This class contains traits along with other individual information (sex, pedigree, etc. ). More...

#include <individual.h>

Collaboration diagram for Individual:

Public Types
typedef int	IDX
Public Member Functions
	Individual ()
	~Individual ()
Individual *	init ()
	Inits parameters and traits.
void	reset ()
	Resets parameters and traits values.
void	show_up ()
	Write some info to stdout.
Individual *	clone ()
	Cloning procedure, clones all the traits present in the individual.
Setters
void	setID (unsigned long value)
void	setAge (unsigned short value)
void	Aging ()
void	setFatherID (unsigned long value)
void	setMotherID (unsigned long value)
void	setFather (Individual *f)
void	setMother (Individual *m)
void	setHome (unsigned short value)
void	setSex (sex_t sex)
void	setCurrentID (unsigned long value)
void	setIsSelfed (bool s)
void	setPedigreeClass (Individual mother, Individual father)
void	setPedigreeClass (unsigned char ped)
Getters
unsigned long	getID ()
unsigned short	getAge ()
unsigned long	getFatherID ()
unsigned long	getMotherID ()
Individual *	getFather ()
Individual *	getMother ()
unsigned short	getHome ()
sex_t	getSex ()
bool	isFemale ()
bool	getIsSelfed ()
unsigned long	getcurrentID ()
double	getFecundity ()
unsigned short	getMatings (unsigned int cat)
	Gives the number of matings that individual had with mates from a given pedigree class.
unsigned short	getLocalMatings ()
	Gives the number of times an individual mated with an individual from the same patch.
unsigned int	getTotMatings ()
	Gives the total number of matings of an individual.
unsigned short	getRealizedFecundity (unsigned int cat)
	Gives the number of surviving offspring for a given pedigree class of mating.
unsigned int	getLocalRealizedFecundity ()
	Gives the total number of surviving offspring when mating occures with mates of the same patch.
unsigned int	getTotRealizedFecundity ()
	Gives the total number of surviving offspring for all categories of mating.
unsigned int	getPedigreeClass ()
	Returns the pedigree class of the individual, as set during offspring creation.
unsigned int	getPedigreeClass (Individual mother, Individual father)
	Returns the pedigree class of two individuals.
implementation
void	store_data (BinaryStorageBuffer *saver)
void	retrieve_data (BinaryStorageBuffer *reader)
Matings and Fecundity
double	setFecundity (double value)
	Sets the fecundity to the value given and returns it.
void	reset_counters ()
	Resets the mating and fecundity counters.
void	addMating (unsigned int category)
	Increments the mating counter according to the pedigree class of the offspring.
void	DidHaveABaby (unsigned int category)
	Increments the mating and realized fecundity counters according to the pedigree class of the offspring.
double	getFecWithHomePatchMate ()
	Returns the proportion of succesfull local matings (i.e.
double	getFecWithOtherPatchMate ()
	Returns the proportion of successfull remote matings.
Trait interface
unsigned int	getTraitNumber ()
	Accessor to the size of the traits table.
std::deque< TTrait * > &	getTraits ()
	Accessot to the traits table itself.
void *	setTrait (IDX T, void *value)
	Sets the phenotype/value of a trait to a particular value.
void	setTraitValue (IDX T)
	Calls the value setting procedure of a particular trait.
void	setTraitValue ()
	Calls the value setting procedure of all traits present in an individual.
void *	getTraitValue (IDX T)
	Accessor to the value (phenotype) of a particular trait.
TTrait *	getTrait (IDX T)
	Trait accessor.
void	addTrait (TTrait *theTrait, IDX pos)
	Adds a trait to the table.
void	removeTrait (IDX T)
	Removes a trait from the table.
void	clearTraits ()
	Clears the traits container.
void	inheritTrait (IDX T, Individual mother, Individual father)
	Calls the inheritance procedure of a particular trait.
void	mutateTrait (IDX T)
	Calls the mutation procedure of a particular trait.
void	createTrait (IDX i, Individual mother, Individual father)
	Sets a particular trait's genotype and phenotype values from the two parents.
Individual *	createTrait (IDX i, bool do_inherit, bool do_mutate)
	Creates an individual's genotypes and phenotypes with optional recombination or mutations on one trait only.
Individual *	create_first_gen ()
	Creates an individual's genotypes and phenotypes for first generation.
Individual *	create ()
	Creates an individual's genotypes and phenotypes with recombination and mutations.
Individual *	create (bool do_inherit, bool do_mutate)
	Creates an individual's genotypes and phenotypes with optional recombination or mutations.
Individual *	create (Individual mother, Individual father)
	Creates an individual, inherit, mutate and set all its trait's values.
void	inherit (Individual mother, Individual father)
	Calls the inheritance procedure of all the traits present in the individual.
void	mutate ()
	Calls the mutation procedure of all the traits present in the individual.
Operators
Individual &	operator= (const Individual &i)
	Assignment, make a deep copy of the parameter values and traits.
bool	operator== (const Individual &i)
	Only checks for traits equivalence.
bool	operator!= (const Individual &i)
Public Attributes
std::deque< TTrait * >	Traits
	The traits table.
Static Public Attributes
static unsigned long	currentID = 0
	The ID counter, reset at the beginning of each simulation.
Private Attributes
unsigned long	_id
	ID tag, unique for one simulation.
unsigned short	_age
	Age.
sex_t	_sex
	Sex tag.
unsigned long	_motherID
	Parents ID tags.
unsigned long	_fatherID
Individual *	_mother
	Parents pointers.
Individual *	_father
unsigned short	_home
	Natal Patch tag.
unsigned char	_pedigreeClass
	Pedigree class of the individual.
double	_fecundity
	Assigned fecundity.
unsigned short	_matings [5]
	Mating counter.
unsigned short	_realizedFecundity [5]
	Number of surviving offspring from the different mating categories (see matings).
unsigned int	_trait_nb
	Number of traits in the table.

Detailed Description

This class contains traits along with other individual information (sex, pedigree, etc. ).

The Individual class can be view as a trait container. It encapsulates the basic interface to manipulate the traits an individual is carrying like initialization, inheritance, mutation and phenotype getter. It also stores the basic individual info like its sex, pedigree (home Patch, mather and father id, etc.) and its mating and fecundity values. It is not a StorableComponent but declares a similar interface to store and retrieve all the previous info to/from a binary file. All individuals in a simulation are instantiated by a call to the IndFactory class (through its derived class Metapop) which contains the individual and traits prototypes.

Definition at line 48 of file individual.h.

Member Typedef Documentation

typedef int Individual::IDX

Definition at line 82 of file individual.h.

Constructor & Destructor Documentation

Individual::Individual ( )

Definition at line 41 of file individual.cc.

References _id, _matings, _realizedFecundity, and currentID.

Referenced by clone().

: _age(0), _sex(MAL),_motherID(0),_fatherID(0),_mother(NULL),_father(NULL),
_home(0),_pedigreeClass(0),_fecundity(0),_trait_nb(0)
{
  _id = currentID++;
  for(unsigned int i = 0; i < 5; i++) {
    _matings[i] = 0; _realizedFecundity[i] = 0;
  }
}

Individual::~Individual ( ) [inline]

Definition at line 87 of file individual.h.

References clearTraits().

{clearTraits();}

Member Function Documentation

void Individual::addMating ( unsigned int category ) [inline]

Increments the mating counter according to the pedigree class of the offspring.

Parameters:

category the pedigree class of the offspring

Definition at line 215 of file individual.h.

References _matings.

Referenced by LCE_Breed_Selection::makeOffspringWithSelection().

  { _matings[category]++; }

void Individual::addTrait	(	TTrait *	theTrait,
		IDX	pos
	)		`[inline]`

Adds a trait to the table.

Parameters:

theTrait	pointer to the trait to add
pos	the position where the trait should be added in the traits table. Used to check that the index of the trait in the table is correctly set.

See also:: IndFactory::makePrototype

Definition at line 284 of file individual.h.

References _trait_nb, fatal(), and Traits.

Referenced by clone().

  { if((int)_trait_nb != pos)
    fatal("Individual::adding a trait to the wrong position (at %i, size %i)!\n",pos,_trait_nb);
    Traits.push_back(theTrait); _trait_nb++;
  }

void Individual::Aging ( ) [inline]

Definition at line 102 of file individual.h.

References _age.

{_age++;}

void Individual::clearTraits ( ) [inline]

Clears the traits container.

Definition at line 296 of file individual.h.

References _trait_nb, and Traits.

Referenced by ~Individual().

  { if(_trait_nb != 0) {for(unsigned int i = 0; i < Traits.size(); ++i) delete Traits[i];
    Traits.clear(); _trait_nb = 0;}
  }

Individual * Individual::clone ( )

Cloning procedure, clones all the traits present in the individual.

Definition at line 149 of file individual.cc.

References _trait_nb, addTrait(), Individual(), and Traits.

Referenced by IndFactory::makeNewIndividual().

{
  Individual* myClone = new Individual();
  
  for(unsigned int i = 0; i < _trait_nb; i++)
    myClone->addTrait(Traits[i]->clone(), i);
  
  return myClone;
}

Individual* Individual::create ( ) [inline]

Creates an individual's genotypes and phenotypes with recombination and mutations.

Definition at line 353 of file individual.h.

References _father, _mother, inherit(), mutate(), and setTraitValue().

Referenced by IndFactory::makeOffsprg(), and LCE_Breed_base::makeOffspring().

  { 
    inherit(_mother, _father);
    mutate();
    setTraitValue();
    return this;
  }

Individual* Individual::create	(	bool	do_inherit,
		bool	do_mutate
	)		`[inline]`

Creates an individual's genotypes and phenotypes with optional recombination or mutations.

Parameters:

do_inherit	if true, do traits inheritance and recombination
do_mutate	if true, performs mutation of the traits

Definition at line 363 of file individual.h.

References _father, _mother, inherit(), mutate(), and setTraitValue().

  { 
    if(do_inherit) inherit(_mother, _father);
    if(do_mutate)  mutate();
    setTraitValue();
    return this;
  }

Individual* Individual::create	(	Individual *	mother,
		Individual *	father
	)		`[inline]`

Creates an individual, inherit, mutate and set all its trait's values.

Parameters:

mother	the mother
father	the father

Definition at line 374 of file individual.h.

References _trait_nb, fatal(), getTrait(), TTrait::inherit(), TTrait::mutate(), TTrait::set_value(), and Traits.

  { if(mother == 0 || father == 0) fatal("Individual::create::received null parents pointer!!!\n");
    TTrait *TT;
    for(unsigned int i = 0; i < _trait_nb; i++) {
      TT = Traits[i];
      TT->inherit(mother->getTrait(i), father->getTrait(i));
      TT->mutate();
      TT->set_value();
    }
    return this;
  }

Individual* Individual::create_first_gen ( ) [inline]

Creates an individual's genotypes and phenotypes for first generation.

Definition at line 339 of file individual.h.

References _fatherID, _motherID, _trait_nb, and Traits.

Referenced by Patch::setNewGeneration().

  {
    for(unsigned int i = 0; i < _trait_nb; i++) {
      Traits[i]->init_sequence();
      Traits[i]->set_value();
    }
    //we have to set the parents ids otherwise the first offspring generation will be made of full sibs only.
    static unsigned long ID = std::numeric_limits< unsigned long >::max();
    _motherID = ID--;
    _fatherID = ID--;
    return this;
  }

void Individual::createTrait	(	IDX	i,
		Individual *	mother,
		Individual *	father
	)		`[inline]`

Sets a particular trait's genotype and phenotype values from the two parents.

Includes its inheritance, mutation and value setting.

Parameters:

i	the index of the trait to create in the traits table
mother	the mother
father	the father

Definition at line 318 of file individual.h.

References fatal(), getTrait(), TTrait::inherit(), TTrait::mutate(), TTrait::set_value(), and Traits.

Referenced by LCE_Breed_Selection::makeOffspringWithSelection().

  { if(mother == 0 || father == 0) fatal("Individual::create::received null pointer!!!\n");
    TTrait* T = Traits[i];
    T->inherit(mother->getTrait(i),father->getTrait(i));
    T->mutate();  
    T->set_value();
  }

Individual* Individual::createTrait	(	IDX	i,
		bool	do_inherit,
		bool	do_mutate
	)		`[inline]`

Creates an individual's genotypes and phenotypes with optional recombination or mutations on one trait only.

Parameters:

i	the index of the trait in the traits' table
do_inherit	if true, does inheritance and recombination of the trait
do_mutate	if true, performs mutation of the trait

Definition at line 330 of file individual.h.

References _father, _mother, inheritTrait(), mutateTrait(), and setTraitValue().

  {
    if(do_inherit) inheritTrait(i, _mother, _father);
    if(do_mutate)  mutateTrait(i);
    setTraitValue(i);
    return this;
  }

void Individual::DidHaveABaby ( unsigned int category ) [inline]

Increments the mating and realized fecundity counters according to the pedigree class of the offspring.

Parameters:

category the pedigree class of the offspring

Definition at line 221 of file individual.h.

References _matings, and _realizedFecundity.

Referenced by IndFactory::makeOffsprg(), LCE_Breed_base::makeOffspring(), and LCE_Breed_Selection::makeOffspringWithSelection().

  { _matings[category]++; _realizedFecundity[category]++; }

unsigned short Individual::getAge ( ) [inline]

Definition at line 119 of file individual.h.

References _age.

{return _age;}

unsigned long Individual::getcurrentID ( ) [inline]

Definition at line 128 of file individual.h.

References currentID.

{return currentID;}

Individual* Individual::getFather ( ) [inline]

Definition at line 122 of file individual.h.

References _father.

Referenced by LCE_Breed_base::makeOffspring(), and LCE_Breed_Selection::makeOffspringWithSelection().

{return _father;}

unsigned long Individual::getFatherID ( ) [inline]

Definition at line 120 of file individual.h.

References _fatherID.

Referenced by getPedigreeClass().

{return _fatherID;}

double Individual::getFecundity ( ) [inline]

Definition at line 129 of file individual.h.

References _fecundity.

{return _fecundity;}

double Individual::getFecWithHomePatchMate ( ) [inline]

Returns the proportion of succesfull local matings (i.e.

those that survived selection).

Definition at line 225 of file individual.h.

References getLocalMatings(), and getLocalRealizedFecundity().

  { 
    unsigned short mate = getLocalMatings();
    return (mate != 0 ? (double) getLocalRealizedFecundity()/mate : 0.0);
  }

double Individual::getFecWithOtherPatchMate ( ) [inline]

Returns the proportion of successfull remote matings.

Returns:: _realizedFecundity[0]/_matings[0]

Definition at line 233 of file individual.h.

References _matings, and _realizedFecundity.

  {
    return (_matings[0] != 0 ? (double) _realizedFecundity[0]/_matings[0] : 0.0);
  }

unsigned short Individual::getHome ( ) [inline]

Definition at line 124 of file individual.h.

References _home.

Referenced by TTDeletMutBitstrFH::FHwrite(), getPedigreeClass(), and TTNeutralGenesFH::write_FSTAT().

{return _home;}

unsigned long Individual::getID ( ) [inline]

Definition at line 118 of file individual.h.

References _id.

Referenced by LCE_Breed_base::breed_cloning(), and IndFactory::makeNewIndividual().

{return _id;}

bool Individual::getIsSelfed ( ) [inline]

Definition at line 127 of file individual.h.

References _pedigreeClass.

{return (_pedigreeClass == 4);}

unsigned short Individual::getLocalMatings ( ) [inline]

Gives the number of times an individual mated with an individual from the same patch.

Definition at line 143 of file individual.h.

References _matings.

Referenced by getFecWithHomePatchMate(), and getTotMatings().

  {
    return _matings[1]+_matings[2]+_matings[3]+_matings[4];
  }

unsigned int Individual::getLocalRealizedFecundity ( ) [inline]

Gives the total number of surviving offspring when mating occures with mates of the same patch.

Definition at line 166 of file individual.h.

References _realizedFecundity.

Referenced by getFecWithHomePatchMate(), and getTotRealizedFecundity().

  {
    return _realizedFecundity[1]+_realizedFecundity[2]+_realizedFecundity[3]+_realizedFecundity[4];
  }

unsigned short Individual::getMatings ( unsigned int cat ) [inline]

Gives the number of matings that individual had with mates from a given pedigree class.

Parameters:

cat	the mating category (= the pedigree class of the offspring): 0 = mates are from different patches 1 = mates are from the same patch 2 = mates are half sib 3 = mates are full sib 4 = selfed mating

Definition at line 138 of file individual.h.

References _matings.

  {
    return _matings[cat];
  }

Individual* Individual::getMother ( ) [inline]

Definition at line 123 of file individual.h.

References _mother.

Referenced by LCE_Breed_base::makeOffspring(), and LCE_Breed_Selection::makeOffspringWithSelection().

{return _mother;}

unsigned long Individual::getMotherID ( ) [inline]

Definition at line 121 of file individual.h.

References _motherID.

Referenced by getPedigreeClass().

{return _motherID;}

unsigned int Individual::getPedigreeClass ( ) [inline]

Returns the pedigree class of the individual, as set during offspring creation.

Definition at line 175 of file individual.h.

References _pedigreeClass.

Referenced by LCE_Selection_base::doViabilitySelection(), TTDeletMutBitstrFH::FHwrite(), LCE_Selection_base::getFitnessFixedEffect(), IndFactory::makeOffsprg(), LCE_Breed_base::makeOffspring(), LCE_Breed_Selection::makeOffspringWithSelection(), setPedigreeClass(), and TTNeutralGenesFH::write_FSTAT().

  {
    return _pedigreeClass;
  }

unsigned int Individual::getPedigreeClass	(	Individual *	mother,
		Individual *	father
	)

Returns the pedigree class of two individuals.

Parameters:

mother	the first individual (e.g.the mother of this individual)
father	the second individual (e.g. the father of this individual)

Returns:

0 = mother and father are from different patches
1 = mother and father are from the same patch
2 = mother and father are half sib
3 = mother and father are full sib
4 = mother and father are the same individual (selfed offspring)

Definition at line 220 of file individual.cc.

References getFatherID(), getHome(), and getMotherID().

{
  if(mother == father) return 4; //selfed

  if(mother->getHome() != father->getHome()) return 0; //outbred between patch
  
  unsigned int mm,mf,fm,ff;
  //mother's parents:
  mm = mother->getMotherID();
  mf = mother->getFatherID();
  //father's parents:
  fm = father->getMotherID();
  ff = father->getFatherID();

  if(mm != fm && mf != ff) return 1; //outbred within patch
    
  else if((mm == fm && mf != ff) || (mm != fm && mf == ff)) return 2; //half sibs
    
  else return 3; //full sibs
}

unsigned short Individual::getRealizedFecundity ( unsigned int cat ) [inline]

Gives the number of surviving offspring for a given pedigree class of mating.

Parameters:

cat	the mating category: 0 = mates are from different patches 1 = mates are from the same patch 2 = mates are half sib 3 = mates are full sib 4 = selfed mating

Definition at line 160 of file individual.h.

References _realizedFecundity.

  {
    return _realizedFecundity[cat];
  }

sex_t Individual::getSex ( ) [inline]

Definition at line 125 of file individual.h.

References _sex.

Referenced by LCE_Breed_Selection::execute(), LCE_Breed::execute(), Metapop::retrieve_data(), LCE_Breed_Wolbachia::wolbachia_model_1(), and LCE_Breed_Wolbachia::wolbachia_model_2().

{return _sex;}

unsigned int Individual::getTotMatings ( ) [inline]

Gives the total number of matings of an individual.

Definition at line 148 of file individual.h.

References _matings, and getLocalMatings().

  {
    return _matings[0] + getLocalMatings();
  }

unsigned int Individual::getTotRealizedFecundity ( ) [inline]

Gives the total number of surviving offspring for all categories of mating.

Definition at line 172 of file individual.h.

References _realizedFecundity, and getLocalRealizedFecundity().

{return _realizedFecundity[0] + getLocalRealizedFecundity( );}

TTrait* Individual::getTrait ( IDX T ) [inline]

Trait accessor.

Parameters:

T	the trait's index in the traits table

Returns:: the pointer to the trait

Definition at line 273 of file individual.h.

References _trait_nb, fatal(), and Traits.

Referenced by create(), createTrait(), TTNeutralGenesFH::FHread(), TTDeletMutBitstrFH::FHread(), TTDeletMutBitstrFH::FHwrite(), getTraitValue(), inherit(), inheritTrait(), mutateTrait(), setTrait(), setTraitValue(), TTNeutralGenesFH::write_FSTAT(), and TTNeutralGenesFH::write_varcompWC().

  { if( T == -1 || !(T < (int)_trait_nb) )
    fatal("Individual::Trying to access a trait not present in the traits table (at %i, size %i)\n",T,_trait_nb);
    return Traits[T]; 
  }

unsigned int Individual::getTraitNumber ( ) [inline]

Accessor to the size of the traits table.

Definition at line 243 of file individual.h.

References _trait_nb.

Referenced by LCE_Selection_base::setParameters().

{ return _trait_nb;}

std::deque<TTrait *>& Individual::getTraits ( ) [inline]

Accessot to the traits table itself.

Returns:: the traits table (a deque)

Definition at line 247 of file individual.h.

References Traits.

{return Traits;}

void* Individual::getTraitValue ( IDX T ) [inline]

Accessor to the value (phenotype) of a particular trait.

Parameters:

T	the trait's index in the traits table

Returns:: the trait's value, using the TTrait interface

Definition at line 267 of file individual.h.

References getTrait(), and TTrait::getValue().

Referenced by LCE_Disperse_EvolDisp::evoldisp(), LCE_Selection_base::getFitnessDirect(), LCE_Selection_base::getFitnessMultivariateGaussian(), LCE_Selection_base::getFitnessMultivariateGaussian_VE(), LCE_Selection_base::getFitnessUnivariateGaussian(), LCE_Selection_base::getFitnessUnivariateGaussian_VE(), TTWolbachiaSH::getMeanFemaleInfection_perPatch(), TTWolbachiaSH::getMeanMaleInfection_perPatch(), TTWolbachiaSH::getMeanOffsprgFemaleInfection_perPatch(), TTWolbachiaSH::getMeanOffsprgInfection(), TTWolbachiaSH::getMeanOffsprgMaleInfection_perPatch(), LCE_Breed_Wolbachia::hasInfectedFemale(), TTWolbachiaSH::setInfectionStats(), LCE_Breed_Wolbachia::wolbachia_model_1(), and LCE_Breed_Wolbachia::wolbachia_model_2().

  { return getTrait(T)->getValue(); }

void Individual::inherit	(	Individual *	mother,
		Individual *	father
	)		`[inline]`

Calls the inheritance procedure of all the traits present in the individual.

Parameters:

mother	the mother
father	the father

Definition at line 389 of file individual.h.

References _trait_nb, getTrait(), inherit(), and Traits.

Referenced by create(), and inherit().

  { for(unsigned int i = 0; i < _trait_nb; i++) Traits[i]->inherit(mother->getTrait(i), father->getTrait(i)); }

void Individual::inheritTrait	(	IDX	T,
		Individual *	mother,
		Individual *	father
	)		`[inline]`

Calls the inheritance procedure of a particular trait.

Parameters:

T	the trait's index in the traits table
mother	the mother
father	the father

Definition at line 305 of file individual.h.

References getTrait(), and TTrait::inherit().

Referenced by createTrait().

  {  getTrait(T)->inherit(mother->getTrait(T), father->getTrait(T)); }

Individual * Individual::init ( )

Inits parameters and traits.

Called by IndFactory::makeNewIndividual() to allocate the traits' sequences memory.

Definition at line 53 of file individual.cc.

References _age, _father, _fatherID, _home, _matings, _mother, _motherID, _pedigreeClass, _realizedFecundity, _trait_nb, error(), and Traits.

Referenced by IndFactory::makeNewIndividual().

{
  _age = 0;
  _pedigreeClass = 0;
  _motherID = 0;
  _fatherID = 0;
  _mother = NULL;
  _father = NULL;
  _home = 0;
  for(unsigned int i = 0; i < 5; i++) {
    _matings[i] = 0; _realizedFecundity[i] = 0;
  }
  
  if(_trait_nb != Traits.size()){
    error("Individual::init: trait counter and table size differ, resetting\n");
    _trait_nb = Traits.size();
  }
  
  for(unsigned int i = 0; i < _trait_nb; i++)
    Traits[i]->init();

  return this;
}

bool Individual::isFemale ( ) [inline]

Definition at line 126 of file individual.h.

References _sex, and FEM.

{return (_sex == FEM);}

void Individual::mutate ( ) [inline]

Calls the mutation procedure of all the traits present in the individual.

Definition at line 393 of file individual.h.

References _trait_nb, mutate(), and Traits.

Referenced by create(), and mutate().

  { for(unsigned int i = 0; i < _trait_nb; i++) Traits[i]->mutate(); }

void Individual::mutateTrait ( IDX T ) [inline]

Calls the mutation procedure of a particular trait.

Parameters:

T	trait's index in the traits table

Definition at line 310 of file individual.h.

References getTrait(), and TTrait::mutate().

Referenced by createTrait().

  {  getTrait(T)->mutate(); }

bool Individual::operator!= ( const Individual & i )

Definition at line 210 of file individual.cc.

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

Individual & Individual::operator= ( const Individual & i )

Assignment, make a deep copy of the parameter values and traits.

Definition at line 161 of file individual.cc.

References _age, _father, _fatherID, _fecundity, _home, _matings, _mother, _motherID, _pedigreeClass, _realizedFecundity, _sex, _trait_nb, error(), fatal(), and Traits.

{
  if(this != &i) {  
    
    if(Traits.size() != i.Traits.size()) fatal("Individual::operator=:not same number of traits in left and right sides of assignment\n");
    if(_trait_nb != i._trait_nb) {
      error("Individual::operator=:trait counters differ, restting\n");
      _trait_nb = i._trait_nb;
    }
    _sex = i._sex;
    _age = i._age;
    _motherID = i._motherID;
    _fatherID = i._fatherID;
    _mother = i._mother;
    _father = i._father;
    _home = i._home;
    _pedigreeClass = i._pedigreeClass;
    _fecundity = i._fecundity;
    for(unsigned int j = 0; j < 5; j++) {
      _matings[j] = i._matings[j];
      _realizedFecundity[j] = i._realizedFecundity[j];
    }

    for(unsigned int t = 0; t < _trait_nb; t++){ 
      if(Traits[t]->get_type().compare(i.Traits[t]->get_type()) != 0) 
        fatal("Individual::operator=: not same kinds of traits on left and right sides of assignment\n");
      (*Traits[t]) = (*i.Traits[t]);
    }
  }
  return *this;
}

bool Individual::operator== ( const Individual & i )

Only checks for traits equivalence.

Definition at line 195 of file individual.cc.

References Traits.

{
  if(this != &i) {
    if(Traits.size() != i.Traits.size()) return false;

    for(unsigned int t = 0; t < Traits.size(); t++)
      if((*Traits[t]) != (*i.Traits[t])) return false;

  //if(_sex != i._sex) return false;
  }
  return true;
}

void Individual::removeTrait ( IDX T ) [inline]

Removes a trait from the table.

Parameters:

T	the trait's index in the traits table

Definition at line 292 of file individual.h.

References _trait_nb, and Traits.

  { delete Traits[T]; Traits.erase(Traits.begin() + T); _trait_nb--;}

void Individual::reset ( )

Resets parameters and traits values.

Does not de-allocate the traits' sequences memory (i.e. is not calling TTrait::reset() on each trait).

Definition at line 79 of file individual.cc.

References _age, _father, _fatherID, _home, _id, _matings, _mother, _motherID, _pedigreeClass, _realizedFecundity, _sex, _trait_nb, MAL, Traits, and warning().

Referenced by IndFactory::makeNewIndividual().

{
  _id = 0;
  _age = 0;
  _sex = MAL;
  _pedigreeClass = 0;
  _motherID = 0;
  _fatherID = 0;
  _mother = NULL;
  _father = NULL;
  _home = 0;
  for(unsigned int i = 0; i < 5; i++) {
    _matings[i] = 0; _realizedFecundity[i] = 0;
  }
   
  if(_trait_nb != Traits.size()){
    warning("Individual::reset: trait counter and table size differ, resetting\n");
    _trait_nb = Traits.size();
  }
}

void Individual::reset_counters ( ) [inline]

Resets the mating and fecundity counters.

Definition at line 206 of file individual.h.

References _matings, and _realizedFecundity.

Referenced by LCE_Breed_base::breed_cloning().

  { 
    for(unsigned int i = 0; i < 5; i++) {
      _matings[i] = 0; _realizedFecundity[i] = 0;
    } }

void Individual::retrieve_data ( BinaryStorageBuffer * reader )

Definition at line 117 of file individual.cc.

References _fatherID, _home, _id, _matings, _motherID, _realizedFecundity, _sex, and BinaryStorageBuffer::read().

Referenced by Metapop::retrieve_data().

{
  reader->read(&_id, sizeof(unsigned long));
  reader->read(&_motherID, sizeof(unsigned long));
  reader->read(&_fatherID, sizeof(unsigned long));
  reader->read(&_sex, sizeof(sex_t));
  reader->read(&_home, sizeof(unsigned short));
  reader->read(&_matings, 2*sizeof(unsigned short));
  reader->read(&_realizedFecundity, 2*sizeof(unsigned short));
//reader->read(&_pedigreeClass, 1);
//reader->read(&_age, sizeof(unsigned short));
}

void Individual::setAge ( unsigned short value ) [inline]

Definition at line 101 of file individual.h.

References _age.

Referenced by LCE_Breed_base::breed_cloning(), and TTDeletMutBitstrFH::FHread().

{_age = value;}

void Individual::setCurrentID ( unsigned long value ) [inline]

Definition at line 109 of file individual.h.

References currentID.

{currentID = value;}

void Individual::setFather ( Individual * f ) [inline]

Definition at line 105 of file individual.h.

References _father.

Referenced by LCE_Breed_base::breed_cloning(), and IndFactory::makeNewIndividual().

{_father = f;}

void Individual::setFatherID ( unsigned long value ) [inline]

Definition at line 103 of file individual.h.

References _fatherID.

Referenced by LCE_Breed_base::breed_cloning(), and IndFactory::makeNewIndividual().

{_fatherID = value;}

double Individual::setFecundity ( double value ) [inline]

Sets the fecundity to the value given and returns it.

Parameters:

value the fecundity

Definition at line 203 of file individual.h.

References _fecundity.

Referenced by LCE_Breed_Selection::execute(), LCE_Breed::execute(), LCE_Breed_Wolbachia::wolbachia_model_1(), and LCE_Breed_Wolbachia::wolbachia_model_2().

{_fecundity = value; return value;}

void Individual::setHome ( unsigned short value ) [inline]

Definition at line 107 of file individual.h.

References _home.

Referenced by LCE_Breed_base::breed_cloning(), and IndFactory::makeNewIndividual().

{_home = value;}

void Individual::setID ( unsigned long value ) [inline]

Definition at line 100 of file individual.h.

References _id.

Referenced by IndFactory::makeNewIndividual().

{_id = value;}

void Individual::setIsSelfed ( bool s ) [inline]

Definition at line 110 of file individual.h.

References _pedigreeClass.

Referenced by LCE_Breed_base::breed_cloning().

{_pedigreeClass = (s ? 4 : 0);}

void Individual::setMother ( Individual * m ) [inline]

Definition at line 106 of file individual.h.

References _mother.

Referenced by LCE_Breed_base::breed_cloning(), and IndFactory::makeNewIndividual().

{_mother = m;}

void Individual::setMotherID ( unsigned long value ) [inline]

Definition at line 104 of file individual.h.

References _motherID.

Referenced by LCE_Breed_base::breed_cloning(), and IndFactory::makeNewIndividual().

{_motherID = value;}

void Individual::setPedigreeClass	(	Individual *	mother,
		Individual *	father
	)		`[inline]`

Definition at line 111 of file individual.h.

References _pedigreeClass, and getPedigreeClass().

Referenced by TTNeutralGenesFH::FHread(), TTDeletMutBitstrFH::FHread(), and IndFactory::makeNewIndividual().

{_pedigreeClass = getPedigreeClass(mother,father);}

void Individual::setPedigreeClass ( unsigned char ped ) [inline]

Definition at line 112 of file individual.h.

References _pedigreeClass.

{_pedigreeClass = ped;}

void Individual::setSex ( sex_t sex ) [inline]

Definition at line 108 of file individual.h.

References _sex.

Referenced by IndFactory::makeNewIndividual().

{_sex = sex;}

void* Individual::setTrait	(	IDX	T,
		void *	value
	)		`[inline]`

Sets the phenotype/value of a trait to a particular value.

Parameters:

T	the trait's index in the traits table
value	the value passed to the trait (using the TTrait interface)

Definition at line 252 of file individual.h.

References getTrait(), and TTrait::set_trait().

Referenced by LCE_Breed_Wolbachia::inoculate_wolbachia().

  { return getTrait(T)->set_trait(value); }

void Individual::setTraitValue ( IDX T ) [inline]

Calls the value setting procedure of a particular trait.

Parameters:

T	the trait's index in the traits table

Definition at line 257 of file individual.h.

References getTrait(), and TTrait::set_value().

  {  getTrait(T)->set_value(); }

void Individual::setTraitValue ( ) [inline]

Calls the value setting procedure of all traits present in an individual.

Definition at line 261 of file individual.h.

References _trait_nb, and Traits.

Referenced by create(), and createTrait().

  { for(unsigned int i = 0; i < _trait_nb; i++) Traits[i]->set_value(); }

void Individual::show_up ( )

Write some info to stdout.

Definition at line 132 of file individual.cc.

References _age, _fatherID, _home, _id, _motherID, _pedigreeClass, _sex, _trait_nb, message(), and Traits.

Referenced by TTDeletMutBitstrFH::FHread().

{
  message("\n Individual ID: %i\n\
           age: %i\n\
           sex: %i\n\
        mother: %i\n\
        father: %i\n\
pedigree class: %i\n\
          home: %i\n\
 traits values: \n",_id,_age,_sex,_motherID,_fatherID, _pedigreeClass,_home);

for(unsigned int i = 0; i < _trait_nb; i++)
  Traits[i]->show_up();
}

void Individual::store_data ( BinaryStorageBuffer * saver )

Definition at line 102 of file individual.cc.

References _fatherID, _home, _id, _matings, _motherID, _realizedFecundity, _sex, and BinaryStorageBuffer::store().

{
  saver->store(&_id, sizeof(unsigned long));
  saver->store(&_motherID, sizeof(unsigned long));
  saver->store(&_fatherID, sizeof(unsigned long));
  saver->store(&_sex, sizeof(sex_t));
  saver->store(&_home, sizeof(unsigned short));
  saver->store(&_matings, 2*sizeof(unsigned short));
  saver->store(&_realizedFecundity, 2*sizeof(unsigned short));
  //saver->store(&_pedigreeClass, 1);
  //saver->store(&_age, sizeof(unsigned short));
}