SeqUtilities.hpp

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/*

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/>.

*/

#ifndef __SEQ_UTILITIES_H__
#define __SEQ_UTILITIES_H__
#include <iterator>
#include <algorithm>
#include <map>
#include <type_traits>

namespace Sequence
{
  template<typename Iterator> 
  std::map<typename std::iterator_traits<Iterator>::value_type,unsigned>
  makeCountList( Iterator beg,  Iterator end)
  {
    typedef typename std::iterator_traits<Iterator>::value_type type;
    typedef typename std::map<type,unsigned> maptype;
    typedef typename maptype::iterator mitr;
    maptype m;
    mitr i;
    while(beg < end)
      {
        i = m.find(*beg);
        if ( i != m.end() )
          {
            (*i).second++;
          }
        else
          {
            m[*beg] = 1;
          }
        beg++;
      }
    return m;
  }

  template<typename Iterator>
  bool
  internalGapCheck(Iterator beg, Iterator end,
                   const char & gapchar = '-',
                   const unsigned & mod = 3)
  {
    //the value type of the iterator must be convertible to a char
    static_assert( std::is_convertible<typename std::iterator_traits<Iterator>::value_type,char>::value,
                   "Iterator's value_type must be convertible to char");

    if(beg==end) return false;
    Iterator itr,effective_end=end-1;
    //find the first non-gap at the end of range
    while(effective_end > beg)
      {
        if (*effective_end != gapchar)
          {
            break;
          }
        else
          {
            --effective_end;
          }
      }
    itr = std::find_if(beg,effective_end,
                       std::bind2nd(std::not_equal_to<char>(),gapchar));
    ++itr;
    unsigned cont_gap = 0;
    while ( itr < effective_end )
      {
        if ( *itr == gapchar )
          {
            cont_gap++;
          }
        else
          {
            if (cont_gap % mod != 0.)
              {
                //gap fails our length requirement
                return true;
              }
            else
              {
                cont_gap = 0;
              }
          }
        itr++;
      }
    return false;
  }
}//namespace Sequence

#endif