TTQuanti_diallelic_full_pleio_epistasis Class Reference

TTQuanti_diallelic_full_pleio : pleiotropic di-allelic loci, max PD = 2. More...

#include <ttquanti_epistasis.h>

Inheritance diagram for TTQuanti_diallelic_full_pleio_epistasis:

Collaboration diagram for TTQuanti_diallelic_full_pleio_epistasis:

Public Member Functions
	TTQuanti_diallelic_full_pleio_epistasis ()
	TTQuanti_diallelic_full_pleio_epistasis (const TTQuanti_diallelic_full_pleio_epistasis &TT)
virtual	~TTQuanti_diallelic_full_pleio_epistasis ()
virtual void	init_sequence ()
virtual TTQuanti_diallelic_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_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_full_pleio : pleiotropic di-allelic loci, max PD = 2.

Constructor & Destructor Documentation

TTQuanti_diallelic_full_pleio_epistasis() [1/2]

TTQuanti_diallelic_full_pleio_epistasis::TTQuanti_diallelic_full_pleio_epistasis ( )

inline

: TTQuanti_diallelic() {}

Referenced by clone().

TTQuanti_diallelic_full_pleio_epistasis() [2/2]

TTQuanti_diallelic_full_pleio_epistasis::TTQuanti_diallelic_full_pleio_epistasis ( const TTQuanti_diallelic_full_pleio_epistasis &  TT )

inline

                                                                                              :
    TTQuanti_diallelic(TT) {}

~TTQuanti_diallelic_full_pleio_epistasis()

virtual TTQuanti_diallelic_full_pleio_epistasis::~TTQuanti_diallelic_full_pleio_epistasis ( )

inlinevirtual

{}

Member Function Documentation

clone()

virtual TTQuanti_diallelic_full_pleio_epistasis* TTQuanti_diallelic_full_pleio_epistasis::clone ( )

inlinevirtual

Implements TTrait.

{return new TTQuanti_diallelic_full_pleio_epistasis(*this);}

References TTQuanti_diallelic_full_pleio_epistasis().

copy_sequence_1locus()

void TTQuanti_diallelic_full_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];
  unsigned char *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_diallelic::_sequence, TProtoQuanti::get_locus_byte_size(), TProtoQuanti::get_num_traits(), and TTrait::get_sequence().

copy_sequence_block()

void TTQuanti_diallelic_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.

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

get_additive_genotype()

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

inlinevirtual

Implements TTQuanti.

{
  double genotype = 0;
  unsigned int L = _myProto->get_num_locus();          //number of loci
  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) {
    genotypes[j] = _myProto->get_seq_diallele_value( pos, _sequence[0][pos] ) + _myProto->get_seq_diallele_value( pos, _sequence[1][pos] );
    pos += _myProto->get_num_traits(); // stride size on the genome (all loci affect each trait)
    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(), TProtoQuanti::get_num_traits(), and TProtoQuanti::get_seq_diallele_value().

get_dominant_genotype()

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

inlinevirtual

Implements TTQuanti.

{
  double genotype = 0;
  unsigned int L = _myProto->get_num_locus();                //number of loci
  unsigned int pos = _myProto->get_locus_seq_pos(0, trait); //starting position
  vector<double> genotypes(L,0);
 
 
  for(unsigned int j = 0; j < L; ++j) {
    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] ),
        j,
        trait);
    pos += _myProto->get_num_traits(); // stride size on the genome (all loci affect each 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_seq_pos(), TProtoQuanti::get_num_locus(), TProtoQuanti::get_num_traits(), and TProtoQuanti::get_seq_diallele_value().

get_epistatic_genotype()

double TTQuanti_diallelic_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) * 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_full_pleio_epistasis::init_sequence ( )

inlinevirtual

Implements TTrait.

{
  //options:
  //0: no variation, init value = one of each allele, mean value is average genotype
  //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_seq_length(); ++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 t = 0; t < _myProto->get_num_traits(); ++t) {
      for(unsigned int i = 0; i < _myProto->get_num_locus(t); i++) { // process trait-wise
        // even locus
        if (i % 2 == 0){
          _sequence[0][ _myProto->get_locus_seq_pos(i, t) ] = 0; //_myProto->get_allele_value(i, 0); //set with the positive allele value
          _sequence[1][ _myProto->get_locus_seq_pos(i, t) ] = 0; //_myProto->get_allele_value(i, 0);
        }
        else { // odd locus
          _sequence[1][ _myProto->get_locus_seq_pos(i, t) ] = 1; // = _myProto->get_allele_value(i, 1); //set with the alternate/negative allele value
          _sequence[0][ _myProto->get_locus_seq_pos(i, t) ] = 1; // = _myProto->get_allele_value(i, 1);
        }
      }
 
    }
  }
}

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

show_up()

void TTQuanti_diallelic_full_pleio_epistasis::show_up ( )

virtual

Implements TTrait.

{
  message("\
          Trait's type: QUANTI (diallelic, 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:");
 
  for(unsigned int i = 0; i < _myProto->get_num_traits(); ++i) {
 
    message("\nt%i (%i loci):\n[0]: ",i+1, _myProto->get_num_locus(i));
 
    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");
 
}

References TTQuanti::_myProto, TTQuanti::_phenotypes, TTQuanti_diallelic::_sequence, TProtoQuanti::get_locus_seq_pos(), TProtoQuanti::get_num_locus(), TProtoQuanti::get_num_traits(), TProtoQuanti::get_seq_length(), and message().

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The documentation for this class was generated from the following files:

• ttquanti_epistasis.h
• ttquanti_epistasis.cc