TTNeutralGenes Class Reference

Microsatellites genome. More...

#include <ttneutralgenes.h>

Inheritance diagram for TTNeutralGenes:

Collaboration diagram for TTNeutralGenes:

Public Member Functions
	TTNeutralGenes ()
	TTNeutralGenes (const TTNeutralGenes &T)
virtual	~TTNeutralGenes ()
Accessors
unsigned int	get_ploidy ()
unsigned int	get_locus_num ()
unsigned int	get_allele_num ()
void	set_proto (TProtoNeutralGenes *proto)
void	set_locus_num (int value)
void	set_allele_num (int value)
void	set_mut_rate (double value)
void	set_2L (unsigned int val)
void	set_recomb_rate (double value)
void	set_mut_model (int value)
void	set_init_model (unsigned short val)
void	set_mut_func_ptr (void(TTNeutralGenes::*theFunc)(void))
void	set_inherit_func_ptr (void(TProtoNeutralGenes::*theFunc)(sex_t, unsigned char *, unsigned char **))
void	set_allele (unsigned int loc, unsigned int al, unsigned char val)
Mutation models
void	mutate_SSM ()
void	mutate_KAM ()
void	mutate_2all ()
void	mutate_NULL ()
Implementations
virtual TTNeutralGenes &	operator= (const TTrait &T)
virtual bool	operator== (const TTrait &T)
virtual bool	operator!= (const TTrait &T)
virtual void	init ()
virtual void	init_sequence ()
virtual void	reset ()
virtual void *	set_trait (void *value)
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 trait_t	get_type () const
virtual void	set_value ()
virtual void *	getValue () const
virtual void	inherit (TTrait *mother, TTrait *father)
virtual void	mutate ()
virtual void	show_up ()
virtual TTNeutralGenes *	clone ()
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
TProtoNeutralGenes *	_myProto
unsigned int	_allele_num
unsigned int	_locus_num
unsigned int	_ploidy
double	_mut_rate
double	_recomb_rate
unsigned int	_mut_model
unsigned int	_2L
unsigned short	_init_model
void(TTNeutralGenes::*	_mutate_func_ptr )(void)
void(TProtoNeutralGenes::*	_inherit_func_ptr )(sex_t, unsigned char *, unsigned char **)
unsigned char **	_sequence
const trait_t	_type

Detailed Description

Microsatellites genome.

Constructor & Destructor Documentation

TTNeutralGenes() [1/2]

TTNeutralGenes::TTNeutralGenes ( )

inline

    : _myProto(0),_allele_num(0),_locus_num(0),_ploidy(2),_mut_rate(0),_recomb_rate(0),_mut_model(0),
    _2L(0), _init_model(0), _mutate_func_ptr(0), _inherit_func_ptr(0), _sequence(0), _type(NTRL) { }

Referenced by clone().

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TTNeutralGenes() [2/2]

TTNeutralGenes::TTNeutralGenes ( const TTNeutralGenes &  T )

inline

    : _myProto(T._myProto),
    _allele_num(T._allele_num), _locus_num(T._locus_num), _ploidy(2), _mut_rate(T._mut_rate),
    _recomb_rate(T._recomb_rate),_mut_model(T._mut_model), _2L(T._2L),
    _init_model(T._init_model),_mutate_func_ptr(T._mutate_func_ptr), _inherit_func_ptr(T._inherit_func_ptr), 
    _sequence(0), _type(NTRL) { }

~TTNeutralGenes()

TTNeutralGenes::~TTNeutralGenes ( )

virtual

{
  if(_sequence != NULL){
    for(unsigned int i = 0; i < _ploidy; i++)
      delete [] _sequence[i];
    delete [] _sequence;
  }
}

References _ploidy, and _sequence.

Member Function Documentation

clone()

virtual TTNeutralGenes * TTNeutralGenes::clone ( )

inlinevirtual

Implements TTrait.

{return new TTNeutralGenes(*this);}

References TTNeutralGenes().

get_allele_num()

unsigned int TTNeutralGenes::get_allele_num ( )

inline

{return _allele_num;}

References _allele_num.

get_allele_value()

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

inlinevirtual

Implements TTrait.

    {return ( !(loc<(int)_locus_num) || !(all<(int)_ploidy) ? 0 : (double)_sequence[all][loc]);}

References _locus_num, _ploidy, and _sequence.

get_locus_num()

unsigned int TTNeutralGenes::get_locus_num ( )

inline

{return _locus_num;}

References _locus_num.

get_ploidy()

unsigned int TTNeutralGenes::get_ploidy ( )

inline

{return _ploidy;}

References _ploidy.

get_sequence()

virtual void ** TTNeutralGenes::get_sequence ( ) const

inlinevirtual

Implements TTrait.

{return (void**)_sequence;}

References _sequence.

get_type()

virtual trait_t TTNeutralGenes::get_type ( ) const

inlinevirtual

Implements TTrait.

{return _type;}

References _type.

getValue()

virtual void * TTNeutralGenes::getValue ( ) const

inlinevirtual

Implements TTrait.

{return 0;}

inherit()

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

virtual

Implements TTrait.

{
  unsigned char** mother_seq = (unsigned char**)mother->get_sequence();
  unsigned char** father_seq = (unsigned char**)father->get_sequence();
 
  (_myProto->* _inherit_func_ptr) (FEM, _sequence[FEM], mother_seq);
 
  (_myProto->* _inherit_func_ptr) (MAL, _sequence[MAL], father_seq);
}

References _inherit_func_ptr, _myProto, _sequence, FEM, TTrait::get_sequence(), and MAL.

init()

void TTNeutralGenes::init ( )

virtual

Implements TTrait.

{
  if(_sequence != NULL)
    fatal("TTNeutralGenes::init::_sequence is not NULL !\n");
 
  //assume _ploidy = 2;
 
  _sequence = new unsigned char* [2];
 
  _sequence[0] = new unsigned char[_locus_num];
  _sequence[1] = new unsigned char[_locus_num];
 
  memset(_sequence[0], 1, _locus_num);
  memset(_sequence[1], 1, _locus_num);
 
}

References _locus_num, _sequence, and fatal().

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

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init_sequence()

void TTNeutralGenes::init_sequence ( )

virtual

Implements TTrait.

{
  if(_sequence == NULL) { //that should never happen
    _sequence = new unsigned char* [_ploidy];
    for(unsigned int i = 0; i < _ploidy; i++)
      _sequence[i] = new unsigned char[_locus_num];
  }
 
  if(_init_model == 1) {
 
    for(unsigned int i = 0; i < _ploidy; ++i)
      for(unsigned int j = 0; j < _locus_num; j++) {
        if(_allele_num > 2)
          _sequence[i][j] = (unsigned char)RAND::Uniform(_allele_num);
        else
          _sequence[i][j] = (unsigned char)RAND::Bernoulli(0.5);
      }
 
  } else if (_init_model == 3 ) {
 
    memset(_sequence[0], 0, _locus_num);
    memset(_sequence[1], 0, _locus_num);
 
    mutate(); //do one round of mutation
 
  } else { //model 0; all monomorphic
 
    memset(_sequence[0], 0, _locus_num);
    memset(_sequence[1], 0, _locus_num);
 
  }
}

References _allele_num, _init_model, _locus_num, _ploidy, _sequence, RAND::Bernoulli(), mutate(), and RAND::Uniform().

mutate()

virtual void TTNeutralGenes::mutate ( )

inlinevirtual

Implements TTrait.

{(this->*_mutate_func_ptr) ();}

References _mutate_func_ptr.

Referenced by init_sequence().

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mutate_2all()

void TTNeutralGenes::mutate_2all ( )

inline

{
  register unsigned int mutAll, mutLocus;
  unsigned int NbMut = RAND::Binomial(_mut_rate, _2L);
 
  for( ; NbMut > 0; NbMut--) {
    mutLocus = RAND::Uniform( _locus_num);
    mutAll = RAND::RandBool(); //RAND::Uniform( _ploidy); <--- only diploids for now
    _sequence[mutAll][mutLocus] = !_sequence[mutAll][mutLocus];
  }
}

References _2L, _locus_num, _mut_rate, _sequence, RAND::Binomial(), RAND::RandBool(), and RAND::Uniform().

Referenced by TProtoNeutralGenes::setParameters().

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mutate_KAM()

void TTNeutralGenes::mutate_KAM

(

)

{
  unsigned int mutAll, mutLocus;
  unsigned char mut;
  unsigned int NbMut = RAND::Binomial(_mut_rate, _2L);
 
  for(; NbMut != 0; NbMut--) {
    mutLocus = RAND::Uniform( _locus_num);
    mutAll = RAND::RandBool(); //RAND::Uniform( _ploidy); <--- only diploids for now
    //assign an arbitrary allele value:
    do{
      mut = (unsigned char) (RAND::Uniform(_allele_num));
    } while (mut == _sequence[mutAll][mutLocus]);
    _sequence[mutAll][mutLocus] = mut;
  }
}

References _2L, _allele_num, _locus_num, _mut_rate, _sequence, RAND::Binomial(), RAND::RandBool(), and RAND::Uniform().

Referenced by TProtoNeutralGenes::setParameters().

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mutate_NULL()

void TTNeutralGenes::mutate_NULL ( )

inline

{ }

Referenced by TProtoNeutralGenes::setParameters().

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mutate_SSM()

void TTNeutralGenes::mutate_SSM

(

)

direction && all == 0

{
  unsigned int mutAll, mutLocus;
  bool direction;
  unsigned int NbMut = RAND::Binomial(_mut_rate, _2L);
 
  for(; NbMut != 0; NbMut--)
  {
    mutLocus = RAND::Uniform( _locus_num);
    mutAll = RAND::RandBool(); //RAND::Uniform( _ploidy); <--- only diploids for now
    direction = RAND::RandBool();
    //alleles values are from 0 to NtrlAll - 1 !!!
    if(direction && _sequence[mutAll][mutLocus] < _allele_num-1)
      _sequence[mutAll][mutLocus] += 1; //one step to the right
    else if(_sequence[mutAll][mutLocus] > 0) // !direction || all==_allele_num
      _sequence[mutAll][mutLocus] -= 1; //one step to the left
    else 
      _sequence[mutAll][mutLocus] += 1;
  }
}

References _2L, _allele_num, _locus_num, _mut_rate, _sequence, RAND::Binomial(), RAND::RandBool(), and RAND::Uniform().

Referenced by TProtoNeutralGenes::setParameters().

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operator!=()

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

virtual

Implements TTrait.

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

operator=()

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

virtual

Implements TTrait.

{
  const TTNeutralGenes& TN = dynamic_cast<const TTNeutralGenes&> (T);
 
  if(this != &TN) {
 
    _locus_num = TN._locus_num;
    _allele_num = TN._allele_num;
    _ploidy = 2; //by default
    _2L = TN._2L;
 
    reset();
 
    init();
 
    memcpy(_sequence[0], TN._sequence[0], _locus_num);
    memcpy(_sequence[1], TN._sequence[1], _locus_num);
 
  }
 
  return *this;
}

References _2L, _allele_num, _locus_num, _ploidy, _sequence, init(), and reset().

operator==()

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

virtual

Implements TTrait.

    {
  if(_type.compare(T.get_type()) != 0) return false;
  const TTNeutralGenes& TN = dynamic_cast<const TTNeutralGenes&> (T);
 
  if(this != &TN) {
    if(_locus_num != TN._locus_num) return false;
    if(_allele_num != TN._allele_num) return false;
    if(_ploidy != TN._ploidy) return false;
  }
  return true;
    }

References _allele_num, _locus_num, _ploidy, _type, and TTrait::get_type().

reset()

void TTNeutralGenes::reset ( )

virtual

Implements TTrait.

{
  if(_sequence != NULL) {
 
    for(unsigned int i = 0; i < _ploidy; i++)  delete [] _sequence[i];
 
    delete [] _sequence;
 
    _sequence = NULL;
  }
}

References _ploidy, and _sequence.

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

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retrieve_data()

virtual bool TTNeutralGenes::retrieve_data ( BinaryStorageBuffer *  reader )

inlinevirtual

Implements StorableComponent.

  { 
    for(unsigned int i = 0; i < _locus_num; ++i)
      for(unsigned int j = 0; j < _ploidy; ++j)
        reader->read(&_sequence[j][i], 1);
    return true;
  }

References _locus_num, _ploidy, _sequence, and BinaryStorageBuffer::read().

set_2L()

void TTNeutralGenes::set_2L ( unsigned int  val )

inline

{_2L = val;}

References _2L.

Referenced by TProtoNeutralGenes::hatch().

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set_allele()

void TTNeutralGenes::set_allele ( unsigned int  loc, unsigned int  al, unsigned char  val  )

inline

{_sequence[al][loc] = val;}

References _sequence.

Referenced by LCE_NtrlInit::init_allele_freq().

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set_allele_num()

void TTNeutralGenes::set_allele_num ( int  value )

inline

{_allele_num = value;}

References _allele_num.

Referenced by TProtoNeutralGenes::hatch().

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set_allele_value()

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

inlinevirtual

Implements TTrait.

    {assert(locus < _locus_num && allele < 2); _sequence[allele][locus] = (unsigned char)value;}

References _locus_num, and _sequence.

set_inherit_func_ptr()

void TTNeutralGenes::set_inherit_func_ptr ( void(TProtoNeutralGenes::*)(sex_t, unsigned char *, unsigned char **)  theFunc )

inline

  {_inherit_func_ptr = theFunc;}

References _inherit_func_ptr.

Referenced by TProtoNeutralGenes::hatch().

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set_init_model()

void TTNeutralGenes::set_init_model ( unsigned short  val )

inline

{_init_model = val;}

References _init_model.

Referenced by TProtoNeutralGenes::hatch().

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set_locus_num()

void TTNeutralGenes::set_locus_num ( int  value )

inline

{_locus_num = value;}

References _locus_num.

Referenced by TProtoNeutralGenes::hatch().

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set_mut_func_ptr()

void TTNeutralGenes::set_mut_func_ptr ( void(TTNeutralGenes::*)(void)  theFunc )

inline

  {_mutate_func_ptr = theFunc;}

References _mutate_func_ptr.

Referenced by TProtoNeutralGenes::hatch().

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set_mut_model()

void TTNeutralGenes::set_mut_model ( int  value )

inline

{_mut_model = value;}

References _mut_model.

Referenced by TProtoNeutralGenes::hatch().

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set_mut_rate()

void TTNeutralGenes::set_mut_rate ( double  value )

inline

{_mut_rate = value;}

References _mut_rate.

Referenced by TProtoNeutralGenes::hatch().

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set_proto()

void TTNeutralGenes::set_proto ( TProtoNeutralGenes *  proto )

inline

{_myProto = proto;}

References _myProto.

Referenced by TProtoNeutralGenes::hatch().

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set_recomb_rate()

void TTNeutralGenes::set_recomb_rate ( double  value )

inline

{_recomb_rate = value;}

References _recomb_rate.

set_sequence()

void TTNeutralGenes::set_sequence ( void **  seq )

virtual

Implements TTrait.

{
  reset(); init();
  memcpy(_sequence[0],seq[0],_locus_num);
  memcpy(_sequence[1],seq[1],_locus_num);
}

References _locus_num, _sequence, init(), and reset().

set_trait()

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

inlinevirtual

Implements TTrait.

{return NULL;}

set_value()

virtual void TTNeutralGenes::set_value ( )

inlinevirtual

Implements TTrait.

{ }

show_up()

void TTNeutralGenes::show_up ( )

virtual

Implements TTrait.

{
  message("\n  Trait's type: ntrl\n\
       locus: %i\n\
     alleles: %i\n\
    _sequence:",_locus_num, _allele_num);
 
  for(unsigned int i = 0; (i < _locus_num && i < 10); i++)
    message("\n              %i %i",(int)_sequence[0][i],(int)_sequence[1][i]);
  if(_locus_num > 10) message("\n              ...");
  message("\n");
}

References _allele_num, _locus_num, _sequence, and message().

store_data()

virtual void TTNeutralGenes::store_data ( BinaryStorageBuffer *  saver )

inlinevirtual

Implements StorableComponent.

  {
    for(unsigned int i = 0; i < _locus_num; ++i)
      for(unsigned int j = 0; j < _ploidy; ++j)
        saver->store(&_sequence[j][i], 1);
  }

References _locus_num, _ploidy, _sequence, and BinaryStorageBuffer::store().

Member Data Documentation

_2L

unsigned int TTNeutralGenes::_2L

private

Referenced by mutate_2all(), mutate_KAM(), mutate_SSM(), operator=(), and set_2L().

_allele_num

unsigned int TTNeutralGenes::_allele_num

private

Referenced by get_allele_num(), init_sequence(), mutate_KAM(), mutate_SSM(), operator=(), operator==(), set_allele_num(), and show_up().

_inherit_func_ptr

void(TProtoNeutralGenes::* TTNeutralGenes::_inherit_func_ptr) (sex_t, unsigned char *, unsigned char **)

private

Referenced by inherit(), and set_inherit_func_ptr().

_init_model

unsigned short TTNeutralGenes::_init_model

private

Referenced by init_sequence(), and set_init_model().

_locus_num

unsigned int TTNeutralGenes::_locus_num

private

Referenced by get_allele_value(), get_locus_num(), init(), init_sequence(), mutate_2all(), mutate_KAM(), mutate_SSM(), operator=(), operator==(), retrieve_data(), set_allele_value(), set_locus_num(), set_sequence(), show_up(), and store_data().

_mut_model

unsigned int TTNeutralGenes::_mut_model

private

Referenced by set_mut_model().

_mut_rate

double TTNeutralGenes::_mut_rate

private

Referenced by mutate_2all(), mutate_KAM(), mutate_SSM(), and set_mut_rate().

_mutate_func_ptr

void(TTNeutralGenes::* TTNeutralGenes::_mutate_func_ptr) (void)

private

Referenced by mutate(), and set_mut_func_ptr().

_myProto

TProtoNeutralGenes* TTNeutralGenes::_myProto

private

Referenced by inherit(), and set_proto().

_ploidy

unsigned int TTNeutralGenes::_ploidy

private

Referenced by get_allele_value(), get_ploidy(), init_sequence(), operator=(), operator==(), reset(), retrieve_data(), store_data(), and ~TTNeutralGenes().

_recomb_rate

double TTNeutralGenes::_recomb_rate

private

Referenced by set_recomb_rate().

_sequence

unsigned char** TTNeutralGenes::_sequence

private

Referenced by get_allele_value(), get_sequence(), inherit(), init(), init_sequence(), mutate_2all(), mutate_KAM(), mutate_SSM(), operator=(), reset(), retrieve_data(), set_allele(), set_allele_value(), set_sequence(), show_up(), store_data(), and ~TTNeutralGenes().

_type

const trait_t TTNeutralGenes::_type

private

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

---

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

• ttneutralgenes.h
• ttneutralgenes.cc