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
void	set_proto (TProtoNeutralGenes *proto)
void	set_mut_func_ptr (void(TTNeutralGenes::*theFunc)(void))
void	set_inherit_func_ptr (void(TProtoNeutralGenes::*theFunc)(sex_t, unsigned char *, const 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) const
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 (const TTrait *mother, const 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	~TTrait ()
Public Member Functions inherited from StorableComponent
virtual	~StorableComponent ()

Private Attributes
TProtoNeutralGenes *	_myProto
void(TTNeutralGenes::*	_mutate_func_ptr )(void)
void(TProtoNeutralGenes::*	_inherit_func_ptr )(sex_t, unsigned char *, const unsigned char **)
unsigned char **	_sequence
const trait_t	_type

Detailed Description

Microsatellites genome.

Constructor & Destructor Documentation

TTNeutralGenes() [1/2]

TTNeutralGenes::TTNeutralGenes ( )

inline

    : _myProto(0), _mutate_func_ptr(0), _inherit_func_ptr(0), _sequence(0), _type(NTRL) { }

Referenced by clone().

TTNeutralGenes() [2/2]

TTNeutralGenes::TTNeutralGenes ( const TTNeutralGenes &  T )

inline

    : _myProto(T._myProto),_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 < _myProto->get_ploidy(); i++)
      delete [] _sequence[i];
    delete [] _sequence;
  }
}

References _myProto, _sequence, and TProtoNeutralGenes::get_ploidy().

Member Function Documentation

clone()

virtual TTNeutralGenes* TTNeutralGenes::clone ( )

inlinevirtual

Implements TTrait.

{return new TTNeutralGenes(*this);}

References TTNeutralGenes().

get_allele_value()

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

virtual

Implements TTrait.

{
  return ( !(loc<(int)_myProto->get_locus_num()) || !(all<(int)_myProto->get_ploidy()) ? 0 : (double)_sequence[all][loc]);
}

References _myProto, _sequence, TProtoNeutralGenes::get_locus_num(), and TProtoNeutralGenes::get_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 ( const TTrait *  mother, const TTrait *  father  )

virtual

Implements TTrait.

{
  const unsigned char** mother_seq = (const unsigned char**)mother->get_sequence();
  const unsigned char** father_seq = (const 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[_myProto->get_locus_num()];
  _sequence[1] = new unsigned char[_myProto->get_locus_num()];
 
  memset(_sequence[0], 1, _myProto->get_locus_num());
  memset(_sequence[1], 1, _myProto->get_locus_num());
 
}

References _myProto, _sequence, fatal(), and TProtoNeutralGenes::get_locus_num().

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

init_sequence()

void TTNeutralGenes::init_sequence ( )

virtual

Implements TTrait.

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

References _myProto, _sequence, RAND::Bernoulli(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_init_model(), TProtoNeutralGenes::get_locus_num(), TProtoNeutralGenes::get_ploidy(), mutate(), and RAND::Uniform().

mutate()

virtual void TTNeutralGenes::mutate ( )

inlinevirtual

Implements TTrait.

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

References _mutate_func_ptr.

Referenced by init_sequence().

mutate_2all()

void TTNeutralGenes::mutate_2all ( )

inline

{
  unsigned int mutAll, mutLocus;
  unsigned int NbMut = _myProto->get_num_mutations();
 
  for( ; NbMut > 0; NbMut--) {
    mutLocus = RAND::Uniform( _myProto->get_locus_num());
    mutAll = RAND::RandBool(); //RAND::Uniform( _ploidy); <--- only diploids for now
    _sequence[mutAll][mutLocus] = !_sequence[mutAll][mutLocus];
  }
}

References _myProto, _sequence, TProtoNeutralGenes::get_locus_num(), TProtoNeutralGenes::get_num_mutations(), RAND::RandBool(), and RAND::Uniform().

Referenced by TProtoNeutralGenes::setParameters().

mutate_KAM()

void TTNeutralGenes::mutate_KAM

(

)

{
  unsigned int mutAll, mutLocus;
  unsigned char mut;
  unsigned int NbMut = _myProto->get_num_mutations();
 
  for(; NbMut != 0; NbMut--) {
    mutLocus = RAND::Uniform( _myProto->get_locus_num());
    mutAll = RAND::RandBool(); //RAND::Uniform( _ploidy); <--- only diploids for now
    //assign an arbitrary allele value:
    do{
      mut = (unsigned char) (RAND::Uniform(_myProto->get_allele_num()));
    } while (mut == _sequence[mutAll][mutLocus]);
    _sequence[mutAll][mutLocus] = mut;
  }
}

References _myProto, _sequence, TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), TProtoNeutralGenes::get_num_mutations(), RAND::RandBool(), and RAND::Uniform().

Referenced by TProtoNeutralGenes::setParameters().

mutate_NULL()

void TTNeutralGenes::mutate_NULL ( )

inline

{ }

Referenced by TProtoNeutralGenes::setParameters().

mutate_SSM()

void TTNeutralGenes::mutate_SSM

(

)

direction && all == 0

{
  unsigned int mutAll, mutLocus;
  bool direction;
  unsigned int NbMut = _myProto->get_num_mutations();
 
  for(; NbMut != 0; NbMut--)
  {
    mutLocus = RAND::Uniform( _myProto->get_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] < _myProto->get_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 _myProto, _sequence, TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), TProtoNeutralGenes::get_num_mutations(), RAND::RandBool(), and RAND::Uniform().

Referenced by TProtoNeutralGenes::setParameters().

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) {
 
    reset();
 
    init();
 
    memcpy(_sequence[0], TN._sequence[0], _myProto->get_locus_num());
    memcpy(_sequence[1], TN._sequence[1], _myProto->get_locus_num());
 
  }
 
  return *this;
}

References _myProto, _sequence, TProtoNeutralGenes::get_locus_num(), 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(_myProto->get_locus_num() != TN._myProto->get_locus_num()) return false;
    if(_myProto->get_allele_num() != TN._myProto->get_allele_num()) return false;
    if(_myProto->get_ploidy() != TN._myProto->get_ploidy()) return false;
  }
  return true;
    }

References _myProto, _type, TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), TProtoNeutralGenes::get_ploidy(), and TTrait::get_type().

reset()

void TTNeutralGenes::reset ( )

virtual

Implements TTrait.

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

References _myProto, _sequence, and TProtoNeutralGenes::get_ploidy().

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

retrieve_data()

bool TTNeutralGenes::retrieve_data ( BinaryStorageBuffer *  reader )

virtual

Implements StorableComponent.

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

References _myProto, _sequence, TProtoNeutralGenes::get_locus_num(), TProtoNeutralGenes::get_ploidy(), and BinaryStorageBuffer::read().

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().

set_allele_value()

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

virtual

Implements TTrait.

{
  assert(locus < _myProto->get_locus_num() && allele < 2);
  _sequence[allele][locus] = (unsigned char)value;
}

References _sequence.

set_inherit_func_ptr()

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

inline

  {_inherit_func_ptr = theFunc;}

References _inherit_func_ptr.

Referenced by TProtoNeutralGenes::hatch().

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().

set_proto()

void TTNeutralGenes::set_proto ( TProtoNeutralGenes *  proto )

inline

{_myProto = proto;}

References _myProto.

Referenced by TProtoNeutralGenes::hatch().

set_sequence()

void TTNeutralGenes::set_sequence ( void **  seq )

virtual

Implements TTrait.

{
  reset(); init();
  memcpy(_sequence[0],seq[0],_myProto->get_locus_num());
  memcpy(_sequence[1],seq[1],_myProto->get_locus_num());
}

References _myProto, _sequence, TProtoNeutralGenes::get_locus_num(), 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:",_myProto->get_locus_num(), _myProto->get_allele_num());
 
  for(unsigned int i = 0; (i < _myProto->get_locus_num() && i < 10); i++)
    message("\n              %i %i",(int)_sequence[0][i],(int)_sequence[1][i]);
  if(_myProto->get_locus_num() > 10) message("\n              ...");
  message("\n");
}

References _myProto, _sequence, TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), and message().

store_data()

void TTNeutralGenes::store_data ( BinaryStorageBuffer *  saver )

virtual

Implements StorableComponent.

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

References _myProto, _sequence, TProtoNeutralGenes::get_locus_num(), TProtoNeutralGenes::get_ploidy(), and BinaryStorageBuffer::store().

Member Data Documentation

_inherit_func_ptr

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

private

Referenced by inherit(), and set_inherit_func_ptr().

_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 get_allele_value(), inherit(), init(), init_sequence(), mutate_2all(), mutate_KAM(), mutate_SSM(), operator=(), operator==(), reset(), retrieve_data(), set_proto(), set_sequence(), show_up(), store_data(), and ~TTNeutralGenes().

_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