TTQuanti_diallelic_no_pleio_epistasis : single or multiple non-pleiotropic traits, di-allelic. More...

#include <ttquanti_epistasis.h>

Inheritance diagram for TTQuanti_diallelic_no_pleio_epistasis:

Collaboration diagram for TTQuanti_diallelic_no_pleio_epistasis:

Public Member Functions
	TTQuanti_diallelic_no_pleio_epistasis ()

	TTQuanti_diallelic_no_pleio_epistasis (const TTQuanti_diallelic_no_pleio_epistasis &TT)

virtual	~TTQuanti_diallelic_no_pleio_epistasis ()

virtual void	init_sequence ()

virtual TTQuanti_diallelic_no_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_diallelic
	TTQuanti_diallelic ()

	TTQuanti_diallelic (const TTQuanti &T)

virtual	~TTQuanti_diallelic ()

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	inherit_free (const TTrait mother, const TTrait father)

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 locus, int allele) const

virtual void	set_allele_value (unsigned int locus, unsigned int allele, double value)

virtual TTQuanti_diallelic &	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)

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_diallelic
unsigned char **	_sequence

Protected Attributes inherited from TTQuanti
double *	_phenotypes

double *	_genotypic_values

TProtoQuanti *	_myProto

Detailed Description

TTQuanti_diallelic_no_pleio_epistasis : single or multiple non-pleiotropic traits, di-allelic.

Constructor & Destructor Documentation

◆ TTQuanti_diallelic_no_pleio_epistasis() [1/2]

TTQuanti_diallelic_no_pleio_epistasis::TTQuanti_diallelic_no_pleio_epistasis ( )

inline

132 : TTQuanti_diallelic() {}

TTQuanti_diallelic::TTQuanti_diallelic

TTQuanti_diallelic()

Definition: ttquanti.h:285

Referenced by clone().

◆ TTQuanti_diallelic_no_pleio_epistasis() [2/2]

TTQuanti_diallelic_no_pleio_epistasis::TTQuanti_diallelic_no_pleio_epistasis ( const TTQuanti_diallelic_no_pleio_epistasis & TT )

inline

134 :

135 TTQuanti_diallelic(TT) {}

◆ ~TTQuanti_diallelic_no_pleio_epistasis()

virtual TTQuanti_diallelic_no_pleio_epistasis::~TTQuanti_diallelic_no_pleio_epistasis ( )

inlinevirtual

137 {}

Member Function Documentation

◆ clone()

virtual TTQuanti_diallelic_no_pleio_epistasis* TTQuanti_diallelic_no_pleio_epistasis::clone ( )

inlinevirtual

Implements TTrait.

141 {return new TTQuanti_diallelic_no_pleio_epistasis(*this);}

TTQuanti_diallelic_no_pleio_epistasis::TTQuanti_diallelic_no_pleio_epistasis

TTQuanti_diallelic_no_pleio_epistasis()

Definition: ttquanti_epistasis.h:132

References TTQuanti_diallelic_no_pleio_epistasis().

◆ copy_sequence_1locus()

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

inlinevirtual

Implements TTQuanti.

 {
   const unsigned char *orig = (const unsigned char*)parent->get_sequence()[chromosome];
  
   _sequence[SEX][at] = orig[at];
 }

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

◆ copy_sequence_block()

void TTQuanti_diallelic_no_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 unsigned char *orig = (const unsigned char*)(parent->get_sequence()[chromosome]);
   unsigned char *seq = _sequence[SEX];
  
   assert(to_locus >= from_locus);
  
   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_diallelic::_sequence, TProtoQuanti::get_locus_byte_size(), and TTrait::get_sequence().

◆ get_additive_genotype()

double TTQuanti_diallelic_no_pleio_epistasis::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
   vector<double> genotypes(L,0);
  
   for(unsigned int j = 0; j < L; ++j, ++pos) {
     genotypes[j] = _myProto->get_seq_diallele_value( pos, _sequence[0][pos] )
         + _myProto->get_seq_diallele_value( pos, _sequence[1][pos] );
     genotype += genotypes[j];
   }
  
   return genotype  + get_epistatic_genotype(genotypes);
 }

References TTQuanti::_myProto, TTQuanti_diallelic::_sequence, get_epistatic_genotype(), TProtoQuanti::get_locus_seq_pos(), TProtoQuanti::get_num_locus(), and TProtoQuanti::get_seq_diallele_value().

◆ get_dominant_genotype()

double TTQuanti_diallelic_no_pleio_epistasis::get_dominant_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
   unsigned int locID;
   vector<double> genotypes(L,0);
  
   for(unsigned int j = 0; j < L; ++j, ++pos) {
     locID = _myProto->get_locus_ID(j, trait);
     genotypes[j] = _myProto->get_genotype_with_dominance(
         _myProto->get_seq_diallele_value( pos, _sequence[0][pos] ) ,
         _myProto->get_seq_diallele_value( pos, _sequence[1][pos] ),
         locID,
         trait);
     genotype += genotypes[j];
   }
  
  
   return genotype + get_epistatic_genotype(genotypes);
 }

References TTQuanti::_myProto, TTQuanti_diallelic::_sequence, get_epistatic_genotype(), TProtoQuanti::get_genotype_with_dominance(), TProtoQuanti::get_locus_ID(), TProtoQuanti::get_locus_seq_pos(), TProtoQuanti::get_num_locus(), and TProtoQuanti::get_seq_diallele_value().

◆ get_epistatic_genotype()

double TTQuanti_diallelic_no_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) * double(genotypes[pos0]) * double(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_diallelic_no_pleio_epistasis::init_sequence ( )

inlinevirtual

Implements TTrait.

 {
   //options:
   //0: no variation, all allele are set to allele 0
   //1: max variation, randomly set alleles at each locus
   //2: no variation and initialize with opposite effect alleles at alternating loci.
  
  
   if (_myProto->get_doInitMutation() == 0){
  
     memset(_sequence[0], 0, _myProto->get_seq_length());
     memset(_sequence[1], 0, _myProto->get_seq_length());
  
   } else  if (_myProto->get_doInitMutation() == 1) {
  
     for(unsigned int i = 0; i < _myProto->get_num_locus(); ++i) {
  
       // randomly set the allelic values
       _sequence[0][ i ] = RAND::RandBool();
       _sequence[1][ i ] = RAND::RandBool();
  
     }
  
   } else {
     //option 2; polarized di-allelic values; even locus set to +a, odd locus set to -a
  
     for(unsigned int i = 0; i < _myProto->get_num_locus(); i++) { // process trait-wise
       // no need to set to 0 since it was initialized that way
       if (i % 2 == 0){
         _sequence[0][ i ] = 0; //_myProto->get_allele_value(i, 0); //set with the positive allele value
         _sequence[1][ i ] = 0; //_myProto->get_allele_value(i, 0);
       }
       else { // odd locus
         _sequence[1][ i ] = 1; // = _myProto->get_allele_value(i, 1); //set with the alternate/negative allele value
         _sequence[0][ i ] = 1; // = _myProto->get_allele_value(i, 1);
       }
     }
   }
  
 }

References TTQuanti::_myProto, TTQuanti_diallelic::_sequence, TProtoQuanti::get_doInitMutation(), TProtoQuanti::get_num_locus(), TProtoQuanti::get_seq_length(), and RAND::RandBool().

◆ show_up()

void TTQuanti_diallelic_no_pleio_epistasis::show_up ( )

virtual

Implements TTrait.

 {
   message("\
           Trait's type: QUANTI (diallelic, no 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("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,",(double)_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,",(double)_sequence[1][ _myProto->get_locus_seq_pos(j, i) ]);
     }
   }
  
   message("\n");
  
 }