TTQuanti_continuous_no_pleio : multiple non-pleiotropic traits. More...

#include <ttquanti.h>

Inheritance diagram for TTQuanti_continuous_no_pleio:

Collaboration diagram for TTQuanti_continuous_no_pleio:

Public Member Functions
	TTQuanti_continuous_no_pleio ()

	TTQuanti_continuous_no_pleio (const TTQuanti_continuous_no_pleio &TT)

virtual	~TTQuanti_continuous_no_pleio ()

virtual void	init_sequence ()

virtual TTQuanti_continuous_no_pleio *	clone ()

virtual void	show_up ()

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 strand, unsigned int from_locus, unsigned int to_locus, const TTQuanti *parent)

virtual void	copy_sequence_1locus (sex_t SEX, unsigned int strand, unsigned int at, const TTQuanti *parent)

Public Member Functions inherited from TTQuanti_continuous
	TTQuanti_continuous ()

	TTQuanti_continuous (const TTQuanti &T)

virtual	~TTQuanti_continuous ()

virtual void	reset ()

virtual void	init ()

virtual void	set_sequence (void **seq)

virtual void **	get_sequence () const

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 TTQuanti_continuous &	operator= (const TTrait &T)

virtual bool	operator== (const TTrait &T)

virtual bool	operator!= (const TTrait &T)

virtual void	store_data (BinaryStorageBuffer *saver)

virtual bool	retrieve_data (BinaryStorageBuffer *reader)

virtual double	get_full_genotype (unsigned int trait)

virtual void	set_allele (int locus, int allele, double value)

virtual void	mutate_add (unsigned int position, unsigned int allele, double value)

virtual void	mutate_inplace (unsigned int position, unsigned int allele, double value)

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)

Public Member Functions inherited from TTQuanti
	TTQuanti ()

	TTQuanti (const TTQuanti &T)

virtual	~TTQuanti ()

virtual trait_t	get_type () const

virtual void	mutate ()

virtual void	inherit (const TTrait mother, const TTrait father)

virtual void *	set_trait (void *value)

virtual void	set_value ()

virtual void *	getValue () const

void	set_proto (TProtoQuanti *proto)

TProtoQuanti *	get_proto ()

double	get_phenotype (unsigned int trai)

void	set_phenotype (unsigned int trait, double value)

void	reset_phenotype_to_genotypic_value ()

Public Member Functions inherited from TTrait
virtual	~TTrait ()

Public Member Functions inherited from StorableComponent
virtual	~StorableComponent ()

Additional Inherited Members
Protected Attributes inherited from TTQuanti_continuous
double **	_sequence

Protected Attributes inherited from TTQuanti
double *	_phenotypes

double *	_genotypic_values

TProtoQuanti *	_myProto

Detailed Description

TTQuanti_continuous_no_pleio : multiple non-pleiotropic traits.

Constructor & Destructor Documentation

◆ TTQuanti_continuous_no_pleio() [1/2]

TTQuanti_continuous_no_pleio::TTQuanti_continuous_no_pleio ( )

inline

229 : TTQuanti_continuous() {}

TTQuanti_continuous::TTQuanti_continuous

TTQuanti_continuous()

Definition: ttquanti.h:117

Referenced by clone().

Here is the caller graph for this function:

◆ TTQuanti_continuous_no_pleio() [2/2]

TTQuanti_continuous_no_pleio::TTQuanti_continuous_no_pleio ( const TTQuanti_continuous_no_pleio & TT )

inline

231 : TTQuanti_continuous(TT) {}

◆ ~TTQuanti_continuous_no_pleio()

virtual TTQuanti_continuous_no_pleio::~TTQuanti_continuous_no_pleio ( )

inlinevirtual

233 {}

Member Function Documentation

◆ clone()

virtual TTQuanti_continuous_no_pleio* TTQuanti_continuous_no_pleio::clone ( )

inlinevirtual

Implements TTrait.

237 {return new TTQuanti_continuous_no_pleio(*this);}

TTQuanti_continuous_no_pleio::TTQuanti_continuous_no_pleio

TTQuanti_continuous_no_pleio()

Definition: ttquanti.h:229

References TTQuanti_continuous_no_pleio().

◆ copy_sequence_1locus()

void TTQuanti_continuous_no_pleio::copy_sequence_1locus	(	sex_t	SEX,
		unsigned int	strand,
		unsigned int	at,
		const TTQuanti *	parent
	)

inlinevirtual

Implements TTQuanti.

 {
   const double *orig = (const double*)parent->get_sequence()[strand];
  
   _sequence[SEX][at] = orig[at];
 }

References TTQuanti_continuous::_sequence, and TTrait::get_sequence().

◆ copy_sequence_block()

void TTQuanti_continuous_no_pleio::copy_sequence_block	(	sex_t	SEX,
		unsigned int	strand,
		unsigned int	from_locus,
		unsigned int	to_locus,
		const TTQuanti *	parent
	)

inlinevirtual

Implements TTQuanti.

 {
   assert(to_locus >= from_locus);
  
   const double *orig = (const double*)parent->get_sequence()[strand];
   double *seq = _sequence[SEX];
  
   size_t block_size = (to_locus - from_locus) * _myProto->get_locus_byte_size();
  
   memcpy(&seq[from_locus], &orig[from_locus], block_size);
  
 }

References TTQuanti::_myProto, TTQuanti_continuous::_sequence, TProtoQuanti::get_locus_byte_size(), and TTrait::get_sequence().

◆ get_additive_genotype()

double TTQuanti_continuous_no_pleio::get_additive_genotype ( const unsigned int trait ) const

inlinevirtual

Implements TTQuanti.

 {
   double genotype = 0;
   unsigned int L = _myProto->get_num_locus(trait);          //number of loci affecting this trait
   unsigned int pos = _myProto->get_locus_seq_pos(0, trait); //starting position, all loci contiguous on the map
  
   // to help with vectorization:
   const double* __restrict__ s0 = _sequence[0] + pos;
   const double* __restrict__ s1 = _sequence[1] + pos;
  
   for (unsigned int j = 0; j < L; ++j)  genotype += s0[j] + s1[j];
  
 //  for(unsigned int j = 0; j < L; ++j, ++pos) {
 //    genotype += _sequence[0][pos] + _sequence[1][pos];
 //  }
  
   return genotype;
 }

References TTQuanti::_myProto, TTQuanti_continuous::_sequence, TProtoQuanti::get_locus_seq_pos(), and TProtoQuanti::get_num_locus().

◆ get_dominant_genotype()

double TTQuanti_continuous_no_pleio::get_dominant_genotype ( const unsigned int trait ) const

inlinevirtual

Implements TTQuanti.

 {
   double genotype = 0, k, a1, a2;
   unsigned int L = _myProto->get_num_locus(trait);          //number of loci affecting this trait
   unsigned int pos = _myProto->get_locus_seq_pos(0, trait); //starting position, all loci contiguous on the map
   unsigned int locID;
  
   const double* __restrict__ s0 = _sequence[0] + pos;
   const double* __restrict__ s1 = _sequence[1] + pos;
   const TMatrix& __restrict__ dom_coef = _myProto->get_dominance_effects();
  
 //  if(_myProto->has_equal_domCoeff()){
 //    k = dom_coef.get(trait, _myProto->get_locus_ID(0, trait));
 //    for (unsigned int j = 0; j < L; ++j) {
 //      double a1 = s0[j], a2 = s1[j];
 //      genotype += a1 + a2 + k * fabs(a2 - a1);
 //    }
 //    return genotype;
 //  }
 //
   //    double a1 = s0[j], a2 = s1[j];
   for (unsigned int j = 0; j < L; ++j) {
     locID = _myProto->get_locus_ID(j, trait);
 //    genotype += _myProto->get_genotype_dominance_k(s0[j], s1[j],
 //                                 _myProto->get_dominance(locID, trait));
     a1 = s0[j]; a2 = s1[j];
     k = dom_coef.get(trait, locID);
     genotype += a1 + a2 + k * fabs(a2 - a1);
   }
  
 //  for(unsigned int j = 0; j < L; ++j, ++pos) {
 //    locID = _myProto->get_locus_ID(j, trait);
 //    genotype += _myProto->get_genotype_dominance_k(_sequence[0][pos], _sequence[1][pos],
 //                             _myProto->get_dominance(locID, trait));
 //  }
  
   return genotype;
 }

References TTQuanti::_myProto, TTQuanti_continuous::_sequence, TProtoQuanti::get_dominance_effects(), TProtoQuanti::get_locus_ID(), TProtoQuanti::get_locus_seq_pos(), and TProtoQuanti::get_num_locus().

◆ init_sequence()

void TTQuanti_continuous_no_pleio::init_sequence ( )

inlinevirtual

Implements TTrait.

 {
   //  cout << "\nStart of TTQuanti_var_pleio::init_sequence!\t\n";
  
   //options:
   //0: no variation, init value = (trait value)/(2*_num_locus)
   //1: init value = (trait value)/(2*_num_locus) + 1 mutation/locus
   //2: init value = (trait value)/(2*_num_locus) + random deviate ~N(0, _init_variance/2*_num_locus)
  
   //Note: the initial values may have been set individually by LCE_quanti
   //      it wouldn't make sense then to store the init values in the prototype
   //      because init values are set patch-specific by LCE_quanti
   //      Problem: without LCE_quanti, the original init values must not change from one replicate
   //      to the other, so we use a local variable
  
  
   //set the allele values from the trait values
   double myinit, initSD;
   for(unsigned int i = 0; i < _myProto->get_num_traits(); ++i){ // process trait-wise
  
     myinit = _myProto->get_init_value(i) / (2 * _myProto->get_num_locus(i)); //divide by num loci affecting that trait
     initSD = sqrt(_myProto->get_init_variance(i)/(2*_myProto->get_num_locus(i)));
  
     for(unsigned int j = 0, pos = _myProto->get_locus_seq_pos(0, i); j < _myProto->get_num_locus(i); ++j, ++pos){
       _sequence[0][ pos ] = myinit;
       _sequence[1][ pos ] = myinit;
     }
  
     if(_myProto->get_doInitMutation() == 2) {
       // add a random deviate from a Normal distribution
       for(unsigned int j = 0, pos = _myProto->get_locus_seq_pos(0, i); j < _myProto->get_num_locus(i); ++j, ++pos){
         _sequence[0][ pos ] += RAND::Gaussian(initSD);
         _sequence[1][ pos ] += RAND::Gaussian(initSD);
       }
     }
  
   }
  
   //add random mutations to allele values
   if(_myProto->get_doInitMutation() == 1) {
  
     for(unsigned int i = 0; i < _myProto->get_num_locus(); i++) {
  
       _sequence[RAND::RandBool()][i] += _myProto->getMutationEffects(i)[0];
  
     }
   }
  
  
  
 }

References TTQuanti::_myProto, TTQuanti_continuous::_sequence, RAND::Gaussian(), TProtoQuanti::get_doInitMutation(), TProtoQuanti::get_init_value(), TProtoQuanti::get_init_variance(), TProtoQuanti::get_locus_seq_pos(), TProtoQuanti::get_num_locus(), TProtoQuanti::get_num_traits(), TProtoQuanti::getMutationEffects(), and RAND::RandBool().

◆ show_up()

void TTQuanti_continuous_no_pleio::show_up ( )

virtual

Implements TTrait.

 {
   message("\
           Trait's type: QUANTI (continuous, no pleiotropy)\n\
           traits: %i\n\
           loci: %i\n\
           seq length: %i\n",_myProto->get_num_traits(),_myProto->get_num_locus()
           ,_myProto->get_seq_length());
  
   for(unsigned int i = 0; i < _myProto->get_num_traits(); i++)
     message("phenotype %i: %f\n",i+1,_phenotypes[i]);
  
   message("genotype:");
  
    for(unsigned int i = 0; i < _myProto->get_num_traits(); ++i) {
  
      message("\ntrait %i (%i loci):\nloci: ",i+1, _myProto->get_num_locus(i));
  
      for(unsigned int j = 0; j < _myProto->get_num_locus(i); ++j) {
            message("%i, ", _myProto->get_locus_ID(j, i));
      }
  
      message("\n[0]: ");
  
      for(unsigned int j = 0; j < _myProto->get_num_locus(i); ++j) {
        message("%.3f,",_sequence[0][ _myProto->get_locus_seq_pos(j, i) ]);
      }
  
      message("\n[1]: ");
  
      for(unsigned int j = 0; j < _myProto->get_num_locus(i); ++j) {
        message("%.3f,",_sequence[1][ _myProto->get_locus_seq_pos(j, i) ]);
      }
    }
  
   message("\n");
  
 }