TTQuanti_continuous_full_pleio : universal pleiotropy. More...

#include <ttquanti_epistasis.h>

Inheritance diagram for TTQuanti_continuous_full_pleio_epistasis:

Collaboration diagram for TTQuanti_continuous_full_pleio_epistasis:

Public Member Functions
	TTQuanti_continuous_full_pleio_epistasis ()

	TTQuanti_continuous_full_pleio_epistasis (const TTQuanti_continuous_full_pleio_epistasis &TT)

virtual	~TTQuanti_continuous_full_pleio_epistasis ()

virtual void	init_sequence ()

virtual TTQuanti_continuous_full_pleio_epistasis *	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 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)

double	get_epistatic_genotype (const vector< double > &genotypes) const

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_full_pleio : universal pleiotropy.

Constructor & Destructor Documentation

◆ TTQuanti_continuous_full_pleio_epistasis() [1/2]

TTQuanti_continuous_full_pleio_epistasis::TTQuanti_continuous_full_pleio_epistasis ( )

inline

44 : TTQuanti_continuous() {}

TTQuanti_continuous::TTQuanti_continuous

TTQuanti_continuous()

Definition: ttquanti.h:118

Referenced by clone().

◆ TTQuanti_continuous_full_pleio_epistasis() [2/2]

TTQuanti_continuous_full_pleio_epistasis::TTQuanti_continuous_full_pleio_epistasis ( const TTQuanti_continuous_full_pleio_epistasis & TT )

inline

46 :

47 TTQuanti_continuous(TT) {}

◆ ~TTQuanti_continuous_full_pleio_epistasis()

virtual TTQuanti_continuous_full_pleio_epistasis::~TTQuanti_continuous_full_pleio_epistasis ( )

inlinevirtual

49 {}

Member Function Documentation

◆ clone()

virtual TTQuanti_continuous_full_pleio_epistasis* TTQuanti_continuous_full_pleio_epistasis::clone ( )

inlinevirtual

Implements TTrait.

53 {return new TTQuanti_continuous_full_pleio_epistasis(*this);}

TTQuanti_continuous_full_pleio_epistasis::TTQuanti_continuous_full_pleio_epistasis

TTQuanti_continuous_full_pleio_epistasis()

Definition: ttquanti_epistasis.h:44

References TTQuanti_continuous_full_pleio_epistasis().

◆ copy_sequence_1locus()

void TTQuanti_continuous_full_pleio_epistasis::copy_sequence_1locus	(	sex_t	SEX,
		unsigned int	chromosome,
		unsigned int	at,
		const TTQuanti *	parent
	)

inlinevirtual

Implements TTQuanti.

 {
   const double *orig = (const double*)parent->get_sequence()[chromosome];
   double *seq = _sequence[SEX];
   unsigned int from_pos = at * _myProto->get_num_traits();
  
   memcpy(&seq[from_pos], &orig[from_pos], _myProto->get_locus_byte_size());
 }

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

◆ copy_sequence_block()

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

inlinevirtual

Implements TTQuanti.

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

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

◆ get_additive_genotype()

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

inlinevirtual

Implements TTQuanti.

 {
   unsigned int loc = trait;  // initial position in the sequence, in the first locus
   unsigned int L = _myProto->get_num_locus(); // same for all traits
   vector<double> genotypes(L,0);
   double genotype = 0;
  
  
   for(unsigned int j = 0; j < L; ++j) {
     // alleles are ordered locus-trait: seq[0]:l0t0,l0t1,l0t2, ..., l1t0,l1t1,l1t2, ...
     genotypes[j] =  _sequence[0][loc] + _sequence[1][loc];
     loc += _myProto->get_num_traits(); // stride size on the genome, between loci
     genotype += genotypes[j];
   }
  
   return genotype + get_epistatic_genotype(genotypes);
 }

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

◆ get_dominant_genotype()

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

virtual

Implements TTQuanti.

 {
   unsigned int loc = trait; // position of first allele in the sequence at first locus
   unsigned int L = _myProto->get_num_locus(); // same for all traits
   vector<double> genotypes(L,0);
   double genotype = 0;
  
   for(unsigned int j = 0; j < L; ++j) {
     genotypes[j] = _myProto->get_genotype_with_dominance( _sequence[0][loc] , _sequence[1][loc], j, trait);
     loc += _myProto->get_num_traits(); // stride size on the genome, between loci
     genotype += genotypes[j];
   }
  
   return genotype + get_epistatic_genotype(genotypes);
 }

References TTQuanti::_myProto, TTQuanti_continuous::_sequence, get_epistatic_genotype(), TProtoQuanti::get_genotype_with_dominance(), TProtoQuanti::get_num_locus(), and TProtoQuanti::get_num_traits().

◆ get_epistatic_genotype()

double TTQuanti_continuous_full_pleio_epistasis::get_epistatic_genotype ( const vector< double > & genotypes ) const

inline

 {
   double genotype = 0;
  
   const TMatrix&  epi_loc_idx = _myProto->get_epi_coef_index();
   const TMatrix&  epi_coef    = _myProto->get_epi_coefs();
   unsigned int pos0, pos1;
  
   // now add the epistatic effects
   for(unsigned int i = 0; i < epi_coef.length(); ++i) {
  
     //  Note _epistatic_coefs_indices has dimensions [_nb_epi_coefs; 2]
     pos0 = epi_loc_idx.get(i,0);
     pos1 = epi_loc_idx.get(i,1);
  
 //    genotype += epi_coef.get(0,i)
 //                   * (_sequence[0][pos0] + _sequence[1][pos0])
 //                   * (_sequence[0][pos1] + _sequence[1][pos1]);
  
     genotype += epi_coef.get(0,i) * genotypes[pos0] * genotypes[pos1];
  
   }
  
   return genotype;
 }

References TTQuanti::_myProto, TMatrix::get(), TProtoQuanti::get_epi_coef_index(), TProtoQuanti::get_epi_coefs(), and TMatrix::length().

Referenced by get_additive_genotype(), and get_dominant_genotype().

◆ init_sequence()

void TTQuanti_continuous_full_pleio_epistasis::init_sequence ( )

inlinevirtual

Implements TTrait.

 {
 //  cout<<" TTQuanti_continuous_full_pleio_epistasis::init_sequence\n";
  
   //options:
   //0: no variation, init value = (trait value)/(2*_num_locus)
   //1: init value = (trait value)/(2*_num_locus) + 1 mutation/locus
   //2: only di-allelic
  
   //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
  
   double my_init[_myProto->get_num_traits()];
  
   for(unsigned int j = 0; j < _myProto->get_num_traits(); j++)
     my_init[j] = _myProto->get_init_value(j) / (2*_myProto->get_num_locus());
  
   unsigned int pos = 0;
  
   for(unsigned int j = 0; j < _myProto->get_num_traits(); ++j) {
     pos = j;
     //set the allele values from the init value, mutations may be added later
     for(unsigned int i = 0; i < _myProto->get_num_locus(); ++i) {
       _sequence[0][pos] = my_init[j];
       _sequence[1][pos] = my_init[j];
       pos += _myProto->get_num_traits();
     }
   }
  
   //add random effects to allele values if needed
   if(_myProto->get_doInitMutation() == 1) {
  
     double *mut;
  
     for(unsigned int i = 0; i < _myProto->get_num_locus(); i++) {
  
       pos = i * _myProto->get_num_traits();
  
       // change only one of the two allele at the locus, randomly
       mut = _myProto->getMutationEffects(i);
  
       for(unsigned int j = 0; j < _myProto->get_num_traits(); j++) {
         _sequence[RAND::RandBool()][pos] += mut[j];
         pos++;
       }
     } // end for_num_locus
   } // end if_doInit == 1
  
   // random deviate to initial additive effect
   if(_myProto->get_doInitMutation() == 2) {
  
     double initSD[_myProto->get_num_traits()];
  
     for(unsigned int j = 0; j < _myProto->get_num_traits(); j++) {
       initSD[j] = sqrt(_myProto->get_init_variance(j) / (2*_myProto->get_num_locus()) );
     }
  
     for(unsigned int i = 0; i < _myProto->get_num_locus(); i++) {
  
       pos = i * _myProto->get_num_traits();
  
       for(unsigned int j = 0; j < _myProto->get_num_traits(); j++) {
         _sequence[0][pos] += RAND::Gaussian(initSD[j]);
         _sequence[1][pos] += RAND::Gaussian(initSD[j]);
         pos++;
       }
     } // end for_num_locus
   } // end if_doInit == 2
  
 //  cout<<" TTQuanti_continuous_full_pleio_epistasis::init_sequence::end\n";
 }

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

◆ show_up()

void TTQuanti_continuous_full_pleio_epistasis::show_up ( )

virtual

Implements TTrait.

 {
   message("\
           Trait's type: QUANTI (continuous, full pleiotropy with epistasis)\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("_sequence: \n0:");
   unsigned int loc;
   for(unsigned int i = 0; i < _myProto->get_num_traits(); ++i) {
     message("\nt%i:",i+1);
     for(unsigned int j = 0; (j < _myProto->get_num_locus()); ++j) {
       loc = j * _myProto->get_num_traits() + i;
       message("%.3f,",_sequence[0][loc]);
     }
   }
   message("\n1:");
   for(unsigned int i = 0; i < _myProto->get_num_traits(); ++i) {
     message("\nt%i:",i+1);
     for(unsigned int j = 0; (j < _myProto->get_num_locus()); ++j) {
       loc = j * _myProto->get_num_traits() + i;
       message("%.3f,",_sequence[1][loc]);
     }
   }
   message("\n");
  
 }