PolyTableSlice.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 __POLY_TABLE_SLICE_HPP__
#define __POLY_TABLE_SLICE_HPP__
#include <vector>
#include <utility>
#include <boost/static_assert.hpp>
#include <boost/type_traits.hpp>
#include <Sequence/SeqConstants.hpp>
#include <Sequence/SeqExceptions.hpp>

namespace Sequence 
{
  template<typename T> class PolyTableSlice
  {
  private:
    BOOST_STATIC_ASSERT( (boost::is_base_and_derived<
                          Sequence::PolyTable,T>::value) );
    mutable T currentSlice;
    typedef std::pair<PolyTable::const_site_iterator,
                      PolyTable::const_site_iterator> range;
    //we store the window info as pointers to the range of sites 
    //in each window
    std::vector< range > windows;
    std::vector< range >::const_iterator windows_begin,windows_end;
    void process_windows(  const PolyTable::const_site_iterator beg,
                           const PolyTable::const_site_iterator end,
                           const unsigned & window_size,
                           const unsigned & step_len,
                           const double & alignment_length,
                           const bool & is_physical,
                           const double & physical_scale = 1.);

  public:
    explicit PolyTableSlice(  const PolyTable::const_site_iterator beg,
                              const PolyTable::const_site_iterator end,
                              const unsigned & window_size_S,
                              const unsigned & window_step_len );

    explicit PolyTableSlice(  const PolyTable::const_site_iterator beg,
                              const PolyTable::const_site_iterator end,
                              const unsigned & window_size,
                              const unsigned & step_len,
                              const double & alignment_length,
                              const double & physical_scale = 1.);
    typedef std::vector< std::pair<PolyTable::const_site_iterator,
                                   PolyTable::const_site_iterator> >::const_iterator const_iterator;
    const_iterator begin() const;
    const_iterator end() const;
    T get_slice(const const_iterator) const throw (Sequence::SeqException);
    unsigned size() const;
    T operator[](const unsigned &) const throw (Sequence::SeqException);
  };
}
#include <Sequence/bits/PolyTableSlice.tcc>

#endif

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