af_spectrum.hpp

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#ifndef GENESIS_POPULATION_PLOTTING_AF_SPECTRUM_H_
#define GENESIS_POPULATION_PLOTTING_AF_SPECTRUM_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
*/
 
#ifdef GENESIS_HTSLIB
 
#include <functional>
#include <string>
#include <utility>
#include <vector>
 
#include "genesis/population/format/vcf_record.hpp"
#include "genesis/population/plotting/heatmap_colorization.hpp"
#include "genesis/population/window/sliding_window_generator.hpp"
#include "genesis/population/window/window.hpp"
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Allele Frequency Window
// =================================================================================================
 
class AlleleFrequencyWindow
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs and Enums
    // -------------------------------------------------------------------------
 
    using AFWindow = Window<double>;
    using self_type = AlleleFrequencyWindow;
    using Spectrum  = HeatmapColorization::Spectrum;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    AlleleFrequencyWindow( size_t width, size_t number_of_bins = 100 );
    ~AlleleFrequencyWindow();
 
    AlleleFrequencyWindow( AlleleFrequencyWindow const& ) = default;
    AlleleFrequencyWindow( AlleleFrequencyWindow&& )      = default;
 
    AlleleFrequencyWindow& operator= ( AlleleFrequencyWindow const& ) = default;
    AlleleFrequencyWindow& operator= ( AlleleFrequencyWindow&& )      = default;
 
    // -------------------------------------------------------------------------
    //     Event Plugin Functionals
    // -------------------------------------------------------------------------
 
    std::function<void( Spectrum const& )> on_chromosome_start;
    std::function<void( Spectrum const& )> on_chromosome_finish;
 
    // -------------------------------------------------------------------------
    //     Settings
    // -------------------------------------------------------------------------
 
    size_t number_of_bins() const
    {
        return number_of_bins_;
    }
 
    bool skip_invalid_records() const
    {
        return skip_invalid_records_;
    }
 
    self_type& skip_invalid_records( bool value )
    {
        skip_invalid_records_ = value;
        return *this;
    }
 
    // -------------------------------------------------------------------------
    //     Window Processing
    // -------------------------------------------------------------------------
 
    void run_vcf( std::string const& vcf_file );
 
    void enqueue( std::string const& chromosome, size_t position, double frequency );
    void enqueue( VcfRecord const& record );
 
    // -------------------------------------------------------------------------
    //     Internal Members
    // -------------------------------------------------------------------------
 
private:
 
    void on_chromosome_start_( std::string const& chromosome, AFWindow::Accumulator& );
 
    void on_chromosome_finish_( std::string const& chromosome, AFWindow::Accumulator& );
 
    void on_emission_( AFWindow const& window );
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    size_t number_of_bins_;
    bool skip_invalid_records_ = true;
 
    SlidingWindowGenerator<double> window_generator_;
    std::vector<Spectrum> spectra_;
 
};
 
} // namespace population
} // namespace genesis
 
#endif // htslib guard
#endif // include guard