base_window.hpp

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#ifndef GENESIS_POPULATION_WINDOW_BASE_WINDOW_H_
#define GENESIS_POPULATION_WINDOW_BASE_WINDOW_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2024 Lucas Czech
 
    This program 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.
 
    This program 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, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include <stdexcept>
#include <string>
#include <unordered_map>
 
#include "genesis/population/genome_region.hpp"
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Genomic Window
// =================================================================================================
 
template<class D>
class BaseWindow
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs and Enums
    // -------------------------------------------------------------------------
 
    using Data = D;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    BaseWindow() = default;
    virtual ~BaseWindow() = default;
 
    BaseWindow( BaseWindow const& ) = default;
    BaseWindow( BaseWindow&& )      = default;
 
    BaseWindow& operator= ( BaseWindow const& ) = default;
    BaseWindow& operator= ( BaseWindow&& )      = default;
 
    // -------------------------------------------------------------------------
    //     Chromosome and Positions
    // -------------------------------------------------------------------------
 
    std::string const& chromosome() const
    {
        return chromosome_;
    }
 
    void chromosome( std::string const& value )
    {
        chromosome_ = value;
    }
 
    size_t first_position() const
    {
        return first_position_;
    }
 
    void first_position( size_t value )
    {
        first_position_ = value;
    }
 
    size_t last_position() const
    {
        return last_position_;
    }
 
    void last_position( size_t value )
    {
        last_position_ = value;
    }
 
    GenomeRegion genome_region() const
    {
        return { chromosome_, first_position_, last_position_ };
    }
 
    size_t width() const
    {
        // We need to do the check here, when this is used.
        if( first_position_ > last_position_ ) {
            throw std::runtime_error(
                "Invalidly set first and last position in the Window, with " +
                std::to_string( first_position_ ) + " > " + std::to_string( last_position_ )
            );
        }
        return last_position_ - first_position_ + 1;
    }
 
    // -------------------------------------------------------------------------
    //     Whole Genome
    // -------------------------------------------------------------------------
 
    bool is_whole_genome() const
    {
        return is_whole_genome_;
    }
 
 
    void is_whole_genome( bool value )
    {
        is_whole_genome_ = value;
    }
 
    std::unordered_map<std::string, size_t> const& chromosomes() const
    {
        return chromosomes_;
    }
 
    std::unordered_map<std::string, size_t>& chromosomes()
    {
        return chromosomes_;
    }
 
    // -------------------------------------------------------------------------
    //     Modifiers and Helpers
    // -------------------------------------------------------------------------
 
    void clear()
    {
        chromosome_     = "";
        first_position_ = 0;
        last_position_  = 0;
        is_whole_genome_ = false;
        chromosomes_.clear();
        clear_();
    }
 
    // -------------------------------------------------------------------------
    //     Virtual Members
    // -------------------------------------------------------------------------
 
protected:
 
    virtual void clear_()
    {
        // Do nothing. Override by derived classes to clear their data.
    }
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    // Normal case of window within chromosome
    std::string chromosome_;
    size_t first_position_ = 0;
    size_t last_position_  = 0;
 
    // Special case of window over whole genome
    bool is_whole_genome_ = false;
    std::unordered_map<std::string, size_t> chromosomes_;
 
};
 
} // namespace population
} // namespace genesis
 
#endif // include guard