TT_BDMI Class Reference

#include <ttbdmi.h>

Inheritance diagram for TT_BDMI:

Collaboration diagram for TT_BDMI:

Public Member Functions
	TT_BDMI ()
	TT_BDMI (const TT_BDMI &T)
virtual	~TT_BDMI ()
void	set_sequence (bitstring **seq)
void	inherit_haplo (const TTrait *mother, const TTrait *father)
void	inherit_diplo (const TTrait *mother, const TTrait *father)
void	mutate_haplo ()
void	mutate_diplo ()
double	viability_haplo ()
double	viability_diplo ()
unsigned int	get_num_mut_haplo (unsigned int loc)
unsigned int	get_num_mut_diplo (unsigned int loc)
const bitstring &	get_bit_sequence (bool chromosome) const
const bitstring *	get_genome_sequence () const
Setters:
void	set_proto (TProtoBDMI *proto)
Implementations
virtual void	init ()
virtual void	init_sequence ()
virtual void	reset ()
virtual void	inherit (const TTrait *mother, const TTrait *father)
virtual void	mutate ()
virtual void *	set_trait (void *value)
virtual void	set_sequence (void **seq)
virtual void	set_value ()
virtual void *	getValue () const
virtual trait_t	get_type () const
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 void	show_up ()
virtual TT_BDMI *	clone ()
virtual TT_BDMI &	operator= (const TTrait &)
virtual bool	operator== (const TTrait &)
virtual bool	operator!= (const TTrait &)
virtual void	store_data (BinaryStorageBuffer *saver)
virtual bool	retrieve_data (BinaryStorageBuffer *reader)
Public Member Functions inherited from TTrait
virtual	~TTrait ()
Public Member Functions inherited from StorableComponent
virtual	~StorableComponent ()

Private Attributes
TProtoBDMI *	_myProto
bitstring	_sequence [2]
double	_phenotype

Static Private Attributes
static unsigned int	_haploGenotCoding [2][2] = {{0,1},{2,3}}
static unsigned int	_diploGenotCoding [2][2] = {{0,1},{2,3}}

Constructor & Destructor Documentation

TT_BDMI() [1/2]

TT_BDMI::TT_BDMI ( )

inline

  : _myProto(0), _phenotype(0) {}

Referenced by clone().

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TT_BDMI() [2/2]

TT_BDMI::TT_BDMI ( const TT_BDMI &  T )

inline

  : _myProto(T._myProto), _phenotype(0){}

~TT_BDMI()

virtual TT_BDMI::~TT_BDMI ( )

inlinevirtual

{ }

Member Function Documentation

clone()

virtual TT_BDMI* TT_BDMI::clone ( )

inlinevirtual

Implements TTrait.

{return new TT_BDMI(*this);}

References TT_BDMI().

get_allele()

unsigned int TT_BDMI::get_allele ( int  loc, int  all  ) const

virtual

Implements TTrait.

{
  assert(loc < _myProto->get_locus_number() && all < 2);
  return (unsigned int)_sequence[all][loc];
}

References _sequence.

get_allele_value()

double TT_BDMI::get_allele_value ( int  loc, int  all  ) const

virtual

Implements TTrait.

{
  if(_myProto->_isHaploid)
          return _myProto->getGenoFitnessHaplo(loc, all);
  else
          return _myProto->getGenoFitnessDiplo(loc, all);
}

References TProtoBDMI::_isHaploid, _myProto, TProtoBDMI::getGenoFitnessDiplo(), and TProtoBDMI::getGenoFitnessHaplo().

get_bit_sequence()

const bitstring& TT_BDMI::get_bit_sequence ( bool  chromosome ) const

inline

{return _sequence[chromosome];}

References _sequence.

Referenced by inherit_haplo().

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get_genome_sequence()

const bitstring* TT_BDMI::get_genome_sequence ( ) const

inline

{return &_sequence[0];}

References _sequence.

Referenced by inherit_diplo(), TTBDMI_FH::write_diplo(), and TTBDMI_FH::write_haplo().

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get_num_mut_diplo()

unsigned int TT_BDMI::get_num_mut_diplo ( unsigned int  loc )

inline

{return _sequence[0][loc] + _sequence[1][loc];}

References _sequence.

Referenced by TTBDMI_SH::countAllele_diplo().

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get_num_mut_haplo()

unsigned int TT_BDMI::get_num_mut_haplo ( unsigned int  loc )

inline

{return _sequence[0][loc];}

References _sequence.

Referenced by TTBDMI_SH::countAllele_haplo().

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get_sequence()

virtual void** TT_BDMI::get_sequence ( ) const

inlinevirtual

Implements TTrait.

                                                         {
    error("calling TT_BDMI::get_sequence()\n");
    return (void**)NULL;
  }

References error().

get_type()

virtual trait_t TT_BDMI::get_type ( ) const

inlinevirtual

Implements TTrait.

{return _myProto->get_type();}

References _myProto, and TProtoBDMI::get_type().

getValue()

virtual void* TT_BDMI::getValue ( ) const

inlinevirtual

Implements TTrait.

{return (void*)&_phenotype;}

References _phenotype.

Referenced by show_up(), TTBDMI_FH::write_diplo(), and TTBDMI_FH::write_haplo().

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inherit()

void TT_BDMI::inherit ( const TTrait *  mother, const TTrait *  father  )

virtual

Implements TTrait.

{
  (this->* _myProto->_inherit_func_ptr) (mother, father);
}

References TProtoBDMI::_inherit_func_ptr, and _myProto.

inherit_diplo()

void TT_BDMI::inherit_diplo	(	const TTrait *	mother,
		const TTrait *	father
	)

{
  const bitstring* mother_seq = dynamic_cast<const TT_BDMI*>(mother)->get_genome_sequence();
  const bitstring* father_seq = dynamic_cast<const TT_BDMI*>(father)->get_genome_sequence();
  
  _myProto->gamete_recombination(FEM, _sequence[FEM], mother_seq);
  _myProto->gamete_recombination(MAL, _sequence[MAL], father_seq);
}

References _myProto, _sequence, FEM, TProtoBDMI::gamete_recombination(), get_genome_sequence(), and MAL.

Referenced by TProtoBDMI::setParameters().

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inherit_haplo()

void TT_BDMI::inherit_haplo	(	const TTrait *	mother,
		const TTrait *	father
	)

{
  bitstring diplogenome[2]; //build a diploid genome; but we copy the incoming sequences, not great...
  diplogenome[0] = dynamic_cast<const TT_BDMI*>(mother)->get_bit_sequence(0);
  diplogenome[1] = dynamic_cast<const TT_BDMI*>(father)->get_bit_sequence(0);
 
  _myProto->gamete_recombination(sex_t(0), _sequence[0], &diplogenome[0]);
}

References _myProto, _sequence, TProtoBDMI::gamete_recombination(), and get_bit_sequence().

Referenced by TProtoBDMI::setParameters().

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init()

void TT_BDMI::init ( )

virtual

Implements TTrait.

{  
  
  _sequence[0].reset(_myProto->_num_locus);
 
  if(!_myProto->_isHaploid)
    _sequence[1].reset(_myProto->_num_locus);
}

References TProtoBDMI::_isHaploid, _myProto, TProtoBDMI::_num_locus, _sequence, and bitstring::reset().

Referenced by operator=(), and set_sequence().

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init_sequence()

void TT_BDMI::init_sequence ( )

virtual

Implements TTrait.

{
  _sequence[0].reset(_myProto->_num_locus);  //sets all bits to 0
 
  if(!_myProto->_isHaploid){
 
    _sequence[1].reset(_myProto->_num_locus);
  }
 
  if(_myProto->isInitSet()) {
 
    for(unsigned int i = 0; i < _myProto->_num_locus; i++) {
 
      if( RAND::Uniform() < _myProto->get_init_freq(i) ) 
        _sequence[0].set(i);
      
      if( !_myProto->_isHaploid )
        if ( RAND::Uniform() < _myProto->get_init_freq(i) )
          _sequence[1].set(i);
    } 
  }
 
}

References TProtoBDMI::_isHaploid, _myProto, TProtoBDMI::_num_locus, _sequence, TProtoBDMI::get_init_freq(), TProtoBDMI::isInitSet(), bitstring::reset(), bitstring::set(), and RAND::Uniform().

Referenced by LCE_Init_BDMI::init_value().

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mutate()

void TT_BDMI::mutate ( )

inlinevirtual

Implements TTrait.

{
  (this->*_myProto->_mutation_func_ptr)();
}

References TProtoBDMI::_mutation_func_ptr, and _myProto.

mutate_diplo()

void TT_BDMI::mutate_diplo ( )

inline

{
  unsigned int NbMut;
  
  NbMut = (unsigned int)RAND::Poisson(_myProto->_genomic_mut_rate);
  
  while(NbMut != 0) {  
    
    _sequence[ RAND::RandBool() ].flip(  RAND::Uniform( _myProto->_num_locus ) );
    
    NbMut--;
  }
}

References TProtoBDMI::_genomic_mut_rate, _myProto, TProtoBDMI::_num_locus, _sequence, bitstring::flip(), RAND::Poisson(), RAND::RandBool(), and RAND::Uniform().

Referenced by TProtoBDMI::setParameters().

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mutate_haplo()

void TT_BDMI::mutate_haplo ( )

inline

{
  unsigned int NbMut;
  
  NbMut = (unsigned int)RAND::Poisson(_myProto->_genomic_mut_rate);
  
  while(NbMut != 0) {  
    
    _sequence[0].flip(  RAND::Uniform( _myProto->_num_locus ) );
    
    NbMut--;
  }
}

References TProtoBDMI::_genomic_mut_rate, _myProto, TProtoBDMI::_num_locus, _sequence, bitstring::flip(), RAND::Poisson(), and RAND::Uniform().

Referenced by TProtoBDMI::setParameters().

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operator!=()

bool TT_BDMI::operator!= ( const TTrait &  T )

virtual

Implements TTrait.

{
  if(!((*this) == T))
    return true;
  else
    return false;
}

operator=()

TT_BDMI & TT_BDMI::operator= ( const TTrait &  T )

virtual

Implements TTrait.

{
  const TT_BDMI& TD = dynamic_cast<const TT_BDMI&> (T);
  if(this != &TD) {
    
    _myProto->_num_locus = TD._myProto->_num_locus;
//    _mut_rate = TD._mut_rate;
//    _recomb_rate = TD._recomb_rate;
//    _genomic_mut_rate = TD._genomic_mut_rate;
    _myProto->_isHaploid = TD._myProto->_isHaploid;
//    _inherit_func_ptr = TD._inherit_func_ptr;
//    _mutation_func_ptr = TD._mutation_func_ptr;
//    _viability_func_ptr = TD._viability_func_ptr;
    //deallocate any previous _sequence memory:
    reset();
    //allocate _sequence memory:
    init();
    //copy _sequence:
    _sequence[0].copy(TD._sequence[0]);
    if(!_myProto->_isHaploid) _sequence[1].copy(TD._sequence[1]);
    
    set_value();
  }
  return *this;
}

References TProtoBDMI::_isHaploid, _myProto, TProtoBDMI::_num_locus, _sequence, bitstring::copy(), init(), reset(), and set_value().

operator==()

bool TT_BDMI::operator== ( const TTrait &  T )

virtual

Implements TTrait.

{
  if(_myProto->get_type().compare(T.get_type()) != 0) return false;
  
  const TT_BDMI& TD = dynamic_cast<const TT_BDMI&> (T);
  if(this != &TD) {
    if(_myProto->_num_locus != TD._myProto->_num_locus) return false;
    if(_myProto->_isHaploid != TD._myProto->_isHaploid) return false;
  }
  return true;
}

References TProtoBDMI::_isHaploid, _myProto, TProtoBDMI::_num_locus, TProtoBDMI::get_type(), and TTrait::get_type().

reset()

void TT_BDMI::reset ( )

virtual

Implements TTrait.

{
  _sequence[0].reset();
  _sequence[1].reset();
}

References _sequence, and bitstring::reset().

Referenced by operator=(), and set_sequence().

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retrieve_data()

bool TT_BDMI::retrieve_data ( BinaryStorageBuffer *  reader )

virtual

Implements StorableComponent.

{
  size_t wnb = _sequence[0].nb_words();
  size_t bytes = wnb * sizeof(bitstring::_ul);
  bitstring::_ul *srce = new bitstring::_ul [wnb];
 
  reader->read(srce, bytes);
  _sequence[0].set_data(srce,wnb);
 
  if(!_myProto->_isHaploid){
    reader->read(srce, bytes);
    _sequence[1].set_data(srce,wnb);
  }
 
  delete [] srce;
 
  return true;
}

References TProtoBDMI::_isHaploid, _myProto, _sequence, bitstring::nb_words(), BinaryStorageBuffer::read(), and bitstring::set_data().

set_allele_value()

void TT_BDMI::set_allele_value ( unsigned int  locus, unsigned int  allele, double  value  )

virtual

Implements TTrait.

{
  _myProto->setGenoFitnessValue(locus, allele, value);
}

References _myProto, and TProtoBDMI::setGenoFitnessValue().

set_proto()

void TT_BDMI::set_proto ( TProtoBDMI *  proto )

inline

{_myProto = proto;}

References _myProto.

Referenced by TProtoBDMI::hatch().

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set_sequence() [1/2]

void TT_BDMI::set_sequence

(

bitstring **

seq

)

{
  reset();
  init();
 
  _sequence[0].copy(*seq[0]);
 
  if(!_myProto->_isHaploid) _sequence[1].copy(*seq[1]);
}

References TProtoBDMI::_isHaploid, _myProto, _sequence, bitstring::copy(), init(), and reset().

set_sequence() [2/2]

virtual void TT_BDMI::set_sequence ( void **  seq )

inlinevirtual

Implements TTrait.

{}

set_trait()

virtual void* TT_BDMI::set_trait ( void *  value )

inlinevirtual

Implements TTrait.

{return NULL;}

set_value()

void TT_BDMI::set_value ( )

inlinevirtual

Implements TTrait.

{
  _phenotype = (this->*_myProto->_viability_func_ptr)();
}

References _myProto, _phenotype, and TProtoBDMI::_viability_func_ptr.

Referenced by LCE_Init_BDMI::init_value(), operator=(), and show_up().

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show_up()

void TT_BDMI::show_up ( )

virtual

Implements TTrait.

{
  set_value();
  std::cout<<"\n   Trait type: dmi"
  <<"\n        value: "<<*(double*)getValue()
  <<"\n     num loci: "<<_myProto->_num_locus
  <<"\nfitness table: "<<endl;
  _myProto->showGenoTable(_myProto->_npair);
  
  cout<<"\n     sequence: "<<endl;
  cout<<"0: ";
  for(unsigned int i = 0; i < _myProto->_num_locus && i < 64; i++)
    cout<<(unsigned int)_sequence[0][i];
  cout<<endl;
  
  if(!_myProto->_isHaploid) {
    cout<<"1: ";
    for(unsigned int i = 0; i < _myProto->_num_locus && i < 64; i++)
      cout<<(unsigned int)_sequence[1][i];
  }
  cout<<endl;
}

References TProtoBDMI::_isHaploid, _myProto, TProtoBDMI::_npair, TProtoBDMI::_num_locus, _sequence, getValue(), set_value(), and TProtoBDMI::showGenoTable().

store_data()

void TT_BDMI::store_data ( BinaryStorageBuffer *  saver )

virtual

Implements StorableComponent.

{
  size_t wnb = _sequence[0].nb_words();
  size_t bytes = sizeof(bitstring::_ul);
 
  for(size_t i = 0; i < wnb; i++)
    saver->store(_sequence[0].getword_atIdx(i), bytes);
 
  if(!_myProto->_isHaploid){
    for(size_t i = 0; i < wnb; i++)
      saver->store(_sequence[1].getword_atIdx(i), bytes);
  }
}

References TProtoBDMI::_isHaploid, _myProto, _sequence, bitstring::getword_atIdx(), bitstring::nb_words(), and BinaryStorageBuffer::store().

viability_diplo()

double TT_BDMI::viability_diplo ( )

inline

{
  double viab = 1;
//cout << "\nTT_BDMI::viability_diplo\n";
//  cout << "  sequence[0].size(): "<<(*_sequence[0]).size()
//  << "  sequence[0].nb_words(): "<<(*_sequence[0]).nb_words()<<endl;
//  cout << "  sequence[1].size(): "<<(*_sequence[1]).size()
//  << "  sequence[1].nb_words(): "<<(*_sequence[1]).nb_words()<<endl;
  
  for (unsigned int pair = 0, i = 0; pair < _myProto->_npair && i < _myProto->_num_locus; ++pair) {
    viab *= 1 + _myProto->getGenoFitnessDiplo( pair , //locus number
            _diploGenotCoding[ _sequence[0][i] ][ _sequence[1][i] ], //first locus
            _diploGenotCoding[ _sequence[0][i+1] ][ _sequence[1][i+1] ]); //second locus
    i += 2;
  }
  return viab; 
}

References _diploGenotCoding, _myProto, TProtoBDMI::_npair, TProtoBDMI::_num_locus, _sequence, and TProtoBDMI::getGenoFitnessDiplo().

Referenced by TProtoBDMI::setParameters().

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viability_haplo()

double TT_BDMI::viability_haplo ( )

inline

{
  double viab = 1;
  
  for (unsigned int pair = 0, i = 0; pair < _myProto->_npair && i < _myProto->_num_locus; ++pair) {
    viab *= 1 + _myProto->getGenoFitnessHaplo( pair , 
                          _haploGenotCoding[ _sequence[0][i] ][ _sequence[0][i+1] ]);
    i += 2;
  }
  return viab;
}

References _haploGenotCoding, _myProto, TProtoBDMI::_npair, TProtoBDMI::_num_locus, _sequence, and TProtoBDMI::getGenoFitnessHaplo().

Referenced by TProtoBDMI::setParameters().

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Member Data Documentation

_diploGenotCoding

unsigned int TT_BDMI::_diploGenotCoding = {{0,1},{2,3}}

staticprivate

Referenced by viability_diplo().

_haploGenotCoding

unsigned int TT_BDMI::_haploGenotCoding = {{0,1},{2,3}}

staticprivate

Referenced by viability_haplo().

_myProto

TProtoBDMI* TT_BDMI::_myProto

private

Referenced by get_allele_value(), get_type(), inherit(), inherit_diplo(), inherit_haplo(), init(), init_sequence(), mutate(), mutate_diplo(), mutate_haplo(), operator=(), operator==(), retrieve_data(), set_allele_value(), set_proto(), set_sequence(), set_value(), show_up(), store_data(), viability_diplo(), and viability_haplo().

_phenotype

double TT_BDMI::_phenotype

private

Referenced by getValue(), and set_value().

_sequence

bitstring TT_BDMI::_sequence[2]

private

Referenced by get_allele(), get_bit_sequence(), get_genome_sequence(), get_num_mut_diplo(), get_num_mut_haplo(), inherit_diplo(), inherit_haplo(), init(), init_sequence(), mutate_diplo(), mutate_haplo(), operator=(), reset(), retrieve_data(), set_sequence(), show_up(), store_data(), viability_diplo(), and viability_haplo().

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

• ttbdmi.h
• ttbdmi.cc