TTDispersal Class Reference

Evolving dispersal trait, codes for female (_type = FDISP) or male (_type = MDISP) sex-specific dispersal rates. More...

#include <ttdispersal.h>

Inheritance diagram for TTDispersal:

Collaboration diagram for TTDispersal:

Public Member Functions
	TTDispersal (sex_t sex)
	TTDispersal (const TTDispersal &TP)
virtual	~TTDispersal ()
Setters
void	set_mut_rate (double val)
void	set_mut_mean (double val)
void	set_init_rate_fem (double val)
void	set_init_rate_mal (double val)
void	set_gender (sex_t val)
void	set_proto (TProtoDispersal *P)
Implementations
virtual void	init ()
virtual void	init_sequence ()
virtual void	reset ()
virtual void	inherit (TTrait *mother, TTrait *father)
virtual void	mutate ()
virtual trait_t	get_type () const
virtual void	set_value ()
virtual void *	getValue () const
virtual void **	get_sequence () const
virtual double	get_allele_value (int loc, int all)
virtual void	set_allele_value (unsigned int locus, unsigned int allele, double value)
virtual void	set_sequence (void **seq)
virtual void *	set_trait (void *value)
virtual void	show_up ()
virtual TTDispersal *	clone ()
virtual TTDispersal &	operator= (const TTrait &TP)
virtual bool	operator== (const TTrait &TP)
virtual bool	operator!= (const TTrait &TP)
virtual void	store_data (BinaryStorageBuffer *saver)
virtual bool	retrieve_data (BinaryStorageBuffer *reader)
Public Member Functions inherited from TTrait
virtual void	init ()=0
	Called to allocate the trait's genotypic sequences. More...
virtual void	init_sequence ()=0
	Called at the start of each replicate, sets the initial genotypes. More...
virtual void	reset ()=0
	Called at the end of each simulation/replicate, deallocates sequence memory. More...
virtual void	inherit (TTrait *mother, TTrait *father)=0
	Inheritance procedure, creates a new trait from mother's and father's traits. More...
virtual void	mutate ()=0
	Mutation procedure, perform mutations on the genes sequence. More...
virtual void *	set_trait (void *value)=0
	Called to set the phenotypic to a particular value or to give context-dependant value(s) to the trait. More...
virtual void	set_sequence (void **seq)=0
	Called to set the sequence pointer to an existing trait. More...
virtual double	get_allele_value (int loc, int all)=0
	Called to read one allele value at a particular locus. More...
virtual void	set_allele_value (unsigned int locus, unsigned int allele, double value)=0
	Called to change the allelic value at a particular locus. More...
virtual void	set_value ()=0
	Tells the trait to set its phenotype from genotype, should be used instead of getValue(). More...
virtual void *	getValue () const =0
	Genotype to phenotype mapper. More...
virtual trait_t	get_type () const =0
	type accessor. More...
virtual void **	get_sequence () const =0
	sequence accessor. More...
virtual void	show_up ()=0
	Writes some info to stdout. More...
virtual TTrait *	clone ()=0
	Returns a copy of itself. More...
virtual	~TTrait ()
Public Member Functions inherited from StorableComponent
virtual void	store_data (BinaryStorageBuffer *saver)=0
	Interface to store the component data (e.g. gene values) into a binary buffer. More...
virtual bool	retrieve_data (BinaryStorageBuffer *reader)=0
	Interface to retrieve the same data from the binary buffer. More...
virtual	~StorableComponent ()

Private Attributes
double	_mut_rate
	The allelic mutation rate. More...
double	_mut_mean
	The mean mutation step. More...
double	_init_rate_fem
	Initial allele for female dispersal. More...
double	_init_rate_mal
	Initial allele for male dispersal. More...
TProtoDispersal *	_myProto
sex_t	_gender
	the gender of the trait, will determine its type. More...
double	_sequence [2]
	The trait's type. More...
double	_phenotype

Detailed Description

Evolving dispersal trait, codes for female (_type = FDISP) or male (_type = MDISP) sex-specific dispersal rates.

Constructor & Destructor Documentation

TTDispersal() [1/2]

TTDispersal::TTDispersal

(

sex_t

sex

)

Parameters

sex	determines the type of this trait (FDISP for female dispersal, MDISP for male dispersal)

: _mut_rate(0), _mut_mean(0.2), _init_rate_fem(-1.0), _init_rate_mal(-1.0), _myProto(0), 
  _gender(sex)
{
//  _type = (_gender == FEM ? FDISP : MDISP);
  _sequence[0] = _sequence[1] = 0;
}

References _sequence.

TTDispersal() [2/2]

TTDispersal::TTDispersal ( const TTDispersal &  TP )

inline

    : _mut_rate(TP._mut_rate), _mut_mean(TP._mut_mean), _init_rate_fem(TP._init_rate_fem), 
    _init_rate_mal(TP._init_rate_mal), _myProto(TP._myProto), _gender(TP._gender), _phenotype(0) //, _type(TP._type)
  {}

~TTDispersal()

virtual TTDispersal::~TTDispersal ( )

inlinevirtual

{ }

Member Function Documentation

clone()

virtual TTDispersal * TTDispersal::clone ( )

inlinevirtual

Implements TTrait.

{return new TTDispersal(*this);}

get_allele_value()

virtual double TTDispersal::get_allele_value ( int  loc, int  all  )

inlinevirtual

Implements TTrait.

{return ( !(all<2) ? 0 : _sequence[all] );}

References _sequence.

get_sequence()

virtual void ** TTDispersal::get_sequence ( ) const

inlinevirtual

Returns

NULL, here the _sequence is not a dble ptr.

Implements TTrait.

{return 0;}

get_type()

virtual trait_t TTDispersal::get_type ( ) const

inlinevirtual

Implements TTrait.

{return (_gender == FEM ? FDISP : MDISP);}

References _gender, FDISP, FEM, and MDISP.

Referenced by show_up().

Here is the caller graph for this function:

getValue()

virtual void * TTDispersal::getValue ( ) const

inlinevirtual

Returns

the dispersal rate, mean of the 2 alleles beard at this dispersal locus.

Implements TTrait.

{return (void*)&_phenotype;}

References _phenotype.

Referenced by show_up().

Here is the caller graph for this function:

inherit()

void TTDispersal::inherit ( TTrait *  mother, TTrait *  father  )

virtual

Implements TTrait.

{
//  if(mother->get_type() != _type || father->get_type() != _type)
//      fatal("TTDispersal::inherit::wrong parent's trait type \n");
  
  _sequence[0] = mother->get_allele_value(0,RAND::RandBool());
  _sequence[1] = father->get_allele_value(0,RAND::RandBool());
}

References _sequence, TTrait::get_allele_value(), and RAND::RandBool().

init()

virtual void TTDispersal::init ( )

inlinevirtual

Implements TTrait.

{ _sequence[0] = 0.0; _sequence[1] = 0.0; }

References _sequence.

Referenced by reset().

Here is the caller graph for this function:

init_sequence()

void TTDispersal::init_sequence ( )

virtual

Implements TTrait.

{
  TMatrix *params;
  unsigned int row;
  
  if ( _myProto->get_init_mode() ) { //this is random mode
    
    params = _myProto->get_init_dist_params();    
    
    if (params->getNbRows() == 2) // means different mean/sd for each sex
      row = _gender;
    else 
      row = 0;
    
    string option = _myProto->get_init_dist() ;
    
    if (option == "normal") {
      
      do { _sequence[0] = params->get(row, 0) + RAND::Gaussian(params->get(row, 1)); }
      while (_sequence[0] < 0.0 || _sequence[0] > 1.0);
      
      do { _sequence[1] = params->get(row, 0) + RAND::Gaussian(params->get(row, 1)); }
      while (_sequence[1] < 0.0 || _sequence[1] > 1.0);
 
    } else if (option == "uniform") {
      
      _sequence[0] = RAND::Uniform();
      _sequence[1] = RAND::Uniform();
      
    } else {
      fatal("dispersal init distribution \"%s\" is not implemented\n",_myProto->get_init_dist().c_str());
    }
    
    
  } else {
    
    _sequence[0] = (_gender == FEM ? _init_rate_fem : _init_rate_mal);
    _sequence[1] = (_gender == FEM ? _init_rate_fem : _init_rate_mal);
    
  }
}

References _gender, _init_rate_fem, _init_rate_mal, _myProto, _sequence, fatal(), FEM, RAND::Gaussian(), TMatrix::get(), TProtoDispersal::get_init_dist(), TProtoDispersal::get_init_dist_params(), TProtoDispersal::get_init_mode(), TMatrix::getNbRows(), and RAND::Uniform().

mutate()

void TTDispersal::mutate ( )

virtual

Implements TTrait.

{
  double step;
  
  unsigned int nbMut = (unsigned int)RAND::Poisson(2*_mut_rate);
  
  unsigned int mut_allele;
  
  for(unsigned int i = 0; i < nbMut; i++) {
    
    step =  -1.0 * _mut_mean * log(1 - RAND::Uniform());
    
    mut_allele = RAND::RandBool();
    
    if(RAND::RandBool())
      _sequence[mut_allele] = ((_sequence[i] + step) > 1.0 ? 1.0 : _sequence[mut_allele] + step);
    else
      _sequence[mut_allele] = ((_sequence[i] - step) < 0.0 ? 0.0 : _sequence[mut_allele] - step);
    
  }
 
}

References _mut_mean, _mut_rate, _sequence, RAND::Poisson(), RAND::RandBool(), and RAND::Uniform().

operator!=()

bool TTDispersal::operator!= ( const TTrait &  TP )

virtual

Implements TTrait.

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

operator=()

TTDispersal & TTDispersal::operator= ( const TTrait &  TP )

virtual

Implements TTrait.

{
  const TTDispersal& TD = dynamic_cast<const TTDispersal&> (T);
  
  if(this != &TD) {
    _gender = TD._gender;
//    _type = TD._type;
    _sequence[0] = TD._sequence[0];
    _sequence[1] = TD._sequence[1];
    _phenotype = TD._phenotype;
  }
  
  return *this;
}

References _gender, _phenotype, and _sequence.

operator==()

bool TTDispersal::operator== ( const TTrait &  TP )

virtual

Implements TTrait.

{
  const TTDispersal& TD = dynamic_cast<const TTDispersal&> (T);
  
  if(this != &TD) {
    if(_gender != TD._gender)  return false;
//    if(_type != TD._type)      return false;
  }
  
  return true;
}

References _gender.

reset()

virtual void TTDispersal::reset ( )

inlinevirtual

Implements TTrait.

{init();}

References init().

retrieve_data()

virtual bool TTDispersal::retrieve_data ( BinaryStorageBuffer *  reader )

inlinevirtual

Implements StorableComponent.

{reader->read(&_sequence, 2 * sizeof(double));return true;}

References _sequence, and BinaryStorageBuffer::read().

set_allele_value()

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

inlinevirtual

Implements TTrait.

    {assert(allele < 2); _sequence[allele] = value;}

References _sequence.

set_gender()

void TTDispersal::set_gender ( sex_t  val )

inline

{_gender = val;}

References _gender.

Referenced by TProtoDispersal::hatch().

Here is the caller graph for this function:

set_init_rate_fem()

void TTDispersal::set_init_rate_fem ( double  val )

inline

{_init_rate_fem = val;}

References _init_rate_fem.

Referenced by TProtoDispersal::hatch().

Here is the caller graph for this function:

set_init_rate_mal()

void TTDispersal::set_init_rate_mal ( double  val )

inline

{_init_rate_mal = val;}

References _init_rate_mal.

Referenced by TProtoDispersal::hatch().

Here is the caller graph for this function:

set_mut_mean()

void TTDispersal::set_mut_mean ( double  val )

inline

{_mut_mean = val;}

References _mut_mean.

Referenced by TProtoDispersal::hatch().

Here is the caller graph for this function:

set_mut_rate()

void TTDispersal::set_mut_rate ( double  val )

inline

{_mut_rate = val;}

References _mut_rate.

Referenced by TProtoDispersal::hatch().

Here is the caller graph for this function:

set_proto()

void TTDispersal::set_proto ( TProtoDispersal *  P )

inline

{_myProto = P;}

References _myProto.

Referenced by TProtoDispersal::hatch().

Here is the caller graph for this function:

set_sequence()

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

inlinevirtual

Implements TTrait.

{ }

set_trait()

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

inlinevirtual

Implements TTrait.

{return value;}

set_value()

virtual void TTDispersal::set_value ( )

inlinevirtual

Implements TTrait.

{_phenotype = (_sequence[0] + _sequence[1])/2.0;}

References _phenotype, and _sequence.

Referenced by show_up().

Here is the caller graph for this function:

show_up()

void TTDispersal::show_up ( )

virtual

Implements TTrait.

{
  set_value();
  message("\n  Trait type: %s\n\
       value: %f\n\
    _sequence: \n\
%f\n\
%f\n",get_type().c_str(), *(double*)getValue(), _sequence[0], _sequence[1]);
}

References _sequence, get_type(), getValue(), message(), and set_value().

store_data()

virtual void TTDispersal::store_data ( BinaryStorageBuffer *  saver )

inlinevirtual

Implements StorableComponent.

{saver->store(&_sequence, 2 * sizeof(double));}

References _sequence, and BinaryStorageBuffer::store().

Member Data Documentation

_gender

sex_t TTDispersal::_gender

private

the gender of the trait, will determine its type.

Referenced by get_type(), init_sequence(), operator=(), operator==(), and set_gender().

_init_rate_fem

double TTDispersal::_init_rate_fem

private

Initial allele for female dispersal.

Referenced by init_sequence(), and set_init_rate_fem().

_init_rate_mal

double TTDispersal::_init_rate_mal

private

Initial allele for male dispersal.

Referenced by init_sequence(), and set_init_rate_mal().

_mut_mean

double TTDispersal::_mut_mean

private

The mean mutation step.

Referenced by mutate(), and set_mut_mean().

_mut_rate

double TTDispersal::_mut_rate

private

The allelic mutation rate.

The mutation distribution is exponential, centered on the allelic value.

Referenced by mutate(), and set_mut_rate().

_myProto

TProtoDispersal* TTDispersal::_myProto

private

Referenced by init_sequence(), and set_proto().

_phenotype

double TTDispersal::_phenotype

private

Referenced by getValue(), operator=(), and set_value().

_sequence

double TTDispersal::_sequence[2]

private

The trait's type.

One diploid locus coding for a sex-specific dispersal rate.

Referenced by get_allele_value(), inherit(), init(), init_sequence(), mutate(), operator=(), retrieve_data(), set_allele_value(), set_value(), show_up(), store_data(), and TTDispersal().

---

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

• ttdispersal.h
• ttdispersal.cc