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

  void stateCounter::operator()(const char &ch) const
    {
      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;
            }
        }
    }

  unsigned stateCounter::nStates(void) const
    {
      unsigned 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;
    }
}

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