':
            ++one;
            break;
          case 'N':
            ++n;
            break;
          default:
            ndna = true;
            break;
          }
      }
  }

  stateCounter::size_type stateCounter::nStates(void) const
  {
    stateCounter::size_type nstates = (a > 0) ? 1 : 0;
    nstates += (g > 0) ? 1 : 0;
    nstates += (c > 0) ? 1 : 0;
    nstates += (t > 0) ? 1 : 0;
    nstates += (zero > 0) ? 1 : 0;
    nstates += (one > 0) ? 1 : 0;
    return nstates;
  }
}