ttneutralgenes_bitstring.h

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/*
 *  @file ttneutralgenes_bitstring.h
 *  Nemo2
 *
 *   Copyright (C) 2026 Frederic Guillaume
 *   frederic.guillaume@helsinki.fi
 *
 *   This file is part of Nemo
 *
 *   Nemo 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 2 of the License, or
 *   (at your option) any later version.
 *
 *   Nemo 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, write to the Free Software
 *   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 *
 *  created on @date 03.03.2026
 *
 *  @author fred
 */
 
#ifndef TTNEUTRALGENES_BITSTRING_H_
#define TTNEUTRALGENES_BITSTRING_H_
 
#include "ttneutralgenes.h"
#include "bitstring.h"
 
// ------------------------------------------------------------------------------
// ------------------------------------------------------------------------------
class TTNeutralGenes_bitstring : public TTNeutralGenes {
 
public:
 
  TTNeutralGenes_bitstring ()
    : TTNeutralGenes(), _sequence(0), _free_recombination(true) { }
 
  TTNeutralGenes_bitstring (const TTNeutralGenes_bitstring& T)
    : TTNeutralGenes(T), _sequence(0), _free_recombination(T._free_recombination) { }
 
  virtual ~TTNeutralGenes_bitstring () { reset(); }
 
  const bitstring& get_bit_sequence (bool chromosome) const
    { return _sequence[chromosome]; }
 
  virtual TTNeutralGenes& operator= (const TTrait& T);
  virtual void    init                 ( );
  virtual void    init_sequence        ( );
  virtual void    reset                ( );
  virtual void**  get_sequence         ( ) const {
    error("calling TTNeutralGenes_bitstring::get_sequence()\n");
    return (void**)NULL;
  }
  virtual unsigned int    get_allele   (int loc, int all) const;
  virtual double  get_allele_value     (int loc, int all) const;
  virtual void    set_allele_value     (unsigned int locus, unsigned int allele, double value);
  virtual void    set_sequence         (void** seq);
  virtual void    inherit              (const TTrait* mother, const TTrait* father);
  virtual void    mutate               ( );
  virtual void    show_up              ( );
  virtual TTNeutralGenes*  clone       ( ) { return new TTNeutralGenes_bitstring(*this); }
 
  //implements StorableComponent
  virtual void    store_data       (BinaryStorageBuffer* saver);
  virtual bool    retrieve_data    (BinaryStorageBuffer* reader);
 
private:
 
  void inherit_low (sex_t SEX, const TTNeutralGenes_bitstring* parent);
 
protected:
 
  bitstring *_sequence;  // array of 2 bitstrings [ploidy]
  bool _free_recombination;
 
};
 
#endif /* TTNEUTRALGENES_BITSTRING_H_ */