ttquanti_bitstring.h

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/*
 *  @file ttquanti_bitstring.h
 *  Nemo2
 *
 *   Copyright (C) 2023-2026 The Authors
 *
 *   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 3 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, see <https://www.gnu.org/licenses/>.
 *
 *  created on @date 10.02.2023
 *
 *  @author fred
 *
 */
 
#ifndef TTQUANTI_BITSTRING_H_
#define TTQUANTI_BITSTRING_H_
 
#include "ttquanti.h"
#include "bitstring.h"
 
// ------------------------------------------------------------------------------
// ------------------------------------------------------------------------------
class TTQuanti_diallelic_bitstring : public TTQuanti  {
 
public:
 
  TTQuanti_diallelic_bitstring () : TTQuanti(), _sequence(0)
  {}
 
  TTQuanti_diallelic_bitstring (const TTQuanti& T) : TTQuanti(T), _sequence(0)
  {}
 
  virtual ~TTQuanti_diallelic_bitstring () {reset();}
 
  virtual bool              get_allele_bit (unsigned int position, unsigned int allele) const;
  virtual void              set_allele_bit (unsigned int position, unsigned int allele, bool value);
  void                      set_bit_sequence (const bitstring* inseq);
  const bitstring&          get_bit_sequence (bool chromosome) const
                               {return _sequence[chromosome];}
  void                      inherit_free (const TTrait* mother, const TTrait* father);
 
  //implements TTrait:
  virtual   void            reset ();
  virtual   void            init  ();
  virtual   void            set_sequence (void** seq);
  virtual   void**          get_sequence () const                   {
    error("calling TTQuanti_diallelic_bitstring::get_sequence()\n");
    return (void**)NULL;
  }
  virtual   unsigned int    get_allele (int loc, int all) const ;
  virtual   double          get_allele_value (int locus, int allele) const;
  virtual   void            set_allele_value (unsigned int locus, unsigned int allele, double value);
 
  virtual   TTQuanti_diallelic_bitstring&       operator= (const TTrait& T);
  virtual   bool            operator== (const TTrait& T);
  virtual   bool            operator!= (const TTrait& T);
 
  //implements StorableComponent:
  virtual   void            store_data    ( BinaryStorageBuffer* saver  );
  virtual   bool            retrieve_data ( BinaryStorageBuffer* reader );
 
  //implements TTQuanti:
  virtual double            get_full_genotype     (unsigned int trait);
  virtual void              mutate_add            (unsigned int position, unsigned int allele, double value)
                               {_sequence[allele].set(position, bool(value));}
  virtual void              mutate_inplace        (unsigned int position, unsigned int allele, double value)
                               {_sequence[allele].flip(position);}
 
protected:
 
  bitstring *_sequence;
 
};
// ------------------------------------------------------------------------------
// ------------------------------------------------------------------------------
class TTQuanti_diallelic_bitstring_no_pleio : public TTQuanti_diallelic_bitstring {
 
public:
  TTQuanti_diallelic_bitstring_no_pleio() : TTQuanti_diallelic_bitstring()
  {}
 
  TTQuanti_diallelic_bitstring_no_pleio(const TTQuanti_diallelic_bitstring_no_pleio& TT) : TTQuanti_diallelic_bitstring(TT)
  {}
 
  virtual ~TTQuanti_diallelic_bitstring_no_pleio() {}
 
  //TTtrait implementation:
  virtual void init  ();
  virtual void init_sequence ();
  virtual TTQuanti_diallelic_bitstring_no_pleio*      clone ()     {return new TTQuanti_diallelic_bitstring_no_pleio(*this);}
  virtual void show_up();
 
  //TTQuanti implementation:
  virtual double get_additive_genotype (const unsigned int trait) const;
  virtual double get_dominant_genotype (const unsigned int trait) const;
  virtual void   copy_sequence_block   (sex_t SEX, unsigned int chromosome, unsigned int from_locus,
      unsigned int to_locus, const TTQuanti *parent);
  virtual void   copy_sequence_1locus  (sex_t SEX, unsigned int chromosome, unsigned int at,
                                                   const TTQuanti *parent);
  // Equal-effects additive genotype (used by get_dominant_genotype for equal-effects-only case)
  double get_additive_genotype_equal_effects (const unsigned int trait) const;
 
};
// ------------------------------------------------------------------------------
// ------------------------------------------------------------------------------
class TTQuanti_diallelic_bitstring_full_pleio : public TTQuanti_diallelic_bitstring {
 
public:
  TTQuanti_diallelic_bitstring_full_pleio () : TTQuanti_diallelic_bitstring() {}
 
  TTQuanti_diallelic_bitstring_full_pleio (const TTQuanti_diallelic_bitstring_full_pleio& TT) : TTQuanti_diallelic_bitstring(TT) {}
 
  virtual ~TTQuanti_diallelic_bitstring_full_pleio () {}
 
  //TTtrait implementation:
  virtual void init_sequence ();
  virtual TTQuanti_diallelic_bitstring_full_pleio*      clone ()     {return new TTQuanti_diallelic_bitstring_full_pleio(*this);}
  virtual void show_up();
 
  //TTQuanti implementation:
  virtual double get_additive_genotype (const unsigned int trait) const;
  virtual double get_dominant_genotype (const unsigned int trait) const;
  virtual void   copy_sequence_block   (sex_t SEX, unsigned int chromosome, unsigned int from_locus,
      unsigned int to_locus, const TTQuanti *parent);
  virtual void   copy_sequence_1locus  (sex_t SEX, unsigned int chromosome, unsigned int at,
                                                   const TTQuanti *parent);
};
// ------------------------------------------------------------------------------
// ------------------------------------------------------------------------------
class TTQuanti_diallelic_bitstring_var_pleio : public TTQuanti_diallelic_bitstring {
 
public:
  TTQuanti_diallelic_bitstring_var_pleio () : TTQuanti_diallelic_bitstring() {}
 
  TTQuanti_diallelic_bitstring_var_pleio (const TTQuanti_diallelic_bitstring_var_pleio& TT) : TTQuanti_diallelic_bitstring(TT) {}
 
  virtual ~TTQuanti_diallelic_bitstring_var_pleio () {}
 
  unsigned int get_sequence_block_size (unsigned int from, unsigned int to);
 
  //TTtrait implementation:
  virtual void init_sequence ();
  virtual TTQuanti_diallelic_bitstring_var_pleio*      clone ()     {return new TTQuanti_diallelic_bitstring_var_pleio(*this);}
  virtual void show_up();
 
  //TTQuanti implementation:
  virtual double get_additive_genotype (const unsigned int trait) const;
  virtual double get_dominant_genotype (const unsigned int trait) const;
  virtual void   copy_sequence_block   (sex_t SEX, unsigned int chromosome, unsigned int from_locus,
      unsigned int to_locus, const TTQuanti *parent);
  virtual void   copy_sequence_1locus  (sex_t SEX, unsigned int chromosome, unsigned int at,
                                                   const TTQuanti *parent);
};
 
 
 
 
#endif /* TTQUANTI_BITSTRING_H_ */