TTWolbachia Class Reference

Trait used to study the dynamics of spread of Wolbachia, an endosymbiotic parasite causing cytoplasmic incompatibility. More...

#include <ttwolbachia.h>

Inheritance diagram for TTWolbachia:

Collaboration diagram for TTWolbachia:

Public Member Functions
	TTWolbachia ()
	TTWolbachia (const TTWolbachia &T)
virtual	~TTWolbachia ()
void	set_transmit_rate (double val)
virtual void	init ()
virtual void	init_sequence ()
virtual void	reset ()
virtual void	inherit (TTrait *mother, 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 double	get_allele_value (int loc, int all)
virtual void	set_allele_value (unsigned int locus, unsigned int allele, double value)
virtual void	show_up ()
virtual TTWolbachia *	clone ()
virtual TTWolbachia &	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)
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	_transmit_rate
bool	_is_infected

Detailed Description

Trait used to study the dynamics of spread of Wolbachia, an endosymbiotic parasite causing cytoplasmic incompatibility.

The trait state is given by a unique haploid "gene" with two alleles, 0 = uninfected and 1 = infected.

Constructor & Destructor Documentation

TTWolbachia() [1/2]

TTWolbachia::TTWolbachia ( )

inline

    : _transmit_rate(0), _is_infected(0) { }

Referenced by clone().

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TTWolbachia() [2/2]

TTWolbachia::TTWolbachia ( const TTWolbachia &  T )

inline

    : _transmit_rate(T._transmit_rate), _is_infected(T._is_infected) { }

~TTWolbachia()

virtual TTWolbachia::~TTWolbachia ( )

inlinevirtual

{}

Member Function Documentation

clone()

virtual TTWolbachia * TTWolbachia::clone ( )

inlinevirtual

Implements TTrait.

{return new TTWolbachia(*this);}

References TTWolbachia().

get_allele_value()

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

inlinevirtual

Implements TTrait.

{return _is_infected;}  

References _is_infected.

get_sequence()

virtual void ** TTWolbachia::get_sequence ( ) const

inlinevirtual

Implements TTrait.

{return NULL;}  

get_type()

virtual trait_t TTWolbachia::get_type ( ) const

inlinevirtual

Implements TTrait.

{return WOLB;}

References WOLB.

Referenced by operator==().

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getValue()

virtual void * TTWolbachia::getValue ( ) const

inlinevirtual

Implements TTrait.

{return (void*)&_is_infected;}

References _is_infected.

inherit()

virtual void TTWolbachia::inherit ( TTrait *  mother, TTrait *  father  )

inlinevirtual

Implements TTrait.

  {  _is_infected = *(bool*)mother->getValue();  }

References _is_infected, and TTrait::getValue().

init()

virtual void TTWolbachia::init ( )

inlinevirtual

Implements TTrait.

{_is_infected = 0;}

References _is_infected.

init_sequence()

virtual void TTWolbachia::init_sequence ( )

inlinevirtual

Implements TTrait.

{_is_infected = 0;}

References _is_infected.

mutate()

virtual void TTWolbachia::mutate ( )

inlinevirtual

Implements TTrait.

  {  _is_infected &= (RAND::Uniform() < _transmit_rate);  }  

References _is_infected, _transmit_rate, and RAND::Uniform().

operator!=()

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

virtual

Implements TTrait.

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

operator=()

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

virtual

Implements TTrait.

{
  const TTWolbachia& TD = dynamic_cast<const TTWolbachia&> (T);
  if(this != &TD) {
    _is_infected = TD._is_infected;
//    _transmit_rate = TD._transmit_rate;
  }
  return *this;
}

References _is_infected.

operator==()

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

virtual

Implements TTrait.

{
  if(this->get_type().compare(T.get_type()) != 0) return false;
//  const TTWolbachia& TD = dynamic_cast<const TTWolbachia&> (T);
//  if(this != &TD) {
//    if(_transmit_rate != TD._transmit_rate) return false;
//  }
  return true;
}

References get_type(), and TTrait::get_type().

reset()

virtual void TTWolbachia::reset ( )

inlinevirtual

Implements TTrait.

{_is_infected = 0;}

References _is_infected.

retrieve_data()

virtual bool TTWolbachia::retrieve_data ( BinaryStorageBuffer *  reader )

inlinevirtual

Implements StorableComponent.

  {
    unsigned char dummy;
    reader->read(&dummy, 1);
    _is_infected = dummy;
    return true;
  }

References _is_infected, and BinaryStorageBuffer::read().

set_allele_value()

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

inlinevirtual

Implements TTrait.

{_is_infected=(bool)value;}  

References _is_infected.

set_sequence()

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

inlinevirtual

Implements TTrait.

{ }

set_trait()

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

inlinevirtual

Implements TTrait.

  {  _is_infected = *(bool*)value; return &_is_infected; }

References _is_infected.

set_transmit_rate()

void TTWolbachia::set_transmit_rate ( double  val )

inline

{_transmit_rate = val;}

References _transmit_rate.

Referenced by TProtoWolbachia::hatch().

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set_value()

virtual void TTWolbachia::set_value ( )

inlinevirtual

Implements TTrait.

{ }

show_up()

virtual void TTWolbachia::show_up ( )

inlinevirtual

Implements TTrait.

{}

store_data()

virtual void TTWolbachia::store_data ( BinaryStorageBuffer *  saver )

inlinevirtual

Implements StorableComponent.

  { 
    unsigned char dummy = static_cast<unsigned char>(_is_infected);
    saver->store(&dummy, 1);
  }

References _is_infected, and BinaryStorageBuffer::store().

Member Data Documentation

_is_infected

bool TTWolbachia::_is_infected

private

Referenced by get_allele_value(), getValue(), inherit(), init(), init_sequence(), mutate(), operator=(), reset(), retrieve_data(), set_allele_value(), set_trait(), and store_data().

_transmit_rate

double TTWolbachia::_transmit_rate

private

Referenced by mutate(), and set_transmit_rate().

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

• ttwolbachia.h
• ttwolbachia.cc